# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 09:28:52 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-[(3,5-dichlorophenyl)methyl]-3-[(1H-imidazol-1-yl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)cc(CNC(=O)c2cccc(Cn3ccnc3)c2)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
 HHM  HHM  N-[(3,5-dichlorophenyl)methyl]-3-[(1H-imidazol-1-yl)methyl]benzamide  ligand  39  24  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HHM
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
 HHM  C21  C   CR6   0  -0.024   4.2863   0.9946  -0.7139
 HHM  C11  C   CR6   0   0.086   3.1009  -0.2767   0.9343
 HHM  C22  C   CR16  0  -0.248   3.0990   0.6800  -0.0735
 HHM  C01  C   CR16  0  -0.226  -2.3967   0.1056  -2.0279
 HHM  C02  C   CR16  0  -0.278  -3.6407   0.4930  -1.5589
 HHM  C03  C   CR6   0   0.127  -3.8080   0.8502  -0.2228
 HHM  C04  C   CR16  0  -0.333  -2.7145   0.8139   0.6281
 HHM  C05  C   CR6   0  -0.017  -1.4623   0.4102   0.1683
 HHM  C06  C   CR16  0  -0.302  -1.3067   0.0596  -1.1686
 HHM  C07  C   C     0   0.531  -0.3226   0.4175   1.1362
 HHM  N08  N   NH1   0  -0.651   0.6453  -0.4887   0.8987
 HHM  O09  O   O     0  -0.477  -0.2969   1.2012   2.0736
 HHM  C10  C   CH2   0  -0.336   1.8391  -0.6209   1.6904
 HHM  N13  N   NR5   0  -0.398  -6.2196   0.4065  -0.0883
 HHM  C14  C   CR15  0  -0.099  -6.3699  -0.8926   0.3097
 HHM  C15  C   CR15  0  -0.215  -7.4939  -1.3391  -0.3234
 HHM  N16  N   N     0  -0.456  -8.0278  -0.3472  -1.0973
 HHM  C17  C   CR15  0   0.096  -7.2368   0.6812  -0.9331
 HHM  C18  C   CR16  0  -0.255   4.2906  -0.9058   1.2837
 HHM  C19  C   CR6   0  -0.028   5.4612  -0.5665   0.6266
 HHM  C20  C   CR16  0  -0.190   5.4845   0.3838  -0.3818
 HHM  CL2  CL  CL    0  -0.113   4.2779   2.1863  -1.9692
 HHM  CL1  CL  CL    0  -0.113   6.9368  -1.3576   1.0634
 HHM  H1   H   HCR6  0   0.277   2.1820   1.1751  -0.3636
 HHM  H2   H   HCR6  0   0.268  -2.2697  -0.1550  -3.0700
 HHM  H3   H   HCR6  0   0.263  -4.4825   0.5200  -2.2403
 HHM  H4   H   HCR6  0   0.261  -2.8381   1.0906   1.6679
 HHM  H5   H   HCR6  0   0.263  -0.3400  -0.2257  -1.5640
 HHM  H6   H   HNH1  0   0.417   0.5036  -1.1763   0.1763
 HHM  H7   H   HCH2  0   0.277   1.9119  -1.6410   2.0715
 HHM  H8   H   HCH2  0   0.283   1.7530   0.0318   2.5593
 HHM  H9   H   HCH2  0   0.286  -5.1267   1.3972   1.3780
 HHM  H10  H   HCH2  0   0.291  -5.3947   2.2885  -0.1080
 HHM  H11  H   HCR5  0   0.292  -5.6854  -1.3713   0.9901
 HHM  H12  H   HCR5  0   0.251  -7.9423  -2.3188  -0.2604
 HHM  H13  H   HCR5  0   0.283  -7.3482   1.6516  -1.3944
 HHM  H14  H   HCR6  0   0.283   4.3022  -1.6585   2.0613
 HHM  H15  H   HCR6  0   0.301   6.4025   0.6352  -0.8941
 HHM  C12  C   CH2   0  -0.378  -5.1501   1.3034   0.2919

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
 HHM  N16  C15  aromatic  1.367  0.020  1.367
 HHM  N16  C17  aromatic  1.308  0.020  1.308
 HHM  C15  C14  aromatic  1.365  0.020  1.365
 HHM  C17  N13  aromatic  1.350  0.020  1.350
 HHM  C14  N13  aromatic  1.367  0.020  1.367
 HHM  N13  C12  single    1.447  0.020  1.447
 HHM  C12  C03  single    1.507  0.020  1.507
 HHM  C03  C02  aromatic  1.393  0.020  1.393
 HHM  C03  C04  aromatic  1.386  0.020  1.386
 HHM  C02  C01  aromatic  1.385  0.020  1.385
 HHM  C04  C05  aromatic  1.394  0.020  1.394
 HHM  C01  C06  aromatic  1.389  0.020  1.389
 HHM  C05  C06  aromatic  1.391  0.020  1.391
 HHM  C05  C07  single    1.495  0.020  1.495
 HHM  CL1  C19  single    1.730  0.020  1.730
 HHM  O09  C07  double    1.222  0.020  1.222
 HHM  C07  N08  single    1.347  0.020  1.347
 HHM  C19  C18  aromatic  1.385  0.020  1.385
 HHM  C19  C20  aromatic  1.386  0.020  1.386
 HHM  C18  C11  aromatic  1.390  0.020  1.390
 HHM  N08  C10  single    1.439  0.020  1.439
 HHM  C20  C21  aromatic  1.385  0.020  1.385
 HHM  C11  C10  single    1.511  0.020  1.511
 HHM  C11  C22  aromatic  1.390  0.020  1.390
 HHM  C21  C22  aromatic  1.385  0.020  1.385
 HHM  C21  CL2  single    1.731  0.020  1.731
 HHM  C22  H1   single    0.930  0.020  1.080
 HHM  C01  H2   single    0.930  0.020  1.080
 HHM  C02  H3   single    0.930  0.020  1.080
 HHM  C04  H4   single    0.930  0.020  1.080
 HHM  C06  H5   single    0.930  0.020  1.080
 HHM  N08  H6   single    0.860  0.020  1.020
 HHM  C10  H7   single    0.970  0.020  1.090
 HHM  C10  H8   single    0.970  0.020  1.090
 HHM  C12  H9   single    0.970  0.020  1.090
 HHM  C12  H10  single    0.970  0.020  1.090
 HHM  C14  H11  single    0.930  0.020  1.080
 HHM  C15  H12  single    0.930  0.020  1.080
 HHM  C17  H13  single    0.930  0.020  1.080
 HHM  C18  H14  single    0.930  0.020  1.080
 HHM  C20  H15  single    0.930  0.020  1.080

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
 HHM  CL2  C21  C20  118.79  3.000
 HHM  CL2  C21  C22  119.17  3.000
 HHM  C20  C21  C22  122.03  3.000
 HHM  C18  C11  C10  119.07  3.000
 HHM  C10  C11  C22  121.24  3.000
 HHM  C18  C11  C22  119.66  3.000
 HHM  H1   C22  C11  120.72  3.000
 HHM  H1   C22  C21  119.91  3.000
 HHM  C11  C22  C21  119.37  3.000
 HHM  H2   C01  C06  119.73  3.000
 HHM  H2   C01  C02  119.95  3.000
 HHM  C06  C01  C02  120.31  3.000
 HHM  H3   C02  C03  120.24  3.000
 HHM  H3   C02  C01  119.47  3.000
 HHM  C03  C02  C01  120.30  3.000
 HHM  C12  C03  C04  120.06  3.000
 HHM  C04  C03  C02  119.16  3.000
 HHM  C12  C03  C02  120.77  3.000
 HHM  H4   C04  C05  119.56  3.000
 HHM  H4   C04  C03  119.51  3.000
 HHM  C05  C04  C03  120.93  3.000
 HHM  C07  C05  C06  122.56  3.000
 HHM  C07  C05  C04  118.03  3.000
 HHM  C06  C05  C04  119.38  3.000
 HHM  H5   C06  C05  121.16  3.000
 HHM  H5   C06  C01  118.91  3.000
 HHM  C05  C06  C01  119.91  3.000
 HHM  O09  C07  N08  123.48  3.000
 HHM  N08  C07  C05  115.49  3.000
 HHM  O09  C07  C05  121.04  3.000
 HHM  H6   N08  C10  116.66  3.000
 HHM  H6   N08  C07  118.98  3.000
 HHM  C10  N08  C07  124.13  3.000
 HHM  H8   C10  H7   106.65  3.000
 HHM  H8   C10  N08  108.55  3.000
 HHM  H7   C10  N08  109.48  3.000
 HHM  H8   C10  C11  109.18  3.000
 HHM  H7   C10  C11  109.39  3.000
 HHM  N08  C10  C11  113.37  3.000
 HHM  C17  N13  C14  107.02  3.000
 HHM  C14  N13  C12  126.44  3.000
 HHM  C17  N13  C12  126.52  3.000
 HHM  H11  C14  C15  132.12  3.000
 HHM  H11  C14  N13  122.43  3.000
 HHM  C15  C14  N13  105.45  3.000
 HHM  H12  C15  N16  121.98  3.000
 HHM  H12  C15  C14  127.73  3.000
 HHM  N16  C15  C14  110.29  3.000
 HHM  C17  N16  C15  105.27  3.000
 HHM  H13  C17  N16  126.19  3.000
 HHM  H13  C17  N13  121.84  3.000
 HHM  N16  C17  N13  111.97  3.000
 HHM  H14  C18  C19  120.16  3.000
 HHM  H14  C18  C11  120.29  3.000
 HHM  C19  C18  C11  119.56  3.000
 HHM  CL1  C19  C20  118.87  3.000
 HHM  C20  C19  C18  121.84  3.000
 HHM  CL1  C19  C18  119.28  3.000
 HHM  H15  C20  C19  121.25  3.000
 HHM  H15  C20  C21  121.22  3.000
 HHM  C19  C20  C21  117.53  3.000
 HHM  H10  C12  H9   106.99  3.000
 HHM  H10  C12  N13  107.32  3.000
 HHM  H9   C12  N13  109.33  3.000
 HHM  H10  C12  C03  110.25  3.000
 HHM  H9   C12  C03  110.29  3.000
 HHM  N13  C12  C03  112.47  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
 HHM  CONST_01  C18  C19  C20  C21     0.00   0.0  0
 HHM  CONST_02  C18  C11  C22  C21     0.00   0.0  0
 HHM  CONST_03  C20  C19  C18  C11     0.00   0.0  0
 HHM  CONST_04  C20  C21  C22  C11     0.00   0.0  0
 HHM  CONST_05  C19  C18  C11  C22     0.00   0.0  0
 HHM  CONST_06  C19  C20  C21  C22     0.00   0.0  0
 HHM  CONST_07  C04  C03  C02  C01     0.00   0.0  0
 HHM  CONST_08  C04  C05  C06  C01     0.00   0.0  0
 HHM  CONST_09  C05  C04  C03  C02     0.00   0.0  0
 HHM  CONST_10  C05  C06  C01  C02     0.00   0.0  0
 HHM  CONST_11  C06  C01  C02  C03     0.00   0.0  0
 HHM  CONST_12  C06  C05  C04  C03     0.00   0.0  0
 HHM  CONST_13  C15  N16  C17  N13     0.00   0.0  0
 HHM  CONST_14  N16  C15  C14  N13     0.00   0.0  0
 HHM  CONST_15  C17  N16  C15  C14     0.00   0.0  0
 HHM  CONST_16  N16  C17  N13  C14     0.00   0.0  0
 HHM  CONST_17  C17  N13  C14  C15     0.00   0.0  0
 HHM  CONST_18  CL1  C19  C20  C21   180.00   0.0  0
 HHM  CONST_19  C10  C11  C22  C21   180.00   0.0  0
 HHM  CONST_20  CL1  C19  C18  C11   180.00   0.0  0
 HHM  CONST_21  CL2  C21  C22  C11   180.00   0.0  0
 HHM  CONST_22  C12  C03  C02  C01   180.00   0.0  0
 HHM  CONST_23  C07  C05  C06  C01   180.00   0.0  0
 HHM  CONST_24  C07  C05  C04  C03   180.00   0.0  0
 HHM  CONST_25  C12  C03  C04  C05   180.00   0.0  0
 HHM  CONST_26  C19  C18  C11  C10   180.00   0.0  0
 HHM  CONST_27  N16  C17  N13  C12   180.00   0.0  0
 HHM  CONST_28  C15  C14  N13  C12   180.00   0.0  0
 HHM  CONST_29  CL2  C21  C20  C19   180.00   0.0  0
 HHM  CONST_30  H14  C18  C11  C22   180.00   0.0  0
 HHM  CONST_31  H15  C20  C21  C22   180.00   0.0  0
 HHM  CONST_32  H4   C04  C03  C02   180.00   0.0  0
 HHM  CONST_33  H5   C06  C01  C02   180.00   0.0  0
 HHM  CONST_34  H2   C01  C02  C03   180.00   0.0  0
 HHM  CONST_35  H3   C02  C03  C04   180.00   0.0  0
 HHM  CONST_36  H12  C15  C14  N13   180.00   0.0  0
 HHM  CONST_37  H13  C17  N13  C14   180.00   0.0  0
 HHM  CONST_38  H11  C14  C15  N16   180.00   0.0  0
 HHM  CONST_39  H1   C22  C11  C18   180.00   0.0  0
 HHM  CONST_40  C10  N08  C07  C05   180.00   0.0  0
 HHM  CONST_41  H6   N08  C07  C05     0.00   0.0  0
 HHM  CONST_42  C10  N08  C07  O09     0.00   0.0  0
 HHM  Var_01    N13  C12  C03  C02    49.31  30.0  2
 HHM  Var_02    C17  N13  C12  C03  -113.06  30.0  2
 HHM  Var_03    N08  C10  C11  C22    31.48  30.0  2
 HHM  Var_04    O09  C07  C05  C04   -28.89  30.0  2
 HHM  Var_05    C07  N08  C10  C11  -114.29  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
 HHM  plan-1  N13  0.020
 HHM  plan-1  C14  0.020
 HHM  plan-1  C15  0.020
 HHM  plan-1  N16  0.020
 HHM  plan-1  C17  0.020
 HHM  plan-1  H11  0.020
 HHM  plan-1  H12  0.020
 HHM  plan-1  H13  0.020
 HHM  plan-1  C12  0.020
 HHM  plan-2  C01  0.020
 HHM  plan-2  C02  0.020
 HHM  plan-2  C03  0.020
 HHM  plan-2  C04  0.020
 HHM  plan-2  C05  0.020
 HHM  plan-2  C06  0.020
 HHM  plan-2  C07  0.020
 HHM  plan-2  H2   0.020
 HHM  plan-2  H3   0.020
 HHM  plan-2  H4   0.020
 HHM  plan-2  H5   0.020
 HHM  plan-2  C12  0.020
 HHM  plan-3  C21  0.020
 HHM  plan-3  C11  0.020
 HHM  plan-3  C22  0.020
 HHM  plan-3  C10  0.020
 HHM  plan-3  C18  0.020
 HHM  plan-3  C19  0.020
 HHM  plan-3  C20  0.020
 HHM  plan-3  CL2  0.020
 HHM  plan-3  CL1  0.020
 HHM  plan-3  H1   0.020
 HHM  plan-3  H14  0.020
 HHM  plan-3  H15  0.020
 HHM  plan-4  C05  0.020
 HHM  plan-4  C07  0.020
 HHM  plan-4  N08  0.020
 HHM  plan-4  O09  0.020
 HHM  plan-4  C10  0.020
 HHM  plan-4  H6   0.020

