# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 02:16:22 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: {1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C)c(Cn2c(CO)nc3ccccc23)c1
#
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
 A7M  A7M  {1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}methanol  ligand  38  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A7M
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
 A7M  C1   C  CR6   0   0.081   1.5400  -0.2976  -0.5431
 A7M  C2   C  CR16  0  -0.346   2.6708   0.4891  -0.7311
 A7M  C3   C  CR6   0   0.100   3.8858   0.2001  -0.1170
 A7M  C4   C  CR16  0  -0.299   3.9411  -0.9178   0.7076
 A7M  C5   C  CR16  0  -0.284   2.8222  -1.7172   0.8922
 A7M  C6   C  CR6   0   0.062   1.6079  -1.4327   0.2746
 A7M  C7   C  CH2   0  -0.397   0.2738   0.0766  -1.2688
 A7M  C9   C  CH3   0  -0.746   0.4309  -2.3409   0.4850
 A7M  N10  N  NR5   0  -0.534  -0.8657   0.3000  -0.3943
 A7M  C12  C  CR56  0   0.129  -2.8585   0.1996   0.5483
 A7M  C17  C  CR16  0  -0.330  -4.1770  -0.2197   0.7235
 A7M  C18  C  CR16  0  -0.276  -4.6914  -1.1330  -0.1782
 A7M  C19  C  CR16  0  -0.275  -3.9152  -1.6252  -1.2386
 A7M  C20  C  CR16  0  -0.311  -2.6058  -1.2191  -1.4287
 A7M  O16  O  OH1   0  -0.659   0.5810   2.8265   0.1158
 A7M  C14  C  CR5   0   0.427  -0.9431   1.1209   0.6952
 A7M  C11  C  CR56  0   0.346  -2.0947  -0.3004  -0.5173
 A7M  N13  N  N     0  -0.479  -2.1093   1.0867   1.2796
 A7M  C21  C  CH3   0  -0.723   5.0824   1.0837  -0.3179
 A7M  H1   H  HCR6  0   0.246   2.6055   1.3492  -1.3885
 A7M  H2   H  HCR6  0   0.246   4.8692  -1.1774   1.2039
 A7M  H3   H  HCR6  0   0.246   2.8979  -2.5935   1.5256
 A7M  H4   H  HCH2  0   0.289   0.4407   0.9624  -1.8813
 A7M  H5   H  HCH2  0   0.283  -0.0053  -0.7257  -1.9535
 A7M  H6   H  HCH3  0   0.251  -0.3169  -1.8991   1.1460
 A7M  H7   H  HCH3  0   0.240  -0.0744  -2.5814  -0.4521
 A7M  H8   H  HCH3  0   0.256   0.7463  -3.2802   0.9373
 A7M  H9   H  HCR6  0   0.254  -4.7758   0.1628   1.5404
 A7M  H10  H  HCR6  0   0.253  -5.7115  -1.4766  -0.0678
 A7M  H11  H  HCR6  0   0.256  -4.3514  -2.3392  -1.9249
 A7M  H12  H  HCR6  0   0.269  -2.0186  -1.6072  -2.2510
 A7M  H13  H  HOH1  0   0.463   1.4870   3.1035   0.2790
 A7M  H14  H  HCH2  0   0.240   1.0091   1.3406   1.5087
 A7M  H15  H  HCH2  0   0.240  -0.1774   2.5316   2.0368
 A7M  H16  H  HCH3  0   0.247   5.1138   1.8777   0.4313
 A7M  H17  H  HCH3  0   0.243   6.0128   0.5229  -0.2335
 A7M  H18  H  HCH3  0   0.243   5.0662   1.5639  -1.2961
 A7M  C15  C  CH2   0  -0.252   0.1843   1.9750   1.1660

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
 A7M  C9   C6   single    1.502  0.020  1.502
 A7M  C5   C6   aromatic  1.392  0.020  1.392
 A7M  C5   C4   aromatic  1.387  0.020  1.387
 A7M  C6   C1   aromatic  1.401  0.020  1.401
 A7M  C4   C3   aromatic  1.390  0.020  1.390
 A7M  C1   C7   single    1.507  0.020  1.507
 A7M  C1   C2   aromatic  1.390  0.020  1.390
 A7M  C3   C2   aromatic  1.392  0.020  1.392
 A7M  C3   C21  single    1.501  0.020  1.501
 A7M  C7   N10  single    1.454  0.020  1.454
 A7M  C20  C19  aromatic  1.384  0.020  1.384
 A7M  C20  C11  aromatic  1.391  0.020  1.391
 A7M  C19  C18  aromatic  1.403  0.020  1.403
 A7M  C11  N10  aromatic  1.373  0.020  1.373
 A7M  C11  C12  aromatic  1.403  0.020  1.403
 A7M  N10  C14  aromatic  1.366  0.020  1.366
 A7M  C18  C17  aromatic  1.383  0.020  1.383
 A7M  C14  C15  single    1.491  0.020  1.491
 A7M  C14  N13  aromatic  1.305  0.020  1.305
 A7M  C12  C17  aromatic  1.395  0.020  1.395
 A7M  C12  N13  aromatic  1.372  0.020  1.372
 A7M  C15  O16  single    1.409  0.020  1.409
 A7M  C2   H1   single    0.930  0.020  1.080
 A7M  C4   H2   single    0.930  0.020  1.080
 A7M  C5   H3   single    0.930  0.020  1.080
 A7M  C7   H4   single    0.970  0.020  1.090
 A7M  C7   H5   single    0.970  0.020  1.090
 A7M  C9   H6   single    0.970  0.020  1.090
 A7M  C9   H7   single    0.970  0.020  1.090
 A7M  C9   H8   single    0.970  0.020  1.090
 A7M  C17  H9   single    0.930  0.020  1.080
 A7M  C18  H10  single    0.930  0.020  1.080
 A7M  C19  H11  single    0.930  0.020  1.080
 A7M  C20  H12  single    0.930  0.020  1.080
 A7M  O16  H13  single    0.850  0.020  0.980
 A7M  C15  H14  single    0.970  0.020  1.090
 A7M  C15  H15  single    0.970  0.020  1.090
 A7M  C21  H16  single    0.970  0.020  1.090
 A7M  C21  H17  single    0.970  0.020  1.090
 A7M  C21  H18  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
 A7M  C7   C1   C6   121.55  3.000
 A7M  C7   C1   C2   118.55  3.000
 A7M  C6   C1   C2   119.87  3.000
 A7M  H1   C2   C3   119.00  3.000
 A7M  H1   C2   C1   118.80  3.000
 A7M  C3   C2   C1   122.20  3.000
 A7M  C21  C3   C4   121.40  3.000
 A7M  C21  C3   C2   120.98  3.000
 A7M  C4   C3   C2   117.61  3.000
 A7M  H2   C4   C5   119.44  3.000
 A7M  H2   C4   C3   119.88  3.000
 A7M  C5   C4   C3   120.67  3.000
 A7M  H3   C5   C6   119.05  3.000
 A7M  H3   C5   C4   119.16  3.000
 A7M  C6   C5   C4   121.79  3.000
 A7M  C9   C6   C5   119.88  3.000
 A7M  C5   C6   C1   117.84  3.000
 A7M  C9   C6   C1   122.28  3.000
 A7M  H5   C7   H4   106.51  3.000
 A7M  H5   C7   N10  106.86  3.000
 A7M  H4   C7   N10  109.46  3.000
 A7M  H5   C7   C1   109.56  3.000
 A7M  H4   C7   C1   110.12  3.000
 A7M  N10  C7   C1   114.02  3.000
 A7M  H8   C9   H7   107.49  3.000
 A7M  H8   C9   H6   107.22  3.000
 A7M  H7   C9   H6   106.98  3.000
 A7M  H8   C9   C6   110.66  3.000
 A7M  H7   C9   C6   112.08  3.000
 A7M  H6   C9   C6   112.16  3.000
 A7M  C11  N10  C14  106.46  3.000
 A7M  C14  N10  C7   128.06  3.000
 A7M  C11  N10  C7   125.48  3.000
 A7M  N13  C12  C11  109.75  3.000
 A7M  N13  C12  C17  130.06  3.000
 A7M  C11  C12  C17  120.19  3.000
 A7M  H9   C17  C18  121.31  3.000
 A7M  H9   C17  C12  120.76  3.000
 A7M  C18  C17  C12  117.93  3.000
 A7M  H10  C18  C19  119.16  3.000
 A7M  H10  C18  C17  119.60  3.000
 A7M  C19  C18  C17  121.25  3.000
 A7M  H11  C19  C20  119.19  3.000
 A7M  H11  C19  C18  119.19  3.000
 A7M  C20  C19  C18  121.61  3.000
 A7M  H12  C20  C11  122.35  3.000
 A7M  H12  C20  C19  120.82  3.000
 A7M  C11  C20  C19  116.82  3.000
 A7M  H13  O16  C15  108.24  3.000
 A7M  N13  C14  C15  123.33  3.000
 A7M  N13  C14  N10  113.08  3.000
 A7M  C15  C14  N10  123.59  3.000
 A7M  C20  C11  C12  122.20  3.000
 A7M  C12  C11  N10  105.27  3.000
 A7M  C20  C11  N10  132.54  3.000
 A7M  C14  N13  C12  105.44  3.000
 A7M  H18  C21  H17  108.00  3.000
 A7M  H18  C21  H16  107.20  3.000
 A7M  H17  C21  H16  107.25  3.000
 A7M  H18  C21  C3   111.57  3.000
 A7M  H17  C21  C3   111.56  3.000
 A7M  H16  C21  C3   111.05  3.000
 A7M  H15  C15  H14  107.12  3.000
 A7M  H15  C15  C14  107.02  3.000
 A7M  H14  C15  C14  109.66  3.000
 A7M  H15  C15  O16  112.25  3.000
 A7M  H14  C15  O16  111.78  3.000
 A7M  C14  C15  O16  108.89  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
 A7M  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 A7M  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 A7M  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 A7M  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 A7M  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 A7M  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 A7M  CONST_07  C19  C20  C11  N10   180.00   0.0  0
 A7M  CONST_08  C17  C12  C11  N10   180.00   0.0  0
 A7M  CONST_09  N13  C12  C11  N10     0.00   0.0  0
 A7M  CONST_10  C12  N13  C14  N10     0.00   0.0  0
 A7M  CONST_11  C19  C20  C11  C12     0.00   0.0  0
 A7M  CONST_12  C14  N10  C11  C12     0.00   0.0  0
 A7M  CONST_13  C19  C18  C17  C12     0.00   0.0  0
 A7M  CONST_14  C20  C19  C18  C17     0.00   0.0  0
 A7M  CONST_15  C20  C11  C12  C17     0.00   0.0  0
 A7M  CONST_16  C14  N13  C12  C17   180.00   0.0  0
 A7M  CONST_17  C11  C20  C19  C18     0.00   0.0  0
 A7M  CONST_18  C11  C12  C17  C18     0.00   0.0  0
 A7M  CONST_19  N13  C12  C17  C18   180.00   0.0  0
 A7M  CONST_20  C14  N10  C11  C20   180.00   0.0  0
 A7M  CONST_21  N13  C12  C11  C20   180.00   0.0  0
 A7M  CONST_22  C11  C12  N13  C14     0.00   0.0  0
 A7M  CONST_23  N13  C14  N10  C11     0.00   0.0  0
 A7M  CONST_24  C21  C3   C2   C1    180.00   0.0  0
 A7M  CONST_25  C9   C6   C1   C2    180.00   0.0  0
 A7M  CONST_26  C7   C1   C2   C3    180.00   0.0  0
 A7M  CONST_27  C9   C6   C5   C4    180.00   0.0  0
 A7M  CONST_28  C7   C1   C6   C5    180.00   0.0  0
 A7M  CONST_29  C21  C3   C4   C5    180.00   0.0  0
 A7M  CONST_30  C20  C11  N10  C7      0.00   0.0  0
 A7M  CONST_31  C12  C11  N10  C7    180.00   0.0  0
 A7M  CONST_32  N13  C14  N10  C7    180.00   0.0  0
 A7M  CONST_33  C15  C14  N13  C12   180.00   0.0  0
 A7M  CONST_34  C11  N10  C14  C15   180.00   0.0  0
 A7M  CONST_35  H3   C5   C6   C1    180.00   0.0  0
 A7M  CONST_36  H2   C4   C3   C2    180.00   0.0  0
 A7M  CONST_37  H1   C2   C3   C4    180.00   0.0  0
 A7M  CONST_38  H12  C20  C11  N10     0.00   0.0  0
 A7M  CONST_39  H10  C18  C17  C12   180.00   0.0  0
 A7M  CONST_40  H11  C19  C18  C17   180.00   0.0  0
 A7M  CONST_41  H9   C17  C18  C19   180.00   0.0  0
 A7M  Var_01    C11  N10  C7   C1   -127.26  30.0  2
 A7M  Var_02    N10  C7   C1   C2   -123.04  30.0  2
 A7M  Var_03    O16  C15  C14  N10    57.25  30.0  2
 A7M  Var_04    H6   C9   C6   C1    -74.51  30.0  2
 A7M  Var_05    H16  C21  C3   C2     89.43  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
 A7M  plan-1  C1   0.020
 A7M  plan-1  C2   0.020
 A7M  plan-1  C3   0.020
 A7M  plan-1  C4   0.020
 A7M  plan-1  C5   0.020
 A7M  plan-1  C6   0.020
 A7M  plan-1  C7   0.020
 A7M  plan-1  C9   0.020
 A7M  plan-1  C21  0.020
 A7M  plan-1  H1   0.020
 A7M  plan-1  H2   0.020
 A7M  plan-1  H3   0.020
 A7M  plan-2  C7   0.020
 A7M  plan-2  N10  0.020
 A7M  plan-2  C12  0.020
 A7M  plan-2  C17  0.020
 A7M  plan-2  C18  0.020
 A7M  plan-2  C19  0.020
 A7M  plan-2  C20  0.020
 A7M  plan-2  C14  0.020
 A7M  plan-2  C11  0.020
 A7M  plan-2  N13  0.020
 A7M  plan-2  H9   0.020
 A7M  plan-2  H10  0.020
 A7M  plan-2  H11  0.020
 A7M  plan-2  H12  0.020
 A7M  plan-2  C15  0.020

