# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 11:46:19 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 4-[(1S)-1-(3-fluoro-4-methoxyphenyl)-2-(2-methoxy-5-nitrophenyl)ethyl]-1H-imidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1F)[C@H](Cc2cc(ccc2OC)[N+]([O-])=O)c3c[nH]c(N)n3
#
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
 B35  B35  4-[(1S)-1-(3-fluoro-4-methoxyphenyl)-2-(2-methoxy-5-nitrophenyl)ethyl]-1H-imidazol-2-amine  ligand  47  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B35
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
 B35  C1    C  CR6    0   0.220  -4.7620   1.1312   0.0415
 B35  C2    C  CR16   0  -0.363  -4.0366   1.5077   1.1646
 B35  C3    C  CR16   0  -0.324  -2.6759   1.2280   1.2511
 B35  C4    C  CR6    0   0.154  -1.9988   0.5698   0.2357
 B35  N     N  N      0  -0.493   0.8689  -1.5869   1.3070
 B35  C5    C  CR16   0  -0.472  -2.7253   0.1974  -0.8975
 B35  C6    C  CH3    0  -0.438  -6.7994   2.0012   0.8612
 B35  C7    C  CH1    0  -0.405  -0.5295   0.2537   0.3704
 B35  C8    C  CR5    0   0.203  -0.2991  -1.1899   0.6990
 B35  C     C  CR6    0   0.480  -4.0686   0.4748  -0.9769
 B35  O     O  O2     0  -0.465  -6.0725   1.3456  -0.1601
 B35  F     F  F      0  -0.314  -4.7546   0.1116  -2.0731
 B35  C9    C  CH2    0  -0.489   0.2565   0.7007  -0.8866
 B35  C10   C  CR6    0   0.054   1.7415   0.5259  -0.7433
 B35  C11   C  CR16   0  -0.333   2.4975   1.5366  -0.1892
 B35  C12   C  CR6    0   0.239   3.8677   1.3781   0.0072
 B35  C13   C  CR16   0  -0.268   4.5029   0.2000  -0.3523
 B35  C14   C  CR16   0  -0.378   3.7617  -0.8187  -0.9177
 B35  C15   C  CR6    0   0.416   2.3889  -0.6669  -1.1225
 B35  O16   O  O2     0  -0.448   1.6254  -1.6014  -1.6808
 B35  C17   C  CH3    0  -0.446   2.1709  -2.8799  -1.9519
 B35  C18   C  CR5    0   0.595   0.8110  -2.8931   1.3676
 B35  N19   N  NR15   0  -0.626  -0.3426  -3.3618   0.8498
 B35  C20   C  CR15   0  -0.135  -1.0746  -2.2733   0.4231
 B35  N21   N  NH2    0  -0.854   1.8130  -3.7203   1.8205
 B35  N22   N  N      1   0.323   4.6324   2.4518   0.5878
 B35  O23   O  O     -1  -0.396   4.0586   3.4828   0.8662
 B35  O24   O  O      0  -0.396   5.8180   2.2806   0.7733
 B35  H2    H  HCR6   0   0.289  -4.5161   2.0253   1.9840
 B35  H3    H  HCR6   0   0.257  -2.1390   1.5390   2.1389
 B35  H5    H  HCR6   0   0.276  -2.2527  -0.3132  -1.7273
 B35  H6    H  HCH3   0   0.231  -6.7872   1.4353   1.7964
 B35  H6A   H  HCH3   0   0.231  -6.4174   3.0074   1.0516
 B35  H6B   H  HCH3   0   0.262  -7.8250   2.0761   0.5094
 B35  H7    H  HCH1   0   0.258  -0.1445   0.8430   1.2098
 B35  H9    H  HCH2   0   0.255  -0.1090   0.1624  -1.7613
 B35  H9A   H  HCH2   0   0.259   0.0437   1.7584  -1.0568
 B35  H11   H  HCR6   0   0.282   2.0053   2.4550   0.1009
 B35  H13   H  HCR6   0   0.293   5.5642   0.0647  -0.2039
 B35  H14   H  HCR6   0   0.290   4.2702  -1.7299  -1.1987
 B35  H17   H  HCH3   0   0.238   2.9698  -2.8323  -2.6952
 B35  H17A  H  HCH3   0   0.236   2.5493  -3.3542  -1.0438
 B35  H17B  H  HCH3   0   0.263   1.3561  -3.4790  -2.3486
 B35  HN19  H  HNR5   0   0.408  -0.6269  -4.3257   0.7890
 B35  H20   H  HCR5   0   0.271  -2.0482  -2.3853  -0.0213
 B35  HN21  H  HNH2   0   0.380   2.5143  -3.2182   2.3425
 B35  HN2A  H  HNH2   0   0.383   1.4992  -4.5313   2.3331

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
 B35  C1   C2    aromatic  1.389  0.020  1.389
 B35  C1   C     aromatic  1.396  0.020  1.396
 B35  C1   O     single    1.343  0.020  1.343
 B35  C2   C3    aromatic  1.392  0.020  1.392
 B35  C2   H2    single    0.930  0.020  1.080
 B35  C3   C4    aromatic  1.387  0.020  1.387
 B35  C3   H3    single    0.930  0.020  1.080
 B35  C4   C5    aromatic  1.397  0.020  1.397
 B35  C4   C7    single    1.509  0.020  1.509
 B35  N    C8    aromatic  1.375  0.020  1.375
 B35  N    C18   aromatic  1.309  0.020  1.309
 B35  C5   C     aromatic  1.374  0.020  1.374
 B35  C5   H5    single    0.930  0.020  1.080
 B35  C6   O     single    1.415  0.020  1.415
 B35  C6   H6    single    0.970  0.020  1.090
 B35  C6   H6A   single    0.970  0.020  1.090
 B35  C6   H6B   single    0.970  0.020  1.090
 B35  C7   C8    single    1.498  0.020  1.498
 B35  C7   C9    single    1.548  0.020  1.548
 B35  C7   H7    single    0.970  0.020  1.090
 B35  C8   C20   aromatic  1.361  0.020  1.361
 B35  C    F     single    1.343  0.020  1.343
 B35  C9   C10   single    1.502  0.020  1.502
 B35  C9   H9    single    0.970  0.020  1.090
 B35  C9   H9A   single    0.970  0.020  1.090
 B35  C10  C11   aromatic  1.378  0.020  1.378
 B35  C10  C15   aromatic  1.409  0.020  1.409
 B35  C11  C12   aromatic  1.393  0.020  1.393
 B35  C11  H11   single    0.930  0.020  1.080
 B35  C12  C13   aromatic  1.386  0.020  1.386
 B35  C12  N22   single    1.440  0.020  1.440
 B35  C13  C14   aromatic  1.381  0.020  1.381
 B35  C13  H13   single    0.930  0.020  1.080
 B35  C14  C15   aromatic  1.396  0.020  1.396
 B35  C14  H14   single    0.930  0.020  1.080
 B35  C15  O16   single    1.330  0.020  1.330
 B35  O16  C17   single    1.416  0.020  1.416
 B35  C17  H17   single    0.970  0.020  1.090
 B35  C17  H17A  single    0.970  0.020  1.090
 B35  C17  H17B  single    0.970  0.020  1.090
 B35  C18  N19   aromatic  1.349  0.020  1.349
 B35  C18  N21   single    1.376  0.020  1.376
 B35  N19  C20   aromatic  1.379  0.020  1.379
 B35  N19  HN19  single    0.860  0.020  1.020
 B35  C20  H20   single    0.930  0.020  1.080
 B35  N21  HN21  single    0.890  0.020  1.040
 B35  N21  HN2A  single    0.890  0.020  1.040
 B35  N22  O23   single    1.212  0.020  1.212
 B35  N22  O24   double    1.212  0.020  1.212

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
 B35  O     C1   C     116.76  3.000
 B35  O     C1   C2    125.99  3.000
 B35  C     C1   C2    117.25  3.000
 B35  H2    C2   C3    118.86  3.000
 B35  H2    C2   C1    120.72  3.000
 B35  C3    C2   C1    120.42  3.000
 B35  H3    C3   C4    119.63  3.000
 B35  H3    C3   C2    118.55  3.000
 B35  C4    C3   C2    121.82  3.000
 B35  C7    C4   C5    121.54  3.000
 B35  C7    C4   C3    120.63  3.000
 B35  C5    C4   C3    117.82  3.000
 B35  C18   N    C8    105.72  3.000
 B35  H5    C5   C     118.53  3.000
 B35  H5    C5   C4    121.37  3.000
 B35  C     C5   C4    120.10  3.000
 B35  H6B   C6   H6A   108.83  3.000
 B35  H6B   C6   H6    108.85  3.000
 B35  H6A   C6   H6    108.89  3.000
 B35  H6B   C6   O     106.44  3.000
 B35  H6A   C6   O     111.89  3.000
 B35  H6    C6   O     111.84  3.000
 B35  H7    C7   C9    106.75  3.000
 B35  H7    C7   C8    107.23  3.000
 B35  C9    C7   C8    112.21  3.000
 B35  H7    C7   C4    107.34  3.000
 B35  C9    C7   C4    111.18  3.000
 B35  C8    C7   C4    111.79  3.000
 B35  C20   C8   C7    129.42  3.000
 B35  C20   C8   N     110.11  3.000
 B35  C7    C8   N     120.37  3.000
 B35  F     C    C5    119.46  3.000
 B35  F     C    C1    117.96  3.000
 B35  C5    C    C1    122.58  3.000
 B35  C6    O    C1    117.83  3.000
 B35  H9A   C9   H9    106.72  3.000
 B35  H9A   C9   C10   108.67  3.000
 B35  H9    C9   C10   110.52  3.000
 B35  H9A   C9   C7    107.89  3.000
 B35  H9    C9   C7    109.79  3.000
 B35  C10   C9   C7    113.01  3.000
 B35  C15   C10  C11   118.48  3.000
 B35  C15   C10  C9    121.80  3.000
 B35  C11   C10  C9    119.69  3.000
 B35  H11   C11  C12   120.42  3.000
 B35  H11   C11  C10   118.74  3.000
 B35  C12   C11  C10   120.84  3.000
 B35  N22   C12  C13   119.67  3.000
 B35  N22   C12  C11   119.61  3.000
 B35  C13   C12  C11   120.72  3.000
 B35  H13   C13  C14   119.42  3.000
 B35  H13   C13  C12   121.41  3.000
 B35  C14   C13  C12   119.17  3.000
 B35  H14   C14  C15   121.08  3.000
 B35  H14   C14  C13   118.42  3.000
 B35  C15   C14  C13   120.50  3.000
 B35  O16   C15  C14   123.35  3.000
 B35  O16   C15  C10   116.37  3.000
 B35  C14   C15  C10   120.28  3.000
 B35  C17   O16  C15   119.58  3.000
 B35  H17B  C17  H17A  108.91  3.000
 B35  H17B  C17  H17   108.91  3.000
 B35  H17A  C17  H17   109.35  3.000
 B35  H17B  C17  O16   106.19  3.000
 B35  H17A  C17  O16   111.49  3.000
 B35  H17   C17  O16   111.87  3.000
 B35  N21   C18  N19   122.70  3.000
 B35  N21   C18  N     125.67  3.000
 B35  N19   C18  N     111.52  3.000
 B35  HN19  N19  C20   125.94  3.000
 B35  HN19  N19  C18   126.70  3.000
 B35  C20   N19  C18   107.36  3.000
 B35  H20   C20  N19   121.72  3.000
 B35  H20   C20  C8    133.03  3.000
 B35  N19   C20  C8    105.26  3.000
 B35  HN2A  N21  HN21  110.70  3.000
 B35  HN2A  N21  C18   115.08  3.000
 B35  HN21  N21  C18   112.18  3.000
 B35  O24   N22  O23   123.23  3.000
 B35  O24   N22  C12   118.40  3.000
 B35  O23   N22  C12   118.38  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
 B35  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 B35  CONST_02  C4    C5   C    C1     0.00   0.0  0
 B35  CONST_03  C5    C    C1   C2     0.00   0.0  0
 B35  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 B35  CONST_05  C     C1   C2   C3     0.00   0.0  0
 B35  CONST_06  C     C5   C4   C3     0.00   0.0  0
 B35  CONST_07  N19   C20  C8   N      0.00   0.0  0
 B35  CONST_08  C20   N19  C18  N      0.00   0.0  0
 B35  CONST_09  N19   C18  N    C8     0.00   0.0  0
 B35  CONST_10  C18   N19  C20  C8     0.00   0.0  0
 B35  CONST_11  C13   C12  C11  C10    0.00   0.0  0
 B35  CONST_12  C13   C14  C15  C10    0.00   0.0  0
 B35  CONST_13  C14   C15  C10  C11    0.00   0.0  0
 B35  CONST_14  C14   C13  C12  C11    0.00   0.0  0
 B35  CONST_15  C15   C10  C11  C12    0.00   0.0  0
 B35  CONST_16  C15   C14  C13  C12    0.00   0.0  0
 B35  CONST_17  C20   C8   N    C18    0.00   0.0  0
 B35  CONST_18  F     C    C1   C2   180.00   0.0  0
 B35  CONST_19  C7    C4   C3   C2   180.00   0.0  0
 B35  CONST_20  O     C1   C2   C3   180.00   0.0  0
 B35  CONST_21  F     C    C5   C4   180.00   0.0  0
 B35  CONST_22  O     C1   C    C5   180.00   0.0  0
 B35  CONST_23  C     C5   C4   C7   180.00   0.0  0
 B35  CONST_24  C18   N    C8   C7   180.00   0.0  0
 B35  CONST_25  N19   C20  C8   C7   180.00   0.0  0
 B35  CONST_26  N21   C18  N    C8   180.00   0.0  0
 B35  CONST_27  C12   C11  C10  C9   180.00   0.0  0
 B35  CONST_28  C14   C15  C10  C9   180.00   0.0  0
 B35  CONST_29  N22   C12  C11  C10  180.00   0.0  0
 B35  CONST_30  O16   C15  C10  C11  180.00   0.0  0
 B35  CONST_31  O16   C15  C14  C13  180.00   0.0  0
 B35  CONST_32  N22   C12  C13  C14  180.00   0.0  0
 B35  CONST_33  N21   C18  N19  C20  180.00   0.0  0
 B35  CONST_34  H3    C3   C2   C1   180.00   0.0  0
 B35  CONST_35  H5    C5   C    C1   180.00   0.0  0
 B35  CONST_36  H2    C2   C3   C4   180.00   0.0  0
 B35  CONST_37  H20   C20  C8   N    180.00   0.0  0
 B35  CONST_38  HN19  N19  C18  N    180.00   0.0  0
 B35  CONST_39  H14   C14  C15  C10  180.00   0.0  0
 B35  CONST_40  H13   C13  C12  C11  180.00   0.0  0
 B35  CONST_41  H11   C11  C12  C13  180.00   0.0  0
 B35  CONST_42  O23   N22  C12  C11    0.00   0.0  0
 B35  CONST_43  O24   N22  C12  C11  180.00   0.0  0
 B35  CONST_44  O23   N22  C12  C13  180.00   0.0  0
 B35  CONST_45  O24   N22  C12  C13    0.00   0.0  0
 B35  Var_01    C     C1   O    C6   179.59  30.0  2
 B35  Var_02    C11   C10  C9   C7   -87.86  30.0  2
 B35  Var_03    H6    C6   O    C1   -61.18  30.0  3
 B35  Var_04    H17   C17  O16  C15  -64.39  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
 B35  chir_01  C7  C4  C8  C9  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
 B35  plan-1  N     0.020
 B35  plan-1  C7    0.020
 B35  plan-1  C8    0.020
 B35  plan-1  C18   0.020
 B35  plan-1  N19   0.020
 B35  plan-1  C20   0.020
 B35  plan-1  N21   0.020
 B35  plan-1  HN19  0.020
 B35  plan-1  H20   0.020
 B35  plan-2  C1    0.020
 B35  plan-2  C2    0.020
 B35  plan-2  C3    0.020
 B35  plan-2  C4    0.020
 B35  plan-2  C5    0.020
 B35  plan-2  C7    0.020
 B35  plan-2  C     0.020
 B35  plan-2  O     0.020
 B35  plan-2  F     0.020
 B35  plan-2  H2    0.020
 B35  plan-2  H3    0.020
 B35  plan-2  H5    0.020
 B35  plan-3  C9    0.020
 B35  plan-3  C10   0.020
 B35  plan-3  C11   0.020
 B35  plan-3  C12   0.020
 B35  plan-3  C13   0.020
 B35  plan-3  C14   0.020
 B35  plan-3  C15   0.020
 B35  plan-3  O16   0.020
 B35  plan-3  N22   0.020
 B35  plan-3  H11   0.020
 B35  plan-3  H13   0.020
 B35  plan-3  H14   0.020
 B35  plan-4  C18   0.020
 B35  plan-4  N21   0.020
 B35  plan-4  HN21  0.020
 B35  plan-4  HN2A  0.020
 B35  plan-5  C12   0.020
 B35  plan-5  N22   0.020
 B35  plan-5  O23   0.020
 B35  plan-5  O24   0.020

