# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 15:12:05 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-(1H-pyrazol-3-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1ccc(n1)c2[nH]c3ccccc3n2
#
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
 L0D  L0D  2-(1H-pyrazol-3-yl)-1H-benzimidazole  ligand  22  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L0D
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
 L0D  C1    C  CR15  0   0.028   4.0762  -0.6480  -0.0241
 L0D  C2    C  CR15  0  -0.506   2.8239  -1.2118  -0.0195
 L0D  C3    C  CR5   0   0.202   1.9527  -0.1067  -0.0173
 L0D  N4    N  N     0  -0.297   2.6216   1.0373  -0.0199
 L0D  N5    N  NR15  0  -0.412   3.8932   0.6842  -0.0241
 L0D  C7    C  CR5   0   0.459   0.5040  -0.1153  -0.0124
 L0D  N8    N  N     0  -0.482  -0.2397  -1.1902  -0.0096
 L0D  C9    C  CR56  0   0.142  -1.5328  -0.7287  -0.0057
 L0D  C10   C  CR16  0  -0.346  -2.7382  -1.4310  -0.0028
 L0D  C11   C  CR16  0  -0.270  -3.9137  -0.7018  -0.0006
 L0D  C12   C  CR16  0  -0.278  -3.9040   0.7017  -0.0008
 L0D  C13   C  CR16  0  -0.312  -2.7192   1.4178  -0.0032
 L0D  C14   C  CR56  0   0.339  -1.5426   0.6780  -0.0061
 L0D  N15   N  NR15  0  -0.708  -0.2221   1.0332  -0.0101
 L0D  HN5   H  HNR5  0   0.429   4.6087   1.3938  -0.0268
 L0D  HN15  H  HNR5  0   0.420   0.1556   1.9681  -0.0155
 L0D  H1    H  HCR5  0   0.298   5.0600  -1.0868  -0.0257
 L0D  H2    H  HCR5  0   0.269   2.5700  -2.2578  -0.0183
 L0D  H10   H  HCR6  0   0.253  -2.7499  -2.5134  -0.0029
 L0D  H11   H  HCR6  0   0.252  -4.8630  -1.2217   0.0011
 L0D  H12   H  HCR6  0   0.255  -4.8446   1.2369   0.0016
 L0D  H13   H  HCR6  0   0.266  -2.7140   2.4998  -0.0022

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
 L0D  C1   C2    aromatic  1.373  0.020  1.373
 L0D  C1   N5    aromatic  1.345  0.020  1.345
 L0D  C1   H1    single    0.930  0.020  1.080
 L0D  C2   C3    aromatic  1.407  0.020  1.407
 L0D  C2   H2    single    0.930  0.020  1.080
 L0D  C3   N4    aromatic  1.325  0.020  1.325
 L0D  C3   C7    single    1.449  0.020  1.449
 L0D  N4   N5    aromatic  1.320  0.020  1.320
 L0D  N5   HN5   single    0.860  0.020  1.020
 L0D  C7   N8    aromatic  1.307  0.020  1.307
 L0D  C7   N15   aromatic  1.359  0.020  1.359
 L0D  N8   C9    aromatic  1.373  0.020  1.373
 L0D  C9   C10   aromatic  1.395  0.020  1.395
 L0D  C9   C14   aromatic  1.407  0.020  1.407
 L0D  C10  C11   aromatic  1.383  0.020  1.383
 L0D  C10  H10   single    0.930  0.020  1.080
 L0D  C11  C12   aromatic  1.404  0.020  1.404
 L0D  C11  H11   single    0.930  0.020  1.080
 L0D  C12  C13   aromatic  1.384  0.020  1.384
 L0D  C12  H12   single    0.930  0.020  1.080
 L0D  C13  C14   aromatic  1.390  0.020  1.390
 L0D  C13  H13   single    0.930  0.020  1.080
 L0D  C14  N15   aromatic  1.367  0.020  1.367
 L0D  N15  HN15  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
 L0D  H1    C1   N5   121.87  3.000
 L0D  H1    C1   C2   131.72  3.000
 L0D  N5    C1   C2   106.41  3.000
 L0D  H2    C2   C3   128.10  3.000
 L0D  H2    C2   C1   127.89  3.000
 L0D  C3    C2   C1   104.01  3.000
 L0D  C7    C3   N4   120.65  3.000
 L0D  C7    C3   C2   127.91  3.000
 L0D  N4    C3   C2   111.43  3.000
 L0D  N5    N4   C3   104.79  3.000
 L0D  HN5   N5   N4   119.71  3.000
 L0D  HN5   N5   C1   126.94  3.000
 L0D  N4    N5   C1   113.35  3.000
 L0D  N15   C7   N8   113.02  3.000
 L0D  N15   C7   C3   121.97  3.000
 L0D  N8    C7   C3   125.02  3.000
 L0D  C9    N8   C7   105.04  3.000
 L0D  C14   C9   C10  119.82  3.000
 L0D  C14   C9   N8   110.04  3.000
 L0D  C10   C9   N8   130.13  3.000
 L0D  H10   C10  C11  121.19  3.000
 L0D  H10   C10  C9   120.85  3.000
 L0D  C11   C10  C9   117.96  3.000
 L0D  H11   C11  C12  119.10  3.000
 L0D  H11   C11  C10  119.48  3.000
 L0D  C12   C11  C10  121.42  3.000
 L0D  H12   C12  C13  119.21  3.000
 L0D  H12   C12  C11  119.24  3.000
 L0D  C13   C12  C11  121.55  3.000
 L0D  H13   C13  C14  121.88  3.000
 L0D  H13   C13  C12  121.43  3.000
 L0D  C14   C13  C12  116.69  3.000
 L0D  N15   C14  C13  132.79  3.000
 L0D  N15   C14  C9   104.65  3.000
 L0D  C13   C14  C9   122.56  3.000
 L0D  HN15  N15  C14  127.05  3.000
 L0D  HN15  N15  C7   125.70  3.000
 L0D  C14   N15  C7   107.25  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
 L0D  CONST_01  N4    C3   C2   C1     0.00  0.0  0
 L0D  CONST_02  C7    C3   C2   C1   180.00  0.0  0
 L0D  CONST_03  C3    N4   N5   C1     0.00  0.0  0
 L0D  CONST_04  N4    N5   C1   C2     0.00  0.0  0
 L0D  CONST_05  N5    N4   C3   C2     0.00  0.0  0
 L0D  CONST_06  N8    C7   C3   C2     0.00  0.0  0
 L0D  CONST_07  N15   C7   C3   C2   180.00  0.0  0
 L0D  CONST_08  N5    C1   C2   C3     0.00  0.0  0
 L0D  CONST_09  C9    N8   C7   C3   180.00  0.0  0
 L0D  CONST_10  C14   N15  C7   C3   180.00  0.0  0
 L0D  CONST_11  N8    C7   C3   N4   180.00  0.0  0
 L0D  CONST_12  N15   C7   C3   N4     0.00  0.0  0
 L0D  CONST_13  C7    C3   N4   N5   180.00  0.0  0
 L0D  CONST_14  C10   C9   N8   C7   180.00  0.0  0
 L0D  CONST_15  C14   C9   N8   C7     0.00  0.0  0
 L0D  CONST_16  C9    C14  N15  C7     0.00  0.0  0
 L0D  CONST_17  C13   C14  N15  C7   180.00  0.0  0
 L0D  CONST_18  C14   N15  C7   N8     0.00  0.0  0
 L0D  CONST_19  C11   C10  C9   N8   180.00  0.0  0
 L0D  CONST_20  C13   C14  C9   N8   180.00  0.0  0
 L0D  CONST_21  N15   C14  C9   N8     0.00  0.0  0
 L0D  CONST_22  N15   C7   N8   C9     0.00  0.0  0
 L0D  CONST_23  C12   C11  C10  C9     0.00  0.0  0
 L0D  CONST_24  C12   C13  C14  C9     0.00  0.0  0
 L0D  CONST_25  C13   C14  C9   C10    0.00  0.0  0
 L0D  CONST_26  N15   C14  C9   C10  180.00  0.0  0
 L0D  CONST_27  C13   C12  C11  C10    0.00  0.0  0
 L0D  CONST_28  C14   C9   C10  C11    0.00  0.0  0
 L0D  CONST_29  C14   C13  C12  C11    0.00  0.0  0
 L0D  CONST_30  N15   C14  C13  C12  180.00  0.0  0
 L0D  CONST_31  HN5   N5   C1   C2   180.00  0.0  0
 L0D  CONST_32  H1    C1   C2   C3   180.00  0.0  0
 L0D  CONST_33  HN15  N15  C7   C3     0.00  0.0  0
 L0D  CONST_34  H2    C2   C3   N4   180.00  0.0  0
 L0D  CONST_35  H10   C10  C9   N8     0.00  0.0  0
 L0D  CONST_36  H11   C11  C10  C9   180.00  0.0  0
 L0D  CONST_37  H13   C13  C14  C9   180.00  0.0  0
 L0D  CONST_38  H12   C12  C11  C10  180.00  0.0  0

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
 L0D  plan-1  C1    0.020
 L0D  plan-1  C2    0.020
 L0D  plan-1  C3    0.020
 L0D  plan-1  N4    0.020
 L0D  plan-1  N5    0.020
 L0D  plan-1  C7    0.020
 L0D  plan-1  HN5   0.020
 L0D  plan-1  H1    0.020
 L0D  plan-1  H2    0.020
 L0D  plan-2  C3    0.020
 L0D  plan-2  C7    0.020
 L0D  plan-2  N8    0.020
 L0D  plan-2  C9    0.020
 L0D  plan-2  C10   0.020
 L0D  plan-2  C11   0.020
 L0D  plan-2  C12   0.020
 L0D  plan-2  C13   0.020
 L0D  plan-2  C14   0.020
 L0D  plan-2  N15   0.020
 L0D  plan-2  HN15  0.020
 L0D  plan-2  H10   0.020
 L0D  plan-2  H11   0.020
 L0D  plan-2  H12   0.020
 L0D  plan-2  H13   0.020

