# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 19:01:53 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 3-(pyrimidin-2-yl)-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cccc(c1)c2[nH]nnn2)c3cccc(c3)c4ncccn4
#
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
 0J7  0J7  3-(pyrimidin-2-yl)-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide  ligand  39  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0J7
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
 0J7  O26  O  O     0  -0.453   0.2430  -0.6679  -0.2426
 0J7  C13  C  C     0   0.533  -0.0408   0.5143  -0.1769
 0J7  N12  N  NH1   0  -0.766   0.8581   1.4941   0.1033
 0J7  C8   C  CR6   0   0.417   2.2311   1.3737   0.3256
 0J7  C7   C  CR16  0  -0.349   2.9842   0.2671  -0.0542
 0J7  C9   C  CR16  0  -0.342   2.8686   2.4553   0.9394
 0J7  C10  C  CR16  0  -0.227   4.2307   2.4277   1.1732
 0J7  C11  C  CR16  0  -0.306   4.9867   1.3261   0.8045
 0J7  C6   C  CR6   0   0.075   4.3573   0.2507   0.1862
 0J7  C5   C  CR5   0   0.503   5.1119  -0.9257  -0.2285
 0J7  N4   N  NR15  0  -0.505   6.4419  -1.0517  -0.2524
 0J7  N3   N  N     0  -0.071   6.7563  -2.2584  -0.6882
 0J7  N2   N  N     0  -0.138   5.6543  -2.8532  -0.9240
 0J7  N1   N  N     0  -0.344   4.6164  -2.0671  -0.6534
 0J7  C14  C  CR6   0  -0.021  -1.4405   0.9909  -0.3892
 0J7  C19  C  CR16  0  -0.293  -1.7328   2.2457  -0.9198
 0J7  C18  C  CR16  0  -0.224  -3.0531   2.6162  -1.1274
 0J7  C17  C  CR16  0  -0.274  -4.0826   1.7498  -0.8011
 0J7  C16  C  CR6   0   0.013  -3.8031   0.4889  -0.2728
 0J7  C15  C  CR16  0  -0.306  -2.4765   0.1154  -0.0831
 0J7  C20  C  CR6   0   0.404  -4.9004  -0.4408   0.0767
 0J7  N25  N  N     0  -0.424  -4.5670  -1.6250   0.5800
 0J7  C24  C  CR16  0  -0.010  -5.5537  -2.4526   0.8905
 0J7  C23  C  CR16  0  -0.355  -6.8842  -2.1167   0.7062
 0J7  C22  C  CR16  0  -0.011  -7.1254  -0.8604   0.1768
 0J7  N21  N  N     0  -0.423  -6.1449  -0.0264  -0.1368
 0J7  H1   H  HNH1  0   0.426   0.4836   2.4128   0.2857
 0J7  H2   H  HCR6  0   0.287   2.5253  -0.5771  -0.5414
 0J7  H3   H  HCR6  0   0.283   2.2908   3.3219   1.2382
 0J7  H4   H  HCR6  0   0.275   4.7064   3.2716   1.6532
 0J7  H5   H  HCR6  0   0.258   6.0485   1.3191   1.0120
 0J7  H6   H  HNR5  0   0.451   7.1699  -0.3919  -0.0175
 0J7  H7   H  HCR6  0   0.272  -0.9449   2.9321  -1.2034
 0J7  H8   H  HCR6  0   0.271  -3.2796   3.5849  -1.5517
 0J7  H9   H  HCR6  0   0.265  -5.1091   2.0488  -0.9603
 0J7  H10  H  HCR6  0   0.262  -2.2504  -0.8631   0.3172
 0J7  H11  H  HCR6  0   0.280  -5.2720  -3.4155   1.3006
 0J7  H12  H  HCR6  0   0.288  -7.6861  -2.7937   0.9608
 0J7  H13  H  HCR6  0   0.280  -8.1368  -0.5134  -0.0001

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
 0J7  C18  C17  aromatic  1.385  0.020  1.385
 0J7  C18  C19  aromatic  1.387  0.020  1.387
 0J7  C17  C16  aromatic  1.395  0.020  1.395
 0J7  C19  C14  aromatic  1.393  0.020  1.393
 0J7  N25  C24  aromatic  1.325  0.020  1.325
 0J7  N25  C20  aromatic  1.329  0.020  1.329
 0J7  C16  C20  single    1.480  0.020  1.480
 0J7  C16  C15  aromatic  1.391  0.020  1.391
 0J7  C24  C23  aromatic  1.385  0.020  1.385
 0J7  C14  C15  aromatic  1.390  0.020  1.390
 0J7  C14  C13  single    1.494  0.020  1.494
 0J7  N1   N2   aromatic  1.330  0.020  1.330
 0J7  N1   C5   aromatic  1.315  0.020  1.315
 0J7  N2   N3   aromatic  1.274  0.020  1.274
 0J7  C20  N21  aromatic  1.329  0.020  1.329
 0J7  N12  C13  single    1.359  0.020  1.359
 0J7  N12  C8   single    1.396  0.020  1.396
 0J7  C13  O26  double    1.218  0.020  1.218
 0J7  C7   C8   aromatic  1.391  0.020  1.391
 0J7  C7   C6   aromatic  1.394  0.020  1.394
 0J7  C23  C22  aromatic  1.384  0.020  1.384
 0J7  C5   C6   single    1.458  0.020  1.458
 0J7  C5   N4   aromatic  1.336  0.020  1.336
 0J7  C8   C9   aromatic  1.397  0.020  1.397
 0J7  N3   N4   aromatic  1.321  0.020  1.321
 0J7  N21  C22  aromatic  1.325  0.020  1.325
 0J7  C6   C11  aromatic  1.391  0.020  1.391
 0J7  C9   C10  aromatic  1.382  0.020  1.382
 0J7  C11  C10  aromatic  1.386  0.020  1.386
 0J7  N12  H1   single    0.860  0.020  1.020
 0J7  C7   H2   single    0.930  0.020  1.080
 0J7  C9   H3   single    0.930  0.020  1.080
 0J7  C10  H4   single    0.930  0.020  1.080
 0J7  C11  H5   single    0.930  0.020  1.080
 0J7  N4   H6   single    0.860  0.020  1.020
 0J7  C19  H7   single    0.930  0.020  1.080
 0J7  C18  H8   single    0.930  0.020  1.080
 0J7  C17  H9   single    0.930  0.020  1.080
 0J7  C15  H10  single    0.930  0.020  1.080
 0J7  C24  H11  single    0.930  0.020  1.080
 0J7  C23  H12  single    0.930  0.020  1.080
 0J7  C22  H13  single    0.930  0.020  1.080

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
 0J7  C14  C13  N12  114.78  3.000
 0J7  N12  C13  O26  123.85  3.000
 0J7  C14  C13  O26  121.37  3.000
 0J7  H1   N12  C8   114.51  3.000
 0J7  H1   N12  C13  116.64  3.000
 0J7  C8   N12  C13  128.41  3.000
 0J7  C9   C8   C7   119.24  3.000
 0J7  C9   C8   N12  116.86  3.000
 0J7  C7   C8   N12  123.87  3.000
 0J7  H2   C7   C6   119.23  3.000
 0J7  H2   C7   C8   121.08  3.000
 0J7  C6   C7   C8   119.69  3.000
 0J7  H3   C9   C10  119.66  3.000
 0J7  H3   C9   C8   119.79  3.000
 0J7  C10  C9   C8   120.55  3.000
 0J7  H4   C10  C11  119.91  3.000
 0J7  H4   C10  C9   119.54  3.000
 0J7  C11  C10  C9   120.56  3.000
 0J7  H5   C11  C6   121.62  3.000
 0J7  H5   C11  C10  119.30  3.000
 0J7  C6   C11  C10  119.07  3.000
 0J7  C5   C6   C11  121.07  3.000
 0J7  C11  C6   C7   120.88  3.000
 0J7  C5   C6   C7   118.05  3.000
 0J7  N1   C5   N4   106.71  3.000
 0J7  N4   C5   C6   126.61  3.000
 0J7  N1   C5   C6   126.68  3.000
 0J7  H6   N4   N3   120.12  3.000
 0J7  H6   N4   C5   130.66  3.000
 0J7  N3   N4   C5   109.20  3.000
 0J7  N2   N3   N4   106.36  3.000
 0J7  N1   N2   N3   111.18  3.000
 0J7  N2   N1   C5   106.55  3.000
 0J7  C15  C14  C19  119.64  3.000
 0J7  C15  C14  C13  117.77  3.000
 0J7  C19  C14  C13  122.55  3.000
 0J7  H7   C19  C18  118.96  3.000
 0J7  H7   C19  C14  121.20  3.000
 0J7  C18  C19  C14  119.82  3.000
 0J7  H8   C18  C17  119.82  3.000
 0J7  H8   C18  C19  119.83  3.000
 0J7  C17  C18  C19  120.36  3.000
 0J7  H9   C17  C16  119.73  3.000
 0J7  H9   C17  C18  119.89  3.000
 0J7  C16  C17  C18  120.38  3.000
 0J7  C20  C16  C15  120.41  3.000
 0J7  C15  C16  C17  119.03  3.000
 0J7  C20  C16  C17  120.56  3.000
 0J7  H10  C15  C16  119.53  3.000
 0J7  H10  C15  C14  119.71  3.000
 0J7  C16  C15  C14  120.76  3.000
 0J7  N21  C20  N25  125.00  3.000
 0J7  N21  C20  C16  117.42  3.000
 0J7  N25  C20  C16  117.59  3.000
 0J7  C24  N25  C20  117.29  3.000
 0J7  H11  C24  C23  121.04  3.000
 0J7  H11  C24  N25  116.76  3.000
 0J7  C23  C24  N25  122.21  3.000
 0J7  H12  C23  C22  121.98  3.000
 0J7  H12  C23  C24  122.01  3.000
 0J7  C22  C23  C24  116.00  3.000
 0J7  H13  C22  N21  116.77  3.000
 0J7  H13  C22  C23  121.03  3.000
 0J7  N21  C22  C23  122.20  3.000
 0J7  C22  N21  C20  117.31  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
 0J7  CONST_01  C5   C6   C7   C8    180.00   0.0  0
 0J7  CONST_02  C11  C6   C7   C8      0.00   0.0  0
 0J7  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 0J7  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 0J7  CONST_05  N1   C5   C6   C7      0.00   0.0  0
 0J7  CONST_06  N4   C5   C6   C7    180.00   0.0  0
 0J7  CONST_07  C10  C11  C6   C7      0.00   0.0  0
 0J7  CONST_08  C6   C7   C8   C9      0.00   0.0  0
 0J7  CONST_09  C6   C11  C10  C9      0.00   0.0  0
 0J7  CONST_10  C5   C6   C11  C10   180.00   0.0  0
 0J7  CONST_11  N1   C5   C6   C11   180.00   0.0  0
 0J7  CONST_12  N4   C5   C6   C11     0.00   0.0  0
 0J7  CONST_13  N2   N1   C5   C6    180.00   0.0  0
 0J7  CONST_14  N3   N4   C5   C6    180.00   0.0  0
 0J7  CONST_15  N3   N2   N1   C5      0.00   0.0  0
 0J7  CONST_16  N2   N3   N4   C5      0.00   0.0  0
 0J7  CONST_17  N2   N1   C5   N4      0.00   0.0  0
 0J7  CONST_18  N1   N2   N3   N4      0.00   0.0  0
 0J7  CONST_19  N1   C5   N4   N3      0.00   0.0  0
 0J7  CONST_20  C17  C18  C19  C14     0.00   0.0  0
 0J7  CONST_21  C17  C16  C15  C14     0.00   0.0  0
 0J7  CONST_22  C20  C16  C15  C14   180.00   0.0  0
 0J7  CONST_23  C16  C17  C18  C19     0.00   0.0  0
 0J7  CONST_24  C16  C15  C14  C19     0.00   0.0  0
 0J7  CONST_25  C20  C16  C17  C18   180.00   0.0  0
 0J7  CONST_26  C15  C16  C17  C18     0.00   0.0  0
 0J7  CONST_27  C15  C14  C19  C18     0.00   0.0  0
 0J7  CONST_28  N25  C20  C16  C17   180.00   0.0  0
 0J7  CONST_29  N21  C20  C16  C17     0.00   0.0  0
 0J7  CONST_30  C24  N25  C20  C16   180.00   0.0  0
 0J7  CONST_31  C22  N21  C20  C16   180.00   0.0  0
 0J7  CONST_32  N25  C20  C16  C15     0.00   0.0  0
 0J7  CONST_33  N21  C20  C16  C15   180.00   0.0  0
 0J7  CONST_34  C23  C24  N25  C20     0.00   0.0  0
 0J7  CONST_35  C23  C22  N21  C20     0.00   0.0  0
 0J7  CONST_36  C22  C23  C24  N25     0.00   0.0  0
 0J7  CONST_37  C22  N21  C20  N25     0.00   0.0  0
 0J7  CONST_38  N21  C20  N25  C24     0.00   0.0  0
 0J7  CONST_39  N21  C22  C23  C24     0.00   0.0  0
 0J7  CONST_40  C18  C19  C14  C13   180.00   0.0  0
 0J7  CONST_41  C16  C15  C14  C13   180.00   0.0  0
 0J7  CONST_42  C6   C7   C8   N12   180.00   0.0  0
 0J7  CONST_43  C10  C9   C8   N12   180.00   0.0  0
 0J7  CONST_44  H4   C10  C9   C8    180.00   0.0  0
 0J7  CONST_45  H3   C9   C8   C7    180.00   0.0  0
 0J7  CONST_46  H5   C11  C6   C7    180.00   0.0  0
 0J7  CONST_47  H2   C7   C8   C9    180.00   0.0  0
 0J7  CONST_48  H6   N4   C5   C6      0.00   0.0  0
 0J7  CONST_49  H8   C18  C19  C14   180.00   0.0  0
 0J7  CONST_50  H9   C17  C18  C19   180.00   0.0  0
 0J7  CONST_51  H10  C15  C14  C19   180.00   0.0  0
 0J7  CONST_52  H7   C19  C18  C17   180.00   0.0  0
 0J7  CONST_53  H11  C24  N25  C20   180.00   0.0  0
 0J7  CONST_54  H13  C22  N21  C20   180.00   0.0  0
 0J7  CONST_55  H12  C23  C24  N25   180.00   0.0  0
 0J7  CONST_56  C14  C13  N12  C8    180.00   0.0  0
 0J7  CONST_59  H1   N12  C8   C7    180.00   0.0  0
 0J7  CONST_60  C8   N12  C13  O26     0.00   0.0  0
 0J7  Var_01    C19  C14  C13  O26  -149.90  30.0  2

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
 0J7  plan-1  C6   0.020
 0J7  plan-1  C5   0.020
 0J7  plan-1  N4   0.020
 0J7  plan-1  N3   0.020
 0J7  plan-1  N2   0.020
 0J7  plan-1  N1   0.020
 0J7  plan-1  H6   0.020
 0J7  plan-2  N12  0.020
 0J7  plan-2  C8   0.020
 0J7  plan-2  C7   0.020
 0J7  plan-2  C9   0.020
 0J7  plan-2  C10  0.020
 0J7  plan-2  C11  0.020
 0J7  plan-2  C6   0.020
 0J7  plan-2  C5   0.020
 0J7  plan-2  H2   0.020
 0J7  plan-2  H3   0.020
 0J7  plan-2  H4   0.020
 0J7  plan-2  H5   0.020
 0J7  plan-3  C13  0.020
 0J7  plan-3  C14  0.020
 0J7  plan-3  C19  0.020
 0J7  plan-3  C18  0.020
 0J7  plan-3  C17  0.020
 0J7  plan-3  C16  0.020
 0J7  plan-3  C15  0.020
 0J7  plan-3  C20  0.020
 0J7  plan-3  H7   0.020
 0J7  plan-3  H8   0.020
 0J7  plan-3  H9   0.020
 0J7  plan-3  H10  0.020
 0J7  plan-4  C16  0.020
 0J7  plan-4  C20  0.020
 0J7  plan-4  N25  0.020
 0J7  plan-4  C24  0.020
 0J7  plan-4  C23  0.020
 0J7  plan-4  C22  0.020
 0J7  plan-4  N21  0.020
 0J7  plan-4  H11  0.020
 0J7  plan-4  H12  0.020
 0J7  plan-4  H13  0.020
 0J7  plan-5  O26  0.020
 0J7  plan-5  C13  0.020
 0J7  plan-5  N12  0.020
 0J7  plan-5  C8   0.020
 0J7  plan-5  C14  0.020
 0J7  plan-5  H1   0.020

