# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:03:09 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 2-({4-[(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2c(Cc3ccc(cc3)C(=O)Nc4ccccc4C(O)=O)c[nH]c2N1
#
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
 OG7  OG7  '2-({4-[(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)benzoic acid'  ligand  46  30  .  2022-07-22  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_OG7
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
 OG7  C10  C  CR16   0  -0.253  -0.0438   0.9112  -1.1065
 OG7  C11  C  CR6    0  -0.055   1.0451   0.3013  -0.4845
 OG7  C12  C  CR16   0  -0.280   0.9243  -1.0290  -0.0875
 OG7  C13  C  CR16   0  -0.309  -0.2524  -1.7264  -0.3159
 OG7  C14  C  C      0   0.515   2.2714   1.1243  -0.2456
 OG7  C15  C  CR6    0   0.350   4.7010   0.8559   0.1854
 OG7  C16  C  CR6    0  -0.230   5.7176  -0.1254   0.2561
 OG7  C17  C  CR16   0  -0.283   7.0167   0.2852   0.5411
 OG7  C18  C  CR16   0  -0.263   7.3398   1.6149   0.7538
 OG7  C01  C  CR56   0   0.650  -5.2447  -0.5707   1.1177
 OG7  C02  C  CR56   0  -0.258  -4.5880  -0.4947  -0.0924
 OG7  C03  C  CR6    0   0.423  -5.0090   0.5157  -1.0360
 OG7  C04  C  CR6    0   0.665  -6.5737   1.2477   0.5535
 OG7  C05  C  CR5    0   0.019  -3.6309  -1.5617  -0.0996
 OG7  C06  C  CR15   0  -0.083  -3.7675  -2.2083   1.0940
 OG7  C08  C  CR6    0   0.140  -1.3348  -1.1237  -0.9490
 OG7  C09  C  CR16   0  -0.299  -1.2119   0.2074  -1.3429
 OG7  C19  C  CR16   0  -0.251   6.3346   2.5674   0.6813
 OG7  C20  C  CR16   0  -0.323   5.0287   2.1996   0.4011
 OG7  C21  C  C      0   0.467   5.4743  -1.6148   0.0350
 OG7  N01  N  NR16   0  -0.732  -6.2410   0.2904   1.4632
 OG7  N02  N  N      0  -0.537  -6.0117   1.3594  -0.6201
 OG7  N03  N  NR15   0  -0.664  -4.7587  -1.5930   1.8345
 OG7  N05  N  NH1    0  -0.791   3.4092   0.4147  -0.0907
 OG7  O02  O  O      0  -0.478   2.1975   2.3457  -0.2144
 OG7  O03  O  O      0  -0.602   4.3000  -1.9769  -0.2512
 OG7  O04  O  OC    -1  -0.558   6.4446  -2.3738   0.1455
 OG7  H1   H  HCR6   0   0.253   0.0271   1.9451  -1.4173
 OG7  H2   H  HCR6   0   0.251   1.7330  -1.5373   0.4214
 OG7  H3   H  HCR6   0   0.251  -0.3268  -2.7574   0.0089
 OG7  H4   H  HCR6   0   0.250   7.7898  -0.4686   0.5949
 OG7  H5   H  HCR6   0   0.248   8.3595   1.9032   0.9723
 OG7  H6   H  HCR5   0   0.282  -3.2379  -3.0576   1.4933
 OG7  H7   H  HCH2   0   0.262  -2.4127  -2.9543  -1.1487
 OG7  H8   H  HCH2   0   0.266  -3.0312  -1.6481  -2.1430
 OG7  H9   H  HCR6   0   0.263  -2.0439   0.6956  -1.8345
 OG7  H10  H  HCR6   0   0.254   6.5617   3.6136   0.8432
 OG7  H11  H  HCR6   0   0.277   4.2674   2.9593   0.3492
 OG7  H12  H  HNR6   0   0.432  -6.6981   0.2380   2.3616
 OG7  H13  H  HNR5   0   0.421  -5.0606  -1.8778   2.7522
 OG7  H14  H  HNH2   0   0.408  -7.8815   2.7446   0.2246
 OG7  H15  H  HNH2   0   0.410  -8.0933   1.9671   1.7357
 OG7  H16  H  HNH1   0   0.447   3.4207  -0.6141  -0.2325
 OG7  C07  C  CH2    0  -0.626  -2.6218  -1.8830  -1.1603
 OG7  N04  N  NH2    0  -0.827  -7.5156   2.1274   0.9284
 OG7  O01  O  O      0  -0.504  -4.5265   0.6423  -2.1615

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
 OG7  N04  C04  single    1.342  0.020  1.342
 OG7  N01  C04  single    1.362  0.020  1.362
 OG7  N01  C01  single    1.361  0.020  1.361
 OG7  C04  N02  double    1.306  0.020  1.306
 OG7  N03  C01  aromatic  1.340  0.020  1.340
 OG7  N03  C06  aromatic  1.382  0.020  1.382
 OG7  C01  C02  aromatic  1.379  0.020  1.379
 OG7  O02  C14  double    1.224  0.020  1.224
 OG7  N02  C03  single    1.375  0.020  1.375
 OG7  C12  C13  aromatic  1.387  0.020  1.387
 OG7  C12  C11  aromatic  1.393  0.020  1.393
 OG7  C06  C05  aromatic  1.364  0.020  1.364
 OG7  C02  C03  single    1.445  0.020  1.445
 OG7  C02  C05  aromatic  1.433  0.020  1.433
 OG7  C13  C08  aromatic  1.391  0.020  1.391
 OG7  C03  O01  double    1.231  0.020  1.231
 OG7  C14  C11  single    1.496  0.020  1.496
 OG7  C14  N05  single    1.350  0.020  1.350
 OG7  C05  C07  single    1.499  0.020  1.499
 OG7  C11  C10  aromatic  1.395  0.020  1.395
 OG7  O03  C21  deloc     1.262  0.020  1.262
 OG7  O04  C21  deloc     1.237  0.020  1.237
 OG7  C21  C16  single    1.525  0.020  1.525
 OG7  C08  C07  single    1.509  0.020  1.509
 OG7  C08  C09  aromatic  1.394  0.020  1.394
 OG7  C16  C15  aromatic  1.415  0.020  1.415
 OG7  C16  C17  aromatic  1.392  0.020  1.392
 OG7  N05  C15  single    1.393  0.020  1.393
 OG7  C15  C20  aromatic  1.400  0.020  1.400
 OG7  C17  C18  aromatic  1.385  0.020  1.385
 OG7  C18  C19  aromatic  1.387  0.020  1.387
 OG7  C20  C19  aromatic  1.385  0.020  1.385
 OG7  C10  C09  aromatic  1.384  0.020  1.384
 OG7  C10  H1   single    0.930  0.020  1.080
 OG7  C12  H2   single    0.930  0.020  1.080
 OG7  C13  H3   single    0.930  0.020  1.080
 OG7  C17  H4   single    0.930  0.020  1.080
 OG7  C18  H5   single    0.930  0.020  1.080
 OG7  C06  H6   single    0.930  0.020  1.080
 OG7  C07  H7   single    0.970  0.020  1.090
 OG7  C07  H8   single    0.970  0.020  1.090
 OG7  C09  H9   single    0.930  0.020  1.080
 OG7  C19  H10  single    0.930  0.020  1.080
 OG7  C20  H11  single    0.930  0.020  1.080
 OG7  N01  H12  single    0.860  0.020  1.020
 OG7  N03  H13  single    0.860  0.020  1.020
 OG7  N04  H14  single    0.890  0.020  1.040
 OG7  N04  H15  single    0.890  0.020  1.040
 OG7  N05  H16  single    0.860  0.020  1.020

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
 OG7  H1   C10  C09  119.48  3.000
 OG7  H1   C10  C11  119.66  3.000
 OG7  C09  C10  C11  120.85  3.000
 OG7  C14  C11  C12  123.42  3.000
 OG7  C14  C11  C10  118.08  3.000
 OG7  C12  C11  C10  118.48  3.000
 OG7  H2   C12  C13  118.38  3.000
 OG7  H2   C12  C11  121.17  3.000
 OG7  C13  C12  C11  120.44  3.000
 OG7  H3   C13  C08  119.68  3.000
 OG7  H3   C13  C12  119.17  3.000
 OG7  C08  C13  C12  121.15  3.000
 OG7  O02  C14  N05  124.93  3.000
 OG7  N05  C14  C11  114.84  3.000
 OG7  O02  C14  C11  120.24  3.000
 OG7  N05  C15  C20  123.49  3.000
 OG7  C20  C15  C16  119.34  3.000
 OG7  N05  C15  C16  117.18  3.000
 OG7  C21  C16  C17  117.82  3.000
 OG7  C17  C16  C15  118.44  3.000
 OG7  C21  C16  C15  123.74  3.000
 OG7  H4   C17  C18  119.66  3.000
 OG7  H4   C17  C16  118.16  3.000
 OG7  C18  C17  C16  122.17  3.000
 OG7  H5   C18  C19  120.70  3.000
 OG7  H5   C18  C17  120.45  3.000
 OG7  C19  C18  C17  118.84  3.000
 OG7  N03  C01  N01  127.76  3.000
 OG7  N03  C01  C02  109.80  3.000
 OG7  N01  C01  C02  122.44  3.000
 OG7  C05  C02  C03  135.38  3.000
 OG7  C05  C02  C01  106.34  3.000
 OG7  C03  C02  C01  118.21  3.000
 OG7  O01  C03  N02  119.96  3.000
 OG7  O01  C03  C02  123.68  3.000
 OG7  N02  C03  C02  116.36  3.000
 OG7  N04  C04  N02  119.79  3.000
 OG7  N02  C04  N01  123.73  3.000
 OG7  N04  C04  N01  116.46  3.000
 OG7  C07  C05  C06  125.80  3.000
 OG7  C07  C05  C02  127.78  3.000
 OG7  C06  C05  C02  106.35  3.000
 OG7  H6   C06  N03  120.33  3.000
 OG7  H6   C06  C05  130.42  3.000
 OG7  N03  C06  C05  109.25  3.000
 OG7  C09  C08  C07  121.08  3.000
 OG7  C09  C08  C13  118.28  3.000
 OG7  C07  C08  C13  120.62  3.000
 OG7  H9   C09  C08  119.42  3.000
 OG7  H9   C09  C10  119.79  3.000
 OG7  C08  C09  C10  120.78  3.000
 OG7  H10  C19  C20  118.98  3.000
 OG7  H10  C19  C18  120.26  3.000
 OG7  C20  C19  C18  120.76  3.000
 OG7  H11  C20  C19  119.27  3.000
 OG7  H11  C20  C15  120.29  3.000
 OG7  C19  C20  C15  120.44  3.000
 OG7  O04  C21  O03  125.05  3.000
 OG7  O04  C21  C16  117.46  3.000
 OG7  O03  C21  C16  117.49  3.000
 OG7  H12  N01  C04  121.36  3.000
 OG7  H12  N01  C01  121.63  3.000
 OG7  C04  N01  C01  116.99  3.000
 OG7  C04  N02  C03  122.22  3.000
 OG7  H13  N03  C06  125.26  3.000
 OG7  H13  N03  C01  126.48  3.000
 OG7  C06  N03  C01  108.26  3.000
 OG7  H16  N05  C15  109.30  3.000
 OG7  H16  N05  C14  120.96  3.000
 OG7  C15  N05  C14  129.65  3.000
 OG7  H8   C07  H7   107.03  3.000
 OG7  H8   C07  C08  109.76  3.000
 OG7  H7   C07  C08  109.21  3.000
 OG7  H8   C07  C05  109.80  3.000
 OG7  H7   C07  C05  109.38  3.000
 OG7  C08  C07  C05  111.55  3.000
 OG7  H15  N04  H14  116.80  3.000
 OG7  H15  N04  C04  121.53  3.000
 OG7  H14  N04  C04  117.54  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
 OG7  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 OG7  CONST_02  C13  C08  C09  C10    0.00   0.0  0
 OG7  CONST_03  C08  C13  C12  C11    0.00   0.0  0
 OG7  CONST_04  C08  C09  C10  C11    0.00   0.0  0
 OG7  CONST_05  C09  C08  C13  C12    0.00   0.0  0
 OG7  CONST_06  C09  C10  C11  C12    0.00   0.0  0
 OG7  CONST_07  C18  C17  C16  C15    0.00   0.0  0
 OG7  CONST_08  C18  C19  C20  C15    0.00   0.0  0
 OG7  CONST_09  C19  C20  C15  C16    0.00   0.0  0
 OG7  CONST_10  C19  C18  C17  C16    0.00   0.0  0
 OG7  CONST_11  C20  C15  C16  C17    0.00   0.0  0
 OG7  CONST_12  C20  C19  C18  C17    0.00   0.0  0
 OG7  CONST_13  C05  C06  N03  C01    0.00   0.0  0
 OG7  CONST_14  C06  C05  C02  C01    0.00   0.0  0
 OG7  CONST_15  C06  N03  C01  C02    0.00   0.0  0
 OG7  CONST_16  N03  C06  C05  C02    0.00   0.0  0
 OG7  CONST_17  N03  C01  C02  C05    0.00   0.0  0
 OG7  CONST_18  N02  C04  N01  C01    0.00   0.0  0
 OG7  CONST_19  N01  C04  N02  C03    0.00   0.0  0
 OG7  CONST_20  C07  C08  C09  C10  180.00   0.0  0
 OG7  CONST_21  C07  C08  C13  C12  180.00   0.0  0
 OG7  CONST_22  C14  C11  C12  C13  180.00   0.0  0
 OG7  CONST_23  C09  C10  C11  C14  180.00   0.0  0
 OG7  CONST_24  N05  C15  C16  C17  180.00   0.0  0
 OG7  CONST_25  C21  C16  C17  C18  180.00   0.0  0
 OG7  CONST_26  C07  C05  C02  C01  180.00   0.0  0
 OG7  CONST_27  C07  C05  C02  C03    0.00   0.0  0
 OG7  CONST_28  N03  C06  C05  C07  180.00   0.0  0
 OG7  CONST_29  N05  C15  C20  C19  180.00   0.0  0
 OG7  CONST_30  C21  C16  C15  C20  180.00   0.0  0
 OG7  CONST_31  N04  C04  N01  C01  180.00   0.0  0
 OG7  CONST_32  N04  C04  N02  C03  180.00   0.0  0
 OG7  CONST_33  H2   C12  C11  C10  180.00   0.0  0
 OG7  CONST_34  H3   C13  C12  C11  180.00   0.0  0
 OG7  CONST_35  H9   C09  C10  C11  180.00   0.0  0
 OG7  CONST_36  H1   C10  C11  C12  180.00   0.0  0
 OG7  CONST_37  H4   C17  C16  C15  180.00   0.0  0
 OG7  CONST_38  H10  C19  C20  C15  180.00   0.0  0
 OG7  CONST_39  H11  C20  C15  C16  180.00   0.0  0
 OG7  CONST_40  H5   C18  C17  C16  180.00   0.0  0
 OG7  CONST_41  H6   C06  N03  C01  180.00   0.0  0
 OG7  CONST_42  H13  N03  C01  C02  180.00   0.0  0
 OG7  CONST_43  H12  N01  C04  N02  180.00   0.0  0
 OG7  CONST_44  C15  N05  C14  C11  180.00   0.0  0
 OG7  CONST_45  C16  C15  N05  C14  180.00   0.0  0
 OG7  CONST_46  C20  C15  N05  C14    0.00   0.0  0
 OG7  CONST_47  H16  N05  C15  C16    0.00   0.0  0
 OG7  CONST_48  H14  N04  C04  N01  180.00   0.0  0
 OG7  CONST_49  H15  N04  C04  N01    0.00   0.0  0
 OG7  CONST_50  O02  C14  N05  C15    0.00   0.0  0
 OG7  Var_01    C05  C07  C08  C13   97.73  30.0  2
 OG7  Var_02    C08  C07  C05  C02   87.60  30.0  2
 OG7  Var_03    O02  C14  C11  C10   21.52  30.0  2
 OG7  Var_04    O03  C21  C16  C15    1.38  30.0  3

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
 OG7  plan-1  C10  0.020
 OG7  plan-1  C11  0.020
 OG7  plan-1  C12  0.020
 OG7  plan-1  C13  0.020
 OG7  plan-1  C14  0.020
 OG7  plan-1  C08  0.020
 OG7  plan-1  C09  0.020
 OG7  plan-1  H1   0.020
 OG7  plan-1  H2   0.020
 OG7  plan-1  H3   0.020
 OG7  plan-1  H9   0.020
 OG7  plan-1  C07  0.020
 OG7  plan-2  C16  0.020
 OG7  plan-2  C21  0.020
 OG7  plan-2  O03  0.020
 OG7  plan-2  O04  0.020
 OG7  plan-3  C15  0.020
 OG7  plan-3  C16  0.020
 OG7  plan-3  C17  0.020
 OG7  plan-3  C18  0.020
 OG7  plan-3  C19  0.020
 OG7  plan-3  C20  0.020
 OG7  plan-3  C21  0.020
 OG7  plan-3  N05  0.020
 OG7  plan-3  H4   0.020
 OG7  plan-3  H5   0.020
 OG7  plan-3  H10  0.020
 OG7  plan-3  H11  0.020
 OG7  plan-4  C01  0.020
 OG7  plan-4  C02  0.020
 OG7  plan-4  C03  0.020
 OG7  plan-4  C04  0.020
 OG7  plan-4  C05  0.020
 OG7  plan-4  C06  0.020
 OG7  plan-4  N01  0.020
 OG7  plan-4  N02  0.020
 OG7  plan-4  N03  0.020
 OG7  plan-4  H6   0.020
 OG7  plan-4  H12  0.020
 OG7  plan-4  H13  0.020
 OG7  plan-4  H14  0.020
 OG7  plan-4  H15  0.020
 OG7  plan-4  C07  0.020
 OG7  plan-4  N04  0.020
 OG7  plan-4  O01  0.020
 OG7  plan-5  C11  0.020
 OG7  plan-5  C14  0.020
 OG7  plan-5  C15  0.020
 OG7  plan-5  N05  0.020
 OG7  plan-5  O02  0.020
 OG7  plan-5  H16  0.020

