# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 04:02:39 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 1-(4-methylphenyl)imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)n2ccnc2
#
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
 P5N  P5N  1-(4-methylphenyl)imidazole  ligand  22  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P5N
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
 P5N  C10  C  CR15  0  -0.117  -15.1636  -19.8823  -0.1532
 P5N  N12  N  N     0  -0.447  -14.4789  -21.6832  -1.2983
 P5N  C13  C  CR15  0   0.087  -15.3799  -22.0450  -0.4270
 P5N  C03  C  CR6   0   0.093  -18.7596  -21.1187   3.3272
 P5N  C04  C  CR16  0  -0.292  -17.8123  -22.1319   3.2006
 P5N  C05  C  CR16  0  -0.284  -16.8387  -22.0917   2.2145
 P5N  C06  C  CR6   0   0.337  -16.8120  -21.0335   1.3150
 P5N  C07  C  CR16  0  -0.283  -17.7492  -20.0141   1.4206
 P5N  C08  C  CR16  0  -0.291  -18.7035  -20.0586   2.4248
 P5N  C11  C  CR15  0  -0.215  -14.3332  -20.3332  -1.1351
 P5N  N09  N  NR5   0  -0.521  -15.8317  -20.9918   0.3002
 P5N  H1   H  HCR5  0   0.298  -15.3169  -18.9035   0.2687
 P5N  H2   H  HCR5  0   0.288  -15.7619  -23.0449  -0.2861
 P5N  H3   H  HCH3  0   0.252  -20.7101  -21.6956   4.0160
 P5N  H4   H  HCH3  0   0.246  -19.4779  -21.7200   5.2664
 P5N  H5   H  HCH3  0   0.246  -20.1321  -20.1832   4.6986
 P5N  H6   H  HCR6  0   0.257  -17.8190  -22.9640   3.8942
 P5N  H7   H  HCR6  0   0.276  -16.0948  -22.8759   2.1606
 P5N  H8   H  HCR6  0   0.277  -17.7476  -19.1908   0.7178
 P5N  H9   H  HCR6  0   0.257  -19.4245  -19.2537   2.4976
 P5N  H10  H  HCR5  0   0.257  -13.6373  -19.7572  -1.7249
 P5N  C01  C  CH3   0  -0.720  -19.8216  -21.1792   4.3853

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
 P5N  N12  C11  aromatic  1.368  0.020  1.368
 P5N  N12  C13  aromatic  1.305  0.020  1.305
 P5N  C11  C10  aromatic  1.363  0.020  1.363
 P5N  C13  N09  aromatic  1.357  0.020  1.357
 P5N  C10  N09  aromatic  1.372  0.020  1.372
 P5N  N09  C06  single    1.412  0.020  1.412
 P5N  C06  C07  aromatic  1.389  0.020  1.389
 P5N  C06  C05  aromatic  1.389  0.020  1.389
 P5N  C07  C08  aromatic  1.386  0.020  1.386
 P5N  C05  C04  aromatic  1.386  0.020  1.386
 P5N  C08  C03  aromatic  1.393  0.020  1.393
 P5N  C04  C03  aromatic  1.393  0.020  1.393
 P5N  C03  C01  single    1.500  0.020  1.500
 P5N  C10  H1   single    0.930  0.020  1.080
 P5N  C13  H2   single    0.930  0.020  1.080
 P5N  C01  H3   single    0.970  0.020  1.090
 P5N  C01  H4   single    0.970  0.020  1.090
 P5N  C01  H5   single    0.970  0.020  1.090
 P5N  C04  H6   single    0.930  0.020  1.080
 P5N  C05  H7   single    0.930  0.020  1.080
 P5N  C07  H8   single    0.930  0.020  1.080
 P5N  C08  H9   single    0.930  0.020  1.080
 P5N  C11  H10  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
 P5N  H1   C10  N09  122.43  3.000
 P5N  H1   C10  C11  132.05  3.000
 P5N  N09  C10  C11  105.50  3.000
 P5N  C11  N12  C13  105.52  3.000
 P5N  H2   C13  N09  122.07  3.000
 P5N  H2   C13  N12  126.04  3.000
 P5N  N09  C13  N12  111.87  3.000
 P5N  C08  C03  C04  117.85  3.000
 P5N  C04  C03  C01  121.07  3.000
 P5N  C08  C03  C01  121.06  3.000
 P5N  H6   C04  C05  118.82  3.000
 P5N  H6   C04  C03  119.76  3.000
 P5N  C05  C04  C03  121.41  3.000
 P5N  H7   C05  C06  120.43  3.000
 P5N  H7   C05  C04  119.81  3.000
 P5N  C06  C05  C04  119.75  3.000
 P5N  N09  C06  C07  120.11  3.000
 P5N  C07  C06  C05  119.80  3.000
 P5N  N09  C06  C05  120.09  3.000
 P5N  H8   C07  C08  119.73  3.000
 P5N  H8   C07  C06  120.52  3.000
 P5N  C08  C07  C06  119.74  3.000
 P5N  H9   C08  C07  118.89  3.000
 P5N  H9   C08  C03  119.67  3.000
 P5N  C07  C08  C03  121.43  3.000
 P5N  H10  C11  N12  122.03  3.000
 P5N  H10  C11  C10  127.62  3.000
 P5N  N12  C11  C10  110.35  3.000
 P5N  C06  N09  C13  126.40  3.000
 P5N  C06  N09  C10  126.84  3.000
 P5N  C13  N09  C10  106.76  3.000
 P5N  H5   C01  H4   108.12  3.000
 P5N  H5   C01  H3   107.32  3.000
 P5N  H4   C01  H3   107.19  3.000
 P5N  H5   C01  C03  111.58  3.000
 P5N  H4   C01  C03  111.54  3.000
 P5N  H3   C01  C03  110.89  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
 P5N  CONST_01  C13  N12  C11  C10    0.00   0.0  0
 P5N  CONST_02  N12  C13  N09  C10    0.00   0.0  0
 P5N  CONST_05  N09  C10  C11  N12    0.00   0.0  0
 P5N  CONST_06  C06  N09  C13  N12  180.00   0.0  0
 P5N  CONST_07  C11  C10  N09  C13    0.00   0.0  0
 P5N  CONST_10  C06  C07  C08  C03    0.00   0.0  0
 P5N  CONST_11  C06  C05  C04  C03    0.00   0.0  0
 P5N  CONST_12  N09  C06  C05  C04  180.00   0.0  0
 P5N  CONST_13  C07  C06  C05  C04    0.00   0.0  0
 P5N  CONST_14  C07  C08  C03  C04    0.00   0.0  0
 P5N  CONST_15  C08  C07  C06  C05    0.00   0.0  0
 P5N  CONST_16  C08  C03  C04  C05    0.00   0.0  0
 P5N  CONST_17  C11  C10  N09  C06  180.00   0.0  0
 P5N  CONST_18  N09  C06  C07  C08  180.00   0.0  0
 P5N  CONST_19  N09  C13  N12  C11    0.00   0.0  0
 P5N  CONST_20  C07  C08  C03  C01  180.00   0.0  0
 P5N  CONST_21  C05  C04  C03  C01  180.00   0.0  0
 P5N  CONST_22  H2   C13  N09  C10  180.00   0.0  0
 P5N  CONST_23  H1   C10  C11  N12  180.00   0.0  0
 P5N  CONST_24  H10  C11  N12  C13  180.00   0.0  0
 P5N  CONST_25  H8   C07  C08  C03  180.00   0.0  0
 P5N  CONST_26  H7   C05  C04  C03  180.00   0.0  0
 P5N  CONST_27  H9   C08  C03  C04  180.00   0.0  0
 P5N  CONST_28  H6   C04  C05  C06  180.00   0.0  0
 P5N  Var_01    H3   C01  C03  C04  -89.62  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
 P5N  plan-1  C10  0.020
 P5N  plan-1  N12  0.020
 P5N  plan-1  C13  0.020
 P5N  plan-1  C06  0.020
 P5N  plan-1  C11  0.020
 P5N  plan-1  N09  0.020
 P5N  plan-1  H1   0.020
 P5N  plan-1  H2   0.020
 P5N  plan-1  H10  0.020
 P5N  plan-2  C03  0.020
 P5N  plan-2  C04  0.020
 P5N  plan-2  C05  0.020
 P5N  plan-2  C06  0.020
 P5N  plan-2  C07  0.020
 P5N  plan-2  C08  0.020
 P5N  plan-2  N09  0.020
 P5N  plan-2  H6   0.020
 P5N  plan-2  H7   0.020
 P5N  plan-2  H8   0.020
 P5N  plan-2  H9   0.020
 P5N  plan-2  C01  0.020

