# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:37:21 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: N-[(S)-(biphenyl-4-ylmethoxy)(hydroxy)phosphoryl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](N[P](O)(=O)OCc1ccc(cc1)c2ccccc2)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
 2GB  2GB  'N-[(S)-(biphenyl-4-ylmethoxy)(hydroxy)phosphoryl]-L-glutamic acid'  ligand  47  27  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2GB
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
 2GB  N    N  NH1   0  -0.792  16.7601  45.2926  42.9797
 2GB  CA   C  CH1   0  -0.168  15.9577  44.4570  42.1092
 2GB  C    C  C     0   0.546  16.7433  43.9206  40.9235
 2GB  OXT  O  OH1   0  -0.575  17.7273  44.7106  40.5303
 2GB  CB   C  CH2   0  -0.488  14.7266  45.2240  41.6133
 2GB  CG   C  CH2   0  -0.589  15.0397  46.4620  40.7845
 2GB  O    O  O     0  -0.445  16.4443  42.8941  40.3656
 2GB  CAP  C  CR16  0  -0.309  26.0574  46.1097  45.4063
 2GB  CAS  C  CR16  0  -0.240  27.3898  45.8781  45.7150
 2GB  CAO  C  CR16  0  -0.266  28.0871  44.8571  45.0823
 2GB  CAR  C  CR16  0  -0.240  27.4405  44.0693  44.1390
 2GB  CAQ  C  CR16  0  -0.310  26.1077  44.3004  43.8317
 2GB  CAN  C  CR6   0   0.087  25.3960  45.3241  44.4603
 2GB  CAI  C  CR6   0   0.078  23.9779  45.5687  44.1293
 2GB  CAM  C  CR16  0  -0.295  23.1046  44.5045  43.8885
 2GB  CAJ  C  CR16  0  -0.278  21.7766  44.7294  43.5720
 2GB  CAL  C  CR16  0  -0.295  23.4728  46.8649  44.0438
 2GB  CAK  C  CR16  0  -0.286  22.1400  47.0886  43.7286
 2GB  CAH  C  CR6   0   0.098  21.2772  46.0275  43.4857
 2GB  CAB  C  CH2   0  -0.283  19.8390  46.2737  43.1409
 2GB  OAT  O  O2    0  -0.583  18.9925  45.7959  44.1992
 2GB  PBA  P  P     0   1.444  17.9389  44.6229  43.9182
 2GB  OAV  O  OH1   0  -0.729  17.2899  44.4703  45.3745
 2GB  OAU  O  O     0  -0.715  18.4769  43.3808  43.3138
 2GB  CD   C  C     0   0.560  13.8065  47.2635  40.4689
 2GB  OE2  O  O     0  -0.442  12.6823  46.9617  40.7833
 2GB  OE1  O  OH1   0  -0.595  14.0975  48.3634  39.7830
 2GB  H1   H  HNH1  0   0.412  16.3321  46.1544  43.2874
 2GB  H2   H  HCH1  0   0.295  15.5768  43.5764  42.6352
 2GB  H3   H  HOH1  0   0.482  18.1643  44.3289  39.7538
 2GB  H4   H  HCH2  0   0.272  14.1446  45.4994  42.4952
 2GB  H5   H  HCH2  0   0.272  14.1077  44.5334  41.0394
 2GB  H6   H  HCH2  0   0.291  15.5122  46.1979  39.8344
 2GB  H7   H  HCH2  0   0.285  15.7499  47.1207  41.2919
 2GB  H9   H  HCR6  0   0.258  27.8830  46.4925  46.4572
 2GB  H10  H  HCR6  0   0.258  29.1266  44.6767  45.3230
 2GB  H11  H  HCR6  0   0.258  27.9774  43.2763  43.6348
 2GB  H12  H  HCR6  0   0.255  25.6230  43.6899  43.0796
 2GB  H13  H  HCR6  0   0.255  23.4630  43.4856  43.9666
 2GB  H14  H  HCR6  0   0.256  21.1216  43.8849  43.3959
 2GB  H15  H  HCR6  0   0.255  24.1262  47.7128  44.2063
 2GB  H16  H  HCR6  0   0.258  21.7741  48.1064  43.6625
 2GB  H17  H  HCH2  0   0.262  19.6483  47.3416  43.0296
 2GB  H18  H  HCH2  0   0.254  19.5822  45.7971  42.1922
 2GB  H19  H  HOH1  0   0.496  17.8342  43.9789  46.0049
 2GB  H20  H  HOH1  0   0.480  13.2859  48.8557  39.5897
 2GB  H8   H  HCR6  0   0.254  25.5219  46.8967  45.9227

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
 2GB  O    C    double    1.206  0.020  1.206
 2GB  OE2  CD   double    1.206  0.020  1.206
 2GB  CD   OE1  single    1.329  0.020  1.329
 2GB  CD   CG   single    1.504  0.020  1.504
 2GB  C    OXT  single    1.322  0.020  1.322
 2GB  C    CA   single    1.520  0.020  1.520
 2GB  CG   CB   single    1.522  0.020  1.522
 2GB  CB   CA   single    1.533  0.020  1.533
 2GB  CA   N    single    1.449  0.020  1.449
 2GB  OAU  PBA  double    1.482  0.020  1.482
 2GB  CAK  CAL  aromatic  1.388  0.020  1.388
 2GB  CAK  CAH  aromatic  1.389  0.020  1.389
 2GB  N    PBA  single    1.649  0.020  1.649
 2GB  CAL  CAI  aromatic  1.394  0.020  1.394
 2GB  CAB  CAH  single    1.499  0.020  1.499
 2GB  CAB  OAT  single    1.437  0.020  1.437
 2GB  CAH  CAJ  aromatic  1.394  0.020  1.394
 2GB  PBA  OAT  single    1.602  0.020  1.602
 2GB  PBA  OAV  single    1.602  0.020  1.602
 2GB  CAI  CAN  single    1.477  0.020  1.477
 2GB  CAI  CAM  aromatic  1.398  0.020  1.398
 2GB  CAP  CAN  aromatic  1.396  0.020  1.396
 2GB  CAP  CAS  aromatic  1.387  0.020  1.387
 2GB  CAJ  CAM  aromatic  1.384  0.020  1.384
 2GB  CAN  CAQ  aromatic  1.396  0.020  1.396
 2GB  CAS  CAO  aromatic  1.389  0.020  1.389
 2GB  CAQ  CAR  aromatic  1.387  0.020  1.387
 2GB  CAO  CAR  aromatic  1.389  0.020  1.389
 2GB  N    H1   single    0.890  0.020  1.040
 2GB  CA   H2   single    0.970  0.020  1.090
 2GB  OXT  H3   single    0.850  0.020  0.980
 2GB  CB   H4   single    0.970  0.020  1.090
 2GB  CB   H5   single    0.970  0.020  1.090
 2GB  CG   H6   single    0.970  0.020  1.090
 2GB  CG   H7   single    0.970  0.020  1.090
 2GB  CAP  H8   single    0.930  0.020  1.080
 2GB  CAS  H9   single    0.930  0.020  1.080
 2GB  CAO  H10  single    0.930  0.020  1.080
 2GB  CAR  H11  single    0.930  0.020  1.080
 2GB  CAQ  H12  single    0.930  0.020  1.080
 2GB  CAM  H13  single    0.930  0.020  1.080
 2GB  CAJ  H14  single    0.930  0.020  1.080
 2GB  CAL  H15  single    0.930  0.020  1.080
 2GB  CAK  H16  single    0.930  0.020  1.080
 2GB  CAB  H17  single    0.970  0.020  1.090
 2GB  CAB  H18  single    0.970  0.020  1.090
 2GB  OAV  H19  single    0.850  0.020  0.980
 2GB  OE1  H20  single    0.850  0.020  0.980

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
 2GB  H1   N    PBA  118.42  3.000
 2GB  H1   N    CA   116.13  3.000
 2GB  PBA  N    CA   120.24  3.000
 2GB  H2   CA   CB   106.17  3.000
 2GB  H2   CA   C    105.72  3.000
 2GB  CB   CA   C    109.83  3.000
 2GB  H2   CA   N    111.60  3.000
 2GB  CB   CA   N    110.52  3.000
 2GB  C    CA   N    112.70  3.000
 2GB  O    C    OXT  123.76  3.000
 2GB  OXT  C    CA   113.95  3.000
 2GB  O    C    CA   122.21  3.000
 2GB  H3   OXT  C    109.79  3.000
 2GB  H5   CB   H4   106.40  3.000
 2GB  H5   CB   CG   110.20  3.000
 2GB  H4   CB   CG   110.13  3.000
 2GB  H5   CB   CA   108.01  3.000
 2GB  H4   CB   CA   107.04  3.000
 2GB  CG   CB   CA   114.70  3.000
 2GB  H7   CG   H6   105.54  3.000
 2GB  H7   CG   CD   107.99  3.000
 2GB  H6   CG   CD   107.49  3.000
 2GB  H7   CG   CB   111.77  3.000
 2GB  H6   CG   CB   111.44  3.000
 2GB  CD   CG   CB   112.26  3.000
 2GB  H8   CAP  CAN  119.85  3.000
 2GB  H8   CAP  CAS  119.35  3.000
 2GB  CAN  CAP  CAS  120.78  3.000
 2GB  H9   CAS  CAO  120.06  3.000
 2GB  H9   CAS  CAP  119.70  3.000
 2GB  CAO  CAS  CAP  120.24  3.000
 2GB  H10  CAO  CAR  120.25  3.000
 2GB  H10  CAO  CAS  120.23  3.000
 2GB  CAR  CAO  CAS  119.52  3.000
 2GB  H11  CAR  CAQ  119.70  3.000
 2GB  H11  CAR  CAO  120.08  3.000
 2GB  CAQ  CAR  CAO  120.22  3.000
 2GB  H12  CAQ  CAN  119.85  3.000
 2GB  H12  CAQ  CAR  119.33  3.000
 2GB  CAN  CAQ  CAR  120.81  3.000
 2GB  CAI  CAN  CAQ  120.67  3.000
 2GB  CAQ  CAN  CAP  118.43  3.000
 2GB  CAI  CAN  CAP  120.90  3.000
 2GB  CAL  CAI  CAM  118.11  3.000
 2GB  CAM  CAI  CAN  120.84  3.000
 2GB  CAL  CAI  CAN  121.05  3.000
 2GB  H13  CAM  CAJ  119.15  3.000
 2GB  H13  CAM  CAI  119.82  3.000
 2GB  CAJ  CAM  CAI  121.02  3.000
 2GB  H14  CAJ  CAH  119.97  3.000
 2GB  H14  CAJ  CAM  119.39  3.000
 2GB  CAH  CAJ  CAM  120.64  3.000
 2GB  H15  CAL  CAK  119.17  3.000
 2GB  H15  CAL  CAI  120.03  3.000
 2GB  CAK  CAL  CAI  120.80  3.000
 2GB  H16  CAK  CAH  119.81  3.000
 2GB  H16  CAK  CAL  119.32  3.000
 2GB  CAH  CAK  CAL  120.87  3.000
 2GB  CAB  CAH  CAK  120.71  3.000
 2GB  CAB  CAH  CAJ  120.73  3.000
 2GB  CAK  CAH  CAJ  118.56  3.000
 2GB  H18  CAB  H17  107.31  3.000
 2GB  H18  CAB  OAT  110.86  3.000
 2GB  H17  CAB  OAT  107.32  3.000
 2GB  H18  CAB  CAH  110.71  3.000
 2GB  H17  CAB  CAH  110.61  3.000
 2GB  OAT  CAB  CAH  109.94  3.000
 2GB  PBA  OAT  CAB  120.12  3.000
 2GB  OAU  PBA  OAV  115.97  3.000
 2GB  OAV  PBA  OAT  100.19  3.000
 2GB  OAU  PBA  OAT  116.51  3.000
 2GB  OAV  PBA  N    105.46  3.000
 2GB  OAT  PBA  N    105.83  3.000
 2GB  OAU  PBA  N    111.58  3.000
 2GB  H19  OAV  PBA  114.40  3.000
 2GB  OE1  CD   OE2  123.10  3.000
 2GB  OE1  CD   CG   111.71  3.000
 2GB  OE2  CD   CG   125.19  3.000
 2GB  H20  OE1  CD   109.88  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
 2GB  CONST_03  CAR  CAQ  CAN  CAP     0.00   0.0  0
 2GB  CONST_04  CAR  CAO  CAS  CAP     0.00   0.0  0
 2GB  CONST_05  CAI  CAN  CAP  CAS   180.00   0.0  0
 2GB  CONST_06  CAQ  CAN  CAP  CAS     0.00   0.0  0
 2GB  CONST_07  CAQ  CAR  CAO  CAS     0.00   0.0  0
 2GB  CONST_08  CAN  CAP  CAS  CAO     0.00   0.0  0
 2GB  CONST_09  CAN  CAQ  CAR  CAO     0.00   0.0  0
 2GB  CONST_10  CAI  CAN  CAQ  CAR   180.00   0.0  0
 2GB  CONST_13  CAK  CAL  CAI  CAN   180.00   0.0  0
 2GB  CONST_14  CAJ  CAM  CAI  CAN   180.00   0.0  0
 2GB  CONST_15  CAH  CAK  CAL  CAI     0.00   0.0  0
 2GB  CONST_16  CAH  CAJ  CAM  CAI     0.00   0.0  0
 2GB  CONST_17  CAK  CAL  CAI  CAM     0.00   0.0  0
 2GB  CONST_18  CAK  CAH  CAJ  CAM     0.00   0.0  0
 2GB  CONST_19  CAL  CAK  CAH  CAJ     0.00   0.0  0
 2GB  CONST_20  CAL  CAI  CAM  CAJ     0.00   0.0  0
 2GB  CONST_21  CAB  CAH  CAJ  CAM   180.00   0.0  0
 2GB  CONST_22  CAB  CAH  CAK  CAL   180.00   0.0  0
 2GB  CONST_23  H12  CAQ  CAN  CAP   180.00   0.0  0
 2GB  CONST_24  H10  CAO  CAS  CAP   180.00   0.0  0
 2GB  CONST_25  H11  CAR  CAO  CAS   180.00   0.0  0
 2GB  CONST_26  H8   CAP  CAS  CAO   180.00   0.0  0
 2GB  CONST_27  H9   CAS  CAO  CAR   180.00   0.0  0
 2GB  CONST_28  H15  CAL  CAI  CAN     0.00   0.0  0
 2GB  CONST_29  H13  CAM  CAI  CAN     0.00   0.0  0
 2GB  CONST_30  H16  CAK  CAL  CAI   180.00   0.0  0
 2GB  CONST_31  H14  CAJ  CAM  CAI   180.00   0.0  0
 2GB  CONST_32  H3   OXT  C    CA    180.00   0.0  0
 2GB  CONST_33  H20  OE1  CD   CG    180.00   0.0  0
 2GB  Var_01    OAT  CAB  CAH  CAJ    66.78  30.0  1
 2GB  Var_02    CD   CG   CB   CA   -173.02  30.0  1
 2GB  Var_03    OAU  PBA  N    CA     27.55  30.0  3
 2GB  Var_04    OE2  CD   CG   CB     -2.38  30.0  2

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
 2GB  chir_01  CA   C  CB   N    positiv
 2GB  chir_02  PBA  N  OAT  OAV  both

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
 2GB  plan-1  CAP  0.020
 2GB  plan-1  CAS  0.020
 2GB  plan-1  CAO  0.020
 2GB  plan-1  CAR  0.020
 2GB  plan-1  CAQ  0.020
 2GB  plan-1  CAN  0.020
 2GB  plan-1  CAI  0.020
 2GB  plan-1  H9   0.020
 2GB  plan-1  H10  0.020
 2GB  plan-1  H11  0.020
 2GB  plan-1  H12  0.020
 2GB  plan-1  H8   0.020
 2GB  plan-2  CAN  0.020
 2GB  plan-2  CAI  0.020
 2GB  plan-2  CAM  0.020
 2GB  plan-2  CAJ  0.020
 2GB  plan-2  CAL  0.020
 2GB  plan-2  CAK  0.020
 2GB  plan-2  CAH  0.020
 2GB  plan-2  CAB  0.020
 2GB  plan-2  H13  0.020
 2GB  plan-2  H14  0.020
 2GB  plan-2  H15  0.020
 2GB  plan-2  H16  0.020
 2GB  plan-3  CA   0.020
 2GB  plan-3  C    0.020
 2GB  plan-3  OXT  0.020
 2GB  plan-3  O    0.020
 2GB  plan-3  H3   0.020
 2GB  plan-4  CG   0.020
 2GB  plan-4  CD   0.020
 2GB  plan-4  OE2  0.020
 2GB  plan-4  OE1  0.020
 2GB  plan-4  H20  0.020

