# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-1137 (Mon Aug 22 05:16:00 2012)
#   - file written: Tue Aug 28 15:03:13 2012
#
#   Inital geometry file: a 122 line input string
#   Ligand name: (E)-N~6~-[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)dihydro-2H-thiopyran-3(4H)-ylidene]-L-lysine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=C1CSC[C@@H](CCC(O)=O)[C@H]1CC(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
C1X        C1X '(E)-N~6~-[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)dihydro-2H-thiopyran-3(4H)-ylidene]-L-lysine' L-peptide 51 25 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_C1X
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
C1X         O4     O   O     .         -6.7137    2.4221   -3.4724
C1X         C11    C   C     .         -6.7147    1.1906   -3.5520
C1X         O3     O   OH1   .         -7.8587    0.6094   -4.0139
C1X         C10    C   CH2   .         -5.6385    0.2102   -3.2162
C1X         C9     C   CH2   .         -4.5837    0.8484   -2.3389
C1X         C8     C   CH1   .         -3.5813   -0.1553   -1.7776
C1X         C7     C   CH2   .         -4.1164   -0.7173   -0.4737
C1X         C5     C   CH2   .         -1.5337   -1.4523    0.0321
C1X         C3     C   CH1   .         -2.1463    0.3866   -1.6519
C1X         C2     C   CH2   .         -1.9783    1.5992   -0.7331
C1X         C1     C   C     .         -1.4329    2.7839   -1.4713
C1X         O1     O   O     .         -0.3209    3.3087   -1.3572
C1X         O2     O   OH1   .         -2.2905    3.3353   -2.3713
C1X         C4     C   C     .         -1.1994   -0.7456   -1.2599
C1X         NZ     N   N     .         -0.2162   -1.2152   -1.9440
C1X         CE     C   CH2   .         -0.2916   -1.7427   -3.2744
C1X         CD     C   CH2   .          0.8221   -1.2372   -4.1956
C1X         CG     C   CH2   .          0.7698    0.2626   -4.3801
C1X         CB     C   CH2   .          1.7040    0.7087   -5.4840
C1X         CA     C   CH1   .          1.4984    2.1774   -5.8954
C1X         N      N   NH2   .          1.3826    3.0820   -4.7838
C1X         C      C   C     .          0.3137    2.2210   -6.8613
C1X         O      O   O     .         -0.8981    2.1699   -6.6181
C1X         S6     S   S2    .         -3.1727   -2.0970    0.0745
C1X         OXT    O   OH1   .          0.6645    2.3338   -8.1682
C1X        H3      H   HOH1  .         -8.5160    1.2958   -4.2134
C1X        H101    H   HCH2  .         -5.1888   -0.1420   -4.1877
C1X        H102    H   HCH2  .         -6.0984   -0.6785   -2.7087
C1X        H9C1    H   HCH2  .         -5.0849    1.3626   -1.4741
C1X        H9C2    H   HCH2  .         -4.0592    1.6500   -2.9218
C1X        H8      H   HCH1  .         -3.5230   -1.0072   -2.5179
C1X        H7C1    H   HCH2  .         -4.1555    0.0785    0.3104
C1X        H7C2    H   HCH2  .         -5.1557   -1.1062   -0.6172
C1X        H5C1    H   HCH2  .         -0.8745   -2.3463    0.1977
C1X        H5C2    H   HCH2  .         -1.3582   -0.7532    0.8869
C1X        HA      H   HCH1  .         -1.8719    0.7394   -2.6909
C1X        H2C1    H   HCH2  .         -2.9654    1.9098   -0.2954
C1X        H2C2    H   HCH2  .         -1.2838    1.3842    0.1199
C1X        H2      H   HOH1  .         -1.8711    4.0994   -2.8126
C1X        HEC1    H   HCH2  .         -1.2750   -1.5743   -3.8007
C1X        HEC2    H   HCH2  .         -0.1641   -2.8607   -3.1593
C1X        HDC1    H   HCH2  .          0.6874   -1.7469   -5.1860
C1X        HDC2    H   HCH2  .          1.8259   -1.5355   -3.7958
C1X        HGC1    H   HCH2  .          1.0492    0.7695   -3.4178
C1X        HGC2    H   HCH2  .         -0.2830    0.5821   -4.6197
C1X        HBC1    H   HCH2  .          1.5509    0.0793   -6.4000
C1X        HBC2    H   HCH2  .          2.7682    0.5776   -5.1526
C1X        HB      H   HCH1  .          2.4063    2.4978   -6.4951
C1X        HN1     H   HNH2  .          2.2612    3.2054   -4.3224
C1X        HN2     H   HNH2  .          1.0151    3.9731   -5.0572
C1X        HXT     H   HOH1  .         -0.1316    2.3565   -8.7255
#
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
C1X   O4      C11   double        1.234 0.020
C1X   C11     O3    single        1.364 0.020
C1X   C11     C10   single        1.494 0.020
C1X   O3     H3     single        0.971 0.020
C1X   C10     C9    single        1.513 0.020
C1X   C10    H101   single        1.127 0.020
C1X   C10    H102   single        1.122 0.020
C1X   C9      C8    single        1.526 0.020
C1X   C9     H9C1   single        1.124 0.020
C1X   C9     H9C2   single        1.121 0.020
C1X   C8      C7    single        1.517 0.020
C1X   C8      C3    single        1.539 0.020
C1X   C8     H8     single        1.130 0.020
C1X   C7      S6    single        1.759 0.020
C1X   C7     H7C1   single        1.118 0.020
C1X   C7     H7C2   single        1.119 0.020
C1X   C5      C4    single        1.510 0.020
C1X   C5      S6    single        1.762 0.020
C1X   C5     H5C1   single        1.123 0.020
C1X   C5     H5C2   single        1.118 0.020
C1X   C3      C2    single        1.531 0.020
C1X   C3      C4    single        1.527 0.020
C1X   C3     HA     single        1.131 0.020
C1X   C2      C1    single        1.499 0.020
C1X   C2     H2C1   single        1.124 0.020
C1X   C2     H2C2   single        1.121 0.020
C1X   C1      O1    double        1.235 0.020
C1X   C1      O2    single        1.360 0.020
C1X   O2     H2     single        0.977 0.020
C1X   C4      NZ    double        1.287 0.020
C1X   NZ      CE    single        1.433 0.020
C1X   CE      CD    single        1.531 0.020
C1X   CE     HEC1   single        1.128 0.020
C1X   CE     HEC2   single        1.131 0.020
C1X   CD      CG    single        1.512 0.020
C1X   CD     HDC1   single        1.122 0.020
C1X   CD     HDC2   single        1.121 0.020
C1X   CG      CB    single        1.513 0.020
C1X   CG     HGC1   single        1.123 0.020
C1X   CG     HGC2   single        1.126 0.020
C1X   CB      CA    single        1.539 0.020
C1X   CB     HBC1   single        1.122 0.020
C1X   CB     HBC2   single        1.122 0.020
C1X   CA      N     single        1.438 0.020
C1X   CA      C     single        1.529 0.020
C1X   CA     HB     single        1.134 0.020
C1X   N      HN1    single        1.000 0.020
C1X   N      HN2    single        1.002 0.020
C1X   C       O     double        1.237 0.020
C1X   C       OXT   single        1.358 0.020
C1X   OXT    HXT    single        0.972 0.020
#
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
C1X   C10     C11     O3          113.62 3.000
C1X   C10     C11     O4          129.77 3.000
C1X   O3      C11     O4          116.61 3.000
C1X  H3       O3      C11         109.64 3.000
C1X  H102     C10    H101         107.81 3.000
C1X  H102     C10     C9          110.95 3.000
C1X  H101     C10     C9          110.70 3.000
C1X  H102     C10     C11         109.04 3.000
C1X  H101     C10     C11         107.38 3.000
C1X   C9      C10     C11         110.83 3.000
C1X  H9C2     C9     H9C1         106.35 3.000
C1X  H9C2     C9      C8          110.74 3.000
C1X  H9C1     C9      C8          108.11 3.000
C1X  H9C2     C9      C10         109.04 3.000
C1X  H9C1     C9      C10         109.16 3.000
C1X   C8      C9      C10         113.19 3.000
C1X  H8       C8      C3          105.71 3.000
C1X  H8       C8      C7          107.58 3.000
C1X   C3      C8      C7          112.90 3.000
C1X  H8       C8      C9          106.79 3.000
C1X   C3      C8      C9          114.27 3.000
C1X   C7      C8      C9          109.15 3.000
C1X  H7C2     C7     H7C1         107.75 3.000
C1X  H7C2     C7      S6          105.40 3.000
C1X  H7C1     C7      S6          111.01 3.000
C1X  H7C2     C7      C8          110.25 3.000
C1X  H7C1     C7      C8          110.58 3.000
C1X   S6      C7      C8          111.66 3.000
C1X  H5C2     C5     H5C1         107.03 3.000
C1X  H5C2     C5      S6          110.88 3.000
C1X  H5C1     C5      S6          104.55 3.000
C1X  H5C2     C5      C4          109.07 3.000
C1X  H5C1     C5      C4          111.64 3.000
C1X   S6      C5      C4          113.44 3.000
C1X  HA       C3      C4          108.46 3.000
C1X  HA       C3      C2          106.12 3.000
C1X   C4      C3      C2          111.42 3.000
C1X  HA       C3      C8          105.13 3.000
C1X   C4      C3      C8          109.76 3.000
C1X   C2      C3      C8          115.48 3.000
C1X  H2C2     C2     H2C1         107.51 3.000
C1X  H2C2     C2      C1          107.51 3.000
C1X  H2C1     C2      C1          107.05 3.000
C1X  H2C2     C2      C3          111.89 3.000
C1X  H2C1     C2      C3          110.88 3.000
C1X   C1      C2      C3          111.75 3.000
C1X   O2      C1      O1          117.17 3.000
C1X   O2      C1      C2          114.64 3.000
C1X   O1      C1      C2          128.18 3.000
C1X  H2       O2      C1          110.20 3.000
C1X   NZ      C4      C3          127.44 3.000
C1X   NZ      C4      C5          116.95 3.000
C1X   C3      C4      C5          115.43 3.000
C1X   CE      NZ      C4          126.00 3.000
C1X  HEC2     CE     HEC1         107.05 3.000
C1X  HEC2     CE      CD          107.79 3.000
C1X  HEC1     CE      CD          107.70 3.000
C1X  HEC2     CE      NZ          105.28 3.000
C1X  HEC1     CE      NZ          115.09 3.000
C1X   CD      CE      NZ          113.50 3.000
C1X  HDC2     CD     HDC1         107.54 3.000
C1X  HDC2     CD      CG          109.78 3.000
C1X  HDC1     CD      CG          109.81 3.000
C1X  HDC2     CD      CE          110.42 3.000
C1X  HDC1     CD      CE          107.09 3.000
C1X   CG      CD      CE          112.07 3.000
C1X  HGC2     CG     HGC1         106.67 3.000
C1X  HGC2     CG      CB          109.77 3.000
C1X  HGC1     CG      CB          109.79 3.000
C1X  HGC2     CG      CD          109.86 3.000
C1X  HGC1     CG      CD          109.55 3.000
C1X   CB      CG      CD          111.10 3.000
C1X  HBC2     CB     HBC1         107.76 3.000
C1X  HBC2     CB      CA          108.49 3.000
C1X  HBC1     CB      CA          107.39 3.000
C1X  HBC2     CB      CG          109.60 3.000
C1X  HBC1     CB      CG          110.24 3.000
C1X   CA      CB      CG          113.19 3.000
C1X  HB       CA      C           106.15 3.000
C1X  HB       CA      N           107.19 3.000
C1X   C       CA      N           114.08 3.000
C1X  HB       CA      CB          107.70 3.000
C1X   C       CA      CB          107.43 3.000
C1X   N       CA      CB          113.86 3.000
C1X  HN2      N      HN1          109.78 3.000
C1X  HN2      N       CA          112.21 3.000
C1X  HN1      N       CA          111.32 3.000
C1X   OXT     C       O           116.47 3.000
C1X   OXT     C       CA          114.22 3.000
C1X   O       C       CA          129.32 3.000
C1X   C5      S6      C7          101.80 3.000
C1X  HXT      OXT     C           110.01 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
C1X CONST_01       H3      O3      C11     O4           -0.01   0.0 0
C1X CONST_02       H2      O2      C1      C2          179.96   0.0 0
C1X CONST_03       HXT     OXT     C       CA         -179.96   0.0 0
C1X Var_01         C4      C5      S6      C7          -48.40  30.0 1
C1X Var_02         S6      C5      C4      C3           55.43  30.0 1
C1X Var_03        H7C1     C7      S6      C5          -71.87  30.0 1
C1X Var_04         C8      C9      C10     C11         170.65  30.0 3
C1X Var_05         O1      C1      C2      C3         -111.01  30.0 3
C1X Var_06         CD      CE      NZ      C4          134.59  30.0 3
C1X Var_07         C9      C10     C11     O4           17.14  30.0 3
C1X Var_08         CG      CD      CE      NZ          -61.93  30.0 3
C1X Var_09         CB      CG      CD      CE         -169.42  30.0 3
C1X Var_10         CA      CB      CG      CD          169.09  30.0 3
#
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
C1X chir_01   C8      C9      C7      C3    positiv
C1X chir_02   C3      C4      C2      C8    positiv
C1X chir_03   CA      CB      N       C     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
C1X plan-1     O4 0.020
C1X plan-1    C11 0.020
C1X plan-1     O3 0.020
C1X plan-1    C10 0.020
C1X plan-1     H3 0.020
C1X plan-2     C2 0.020
C1X plan-2     C1 0.020
C1X plan-2     O1 0.020
C1X plan-2     O2 0.020
C1X plan-2     H2 0.020
C1X plan-3     CA 0.020
C1X plan-3      C 0.020
C1X plan-3      O 0.020
C1X plan-3    OXT 0.020
C1X plan-3    HXT 0.020
