# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 14:09:18 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 3,5-bis(fluoranyl)-~{N}-oxidanyl-4-[(5-pyrimidin-2-yl-1,2,3,4-tetrazol-2-yl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1cc(F)c(Cn2nnc(n2)c3ncccn3)c(F)c1
#
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
 V05  V05  "3,5-bis(fluoranyl)-~{N}-oxidanyl-4-[(5-pyrimidin-2-yl-1,2,3,4-tetrazol-2-yl)methyl]benzamide"
  ligand  33  24  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V05
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
 V05  C4   C  CR6   0   0.595   3.9375   4.4201  29.4511
 V05  C5   C  CR6   0  -0.295   3.8658   3.1576  28.8764
 V05  C6   C  CH2   0  -0.372   3.4231   1.9555  29.6550
 V05  C11  C  CR16  0  -0.015   9.1492  -1.0916  28.9347
 V05  C7   C  CR5   0   0.337   6.3190   0.3427  30.6079
 V05  C8   C  CR6   0   0.371   7.5946  -0.3469  30.3865
 V05  C9   C  CR16  0  -0.017   9.3710  -1.4282  31.2534
 V05  C10  C  CR16  0  -0.337   9.8916  -1.6087  29.9832
 V05  C12  C  CR6   0   0.598   4.2459   3.0714  27.5460
 V05  C13  C  CR16  0  -0.444   4.6749   4.1588  26.8117
 V05  N1   N  NH1   0  -0.366   6.1998   6.4462  25.8871
 V05  N2   N  NR5   0  -0.097   4.5538   1.3086  30.3012
 V05  C3   C  CR16  0  -0.441   4.3367   5.5430  28.7597
 V05  N3   N  N     0  -0.049   4.6634   1.1893  31.5958
 V05  O1   O  O     0  -0.448   4.5681   7.6962  26.8405
 V05  C1   C  C     0   0.495   5.1404   6.6337  26.6896
 V05  O2   O  OH1   0  -0.532   6.6119   7.4303  25.0472
 V05  C2   C  CR6   0  -0.030   4.7250   5.4008  27.4329
 V05  F1   F  F     0  -0.294   3.5971   4.5448  30.7362
 V05  N4   N  N     0  -0.317   5.7758   0.5756  31.8139
 V05  N5   N  N     0  -0.404   8.2233  -0.7970  31.4619
 V05  N6   N  N     0  -0.406   8.0002  -0.4602  29.1299
 V05  N7   N  N     0  -0.241   5.5549   0.8040  29.6379
 V05  F2   F  F     0  -0.294   4.1876   1.8813  26.9462
 V05  H1   H  HCH2  0   0.321   2.7221   2.2160  30.4435
 V05  H2   H  HCH2  0   0.323   2.9369   1.2224  29.0143
 V05  H4   H  HCR6  0   0.285   9.8899  -1.8013  32.1285
 V05  H5   H  HCR6  0   0.292  10.8262  -2.1243  29.8190
 V05  H6   H  HCR6  0   0.299   4.9372   4.0264  25.7700
 V05  H7   H  HNH1  0   0.427   6.7024   5.5727  25.8145
 V05  H8   H  HCR6  0   0.296   4.3599   6.5052  29.2536
 V05  H9   H  HOH1  0   0.479   7.2716   7.9473  25.5307
 V05  H3   H  HCR6  0   0.285   9.4866  -1.1874  27.9092

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
 V05  O2   N1   single    1.358  0.020  1.358
 V05  N1   C1   single    1.342  0.020  1.342
 V05  F2   C12  single    1.334  0.020  1.334
 V05  C13  C12  aromatic  1.380  0.020  1.380
 V05  C13  C2   aromatic  1.390  0.020  1.390
 V05  C1   O1   double    1.216  0.020  1.216
 V05  C1   C2   single    1.498  0.020  1.498
 V05  C12  C5   aromatic  1.386  0.020  1.386
 V05  C2   C3   aromatic  1.390  0.020  1.390
 V05  C5   C6   single    1.499  0.020  1.499
 V05  C5   C4   aromatic  1.389  0.020  1.389
 V05  C3   C4   aromatic  1.378  0.020  1.378
 V05  C11  N6   aromatic  1.325  0.020  1.325
 V05  C11  C10  aromatic  1.385  0.020  1.385
 V05  N6   C8   aromatic  1.325  0.020  1.325
 V05  C6   N2   single    1.454  0.020  1.454
 V05  C4   F1   single    1.335  0.020  1.335
 V05  N7   N2   aromatic  1.303  0.020  1.303
 V05  N7   C7   aromatic  1.318  0.020  1.318
 V05  N2   N3   aromatic  1.305  0.020  1.305
 V05  C10  C9   aromatic  1.385  0.020  1.385
 V05  C8   C7   single    1.467  0.020  1.467
 V05  C8   N5   aromatic  1.325  0.020  1.325
 V05  C7   N4   aromatic  1.343  0.020  1.343
 V05  N3   N4   aromatic  1.289  0.020  1.289
 V05  C9   N5   aromatic  1.326  0.020  1.326
 V05  C6   H1   single    0.970  0.020  1.090
 V05  C6   H2   single    0.970  0.020  1.090
 V05  C11  H3   single    0.930  0.020  1.080
 V05  C9   H4   single    0.930  0.020  1.080
 V05  C10  H5   single    0.930  0.020  1.080
 V05  C13  H6   single    0.930  0.020  1.080
 V05  N1   H7   single    0.860  0.020  1.020
 V05  C3   H8   single    0.930  0.020  1.080
 V05  O2   H9   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
 V05  F1   C4   C3   118.73  3.000
 V05  F1   C4   C5   118.03  3.000
 V05  C3   C4   C5   123.24  3.000
 V05  C12  C5   C6   121.97  3.000
 V05  C6   C5   C4   121.95  3.000
 V05  C12  C5   C4   116.07  3.000
 V05  H2   C6   H1   107.48  3.000
 V05  H2   C6   N2   108.02  3.000
 V05  H1   C6   N2   106.60  3.000
 V05  H2   C6   C5   111.49  3.000
 V05  H1   C6   C5   112.03  3.000
 V05  N2   C6   C5   110.97  3.000
 V05  H3   C11  N6   116.83  3.000
 V05  H3   C11  C10  121.09  3.000
 V05  N6   C11  C10  122.08  3.000
 V05  N7   C7   N4   111.45  3.000
 V05  N4   C7   C8   124.67  3.000
 V05  N7   C7   C8   123.88  3.000
 V05  N6   C8   N5   126.55  3.000
 V05  N5   C8   C7   116.74  3.000
 V05  N6   C8   C7   116.71  3.000
 V05  H4   C9   N5   116.82  3.000
 V05  H4   C9   C10  121.06  3.000
 V05  N5   C9   C10  122.12  3.000
 V05  H5   C10  C9   121.82  3.000
 V05  H5   C10  C11  121.81  3.000
 V05  C9   C10  C11  116.37  3.000
 V05  F2   C12  C13  118.51  3.000
 V05  C13  C12  C5   123.14  3.000
 V05  F2   C12  C5   118.35  3.000
 V05  H6   C13  C2   122.06  3.000
 V05  H6   C13  C12  119.40  3.000
 V05  C2   C13  C12  118.52  3.000
 V05  H7   N1   O2   115.54  3.000
 V05  H7   N1   C1   123.80  3.000
 V05  O2   N1   C1   120.54  3.000
 V05  N7   N2   N3   113.91  3.000
 V05  N3   N2   C6   123.16  3.000
 V05  N7   N2   C6   122.93  3.000
 V05  H8   C3   C2   121.39  3.000
 V05  H8   C3   C4   120.13  3.000
 V05  C2   C3   C4   118.47  3.000
 V05  N4   N3   N2   106.50  3.000
 V05  C2   C1   O1   121.79  3.000
 V05  C2   C1   N1   113.61  3.000
 V05  O1   C1   N1   124.58  3.000
 V05  H9   O2   N1   106.56  3.000
 V05  C1   C2   C3   117.84  3.000
 V05  C3   C2   C13  120.54  3.000
 V05  C1   C2   C13  121.58  3.000
 V05  N3   N4   C7   106.24  3.000
 V05  C9   N5   C8   116.41  3.000
 V05  C8   N6   C11  116.47  3.000
 V05  N2   N7   C7   101.91  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
 V05  CONST_01  C13  C12  C5   C4      0.00   0.0  0
 V05  CONST_02  C13  C2   C3   C4      0.00   0.0  0
 V05  CONST_03  C2   C13  C12  C5      0.00   0.0  0
 V05  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 V05  CONST_05  C7   C8   N6   C11   180.00   0.0  0
 V05  CONST_06  N5   C8   N6   C11     0.00   0.0  0
 V05  CONST_07  N5   C9   C10  C11     0.00   0.0  0
 V05  CONST_08  N3   N2   N7   C7      0.00   0.0  0
 V05  CONST_09  C9   N5   C8   C7    180.00   0.0  0
 V05  CONST_10  N2   N3   N4   C7      0.00   0.0  0
 V05  CONST_11  C10  C11  N6   C8      0.00   0.0  0
 V05  CONST_12  N2   N7   C7   C8    180.00   0.0  0
 V05  CONST_13  N3   N4   C7   C8    180.00   0.0  0
 V05  CONST_14  C10  C9   N5   C8      0.00   0.0  0
 V05  CONST_15  N6   C11  C10  C9      0.00   0.0  0
 V05  CONST_16  N6   C8   N5   C9      0.00   0.0  0
 V05  CONST_17  C3   C2   C13  C12     0.00   0.0  0
 V05  CONST_18  C3   C4   C5   C12     0.00   0.0  0
 V05  CONST_19  N4   C7   N7   N2      0.00   0.0  0
 V05  CONST_20  N7   C7   N4   N3      0.00   0.0  0
 V05  CONST_21  N6   C8   C7   N4    180.00   0.0  0
 V05  CONST_22  N5   C8   C7   N4      0.00   0.0  0
 V05  CONST_23  N7   N2   N3   N4      0.00   0.0  0
 V05  CONST_24  N7   C7   C8   N5    180.00   0.0  0
 V05  CONST_25  N7   C7   C8   N6      0.00   0.0  0
 V05  CONST_26  F2   C12  C5   C4    180.00   0.0  0
 V05  CONST_27  C1   C2   C3   C4    180.00   0.0  0
 V05  CONST_28  C13  C12  C5   C6    180.00   0.0  0
 V05  CONST_29  C3   C4   C5   C6    180.00   0.0  0
 V05  CONST_30  C7   N7   N2   C6    180.00   0.0  0
 V05  CONST_31  N4   N3   N2   C6    180.00   0.0  0
 V05  CONST_32  C1   C2   C13  C12   180.00   0.0  0
 V05  CONST_33  F1   C4   C5   C12   180.00   0.0  0
 V05  CONST_34  F2   C12  C13  C2    180.00   0.0  0
 V05  CONST_35  F1   C4   C3   C2    180.00   0.0  0
 V05  CONST_36  H6   C13  C12  C5    180.00   0.0  0
 V05  CONST_37  H8   C3   C4   C5    180.00   0.0  0
 V05  CONST_38  H4   C9   C10  C11   180.00   0.0  0
 V05  CONST_39  H3   C11  N6   C8    180.00   0.0  0
 V05  CONST_40  H4   C9   N5   C8    180.00   0.0  0
 V05  CONST_41  H3   C11  C10  C9    180.00   0.0  0
 V05  CONST_42  H8   C3   C2   C13   180.00   0.0  0
 V05  CONST_43  H6   C13  C2   C3    180.00   0.0  0
 V05  CONST_44  H5   C10  C9   N5    180.00   0.0  0
 V05  CONST_45  H5   C10  C11  N6    180.00   0.0  0
 V05  CONST_46  C2   C1   N1   O2    180.00   0.0  0
 V05  CONST_47  H7   N1   C1   C2      0.00   0.0  0
 V05  CONST_48  O2   N1   C1   O1      0.00   0.0  0
 V05  CONST_49  H7   N1   C1   O1    180.00   0.0  0
 V05  Var_01    N2   C6   C5   C4    -89.35  30.0  2
 V05  Var_02    N7   N2   C6   C5    -61.39  30.0  2
 V05  Var_03    N3   N2   C6   C5    118.09  30.0  2
 V05  Var_04    N2   C6   C5   C12    89.72  30.0  2
 V05  Var_05    N1   C1   C2   C13   -42.73  30.0  2
 V05  Var_06    O1   C1   C2   C13   138.64  30.0  2
 V05  Var_07    C3   C2   C1   N1    139.78  30.0  2
 V05  Var_08    O1   C1   C2   C3    -38.85  30.0  2
 V05  Var_09    H1   C6   C5   C4     29.68  30.0  2
 V05  Var_10    H2   C6   C5   C4    150.19  30.0  2
 V05  Var_11    H1   C6   C5   C12  -151.25  30.0  2
 V05  Var_12    H2   C6   C5   C12   -30.75  30.0  2
 V05  Var_13    H1   C6   N2   N3     -4.15  30.0  2
 V05  Var_14    H2   C6   N2   N3   -119.41  30.0  2
 V05  Var_15    H1   C6   N2   N7    176.37  30.0  2
 V05  Var_16    H2   C6   N2   N7     61.11  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
 V05  plan-1  C6   0.020
 V05  plan-1  C7   0.020
 V05  plan-1  C8   0.020
 V05  plan-1  N2   0.020
 V05  plan-1  N3   0.020
 V05  plan-1  N4   0.020
 V05  plan-1  N7   0.020
 V05  plan-2  C11  0.020
 V05  plan-2  C7   0.020
 V05  plan-2  C8   0.020
 V05  plan-2  C9   0.020
 V05  plan-2  C10  0.020
 V05  plan-2  N5   0.020
 V05  plan-2  N6   0.020
 V05  plan-2  H4   0.020
 V05  plan-2  H5   0.020
 V05  plan-2  H3   0.020
 V05  plan-3  C4   0.020
 V05  plan-3  C5   0.020
 V05  plan-3  C6   0.020
 V05  plan-3  C12  0.020
 V05  plan-3  C13  0.020
 V05  plan-3  C3   0.020
 V05  plan-3  C1   0.020
 V05  plan-3  C2   0.020
 V05  plan-3  F1   0.020
 V05  plan-3  F2   0.020
 V05  plan-3  H6   0.020
 V05  plan-3  H8   0.020
 V05  plan-4  N1   0.020
 V05  plan-4  O1   0.020
 V05  plan-4  C1   0.020
 V05  plan-4  O2   0.020
 V05  plan-4  C2   0.020
 V05  plan-4  H7   0.020

