# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:03:12 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-(1-propylpiperidin-4-yl)-1H-benzimidazole-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN1CCC(CC1)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
 AAI  AAI  2-(1-propylpiperidin-4-yl)-1H-benzimidazole-7-carboxamide  ligand  43  21  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AAI
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
 AAI  C1    C  CR5   0   0.489  -0.4155  -1.0553  -0.2830
 AAI  N2    N  NR15  0  -0.695  -1.1061   0.1007  -0.0805
 AAI  C3    C  CR56  0   0.339  -2.4316  -0.2114  -0.0001
 AAI  C4    C  CR56  0   0.144  -2.4717  -1.6079  -0.1664
 AAI  N5    N  N     0  -0.475  -1.1988  -2.0979  -0.3404
 AAI  C6    C  CR6   0  -0.092  -3.5823   0.5581   0.1950
 AAI  C7    C  CR16  0  -0.331  -4.7855  -0.1427   0.2139
 AAI  C8    C  CR16  0  -0.258  -4.8389  -1.5287   0.0494
 AAI  C9    C  CR16  0  -0.337  -3.6896  -2.2780  -0.1413
 AAI  C10   C  C     0   0.521  -3.4503   2.0308   0.3597
 AAI  N11   N  NH2   0  -0.824  -4.5668   2.7363   0.5767
 AAI  O12   O  O     0  -0.495  -2.3448   2.5633   0.2947
 AAI  C13   C  CH1   0  -0.391   1.0690  -1.0820  -0.3971
 AAI  C14   C  CH2   0  -0.425   1.5976  -0.1332  -1.4749
 AAI  C15   C  CH2   0  -0.281   3.1159  -0.1839  -1.5258
 AAI  N16   N  NT    0  -0.421   3.7049   0.1531  -0.2426
 AAI  C17   C  CH2   0  -0.288   3.2614  -0.7722   0.7845
 AAI  C18   C  CH2   0  -0.418   1.7482  -0.7532   0.9354
 AAI  C19   C  CH2   0  -0.244   5.1523   0.2264  -0.3407
 AAI  C20   C  CH2   0  -0.451   5.8312   0.8257   0.8844
 AAI  C21   C  CH3   0  -0.664   7.3115   1.0786   0.6327
 AAI  H2    H  HNR5  0   0.416  -0.7326   1.0334   0.0009
 AAI  H7    H  HCR6  0   0.250  -5.7244   0.3759   0.3584
 AAI  H8    H  HCR6  0   0.262  -5.8019  -2.0206   0.0719
 AAI  H9    H  HCR6  0   0.262  -3.7366  -3.3520  -0.2663
 AAI  H111  H  HNH2  0   0.417  -5.4809   2.3265   0.6430
 AAI  H112  H  HNH2  0   0.408  -4.5079   3.7356   0.6834
 AAI  H13   H  HCH1  0   0.260   1.3356  -2.1060  -0.6759
 AAI  H141  H  HCH2  0   0.249   1.1924  -0.4023  -2.4525
 AAI  H142  H  HCH2  0   0.222   1.2838   0.8943  -1.2660
 AAI  H151  H  HCH2  0   0.189   3.4318  -1.1866  -1.8679
 AAI  H152  H  HCH2  0   0.240   3.4733   0.5274  -2.2741
 AAI  H171  H  HCH2  0   0.189   3.5944  -1.8043   0.5677
 AAI  H172  H  HCH2  0   0.245   3.7083  -0.4948   1.7397
 AAI  H181  H  HCH2  0   0.225   1.4364   0.2367   1.2827
 AAI  H182  H  HCH2  0   0.248   1.4527  -1.4729   1.7017
 AAI  H191  H  HCH2  0   0.183   5.5943  -0.7637  -0.5544
 AAI  H192  H  HCH2  0   0.221   5.3901   0.8571  -1.2031
 AAI  H201  H  HCH2  0   0.218   5.3295   1.7616   1.1451
 AAI  H202  H  HCH2  0   0.222   5.7271   0.1641   1.7477
 AAI  H211  H  HCH3  0   0.219   7.8294   0.1583   0.3556
 AAI  H212  H  HCH3  0   0.219   7.4615   1.7970  -0.1752
 AAI  H213  H  HCH3  0   0.231   7.8027   1.4746   1.5216

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
 AAI  O12  C10   double    1.229  0.020  1.229
 AAI  C10  N11   single    1.338  0.020  1.338
 AAI  C10  C6    single    1.488  0.020  1.488
 AAI  C7   C6    aromatic  1.393  0.020  1.393
 AAI  C7   C8    aromatic  1.397  0.020  1.397
 AAI  C6   C3    aromatic  1.398  0.020  1.398
 AAI  C8   C9    aromatic  1.385  0.020  1.385
 AAI  C3   N2    aromatic  1.364  0.020  1.364
 AAI  C3   C4    aromatic  1.407  0.020  1.407
 AAI  N2   C1    aromatic  1.362  0.020  1.362
 AAI  C9   C4    aromatic  1.390  0.020  1.390
 AAI  C4   N5    aromatic  1.375  0.020  1.375
 AAI  C1   N5    aromatic  1.305  0.020  1.305
 AAI  C1   C13   single    1.489  0.020  1.489
 AAI  C13  C18   single    1.531  0.020  1.531
 AAI  C13  C14   single    1.530  0.020  1.530
 AAI  C18  C17   single    1.521  0.020  1.521
 AAI  C14  C15   single    1.520  0.020  1.520
 AAI  C17  N16   single    1.452  0.020  1.452
 AAI  C15  N16   single    1.452  0.020  1.452
 AAI  N16  C19   single    1.453  0.020  1.453
 AAI  C20  C19   single    1.523  0.020  1.523
 AAI  C20  C21   single    1.523  0.020  1.523
 AAI  N2   H2    single    0.860  0.020  1.020
 AAI  C7   H7    single    0.930  0.020  1.080
 AAI  C8   H8    single    0.930  0.020  1.080
 AAI  C9   H9    single    0.930  0.020  1.080
 AAI  N11  H111  single    0.860  0.020  1.020
 AAI  N11  H112  single    0.860  0.020  1.020
 AAI  C13  H13   single    0.970  0.020  1.090
 AAI  C14  H141  single    0.970  0.020  1.090
 AAI  C14  H142  single    0.970  0.020  1.090
 AAI  C15  H151  single    0.970  0.020  1.090
 AAI  C15  H152  single    0.970  0.020  1.090
 AAI  C17  H171  single    0.970  0.020  1.090
 AAI  C17  H172  single    0.970  0.020  1.090
 AAI  C18  H181  single    0.970  0.020  1.090
 AAI  C18  H182  single    0.970  0.020  1.090
 AAI  C19  H191  single    0.970  0.020  1.090
 AAI  C19  H192  single    0.970  0.020  1.090
 AAI  C20  H201  single    0.970  0.020  1.090
 AAI  C20  H202  single    0.970  0.020  1.090
 AAI  C21  H211  single    0.970  0.020  1.090
 AAI  C21  H212  single    0.970  0.020  1.090
 AAI  C21  H213  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
 AAI  C13   C1   N5    125.49  3.000
 AAI  C13   C1   N2    122.15  3.000
 AAI  N5    C1   N2    112.35  3.000
 AAI  H2    N2   C3    124.54  3.000
 AAI  H2    N2   C1    127.56  3.000
 AAI  C3    N2   C1    107.90  3.000
 AAI  C6    C3   C4    122.64  3.000
 AAI  C4    C3   N2    104.35  3.000
 AAI  C6    C3   N2    133.01  3.000
 AAI  C9    C4   N5    129.91  3.000
 AAI  N5    C4   C3    110.01  3.000
 AAI  C9    C4   C3    120.08  3.000
 AAI  C4    N5   C1    105.39  3.000
 AAI  C10   C6   C7    124.98  3.000
 AAI  C7    C6   C3    115.85  3.000
 AAI  C10   C6   C3    119.16  3.000
 AAI  H7    C7   C8    117.26  3.000
 AAI  H7    C7   C6    120.68  3.000
 AAI  C8    C7   C6    122.06  3.000
 AAI  H8    C8   C9    119.71  3.000
 AAI  H8    C8   C7    118.88  3.000
 AAI  C9    C8   C7    121.42  3.000
 AAI  H9    C9   C8    121.11  3.000
 AAI  H9    C9   C4    120.95  3.000
 AAI  C8    C9   C4    117.94  3.000
 AAI  O12   C10  N11   122.05  3.000
 AAI  N11   C10  C6    117.76  3.000
 AAI  O12   C10  C6    120.19  3.000
 AAI  H112  N11  H111  116.84  3.000
 AAI  H112  N11  C10   119.45  3.000
 AAI  H111  N11  C10   123.72  3.000
 AAI  H13   C13  C18   108.33  3.000
 AAI  H13   C13  C14   108.46  3.000
 AAI  C18   C13  C14   109.06  3.000
 AAI  H13   C13  C1    106.21  3.000
 AAI  C14   C13  C1    112.78  3.000
 AAI  C18   C13  C1    111.82  3.000
 AAI  H142  C14  H141  107.20  3.000
 AAI  H142  C14  C15   108.91  3.000
 AAI  H141  C14  C15   109.42  3.000
 AAI  H142  C14  C13   110.40  3.000
 AAI  H141  C14  C13   110.47  3.000
 AAI  C15   C14  C13   110.37  3.000
 AAI  H152  C15  H151  106.56  3.000
 AAI  H152  C15  N16   108.76  3.000
 AAI  H151  C15  N16   111.60  3.000
 AAI  H152  C15  C14   109.15  3.000
 AAI  H151  C15  C14   109.03  3.000
 AAI  N16   C15  C14   111.59  3.000
 AAI  C19   N16  C17   112.60  3.000
 AAI  C19   N16  C15   110.87  3.000
 AAI  C17   N16  C15   110.70  3.000
 AAI  H172  C17  H171  106.60  3.000
 AAI  H172  C17  C18   108.52  3.000
 AAI  H171  C17  C18   109.31  3.000
 AAI  H172  C17  N16   109.42  3.000
 AAI  H171  C17  N16   111.35  3.000
 AAI  C18   C17  N16   111.48  3.000
 AAI  H182  C18  H181  107.24  3.000
 AAI  H182  C18  C17   109.31  3.000
 AAI  H181  C18  C17   109.04  3.000
 AAI  H182  C18  C13   110.43  3.000
 AAI  H181  C18  C13   110.11  3.000
 AAI  C17   C18  C13   110.63  3.000
 AAI  H192  C19  H191  106.08  3.000
 AAI  H192  C19  C20   108.07  3.000
 AAI  H191  C19  C20   109.25  3.000
 AAI  H192  C19  N16   107.39  3.000
 AAI  H191  C19  N16   111.49  3.000
 AAI  C20   C19  N16   114.18  3.000
 AAI  H202  C20  H201  106.63  3.000
 AAI  H202  C20  C21   108.89  3.000
 AAI  H201  C20  C21   110.08  3.000
 AAI  H202  C20  C19   110.78  3.000
 AAI  H201  C20  C19   108.90  3.000
 AAI  C21   C20  C19   111.45  3.000
 AAI  H213  C21  H212  107.61  3.000
 AAI  H213  C21  H211  107.43  3.000
 AAI  H212  C21  H211  107.57  3.000
 AAI  H213  C21  C20   111.32  3.000
 AAI  H212  C21  C20   111.42  3.000
 AAI  H211  C21  C20   111.29  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
 AAI  CONST_01  C6    C3   N2   C1    180.00   0.0  0
 AAI  CONST_02  C4    C3   N2   C1      0.00   0.0  0
 AAI  CONST_03  C3    C4   N5   C1      0.00   0.0  0
 AAI  CONST_04  C9    C4   N5   C1    180.00   0.0  0
 AAI  CONST_05  C7    C6   C3   N2    180.00   0.0  0
 AAI  CONST_06  C9    C4   C3   N2    180.00   0.0  0
 AAI  CONST_07  N5    C4   C3   N2      0.00   0.0  0
 AAI  CONST_08  C4    N5   C1   N2      0.00   0.0  0
 AAI  CONST_09  C8    C7   C6   C3      0.00   0.0  0
 AAI  CONST_10  N5    C1   N2   C3      0.00   0.0  0
 AAI  CONST_11  C8    C9   C4   C3      0.00   0.0  0
 AAI  CONST_12  C7    C6   C3   C4      0.00   0.0  0
 AAI  CONST_13  C7    C8   C9   C4      0.00   0.0  0
 AAI  CONST_14  C6    C3   C4   N5    180.00   0.0  0
 AAI  CONST_15  C8    C9   C4   N5    180.00   0.0  0
 AAI  CONST_16  C9    C8   C7   C6      0.00   0.0  0
 AAI  CONST_17  C9    C4   C3   C6      0.00   0.0  0
 AAI  CONST_18  C13   C1   N2   C3    180.00   0.0  0
 AAI  CONST_19  C13   C1   N5   C4    180.00   0.0  0
 AAI  CONST_20  C10   C6   C3   N2      0.00   0.0  0
 AAI  CONST_21  C10   C6   C3   C4    180.00   0.0  0
 AAI  CONST_22  C10   C6   C7   C8    180.00   0.0  0
 AAI  CONST_23  H7    C7   C6   C3    180.00   0.0  0
 AAI  CONST_24  H9    C9   C4   C3    180.00   0.0  0
 AAI  CONST_25  H2    N2   C3   C4    180.00   0.0  0
 AAI  CONST_26  H8    C8   C9   C4    180.00   0.0  0
 AAI  CONST_27  H111  N11  C10  C6      0.00   0.0  0
 AAI  CONST_28  H112  N11  C10  C6    180.00   0.0  0
 AAI  Var_01    N16   C17  C18  C13    57.16  30.0  1
 AAI  Var_02    N16   C15  C14  C13   -57.64  30.0  1
 AAI  Var_03    C17   N16  C15  C14    59.79  30.0  1
 AAI  Var_04    C18   C17  N16  C15   -59.44  30.0  1
 AAI  Var_05    O12   C10  C6   C3      1.61  30.0  3
 AAI  Var_06    C20   C19  N16  C15   169.12  30.0  3
 AAI  Var_07    C21   C20  C19  N16  -170.93  30.0  1
 AAI  Var_08    H211  C21  C20  C19   -58.20  30.0  3

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
 AAI  chir_01  C13  C1  C18  C14  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
 AAI  plan-1  C1    0.020
 AAI  plan-1  N2    0.020
 AAI  plan-1  C3    0.020
 AAI  plan-1  C4    0.020
 AAI  plan-1  N5    0.020
 AAI  plan-1  C6    0.020
 AAI  plan-1  C7    0.020
 AAI  plan-1  C8    0.020
 AAI  plan-1  C9    0.020
 AAI  plan-1  C10   0.020
 AAI  plan-1  C13   0.020
 AAI  plan-1  H2    0.020
 AAI  plan-1  H7    0.020
 AAI  plan-1  H8    0.020
 AAI  plan-1  H9    0.020
 AAI  plan-2  C6    0.020
 AAI  plan-2  C10   0.020
 AAI  plan-2  N11   0.020
 AAI  plan-2  O12   0.020
 AAI  plan-2  H111  0.020
 AAI  plan-2  H112  0.020

