# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 22 16:35:03 2016
#
#   Inital geometry file: a 166 line input string
#   Ligand name: O-[(R)-hydroxy{[(3R)-3-hydroxy-4-{[3-({2-[(2-hydroxybenzoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-2,2-dimethyl-4-oxobutyl]oxy}phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(=O)OC[C@H](N)C(O)=O)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)c1ccccc1O
#
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
4HJ        4HJ 'O-[(R)-hydroxy{[(3R)-3-hydroxy-4-{[3-({2-[(2-hydroxybenzoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-2,2-dimethyl-4-oxobutyl]oxy}phosphoryl]-L-serine' L-peptide 67 37 .
2016-04-22 2016-04-22
;
CIF prepared directly in eLBOW
;
#
data_comp_4HJ
#
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
4HJ         N      N   NH2    0    .      -5.3159    1.7668    1.5945
4HJ         CA     C   CH1    0    .      -4.3786    2.8367    1.3036
4HJ         CAA    C   CR16   0    .       9.9826    2.4968   -0.7721
4HJ         C      C   C      0    .      -5.0538    4.2440    1.2331
4HJ         O      O   O      0    .      -6.2679    4.3267    0.8835
4HJ         CB     C   CH2    0    .      -3.5555    2.6612    0.0109
4HJ         OG     O   O2     0    .      -2.6347    1.6049    0.1541
4HJ         CZ1    C   CR16   0    .       9.6096    2.6934    0.5475
4HJ         CZ2    C   CR16   0    .       9.0833    1.9351   -1.6845
4HJ         CJ     C   CH2    0    .      -3.6871   -1.7864   -0.6288
4HJ         CK     C   CT     0    .      -4.2498   -2.4042    0.6723
4HJ         CL1    C   CH3    0    .      -3.5677   -1.7801    1.8783
4HJ         CL2    C   CH3    0    .      -5.7425   -2.1159    0.7514
4HJ         CM     C   C      0    .      -2.6289   -4.3412    0.2486
4HJ         OM     O   OH1    0    .      -4.9670   -4.6068   -0.1674
4HJ         NN     N   NH1    0    .      -1.5942   -4.2101    1.1708
4HJ         ON     O   O      0    .      -2.4443   -4.8219   -0.8884
4HJ         P      P   P      0    .      -2.5067    0.5219   -1.0435
4HJ         O1P    O   O      0    .      -1.2887   -0.2919   -0.7740
4HJ         O2P    O   OP    -1    .      -2.7827    1.1037   -2.3677
4HJ         O3P    O   O2     0    .      -3.8262   -0.4087   -0.6281
4HJ         CX     C   CR6    0    .       7.4066    1.7355    0.0676
4HJ         CL3    C   CH1    0    .      -4.0485   -3.9368    0.6763
4HJ         CO     C   CH2    0    .      -0.2427   -4.0269    0.6868
4HJ         CP     C   CH2    0    .      -0.0438   -2.6637    0.0314
4HJ         CQ     C   C      0    .       1.4013   -2.3257   -0.2299
4HJ         CS     C   CH2    0    .       2.9105   -0.5941   -1.1155
4HJ         CT     C   CH2    0    .       3.7858   -0.2281    0.0849
4HJ         CV     C   C      0    .       6.0580    1.3073    0.4822
4HJ         CY1    C   CR6    0    .       8.3141    2.3231    0.9728
4HJ         CY2    C   CR16   0    .       7.8131    1.5621   -1.2668
4HJ         NR     N   NH1    0    .       1.6117   -1.0765   -0.7760
4HJ         OR     O   O      0    .       2.3525   -3.1076    0.0104
4HJ         OW     O   O      0    .       5.5012    1.7657    1.4946
4HJ         SU     S   S2     0    .       5.4063    0.1138   -0.5575
4HJ         H      H   HNH2   0    .      -6.2423    2.0713    1.3458
4HJ         H1     H   HNH2   0    .      -5.0994    0.9599    1.0388
4HJ         HA     H   HCH1   0    .      -3.6432    2.8568    2.1599
4HJ         HB3    H   HCH2   0    .      -4.2136    2.4659   -0.8783
4HJ         HB2    H   HCH2   0    .      -2.9762    3.6143   -0.1492
4HJ         HZ2    H   HCR6   0    .       9.3811    1.7916   -2.7325
4HJ         HZ     H   HOH1   0    .       7.1273    2.3849    2.4942
4HJ         HJ2    H   HCH2   0    .      -2.6028   -2.0733   -0.7430
4HJ         HJ3    H   HCH2   0    .      -4.2803   -2.2188   -1.4881
4HJ        HL12    H   HCH3   0    .      -3.9725   -0.7466    2.0342
4HJ        HL11    H   HCH3   0    .      -3.7519   -2.3825    2.7999
4HJ        HL13    H   HCH3   0    .      -2.4681   -1.6762    1.7138
4HJ        HL22    H   HCH3   0    .      -6.2866   -2.6439   -0.0680
4HJ        HL21    H   HCH3   0    .      -6.1525   -2.4560    1.7317
4HJ        HL23    H   HCH3   0    .      -5.9070   -1.0152    0.6413
4HJ         HM     H   HOH1   0    .      -4.7425   -4.3687   -1.0784
4HJ         HN     H   HNH1   0    .      -1.8210   -3.6649    1.9762
4HJ         HL3    H   HCH1   0    .      -4.2797   -4.3404    1.7031
4HJ         HO2    H   HCH2   0    .       0.4599   -4.1411    1.5585
4HJ         HO3    H   HCH2   0    .      -0.0164   -4.8390   -0.0590
4HJ         HP2    H   HCH2   0    .      -0.5993   -2.6262   -0.9493
4HJ         HP3    H   HCH2   0    .      -0.4949   -1.8395    0.6583
4HJ         HS2    H   HCH2   0    .       2.7884    0.3159   -1.7694
4HJ         HS3    H   HCH2   0    .       3.4562   -1.3917   -1.7026
4HJ         HT3    H   HCH2   0    .       3.3837    0.6543    0.6375
4HJ         HT2    H   HCH2   0    .       3.8481   -1.0925    0.7914
4HJ         HY2    H   HCR6   0    .       7.1056    1.1248   -1.9944
4HJ         HR     H   HNH1   0    .       0.8103   -0.4757   -0.8965
4HJ         OXT    O   OC    -1    .      -4.3458    5.2463    1.5365
4HJ         HAA    H   HCR6   0    .      10.9894    2.7897   -1.1051
4HJ         OZ     O   OH1    0    .       8.0615    2.5666    2.2938
4HJ         HZ1    H   HCR6   0    .      10.2977    3.1396    1.2788
#
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
4HJ   O1P     P     deloc         1.489 0.020     1.489
4HJ   ON      CM    double        1.248 0.020     1.248
4HJ   NN      CM    single        1.392 0.020     1.392
4HJ   NN      CO    single        1.447 0.020     1.447
4HJ   CM      CL3   single        1.537 0.020     1.537
4HJ   C       O     deloc         1.266 0.020     1.266
4HJ   C       CA    single        1.563 0.020     1.563
4HJ   CP      CO    single        1.526 0.020     1.526
4HJ   CP      CQ    single        1.507 0.020     1.507
4HJ   OG      P     single        1.620 0.020     1.620
4HJ   OG      CB    single        1.409 0.020     1.409
4HJ   P       O2P   deloc         1.472 0.020     1.472
4HJ   P       O3P   single        1.667 0.020     1.667
4HJ   CJ      O3P   single        1.385 0.020     1.385
4HJ   CJ      CK    single        1.546 0.020     1.546
4HJ   OR      CQ    double        1.255 0.020     1.255
4HJ   CL3     OM    single        1.416 0.020     1.416
4HJ   CL3     CK    single        1.546 0.020     1.546
4HJ   N       CA    single        1.452 0.020     1.452
4HJ   CQ      NR    single        1.379 0.020     1.379
4HJ   CA      CB    single        1.543 0.020     1.543
4HJ   CK      CL2   single        1.522 0.020     1.522
4HJ   CK      CL1   single        1.520 0.020     1.520
4HJ   NR      CS    single        1.426 0.020     1.426
4HJ   CS      CT    single        1.530 0.020     1.530
4HJ   CT      SU    single        1.776 0.020     1.776
4HJ   CAA     CZ2   aromatic      1.399 0.020     1.399
4HJ   CAA     CZ1   aromatic      1.385 0.020     1.385
4HJ   CZ2     CY2   aromatic      1.388 0.020     1.388
4HJ   CZ1     CY1   aromatic      1.413 0.020     1.413
4HJ   CY2     CX    aromatic      1.406 0.020     1.406
4HJ   CY1     CX    aromatic      1.410 0.020     1.410
4HJ   CY1     OZ    single        1.367 0.020     1.367
4HJ   CX      CV    single        1.474 0.020     1.474
4HJ   SU      CV    single        1.712 0.020     1.712
4HJ   CV      OW    double        1.243 0.020     1.243
4HJ   N       H     single        0.860 0.020     1.020
4HJ   N       H1    single        0.890 0.020     1.040
4HJ   CA      HA    single        0.970 0.020     1.090
4HJ   CAA     HAA   single        0.930 0.020     1.080
4HJ   CB      HB3   single        0.970 0.020     1.090
4HJ   CB      HB2   single        0.970 0.020     1.090
4HJ   CZ1     HZ1   single        0.930 0.020     1.080
4HJ   CZ2     HZ2   single        0.930 0.020     1.080
4HJ   OZ      HZ    single        0.850 0.020     0.980
4HJ   CJ      HJ2   single        0.970 0.020     1.090
4HJ   CJ      HJ3   single        0.970 0.020     1.090
4HJ   CL1    HL12   single        0.970 0.020     1.090
4HJ   CL1    HL11   single        0.970 0.020     1.090
4HJ   CL1    HL13   single        0.970 0.020     1.090
4HJ   CL2    HL22   single        0.970 0.020     1.090
4HJ   CL2    HL21   single        0.970 0.020     1.090
4HJ   CL2    HL23   single        0.970 0.020     1.090
4HJ   OM      HM    single        0.850 0.020     0.980
4HJ   NN      HN    single        0.890 0.020     1.040
4HJ   CL3     HL3   single        0.970 0.020     1.090
4HJ   CO      HO2   single        0.970 0.020     1.090
4HJ   CO      HO3   single        0.970 0.020     1.090
4HJ   CP      HP2   single        0.970 0.020     1.090
4HJ   CP      HP3   single        0.970 0.020     1.090
4HJ   CS      HS2   single        0.970 0.020     1.090
4HJ   CS      HS3   single        0.970 0.020     1.090
4HJ   CT      HT3   single        0.970 0.020     1.090
4HJ   CT      HT2   single        0.970 0.020     1.090
4HJ   CY2     HY2   single        0.930 0.020     1.080
4HJ   NR      HR    single        0.860 0.020     1.020
4HJ   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
4HJ   H1      N       H           107.76 3.000
4HJ   H1      N       CA          110.02 3.000
4HJ   H       N       CA          108.77 3.000
4HJ   HA      CA      CB          106.86 3.000
4HJ   HA      CA      C           107.44 3.000
4HJ   CB      CA      C           107.17 3.000
4HJ   HA      CA      N           106.36 3.000
4HJ   CB      CA      N           115.38 3.000
4HJ   C       CA      N           113.19 3.000
4HJ   HAA     CAA     CZ2         119.85 3.000
4HJ   HAA     CAA     CZ1         119.80 3.000
4HJ   CZ2     CAA     CZ1         120.34 3.000
4HJ   OXT     C       O           123.48 3.000
4HJ   OXT     C       CA          117.47 3.000
4HJ   O       C       CA          119.05 3.000
4HJ   HB2     CB      HB3         109.62 3.000
4HJ   HB2     CB      OG          108.22 3.000
4HJ   HB3     CB      OG          109.46 3.000
4HJ   HB2     CB      CA          107.29 3.000
4HJ   HB3     CB      CA          111.75 3.000
4HJ   OG      CB      CA          110.42 3.000
4HJ   P       OG      CB          118.55 3.000
4HJ   HZ1     CZ1     CY1         118.70 3.000
4HJ   HZ1     CZ1     CAA         121.53 3.000
4HJ   CY1     CZ1     CAA         119.76 3.000
4HJ   HZ2     CZ2     CY2         119.99 3.000
4HJ   HZ2     CZ2     CAA         120.02 3.000
4HJ   CY2     CZ2     CAA         120.00 3.000
4HJ   HJ3     CJ      HJ2         109.30 3.000
4HJ   HJ3     CJ      O3P         109.16 3.000
4HJ   HJ2     CJ      O3P         110.48 3.000
4HJ   HJ3     CJ      CK          107.21 3.000
4HJ   HJ2     CJ      CK          109.48 3.000
4HJ   O3P     CJ      CK          111.13 3.000
4HJ   CL3     CK      CL2         108.38 3.000
4HJ   CL2     CK      CL1         108.73 3.000
4HJ   CL3     CK      CL1         110.29 3.000
4HJ   CL1     CK      CJ          109.90 3.000
4HJ   CL2     CK      CJ          108.96 3.000
4HJ   CL3     CK      CJ          110.55 3.000
4HJ  HL13     CL1    HL11         109.53 3.000
4HJ  HL13     CL1    HL12         106.88 3.000
4HJ  HL11     CL1    HL12         108.85 3.000
4HJ  HL13     CL1     CK          111.30 3.000
4HJ  HL11     CL1     CK          111.07 3.000
4HJ  HL12     CL1     CK          109.08 3.000
4HJ  HL23     CL2    HL21         109.42 3.000
4HJ  HL23     CL2    HL22         108.76 3.000
4HJ  HL21     CL2    HL22         108.76 3.000
4HJ  HL23     CL2     CK          109.00 3.000
4HJ  HL21     CL2     CK          110.38 3.000
4HJ  HL22     CL2     CK          110.49 3.000
4HJ   CL3     CM      ON          119.44 3.000
4HJ   CL3     CM      NN          118.52 3.000
4HJ   ON      CM      NN          121.99 3.000
4HJ   HM      OM      CL3         107.10 3.000
4HJ   HN      NN      CO          114.37 3.000
4HJ   HN      NN      CM          114.63 3.000
4HJ   CO      NN      CM          118.98 3.000
4HJ   O3P     P       O2P         107.23 3.000
4HJ   O3P     P       O1P         107.29 3.000
4HJ   O2P     P       O1P         122.13 3.000
4HJ   O3P     P       OG           97.27 3.000
4HJ   O2P     P       OG          112.70 3.000
4HJ   O1P     P       OG          107.23 3.000
4HJ   P       O3P     CJ          118.40 3.000
4HJ   CY2     CX      CY1         118.34 3.000
4HJ   CY1     CX      CV          121.95 3.000
4HJ   CY2     CX      CV          119.71 3.000
4HJ   HL3     CL3     OM          103.91 3.000
4HJ   HL3     CL3     CM          110.41 3.000
4HJ   OM      CL3     CM          108.00 3.000
4HJ   HL3     CL3     CK          109.31 3.000
4HJ   OM      CL3     CK          112.53 3.000
4HJ   CM      CL3     CK          112.36 3.000
4HJ   HO3     CO      HO2         108.33 3.000
4HJ   HO3     CO      CP          109.50 3.000
4HJ   HO2     CO      CP          110.00 3.000
4HJ   HO3     CO      NN          108.54 3.000
4HJ   HO2     CO      NN          108.13 3.000
4HJ   CP      CO      NN          112.24 3.000
4HJ   HP3     CP      HP2         105.17 3.000
4HJ   HP3     CP      CQ          108.40 3.000
4HJ   HP2     CP      CQ          108.31 3.000
4HJ   HP3     CP      CO          111.19 3.000
4HJ   HP2     CP      CO          109.82 3.000
4HJ   CQ      CP      CO          113.57 3.000
4HJ   OR      CQ      NR          121.64 3.000
4HJ   NR      CQ      CP          114.71 3.000
4HJ   OR      CQ      CP          123.65 3.000
4HJ   HS3     CS      HS2         108.69 3.000
4HJ   HS3     CS      NR          108.93 3.000
4HJ   HS2     CS      NR          108.21 3.000
4HJ   HS3     CS      CT          107.45 3.000
4HJ   HS2     CS      CT          108.90 3.000
4HJ   NR      CS      CT          114.52 3.000
4HJ   HT2     CT      HT3         108.57 3.000
4HJ   HT2     CT      SU          109.05 3.000
4HJ   HT3     CT      SU          110.83 3.000
4HJ   HT2     CT      CS          110.04 3.000
4HJ   HT3     CT      CS          111.81 3.000
4HJ   SU      CT      CS          106.51 3.000
4HJ   SU      CV      OW          125.54 3.000
4HJ   OW      CV      CX          122.11 3.000
4HJ   SU      CV      CX          112.33 3.000
4HJ   CX      CY1     OZ          125.15 3.000
4HJ   OZ      CY1     CZ1         114.44 3.000
4HJ   CX      CY1     CZ1         120.40 3.000
4HJ   HY2     CY2     CX          119.26 3.000
4HJ   HY2     CY2     CZ2         119.61 3.000
4HJ   CX      CY2     CZ2         121.13 3.000
4HJ   HR      NR      CS          119.56 3.000
4HJ   HR      NR      CQ          117.74 3.000
4HJ   CS      NR      CQ          122.64 3.000
4HJ   CV      SU      CT          105.18 3.000
4HJ   HZ      OZ      CY1         110.08 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
4HJ CONST_01       CX      CY2     CZ2     CAA          -0.13   0.0 0
4HJ CONST_02       CX      CY1     CZ1     CAA           1.01   0.0 0
4HJ CONST_03       CY2     CZ2     CAA     CZ1          -0.49   0.0 0
4HJ CONST_04       CY2     CX      CY1     CZ1          -1.60   0.0 0
4HJ CONST_05       CY1     CZ1     CAA     CZ2           0.05   0.0 0
4HJ CONST_06       CY1     CX      CY2     CZ2           1.17   0.0 0
4HJ CONST_07       OZ      CY1     CZ1     CAA        -179.91   0.0 0
4HJ CONST_08       CV      CX      CY1     CZ1         178.55   0.0 0
4HJ CONST_09       CV      CX      CY2     CZ2        -178.98   0.0 0
4HJ CONST_10       CY2     CX      CY1     OZ          179.42   0.0 0
4HJ CONST_11       HY2     CY2     CZ2     CAA         179.62   0.0 0
4HJ CONST_12       HZ2     CZ2     CAA     CZ1         179.34   0.0 0
4HJ CONST_13       HZ1     CZ1     CAA     CZ2        -179.55   0.0 0
4HJ CONST_14       HAA     CAA     CZ1     CY1         179.69   0.0 0
4HJ CONST_15       CO      NN      CM      ON           28.73   0.0 0
4HJ CONST_16       CO      NN      CM      CL3        -154.04   0.0 0
4HJ CONST_17       CS      NR      CQ      CP         -178.73   0.0 0
4HJ CONST_18       OR      CQ      NR      CS            0.63   0.0 0
4HJ CONST_19       HN      NN      CM      ON          169.34   0.0 0
4HJ CONST_20       HR      NR      CQ      CP            4.03   0.0 0
4HJ Var_01         SU      CV      CX      CY1        -157.37  30.0 2
4HJ Var_02         O1P     P       OG      CB          168.16  30.0 3
4HJ Var_03         O3P     CJ      CK      CL1         -56.30  30.0 1
4HJ Var_04         CP      CO      NN      CM           69.24  30.0 3
4HJ Var_05         CQ      CP      CO      NN          168.25  30.0 1
4HJ Var_06         OR      CQ      CP      CO            2.99  30.0 3
4HJ Var_07         CT      CS      NR      CQ          -72.48  30.0 3
4HJ Var_08         SU      CT      CS      NR          171.99  30.0 3
4HJ Var_09        HL22     CL2     CK      CJ           65.67  30.0 3
4HJ Var_10        HL12     CL1     CK      CJ           74.92  30.0 3
4HJ Var_11         HB3     CB      OG      P            10.50  30.0 3
4HJ Var_12         HT3     CT      SU      CV           26.41  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
4HJ chir_01   CA      C       N       CB    negativ
4HJ chir_03   CL3     CM      OM      CK    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
4HJ plan-1    CAA 0.020
4HJ plan-1    CZ1 0.020
4HJ plan-1    CZ2 0.020
4HJ plan-1     CX 0.020
4HJ plan-1     CV 0.020
4HJ plan-1    CY1 0.020
4HJ plan-1    CY2 0.020
4HJ plan-1    HZ2 0.020
4HJ plan-1    HY2 0.020
4HJ plan-1    HAA 0.020
4HJ plan-1     OZ 0.020
4HJ plan-1    HZ1 0.020
4HJ plan-2     CX 0.020
4HJ plan-2     CV 0.020
4HJ plan-2     OW 0.020
4HJ plan-2     SU 0.020
4HJ plan-3     CM 0.020
4HJ plan-3     NN 0.020
4HJ plan-3     ON 0.020
4HJ plan-3    CL3 0.020
4HJ plan-3     CO 0.020
4HJ plan-3     HN 0.020
4HJ plan-4     CP 0.020
4HJ plan-4     CQ 0.020
4HJ plan-4     CS 0.020
4HJ plan-4     NR 0.020
4HJ plan-4     OR 0.020
4HJ plan-4     HR 0.020
4HJ plan-5     CA 0.020
4HJ plan-5      C 0.020
4HJ plan-5      O 0.020
4HJ plan-5    OXT 0.020
