# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 05:34:58 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (5-methanoyl-2-nitro-phenyl) 2-methyl-6-(trifluoromethyl)pyridine-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(ccc1C(=O)Oc2cc(C=O)ccc2[N+]([O-])=O)C(F)(F)F
#
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
 V4B  V4B  '(5-methanoyl-2-nitro-phenyl) 2-methyl-6-(trifluoromethyl)pyridine-3-carboxylate'  ligand  34  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V4B
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
 V4B  C01  C  CH3    0  -0.739  24.6646  16.4778  -0.2510
 V4B  C02  C  CR6    0   0.273  25.1712  17.0597   1.0338
 V4B  C03  C  CR6    0  -0.151  25.0574  18.4145   1.4037
 V4B  C04  C  C      0   0.547  24.4862  19.4970   0.5676
 V4B  C06  C  CR6    0   0.425  24.0960  20.1702  -1.6340
 V4B  C07  C  CR6    0   0.200  24.6805  21.4213  -1.8213
 V4B  C11  C  CR16   0  -0.269  24.1719  22.3123  -2.7566
 V4B  C12  C  CR16   0  -0.261  23.0840  21.9531  -3.5257
 V4B  C13  C  CR6    0   0.004  22.4912  20.7082  -3.3413
 V4B  C14  C  C1     0   0.132  21.3168  20.2949  -4.1441
 V4B  C15  C  CR16   0  -0.348  22.9903  19.8279  -2.3908
 V4B  C17  C  CR16   0  -0.118  25.4973  18.8030   2.6627
 V4B  C18  C  CR16   0  -0.308  26.0775  17.8794   3.5135
 V4B  C19  C  CR6    0   0.005  26.1771  16.5847   3.0461
 V4B  C20  C  CT     0   1.051  26.8465  15.4996   3.8534
 V4B  F21  F  F      0  -0.309  28.0585  15.2241   3.3583
 V4B  F22  F  F      0  -0.298  27.0092  15.8525   5.1300
 V4B  F23  F  F      0  -0.302  26.1445  14.3670   3.8351
 V4B  N08  N  N      1   0.336  25.8517  21.8381  -1.0622
 V4B  N24  N  N      0  -0.441  25.7319  16.1900   1.8657
 V4B  O05  O  O2     0  -0.481  24.5681  19.2405  -0.7505
 V4B  O09  O  O      0  -0.362  26.6335  20.9868  -0.7146
 V4B  O10  O  O     -1  -0.351  25.9768  23.0168  -0.8442
 V4B  O16  O  O      0  -0.387  24.0308  20.5177   0.9988
 V4B  H1   H  HCH3   0   0.262  24.6652  15.3937  -0.1698
 V4B  H2   H  HCH3   0   0.260  23.6531  16.8070  -0.4831
 V4B  H3   H  HCH3   0   0.267  25.3012  16.7526  -1.0920
 V4B  H4   H  HCR6   0   0.312  24.6349  23.2792  -2.8927
 V4B  H5   H  HCR6   0   0.291  22.6982  22.6417  -4.2648
 V4B  H6   H  H      0   0.215  20.9178  19.2957  -3.9000
 V4B  H9   H  HCR6   0   0.307  22.5251  18.8614  -2.2348
 V4B  H10  H  HCR6   0   0.295  25.4019  19.8329   2.9788
 V4B  H11  H  HCR6   0   0.295  26.4329  18.1764   4.4890
 V4B  O1   O  O      0  -0.350  20.8215  20.9797  -5.0021

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
 V4B  C14  C13  single    1.481  0.020  1.481
 V4B  C13  C12  aromatic  1.391  0.020  1.391
 V4B  C13  C15  aromatic  1.388  0.020  1.388
 V4B  C12  C11  aromatic  1.380  0.020  1.380
 V4B  C15  C06  aromatic  1.383  0.020  1.383
 V4B  C11  C07  aromatic  1.388  0.020  1.388
 V4B  C06  C07  aromatic  1.393  0.020  1.393
 V4B  C06  O05  single    1.367  0.020  1.367
 V4B  C07  N08  single    1.457  0.020  1.457
 V4B  O05  C04  single    1.345  0.020  1.345
 V4B  N08  O09  double    1.207  0.020  1.207
 V4B  N08  O10  single    1.205  0.020  1.205
 V4B  C04  O16  double    1.198  0.020  1.198
 V4B  C04  C03  single    1.482  0.020  1.482
 V4B  C01  C02  single    1.499  0.020  1.499
 V4B  C03  C02  aromatic  1.409  0.020  1.409
 V4B  C03  C17  aromatic  1.389  0.020  1.389
 V4B  C02  N24  aromatic  1.328  0.020  1.328
 V4B  C17  C18  aromatic  1.383  0.020  1.383
 V4B  N24  C19  aromatic  1.322  0.020  1.322
 V4B  C18  C19  aromatic  1.380  0.020  1.380
 V4B  C19  C20  single    1.509  0.020  1.509
 V4B  F21  C20  single    1.338  0.020  1.338
 V4B  C20  F23  single    1.333  0.020  1.333
 V4B  C20  F22  single    1.334  0.020  1.334
 V4B  C01  H1   single    0.970  0.020  1.090
 V4B  C01  H2   single    0.970  0.020  1.090
 V4B  C01  H3   single    0.970  0.020  1.090
 V4B  C11  H4   single    0.930  0.020  1.080
 V4B  C12  H5   single    0.930  0.020  1.080
 V4B  C14  H6   single    0.930  0.020  1.080
 V4B  C15  H9   single    0.930  0.020  1.080
 V4B  C17  H10  single    0.930  0.020  1.080
 V4B  C18  H11  single    0.930  0.020  1.080
 V4B  C14  O1   double    1.204  0.020  1.204

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
 V4B  H3   C01  H2   107.57  3.000
 V4B  H3   C01  H1   107.98  3.000
 V4B  H2   C01  H1   108.54  3.000
 V4B  H3   C01  C02  111.48  3.000
 V4B  H2   C01  C02  112.30  3.000
 V4B  H1   C01  C02  108.84  3.000
 V4B  N24  C02  C03  119.97  3.000
 V4B  N24  C02  C01  115.19  3.000
 V4B  C03  C02  C01  124.82  3.000
 V4B  C17  C03  C04  115.41  3.000
 V4B  C17  C03  C02  118.77  3.000
 V4B  C04  C03  C02  125.82  3.000
 V4B  O16  C04  O05  122.56  3.000
 V4B  O16  C04  C03  124.45  3.000
 V4B  O05  C04  C03  112.96  3.000
 V4B  O05  C06  C15  117.49  3.000
 V4B  O05  C06  C07  123.55  3.000
 V4B  C15  C06  C07  118.95  3.000
 V4B  N08  C07  C11  117.52  3.000
 V4B  N08  C07  C06  121.61  3.000
 V4B  C11  C07  C06  120.87  3.000
 V4B  H4   C11  C12  120.03  3.000
 V4B  H4   C11  C07  120.14  3.000
 V4B  C12  C11  C07  119.82  3.000
 V4B  H5   C12  C13  120.56  3.000
 V4B  H5   C12  C11  119.77  3.000
 V4B  C13  C12  C11  119.67  3.000
 V4B  C15  C13  C14  118.63  3.000
 V4B  C15  C13  C12  120.33  3.000
 V4B  C14  C13  C12  121.04  3.000
 V4B  O1   C14  H6   121.59  3.000
 V4B  O1   C14  C13  123.60  3.000
 V4B  H6   C14  C13  114.80  3.000
 V4B  H9   C15  C13  120.64  3.000
 V4B  H9   C15  C06  119.02  3.000
 V4B  C13  C15  C06  120.34  3.000
 V4B  H10  C17  C18  119.55  3.000
 V4B  H10  C17  C03  120.21  3.000
 V4B  C18  C17  C03  120.23  3.000
 V4B  H11  C18  C19  122.70  3.000
 V4B  H11  C18  C17  120.66  3.000
 V4B  C19  C18  C17  116.64  3.000
 V4B  N24  C19  C20  114.36  3.000
 V4B  C20  C19  C18  121.70  3.000
 V4B  N24  C19  C18  123.93  3.000
 V4B  F23  C20  F22  107.58  3.000
 V4B  F22  C20  F21  107.34  3.000
 V4B  F23  C20  F21  107.28  3.000
 V4B  F22  C20  C19  112.07  3.000
 V4B  F23  C20  C19  111.72  3.000
 V4B  F21  C20  C19  110.61  3.000
 V4B  O10  N08  O09  124.79  3.000
 V4B  O10  N08  C07  117.23  3.000
 V4B  O09  N08  C07  117.97  3.000
 V4B  C19  N24  C02  120.41  3.000
 V4B  C06  O05  C04  118.86  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
 V4B  CONST_01  C18  C17  C03  C02     0.00   0.0  0
 V4B  CONST_02  C18  C19  N24  C02     0.00   0.0  0
 V4B  CONST_03  C19  N24  C02  C03     0.00   0.0  0
 V4B  CONST_04  C19  C18  C17  C03     0.00   0.0  0
 V4B  CONST_05  C12  C13  C15  C06     0.00   0.0  0
 V4B  CONST_06  C12  C11  C07  C06     0.00   0.0  0
 V4B  CONST_07  C13  C12  C11  C07     0.00   0.0  0
 V4B  CONST_08  C13  C15  C06  C07     0.00   0.0  0
 V4B  CONST_09  C15  C13  C12  C11     0.00   0.0  0
 V4B  CONST_10  C15  C06  C07  C11     0.00   0.0  0
 V4B  CONST_11  N24  C02  C03  C17     0.00   0.0  0
 V4B  CONST_12  N24  C19  C18  C17     0.00   0.0  0
 V4B  CONST_13  C17  C03  C02  C01   180.00   0.0  0
 V4B  CONST_14  C19  N24  C02  C01   180.00   0.0  0
 V4B  CONST_15  C20  C19  N24  C02   180.00   0.0  0
 V4B  CONST_16  N24  C02  C03  C04   180.00   0.0  0
 V4B  CONST_17  C18  C17  C03  C04   180.00   0.0  0
 V4B  CONST_18  C14  C13  C15  C06   180.00   0.0  0
 V4B  CONST_19  C14  C13  C12  C11   180.00   0.0  0
 V4B  CONST_20  O05  C06  C07  C11   180.00   0.0  0
 V4B  CONST_21  N08  C07  C11  C12   180.00   0.0  0
 V4B  CONST_22  O05  C06  C15  C13   180.00   0.0  0
 V4B  CONST_23  N08  C07  C06  C15   180.00   0.0  0
 V4B  CONST_24  C20  C19  C18  C17   180.00   0.0  0
 V4B  CONST_25  H10  C17  C03  C02   180.00   0.0  0
 V4B  CONST_26  H11  C18  C17  C03   180.00   0.0  0
 V4B  CONST_27  H4   C11  C07  C06   180.00   0.0  0
 V4B  CONST_28  H5   C12  C11  C07   180.00   0.0  0
 V4B  CONST_29  H9   C15  C06  C07   180.00   0.0  0
 V4B  Var_01    O05  C04  C03  C02   -25.54  30.0  2
 V4B  Var_02    C15  C06  O05  C04  -113.67  30.0  3
 V4B  Var_03    O1   C14  C13  C12     1.21  30.0  2
 V4B  Var_04    F21  C20  C19  C18  -104.47  30.0  2
 V4B  Var_05    H1   C01  C02  C03  -166.32  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
 V4B  plan-1  C01  0.020
 V4B  plan-1  C02  0.020
 V4B  plan-1  C03  0.020
 V4B  plan-1  C04  0.020
 V4B  plan-1  C17  0.020
 V4B  plan-1  C18  0.020
 V4B  plan-1  C19  0.020
 V4B  plan-1  C20  0.020
 V4B  plan-1  N24  0.020
 V4B  plan-1  H10  0.020
 V4B  plan-1  H11  0.020
 V4B  plan-2  C06  0.020
 V4B  plan-2  C07  0.020
 V4B  plan-2  C11  0.020
 V4B  plan-2  C12  0.020
 V4B  plan-2  C13  0.020
 V4B  plan-2  C14  0.020
 V4B  plan-2  C15  0.020
 V4B  plan-2  N08  0.020
 V4B  plan-2  O05  0.020
 V4B  plan-2  H4   0.020
 V4B  plan-2  H5   0.020
 V4B  plan-2  H9   0.020
 V4B  plan-3  C07  0.020
 V4B  plan-3  N08  0.020
 V4B  plan-3  O09  0.020
 V4B  plan-3  O10  0.020
 V4B  plan-4  C03  0.020
 V4B  plan-4  C04  0.020
 V4B  plan-4  O05  0.020
 V4B  plan-4  O16  0.020
 V4B  plan-5  C13  0.020
 V4B  plan-5  C14  0.020
 V4B  plan-5  H6   0.020
 V4B  plan-5  O1   0.020

