# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 14:31:59 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-[5-[3-(trifluoromethyl)phenyl]-1H-pyrazol-4-yl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(c1)c2[nH]ncc2c3ccncc3
#
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
 6NM  6NM  4-[5-[3-(trifluoromethyl)phenyl]-1H-pyrazol-4-yl]pyridine  ligand  31  21  .  2022-07-23  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_6NM
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
 6NM  C1   C  CR16  0  -0.226   1.6996   2.6825  -1.4146
 6NM  C2   C  CR16  0  -0.287   0.3623   2.5945  -1.0666
 6NM  C6   C  CR16  0  -0.288   2.6092   1.7391  -0.9584
 6NM  C17  C  CR16  0  -0.386  -2.7165  -2.0273   0.7081
 6NM  C21  C  CR16  0  -0.389  -1.3640  -1.4292  -1.1521
 6NM  C4   C  CR16  0  -0.324   0.8306   0.6216   0.2231
 6NM  C18  C  CR16  0  -0.060  -2.5026  -3.3530   0.3682
 6NM  C20  C  CR16  0  -0.057  -1.2071  -2.7823  -1.4009
 6NM  C13  C  CR15  0  -0.094  -3.5598   0.9589   0.7195
 6NM  C3   C  CR6   0   0.041  -0.0837   1.5610  -0.2421
 6NM  C16  C  CR6   0   0.121  -2.1337  -1.0220  -0.0627
 6NM  C12  C  CR5   0  -0.170  -2.3571   0.3848   0.2582
 6NM  C5   C  CR6   0  -0.171   2.1674   0.7068  -0.1419
 6NM  C11  C  CR5   0   0.451  -1.4914   1.4642   0.1444
 6NM  C7   C  CT    0   1.056   3.1129  -0.3248   0.3906
 6NM  N19  N  N     0  -0.411  -1.7598  -3.7393  -0.6629
 6NM  N15  N  NR15  0  -0.495  -2.2038   2.5432   0.5169
 6NM  N14  N  N     0  -0.246  -3.4509   2.2624   0.8679
 6NM  F8   F  F     0  -0.301   4.3346  -0.2266  -0.1387
 6NM  F9   F  F     0  -0.314   3.2524  -0.2245   1.7208
 6NM  F10  F  F     0  -0.312   2.6767  -1.5680   0.1461
 6NM  H1   H  HCR6  0   0.276   2.0367   3.4863  -2.0545
 6NM  H2   H  HCR6  0   0.273  -0.3384   3.3224  -1.4556
 6NM  H6   H  HCR6  0   0.278   3.6475   1.8199  -1.2478
 6NM  H18  H  HCR6  0   0.264  -2.9489  -4.1395   0.9669
 6NM  H21  H  HCR6  0   0.266  -0.8978  -0.7098  -1.8119
 6NM  H20  H  HCR6  0   0.264  -0.6085  -3.1061  -2.2454
 6NM  H4   H  HCR6  0   0.282   0.4880  -0.1726   0.8748
 6NM  H13  H  HCR5  0   0.269  -4.4967   0.4600   0.9183
 6NM  H15  H  HNR5  0   0.427  -1.8641   3.4895   0.6023
 6NM  H17  H  HCR6  0   0.265  -3.3195  -1.7877   1.5741

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
 6NM  C1   C2   aromatic  1.385  0.020  1.385
 6NM  C1   C6   aromatic  1.388  0.020  1.388
 6NM  C2   C3   aromatic  1.395  0.020  1.395
 6NM  C6   C5   aromatic  1.388  0.020  1.388
 6NM  C17  C18  aromatic  1.385  0.020  1.385
 6NM  C17  C16  aromatic  1.394  0.020  1.394
 6NM  C21  C20  aromatic  1.385  0.020  1.385
 6NM  C21  C16  aromatic  1.395  0.020  1.395
 6NM  C4   C3   aromatic  1.391  0.020  1.391
 6NM  C4   C5   aromatic  1.388  0.020  1.388
 6NM  C18  N19  aromatic  1.328  0.020  1.328
 6NM  C20  N19  aromatic  1.329  0.020  1.329
 6NM  C13  C12  aromatic  1.410  0.020  1.410
 6NM  C13  N14  aromatic  1.316  0.020  1.316
 6NM  C3   C11  single    1.463  0.020  1.463
 6NM  C16  C12  single    1.460  0.020  1.460
 6NM  C12  C11  aromatic  1.388  0.020  1.388
 6NM  C5   C7   single    1.497  0.020  1.497
 6NM  C11  N15  aromatic  1.346  0.020  1.346
 6NM  C7   F8   single    1.335  0.020  1.335
 6NM  C7   F9   single    1.341  0.020  1.341
 6NM  C7   F10  single    1.340  0.020  1.340
 6NM  N15  N14  aromatic  1.326  0.020  1.326
 6NM  C1   H1   single    0.930  0.020  1.080
 6NM  C2   H2   single    0.930  0.020  1.080
 6NM  C6   H6   single    0.930  0.020  1.080
 6NM  C17  H17  single    0.930  0.020  1.080
 6NM  C18  H18  single    0.930  0.020  1.080
 6NM  C21  H21  single    0.930  0.020  1.080
 6NM  C20  H20  single    0.930  0.020  1.080
 6NM  C4   H4   single    0.930  0.020  1.080
 6NM  C13  H13  single    0.930  0.020  1.080
 6NM  N15  H15  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
 6NM  H1   C1   C6   119.71  3.000
 6NM  H1   C1   C2   119.81  3.000
 6NM  C6   C1   C2   120.48  3.000
 6NM  H2   C2   C3   120.23  3.000
 6NM  H2   C2   C1   119.48  3.000
 6NM  C3   C2   C1   120.29  3.000
 6NM  H6   C6   C5   121.25  3.000
 6NM  H6   C6   C1   119.39  3.000
 6NM  C5   C6   C1   119.36  3.000
 6NM  H17  C17  C16  121.04  3.000
 6NM  H17  C17  C18  119.63  3.000
 6NM  C16  C17  C18  119.32  3.000
 6NM  H21  C21  C16  121.34  3.000
 6NM  H21  C21  C20  119.43  3.000
 6NM  C16  C21  C20  119.23  3.000
 6NM  H4   C4   C5   120.52  3.000
 6NM  H4   C4   C3   119.25  3.000
 6NM  C5   C4   C3   120.23  3.000
 6NM  H18  C18  N19  116.60  3.000
 6NM  H18  C18  C17  119.67  3.000
 6NM  N19  C18  C17  123.73  3.000
 6NM  H20  C20  N19  116.55  3.000
 6NM  H20  C20  C21  119.62  3.000
 6NM  N19  C20  C21  123.83  3.000
 6NM  H13  C13  N14  120.56  3.000
 6NM  H13  C13  C12  127.73  3.000
 6NM  N14  C13  C12  111.68  3.000
 6NM  C11  C3   C4   119.96  3.000
 6NM  C11  C3   C2   120.85  3.000
 6NM  C4   C3   C2   119.19  3.000
 6NM  C12  C16  C21  122.51  3.000
 6NM  C12  C16  C17  120.61  3.000
 6NM  C21  C16  C17  116.87  3.000
 6NM  C11  C12  C16  129.47  3.000
 6NM  C11  C12  C13  104.01  3.000
 6NM  C16  C12  C13  126.48  3.000
 6NM  C7   C5   C4   118.18  3.000
 6NM  C7   C5   C6   121.37  3.000
 6NM  C4   C5   C6   120.44  3.000
 6NM  N15  C11  C12  105.70  3.000
 6NM  N15  C11  C3   121.97  3.000
 6NM  C12  C11  C3   132.30  3.000
 6NM  F10  C7   F9   106.51  3.000
 6NM  F10  C7   F8   107.08  3.000
 6NM  F9   C7   F8   107.01  3.000
 6NM  F10  C7   C5   111.64  3.000
 6NM  F9   C7   C5   111.53  3.000
 6NM  F8   C7   C5   112.72  3.000
 6NM  C20  N19  C18  117.02  3.000
 6NM  H15  N15  N14  119.54  3.000
 6NM  H15  N15  C11  126.67  3.000
 6NM  N14  N15  C11  113.67  3.000
 6NM  N15  N14  C13  104.93  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
 6NM  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 6NM  CONST_02  C11  C3   C2   C1   180.00   0.0  0
 6NM  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 6NM  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 6NM  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 6NM  CONST_08  C3   C2   C1   C6     0.00   0.0  0
 6NM  CONST_09  C3   C4   C5   C6     0.00   0.0  0
 6NM  CONST_10  C20  N19  C18  C17    0.00   0.0  0
 6NM  CONST_11  C20  C21  C16  C17    0.00   0.0  0
 6NM  CONST_14  C18  N19  C20  C21    0.00   0.0  0
 6NM  CONST_15  C18  C17  C16  C21    0.00   0.0  0
 6NM  CONST_20  C12  C16  C17  C18  180.00   0.0  0
 6NM  CONST_21  C12  C16  C21  C20  180.00   0.0  0
 6NM  CONST_22  C3   C11  C12  C13  180.00   0.0  0
 6NM  CONST_23  N15  C11  C12  C13    0.00   0.0  0
 6NM  CONST_24  C11  N15  N14  C13    0.00   0.0  0
 6NM  CONST_25  C16  C12  C11  C3     0.00   0.0  0
 6NM  CONST_26  N14  N15  C11  C3   180.00   0.0  0
 6NM  CONST_27  N19  C18  C17  C16    0.00   0.0  0
 6NM  CONST_28  N19  C20  C21  C16    0.00   0.0  0
 6NM  CONST_29  N14  C13  C12  C16  180.00   0.0  0
 6NM  CONST_30  N15  C11  C12  C16  180.00   0.0  0
 6NM  CONST_31  N15  N14  C13  C12    0.00   0.0  0
 6NM  CONST_32  N14  N15  C11  C12    0.00   0.0  0
 6NM  CONST_33  C11  C3   C4   C5   180.00   0.0  0
 6NM  CONST_34  N14  C13  C12  C11    0.00   0.0  0
 6NM  CONST_35  C7   C5   C6   C1   180.00   0.0  0
 6NM  CONST_36  C7   C5   C4   C3   180.00   0.0  0
 6NM  CONST_37  H6   C6   C1   C2   180.00   0.0  0
 6NM  CONST_38  H4   C4   C3   C2   180.00   0.0  0
 6NM  CONST_39  H2   C2   C1   C6   180.00   0.0  0
 6NM  CONST_40  H21  C21  C16  C17  180.00   0.0  0
 6NM  CONST_41  H17  C17  C16  C21  180.00   0.0  0
 6NM  CONST_42  H20  C20  N19  C18  180.00   0.0  0
 6NM  CONST_43  H18  C18  N19  C20  180.00   0.0  0
 6NM  CONST_44  H15  N15  N14  C13  180.00   0.0  0
 6NM  CONST_45  H1   C1   C2   C3   180.00   0.0  0
 6NM  CONST_46  H13  C13  C12  C16    0.00   0.0  0
 6NM  Var_01    F8   C7   C5   C6    -7.93  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
 6NM  plan-1  C13  0.020
 6NM  plan-1  C3   0.020
 6NM  plan-1  C16  0.020
 6NM  plan-1  C12  0.020
 6NM  plan-1  C11  0.020
 6NM  plan-1  N15  0.020
 6NM  plan-1  N14  0.020
 6NM  plan-1  H13  0.020
 6NM  plan-1  H15  0.020
 6NM  plan-2  C1   0.020
 6NM  plan-2  C2   0.020
 6NM  plan-2  C6   0.020
 6NM  plan-2  C4   0.020
 6NM  plan-2  C3   0.020
 6NM  plan-2  C5   0.020
 6NM  plan-2  C11  0.020
 6NM  plan-2  C7   0.020
 6NM  plan-2  H1   0.020
 6NM  plan-2  H2   0.020
 6NM  plan-2  H6   0.020
 6NM  plan-2  H4   0.020
 6NM  plan-3  C17  0.020
 6NM  plan-3  C21  0.020
 6NM  plan-3  C18  0.020
 6NM  plan-3  C20  0.020
 6NM  plan-3  C16  0.020
 6NM  plan-3  C12  0.020
 6NM  plan-3  N19  0.020
 6NM  plan-3  H18  0.020
 6NM  plan-3  H21  0.020
 6NM  plan-3  H20  0.020
 6NM  plan-3  H17  0.020

