# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 00:44:01 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: methyl ~{N}-(5-butyl-1~{H}-benzimidazol-2-yl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCc1ccc2[nH]c(NC(=O)OC)nc2c1
#
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
 H1C  H1C  "methyl ~{N}-(5-butyl-1~{H}-benzimidazol-2-yl)carbamate"  ligand  35  18  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H1C
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
 H1C  C01  C  CR16  0  -0.328  16.1319  64.1394  39.9244
 H1C  C02  C  CR16  0  -0.290  17.1401  63.5637  39.1672
 H1C  C03  C  CR56  0   0.327  17.2483  63.9838  37.8507
 H1C  C04  C  CR56  0   0.178  16.3891  64.9436  37.2978
 H1C  C05  C  CR16  0  -0.409  15.3870  65.5111  38.0800
 H1C  C06  C  CR6   0   0.125  15.2552  65.1053  39.4020
 H1C  C08  C  CR5   0   0.690  17.7133  64.3759  35.7427
 H1C  C11  C  C     0   0.737  18.0564  64.7670  33.3525
 H1C  C14  C  CH3   0  -0.418  18.7901  64.9087  31.1269
 H1C  C15  C  CH2   0  -0.504  14.2060  65.7168  40.2896
 H1C  C16  C  CH2   0  -0.402  14.7623  66.8106  41.2022
 H1C  C17  C  CH2   0  -0.421  13.6960  67.4230  42.1007
 H1C  C18  C  CH3   0  -0.659  14.2451  68.5068  43.0178
 H1C  N07  N  NR15  0  -0.736  18.0910  63.6381  36.8212
 H1C  N09  N  N     0  -0.485  16.7092  65.1697  35.9773
 H1C  N10  N  NH1   0  -0.773  18.4042  64.2278  34.5646
 H1C  O12  O  O2    0  -0.472  18.9798  64.4322  32.4573
 H1C  O13  O  O     0  -0.459  17.0786  65.4292  33.1232
 H1C  H1   H  HCR6  0   0.241  16.0114  63.8287  40.9557
 H1C  H2   H  HCR6  0   0.260  17.8014  62.8170  39.5870
 H1C  H3   H  HCR6  0   0.240  14.7180  66.2535  37.6602
 H1C  H4   H  HCH3  0   0.253  19.6363  64.5361  30.5574
 H1C  H5   H  HCH3  0   0.240  17.8668  64.5267  30.6920
 H1C  H6   H  HCH3  0   0.240  18.7828  65.9977  31.0898
 H1C  H7   H  HCH2  0   0.233  13.4033  66.1363  39.6772
 H1C  H8   H  HCH2  0   0.231  13.7473  64.9396  40.9087
 H1C  H9   H  HCH2  0   0.215  15.5660  66.3938  41.8183
 H1C  H10  H  HCH2  0   0.215  15.2220  67.5934  40.5899
 H1C  H11  H  HCH2  0   0.213  12.8955  67.8380  41.4806
 H1C  H12  H  HCH2  0   0.212  13.2341  66.6337  42.7019
 H1C  H13  H  HCH3  0   0.225  13.4657  68.9228  43.6570
 H1C  H14  H  HCH3  0   0.216  15.0298  68.1133  43.6663
 H1C  H15  H  HCH3  0   0.216  14.6753  69.3294  42.4435
 H1C  H16  H  HNR5  0   0.422  18.8308  62.9525  36.8533
 H1C  H18  H  HNH1  0   0.429  19.2391  63.6598  34.5886

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
 H1C  C14  O12  single    1.426  0.020  1.426
 H1C  O12  C11  single    1.329  0.020  1.329
 H1C  O13  C11  double    1.203  0.020  1.203
 H1C  C11  N10  single    1.371  0.020  1.371
 H1C  N10  C08  single    1.374  0.020  1.374
 H1C  C08  N09  aromatic  1.301  0.020  1.301
 H1C  C08  N07  aromatic  1.360  0.020  1.360
 H1C  N09  C04  aromatic  1.377  0.020  1.377
 H1C  N07  C03  aromatic  1.375  0.020  1.375
 H1C  C04  C03  aromatic  1.402  0.020  1.402
 H1C  C04  C05  aromatic  1.392  0.020  1.392
 H1C  C03  C02  aromatic  1.386  0.020  1.386
 H1C  C05  C06  aromatic  1.389  0.020  1.389
 H1C  C02  C01  aromatic  1.386  0.020  1.386
 H1C  C06  C01  aromatic  1.405  0.020  1.405
 H1C  C06  C15  single    1.504  0.020  1.504
 H1C  C15  C16  single    1.529  0.020  1.529
 H1C  C16  C17  single    1.523  0.020  1.523
 H1C  C17  C18  single    1.522  0.020  1.522
 H1C  C01  H1   single    0.930  0.020  1.080
 H1C  C02  H2   single    0.930  0.020  1.080
 H1C  C05  H3   single    0.930  0.020  1.080
 H1C  C14  H4   single    0.970  0.020  1.090
 H1C  C14  H5   single    0.970  0.020  1.090
 H1C  C14  H6   single    0.970  0.020  1.090
 H1C  C15  H7   single    0.970  0.020  1.090
 H1C  C15  H8   single    0.970  0.020  1.090
 H1C  C16  H9   single    0.970  0.020  1.090
 H1C  C16  H10  single    0.970  0.020  1.090
 H1C  C17  H11  single    0.970  0.020  1.090
 H1C  C17  H12  single    0.970  0.020  1.090
 H1C  C18  H13  single    0.970  0.020  1.090
 H1C  C18  H14  single    0.970  0.020  1.090
 H1C  C18  H15  single    0.970  0.020  1.090
 H1C  N07  H16  single    0.860  0.020  1.020
 H1C  N10  H18  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
 H1C  H1   C01  C06  118.78  3.000
 H1C  H1   C01  C02  118.79  3.000
 H1C  C06  C01  C02  122.43  3.000
 H1C  H2   C02  C03  121.99  3.000
 H1C  H2   C02  C01  121.28  3.000
 H1C  C03  C02  C01  116.73  3.000
 H1C  N07  C03  C04  104.63  3.000
 H1C  C04  C03  C02  122.30  3.000
 H1C  N07  C03  C02  133.07  3.000
 H1C  N09  C04  C05  129.72  3.000
 H1C  C05  C04  C03  119.91  3.000
 H1C  N09  C04  C03  110.37  3.000
 H1C  H3   C05  C06  120.67  3.000
 H1C  H3   C05  C04  120.39  3.000
 H1C  C06  C05  C04  118.94  3.000
 H1C  C15  C06  C05  120.60  3.000
 H1C  C15  C06  C01  119.68  3.000
 H1C  C05  C06  C01  119.70  3.000
 H1C  N10  C08  N09  127.48  3.000
 H1C  N09  C08  N07  113.71  3.000
 H1C  N10  C08  N07  118.81  3.000
 H1C  O13  C11  O12  125.10  3.000
 H1C  O13  C11  N10  126.23  3.000
 H1C  O12  C11  N10  108.67  3.000
 H1C  H6   C14  H5   109.34  3.000
 H1C  H6   C14  H4   109.29  3.000
 H1C  H5   C14  H4   109.31  3.000
 H1C  H6   C14  O12  111.50  3.000
 H1C  H5   C14  O12  111.59  3.000
 H1C  H4   C14  O12  105.72  3.000
 H1C  H8   C15  H7   106.36  3.000
 H1C  H8   C15  C16  108.84  3.000
 H1C  H7   C15  C16  109.08  3.000
 H1C  H8   C15  C06  109.72  3.000
 H1C  H7   C15  C06  109.73  3.000
 H1C  C16  C15  C06  112.90  3.000
 H1C  H10  C16  H9   106.18  3.000
 H1C  H10  C16  C17  109.66  3.000
 H1C  H9   C16  C17  109.57  3.000
 H1C  H10  C16  C15  109.29  3.000
 H1C  H9   C16  C15  109.30  3.000
 H1C  C17  C16  C15  112.64  3.000
 H1C  H12  C17  H11  106.03  3.000
 H1C  H12  C17  C18  109.56  3.000
 H1C  H11  C17  C18  109.59  3.000
 H1C  H12  C17  C16  109.24  3.000
 H1C  H11  C17  C16  109.29  3.000
 H1C  C18  C17  C16  112.90  3.000
 H1C  H15  C18  H14  107.51  3.000
 H1C  H15  C18  H13  107.61  3.000
 H1C  H14  C18  H13  107.64  3.000
 H1C  H15  C18  C17  111.21  3.000
 H1C  H14  C18  C17  111.14  3.000
 H1C  H13  C18  C17  111.53  3.000
 H1C  H16  N07  C08  126.68  3.000
 H1C  H16  N07  C03  126.62  3.000
 H1C  C08  N07  C03  106.69  3.000
 H1C  C08  N09  C04  104.60  3.000
 H1C  H18  N10  C11  116.85  3.000
 H1C  H18  N10  C08  117.13  3.000
 H1C  C11  N10  C08  126.02  3.000
 H1C  C14  O12  C11  116.86  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
 H1C  CONST_01  N07  C03  C02  C01   180.00   0.0  0
 H1C  CONST_02  C04  C03  C02  C01     0.00   0.0  0
 H1C  CONST_03  C04  C05  C06  C01     0.00   0.0  0
 H1C  CONST_04  C08  N07  C03  C02   180.00   0.0  0
 H1C  CONST_05  N09  C04  C03  C02   180.00   0.0  0
 H1C  CONST_06  C05  C04  C03  C02     0.00   0.0  0
 H1C  CONST_07  C05  C06  C01  C02     0.00   0.0  0
 H1C  CONST_08  N09  C08  N07  C03     0.00   0.0  0
 H1C  CONST_09  C08  N09  C04  C03     0.00   0.0  0
 H1C  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 H1C  CONST_11  C06  C01  C02  C03     0.00   0.0  0
 H1C  CONST_12  N07  C08  N09  C04     0.00   0.0  0
 H1C  CONST_13  C08  N07  C03  C04     0.00   0.0  0
 H1C  CONST_14  C08  N09  C04  C05   180.00   0.0  0
 H1C  CONST_15  N07  C03  C04  C05   180.00   0.0  0
 H1C  CONST_16  N09  C04  C05  C06   180.00   0.0  0
 H1C  CONST_17  N09  C04  C03  N07     0.00   0.0  0
 H1C  CONST_18  C15  C06  C01  C02   180.00   0.0  0
 H1C  CONST_19  N10  C08  N07  C03   180.00   0.0  0
 H1C  CONST_20  N10  C08  N09  C04   180.00   0.0  0
 H1C  CONST_21  C15  C06  C05  C04   180.00   0.0  0
 H1C  CONST_22  H3   C05  C06  C01   180.00   0.0  0
 H1C  CONST_23  H16  N07  C03  C02     0.00   0.0  0
 H1C  CONST_24  H3   C05  C04  C03   180.00   0.0  0
 H1C  CONST_25  H1   C01  C02  C03   180.00   0.0  0
 H1C  CONST_26  H16  N07  C03  C04   180.00   0.0  0
 H1C  CONST_27  H2   C02  C03  C04   180.00   0.0  0
 H1C  CONST_28  H1   C01  C06  C05   180.00   0.0  0
 H1C  CONST_29  H2   C02  C01  C06   180.00   0.0  0
 H1C  CONST_30  H2   C02  C03  N07     0.00   0.0  0
 H1C  CONST_31  H16  N07  C08  N09   180.00   0.0  0
 H1C  CONST_32  H3   C05  C04  N09     0.00   0.0  0
 H1C  CONST_33  N09  C08  N10  C11     0.00   0.0  0
 H1C  CONST_34  N07  C08  N10  C11   180.00   0.0  0
 H1C  CONST_35  H18  N10  C08  N07     0.00   0.0  0
 H1C  CONST_36  H18  N10  C08  N09   180.00   0.0  0
 H1C  CONST_37  O12  C11  N10  C08   180.00   0.0  0
 H1C  CONST_38  O13  C11  N10  C08     0.00   0.0  0
 H1C  Var_01    C16  C15  C06  C01    79.21  30.0  2
 H1C  Var_02    C16  C15  C06  C05   -99.17  30.0  2
 H1C  Var_03    H7   C15  C06  C01  -158.89  30.0  2
 H1C  Var_04    H8   C15  C06  C01   -42.38  30.0  2
 H1C  Var_05    H7   C15  C06  C05    22.73  30.0  2
 H1C  Var_06    H8   C15  C06  C05   139.24  30.0  2
 H1C  Var_07    C17  C16  C15  C06  -179.85  30.0  3
 H1C  Var_08    H9   C16  C15  C06   -57.80  30.0  3
 H1C  Var_09    H10  C16  C15  C06    58.00  30.0  3
 H1C  Var_10    O13  C11  O12  C14     0.44  30.0  3
 H1C  Var_11    N10  C11  O12  C14  -179.85  30.0  3
 H1C  Var_12    C18  C17  C16  C15   179.65  30.0  3
 H1C  Var_13    H4   C14  O12  C11   179.93  30.0  3
 H1C  Var_14    H5   C14  O12  C11   -61.33  30.0  3
 H1C  Var_15    H6   C14  O12  C11    61.26  30.0  3
 H1C  Var_16    H11  C17  C16  C15   -58.11  30.0  3
 H1C  Var_17    H12  C17  C16  C15    57.49  30.0  3
 H1C  Var_18    H13  C18  C17  C16  -179.46  30.0  3
 H1C  Var_19    H14  C18  C17  C16   -59.33  30.0  3
 H1C  Var_20    H15  C18  C17  C16    60.41  30.0  3
 H1C  Var_21    H7   C15  C16  C17    57.88  30.0  2
 H1C  Var_22    H8   C15  C16  C17   -57.77  30.0  2
 H1C  Var_23    H9   C16  C17  C18    57.76  30.0  1
 H1C  Var_24    H10  C16  C17  C18   -58.41  30.0  1
 H1C  Var_25    H18  N10  C11  O12    -2.28  30.0  2
 H1C  Var_26    H18  N10  C11  O13   177.43  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
 H1C  plan-1  C01  0.020
 H1C  plan-1  C02  0.020
 H1C  plan-1  C03  0.020
 H1C  plan-1  C04  0.020
 H1C  plan-1  C05  0.020
 H1C  plan-1  C06  0.020
 H1C  plan-1  C08  0.020
 H1C  plan-1  C15  0.020
 H1C  plan-1  N07  0.020
 H1C  plan-1  N09  0.020
 H1C  plan-1  N10  0.020
 H1C  plan-1  H1   0.020
 H1C  plan-1  H2   0.020
 H1C  plan-1  H3   0.020
 H1C  plan-1  H16  0.020
 H1C  plan-2  C08  0.020
 H1C  plan-2  C11  0.020
 H1C  plan-2  N10  0.020
 H1C  plan-2  H18  0.020
 H1C  plan-3  C11  0.020
 H1C  plan-3  N10  0.020
 H1C  plan-3  O12  0.020
 H1C  plan-3  O13  0.020

