# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 26 19:50:41 2016
#
#   Inital geometry file: a 169 line input string
#   Ligand name: (2R)-2-{(1R)-2-[(2S)-2-amino-2-carboxylatoethoxy]-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylate
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](COC(=O)[C@@H](NC(=O)Cc1sccc1)[C@@H]2NC(=C(CS2)\C=C\c3ccc(cc3[N+]([O-])=O)[N+]([O-])=O)C([O-])=O)C([O-])=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
NC1        NC1 '(2R)-2-{(1R)-2-[(2S)-2-amino-2-carboxylatoethoxy]-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylate' L-peptide 63 42 .
2016-04-26 2016-04-26
;
CIF prepared directly in eLBOW
;
#
data_comp_NC1
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
NC1         S1     S   S2     0    .       3.1644   -1.8203   -3.4486
NC1         C2     C   CR16   0    .       1.8432   -3.0332   -3.5471
NC1         N3     N   NR16   0    .       0.5511   -2.4625   -3.2724
NC1         C4     C   CR6    0    .       0.3413   -1.5310   -2.3329
NC1         C5     C   CR6    0    .       1.3707   -0.9507   -1.5381
NC1         C6     C   C      0    .       2.8061   -1.1308   -1.8602
NC1         C9     C   CH1    0    .       1.9781   -3.7728   -4.9066
NC1         N10    N   NH1    0    .       1.5156   -3.0472   -6.0522
NC1         C11    C   C      0    .       2.3581   -2.7481   -7.1120
NC1         O12    O   O      0    .       3.5967   -2.8736   -7.0186
NC1         C13    C   CH2    0    .       1.6953   -2.1977   -8.3714
NC1         C14    C   CR5    0    .       1.9440   -3.0626   -9.5348
NC1         S15    S   S2     0    .       3.1961   -2.8022  -10.6474
NC1         C16    C   CR15   0    .       2.7567   -4.1008  -11.6079
NC1         C17    C   CR15   0    .       1.6616   -4.7608  -11.0995
NC1         C18    C   CR15   0    .       1.1821   -4.1558   -9.8928
NC1         C19    C   C      0    .      -1.1583   -1.0770   -2.1292
NC1         O20    O   O      0    .      -1.6758   -1.3866   -1.0317
NC1         O21    O   OC    -1    .      -1.6641   -0.4617   -3.0905
NC1         C22    C   C1     0    .       1.0181   -0.1921   -0.4243
NC1         C23    C   C1     0    .       1.9301    0.4105    0.4499
NC1         C24    C   CR6    0    .       1.5805    1.1637    1.5696
NC1         C25    C   CR6    0    .       2.5390    1.7916    2.4415
NC1         C26    C   CR16   0    .       2.1421    2.6275    3.4961
NC1         C27    C   CR6    0    .       0.7874    2.8301    3.7622
NC1         C28    C   CR16   0    .      -0.1912    2.1881    2.9507
NC1         C29    C   CR16   0    .       0.2022    1.3963    1.9119
NC1         N30    N   N      1    .       3.9930    1.6095    2.2855
NC1         O31    O   O     -1    .       4.7312    2.4573    2.7364
NC1         O32    O   O      0    .       4.4535    0.6310    1.7569
NC1         N33    N   N      1    .       0.3710    3.6889    4.8702
NC1         O34    O   O     -1    .      -0.8047    3.8692    5.0802
NC1         O35    O   O      0    .       1.2050    4.2120    5.5713
NC1         N      N   NH2    0    .      -3.0429   -6.5574   -6.2642
NC1         CA     C   CH1    0    .      -1.9932   -5.5644   -6.0775
NC1         CB     C   CH2    0    .      -0.9157   -6.1059   -5.1199
NC1         C      C   C      0    .      -1.3184   -5.1133   -7.4044
NC1         O      O   O      0    .      -0.8695   -3.9313   -7.4794
NC1         OXT    O   OC    -1    .      -1.2566   -5.9336   -8.3640
NC1         H9     H   HCR6   0    .       2.0513   -3.8026   -2.7434
NC1         H8     H   HNR6   0    .      -0.2181   -2.7528   -3.8503
NC1         H6     H   H      0    .       3.3243   -0.1346   -1.8733
NC1         H7     H   H      0    .       3.2947   -1.7569   -1.0699
NC1         H10    H   HCH1   0    .       3.0838   -4.0097   -5.0301
NC1         H11    H   HNH1   0    .       0.5229   -3.0794   -6.2336
NC1         H12    H   HCH2   0    .       2.1163   -1.1700   -8.5359
NC1         H13    H   HCH2   0    .       0.5776   -2.1106   -8.2316
NC1         H14    H   HCR5   0    .       3.2980   -4.3661  -12.5116
NC1         H15    H   HCR5   0    .       1.1906   -5.6428  -11.5372
NC1         H16    H   HCR5   0    .       0.3051   -4.5251   -9.3243
NC1         H5     H   H      0    .      -0.0694   -0.0945   -0.2199
NC1         H4     H   H      0    .       2.9995    0.2609    0.2282
NC1         H1     H   HCR6   0    .       2.9050    3.1263    4.1261
NC1        HC28    H   HCR6   0    .      -1.2604    2.3409    3.1739
NC1         H3     H   HCR6   0    .      -0.5746    0.9065    1.3016
NC1         H2     H   HNH2   0    .      -3.7858   -6.1224   -6.7806
NC1         H19    H   HCH1   0    .      -2.4497   -4.6494   -5.6003
NC1         HB2    H   HCH2   0    .      -1.3573   -6.5011   -4.1685
NC1         HB3    H   HCH2   0    .      -0.2888   -6.8913   -5.6135
NC1         C7     C   C      0    .       1.2416   -5.1122   -4.7701
NC1         OG     O   O2     0    .      -0.1103   -4.9734   -4.7429
NC1         O8     O   O      0    .       1.7546   -6.2269   -4.6706
NC1         H      H   HNH2   0    .      -2.6766   -7.2937   -6.8447
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
NC1   S1      C2    single        1.796 0.020     1.796
NC1   S1      C6    single        1.768 0.020     1.768
NC1   C2      N3    single        1.439 0.020     1.439
NC1   C2      C9    single        1.554 0.020     1.554
NC1   C2      H9    single        0.970 0.020     1.090
NC1   N3      C4    single        1.339 0.020     1.339
NC1   N3      H8    single        0.860 0.020     1.020
NC1   C4      C5    double        1.424 0.020     1.424
NC1   C4      C19   single        1.580 0.020     1.580
NC1   C5      C6    single        1.482 0.020     1.482
NC1   C5      C22   single        1.393 0.020     1.393
NC1   C6      H6    single        0.970 0.020     1.090
NC1   C6      H7    single        0.970 0.020     1.090
NC1   C7      O8    double        1.231 0.020     1.231
NC1   C7      C9    single        1.535 0.020     1.535
NC1   C7      OG    single        1.359 0.020     1.359
NC1   C9      N10   single        1.433 0.020     1.433
NC1   C9      H10   single        0.970 0.020     1.090
NC1   N10     C11   single        1.386 0.020     1.386
NC1   N10     H11   single        0.890 0.020     1.040
NC1   C11     O12   double        1.248 0.020     1.248
NC1   C11     C13   single        1.526 0.020     1.526
NC1   C13     C14   single        1.471 0.020     1.471
NC1   C13     H12   single        0.970 0.020     1.090
NC1   C13     H13   single        0.970 0.020     1.090
NC1   C14     S15   aromatic      1.695 0.020     1.695
NC1   C14     C18   aromatic      1.380 0.020     1.380
NC1   S15     C16   aromatic      1.674 0.020     1.674
NC1   C16     C17   aromatic      1.376 0.020     1.376
NC1   C16     H14   single        0.930 0.020     1.080
NC1   C17     C18   aromatic      1.432 0.020     1.432
NC1   C17     H15   single        0.930 0.020     1.080
NC1   C18     H16   single        0.930 0.020     1.080
NC1   C19     O20   deloc         1.252 0.020     1.252
NC1   C19     O21   deloc         1.248 0.020     1.248
NC1   C22     C23   double        1.400 0.020     1.400
NC1   C22     H5    single        0.930 0.020     1.080
NC1   C23     C24   single        1.394 0.020     1.394
NC1   C23     H4    single        0.930 0.020     1.080
NC1   C24     C25   aromatic      1.440 0.020     1.440
NC1   C24     C29   aromatic      1.439 0.020     1.439
NC1   C25     C26   aromatic      1.403 0.020     1.403
NC1   C25     N30   single        1.474 0.020     1.474
NC1   C26     C27   aromatic      1.395 0.020     1.395
NC1   C26     H1    single        0.930 0.020     1.080
NC1   C27     C28   aromatic      1.424 0.020     1.424
NC1   C27     N33   single        1.462 0.020     1.462
NC1   C28     C29   aromatic      1.364 0.020     1.364
NC1   C28    HC28   single        0.930 0.020     1.080
NC1   C29     H3    single        0.930 0.020     1.080
NC1   N30     O31   single        1.211 0.020     1.211
NC1   N30     O32   double        1.204 0.020     1.204
NC1   N33     O34   single        1.208 0.020     1.208
NC1   N33     O35   double        1.209 0.020     1.209
NC1   N       CA    single        1.457 0.020     1.457
NC1   N       H     single        0.860 0.020     1.020
NC1   N       H2    single        0.890 0.020     1.040
NC1   CA      CB    single        1.540 0.020     1.540
NC1   CA      C     single        1.556 0.020     1.556
NC1   CA      H19   single        0.970 0.020     1.090
NC1   CB      OG    single        1.440 0.020     1.440
NC1   CB      HB2   single        0.970 0.020     1.090
NC1   CB      HB3   single        0.970 0.020     1.090
NC1   C       O     deloc         1.267 0.020     1.267
NC1   C       OXT   deloc         1.264 0.020     1.264
#
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
NC1   C6      S1      C2           99.41 3.000
NC1   H9      C2      C9          106.37 3.000
NC1   H9      C2      N3          107.40 3.000
NC1   C9      C2      N3          115.71 3.000
NC1   H9      C2      S1          106.55 3.000
NC1   C9      C2      S1          107.79 3.000
NC1   N3      C2      S1          112.47 3.000
NC1   H8      N3      C4          118.96 3.000
NC1   H8      N3      C2          117.58 3.000
NC1   C4      N3      C2          123.39 3.000
NC1   C19     C4      C5          119.80 3.000
NC1   C19     C4      N3          116.04 3.000
NC1   C5      C4      N3          124.16 3.000
NC1   C22     C5      C6          119.02 3.000
NC1   C22     C5      C4          119.02 3.000
NC1   C6      C5      C4          121.95 3.000
NC1   H7      C6      H6          107.62 3.000
NC1   H7      C6      C5          109.69 3.000
NC1   H6      C6      C5          109.98 3.000
NC1   H7      C6      S1          109.11 3.000
NC1   H6      C6      S1          104.00 3.000
NC1   C5      C6      S1          116.03 3.000
NC1   H10     C9      N10         109.42 3.000
NC1   H10     C9      C7          107.12 3.000
NC1   N10     C9      C7          110.99 3.000
NC1   H10     C9      C2          106.17 3.000
NC1   N10     C9      C2          115.51 3.000
NC1   C7      C9      C2          107.22 3.000
NC1   H11     N10     C11         117.84 3.000
NC1   H11     N10     C9          116.42 3.000
NC1   C11     N10     C9          121.62 3.000
NC1   C13     C11     O12         121.93 3.000
NC1   C13     C11     N10         116.41 3.000
NC1   O12     C11     N10         121.60 3.000
NC1   H13     C13     H12         108.57 3.000
NC1   H13     C13     C14         108.09 3.000
NC1   H12     C13     C14         111.03 3.000
NC1   H13     C13     C11         110.82 3.000
NC1   H12     C13     C11         106.75 3.000
NC1   C14     C13     C11         111.55 3.000
NC1   C18     C14     S15         111.06 3.000
NC1   C18     C14     C13         125.29 3.000
NC1   S15     C14     C13         123.62 3.000
NC1   C16     S15     C14          93.64 3.000
NC1   H14     C16     C17         125.93 3.000
NC1   H14     C16     S15         122.42 3.000
NC1   C17     C16     S15         111.65 3.000
NC1   H15     C17     C18         122.32 3.000
NC1   H15     C17     C16         125.65 3.000
NC1   C18     C17     C16         112.03 3.000
NC1   H16     C18     C17         123.79 3.000
NC1   H16     C18     C14         124.59 3.000
NC1   C17     C18     C14         111.62 3.000
NC1   O21     C19     O20         128.99 3.000
NC1   O21     C19     C4          115.27 3.000
NC1   O20     C19     C4          115.74 3.000
NC1   H5      C22     C23         119.02 3.000
NC1   H5      C22     C5          116.29 3.000
NC1   C23     C22     C5          124.67 3.000
NC1   H4      C23     C24         118.56 3.000
NC1   H4      C23     C22         116.62 3.000
NC1   C24     C23     C22         124.81 3.000
NC1   C29     C24     C25         115.03 3.000
NC1   C29     C24     C23         121.24 3.000
NC1   C25     C24     C23         123.71 3.000
NC1   N30     C25     C26         115.61 3.000
NC1   N30     C25     C24         122.61 3.000
NC1   C26     C25     C24         121.78 3.000
NC1   H1      C26     C27         119.65 3.000
NC1   H1      C26     C25         120.06 3.000
NC1   C27     C26     C25         120.29 3.000
NC1   N33     C27     C28         120.05 3.000
NC1   N33     C27     C26         120.41 3.000
NC1   C28     C27     C26         119.54 3.000
NC1  HC28     C28     C29         120.94 3.000
NC1  HC28     C28     C27         119.23 3.000
NC1   C29     C28     C27         119.83 3.000
NC1   H3      C29     C28         118.44 3.000
NC1   H3      C29     C24         118.11 3.000
NC1   C28     C29     C24         123.45 3.000
NC1   O32     N30     O31         119.95 3.000
NC1   O32     N30     C25         121.63 3.000
NC1   O31     N30     C25         118.39 3.000
NC1   O35     N33     O34         120.41 3.000
NC1   O35     N33     C27         119.81 3.000
NC1   O34     N33     C27         119.77 3.000
NC1   H2      N       H           106.84 3.000
NC1   H2      N       CA          107.69 3.000
NC1   H       N       CA          108.07 3.000
NC1   H19     CA      C           107.52 3.000
NC1   H19     CA      CB          107.77 3.000
NC1   C       CA      CB          109.20 3.000
NC1   H19     CA      N           108.39 3.000
NC1   C       CA      N           113.63 3.000
NC1   CB      CA      N           110.14 3.000
NC1   HB3     CB      HB2         110.33 3.000
NC1   HB3     CB      OG          110.73 3.000
NC1   HB2     CB      OG          105.99 3.000
NC1   HB3     CB      CA          111.36 3.000
NC1   HB2     CB      CA          112.09 3.000
NC1   OG      CB      CA          106.12 3.000
NC1   OXT     C       O           122.92 3.000
NC1   OXT     C       CA          118.73 3.000
NC1   O       C       CA          118.35 3.000
NC1   OG      C7      C9          112.95 3.000
NC1   OG      C7      O8          120.35 3.000
NC1   C9      C7      O8          126.69 3.000
NC1   CB      OG      C7          118.08 3.000
#
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
NC1 CONST_01       C17     C16     S15     C14          -0.45   0.0 0
NC1 CONST_02       C16     C17     C18     C14          -0.33   0.0 0
NC1 CONST_03       C17     C18     C14     S15          -0.01   0.0 0
NC1 CONST_04       C18     C17     C16     S15           0.52   0.0 0
NC1 CONST_05       C18     C14     S15     C16           0.26   0.0 0
NC1 CONST_06       C27     C26     C25     C24           2.62   0.0 0
NC1 CONST_07       C27     C28     C29     C24          -0.20   0.0 0
NC1 CONST_08       C28     C29     C24     C25           2.29   0.0 0
NC1 CONST_09       C28     C27     C26     C25          -0.34   0.0 0
NC1 CONST_10       C29     C24     C25     C26          -3.48   0.0 0
NC1 CONST_11       C29     C28     C27     C26          -0.85   0.0 0
NC1 CONST_12       C16     S15     C14     C13        -177.92   0.0 0
NC1 CONST_13       C17     C18     C14     C13         178.14   0.0 0
NC1 CONST_14       C26     C25     C24     C23         174.89   0.0 0
NC1 CONST_15       C28     C29     C24     C23        -176.12   0.0 0
NC1 CONST_16       N33     C27     C26     C25         179.31   0.0 0
NC1 CONST_17       N30     C25     C26     C27        -177.71   0.0 0
NC1 CONST_18       N30     C25     C24     C29         176.89   0.0 0
NC1 CONST_19       N33     C27     C28     C29         179.49   0.0 0
NC1 CONST_20       H14     C16     S15     C14        -179.99   0.0 0
NC1 CONST_21       H15     C17     C18     C14         179.60   0.0 0
NC1 CONST_22       H16     C18     C14     S15        -179.87   0.0 0
NC1 CONST_23       H1      C26     C25     C24        -177.71   0.0 0
NC1 CONST_24      HC28     C28     C29     C24         179.76   0.0 0
NC1 CONST_25       H3      C29     C24     C25        -177.62   0.0 0
NC1 CONST_26       O31     N30     C25     C24         156.61   0.0 0
NC1 CONST_27       O32     N30     C25     C24         -25.33   0.0 0
NC1 CONST_28       O31     N30     C25     C26         -23.05   0.0 0
NC1 CONST_29       O32     N30     C25     C26         155.01   0.0 0
NC1 CONST_30       O34     N33     C27     C26         179.11   0.0 0
NC1 CONST_31       O35     N33     C27     C26          -1.01   0.0 0
NC1 CONST_32       O34     N33     C27     C28          -1.24   0.0 0
NC1 CONST_33       O35     N33     C27     C28         178.64   0.0 0
NC1 CONST_34       O12     C11     N10     C9          -13.35   0.0 0
NC1 CONST_35       C13     C11     N10     C9          169.39   0.0 0
NC1 CONST_36       H11     N10     C11     O12        -169.69   0.0 0
NC1 Var_01         C4      C5      C6      S1           11.89  30.0 1
NC1 Var_02         C5      C6      S1      C2          -38.87  30.0 1
NC1 Var_03         C5      C4      N3      C2            2.96  30.0 1
NC1 Var_04         C6      C5      C4      N3           12.34  30.0 1
NC1 Var_05         C24     C23     C22     C5         -179.61   0.0 2
NC1 Var_06         O20     C19     C4      N3          113.04  30.0 2
NC1 Var_07         C23     C22     C5      C4          178.82  30.0 2
NC1 Var_08         S15     C14     C13     C11         -95.40  30.0 2
NC1 Var_09         C25     C24     C23     C22        -178.96  30.0 2
NC1 Var_10         O31     N30     C25     C24         156.61  30.0 2
NC1 Var_11         O34     N33     C27     C26         179.11  30.0 2
NC1 Var_12         C14     C13     C11     N10        -120.05  30.0 3
NC1 Var_13         CA      CB      OG      C7         -134.00  30.0 1
#
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
NC1 chir_01   C2      S1      N3      C9    negativ
NC1 chir_02   C9      N10     C2      C7    negativ
NC1 chir_03   CA      N       C       CB    positiv
#
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
NC1 plan-1    C13 0.020
NC1 plan-1    C14 0.020
NC1 plan-1    S15 0.020
NC1 plan-1    C16 0.020
NC1 plan-1    C17 0.020
NC1 plan-1    C18 0.020
NC1 plan-1    H14 0.020
NC1 plan-1    H15 0.020
NC1 plan-1    H16 0.020
NC1 plan-2     C9 0.020
NC1 plan-2     C7 0.020
NC1 plan-2     OG 0.020
NC1 plan-2     O8 0.020
NC1 plan-3     C5 0.020
NC1 plan-3    C22 0.020
NC1 plan-3    C23 0.020
NC1 plan-3    C24 0.020
NC1 plan-3     H5 0.020
NC1 plan-3     H4 0.020
NC1 plan-4    C23 0.020
NC1 plan-4    C24 0.020
NC1 plan-4    C25 0.020
NC1 plan-4    C26 0.020
NC1 plan-4    C27 0.020
NC1 plan-4    C28 0.020
NC1 plan-4    C29 0.020
NC1 plan-4    N30 0.020
NC1 plan-4    N33 0.020
NC1 plan-4     H1 0.020
NC1 plan-4   HC28 0.020
NC1 plan-4     H3 0.020
NC1 plan-5    C25 0.020
NC1 plan-5    N30 0.020
NC1 plan-5    O31 0.020
NC1 plan-5    O32 0.020
NC1 plan-6    C27 0.020
NC1 plan-6    N33 0.020
NC1 plan-6    O34 0.020
NC1 plan-6    O35 0.020
NC1 plan-7     C9 0.020
NC1 plan-7    N10 0.020
NC1 plan-7    C11 0.020
NC1 plan-7    O12 0.020
NC1 plan-7    C13 0.020
NC1 plan-7    H11 0.020
NC1 plan-8     C2 0.020
NC1 plan-8     N3 0.020
NC1 plan-8     C4 0.020
NC1 plan-8     H8 0.020
NC1 plan-9     C4 0.020
NC1 plan-9    C19 0.020
NC1 plan-9    O20 0.020
NC1 plan-9    O21 0.020
NC1 plan-10     CA 0.020
NC1 plan-10      C 0.020
NC1 plan-10      O 0.020
NC1 plan-10    OXT 0.020
