# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:38:12 2021
#   Inital geometry file: a 59 line input string
#   Ligand name: (5R)-2-methyl-4,5,6,7-tetrahydro-1H-benzimidazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c2CC[C@@H](N)Cc2n1
#
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
 WUS  WUS  (5R)-2-methyl-4,5,6,7-tetrahydro-1H-benzimidazol-5-amine  ligand  24  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WUS
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
 WUS  C10  C  CR5   0   0.090  62.2605  -78.5677   8.3544
 WUS  C01  C  CH3   0  -0.746  62.9602  -75.6861   6.3248
 WUS  C02  C  CR5   0   0.387  62.6871  -76.7266   7.3509
 WUS  N03  N  NR15  0  -0.654  62.6370  -76.4572   8.6775
 WUS  C04  C  CR5   0   0.286  62.3628  -77.6265   9.3338
 WUS  C05  C  CH2   0  -0.509  62.2077  -77.8507  10.7939
 WUS  C06  C  CH2   0  -0.456  61.5721  -79.2303  10.9940
 WUS  C07  C  CH1   0  -0.088  62.2067  -80.3107  10.1053
 WUS  C08  C  CH2   0  -0.506  61.9745  -80.0064   8.6228
 WUS  N09  N  NH2   0  -0.794  61.7492  -81.6619  10.3954
 WUS  N11  N  N     0  -0.483  62.4627  -77.9991   7.1236
 WUS  H1   H  HCH3  0   0.255  62.9799  -76.1419   5.3375
 WUS  H2   H  HCH3  0   0.253  62.1939  -74.9093   6.3241
 WUS  H3   H  HCH3  0   0.252  63.9210  -75.1968   6.4918
 WUS  H4   H  HNR5  0   0.408  62.7822  -75.5551   9.1028
 WUS  H5   H  HCH2  0   0.241  63.1776  -77.8078  11.3007
 WUS  H6   H  HCH2  0   0.249  61.5881  -77.0775  11.2557
 WUS  H7   H  HCH2  0   0.221  60.5003  -79.1762  10.7723
 WUS  H8   H  HCH2  0   0.234  61.6648  -79.5237  12.0426
 WUS  H9   H  HCH1  0   0.223  63.2890  -80.2933  10.2827
 WUS  H10  H  HCH2  0   0.224  60.9367  -80.2497   8.3609
 WUS  H11  H  HCH2  0   0.238  62.6064  -80.6536   8.0089
 WUS  H12  H  HNH2  0   0.343  61.9267  -81.8753  11.3697
 WUS  H13  H  HNH2  0   0.334  60.7412  -81.7042  10.2891

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
 WUS  C01  C02  single    1.487  0.020  1.487
 WUS  N11  C02  aromatic  1.312  0.020  1.312
 WUS  N11  C10  aromatic  1.371  0.020  1.371
 WUS  C02  N03  aromatic  1.355  0.020  1.355
 WUS  C10  C08  single    1.491  0.020  1.491
 WUS  C10  C04  aromatic  1.362  0.020  1.362
 WUS  N03  C04  aromatic  1.369  0.020  1.369
 WUS  C08  C07  single    1.531  0.020  1.531
 WUS  C04  C05  single    1.485  0.020  1.485
 WUS  C07  N09  single    1.456  0.020  1.456
 WUS  C07  C06  single    1.536  0.020  1.536
 WUS  C05  C06  single    1.532  0.020  1.532
 WUS  C01  H1   single    0.970  0.020  1.090
 WUS  C01  H2   single    0.970  0.020  1.090
 WUS  C01  H3   single    0.970  0.020  1.090
 WUS  N03  H4   single    0.860  0.020  1.020
 WUS  C05  H5   single    0.970  0.020  1.090
 WUS  C05  H6   single    0.970  0.020  1.090
 WUS  C06  H7   single    0.970  0.020  1.090
 WUS  C06  H8   single    0.970  0.020  1.090
 WUS  C07  H9   single    0.970  0.020  1.090
 WUS  C08  H10  single    0.970  0.020  1.090
 WUS  C08  H11  single    0.970  0.020  1.090
 WUS  N09  H12  single    0.890  0.020  1.040
 WUS  N09  H13  single    0.890  0.020  1.040

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
 WUS  N11  C10  C08  126.16  3.000
 WUS  C08  C10  C04  123.48  3.000
 WUS  N11  C10  C04  110.36  3.000
 WUS  H3   C01  H2   107.41  3.000
 WUS  H3   C01  H1   108.12  3.000
 WUS  H2   C01  H1   108.09  3.000
 WUS  H3   C01  C02  111.71  3.000
 WUS  H2   C01  C02  111.70  3.000
 WUS  H1   C01  C02  109.67  3.000
 WUS  N11  C02  N03  110.87  3.000
 WUS  N03  C02  C01  122.92  3.000
 WUS  N11  C02  C01  126.21  3.000
 WUS  H4   N03  C04  126.24  3.000
 WUS  H4   N03  C02  125.87  3.000
 WUS  C04  N03  C02  107.88  3.000
 WUS  C05  C04  N03  128.41  3.000
 WUS  C05  C04  C10  126.48  3.000
 WUS  N03  C04  C10  105.11  3.000
 WUS  H6   C05  H5   106.19  3.000
 WUS  H6   C05  C06  110.27  3.000
 WUS  H5   C05  C06  110.01  3.000
 WUS  H6   C05  C04  111.57  3.000
 WUS  H5   C05  C04  110.89  3.000
 WUS  C06  C05  C04  107.92  3.000
 WUS  H8   C06  H7   106.88  3.000
 WUS  H8   C06  C07  109.34  3.000
 WUS  H7   C06  C07  108.77  3.000
 WUS  H8   C06  C05  109.38  3.000
 WUS  H7   C06  C05  109.57  3.000
 WUS  C07  C06  C05  112.72  3.000
 WUS  H9   C07  N09  107.01  3.000
 WUS  H9   C07  C08  107.64  3.000
 WUS  N09  C07  C08  109.25  3.000
 WUS  H9   C07  C06  107.63  3.000
 WUS  N09  C07  C06  114.06  3.000
 WUS  C08  C07  C06  110.96  3.000
 WUS  H11  C08  H10  106.34  3.000
 WUS  H11  C08  C07  109.78  3.000
 WUS  H10  C08  C07  109.29  3.000
 WUS  H11  C08  C10  111.05  3.000
 WUS  H10  C08  C10  110.63  3.000
 WUS  C07  C08  C10  109.69  3.000
 WUS  H13  N09  H12  105.43  3.000
 WUS  H13  N09  C07  109.27  3.000
 WUS  H12  N09  C07  109.40  3.000
 WUS  C02  N11  C10  105.78  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
 WUS  CONST_01  N03  C02  N11  C10    0.00   0.0  0
 WUS  CONST_02  C02  N03  C04  C10    0.00   0.0  0
 WUS  CONST_03  C04  C10  N11  C02    0.00   0.0  0
 WUS  CONST_04  N11  C10  C04  N03    0.00   0.0  0
 WUS  CONST_05  N11  C02  N03  C04    0.00   0.0  0
 WUS  CONST_06  C01  C02  N11  C10  180.00   0.0  0
 WUS  CONST_07  C04  N03  C02  C01  180.00   0.0  0
 WUS  CONST_08  H4   N03  C04  C10  180.00   0.0  0
 WUS  Var_01    C06  C05  C04  C10  -13.99  30.0  1
 WUS  Var_02    C07  C08  C10  C04  -15.69  30.0  1
 WUS  Var_03    C07  C06  C05  C04   44.64  30.0  1
 WUS  Var_04    H1   C01  C02  N03  178.34  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 WUS  chir_01  C07  C08  N09  C06  positiv

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
 WUS  plan-1  C10  0.020
 WUS  plan-1  C01  0.020
 WUS  plan-1  C02  0.020
 WUS  plan-1  N03  0.020
 WUS  plan-1  C04  0.020
 WUS  plan-1  C05  0.020
 WUS  plan-1  C08  0.020
 WUS  plan-1  N11  0.020
 WUS  plan-1  H4   0.020

