# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:44:56 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: S-{2-[(E)-(1-carboxyethylidene)amino]ethyl}-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=NCCSC[C@H](N)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
 KPY  KPY  S-{2-[(E)-(1-carboxyethylidene)amino]ethyl}-L-cysteine  L-peptide  27  15  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_KPY
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
 KPY  NZ    N  N      0  -0.364  -11.0006  17.4558  15.8439
 KPY  CE    C  CH2    0  -0.304   -9.8027  16.8314  15.3262
 KPY  CD    C  CH2    0  -0.541  -10.0428  15.3416  15.1438
 KPY  SG    S  S2     0  -0.060   -8.5303  14.5581  14.5181
 KPY  CB    C  CH2    0  -0.525   -9.0490  12.8187  14.5885
 KPY  CA    C  CH1    0  -0.201   -7.9643  11.8922  14.0429
 KPY  C     C  C      0   0.389   -6.6469  12.1024  14.8300
 KPY  O     O  O      0  -0.607   -6.6224  11.6143  15.9792
 KPY  N     N  NH2    0  -0.790   -8.4856  10.5297  14.1053
 KPY  OL1   O  OC    -1  -0.588  -13.0578  18.6982  17.2465
 KPY  CL    C  C      0   0.366  -12.3100  19.3643  16.5129
 KPY  OL2   O  O      0  -0.593  -12.4915  20.5158  16.0718
 KPY  CI    C  C      0   0.081  -10.9993  18.7086  16.0517
 KPY  CK    C  CH3    0  -0.747   -9.8211  19.6076  15.8023
 KPY  OXT   O  OC    -1  -0.603   -5.7412  12.7462  14.2658
 KPY  HE1C  H  HCH2   0   0.230   -9.5035  17.2756  14.3686
 KPY  HE2C  H  HCH2   0   0.231   -8.9539  16.9771  16.0062
 KPY  HD1C  H  HCH2   0   0.254  -10.3123  14.8873  16.0997
 KPY  HD2C  H  HCH2   0   0.253  -10.8653  15.1712  14.4460
 KPY  HB1C  H  HCH2   0   0.246   -9.2695  12.5584  15.6269
 KPY  HB2C  H  HCH2   0   0.256   -9.9647  12.6965  14.0070
 KPY  HA    H  HCH1   0   0.212   -7.8007  12.1402  12.9904
 KPY  HN1   H  HNH2   0   0.339   -7.8692   9.9210  13.5797
 KPY  HN2   H  HNH2   0   0.326   -8.4046  10.2181  15.0674
 KPY  HK1C  H  HCH3   0   0.249   -9.9682  20.5976  16.2239
 KPY  HK2C  H  HCH3   0   0.241   -8.9050  19.1839  16.2177
 KPY  HK3C  H  HCH3   0   0.249   -9.6469  19.7273  14.7290

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
 KPY  NZ   CE    single  1.447  0.020  1.447
 KPY  NZ   CI    double  1.270  0.020  1.270
 KPY  CE   CD    single  1.520  0.020  1.520
 KPY  CD   SG    single  1.815  0.020  1.815
 KPY  CB   SG    single  1.817  0.020  1.817
 KPY  CB   CA    single  1.530  0.020  1.530
 KPY  CA   C     single  1.525  0.021  1.525
 KPY  CA   N     single  1.458  0.019  1.458
 KPY  C    O     deloc   1.231  0.020  1.231
 KPY  C    OXT   deloc   1.246  0.020  1.246
 KPY  OL1  CL    deloc   1.241  0.020  1.241
 KPY  CL   OL2   deloc   1.246  0.020  1.246
 KPY  CL   CI    single  1.536  0.020  1.536
 KPY  CI   CK    single  1.503  0.020  1.503
 KPY  CE   HE1C  single  0.970  0.020  1.090
 KPY  CE   HE2C  single  0.970  0.020  1.090
 KPY  CD   HD1C  single  0.970  0.020  1.090
 KPY  CD   HD2C  single  0.970  0.020  1.090
 KPY  CB   HB1C  single  0.970  0.020  1.090
 KPY  CB   HB2C  single  0.970  0.020  1.090
 KPY  CA   HA    single  0.970  0.020  0.970
 KPY  N    HN1   single  0.890  0.020  1.040
 KPY  N    HN2   single  0.890  0.020  1.040
 KPY  CK   HK1C  single  0.970  0.020  1.090
 KPY  CK   HK2C  single  0.970  0.020  1.090
 KPY  CK   HK3C  single  0.970  0.020  1.090

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
 KPY  CI    NZ  CE    118.91  3.000
 KPY  HE2C  CE  HE1C  106.03  3.000
 KPY  HE2C  CE  CD    109.07  3.000
 KPY  HE1C  CE  CD    109.58  3.000
 KPY  HE2C  CE  NZ    111.19  3.000
 KPY  HE1C  CE  NZ    111.31  3.000
 KPY  CD    CE  NZ    109.59  3.000
 KPY  HD2C  CD  HD1C  107.97  3.000
 KPY  HD2C  CD  SG    109.88  3.000
 KPY  HD1C  CD  SG    109.14  3.000
 KPY  HD2C  CD  CE    110.40  3.000
 KPY  HD1C  CD  CE    109.98  3.000
 KPY  SG    CD  CE    109.45  3.000
 KPY  CB    SG  CD     99.32  3.000
 KPY  HB2C  CB  HB1C  108.07  3.000
 KPY  HB2C  CB  CA    109.73  3.000
 KPY  HB1C  CB  CA    109.77  3.000
 KPY  HB2C  CB  SG    109.03  3.000
 KPY  HB1C  CB  SG    108.81  3.000
 KPY  CA    CB  SG    111.36  3.000
 KPY  HA    CA  N     110.00  3.000
 KPY  HA    CA  C     109.00  3.000
 KPY  N     CA  C     111.00  2.800
 KPY  HA    CA  CB    109.00  3.000
 KPY  N     CA  CB    110.50  1.700
 KPY  C     CA  CB    110.10  1.900
 KPY  OXT   C   O     127.18  3.000
 KPY  OXT   C   CA    117.27  3.000
 KPY  O     C   CA    120.80  1.700
 KPY  HN2   N   HN1   105.00  3.000
 KPY  HN2   N   CA    107.37  3.000
 KPY  HN1   N   CA    108.74  3.000
 KPY  CI    CL  OL2   114.35  3.000
 KPY  CI    CL  OL1   117.54  3.000
 KPY  OL2   CL  OL1   128.10  3.000
 KPY  CK    CI  CL    117.60  3.000
 KPY  CK    CI  NZ    124.32  3.000
 KPY  CL    CI  NZ    117.98  3.000
 KPY  HK3C  CK  HK2C  106.40  3.000
 KPY  HK3C  CK  HK1C  107.62  3.000
 KPY  HK2C  CK  HK1C  108.65  3.000
 KPY  HK3C  CK  CI    110.68  3.000
 KPY  HK2C  CK  CI    111.26  3.000
 KPY  HK1C  CK  CI    112.00  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
 KPY  Var_01  CL    CI  NZ  CE   176.03   0.0  2
 KPY  Var_02  SG    CD  CE  NZ  -179.15  30.0  3
 KPY  Var_03  OL1   CL  CI  NZ    33.86  30.0  2
 KPY  Var_04  CA    CB  SG  CD   177.34  30.0  1
 KPY  Var_05  HK1C  CK  CI  NZ  -168.90  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
 KPY  chir_01  CA  CB  C  N  negativ

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
 KPY  plan-1  CA   0.020
 KPY  plan-1  C    0.020
 KPY  plan-1  O    0.020
 KPY  plan-1  OXT  0.020
 KPY  plan-2  OL1  0.020
 KPY  plan-2  CL   0.020
 KPY  plan-2  OL2  0.020
 KPY  plan-2  CI   0.020
 KPY  plan-3  NZ   0.020
 KPY  plan-3  CE   0.020
 KPY  plan-3  CL   0.020
 KPY  plan-3  CI   0.020
 KPY  plan-3  CK   0.020

