# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:56:25 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (2S)-2-amino-5-({(1R)-2-[(carboxylatomethyl)amino]-1-[(nitrososulfanyl)methyl]-2-oxoethyl}amino)-5-oxopentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC([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
 GSN  GSN  (2S)-2-amino-5-({(1R)-2-[(carboxylatomethyl)amino]-1-[(nitrososulfanyl)methyl]-2-oxoethyl}amino)-5-oxopentanoate  ligand  36  22  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GSN
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
 GSN  OXT   O  OC    -1  -0.608   6.5078   0.7071  -0.8563
 GSN  C     C  C      0   0.384   5.7046   0.2772  -0.0043
 GSN  O     O  O      0  -0.618   5.7525  -0.8302   0.5697
 GSN  CA    C  CH1    0  -0.213   4.5022   1.1817   0.3667
 GSN  N     N  NH2    0  -0.787   4.6154   2.5722  -0.0450
 GSN  CB    C  CH2    0  -0.422   3.2275   0.5688  -0.2185
 GSN  CAG   C  CH2    0  -0.560   1.9612   1.2797   0.2504
 GSN  CAH   C  C      0   0.553   0.7250   0.7133  -0.4050
 GSN  OAI   O  O      0  -0.494   0.6167   0.6248  -1.6192
 GSN  NAJ   N  NH1    0  -0.630  -0.2417   0.3086   0.4473
 GSN  CAK   C  CH1    0  -0.203  -1.4820  -0.2803   0.0318
 GSN  CAL   C  CH2    0  -0.597  -1.5503  -1.7657   0.4111
 GSN  SAM   S  S2     0   0.212  -0.2112  -2.7291  -0.3065
 GSN  NAN   N  N      0  -0.001   0.9113  -2.5260   1.0376
 GSN  OAV   O  O      0  -0.247   1.9757  -3.0134   0.8822
 GSN  CAO   C  C      0   0.559  -2.6553   0.4280   0.7121
 GSN  OAP   O  O      0  -0.500  -2.5697   0.8068   1.8737
 GSN  NAQ   N  NH1    0  -0.625  -3.7493   0.5333  -0.0346
 GSN  CAR   C  CH2    0  -0.414  -5.0053   1.0662   0.4291
 GSN  CAS   C  C      0   0.401  -6.0717   0.9875  -0.6836
 GSN  OAU   O  OC    -1  -0.607  -7.1988   1.4026  -0.3676
 GSN  OAT   O  O      0  -0.598  -5.7087   0.5244  -1.7820
 GSN  HA    H  HCH1   0   0.210   4.4037   1.1668   1.4584
 GSN  HN1   H  HNH2   0   0.336   5.3705   3.0048   0.4732
 GSN  HN2   H  HNH2   0   0.324   4.9338   2.5824  -1.0078
 GSN  HB1   H  HCH2   0   0.221   3.2808   0.6013  -1.3110
 GSN  HB2   H  HCH2   0   0.226   3.1847  -0.4853   0.0615
 GSN  HAG1  H  HCH2   0   0.240   1.8888   1.2261   1.3396
 GSN  HAG2  H  HCH2   0   0.265   2.0309   2.3389  -0.0079
 GSN  HAJ   H  HNH1   0   0.399  -0.0986   0.4296   1.4378
 GSN  HAK   H  HCH1   0   0.294  -1.5566  -0.1829  -1.0514
 GSN  HAL1  H  HCH2   0   0.302  -1.5017  -1.8926   1.4949
 GSN  HAL2  H  HCH2   0   0.315  -2.4845  -2.2114   0.0678
 GSN  HAQ   H  HNH1   0   0.393  -3.7545   0.2264  -0.9982
 GSN  HAR1  H  HCH2   0   0.246  -5.3581   0.5145   1.3052
 GSN  HAR2  H  HCH2   0   0.246  -4.8938   2.1088   0.7417

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
 GSN  OXT  C     single  1.247  0.020  1.247
 GSN  C    O     double  1.248  0.020  1.248
 GSN  C    CA    single  1.550  0.020  1.550
 GSN  CA   N     single  1.455  0.020  1.455
 GSN  CA   CB    single  1.531  0.020  1.531
 GSN  CA   HA    single  0.970  0.020  1.090
 GSN  N    HN1   single  0.890  0.020  1.040
 GSN  N    HN2   single  0.890  0.020  1.040
 GSN  CB   CAG   single  1.526  0.020  1.526
 GSN  CB   HB1   single  0.970  0.020  1.090
 GSN  CB   HB2   single  0.970  0.020  1.090
 GSN  CAG  CAH   single  1.509  0.020  1.509
 GSN  CAG  HAG1  single  0.970  0.020  1.090
 GSN  CAG  HAG2  single  0.970  0.020  1.090
 GSN  CAH  OAI   double  1.222  0.020  1.222
 GSN  CAH  NAJ   single  1.351  0.020  1.351
 GSN  NAJ  CAK   single  1.434  0.020  1.434
 GSN  NAJ  HAJ   single  0.860  0.020  1.020
 GSN  CAK  CAL   single  1.535  0.020  1.535
 GSN  CAK  CAO   single  1.530  0.020  1.530
 GSN  CAK  HAK   single  0.970  0.020  1.090
 GSN  CAL  SAM   single  1.799  0.020  1.799
 GSN  CAL  HAL1  single  0.970  0.020  1.090
 GSN  CAL  HAL2  single  0.970  0.020  1.090
 GSN  SAM  NAN   single  1.763  0.020  1.763
 GSN  NAN  OAV   double  1.181  0.020  1.181
 GSN  CAO  OAP   double  1.225  0.020  1.225
 GSN  CAO  NAQ   single  1.329  0.020  1.329
 GSN  NAQ  CAR   single  1.441  0.020  1.441
 GSN  NAQ  HAQ   single  0.860  0.020  1.020
 GSN  CAR  CAS   single  1.543  0.020  1.543
 GSN  CAR  HAR1  single  0.970  0.020  1.090
 GSN  CAR  HAR2  single  0.970  0.020  1.090
 GSN  CAS  OAU   single  1.242  0.020  1.242
 GSN  CAS  OAT   double  1.246  0.020  1.246

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
 GSN  CA    C    O     115.94  3.000
 GSN  CA    C    OXT   117.51  3.000
 GSN  O     C    OXT   126.53  3.000
 GSN  HA    CA   CB    107.48  3.000
 GSN  HA    CA   N     107.57  3.000
 GSN  CB    CA   N     109.84  3.000
 GSN  HA    CA   C     107.47  3.000
 GSN  CB    CA   C     108.72  3.000
 GSN  N     CA   C     115.46  3.000
 GSN  HN2   N    HN1   104.32  3.000
 GSN  HN2   N    CA    107.62  3.000
 GSN  HN1   N    CA    108.76  3.000
 GSN  HB2   CB   HB1   106.66  3.000
 GSN  HB2   CB   CAG   109.79  3.000
 GSN  HB1   CB   CAG   109.47  3.000
 GSN  HB2   CB   CA    108.74  3.000
 GSN  HB1   CB   CA    109.22  3.000
 GSN  CAG   CB   CA    112.77  3.000
 GSN  HAG2  CAG  HAG1  106.70  3.000
 GSN  HAG2  CAG  CAH   108.27  3.000
 GSN  HAG1  CAG  CAH   111.11  3.000
 GSN  HAG2  CAG  CB    109.03  3.000
 GSN  HAG1  CAG  CB    109.77  3.000
 GSN  CAH   CAG  CB    111.80  3.000
 GSN  NAJ   CAH  OAI   122.80  3.000
 GSN  NAJ   CAH  CAG   115.12  3.000
 GSN  OAI   CAH  CAG   122.08  3.000
 GSN  HAJ   NAJ  CAK   117.17  3.000
 GSN  HAJ   NAJ  CAH   118.84  3.000
 GSN  CAK   NAJ  CAH   123.99  3.000
 GSN  HAK   CAK  CAO   110.36  3.000
 GSN  HAK   CAK  CAL   109.21  3.000
 GSN  CAO   CAK  CAL   107.70  3.000
 GSN  HAK   CAK  NAJ   108.08  3.000
 GSN  CAO   CAK  NAJ   110.13  3.000
 GSN  CAL   CAK  NAJ   111.36  3.000
 GSN  HAL2  CAL  HAL1  107.64  3.000
 GSN  HAL2  CAL  SAM   107.05  3.000
 GSN  HAL1  CAL  SAM   107.48  3.000
 GSN  HAL2  CAL  CAK   110.85  3.000
 GSN  HAL1  CAL  CAK   110.83  3.000
 GSN  SAM   CAL  CAK   112.75  3.000
 GSN  NAN   SAM  CAL    96.21  3.000
 GSN  OAV   NAN  SAM   115.22  3.000
 GSN  NAQ   CAO  OAP   124.47  3.000
 GSN  NAQ   CAO  CAK   114.72  3.000
 GSN  OAP   CAO  CAK   120.75  3.000
 GSN  HAQ   NAQ  CAR   114.48  3.000
 GSN  HAQ   NAQ  CAO   121.04  3.000
 GSN  CAR   NAQ  CAO   124.48  3.000
 GSN  HAR2  CAR  HAR1  106.53  3.000
 GSN  HAR2  CAR  CAS   108.97  3.000
 GSN  HAR1  CAR  CAS   109.21  3.000
 GSN  HAR2  CAR  NAQ   110.82  3.000
 GSN  HAR1  CAR  NAQ   110.63  3.000
 GSN  CAS   CAR  NAQ   110.58  3.000
 GSN  OAT   CAS  OAU   127.80  3.000
 GSN  OAT   CAS  CAR   116.95  3.000
 GSN  OAU   CAS  CAR   115.25  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
 GSN  CONST_01  CAK   NAJ  CAH  CAG   180.00   0.0  0
 GSN  CONST_02  CAK   NAJ  CAH  OAI     0.00   0.0  0
 GSN  CONST_03  CAR   NAQ  CAO  CAK   180.00   0.0  0
 GSN  CONST_04  CAR   NAQ  CAO  OAP     0.00   0.0  0
 GSN  CONST_05  HAJ   NAJ  CAH  CAG     0.00   0.0  0
 GSN  CONST_06  HAQ   NAQ  CAO  CAK     0.00   0.0  0
 GSN  Var_01    CAH   CAG  CB   CA    176.48  30.0  3
 GSN  Var_02    OAI   CAH  CAG  CB    -53.98  30.0  3
 GSN  Var_03    CAS   CAR  NAQ  CAO  -177.77  30.0  3
 GSN  Var_04    OAU   CAS  CAR  NAQ   178.71  30.0  3
 GSN  Var_05    HAL1  CAL  SAM  NAN   -32.02  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
 GSN  chir_01  CA   C    N    CB   negativ
 GSN  chir_02  CAK  NAJ  CAL  CAO  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
 GSN  plan-1  CAG  0.020
 GSN  plan-1  CAH  0.020
 GSN  plan-1  OAI  0.020
 GSN  plan-1  NAJ  0.020
 GSN  plan-1  CAK  0.020
 GSN  plan-1  HAJ  0.020
 GSN  plan-2  CAK  0.020
 GSN  plan-2  CAO  0.020
 GSN  plan-2  OAP  0.020
 GSN  plan-2  NAQ  0.020
 GSN  plan-2  CAR  0.020
 GSN  plan-2  HAQ  0.020
 GSN  plan-3  OXT  0.020
 GSN  plan-3  C    0.020
 GSN  plan-3  O    0.020
 GSN  plan-3  CA   0.020
 GSN  plan-4  CAR  0.020
 GSN  plan-4  CAS  0.020
 GSN  plan-4  OAU  0.020
 GSN  plan-4  OAT  0.020
 GSN  plan-5  SAM  0.020
 GSN  plan-5  NAN  0.020
 GSN  plan-5  OAV  0.020

