# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:37:14 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-[(2R)-2-methylpyrrolidin-2-yl]-1H-benzimidazole-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(CCCN1)c2[nH]c3c(cccc3C(N)=O)n2
#
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
 78P  78P  2-[(2R)-2-methylpyrrolidin-2-yl]-1H-benzimidazole-7-carboxamide  ligand  34  18  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_78P
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
 78P  C4    C  CR56  0   0.337  -1.2163   0.2651  -0.0436
 78P  C5    C  CR6   0  -0.090  -2.5635  -0.0797   0.1027
 78P  C6    C  CR16  0  -0.331  -3.4744   0.9657  -0.0213
 78P  C8    C  CR5   0   0.482   0.9722   0.4060  -0.2081
 78P  C10   C  C     0   0.519  -2.9254  -1.4962   0.3796
 78P  C13   C  CT    0  -0.056   2.3859  -0.0741  -0.2717
 78P  C15   C  CH2   0  -0.322   4.0533  -1.2055   0.8964
 78P  C17   C  CH2   0  -0.416   3.4124   1.0074   0.0993
 78P  C1    C  CR16  0  -0.258  -3.0701   2.2775  -0.2801
 78P  C2    C  CR16  0  -0.338  -1.7326   2.6040  -0.4266
 78P  C3    C  CR56  0   0.145  -0.7966   1.5826  -0.3066
 78P  N7    N  N     0  -0.468   0.5735   1.6313  -0.4018
 78P  N9    N  NR15  0  -0.687  -0.0580  -0.4541   0.0097
 78P  N11   N  NH2   0  -0.823  -4.2266  -1.8066   0.4349
 78P  O12   O  O     0  -0.493  -2.0455  -2.3360   0.5505
 78P  N14   N  NH1   0  -0.589   2.5996  -1.1392   0.7136
 78P  C16   C  CH2   0  -0.489   4.6335   0.1834   0.5239
 78P  C18   C  CH3   0  -0.637   2.6512  -0.6149  -1.6816
 78P  H6    H  HCR6  0   0.250  -4.5361   0.7878   0.0880
 78P  H151  H  HCH2  0   0.244   4.2737  -1.4890   1.9248
 78P  H152  H  HCH2  0   0.230   4.4766  -1.9817   0.2562
 78P  H171  H  HCH2  0   0.240   3.6192   1.6997  -0.7172
 78P  H172  H  HCH2  0   0.236   3.0327   1.5945   0.9377
 78P  H1    H  HCR6  0   0.262  -3.8235   3.0485  -0.3654
 78P  H2    H  HCR6  0   0.262  -1.4215   3.6210  -0.6272
 78P  H9    H  HNR5  0   0.415   0.0136  -1.4430   0.1920
 78P  H111  H  HNH2  0   0.416  -4.9631  -1.1509   0.2464
 78P  H112  H  HNH2  0   0.407  -4.5010  -2.7590   0.6110
 78P  H141  H  HNH1  0   0.349   2.1965  -0.8368   1.5944
 78P  H161  H  HCH2  0   0.243   5.1534   0.6463   1.3623
 78P  H162  H  HCH2  0   0.238   5.3559   0.0954  -0.2880
 78P  H181  H  HCH3  0   0.245   3.6780  -0.9691  -1.7801
 78P  H182  H  HCH3  0   0.238   1.9863  -1.4469  -1.9150
 78P  H183  H  HCH3  0   0.238   2.4997   0.1676  -2.4253

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
 78P  C18  C13   single    1.533  0.020  1.533
 78P  C13  C17   single    1.537  0.020  1.537
 78P  C13  N14   single    1.467  0.020  1.467
 78P  C13  C8    single    1.494  0.020  1.494
 78P  C17  C16   single    1.533  0.020  1.533
 78P  N14  C15   single    1.467  0.020  1.467
 78P  N7   C8    aromatic  1.303  0.020  1.303
 78P  N7   C3    aromatic  1.374  0.020  1.374
 78P  C8   N9    aromatic  1.360  0.020  1.360
 78P  C15  C16   single    1.551  0.020  1.551
 78P  N9   C4    aromatic  1.364  0.020  1.364
 78P  C3   C2    aromatic  1.390  0.020  1.390
 78P  C3   C4    aromatic  1.408  0.020  1.408
 78P  C2   C1    aromatic  1.385  0.020  1.385
 78P  C4   C5    aromatic  1.398  0.020  1.398
 78P  C1   C6    aromatic  1.397  0.020  1.397
 78P  C5   C6    aromatic  1.392  0.020  1.392
 78P  C5   C10   single    1.488  0.020  1.488
 78P  N11  C10   single    1.339  0.020  1.339
 78P  C10  O12   double    1.228  0.020  1.228
 78P  C6   H6    single    0.930  0.020  1.080
 78P  C15  H151  single    0.970  0.020  1.090
 78P  C15  H152  single    0.970  0.020  1.090
 78P  C17  H171  single    0.970  0.020  1.090
 78P  C17  H172  single    0.970  0.020  1.090
 78P  C1   H1    single    0.930  0.020  1.080
 78P  C2   H2    single    0.930  0.020  1.080
 78P  N9   H9    single    0.860  0.020  1.020
 78P  N11  H111  single    0.860  0.020  1.020
 78P  N11  H112  single    0.860  0.020  1.020
 78P  N14  H141  single    0.890  0.020  1.040
 78P  C16  H161  single    0.970  0.020  1.090
 78P  C16  H162  single    0.970  0.020  1.090
 78P  C18  H181  single    0.970  0.020  1.090
 78P  C18  H182  single    0.970  0.020  1.090
 78P  C18  H183  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
 78P  N9    C4   C3    104.34  3.000
 78P  C3    C4   C5    122.52  3.000
 78P  N9    C4   C5    133.14  3.000
 78P  C10   C5   C6    124.91  3.000
 78P  C10   C5   C4    119.24  3.000
 78P  C6    C5   C4    115.85  3.000
 78P  H6    C6   C1    117.20  3.000
 78P  H6    C6   C5    120.64  3.000
 78P  C1    C6   C5    122.16  3.000
 78P  N9    C8   N7    112.76  3.000
 78P  N9    C8   C13   121.36  3.000
 78P  N7    C8   C13   125.82  3.000
 78P  O12   C10  N11   122.14  3.000
 78P  O12   C10  C5    120.17  3.000
 78P  N11   C10  C5    117.69  3.000
 78P  C18   C13  N14   109.66  3.000
 78P  N14   C13  C17   104.57  3.000
 78P  C18   C13  C17   110.78  3.000
 78P  N14   C13  C8    110.03  3.000
 78P  C17   C13  C8    113.30  3.000
 78P  C18   C13  C8    108.43  3.000
 78P  H152  C15  H151  106.87  3.000
 78P  H152  C15  C16   110.54  3.000
 78P  H151  C15  C16   112.60  3.000
 78P  H152  C15  N14   110.08  3.000
 78P  H151  C15  N14   109.27  3.000
 78P  C16   C15  N14   107.49  3.000
 78P  H172  C17  H171  107.44  3.000
 78P  H172  C17  C16   110.69  3.000
 78P  H171  C17  C16   113.43  3.000
 78P  H172  C17  C13   109.37  3.000
 78P  H171  C17  C13   113.13  3.000
 78P  C16   C17  C13   102.75  3.000
 78P  H1    C1   C2    119.78  3.000
 78P  H1    C1   C6    118.85  3.000
 78P  C2    C1   C6    121.37  3.000
 78P  H2    C2   C3    120.85  3.000
 78P  H2    C2   C1    121.25  3.000
 78P  C3    C2   C1    117.90  3.000
 78P  N7    C3   C2    129.72  3.000
 78P  C2    C3   C4    120.20  3.000
 78P  N7    C3   C4    110.08  3.000
 78P  C3    N7   C8    105.16  3.000
 78P  H9    N9   C8    126.57  3.000
 78P  H9    N9   C4    125.76  3.000
 78P  C8    N9   C4    107.67  3.000
 78P  H112  N11  H111  116.80  3.000
 78P  H112  N11  C10   119.43  3.000
 78P  H111  N11  C10   123.63  3.000
 78P  H141  N14  C15   107.40  3.000
 78P  H141  N14  C13   107.99  3.000
 78P  C15   N14  C13   105.13  3.000
 78P  H162  C16  H161  106.92  3.000
 78P  H162  C16  C17   111.40  3.000
 78P  H161  C16  C17   111.39  3.000
 78P  H162  C16  C15   110.77  3.000
 78P  H161  C16  C15   111.97  3.000
 78P  C17   C16  C15   104.48  3.000
 78P  H183  C18  H182  108.48  3.000
 78P  H183  C18  H181  107.60  3.000
 78P  H182  C18  H181  107.88  3.000
 78P  H183  C18  C13   110.49  3.000
 78P  H182  C18  C13   111.13  3.000
 78P  H181  C18  C13   111.13  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
 78P  CONST_01  N7    C8   N9   C4      0.00   0.0  0
 78P  CONST_02  C8    N7   C3   C4      0.00   0.0  0
 78P  CONST_03  C1    C2   C3   C4      0.00   0.0  0
 78P  CONST_04  C1    C6   C5   C4      0.00   0.0  0
 78P  CONST_05  C8    N9   C4   C5    180.00   0.0  0
 78P  CONST_06  N7    C3   C4   C5    180.00   0.0  0
 78P  CONST_07  C2    C3   C4   C5      0.00   0.0  0
 78P  CONST_08  C2    C1   C6   C5      0.00   0.0  0
 78P  CONST_09  C3    C2   C1   C6      0.00   0.0  0
 78P  CONST_10  N9    C4   C5   C6    180.00   0.0  0
 78P  CONST_11  C3    C4   C5   C6      0.00   0.0  0
 78P  CONST_12  C2    C3   N7   C8    180.00   0.0  0
 78P  CONST_13  C3    C4   N9   C8      0.00   0.0  0
 78P  CONST_14  N7    C3   C2   C1    180.00   0.0  0
 78P  CONST_15  N9    C4   C3   C2    180.00   0.0  0
 78P  CONST_16  N9    C8   N7   C3      0.00   0.0  0
 78P  CONST_17  N9    C4   C3   N7      0.00   0.0  0
 78P  CONST_18  C13   C8   N9   C4    180.00   0.0  0
 78P  CONST_19  C3    N7   C8   C13   180.00   0.0  0
 78P  CONST_20  N9    C4   C5   C10     0.00   0.0  0
 78P  CONST_21  C3    C4   C5   C10   180.00   0.0  0
 78P  CONST_22  C1    C6   C5   C10   180.00   0.0  0
 78P  CONST_23  H2    C2   C3   C4    180.00   0.0  0
 78P  CONST_24  H6    C6   C5   C4    180.00   0.0  0
 78P  CONST_25  H9    N9   C4   C5      0.00   0.0  0
 78P  CONST_26  H1    C1   C6   C5    180.00   0.0  0
 78P  CONST_27  H111  N11  C10  C5      0.00   0.0  0
 78P  CONST_28  H112  N11  C10  C5    180.00   0.0  0
 78P  Var_01    C15   C16  C17  C13   -21.69  30.0  1
 78P  Var_02    C16   C15  N14  C13    24.81  30.0  1
 78P  Var_03    N14   C15  C16  C17    -1.07  30.0  1
 78P  Var_04    N11   C10  C5   C4   -176.10  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
 78P  chir_01  C13  C17  N14  C8  negativ

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
 78P  plan-1  C4    0.020
 78P  plan-1  C5    0.020
 78P  plan-1  C6    0.020
 78P  plan-1  C8    0.020
 78P  plan-1  C10   0.020
 78P  plan-1  C13   0.020
 78P  plan-1  C1    0.020
 78P  plan-1  C2    0.020
 78P  plan-1  C3    0.020
 78P  plan-1  N7    0.020
 78P  plan-1  N9    0.020
 78P  plan-1  H6    0.020
 78P  plan-1  H1    0.020
 78P  plan-1  H2    0.020
 78P  plan-1  H9    0.020
 78P  plan-2  C5    0.020
 78P  plan-2  C10   0.020
 78P  plan-2  N11   0.020
 78P  plan-2  O12   0.020
 78P  plan-2  H111  0.020
 78P  plan-2  H112  0.020

