# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 14:14:53 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N-[(4-fluorophenyl)methyl]-2-(propan-2-yl)-1H-imidazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1[nH]c(cn1)C(=O)NCc2ccc(F)cc2
#
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
 LEY  LEY  N-[(4-fluorophenyl)methyl]-2-(propan-2-yl)-1H-imidazole-5-carboxamide  ligand  35  19  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LEY
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
 LEY  N1   N  NR15  0  -0.658  -2.3488   0.1577  -0.0806
 LEY  N3   N  NH1   0  -0.654   0.1629  -1.2683   0.2670
 LEY  C4   C  CR5   0   0.475  -3.6699   0.4202  -0.1191
 LEY  C5   C  CR5   0   0.163  -2.1807  -1.1993  -0.2116
 LEY  C6   C  CR15  0  -0.203  -3.4525  -1.6964  -0.3146
 LEY  C7   C  C     0   0.512  -0.9088  -1.9311  -0.2141
 LEY  C8   C  CH2   0  -0.326   1.4815  -1.8644   0.3302
 LEY  C10  C  CR16  0  -0.264   2.6526   0.0455  -0.8144
 LEY  C13  C  CR16  0  -0.397   4.4440   0.3140   1.2923
 LEY  C1   C  CH3   0  -0.654  -3.6627   2.6080   1.0988
 LEY  C11  C  CR16  0  -0.396   3.6364   1.0192  -0.8747
 LEY  C12  C  CR6   0   0.515   4.5175   1.1341   0.1856
 LEY  C14  C  CR16  0  -0.289   3.4483  -0.6546   1.3333
 LEY  C2   C  CH1   0  -0.360  -4.2312   1.8041  -0.0696
 LEY  C3   C  CH3   0  -0.647  -4.0095   2.5275  -1.4006
 LEY  C9   C  CR6   0   0.064   2.5472  -0.8035   0.2863
 LEY  N2   N  N     0  -0.448  -4.3631  -0.6906  -0.2502
 LEY  O1   O  O     0  -0.488  -0.8530  -3.0755  -0.6447
 LEY  H1   H  HNR5  0   0.415  -1.6184   0.8521  -0.0483
 LEY  H2   H  HNH1  0   0.400   0.0198  -0.4417   0.8257
 LEY  H3   H  HCR5  0   0.266  -3.7450  -2.7305  -0.4132
 LEY  H4   H  HCH2  0   0.260   1.5938  -2.4718   1.2330
 LEY  H5   H  HCH2  0   0.268   1.5892  -2.5393  -0.5191
 LEY  H6   H  HCR6  0   0.264   1.9595  -0.0538  -1.6409
 LEY  H7   H  HCR6  0   0.281   5.1435   0.4281   2.1096
 LEY  H8   H  HCH3  0   0.242  -3.8259   2.1032   2.0512
 LEY  H9   H  HCH3  0   0.220  -2.5903   2.7823   0.9874
 LEY  H10  H  HCH3  0   0.243  -4.1436   3.5848   1.1506
 LEY  H11  H  HCR6  0   0.281   3.7198   1.6747  -1.7316
 LEY  H12  H  HCR6  0   0.267   3.3794  -1.3009   2.1995
 LEY  H13  H  HCH1  0   0.263  -5.3061   1.6828   0.0802
 LEY  H14  H  HCH3  0   0.223  -2.9468   2.6799  -1.5986
 LEY  H15  H  HCH3  0   0.240  -4.4319   1.9667  -2.2345
 LEY  H16  H  HCH3  0   0.240  -4.4869   3.5076  -1.3792
 LEY  F1   F  F     0  -0.316   5.4739   2.0758   0.1342

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
 LEY  C2   C1   single    1.528  0.020  1.528
 LEY  C2   C3   single    1.531  0.020  1.531
 LEY  C2   C4   single    1.494  0.020  1.494
 LEY  C4   N2   aromatic  1.316  0.020  1.316
 LEY  C4   N1   aromatic  1.348  0.020  1.348
 LEY  N2   C6   aromatic  1.358  0.020  1.358
 LEY  N1   C5   aromatic  1.374  0.020  1.374
 LEY  C6   C5   aromatic  1.369  0.020  1.369
 LEY  C5   C7   single    1.467  0.020  1.467
 LEY  C7   N3   single    1.349  0.020  1.349
 LEY  C7   O1   double    1.224  0.020  1.224
 LEY  N3   C8   single    1.448  0.020  1.448
 LEY  C8   C9   single    1.504  0.020  1.504
 LEY  C9   C14  aromatic  1.389  0.020  1.389
 LEY  C9   C10  aromatic  1.394  0.020  1.394
 LEY  C14  C13  aromatic  1.390  0.020  1.390
 LEY  C10  C11  aromatic  1.386  0.020  1.386
 LEY  C13  C12  aromatic  1.379  0.020  1.379
 LEY  C11  C12  aromatic  1.383  0.020  1.383
 LEY  C12  F1   single    1.343  0.020  1.343
 LEY  N1   H1   single    0.860  0.020  1.020
 LEY  N3   H2   single    0.860  0.020  1.020
 LEY  C6   H3   single    0.930  0.020  1.080
 LEY  C8   H4   single    0.970  0.020  1.090
 LEY  C8   H5   single    0.970  0.020  1.090
 LEY  C10  H6   single    0.930  0.020  1.080
 LEY  C13  H7   single    0.930  0.020  1.080
 LEY  C1   H8   single    0.970  0.020  1.090
 LEY  C1   H9   single    0.970  0.020  1.090
 LEY  C1   H10  single    0.970  0.020  1.090
 LEY  C11  H11  single    0.930  0.020  1.080
 LEY  C14  H12  single    0.930  0.020  1.080
 LEY  C2   H13  single    0.970  0.020  1.090
 LEY  C3   H14  single    0.970  0.020  1.090
 LEY  C3   H15  single    0.970  0.020  1.090
 LEY  C3   H16  single    0.970  0.020  1.090

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
 LEY  H1   N1   C5   126.49  3.000
 LEY  H1   N1   C4   125.24  3.000
 LEY  C5   N1   C4   108.04  3.000
 LEY  H2   N3   C8   116.27  3.000
 LEY  H2   N3   C7   119.20  3.000
 LEY  C8   N3   C7   122.46  3.000
 LEY  N2   C4   C2   125.96  3.000
 LEY  N2   C4   N1   110.79  3.000
 LEY  C2   C4   N1   123.21  3.000
 LEY  C7   C5   C6   128.60  3.000
 LEY  C7   C5   N1   126.79  3.000
 LEY  C6   C5   N1   104.60  3.000
 LEY  H3   C6   N2   122.15  3.000
 LEY  H3   C6   C5   127.33  3.000
 LEY  N2   C6   C5   110.51  3.000
 LEY  O1   C7   C5   120.42  3.000
 LEY  O1   C7   N3   123.27  3.000
 LEY  C5   C7   N3   116.30  3.000
 LEY  H5   C8   H4   106.80  3.000
 LEY  H5   C8   C9   110.11  3.000
 LEY  H4   C8   C9   110.05  3.000
 LEY  H5   C8   N3   108.11  3.000
 LEY  H4   C8   N3   110.98  3.000
 LEY  C9   C8   N3   110.70  3.000
 LEY  H6   C10  C9   119.89  3.000
 LEY  H6   C10  C11  119.05  3.000
 LEY  C9   C10  C11  121.06  3.000
 LEY  H7   C13  C14  120.96  3.000
 LEY  H7   C13  C12  120.59  3.000
 LEY  C14  C13  C12  118.44  3.000
 LEY  H10  C1   H9   107.16  3.000
 LEY  H10  C1   H8   107.91  3.000
 LEY  H9   C1   H8   108.06  3.000
 LEY  H10  C1   C2   110.10  3.000
 LEY  H9   C1   C2   111.79  3.000
 LEY  H8   C1   C2   111.64  3.000
 LEY  H11  C11  C12  120.50  3.000
 LEY  H11  C11  C10  120.99  3.000
 LEY  C12  C11  C10  118.51  3.000
 LEY  F1   C12  C11  118.84  3.000
 LEY  F1   C12  C13  119.04  3.000
 LEY  C11  C12  C13  122.11  3.000
 LEY  H12  C14  C9   119.84  3.000
 LEY  H12  C14  C13  119.02  3.000
 LEY  C9   C14  C13  121.14  3.000
 LEY  H13  C2   C3   108.32  3.000
 LEY  H13  C2   C1   108.64  3.000
 LEY  C3   C2   C1   111.24  3.000
 LEY  H13  C2   C4   105.75  3.000
 LEY  C3   C2   C4   110.76  3.000
 LEY  C1   C2   C4   111.89  3.000
 LEY  H16  C3   H15  107.93  3.000
 LEY  H16  C3   H14  107.71  3.000
 LEY  H15  C3   H14  108.08  3.000
 LEY  H16  C3   C2   110.14  3.000
 LEY  H15  C3   C2   111.46  3.000
 LEY  H14  C3   C2   111.38  3.000
 LEY  C14  C9   C10  118.73  3.000
 LEY  C10  C9   C8   120.40  3.000
 LEY  C14  C9   C8   120.87  3.000
 LEY  C6   N2   C4   106.06  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
 LEY  CONST_01  C6   N2   C4   N1     0.00   0.0  0
 LEY  CONST_02  N2   C6   C5   N1     0.00   0.0  0
 LEY  CONST_03  C5   C6   N2   C4     0.00   0.0  0
 LEY  CONST_04  C6   C5   N1   C4     0.00   0.0  0
 LEY  CONST_05  N2   C4   N1   C5     0.00   0.0  0
 LEY  CONST_06  C13  C14  C9   C10    0.00   0.0  0
 LEY  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 LEY  CONST_08  C14  C9   C10  C11    0.00   0.0  0
 LEY  CONST_09  C14  C13  C12  C11    0.00   0.0  0
 LEY  CONST_10  C9   C14  C13  C12    0.00   0.0  0
 LEY  CONST_11  C9   C10  C11  C12    0.00   0.0  0
 LEY  CONST_12  C7   C5   N1   C4   180.00   0.0  0
 LEY  CONST_13  C2   C4   N1   C5   180.00   0.0  0
 LEY  CONST_14  C2   C4   N2   C6   180.00   0.0  0
 LEY  CONST_15  N2   C6   C5   C7   180.00   0.0  0
 LEY  CONST_16  C13  C14  C9   C8   180.00   0.0  0
 LEY  CONST_17  C11  C10  C9   C8   180.00   0.0  0
 LEY  CONST_18  F1   C12  C11  C10  180.00   0.0  0
 LEY  CONST_19  F1   C12  C13  C14  180.00   0.0  0
 LEY  CONST_20  H3   C6   C5   N1   180.00   0.0  0
 LEY  CONST_21  H1   N1   C5   C6   180.00   0.0  0
 LEY  CONST_22  H12  C14  C9   C10  180.00   0.0  0
 LEY  CONST_23  H11  C11  C12  C13  180.00   0.0  0
 LEY  CONST_24  H7   C13  C12  C11  180.00   0.0  0
 LEY  CONST_25  H6   C10  C11  C12  180.00   0.0  0
 LEY  CONST_26  C8   N3   C7   C5   180.00   0.0  0
 LEY  CONST_28  O1   C7   N3   C8     0.00   0.0  0
 LEY  Var_01    C1   C2   C4   N1   -51.02  30.0  3
 LEY  Var_02    N3   C7   C5   N1    16.74  30.0  2
 LEY  Var_03    C14  C9   C8   N3   119.70  30.0  2
 LEY  Var_04    C9   C8   N3   C7   153.98  30.0  3
 LEY  Var_05    H8   C1   C2   C4   -56.09  30.0  3
 LEY  Var_06    H14  C3   C2   C4   -64.74  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
 LEY  plan-1  N1   0.020
 LEY  plan-1  C4   0.020
 LEY  plan-1  C5   0.020
 LEY  plan-1  C6   0.020
 LEY  plan-1  C7   0.020
 LEY  plan-1  C2   0.020
 LEY  plan-1  N2   0.020
 LEY  plan-1  H1   0.020
 LEY  plan-1  H3   0.020
 LEY  plan-2  C8   0.020
 LEY  plan-2  C10  0.020
 LEY  plan-2  C13  0.020
 LEY  plan-2  C11  0.020
 LEY  plan-2  C12  0.020
 LEY  plan-2  C14  0.020
 LEY  plan-2  C9   0.020
 LEY  plan-2  H6   0.020
 LEY  plan-2  H7   0.020
 LEY  plan-2  H11  0.020
 LEY  plan-2  H12  0.020
 LEY  plan-2  F1   0.020
 LEY  plan-3  N3   0.020
 LEY  plan-3  C5   0.020
 LEY  plan-3  C7   0.020
 LEY  plan-3  C8   0.020
 LEY  plan-3  O1   0.020
 LEY  plan-3  H2   0.020

