# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 05:51:40 2022
#   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  52  31  .  2022-03-18  2022-03-18
;
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  -0.485  11.2145   2.1480  11.6050
 GPB  C2    C  CR6    0   0.508  11.9222   1.2027  12.2099
 GPB  NA2   N  NH2    0  -0.826  11.6401  -0.0913  11.8977
 GPB  N3    N  N      0  -0.492  12.8712   1.3910  13.1434
 GPB  C4    C  CR6    0   0.218  13.1660   2.6253  13.5272
 GPB  C5    C  CH3    0  -0.757  14.2444   2.7690  14.5529
 GPB  C4A   C  CR56   0  -0.071  12.4953   3.7155  12.9666
 GPB  C6    C  CR5    0  -0.027  12.4841   5.1524  13.0875
 GPB  C7    C  CR15   0  -0.062  11.5338   5.5855  12.2151
 GPB  N8    N  NR15   0  -0.673  10.9551   4.5163  11.5634
 GPB  C8A   C  CR56   0   0.508  11.5221   3.3744  12.0034
 GPB  C9    C  CH2    0  -0.546  13.3507   6.0414  13.9164
 GPB  C10   C  CH2    0  -0.517  14.7976   6.1487  13.4032
 GPB  C11   C  CR6    0  -0.045  14.9109   7.5922   9.3403
 GPB  C12   C  CR16   0  -0.262  15.0385   6.2330   9.6154
 GPB  C13   C  CR16   0  -0.287  15.0036   5.7701  10.9205
 GPB  C14   C  CR6    0   0.140  14.8666   6.6501  11.9914
 GPB  C15   C  CR16   0  -0.296  14.7569   8.0101  11.7128
 GPB  C16   C  CR16   0  -0.281  14.7733   8.4775  10.4081
 GPB  O     O  O      0  -0.504  15.5855   7.3885   7.0753
 GPB  N     N  NH1    0  -0.647  14.3323   9.1833   7.6391
 GPB  CA    C  CH1    0  -0.177  14.3207   9.8464   6.3507
 GPB  CB    C  CH2    0  -0.411  13.2818   9.2005   5.4183
 GPB  CG    C  CH2    0  -0.583  13.3432   9.6723   3.9745
 GPB  CD    C  C      0   0.407  12.4278   8.9211   2.9849
 GPB  OE1   O  O      0  -0.627  12.5841   9.2124   1.7799
 GPB  OE2   O  OC    -1  -0.606  11.6063   8.1042   3.4485
 GPB  CT    C  C      0   0.413  14.0135  11.3456   6.5929
 GPB  O1    O  OC    -1  -0.600  13.3442  11.6086   7.6149
 GPB  O2    O  O      0  -0.591  14.4339  12.1473   5.7417
 GPB  HA22  H  HNH2   0   0.384  12.3393  -0.7765  12.1288
 GPB  HA21  H  HNH2   0   0.384  11.1460  -0.2571  11.0370
 GPB  H53   H  HCH3   0   0.251  14.0462   3.5852  15.2453
 GPB  H52   H  HCH3   0   0.259  14.3577   1.8466  15.1187
 GPB  H51   H  HCH3   0   0.259  15.2006   2.9781  14.0680
 GPB  H7    H  HCR5   0   0.281  11.2228   6.5942  11.9942
 GPB  H8    H  HNR5   0   0.405  10.2194   4.5755  10.8783
 GPB  H91   H  HCH2   0   0.250  12.9111   7.0417  13.9347
 GPB  H92   H  HCH2   0   0.245  13.3760   5.7037  14.9555
 GPB  H101  H  HCH2   0   0.250  15.3467   6.8223  14.0647
 GPB  H102  H  HCH2   0   0.252  15.2868   5.1756  13.4715
 GPB  H12   H  HCR6   0   0.250  15.1589   5.5296   8.8017
 GPB  H13   H  HCR6   0   0.246  15.0888   4.7068  11.1113
 GPB  H15   H  HCR6   0   0.249  14.6667   8.7178  12.5289
 GPB  H16   H  HCR6   0   0.251  14.7103   9.5459  10.2395
 GPB  H     H  HNH1   0   0.387  13.7908   9.6616   8.3452
 GPB  HA1   H  HCH1   0   0.218  15.3109   9.7518   5.8966
 GPB  HB2   H  HCH2   0   0.215  13.4386   8.1199   5.4468
 GPB  HB1   H  HCH2   0   0.200  12.2852   9.3732   5.8353
 GPB  HG2   H  HCH2   0   0.222  13.1003  10.7370   3.9135
 GPB  HG1   H  HCH2   0   0.206  14.3744   9.5995   3.6108
 GPB  C     C  C      0   0.513  14.9739   8.0453   7.9142

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  1.327  0.020  1.327
 GPB  N1   C8A   aromatic  1.326  0.020  1.326
 GPB  C2   NA2   single    1.361  0.020  1.361
 GPB  C2   N3    aromatic  1.344  0.020  1.344
 GPB  NA2  HA22  single    0.890  0.020  1.040
 GPB  NA2  HA21  single    0.890  0.020  1.040
 GPB  N3   C4    aromatic  1.326  0.020  1.326
 GPB  C4   C5    single    1.495  0.020  1.495
 GPB  C4   C4A   aromatic  1.397  0.020  1.397
 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  1.442  0.020  1.442
 GPB  C4A  C8A   aromatic  1.411  0.020  1.411
 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    1.539  0.020  1.539
 GPB  C9   H91   single    0.970  0.020  1.090
 GPB  C9   H92   single    0.970  0.020  1.090
 GPB  C10  C14   single    1.500  0.020  1.500
 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  1.394  0.020  1.394
 GPB  C11  C     single    1.498  0.020  1.498
 GPB  C12  C13   aromatic  1.385  0.020  1.385
 GPB  C12  H12   single    0.930  0.020  1.080
 GPB  C13  C14   aromatic  1.393  0.020  1.393
 GPB  C13  H13   single    0.930  0.020  1.080
 GPB  C14  C15   aromatic  1.393  0.020  1.393
 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    1.229  0.020  1.229
 GPB  C    N     single    1.335  0.020  1.335
 GPB  N    CA    single    1.449  0.020  1.449
 GPB  N    H     single    0.860  0.020  1.020
 GPB  CA   CB    single    1.538  0.020  1.538
 GPB  CA   CT    single    1.549  0.020  1.549
 GPB  CA   HA1   single    0.970  0.020  1.090
 GPB  CB   CG    single    1.520  0.020  1.520
 GPB  CB   HB2   single    0.970  0.020  1.090
 GPB  CB   HB1   single    0.970  0.020  1.090
 GPB  CG   CD    single    1.543  0.020  1.543
 GPB  CG   HG2   single    0.970  0.020  1.090
 GPB  CG   HG1   single    0.970  0.020  1.090
 GPB  CD   OE1   deloc     1.250  0.020  1.250
 GPB  CD   OE2   deloc     1.248  0.020  1.248
 GPB  CT   O1    deloc     1.250  0.020  1.250
 GPB  CT   O2    deloc     1.243  0.020  1.243

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    113.48  3.000
 GPB  N3    C2   NA2   116.03  3.000
 GPB  N3    C2   N1    126.39  3.000
 GPB  NA2   C2   N1    117.54  3.000
 GPB  HA21  NA2  HA22  115.19  3.000
 GPB  HA21  NA2  C2    117.05  3.000
 GPB  HA22  NA2  C2    116.81  3.000
 GPB  C4    N3   C2    119.23  3.000
 GPB  C4A   C4   C5    123.12  3.000
 GPB  C4A   C4   N3    120.23  3.000
 GPB  C5    C4   N3    116.64  3.000
 GPB  H51   C5   H52   107.58  3.000
 GPB  H51   C5   H53   107.36  3.000
 GPB  H52   C5   H53   108.89  3.000
 GPB  H51   C5   C4    110.20  3.000
 GPB  H52   C5   C4    110.51  3.000
 GPB  H53   C5   C4    112.15  3.000
 GPB  C8A   C4A  C6    107.02  3.000
 GPB  C8A   C4A  C4    114.60  3.000
 GPB  C6    C4A  C4    138.37  3.000
 GPB  C9    C6   C7    124.88  3.000
 GPB  C9    C6   C4A   129.46  3.000
 GPB  C7    C6   C4A   105.59  3.000
 GPB  H7    C7   N8    120.48  3.000
 GPB  H7    C7   C6    129.08  3.000
 GPB  N8    C7   C6    110.44  3.000
 GPB  H8    N8   C8A   125.37  3.000
 GPB  H8    N8   C7    125.61  3.000
 GPB  C8A   N8   C7    109.01  3.000
 GPB  N8    C8A  C4A   107.94  3.000
 GPB  N8    C8A  N1    126.00  3.000
 GPB  C4A   C8A  N1    126.06  3.000
 GPB  H92   C9   H91   106.03  3.000
 GPB  H92   C9   C10   108.47  3.000
 GPB  H91   C9   C10   108.67  3.000
 GPB  H92   C9   C6    110.94  3.000
 GPB  H91   C9   C6    108.72  3.000
 GPB  C10   C9   C6    113.71  3.000
 GPB  H102  C10  H101  106.67  3.000
 GPB  H102  C10  C14   109.66  3.000
 GPB  H101  C10  C14   109.92  3.000
 GPB  H102  C10  C9    109.78  3.000
 GPB  H101  C10  C9    108.28  3.000
 GPB  C14   C10  C9    112.36  3.000
 GPB  C     C11  C16   122.78  3.000
 GPB  C     C11  C12   118.65  3.000
 GPB  C16   C11  C12   118.53  3.000
 GPB  H12   C12  C13   119.61  3.000
 GPB  H12   C12  C11   119.73  3.000
 GPB  C13   C12  C11   120.66  3.000
 GPB  H13   C13  C14   119.49  3.000
 GPB  H13   C13  C12   119.45  3.000
 GPB  C14   C13  C12   121.05  3.000
 GPB  C15   C14  C13   118.09  3.000
 GPB  C15   C14  C10   120.75  3.000
 GPB  C13   C14  C10   121.14  3.000
 GPB  H15   C15  C16   119.31  3.000
 GPB  H15   C15  C14   119.57  3.000
 GPB  C16   C15  C14   121.12  3.000
 GPB  H16   C16  C15   118.58  3.000
 GPB  H16   C16  C11   120.85  3.000
 GPB  C15   C16  C11   120.54  3.000
 GPB  H     N    CA    113.61  3.000
 GPB  H     N    C     121.14  3.000
 GPB  CA    N    C     125.25  3.000
 GPB  HA1   CA   CT    109.16  3.000
 GPB  HA1   CA   CB    108.88  3.000
 GPB  CT    CA   CB    111.54  3.000
 GPB  HA1   CA   N     108.81  3.000
 GPB  CT    CA   N     107.78  3.000
 GPB  CB    CA   N     110.62  3.000
 GPB  HB1   CB   HB2   106.08  3.000
 GPB  HB1   CB   CG    110.47  3.000
 GPB  HB2   CB   CG    109.03  3.000
 GPB  HB1   CB   CA    108.54  3.000
 GPB  HB2   CB   CA    107.62  3.000
 GPB  CG    CB   CA    114.71  3.000
 GPB  HG1   CG   HG2   104.78  3.000
 GPB  HG1   CG   CD    108.24  3.000
 GPB  HG2   CG   CD    107.84  3.000
 GPB  HG1   CG   CB    109.43  3.000
 GPB  HG2   CG   CB    110.26  3.000
 GPB  CD    CG   CB    115.72  3.000
 GPB  OE2   CD   OE1   126.39  3.000
 GPB  OE2   CD   CG    118.10  3.000
 GPB  OE1   CD   CG    115.51  3.000
 GPB  O2    CT   O1    127.27  3.000
 GPB  O2    CT   CA    116.75  3.000
 GPB  O1    CT   CA    115.96  3.000
 GPB  N     C    O     123.67  3.000
 GPB  N     C    C11   115.71  3.000
 GPB  O     C    C11   120.62  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  Var_01    C10  C9   C6   C4A    71.75  30.0  2
 GPB  Var_02    C14  C10  C9   C6     57.91  30.0  3
 GPB  Var_03    C13  C14  C10  C9    -97.85  30.0  2
 GPB  Var_04    O    C    C11  C12   -26.33  30.0  2
 GPB  Var_05    H53  C5   C4   N3   -144.34  30.0  2
 GPB  Var_06    CD   CG   CB   CA    173.01  30.0  3
 GPB  Var_07    OE1  CD   CG   CB   -172.65  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-6  CA    0.020
 GPB  plan-6  CT    0.020
 GPB  plan-6  O1    0.020
 GPB  plan-6  O2    0.020

