# 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 15:22:18 2012
#
#   Inital geometry file: a 127 line input string
#   Ligand name: (E)-N~6~-[(1S,4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)-1-oxidodihydro-2H-thiopyran-3(4H)-ylidene]-L-lysine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=C1C[S@@](=O)C[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
OBS        OBS '(E)-N~6~-[(1S,4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)-1-oxidodihydro-2H-thiopyran-3(4H)-ylidene]-L-lysine' L-peptide 52 26 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_OBS
#
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
OBS         O4     O   O     .          3.6722   -3.0628   -6.9581
OBS         C11    C   C     .          3.2584   -3.9130   -6.1652
OBS         O3     O   OH1   .          3.3985   -5.2168   -6.5370
OBS         C10    C   CH2   .          2.6123   -3.7378   -4.8283
OBS         C9     C   CH2   .          3.1189   -2.4895   -4.1372
OBS         C8     C   CH1   .          2.2621   -2.0977   -2.9397
OBS         C7     C   CH2   .          1.3928   -0.9101   -3.2984
OBS         C5     C   CH2   .          1.1624   -0.7740   -0.3548
OBS         C3     C   CH1   .          3.0733   -1.8898   -1.6461
OBS         C2     C   CH2   .          3.9768   -0.6582   -1.6448
OBS         C1     C   C     .          4.9021   -0.6687   -0.4681
OBS         O1     O   O     .          5.5066   -1.6164    0.0436
OBS         O2     O   OH1   .          5.0839    0.5553    0.0982
OBS         C4     C   C     .          2.1360   -1.9150   -0.4363
OBS         NZ     N   N     .          1.9929   -2.8939    0.3893
OBS         CE     C   CH2   .          2.9936   -3.2559    1.3568
OBS         CD     C   CH2   .          2.4783   -4.2618    2.3870
OBS         CG     C   CH2   .          1.5882   -3.6073    3.4209
OBS         CB     C   CH2   .          1.1902   -4.6006    4.4904
OBS         CA     C   CH1   .          0.2605   -3.9610    5.5346
OBS         N      N   NH2   .          0.9623   -3.2791    6.5961
OBS         C      C   C     .         -0.6934   -5.0428    6.0362
OBS         O      O   O     .         -0.4465   -6.2235    6.3020
OBS         OXT    O   OH1   .         -1.9781   -4.6297    6.2053
OBS         S6     S   S3    .          0.4349   -0.4235   -1.9137
OBS         O5     O   O     .         -0.8922    0.2368   -2.0440
OBS        H3      H   HOH1  .          3.8226   -5.2653   -7.4103
OBS        H101    H   HCH2  .          2.8083   -4.6508   -4.2046
OBS        H102    H   HCH2  .          1.5034   -3.6726   -4.9990
OBS        H9C1    H   HCH2  .          3.1168   -1.6379   -4.8720
OBS        H9C2    H   HCH2  .          4.1849   -2.6386   -3.8245
OBS        H8      H   HCH1  .          1.5760   -2.9730   -2.7351
OBS        H7C1    H   HCH2  .          2.0122   -0.0732   -3.7088
OBS        H7C2    H   HCH2  .          0.6770   -1.1957   -4.1125
OBS        H5C1    H   HCH2  .          0.3153   -1.0070    0.3476
OBS        H5C2    H   HCH2  .          1.6786    0.1182    0.0861
OBS        HA      H   HCH1  .          3.7660   -2.7823   -1.5721
OBS        H2C1    H   HCH2  .          4.6325   -0.6578   -2.5578
OBS        H2C2    H   HCH2  .          3.4012    0.3049   -1.6538
OBS        H2      H   HOH1  .          5.6918    0.4807    0.8530
OBS        HEC1    H   HCH2  .          3.3647   -2.3397    1.9082
OBS        HEC2    H   HCH2  .          3.8847   -3.7192    0.8391
OBS        HDC1    H   HCH2  .          3.3747   -4.7111    2.8905
OBS        HDC2    H   HCH2  .          1.9238   -5.0927    1.8790
OBS        HGC1    H   HCH2  .          0.6673   -3.2009    2.9251
OBS        HGC2    H   HCH2  .          2.1253   -2.7390    3.8858
OBS        HBC1    H   HCH2  .          2.1047   -5.0144    4.9899
OBS        HBC2    H   HCH2  .          0.6382   -5.4597    4.0230
OBS        HB      H   HCH1  .         -0.3861   -3.1906    5.0105
OBS        HN1     H   HNH2  .          0.8030   -3.7320    7.4756
OBS        HN2     H   HNH2  .          1.9464   -3.2418    6.4169
OBS        HXT     H   HOH1  .         -2.5213   -5.3699    6.5245
#
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
OBS   O4      C11   double        1.234 0.020
OBS   C11     O3    single        1.363 0.020
OBS   C11     C10   single        1.495 0.020
OBS   O3     H3     single        0.972 0.020
OBS   C10     C9    single        1.514 0.020
OBS   C10    H101   single        1.123 0.020
OBS   C10    H102   single        1.124 0.020
OBS   C9      C8    single        1.524 0.020
OBS   C9     H9C1   single        1.125 0.020
OBS   C9     H9C2   single        1.121 0.020
OBS   C8      C7    single        1.515 0.020
OBS   C8      C3    single        1.541 0.020
OBS   C8     H8     single        1.131 0.020
OBS   C7      S6    single        1.753 0.020
OBS   C7     H7C1   single        1.119 0.020
OBS   C7     H7C2   single        1.121 0.020
OBS   C5      C4    single        1.502 0.020
OBS   C5      S6    single        1.756 0.020
OBS   C5     H5C1   single        1.125 0.020
OBS   C5     H5C2   single        1.121 0.020
OBS   C3      C2    single        1.527 0.020
OBS   C3      C4    single        1.531 0.020
OBS   C3     HA     single        1.132 0.020
OBS   C2      C1    single        1.497 0.020
OBS   C2     H2C1   single        1.124 0.020
OBS   C2     H2C2   single        1.122 0.020
OBS   C1      O1    double        1.235 0.020
OBS   C1      O2    single        1.361 0.020
OBS   O2     H2     single        0.972 0.020
OBS   C4      NZ    double        1.289 0.020
OBS   NZ      CE    single        1.438 0.020
OBS   CE      CD    single        1.529 0.020
OBS   CE     HEC1   single        1.132 0.020
OBS   CE     HEC2   single        1.130 0.020
OBS   CD      CG    single        1.513 0.020
OBS   CD     HDC1   single        1.122 0.020
OBS   CD     HDC2   single        1.121 0.020
OBS   CG      CB    single        1.513 0.020
OBS   CG     HGC1   single        1.122 0.020
OBS   CG     HGC2   single        1.122 0.020
OBS   CB      CA    single        1.537 0.020
OBS   CB     HBC1   single        1.121 0.020
OBS   CB     HBC2   single        1.123 0.020
OBS   CA      N     single        1.444 0.020
OBS   CA      C     single        1.527 0.020
OBS   CA     HB     single        1.134 0.020
OBS   N      HN1    single        1.002 0.020
OBS   N      HN2    single        1.001 0.020
OBS   C       O     double        1.235 0.020
OBS   C       OXT   single        1.360 0.020
OBS   OXT    HXT    single        0.972 0.020
OBS   S6      O5    double        1.488 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
OBS   C10     C11     O3          113.60 3.000
OBS   C10     C11     O4          129.70 3.000
OBS   O3      C11     O4          116.70 3.000
OBS  H3       O3      C11         109.73 3.000
OBS  H102     C10    H101         107.68 3.000
OBS  H102     C10     C9          110.59 3.000
OBS  H101     C10     C9          111.01 3.000
OBS  H102     C10     C11         107.29 3.000
OBS  H101     C10     C11         109.02 3.000
OBS   C9      C10     C11         111.11 3.000
OBS  H9C2     C9     H9C1         106.54 3.000
OBS  H9C2     C9      C8          110.47 3.000
OBS  H9C1     C9      C8          108.52 3.000
OBS  H9C2     C9      C10         109.62 3.000
OBS  H9C1     C9      C10         108.99 3.000
OBS   C8      C9      C10         112.49 3.000
OBS  H8       C8      C3          105.78 3.000
OBS  H8       C8      C7          107.55 3.000
OBS   C3      C8      C7          113.27 3.000
OBS  H8       C8      C9          106.52 3.000
OBS   C3      C8      C9          113.48 3.000
OBS   C7      C8      C9          109.76 3.000
OBS  H7C2     C7     H7C1         106.12 3.000
OBS  H7C2     C7      S6          107.19 3.000
OBS  H7C1     C7      S6          112.62 3.000
OBS  H7C2     C7      C8          109.80 3.000
OBS  H7C1     C7      C8          110.82 3.000
OBS   S6      C7      C8          110.13 3.000
OBS  H5C2     C5     H5C1         105.42 3.000
OBS  H5C2     C5      S6          112.40 3.000
OBS  H5C1     C5      S6          106.49 3.000
OBS  H5C2     C5      C4          109.11 3.000
OBS  H5C1     C5      C4          111.39 3.000
OBS   S6      C5      C4          111.84 3.000
OBS  HA       C3      C4          108.06 3.000
OBS  HA       C3      C2          105.88 3.000
OBS   C4      C3      C2          112.02 3.000
OBS  HA       C3      C8          105.70 3.000
OBS   C4      C3      C8          109.81 3.000
OBS   C2      C3      C8          114.89 3.000
OBS  H2C2     C2     H2C1         107.01 3.000
OBS  H2C2     C2      C1          109.23 3.000
OBS  H2C1     C2      C1          106.13 3.000
OBS  H2C2     C2      C3          112.87 3.000
OBS  H2C1     C2      C3          110.17 3.000
OBS   C1      C2      C3          111.14 3.000
OBS   O2      C1      O1          116.90 3.000
OBS   O2      C1      C2          113.79 3.000
OBS   O1      C1      C2          129.31 3.000
OBS  H2       O2      C1          109.73 3.000
OBS   NZ      C4      C3          125.94 3.000
OBS   NZ      C4      C5          118.06 3.000
OBS   C3      C4      C5          115.29 3.000
OBS   CE      NZ      C4          123.02 3.000
OBS  HEC2     CE     HEC1         107.25 3.000
OBS  HEC2     CE      CD          107.74 3.000
OBS  HEC1     CE      CD          108.35 3.000
OBS  HEC2     CE      NZ          110.10 3.000
OBS  HEC1     CE      NZ          110.61 3.000
OBS   CD      CE      NZ          112.60 3.000
OBS  HDC2     CD     HDC1         107.56 3.000
OBS  HDC2     CD      CG          109.84 3.000
OBS  HDC1     CD      CG          109.67 3.000
OBS  HDC2     CD      CE          110.43 3.000
OBS  HDC1     CD      CE          107.25 3.000
OBS   CG      CD      CE          111.96 3.000
OBS  HGC2     CG     HGC1         107.21 3.000
OBS  HGC2     CG      CB          109.95 3.000
OBS  HGC1     CG      CB          109.53 3.000
OBS  HGC2     CG      CD          109.65 3.000
OBS  HGC1     CG      CD          109.73 3.000
OBS   CB      CG      CD          110.72 3.000
OBS  HBC2     CB     HBC1         107.70 3.000
OBS  HBC2     CB      CA          107.68 3.000
OBS  HBC1     CB      CA          110.13 3.000
OBS  HBC2     CB      CG          109.72 3.000
OBS  HBC1     CB      CG          110.04 3.000
OBS   CA      CB      CG          111.47 3.000
OBS  HB       CA      C           106.07 3.000
OBS  HB       CA      N           107.22 3.000
OBS   C       CA      N           113.37 3.000
OBS  HB       CA      CB          108.27 3.000
OBS   C       CA      CB          107.82 3.000
OBS   N       CA      CB          113.70 3.000
OBS  HN2      N      HN1          109.29 3.000
OBS  HN2      N       CA          111.33 3.000
OBS  HN1      N       CA          110.77 3.000
OBS   OXT     C       O           116.90 3.000
OBS   OXT     C       CA          114.57 3.000
OBS   O       C       CA          128.54 3.000
OBS  HXT      OXT     C           109.72 3.000
OBS   O5      S6      C5          122.41 3.000
OBS   O5      S6      C7          122.78 3.000
OBS   C5      S6      C7          114.81 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
OBS CONST_01       H3      O3      C11     O4           -0.02   0.0 0
OBS CONST_02       H2      O2      C1      C2          179.99   0.0 0
OBS CONST_03       HXT     OXT     C       CA          179.99   0.0 0
OBS Var_01         C5      S6      C7      C8           28.49  30.0 1
OBS Var_02         C4      C5      S6      C7          -24.92  30.0 1
OBS Var_03         S6      C5      C4      C3           43.34  30.0 1
OBS Var_04         C8      C9      C10     C11         166.49  30.0 3
OBS Var_05         O1      C1      C2      C3           39.44  30.0 3
OBS Var_06         CD      CE      NZ      C4          168.79  30.0 3
OBS Var_07         C9      C10     C11     O4          -30.73  30.0 3
OBS Var_08         CG      CD      CE      NZ          -76.34  30.0 3
OBS Var_09         CB      CG      CD      CE         -175.19  30.0 3
OBS Var_10         CA      CB      CG      CD         -178.80  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
OBS chir_01   C8      C9      C7      C3    positiv
OBS chir_02   C3      C4      C2      C8    positiv
OBS 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
OBS plan-1     O4 0.020
OBS plan-1    C11 0.020
OBS plan-1     O3 0.020
OBS plan-1    C10 0.020
OBS plan-1     H3 0.020
OBS plan-2     C2 0.020
OBS plan-2     C1 0.020
OBS plan-2     O1 0.020
OBS plan-2     O2 0.020
OBS plan-2     H2 0.020
OBS plan-3     CA 0.020
OBS plan-3      C 0.020
OBS plan-3      O 0.020
OBS plan-3    OXT 0.020
OBS plan-3    HXT 0.020
OBS plan-4     C7 0.020
OBS plan-4     C5 0.020
OBS plan-4     S6 0.020
OBS plan-4     O5 0.020
