# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:22:32 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: L-gamma-glutamyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CO[P](O)(=O)N[C@@H](CCC(O)=O)C(O)=O)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
 2G2  2G2  L-gamma-glutamyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine  ligand  51  29  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2G2
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
 2G2  OXT  O  OH1   0  -0.594  -7.7999   0.2428  -1.8960
 2G2  C    C  C     0   0.524  -7.9211   0.4033  -0.5832
 2G2  O    O  O     0  -0.439  -8.9343   0.1591   0.0224
 2G2  CA   C  CH1   0  -0.212  -6.6377   0.9275   0.0522
 2G2  N    N  NH2   0  -0.777  -6.8009   1.3385   1.4248
 2G2  CB   C  CH2   0  -0.432  -5.5296  -0.1290  -0.0643
 2G2  CAN  C  CH2   0  -0.578  -4.1961   0.4072   0.4345
 2G2  CAV  C  C     0   0.575  -3.0913  -0.6193   0.3581
 2G2  OAC  O  O     0  -0.493  -3.2748  -1.8091   0.5641
 2G2  NAR  N  NH1   0  -0.638  -1.8762  -0.1204   0.0476
 2G2  CBA  C  CH1   0  -0.243  -0.6899  -0.9237   0.0669
 2G2  CAX  C  C     0   0.562  -0.1708  -1.0958   1.4915
 2G2  OAJ  O  OH1   0  -0.593   0.9307  -1.8337   1.5163
 2G2  OAE  O  O     0  -0.418  -0.6969  -0.6336   2.4663
 2G2  CAQ  C  CH2   0  -0.201   0.3738  -0.3343  -0.8421
 2G2  OAT  O  O2    0  -0.602   0.7846   0.9067  -0.2710
 2G2  PBC  P  P     0   1.440   1.8685   1.8170  -1.0437
 2G2  OAL  O  OH1   0  -0.767   1.8444   3.1009  -0.1052
 2G2  OAG  O  O     0  -0.707   1.5638   2.0802  -2.4658
 2G2  NAS  N  NH1   0  -0.788   3.3038   1.0126  -0.8441
 2G2  CBB  C  CH1   0  -0.237   3.8320   0.4701   0.3861
 2G2  CAY  C  C     0   0.624   4.4681   1.5608   1.2472
 2G2  OAK  O  O     0  -0.468   4.1984   2.7384   1.1427
 2G2  OAF  O  OH1   0  -0.566   5.3046   1.0974   2.1450
 2G2  CAP  C  CH2   0  -0.447   4.7861  -0.6893   0.0905
 2G2  CAM  C  CH2   0  -0.593   4.0838  -1.8110  -0.6555
 2G2  CAU  C  C     0   0.564   4.9966  -2.9654  -0.9630
 2G2  OAH  O  O     0  -0.442   6.1682  -3.0186  -0.6839
 2G2  OAB  O  OH1   0  -0.595   4.3548  -3.9421  -1.5949
 2G2  H1   H  HOH1  0   0.482  -8.6259  -0.1005  -2.2690
 2G2  H2   H  HCH1  0   0.272  -6.3312   1.8031  -0.5310
 2G2  H3   H  HNH2  0   0.356  -7.4708   2.0930   1.4962
 2G2  H4   H  HNH2  0   0.345  -7.1679   0.5743   1.9790
 2G2  H6   H  HCH2  0   0.243  -5.8178  -1.0150   0.5071
 2G2  H7   H  HCH2  0   0.254  -5.4301  -0.4425  -1.1045
 2G2  H8   H  HCH2  0   0.255  -3.9198   1.3047  -0.1251
 2G2  H9   H  HCH2  0   0.282  -4.2891   0.7161   1.4788
 2G2  H10  H  HNH1  0   0.406  -1.7673   0.8802  -0.0121
 2G2  H11  H  HCH1  0   0.322  -0.9233  -1.9190  -0.3230
 2G2  H12  H  HOH1  0   0.489   1.2526  -1.9336   2.4254
 2G2  H13  H  HCH2  0   0.266   1.2173  -1.0209  -0.9291
 2G2  H14  H  HCH2  0   0.277  -0.0488  -0.1845  -1.8378
 2G2  H15  H  HOH1  0   0.499   2.6868   3.1865   0.3957
 2G2  H16  H  HNH1  0   0.414   3.9925   1.1758  -1.5670
 2G2  H17  H  HCH1  0   0.304   2.9995   0.0805   0.9856
 2G2  H18  H  HOH1  0   0.496   5.6405   1.8160   2.7041
 2G2  H19  H  HCH2  0   0.259   5.6359  -0.3194  -0.4891
 2G2  H20  H  HCH2  0   0.271   5.1838  -1.0739   1.0282
 2G2  H21  H  HCH2  0   0.280   3.2414  -2.1902  -0.0690
 2G2  H22  H  HCH2  0   0.289   3.6559  -1.4573  -1.5975
 2G2  H23  H  HOH1  0   0.480   4.9649  -4.6706  -1.7838

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
 2G2  O    C    double  1.205  0.020  1.205
 2G2  OAK  CAY  double  1.213  0.020  1.213
 2G2  OAH  CAU  double  1.206  0.020  1.206
 2G2  C    OXT  single  1.328  0.020  1.328
 2G2  C    CA   single  1.525  0.020  1.525
 2G2  CAU  OAB  single  1.329  0.020  1.329
 2G2  CAU  CAM  single  1.503  0.020  1.503
 2G2  CAY  OAF  single  1.312  0.020  1.312
 2G2  CAY  CBB  single  1.528  0.020  1.528
 2G2  CAM  CAP  single  1.519  0.020  1.519
 2G2  CAP  CBB  single  1.530  0.020  1.530
 2G2  CA   CB   single  1.535  0.020  1.535
 2G2  CA   N    single  1.442  0.020  1.442
 2G2  CBB  NAS  single  1.445  0.020  1.445
 2G2  CB   CAN  single  1.521  0.020  1.521
 2G2  OAG  PBC  double  1.478  0.020  1.478
 2G2  NAS  PBC  single  1.657  0.020  1.657
 2G2  CAN  CAV  single  1.510  0.020  1.510
 2G2  CAQ  CBA  single  1.518  0.020  1.518
 2G2  CAQ  OAT  single  1.427  0.020  1.427
 2G2  CAV  OAC  double  1.221  0.020  1.221
 2G2  CAV  NAR  single  1.350  0.020  1.350
 2G2  PBC  OAT  single  1.613  0.020  1.613
 2G2  PBC  OAL  single  1.591  0.020  1.591
 2G2  NAR  CBA  single  1.433  0.020  1.433
 2G2  CBA  CAX  single  1.526  0.020  1.526
 2G2  CAX  OAE  double  1.200  0.020  1.200
 2G2  CAX  OAJ  single  1.326  0.020  1.326
 2G2  OXT  H1   single  0.850  0.020  0.980
 2G2  CA   H2   single  0.970  0.020  1.090
 2G2  N    H3   single  0.890  0.020  1.040
 2G2  N    H4   single  0.890  0.020  1.040
 2G2  CB   H6   single  0.970  0.020  1.090
 2G2  CB   H7   single  0.970  0.020  1.090
 2G2  CAN  H8   single  0.970  0.020  1.090
 2G2  CAN  H9   single  0.970  0.020  1.090
 2G2  NAR  H10  single  0.860  0.020  1.020
 2G2  CBA  H11  single  0.970  0.020  1.090
 2G2  OAJ  H12  single  0.850  0.020  0.980
 2G2  CAQ  H13  single  0.970  0.020  1.090
 2G2  CAQ  H14  single  0.970  0.020  1.090
 2G2  OAL  H15  single  0.850  0.020  0.980
 2G2  NAS  H16  single  0.890  0.020  1.040
 2G2  CBB  H17  single  0.970  0.020  1.090
 2G2  OAF  H18  single  0.850  0.020  0.980
 2G2  CAP  H19  single  0.970  0.020  1.090
 2G2  CAP  H20  single  0.970  0.020  1.090
 2G2  CAM  H21  single  0.970  0.020  1.090
 2G2  CAM  H22  single  0.970  0.020  1.090
 2G2  OAB  H23  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
 2G2  H1   OXT  C    110.21  3.000
 2G2  CA   C    O    124.59  3.000
 2G2  CA   C    OXT  112.12  3.000
 2G2  O    C    OXT  123.28  3.000
 2G2  H2   CA   CB   107.91  3.000
 2G2  H2   CA   N    108.09  3.000
 2G2  CB   CA   N    110.48  3.000
 2G2  H2   CA   C    106.76  3.000
 2G2  N    CA   C    113.54  3.000
 2G2  CB   CA   C    109.83  3.000
 2G2  H4   N    H3   106.51  3.000
 2G2  H4   N    CA   110.29  3.000
 2G2  H3   N    CA   110.77  3.000
 2G2  H7   CB   H6   106.83  3.000
 2G2  H7   CB   CAN  109.51  3.000
 2G2  H6   CB   CAN  110.21  3.000
 2G2  H7   CB   CA   109.62  3.000
 2G2  H6   CB   CA   109.13  3.000
 2G2  CAN  CB   CA   111.42  3.000
 2G2  H9   CAN  H8   106.18  3.000
 2G2  H9   CAN  CAV  107.62  3.000
 2G2  H8   CAN  CAV  110.32  3.000
 2G2  H9   CAN  CB   109.77  3.000
 2G2  H8   CAN  CB   110.07  3.000
 2G2  CAV  CAN  CB   112.65  3.000
 2G2  NAR  CAV  OAC  122.29  3.000
 2G2  NAR  CAV  CAN  114.77  3.000
 2G2  OAC  CAV  CAN  122.94  3.000
 2G2  H10  NAR  CBA  117.88  3.000
 2G2  H10  NAR  CAV  118.54  3.000
 2G2  CBA  NAR  CAV  122.35  3.000
 2G2  H11  CBA  CAQ  106.81  3.000
 2G2  H11  CBA  CAX  107.62  3.000
 2G2  CAQ  CBA  CAX  111.37  3.000
 2G2  H11  CBA  NAR  109.18  3.000
 2G2  CAX  CBA  NAR  110.94  3.000
 2G2  CAQ  CBA  NAR  110.76  3.000
 2G2  OAE  CAX  OAJ  124.27  3.000
 2G2  OAJ  CAX  CBA  111.27  3.000
 2G2  OAE  CAX  CBA  124.45  3.000
 2G2  H12  OAJ  CAX  110.53  3.000
 2G2  H14  CAQ  H13  108.23  3.000
 2G2  H14  CAQ  OAT  110.92  3.000
 2G2  H13  CAQ  OAT  110.90  3.000
 2G2  H14  CAQ  CBA  109.15  3.000
 2G2  H13  CAQ  CBA  110.19  3.000
 2G2  OAT  CAQ  CBA  107.44  3.000
 2G2  PBC  OAT  CAQ  119.52  3.000
 2G2  NAS  PBC  OAG  112.39  3.000
 2G2  NAS  PBC  OAL  109.50  3.000
 2G2  OAG  PBC  OAL  114.89  3.000
 2G2  OAL  PBC  OAT   99.37  3.000
 2G2  NAS  PBC  OAT  104.50  3.000
 2G2  OAG  PBC  OAT  115.03  3.000
 2G2  H15  OAL  PBC  110.96  3.000
 2G2  H16  NAS  CBB  114.84  3.000
 2G2  H16  NAS  PBC  115.16  3.000
 2G2  CBB  NAS  PBC  126.98  3.000
 2G2  H17  CBB  CAP  108.03  3.000
 2G2  H17  CBB  CAY  105.15  3.000
 2G2  CAP  CBB  CAY  112.96  3.000
 2G2  H17  CBB  NAS  108.73  3.000
 2G2  CAP  CBB  NAS  110.37  3.000
 2G2  CAY  CBB  NAS  111.35  3.000
 2G2  OAF  CAY  OAK  122.95  3.000
 2G2  OAF  CAY  CBB  113.51  3.000
 2G2  OAK  CAY  CBB  123.50  3.000
 2G2  H18  OAF  CAY  110.70  3.000
 2G2  H20  CAP  H19  106.99  3.000
 2G2  H20  CAP  CAM  109.33  3.000
 2G2  H19  CAP  CAM  110.42  3.000
 2G2  H20  CAP  CBB  109.21  3.000
 2G2  H19  CAP  CBB  109.31  3.000
 2G2  CAM  CAP  CBB  111.47  3.000
 2G2  H22  CAM  H21  105.82  3.000
 2G2  H22  CAM  CAU  108.05  3.000
 2G2  H21  CAM  CAU  108.12  3.000
 2G2  H22  CAM  CAP  111.41  3.000
 2G2  H21  CAM  CAP  110.39  3.000
 2G2  CAU  CAM  CAP  112.75  3.000
 2G2  OAB  CAU  OAH  123.17  3.000
 2G2  OAB  CAU  CAM  111.62  3.000
 2G2  OAH  CAU  CAM  125.21  3.000
 2G2  H23  OAB  CAU  109.96  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
 2G2  CONST_01  CBA  NAR  CAV  CAN  180.00   0.0  0
 2G2  CONST_02  CBA  NAR  CAV  OAC    0.00   0.0  0
 2G2  CONST_03  H10  NAR  CAV  CAN    0.00   0.0  0
 2G2  CONST_04  H1   OXT  C    O      0.00   0.0  0
 2G2  CONST_05  H12  OAJ  CAX  CBA  180.00   0.0  0
 2G2  CONST_06  H18  OAF  CAY  CBB  180.00   0.0  0
 2G2  CONST_07  H23  OAB  CAU  CAM  180.00   0.0  0
 2G2  Var_01    CAV  CAN  CB   CA   178.85  30.0  3
 2G2  Var_02    OAC  CAV  CAN  CB   -35.67  30.0  3
 2G2  Var_03    OAG  PBC  OAT  CAQ   50.82  30.0  1
 2G2  Var_04    CBB  NAS  PBC  OAT  -47.26  30.0  1
 2G2  Var_05    CAU  CAM  CAP  CBB  179.90  30.0  1
 2G2  Var_06    OAH  CAU  CAM  CAP   -1.24  30.0  2
 2G2  Var_07    H13  CAQ  OAT  PBC   62.26  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
 2G2  chir_01  CA   C    CB   N    positiv
 2G2  chir_02  CBA  NAR  CAQ  CAX  negativ
 2G2  chir_04  CBB  NAS  CAY  CAP  positiv
 2G2  chir_05  PBC  NAS  OAT  OAL  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
 2G2  plan-1  CAN  0.020
 2G2  plan-1  CAV  0.020
 2G2  plan-1  OAC  0.020
 2G2  plan-1  NAR  0.020
 2G2  plan-1  CBA  0.020
 2G2  plan-1  H10  0.020
 2G2  plan-2  OXT  0.020
 2G2  plan-2  C    0.020
 2G2  plan-2  O    0.020
 2G2  plan-2  CA   0.020
 2G2  plan-2  H1   0.020
 2G2  plan-3  CBA  0.020
 2G2  plan-3  CAX  0.020
 2G2  plan-3  OAJ  0.020
 2G2  plan-3  OAE  0.020
 2G2  plan-3  H12  0.020
 2G2  plan-4  CBB  0.020
 2G2  plan-4  CAY  0.020
 2G2  plan-4  OAK  0.020
 2G2  plan-4  OAF  0.020
 2G2  plan-4  H18  0.020
 2G2  plan-5  CAM  0.020
 2G2  plan-5  CAU  0.020
 2G2  plan-5  OAH  0.020
 2G2  plan-5  OAB  0.020
 2G2  plan-5  H23  0.020

