# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 01:55:35 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-6-fluoro-1H-benzimidazol-2-yl}-6-{[(1S,2S)-2-methylcyclohexyl]oxy}phenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCCC[C@@H]1Oc2cccc(c2[O-])c3[nH]c4cc(F)c(cc4n3)C(N)=[NH2+]
#
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
 CR9  CR9  2-{5-[amino(iminio)methyl]-6-fluoro-1H-benzimidazol-2-yl}-6-{[(1S,2S)-2-methylcyclohexyl]oxy}phenolate  ligand  51  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CR9
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
 CR9  C1    C  CR6    0  -0.228  -5.3016  -0.5871   0.1496
 CR9  C2    C  CR6    0   0.549  -5.5149   0.7344  -0.2658
 CR9  F2    F  F      0  -0.305  -6.7691   1.1313  -0.5302
 CR9  C3    C  CR16   0  -0.465  -4.4966   1.6409  -0.4568
 CR9  C4    C  CR56   0   0.376  -3.2154   1.1740  -0.2026
 CR9  C5    C  CR56   0   0.156  -2.9486  -0.1458   0.2171
 CR9  C6    C  CR16   0  -0.356  -3.9973  -1.0325   0.3860
 CR9  C7    C  C      0   0.592  -6.4119  -1.5325   0.3123
 CR9  N1    N  NH2    0  -0.758  -7.5137  -1.1756   0.9270
 CR9  N2    N  NC2    1  -0.757  -6.2620  -2.7510  -0.1514
 CR9  N3    N  NR15   0  -0.738  -1.9971   1.7580  -0.2758
 CR9  N4    N  N      0  -0.476  -1.6044  -0.3272   0.3888
 CR9  C8    C  CR5    0   0.486  -1.0418   0.8224   0.0837
 CR9  C1'   C  CR6    0  -0.242   0.3619   1.1631   0.0957
 CR9  C2'   C  CR16   0  -0.310   0.7384   2.5260   0.0594
 CR9  C3'   C  CR16   0  -0.308   2.0512   2.9065   0.0283
 CR9  C4'   C  CR16   0  -0.377   3.0605   1.9195   0.0335
 CR9  C5'   C  CR6    0   0.236   2.7357   0.5895   0.0806
 CR9  C6'   C  CR6    0   0.211   1.3525   0.1222   0.1156
 CR9  O6'   O  OC    -1  -0.547   1.1091  -1.1033   0.1389
 CR9  O5'   O  O2     0  -0.488   3.6232  -0.4330   0.0851
 CR9  C1B   C  CH1    0  -0.256   5.6709  -1.4539  -0.5529
 CR9  C2B   C  CH2    0  -0.421   7.1811  -1.2310  -0.6654
 CR9  C3B   C  CH2    0  -0.432   7.8050  -0.7867   0.6525
 CR9  C4B   C  CH2    0  -0.439   7.1156   0.4616   1.1901
 CR9  C5B   C  CH2    0  -0.467   5.6126   0.2361   1.3175
 CR9  C6B   C  CH1    0   0.077   5.0121  -0.1802  -0.0229
 CR9  C1A   C  CH3    0  -0.655   5.0856  -1.8868  -1.8918
 CR9  HC3   H  HCR6   0   0.297  -4.7035   2.6474  -0.7949
 CR9  HC6   H  HCR6   0   0.285  -3.8099  -2.0456   0.7189
 CR9  HH11  H  HNH2   0   0.443  -7.5846  -0.2909   1.4015
 CR9  HH12  H  HNH2   0   0.437  -8.3037  -1.7983   1.0093
 CR9  HH21  H  HNC2   0   0.437  -6.9444  -3.4760   0.0119
 CR9  HH22  H  HNC2   0   0.447  -5.4705  -2.9880  -0.7270
 CR9  HN3   H  HNR5   0   0.422  -1.8201   2.6906  -0.6113
 CR9  HC2'  H  HCR6   0   0.223  -0.0162   3.3030   0.0884
 CR9  HC3'  H  HCR6   0   0.229   2.3233   3.9534   0.0149
 CR9  HC4'  H  HCR6   0   0.253   4.0940   2.2424   0.0094
 CR9  H1B   H  HCH1   0   0.216   5.5014  -2.2510   0.1835
 CR9  H2A   H  HCH2   0   0.230   7.6564  -2.1511  -1.0158
 CR9  H2B   H  HCH2   0   0.208   7.3724  -0.4729  -1.4350
 CR9  H3A   H  HCH2   0   0.212   7.7097  -1.5941   1.3858
 CR9  H3B   H  HCH2   0   0.229   8.8746  -0.6068   0.5218
 CR9  H4A   H  HCH2   0   0.233   7.5334   0.7439   2.1589
 CR9  H4B   H  HCH2   0   0.214   7.3036   1.3026   0.5135
 CR9  H5A   H  HCH2   0   0.220   5.4220  -0.5568   2.0496
 CR9  H5B   H  HCH2   0   0.240   5.1239   1.1370   1.6939
 CR9  H6B   H  HCH1   0   0.199   5.1923   0.6158  -0.7629
 CR9  H1AA  H  HCH3   0   0.224   5.6010  -2.7731  -2.2654
 CR9  H1AB  H  HCH3   0   0.234   4.0252  -2.1242  -1.8184
 CR9  H1AC  H  HCH3   0   0.211   5.2027  -1.0981  -2.6394

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
 CR9  C1   C2    aromatic  1.402  0.020  1.402
 CR9  C1   C6    aromatic  1.398  0.020  1.398
 CR9  C1   C7    single    1.467  0.020  1.467
 CR9  C2   F2    single    1.342  0.020  1.342
 CR9  C2   C3    aromatic  1.377  0.020  1.377
 CR9  C3   C4    aromatic  1.387  0.020  1.387
 CR9  C3   HC3   single    0.930  0.020  1.080
 CR9  C4   C5    aromatic  1.410  0.020  1.410
 CR9  C4   N3    aromatic  1.353  0.020  1.353
 CR9  C5   C6    aromatic  1.384  0.020  1.384
 CR9  C5   N4    aromatic  1.367  0.020  1.367
 CR9  C6   HC6   single    0.930  0.020  1.080
 CR9  C7   N1    single    1.311  0.020  1.311
 CR9  C7   N2    double    1.312  0.020  1.312
 CR9  N1   HH11  single    0.860  0.020  1.020
 CR9  N1   HH12  single    0.860  0.020  1.020
 CR9  N2   HH21  single    0.860  0.020  1.020
 CR9  N2   HH22  single    0.860  0.020  1.020
 CR9  N3   C8    aromatic  1.385  0.020  1.385
 CR9  N3   HN3   single    0.860  0.020  1.020
 CR9  N4   C8    aromatic  1.316  0.020  1.316
 CR9  C8   C1'   single    1.444  0.020  1.444
 CR9  C1'  C2'   aromatic  1.414  0.020  1.414
 CR9  C1'  C6'   aromatic  1.437  0.020  1.437
 CR9  C2'  C3'   aromatic  1.367  0.020  1.367
 CR9  C2'  HC2'  single    0.930  0.020  1.080
 CR9  C3'  C4'   aromatic  1.412  0.020  1.412
 CR9  C3'  HC3'  single    0.930  0.020  1.080
 CR9  C4'  C5'   aromatic  1.370  0.020  1.370
 CR9  C4'  HC4'  single    0.930  0.020  1.080
 CR9  C5'  C6'   aromatic  1.460  0.020  1.460
 CR9  C5'  O5'   single    1.354  0.020  1.354
 CR9  C6'  O6'   single    1.250  0.020  1.250
 CR9  O5'  C6B   single    1.416  0.020  1.416
 CR9  C1B  C2B   single    1.531  0.020  1.531
 CR9  C1B  C6B   single    1.529  0.020  1.529
 CR9  C1B  C1A   single    1.524  0.020  1.524
 CR9  C1B  H1B   single    0.970  0.020  1.090
 CR9  C2B  C3B   single    1.524  0.020  1.524
 CR9  C2B  H2A   single    0.970  0.020  1.090
 CR9  C2B  H2B   single    0.970  0.020  1.090
 CR9  C3B  C4B   single    1.524  0.020  1.524
 CR9  C3B  H3A   single    0.970  0.020  1.090
 CR9  C3B  H3B   single    0.970  0.020  1.090
 CR9  C4B  C5B   single    1.525  0.020  1.525
 CR9  C4B  H4A   single    0.970  0.020  1.090
 CR9  C4B  H4B   single    0.970  0.020  1.090
 CR9  C5B  C6B   single    1.527  0.020  1.527
 CR9  C5B  H5A   single    0.970  0.020  1.090
 CR9  C5B  H5B   single    0.970  0.020  1.090
 CR9  C6B  H6B   single    0.970  0.020  1.090
 CR9  C1A  H1AA  single    0.970  0.020  1.090
 CR9  C1A  H1AB  single    0.970  0.020  1.090
 CR9  C1A  H1AC  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
 CR9  C7    C1   C6    118.80  3.000
 CR9  C7    C1   C2    121.68  3.000
 CR9  C6    C1   C2    119.50  3.000
 CR9  C3    C2   F2    117.98  3.000
 CR9  C3    C2   C1    123.33  3.000
 CR9  F2    C2   C1    118.66  3.000
 CR9  HC3   C3   C4    123.17  3.000
 CR9  HC3   C3   C2    120.97  3.000
 CR9  C4    C3   C2    115.86  3.000
 CR9  N3    C4   C5    104.46  3.000
 CR9  N3    C4   C3    132.57  3.000
 CR9  C5    C4   C3    122.97  3.000
 CR9  N4    C5   C6    130.15  3.000
 CR9  N4    C5   C4    110.33  3.000
 CR9  C6    C5   C4    119.52  3.000
 CR9  HC6   C6   C5    120.40  3.000
 CR9  HC6   C6   C1    120.76  3.000
 CR9  C5    C6   C1    118.82  3.000
 CR9  N2    C7   N1    120.95  3.000
 CR9  N2    C7   C1    118.21  3.000
 CR9  N1    C7   C1    120.83  3.000
 CR9  HH12  N1   HH11  116.66  3.000
 CR9  HH12  N1   C7    121.88  3.000
 CR9  HH11  N1   C7    121.30  3.000
 CR9  HH22  N2   HH21  117.07  3.000
 CR9  HH22  N2   C7    120.68  3.000
 CR9  HH21  N2   C7    122.19  3.000
 CR9  HN3   N3   C8    126.24  3.000
 CR9  HN3   N3   C4    125.18  3.000
 CR9  C8    N3   C4    108.39  3.000
 CR9  C8    N4   C5    105.98  3.000
 CR9  C1'   C8   N4    128.29  3.000
 CR9  C1'   C8   N3    120.88  3.000
 CR9  N4    C8   N3    110.83  3.000
 CR9  C6'   C1'  C2'   120.98  3.000
 CR9  C6'   C1'  C8    119.95  3.000
 CR9  C2'   C1'  C8    119.06  3.000
 CR9  HC2'  C2'  C3'   118.02  3.000
 CR9  HC2'  C2'  C1'   120.33  3.000
 CR9  C3'   C2'  C1'   121.63  3.000
 CR9  HC3'  C3'  C4'   119.79  3.000
 CR9  HC3'  C3'  C2'   120.75  3.000
 CR9  C4'   C3'  C2'   119.46  3.000
 CR9  HC4'  C4'  C5'   121.10  3.000
 CR9  HC4'  C4'  C3'   118.27  3.000
 CR9  C5'   C4'  C3'   120.62  3.000
 CR9  O5'   C5'  C6'   112.28  3.000
 CR9  O5'   C5'  C4'   125.30  3.000
 CR9  C6'   C5'  C4'   122.42  3.000
 CR9  O6'   C6'  C5'   119.92  3.000
 CR9  O6'   C6'  C1'   125.19  3.000
 CR9  C5'   C6'  C1'   114.88  3.000
 CR9  C6B   O5'  C5'   120.52  3.000
 CR9  H1B   C1B  C1A   108.88  3.000
 CR9  H1B   C1B  C6B   107.80  3.000
 CR9  C1A   C1B  C6B   112.07  3.000
 CR9  H1B   C1B  C2B   107.89  3.000
 CR9  C1A   C1B  C2B   110.84  3.000
 CR9  C6B   C1B  C2B   109.22  3.000
 CR9  H2B   C2B  H2A   106.31  3.000
 CR9  H2B   C2B  C3B   109.50  3.000
 CR9  H2A   C2B  C3B   110.16  3.000
 CR9  H2B   C2B  C1B   108.91  3.000
 CR9  H2A   C2B  C1B   109.26  3.000
 CR9  C3B   C2B  C1B   112.51  3.000
 CR9  H3B   C3B  H3A   106.66  3.000
 CR9  H3B   C3B  C4B   110.50  3.000
 CR9  H3A   C3B  C4B   109.17  3.000
 CR9  H3B   C3B  C2B   110.20  3.000
 CR9  H3A   C3B  C2B   109.18  3.000
 CR9  C4B   C3B  C2B   111.01  3.000
 CR9  H4B   C4B  H4A   106.48  3.000
 CR9  H4B   C4B  C5B   109.52  3.000
 CR9  H4A   C4B  C5B   109.95  3.000
 CR9  H4B   C4B  C3B   109.47  3.000
 CR9  H4A   C4B  C3B   110.58  3.000
 CR9  C5B   C4B  C3B   110.74  3.000
 CR9  H5B   C5B  H5A   106.78  3.000
 CR9  H5B   C5B  C6B   110.58  3.000
 CR9  H5A   C5B  C6B   108.72  3.000
 CR9  H5B   C5B  C4B   110.36  3.000
 CR9  H5A   C5B  C4B   109.53  3.000
 CR9  C6B   C5B  C4B   110.77  3.000
 CR9  H6B   C6B  C5B   109.18  3.000
 CR9  H6B   C6B  C1B   107.37  3.000
 CR9  C5B   C6B  C1B   111.23  3.000
 CR9  H6B   C6B  O5'   109.92  3.000
 CR9  C5B   C6B  O5'   111.57  3.000
 CR9  C1B   C6B  O5'   107.48  3.000
 CR9  H1AC  C1A  H1AB  107.92  3.000
 CR9  H1AC  C1A  H1AA  107.53  3.000
 CR9  H1AB  C1A  H1AA  107.81  3.000
 CR9  H1AC  C1A  C1B   110.78  3.000
 CR9  H1AB  C1A  C1B   112.13  3.000
 CR9  H1AA  C1A  C1B   110.49  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
 CR9  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 CR9  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 CR9  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 CR9  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 CR9  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 CR9  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 CR9  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 CR9  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 CR9  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 CR9  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 CR9  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 CR9  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 CR9  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 CR9  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 CR9  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 CR9  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 CR9  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 CR9  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 CR9  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 CR9  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 CR9  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 CR9  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 CR9  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 CR9  CONST_28  C5'   C6'  C1'  C2'    0.00   0.0  0
 CR9  CONST_29  C5'   C4'  C3'  C2'    0.00   0.0  0
 CR9  CONST_30  C6'   C1'  C2'  C3'    0.00   0.0  0
 CR9  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 CR9  CONST_32  C6    C1   C2   F2   180.00   0.0  0
 CR9  CONST_33  C4    C3   C2   F2   180.00   0.0  0
 CR9  CONST_34  C7    C1   C2   C3   180.00   0.0  0
 CR9  CONST_35  C7    C1   C6   C5   180.00   0.0  0
 CR9  CONST_36  O6'   C6'  C1'  C8     0.00   0.0  0
 CR9  CONST_37  O5'   C5'  C6'  C1'  180.00   0.0  0
 CR9  CONST_38  O6'   C6'  C1'  C2'  180.00   0.0  0
 CR9  CONST_39  O5'   C5'  C4'  C3'  180.00   0.0  0
 CR9  CONST_40  O6'   C6'  C5'  C4'  180.00   0.0  0
 CR9  CONST_41  HC3   C3   C2   C1   180.00   0.0  0
 CR9  CONST_42  HC6   C6   C1   C2   180.00   0.0  0
 CR9  CONST_43  HN3   N3   C4   C3     0.00   0.0  0
 CR9  CONST_44  HC2'  C2'  C1'  C8     0.00   0.0  0
 CR9  CONST_45  HC3'  C3'  C2'  C1'  180.00   0.0  0
 CR9  CONST_46  HC4'  C4'  C3'  C2'  180.00   0.0  0
 CR9  CONST_47  HH11  N1   C7   C1     0.00   0.0  0
 CR9  CONST_48  HH12  N1   C7   C1   180.00   0.0  0
 CR9  CONST_49  HH21  N2   C7   C1   180.00   0.0  0
 CR9  CONST_50  HH22  N2   C7   C1     0.00   0.0  0
 CR9  Var_01    C4B   C3B  C2B  C1B  -55.36  30.0  1
 CR9  Var_02    C5B   C4B  C3B  C2B   54.96  30.0  1
 CR9  Var_03    C6B   C5B  C4B  C3B  -56.65  30.0  1
 CR9  Var_04    N1    C7   C1   C2   -45.23  30.0  2

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
 CR9  chir_01  C1B  C2B  C6B  C1A  negativ
 CR9  chir_02  C6B  O5'  C5B  C1B  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
 CR9  plan-1  C8    0.020
 CR9  plan-1  C1'   0.020
 CR9  plan-1  C2'   0.020
 CR9  plan-1  C3'   0.020
 CR9  plan-1  C4'   0.020
 CR9  plan-1  C5'   0.020
 CR9  plan-1  C6'   0.020
 CR9  plan-1  O6'   0.020
 CR9  plan-1  O5'   0.020
 CR9  plan-1  HC2'  0.020
 CR9  plan-1  HC3'  0.020
 CR9  plan-1  HC4'  0.020
 CR9  plan-2  C1    0.020
 CR9  plan-2  C2    0.020
 CR9  plan-2  F2    0.020
 CR9  plan-2  C3    0.020
 CR9  plan-2  C4    0.020
 CR9  plan-2  C5    0.020
 CR9  plan-2  C6    0.020
 CR9  plan-2  C7    0.020
 CR9  plan-2  N3    0.020
 CR9  plan-2  N4    0.020
 CR9  plan-2  C8    0.020
 CR9  plan-2  C1'   0.020
 CR9  plan-2  HC3   0.020
 CR9  plan-2  HC6   0.020
 CR9  plan-2  HN3   0.020
 CR9  plan-3  C1    0.020
 CR9  plan-3  C7    0.020
 CR9  plan-3  N1    0.020
 CR9  plan-3  N2    0.020
 CR9  plan-3  HH11  0.020
 CR9  plan-3  HH12  0.020
 CR9  plan-3  HH21  0.020
 CR9  plan-3  HH22  0.020

