# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 00:16:17 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 1-pentyl-4-phenyl-imidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCn1cc(nc1N)c2ccccc2
#
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
 MBL  MBL  1-pentyl-4-phenyl-imidazol-2-amine  ligand  36  17  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MBL
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
 MBL  N2   N  NH2   0  -0.858  -1.0902   2.7858  -0.0875
 MBL  C8   C  CR5   0   0.601  -0.3135   1.6550  -0.1746
 MBL  N    N  NR5   0  -0.454  -0.7960   0.4853  -0.6593
 MBL  C9   C  CH2   0  -0.319  -2.1662   0.2001  -1.0312
 MBL  C10  C  CH2   0  -0.432  -3.0249  -0.2136   0.1564
 MBL  C11  C  CH2   0  -0.415  -4.4532  -0.5419  -0.2578
 MBL  C12  C  CH2   0  -0.420  -5.3263  -0.9665   0.9162
 MBL  C13  C  CH3   0  -0.662  -6.7510  -1.3057   0.5010
 MBL  C7   C  CR15  0  -0.128   0.2521  -0.4043  -0.6622
 MBL  N1   N  N     0  -0.518   0.9619   1.5788   0.1057
 MBL  C6   C  CR5   0   0.148   1.3331   0.2896  -0.1989
 MBL  C3   C  CR6   0   0.044   2.7057  -0.1753  -0.0209
 MBL  C1   C  CR16  0  -0.344   3.0534  -1.5139  -0.2298
 MBL  C5   C  CR16  0  -0.311   3.7096   0.7143   0.3683
 MBL  C4   C  CR16  0  -0.239   5.0169   0.2813   0.5386
 MBL  C2   C  CR16  0  -0.276   5.3507  -1.0494   0.3252
 MBL  C    C  CR16  0  -0.236   4.3592  -1.9447  -0.0603
 MBL  H1   H  HNH2  0   0.390  -2.0176   2.6476   0.2876
 MBL  H2   H  HNH2  0   0.388  -0.6219   3.5290   0.4083
 MBL  H3   H  HCH2  0   0.261  -2.5800   1.0852  -1.5199
 MBL  H4   H  HCH2  0   0.268  -2.1477  -0.5911  -1.7812
 MBL  H5   H  HCH2  0   0.234  -2.5691  -1.0827   0.6395
 MBL  H6   H  HCH2  0   0.225  -3.0334   0.5863   0.9045
 MBL  H7   H  HCH2  0   0.217  -4.9018   0.3289  -0.7482
 MBL  H8   H  HCH2  0   0.217  -4.4397  -1.3405  -1.0075
 MBL  H9   H  HCH2  0   0.214  -4.8733  -1.8329   1.4080
 MBL  H10  H  HCH2  0   0.215  -5.3424  -0.1678   1.6639
 MBL  H11  H  HCH3  0   0.227  -7.3529  -1.6130   1.3571
 MBL  H12  H  HCH3  0   0.217  -7.2459  -0.4478   0.0421
 MBL  H13  H  HCH3  0   0.217  -6.7679  -2.1225  -0.2229
 MBL  H14  H  HCR5  0   0.284   0.1242  -1.4208  -0.9960
 MBL  H15  H  HCR6  0   0.240   2.2964  -2.2315  -0.5227
 MBL  H16  H  HCR6  0   0.245   3.4610   1.7538   0.5369
 MBL  H17  H  HCR6  0   0.252   5.7796   0.9894   0.8379
 MBL  H18  H  HCR6  0   0.252   6.3706  -1.3861   0.4589
 MBL  H19  H  HCR6  0   0.254   4.6031  -2.9861  -0.2278

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
 MBL  C    C1   aromatic  1.385  0.020  1.385
 MBL  C    C2   aromatic  1.390  0.020  1.390
 MBL  C1   C3   aromatic  1.399  0.020  1.399
 MBL  C2   C4   aromatic  1.388  0.020  1.388
 MBL  C7   C6   aromatic  1.366  0.020  1.366
 MBL  C7   N    aromatic  1.375  0.020  1.375
 MBL  C3   C6   single    1.460  0.020  1.460
 MBL  C3   C5   aromatic  1.397  0.020  1.397
 MBL  C11  C12  single    1.523  0.020  1.523
 MBL  C11  C10  single    1.523  0.020  1.523
 MBL  C13  C12  single    1.522  0.020  1.522
 MBL  C4   C5   aromatic  1.388  0.020  1.388
 MBL  C9   N    single    1.448  0.020  1.448
 MBL  C9   C10  single    1.523  0.020  1.523
 MBL  C6   N1   aromatic  1.376  0.020  1.376
 MBL  N    C8   aromatic  1.355  0.020  1.355
 MBL  N1   C8   aromatic  1.308  0.020  1.308
 MBL  C8   N2   single    1.375  0.020  1.375
 MBL  N2   H1   single    0.890  0.020  1.040
 MBL  N2   H2   single    0.890  0.020  1.040
 MBL  C9   H3   single    0.970  0.020  1.090
 MBL  C9   H4   single    0.970  0.020  1.090
 MBL  C10  H5   single    0.970  0.020  1.090
 MBL  C10  H6   single    0.970  0.020  1.090
 MBL  C11  H7   single    0.970  0.020  1.090
 MBL  C11  H8   single    0.970  0.020  1.090
 MBL  C12  H9   single    0.970  0.020  1.090
 MBL  C12  H10  single    0.970  0.020  1.090
 MBL  C13  H11  single    0.970  0.020  1.090
 MBL  C13  H12  single    0.970  0.020  1.090
 MBL  C13  H13  single    0.970  0.020  1.090
 MBL  C7   H14  single    0.930  0.020  1.080
 MBL  C1   H15  single    0.930  0.020  1.080
 MBL  C5   H16  single    0.930  0.020  1.080
 MBL  C4   H17  single    0.930  0.020  1.080
 MBL  C2   H18  single    0.930  0.020  1.080
 MBL  C    H19  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
 MBL  H2   N2   H1   110.15  3.000
 MBL  H2   N2   C8   112.03  3.000
 MBL  H1   N2   C8   115.46  3.000
 MBL  N1   C8   N    111.93  3.000
 MBL  N1   C8   N2   125.82  3.000
 MBL  N    C8   N2   122.12  3.000
 MBL  C7   N    C9   126.40  3.000
 MBL  C9   N    C8   126.78  3.000
 MBL  C7   N    C8   106.74  3.000
 MBL  H4   C9   H3   106.65  3.000
 MBL  H4   C9   C10  110.42  3.000
 MBL  H3   C9   C10  110.82  3.000
 MBL  H4   C9   N    107.67  3.000
 MBL  H3   C9   N    108.29  3.000
 MBL  C10  C9   N    112.75  3.000
 MBL  H6   C10  H5   106.37  3.000
 MBL  H6   C10  C11  109.63  3.000
 MBL  H5   C10  C11  109.86  3.000
 MBL  H6   C10  C9   109.80  3.000
 MBL  H5   C10  C9   108.98  3.000
 MBL  C11  C10  C9   112.04  3.000
 MBL  H8   C11  H7   106.15  3.000
 MBL  H8   C11  C12  109.34  3.000
 MBL  H7   C11  C12  109.38  3.000
 MBL  H8   C11  C10  109.37  3.000
 MBL  H7   C11  C10  109.54  3.000
 MBL  C12  C11  C10  112.83  3.000
 MBL  H10  C12  H9   106.07  3.000
 MBL  H10  C12  C13  109.59  3.000
 MBL  H9   C12  C13  109.49  3.000
 MBL  H10  C12  C11  109.36  3.000
 MBL  H9   C12  C11  109.26  3.000
 MBL  C13  C12  C11  112.85  3.000
 MBL  H13  C13  H12  107.60  3.000
 MBL  H13  C13  H11  107.53  3.000
 MBL  H12  C13  H11  107.53  3.000
 MBL  H13  C13  C12  111.23  3.000
 MBL  H12  C13  C12  111.34  3.000
 MBL  H11  C13  C12  111.42  3.000
 MBL  H14  C7   C6   132.72  3.000
 MBL  H14  C7   N    121.38  3.000
 MBL  C6   C7   N    105.90  3.000
 MBL  C6   N1   C8   105.68  3.000
 MBL  C3   C6   N1   121.67  3.000
 MBL  N1   C6   C7   109.74  3.000
 MBL  C3   C6   C7   128.59  3.000
 MBL  C5   C3   C1   118.20  3.000
 MBL  C5   C3   C6   120.45  3.000
 MBL  C1   C3   C6   121.35  3.000
 MBL  H15  C1   C    119.05  3.000
 MBL  H15  C1   C3   120.04  3.000
 MBL  C    C1   C3   120.90  3.000
 MBL  H16  C5   C4   119.82  3.000
 MBL  H16  C5   C3   119.35  3.000
 MBL  C4   C5   C3   120.83  3.000
 MBL  H17  C4   C2   120.00  3.000
 MBL  H17  C4   C5   119.56  3.000
 MBL  C2   C4   C5   120.45  3.000
 MBL  H18  C2   C    120.39  3.000
 MBL  H18  C2   C4   120.38  3.000
 MBL  C    C2   C4   119.23  3.000
 MBL  H19  C    C2   120.11  3.000
 MBL  H19  C    C1   119.51  3.000
 MBL  C2   C    C1   120.38  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
 MBL  CONST_01  C6   C7   N    C8      0.00   0.0  0
 MBL  CONST_02  C7   C6   N1   C8      0.00   0.0  0
 MBL  CONST_03  C3   C6   N1   C8    180.00   0.0  0
 MBL  CONST_04  C3   C6   C7   N     180.00   0.0  0
 MBL  CONST_05  N1   C6   C7   N       0.00   0.0  0
 MBL  CONST_06  C6   N1   C8   N       0.00   0.0  0
 MBL  CONST_07  C1   C3   C6   C7      0.00   0.0  0
 MBL  CONST_08  C5   C3   C6   C7    180.00   0.0  0
 MBL  CONST_09  N1   C8   N    C7      0.00   0.0  0
 MBL  CONST_10  C1   C3   C6   N1    180.00   0.0  0
 MBL  CONST_11  C5   C3   C6   N1      0.00   0.0  0
 MBL  CONST_12  C    C1   C3   C6    180.00   0.0  0
 MBL  CONST_13  C4   C5   C3   C6    180.00   0.0  0
 MBL  CONST_14  C2   C    C1   C3      0.00   0.0  0
 MBL  CONST_15  C2   C4   C5   C3      0.00   0.0  0
 MBL  CONST_16  C4   C2   C    C1      0.00   0.0  0
 MBL  CONST_17  C4   C5   C3   C1      0.00   0.0  0
 MBL  CONST_18  C    C1   C3   C5      0.00   0.0  0
 MBL  CONST_19  C    C2   C4   C5      0.00   0.0  0
 MBL  CONST_20  C7   N    C8   N2    180.00   0.0  0
 MBL  CONST_21  C6   N1   C8   N2    180.00   0.0  0
 MBL  CONST_22  C6   C7   N    C9    180.00   0.0  0
 MBL  CONST_23  N1   C8   N    C9    180.00   0.0  0
 MBL  CONST_24  H14  C7   N    C8    180.00   0.0  0
 MBL  CONST_25  H15  C1   C3   C6      0.00   0.0  0
 MBL  CONST_26  H16  C5   C3   C6      0.00   0.0  0
 MBL  CONST_27  H19  C    C1   C3    180.00   0.0  0
 MBL  CONST_28  H17  C4   C5   C3    180.00   0.0  0
 MBL  CONST_29  H18  C2   C    C1    180.00   0.0  0
 MBL  CONST_31  H2   N2   C8   N     180.00   0.0  0
 MBL  Var_01    C10  C9   N    C8    -84.15  30.0  3
 MBL  Var_02    C11  C10  C9   N    -178.62  30.0  3
 MBL  Var_03    C12  C11  C10  C9    179.64  30.0  1
 MBL  Var_04    C13  C12  C11  C10  -179.53  30.0  3
 MBL  Var_05    H11  C13  C12  C11   179.60  30.0  3

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
 MBL  plan-1  N2   0.020
 MBL  plan-1  C8   0.020
 MBL  plan-1  N    0.020
 MBL  plan-1  C9   0.020
 MBL  plan-1  C7   0.020
 MBL  plan-1  N1   0.020
 MBL  plan-1  C6   0.020
 MBL  plan-1  C3   0.020
 MBL  plan-1  H14  0.020
 MBL  plan-2  C6   0.020
 MBL  plan-2  C3   0.020
 MBL  plan-2  C1   0.020
 MBL  plan-2  C5   0.020
 MBL  plan-2  C4   0.020
 MBL  plan-2  C2   0.020
 MBL  plan-2  C    0.020
 MBL  plan-2  H15  0.020
 MBL  plan-2  H16  0.020
 MBL  plan-2  H17  0.020
 MBL  plan-2  H18  0.020
 MBL  plan-2  H19  0.020
 MBL  plan-3  N2   0.020
 MBL  plan-3  C8   0.020
 MBL  plan-3  H1   0.020
 MBL  plan-3  H2   0.020

