# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:03:00 2021
#   Inital geometry file: a 135 line input string
#   Ligand name: N-({4-[2-(2-amino-4-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]phenyl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)nc2[nH]cc(CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)c12
#
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
 GPB  GPB  'N-({4-[2-(2-amino-4-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]phenyl}carbonyl)-L-glutamic acid'  ligand  54  31  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GPB
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
 GPB  N1    N  N     0  -0.488  12.6081   1.4621  11.1600
 GPB  C2    C  CR6   0   0.510  13.3123   0.8070  12.0731
 GPB  NA2   N  NH2   0  -0.827  13.5419  -0.5173  11.8614
 GPB  N3    N  N     0  -0.496  13.7940   1.3116  13.2239
 GPB  C4    C  CR6   0   0.220  13.5751   2.5862  13.5125
 GPB  C5    C  CH3   0  -0.761  14.1256   3.0957  14.8056
 GPB  C4A   C  CR56  0  -0.070  12.8561   3.3940  12.6272
 GPB  C6    C  CR5   0  -0.044  12.3976   4.7580  12.5483
 GPB  C7    C  CR15  0  -0.046  11.7107   4.8452  11.3767
 GPB  N8    N  NR15  0  -0.672  11.7114   3.6292  10.7270
 GPB  C8A   C  CR56  0   0.508  12.4007   2.7361  11.4661
 GPB  C9    C  CH2   0  -0.539  12.6783   5.9021  13.4651
 GPB  C10   C  CH2   0  -0.523  14.0994   6.4754  13.3065
 GPB  C11   C  CR6   0  -0.057  14.7457   7.7997   9.2593
 GPB  C12   C  CR16  0  -0.257  15.1147   6.5150   9.6522
 GPB  C13   C  CR16  0  -0.268  14.9115   6.0947  10.9547
 GPB  C14   C  CR6   0   0.143  14.3633   6.9499  11.9089
 GPB  C15   C  CR16  0  -0.297  14.0208   8.2408  11.5169
 GPB  C16   C  CR16  0  -0.280  14.2036   8.6630  10.2091
 GPB  O     O  O     0  -0.482  15.8870   7.7056   7.1836
 GPB  N     N  NH1   0  -0.649  14.1438   9.1319   7.3484
 GPB  CA    C  CH1   0  -0.223  14.2875   9.7289   6.0494
 GPB  CB    C  CH2   0  -0.454  12.9337   9.8730   5.3537
 GPB  CG    C  CH2   0  -0.557  12.2947   8.5086   5.1107
 GPB  CD    C  C     0   0.540  10.9293   8.5604   4.4806
 GPB  OE1   O  O     0  -0.447  10.0048   7.8544   4.8000
 GPB  OE2   O  OH1   0  -0.590  10.8503   9.4563   3.5035
 GPB  CT    C  C     0   0.568  15.0222  11.0650   6.0913
 GPB  O1    O  OH1   0  -0.576  15.6682  11.2643   7.2257
 GPB  O2    O  O     0  -0.440  15.0336  11.8376   5.1664
 GPB  HA22  H  HNH2  0   0.385  14.2899  -0.9357  12.3878
 GPB  HA21  H  HNH2  0   0.385  13.4448  -0.8533  10.9180
 GPB  H53   H  HCH3  0   0.254  13.3498   3.5744  15.4033
 GPB  H52   H  HCH3  0   0.261  14.5614   2.2846  15.3843
 GPB  H51   H  HCH3  0   0.258  14.9013   3.8427  14.6311
 GPB  H7    H  HCR5  0   0.280  11.2241   5.6998  10.9348
 GPB  H8    H  HNR5  0   0.406  11.2631   3.4362   9.8466
 GPB  H91   H  HCH2  0   0.251  11.9558   6.6990  13.2720
 GPB  H92   H  HCH2  0   0.245  12.5376   5.6119  14.5089
 GPB  H101  H  HCH2  0   0.253  14.2208   7.2988  14.0135
 GPB  H102  H  HCH2  0   0.250  14.8315   5.7137  13.5811
 GPB  H12   H  HCR6  0   0.256  15.5521   5.8368   8.9312
 GPB  H13   H  HCR6  0   0.247  15.1838   5.0848  11.2369
 GPB  H15   H  HCR6  0   0.253  13.6101   8.9315  12.2442
 GPB  H16   H  HCR6  0   0.256  13.9444   9.6834   9.9529
 GPB  H     H  HNH1  0   0.411  13.3996   9.4803   7.9322
 GPB  HA1   H  HCH1  0   0.309  14.9190   9.0689   5.4451
 GPB  HB2   H  HCH2  0   0.259  12.2754  10.4983   5.9638
 GPB  HB1   H  HCH2  0   0.269  13.0837  10.3917   4.4088
 GPB  HG2   H  HCH2  0   0.285  12.9390   7.9202   4.4477
 GPB  HG1   H  HCH2  0   0.271  12.2078   7.9458   6.0395
 GPB  HE2O  H  HOH1  0   0.482   9.9622   9.4473   3.1157
 GPB  H1O   H  HOH1  0   0.486  16.1478  12.1062   7.1892
 GPB  C     C  C     0   0.540  14.9887   8.2061   7.8451

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
 GPB  N1   C2    aromatic  1.326  0.020  1.326
 GPB  N1   C8A   aromatic  1.327  0.020  1.327
 GPB  C2   NA2   single    1.361  0.020  1.361
 GPB  C2   N3    aromatic  1.346  0.020  1.346
 GPB  NA2  HA22  single    0.890  0.020  1.040
 GPB  NA2  HA21  single    0.890  0.020  1.040
 GPB  N3   C4    aromatic  1.325  0.020  1.325
 GPB  C4   C5    single    1.495  0.020  1.495
 GPB  C4   C4A   aromatic  1.398  0.020  1.398
 GPB  C5   H53   single    0.970  0.020  1.090
 GPB  C5   H52   single    0.970  0.020  1.090
 GPB  C5   H51   single    0.970  0.020  1.090
 GPB  C4A  C6    aromatic  1.441  0.020  1.441
 GPB  C4A  C8A   aromatic  1.410  0.020  1.410
 GPB  C6   C7    aromatic  1.361  0.020  1.361
 GPB  C6   C9    single    1.493  0.020  1.493
 GPB  C7   N8    aromatic  1.379  0.020  1.379
 GPB  C7   H7    single    0.930  0.020  1.080
 GPB  N8   C8A   aromatic  1.349  0.020  1.349
 GPB  N8   H8    single    0.860  0.020  1.020
 GPB  C9   C10   single    1.541  0.020  1.541
 GPB  C9   H91   single    0.970  0.020  1.090
 GPB  C9   H92   single    0.970  0.020  1.090
 GPB  C10  C14   single    1.499  0.020  1.499
 GPB  C10  H101  single    0.970  0.020  1.090
 GPB  C10  H102  single    0.970  0.020  1.090
 GPB  C11  C12   aromatic  1.393  0.020  1.393
 GPB  C11  C16   aromatic  1.393  0.020  1.393
 GPB  C11  C     single    1.491  0.020  1.491
 GPB  C12  C13   aromatic  1.384  0.020  1.384
 GPB  C12  H12   single    0.930  0.020  1.080
 GPB  C13  C14   aromatic  1.394  0.020  1.394
 GPB  C13  H13   single    0.930  0.020  1.080
 GPB  C14  C15   aromatic  1.392  0.020  1.392
 GPB  C15  C16   aromatic  1.386  0.020  1.386
 GPB  C15  H15   single    0.930  0.020  1.080
 GPB  C16  H16   single    0.930  0.020  1.080
 GPB  C    O     double    1.223  0.020  1.223
 GPB  C    N     single    1.348  0.020  1.348
 GPB  N    CA    single    1.437  0.020  1.437
 GPB  N    H     single    0.860  0.020  1.020
 GPB  CA   CB    single    1.529  0.020  1.529
 GPB  CA   CT    single    1.525  0.020  1.525
 GPB  CA   HA1   single    0.970  0.020  1.090
 GPB  CB   CG    single    1.526  0.020  1.526
 GPB  CB   HB2   single    0.970  0.020  1.090
 GPB  CB   HB1   single    0.970  0.020  1.090
 GPB  CG   CD    single    1.505  0.020  1.505
 GPB  CG   HG2   single    0.970  0.020  1.090
 GPB  CG   HG1   single    0.970  0.020  1.090
 GPB  CD   OE1   double    1.206  0.020  1.206
 GPB  CD   OE2   single    1.328  0.020  1.328
 GPB  OE2  HE2O  single    0.850  0.020  0.980
 GPB  CT   O1    single    1.321  0.020  1.321
 GPB  CT   O2    double    1.205  0.020  1.205
 GPB  O1   H1O   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
 GPB  C8A   N1   C2    113.49  3.000
 GPB  N3    C2   NA2   115.95  3.000
 GPB  N3    C2   N1    126.41  3.000
 GPB  NA2   C2   N1    117.60  3.000
 GPB  HA21  NA2  HA22  115.06  3.000
 GPB  HA21  NA2  C2    117.04  3.000
 GPB  HA22  NA2  C2    116.68  3.000
 GPB  C4    N3   C2    119.20  3.000
 GPB  C4A   C4   C5    122.71  3.000
 GPB  C4A   C4   N3    120.20  3.000
 GPB  C5    C4   N3    117.10  3.000
 GPB  H51   C5   H52   108.11  3.000
 GPB  H51   C5   H53   107.04  3.000
 GPB  H52   C5   H53   108.71  3.000
 GPB  H51   C5   C4    110.91  3.000
 GPB  H52   C5   C4    110.71  3.000
 GPB  H53   C5   C4    111.22  3.000
 GPB  C8A   C4A  C6    107.08  3.000
 GPB  C8A   C4A  C4    114.71  3.000
 GPB  C6    C4A  C4    138.19  3.000
 GPB  C9    C6   C7    125.07  3.000
 GPB  C9    C6   C4A   129.20  3.000
 GPB  C7    C6   C4A   105.56  3.000
 GPB  H7    C7   N8    120.41  3.000
 GPB  H7    C7   C6    129.16  3.000
 GPB  N8    C7   C6    110.42  3.000
 GPB  H8    N8   C8A   125.44  3.000
 GPB  H8    N8   C7    125.53  3.000
 GPB  C8A   N8   C7    109.03  3.000
 GPB  N8    C8A  C4A   107.90  3.000
 GPB  N8    C8A  N1    126.11  3.000
 GPB  C4A   C8A  N1    125.98  3.000
 GPB  H92   C9   H91   106.10  3.000
 GPB  H92   C9   C10   108.42  3.000
 GPB  H91   C9   C10   108.68  3.000
 GPB  H92   C9   C6    111.03  3.000
 GPB  H91   C9   C6    109.03  3.000
 GPB  C10   C9   C6    113.30  3.000
 GPB  H102  C10  H101  106.78  3.000
 GPB  H102  C10  C14   109.71  3.000
 GPB  H101  C10  C14   110.20  3.000
 GPB  H102  C10  C9    109.46  3.000
 GPB  H101  C10  C9    108.45  3.000
 GPB  C14   C10  C9    112.09  3.000
 GPB  C     C11  C16   122.75  3.000
 GPB  C     C11  C12   118.39  3.000
 GPB  C16   C11  C12   118.83  3.000
 GPB  H12   C12  C13   119.74  3.000
 GPB  H12   C12  C11   119.81  3.000
 GPB  C13   C12  C11   120.44  3.000
 GPB  H13   C13  C14   119.50  3.000
 GPB  H13   C13  C12   119.44  3.000
 GPB  C14   C13  C12   121.06  3.000
 GPB  C15   C14  C13   118.23  3.000
 GPB  C15   C14  C10   120.84  3.000
 GPB  C13   C14  C10   120.88  3.000
 GPB  H15   C15  C16   119.27  3.000
 GPB  H15   C15  C14   119.68  3.000
 GPB  C16   C15  C14   121.04  3.000
 GPB  H16   C16  C15   118.57  3.000
 GPB  H16   C16  C11   121.02  3.000
 GPB  C15   C16  C11   120.38  3.000
 GPB  H     N    CA    116.99  3.000
 GPB  H     N    C     119.13  3.000
 GPB  CA    N    C     123.76  3.000
 GPB  HA1   CA   CT    105.38  3.000
 GPB  HA1   CA   CB    108.44  3.000
 GPB  CT    CA   CB    110.88  3.000
 GPB  HA1   CA   N     107.82  3.000
 GPB  CT    CA   N     112.79  3.000
 GPB  CB    CA   N     111.23  3.000
 GPB  HB1   CB   HB2   107.15  3.000
 GPB  HB1   CB   CG    110.22  3.000
 GPB  HB2   CB   CG    110.35  3.000
 GPB  HB1   CB   CA    108.54  3.000
 GPB  HB2   CB   CA    109.45  3.000
 GPB  CG    CB   CA    111.03  3.000
 GPB  HG1   CG   HG2   106.58  3.000
 GPB  HG1   CG   CD    107.61  3.000
 GPB  HG2   CG   CD    107.38  3.000
 GPB  HG1   CG   CB    111.07  3.000
 GPB  HG2   CG   CB    109.28  3.000
 GPB  CD    CG   CB    114.57  3.000
 GPB  OE2   CD   OE1   122.96  3.000
 GPB  OE2   CD   CG    112.67  3.000
 GPB  OE1   CD   CG    124.36  3.000
 GPB  HE2O  OE2  CD    110.04  3.000
 GPB  O2    CT   O1    123.91  3.000
 GPB  O2    CT   CA    123.03  3.000
 GPB  O1    CT   CA    113.04  3.000
 GPB  H1O   O1   CT    109.92  3.000
 GPB  N     C    O     122.83  3.000
 GPB  N     C    C11   115.74  3.000
 GPB  O     C    C11   121.42  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
 GPB  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 GPB  CONST_02  C4    C4A  C8A  N1      0.00   0.0  0
 GPB  CONST_03  C6    C4A  C8A  N1    180.00   0.0  0
 GPB  CONST_04  C7    N8   C8A  N1    180.00   0.0  0
 GPB  CONST_05  C4A   C8A  N1   C2      0.00   0.0  0
 GPB  CONST_06  N8    C8A  N1   C2    180.00   0.0  0
 GPB  CONST_07  C4A   C4   N3   C2      0.00   0.0  0
 GPB  CONST_08  C8A   N1   C2   N3      0.00   0.0  0
 GPB  CONST_09  C6    C4A  C4   N3    180.00   0.0  0
 GPB  CONST_10  C8A   C4A  C4   N3      0.00   0.0  0
 GPB  CONST_11  C7    C6   C4A  C4    180.00   0.0  0
 GPB  CONST_12  N8    C8A  C4A  C4    180.00   0.0  0
 GPB  CONST_13  N8    C7   C6   C4A     0.00   0.0  0
 GPB  CONST_14  C7    N8   C8A  C4A     0.00   0.0  0
 GPB  CONST_15  N8    C8A  C4A  C6      0.00   0.0  0
 GPB  CONST_16  C8A   N8   C7   C6      0.00   0.0  0
 GPB  CONST_17  C8A   C4A  C6   C7      0.00   0.0  0
 GPB  CONST_18  C14   C13  C12  C11     0.00   0.0  0
 GPB  CONST_19  C14   C15  C16  C11     0.00   0.0  0
 GPB  CONST_20  C15   C16  C11  C12     0.00   0.0  0
 GPB  CONST_21  C15   C14  C13  C12     0.00   0.0  0
 GPB  CONST_22  C16   C11  C12  C13     0.00   0.0  0
 GPB  CONST_23  C16   C15  C14  C13     0.00   0.0  0
 GPB  CONST_24  C5    C4   N3   C2    180.00   0.0  0
 GPB  CONST_25  C8A   N1   C2   NA2   180.00   0.0  0
 GPB  CONST_26  C4    N3   C2   NA2   180.00   0.0  0
 GPB  CONST_27  C9    C6   C4A  C4      0.00   0.0  0
 GPB  CONST_28  C6    C4A  C4   C5      0.00   0.0  0
 GPB  CONST_29  C8A   C4A  C4   C5    180.00   0.0  0
 GPB  CONST_30  C9    C6   C7   N8    180.00   0.0  0
 GPB  CONST_31  C9    C6   C4A  C8A   180.00   0.0  0
 GPB  CONST_32  C12   C13  C14  C10   180.00   0.0  0
 GPB  CONST_33  C16   C15  C14  C10   180.00   0.0  0
 GPB  CONST_34  C     C11  C12  C13   180.00   0.0  0
 GPB  CONST_35  C     C11  C16  C15   180.00   0.0  0
 GPB  CONST_36  H8    N8   C8A  N1      0.00   0.0  0
 GPB  CONST_37  H7    C7   C6   C4A   180.00   0.0  0
 GPB  CONST_38  H13   C13  C12  C11   180.00   0.0  0
 GPB  CONST_39  H15   C15  C16  C11   180.00   0.0  0
 GPB  CONST_40  H16   C16  C11  C12   180.00   0.0  0
 GPB  CONST_41  H12   C12  C13  C14   180.00   0.0  0
 GPB  CONST_44  CA    N    C    C11   180.00   0.0  0
 GPB  CONST_45  H     N    C    C11     0.00   0.0  0
 GPB  CONST_46  CA    N    C    O       0.00   0.0  0
 GPB  CONST_47  H1O   O1   CT   CA    180.00   0.0  0
 GPB  CONST_48  HE2O  OE2  CD   CG    180.00   0.0  0
 GPB  Var_01    C10   C9   C6   C4A    74.89  30.0  2
 GPB  Var_02    C14   C10  C9   C6     58.43  30.0  3
 GPB  Var_03    C13   C14  C10  C9    -90.86  30.0  2
 GPB  Var_04    O     C    C11  C12   -27.27  30.0  2
 GPB  Var_05    H53   C5   C4   N3   -126.57  30.0  2
 GPB  Var_06    CD    CG   CB   CA    177.54  30.0  3
 GPB  Var_07    OE1   CD   CG   CB   -139.08  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
 GPB  chir_01  CA  N  CB  CT  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
 GPB  plan-1  C10   0.020
 GPB  plan-1  C11   0.020
 GPB  plan-1  C12   0.020
 GPB  plan-1  C13   0.020
 GPB  plan-1  C14   0.020
 GPB  plan-1  C15   0.020
 GPB  plan-1  C16   0.020
 GPB  plan-1  H12   0.020
 GPB  plan-1  H13   0.020
 GPB  plan-1  H15   0.020
 GPB  plan-1  H16   0.020
 GPB  plan-1  C     0.020
 GPB  plan-2  N1    0.020
 GPB  plan-2  C2    0.020
 GPB  plan-2  NA2   0.020
 GPB  plan-2  N3    0.020
 GPB  plan-2  C4    0.020
 GPB  plan-2  C5    0.020
 GPB  plan-2  C4A   0.020
 GPB  plan-2  C6    0.020
 GPB  plan-2  C7    0.020
 GPB  plan-2  N8    0.020
 GPB  plan-2  C8A   0.020
 GPB  plan-2  C9    0.020
 GPB  plan-2  H7    0.020
 GPB  plan-2  H8    0.020
 GPB  plan-3  C11   0.020
 GPB  plan-3  O     0.020
 GPB  plan-3  N     0.020
 GPB  plan-3  CA    0.020
 GPB  plan-3  H     0.020
 GPB  plan-3  C     0.020
 GPB  plan-4  C2    0.020
 GPB  plan-4  NA2   0.020
 GPB  plan-4  HA22  0.020
 GPB  plan-4  HA21  0.020
 GPB  plan-5  CG    0.020
 GPB  plan-5  CD    0.020
 GPB  plan-5  OE1   0.020
 GPB  plan-5  OE2   0.020
 GPB  plan-5  HE2O  0.020
 GPB  plan-6  CA    0.020
 GPB  plan-6  CT    0.020
 GPB  plan-6  O1    0.020
 GPB  plan-6  O2    0.020
 GPB  plan-6  H1O   0.020

