# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:22:54 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-fluoro-2-(2-hydroxy-3-{[(1S,2S)-2-methylcyclohexyl]oxy}phenyl)-1H-indole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCCC[C@@H]1Oc2cccc(c2O)c3[nH]c4cc(F)c(cc4c3)C(N)=N
#
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
 134  134  6-fluoro-2-(2-hydroxy-3-{[(1S,2S)-2-methylcyclohexyl]oxy}phenyl)-1H-indole-5-carboximidamide  ligand  52  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_134
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
 134  C1    C  CR6   0  -0.185  -5.5733   0.0084   0.1538
 134  C2    C  CR6   0   0.521  -5.0988  -1.3142   0.1417
 134  F2    F  F     0  -0.308  -5.9753  -2.3164   0.3129
 134  C3    C  CR16  0  -0.475  -3.7732  -1.6472   0.0032
 134  C4    C  CR56  0   0.357  -2.8776  -0.5898  -0.1432
 134  C5    C  CR56  0   0.090  -3.2996   0.7574  -0.1347
 134  C6    C  CR16  0  -0.360  -4.6561   1.0412   0.0264
 134  C7    C  C     0   0.337  -7.0261   0.3107   0.2715
 134  N1    N  NH2   0  -0.809  -7.3104   1.3308   1.1331
 134  N2    N  N     0  -0.650  -7.8602  -0.3191  -0.4616
 134  N3    N  NR15  0  -0.740  -1.5306  -0.5972  -0.3054
 134  CN4   C  CR15  0  -0.446  -2.1305   1.5533  -0.3080
 134  C8    C  CR5   0   0.374  -1.0659   0.6944  -0.4129
 134  C1'   C  CR6   0  -0.065   0.3385   1.0335  -0.6390
 134  C2'   C  CR16  0  -0.338   0.6466   2.2160  -1.3278
 134  C3'   C  CR16  0  -0.257   1.9552   2.5887  -1.5451
 134  C4'   C  CR16  0  -0.375   3.0041   1.7943  -1.0851
 134  C5'   C  CR6   0   0.344   2.7228   0.6241  -0.4022
 134  C6'   C  CR6   0   0.221   1.3878   0.2423  -0.1777
 134  O6'   O  OH1   0  -0.632   1.1236  -0.8936   0.4992
 134  O5'   O  O2    0  -0.525   3.6194  -0.2483   0.1005
 134  C1B   C  CH1   0  -0.260   5.7031  -1.3936   0.1193
 134  C2B   C  CH2   0  -0.423   7.2202  -1.2091   0.0277
 134  C3B   C  CH2   0  -0.432   7.7523  -0.1849   1.0227
 134  C4B   C  CH2   0  -0.442   7.0390   1.1510   0.8573
 134  C5B   C  CH2   0  -0.466   5.5282   0.9767   0.9727
 134  C6B   C  CH1   0   0.069   5.0235  -0.0369  -0.0478
 134  CM    C  CH3   0  -0.655   5.2204  -2.4132  -0.9053
 134  HC3   H  HCR6  0   0.281  -3.4552  -2.6818   0.0136
 134  HC6   H  HCR6  0   0.264  -5.0005   2.0679   0.0291
 134  HH11  H  HNH2  0   0.395  -6.6771   1.5040   1.8956
 134  HH12  H  HNH2  0   0.390  -8.2784   1.5106   1.3478
 134  HH21  H  H     0   0.319  -8.8124  -0.0165  -0.2705
 134  HN3   H  HNR5  0   0.413  -0.9586  -1.4231  -0.3616
 134  HN4   H  HCR5  0   0.255  -2.0803   2.6302  -0.3342
 134  HC'2  H  HCR6  0   0.253  -0.1597   2.8307  -1.7049
 134  HC'3  H  HCR6  0   0.258   2.1773   3.5000  -2.0833
 134  HC'4  H  HCR6  0   0.281   4.0230   2.1039  -1.2713
 134  HO'6  H  HOH1  0   0.476   1.9529  -1.3329   0.7293
 134  H1'   H  HCH1  0   0.225   5.4653  -1.7616   1.1262
 134  H2'1  H  HCH2  0   0.235   7.7056  -2.1759   0.1826
 134  H2'2  H  HCH2  0   0.213   7.4780  -0.8930  -0.9900
 134  H3'1  H  HCH2  0   0.214   7.6051  -0.5532   2.0437
 134  H3'2  H  HCH2  0   0.232   8.8293  -0.0598   0.8885
 134  H4'1  H  HCH2  0   0.237   7.3849   1.8706   1.6021
 134  H4'2  H  HCH2  0   0.218   7.2847   1.5754  -0.1222
 134  H5'1  H  HCH2  0   0.228   5.2754   0.6190   1.9762
 134  H5'2  H  HCH2  0   0.245   5.0281   1.9391   0.8431
 134  H6'   H  HCH1  0   0.220   5.2283   0.3246  -1.0658
 134  HM1   H  HCH3  0   0.229   5.7416  -3.3624  -0.7700
 134  HM2   H  HCH3  0   0.233   4.1522  -2.6112  -0.8237
 134  HM3   H  HCH3  0   0.216   5.4230  -2.0696  -1.9227

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
 134  C1   C2    aromatic  1.405  0.020  1.405
 134  C1   C6    aromatic  1.387  0.020  1.387
 134  C1   C7    single    1.489  0.020  1.489
 134  C2   F2    single    1.342  0.020  1.342
 134  C2   C3    aromatic  1.374  0.020  1.374
 134  C3   C4    aromatic  1.393  0.020  1.393
 134  C3   HC3   single    0.930  0.020  1.080
 134  C4   C5    aromatic  1.412  0.020  1.412
 134  C4   N3    aromatic  1.357  0.020  1.357
 134  C5   C6    aromatic  1.395  0.020  1.395
 134  C5   CN4   aromatic  1.425  0.020  1.425
 134  C6   HC6   single    0.930  0.020  1.080
 134  C7   N1    single    1.365  0.020  1.365
 134  C7   N2    double    1.277  0.020  1.277
 134  N1   HH11  single    0.890  0.020  1.040
 134  N1   HH12  single    0.890  0.020  1.040
 134  N2   HH21  single    0.890  0.020  1.040
 134  N3   C8    aromatic  1.377  0.020  1.377
 134  N3   HN3   single    0.860  0.020  1.020
 134  CN4  C8    aromatic  1.372  0.020  1.372
 134  CN4  HN4   single    0.930  0.020  1.080
 134  C8   C1'   single    1.462  0.020  1.462
 134  C1'  C2'   aromatic  1.403  0.020  1.403
 134  C1'  C6'   aromatic  1.393  0.020  1.393
 134  C2'  C3'   aromatic  1.378  0.020  1.378
 134  C2'  HC'2  single    0.930  0.020  1.080
 134  C3'  C4'   aromatic  1.394  0.020  1.394
 134  C3'  HC'3  single    0.930  0.020  1.080
 134  C4'  C5'   aromatic  1.384  0.020  1.384
 134  C4'  HC'4  single    0.930  0.020  1.080
 134  C5'  C6'   aromatic  1.406  0.020  1.406
 134  C5'  O5'   single    1.348  0.020  1.348
 134  C6'  O6'   single    1.348  0.020  1.348
 134  O6'  HO'6  single    0.850  0.020  0.980
 134  O5'  C6B   single    1.428  0.020  1.428
 134  C1B  C2B   single    1.531  0.020  1.531
 134  C1B  C6B   single    1.527  0.020  1.527
 134  C1B  CM    single    1.524  0.020  1.524
 134  C1B  H1'   single    0.970  0.020  1.090
 134  C2B  C3B   single    1.524  0.020  1.524
 134  C2B  H2'1  single    0.970  0.020  1.090
 134  C2B  H2'2  single    0.970  0.020  1.090
 134  C3B  C4B   single    1.523  0.020  1.523
 134  C3B  H3'1  single    0.970  0.020  1.090
 134  C3B  H3'2  single    0.970  0.020  1.090
 134  C4B  C5B   single    1.525  0.020  1.525
 134  C4B  H4'1  single    0.970  0.020  1.090
 134  C4B  H4'2  single    0.970  0.020  1.090
 134  C5B  C6B   single    1.524  0.020  1.524
 134  C5B  H5'1  single    0.970  0.020  1.090
 134  C5B  H5'2  single    0.970  0.020  1.090
 134  C6B  H6'   single    0.970  0.020  1.090
 134  CM   HM1   single    0.970  0.020  1.090
 134  CM   HM2   single    0.970  0.020  1.090
 134  CM   HM3   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
 134  C7    C1   C6    120.09  3.000
 134  C7    C1   C2    121.42  3.000
 134  C6    C1   C2    118.47  3.000
 134  C3    C2   F2    117.51  3.000
 134  C3    C2   C1    123.70  3.000
 134  F2    C2   C1    118.76  3.000
 134  HC3   C3   C4    122.52  3.000
 134  HC3   C3   C2    120.94  3.000
 134  C4    C3   C2    116.54  3.000
 134  N3    C4   C5    107.62  3.000
 134  N3    C4   C3    130.28  3.000
 134  C5    C4   C3    122.10  3.000
 134  CN4   C5   C6    134.28  3.000
 134  CN4   C5   C4    106.68  3.000
 134  C6    C5   C4    119.04  3.000
 134  HC6   C6   C5    120.15  3.000
 134  HC6   C6   C1    119.70  3.000
 134  C5    C6   C1    120.13  3.000
 134  N2    C7   N1    126.51  3.000
 134  N2    C7   C1    119.48  3.000
 134  N1    C7   C1    113.88  3.000
 134  HH12  N1   HH11  114.36  3.000
 134  HH12  N1   C7    117.89  3.000
 134  HH11  N1   C7    118.41  3.000
 134  HH21  N2   C7    110.91  3.000
 134  HN3   N3   C8    125.01  3.000
 134  HN3   N3   C4    125.13  3.000
 134  C8    N3   C4    109.84  3.000
 134  HN4   CN4  C8    125.96  3.000
 134  HN4   CN4  C5    126.80  3.000
 134  C8    CN4  C5    107.23  3.000
 134  C1'   C8   CN4   127.73  3.000
 134  C1'   C8   N3    123.63  3.000
 134  CN4   C8   N3    108.63  3.000
 134  C6'   C1'  C2'   118.42  3.000
 134  C6'   C1'  C8    122.73  3.000
 134  C2'   C1'  C8    118.84  3.000
 134  HC'2  C2'  C3'   119.95  3.000
 134  HC'2  C2'  C1'   119.11  3.000
 134  C3'   C2'  C1'   120.94  3.000
 134  HC'3  C3'  C4'   119.34  3.000
 134  HC'3  C3'  C2'   120.10  3.000
 134  C4'   C3'  C2'   120.56  3.000
 134  HC'4  C4'  C5'   121.25  3.000
 134  HC'4  C4'  C3'   119.29  3.000
 134  C5'   C4'  C3'   119.47  3.000
 134  O5'   C5'  C6'   113.34  3.000
 134  O5'   C5'  C4'   126.58  3.000
 134  C6'   C5'  C4'   120.08  3.000
 134  O6'   C6'  C5'   119.65  3.000
 134  O6'   C6'  C1'   119.81  3.000
 134  C5'   C6'  C1'   120.54  3.000
 134  HO'6  O6'  C6'   109.53  3.000
 134  C6B   O5'  C5'   121.30  3.000
 134  H1'   C1B  CM    108.89  3.000
 134  H1'   C1B  C6B   107.57  3.000
 134  CM    C1B  C6B   112.33  3.000
 134  H1'   C1B  C2B   108.05  3.000
 134  CM    C1B  C2B   110.74  3.000
 134  C6B   C1B  C2B   109.12  3.000
 134  H2'2  C2B  H2'1  106.40  3.000
 134  H2'2  C2B  C3B   109.28  3.000
 134  H2'1  C2B  C3B   110.30  3.000
 134  H2'2  C2B  C1B   108.86  3.000
 134  H2'1  C2B  C1B   108.97  3.000
 134  C3B   C2B  C1B   112.82  3.000
 134  H3'2  C3B  H3'1  106.59  3.000
 134  H3'2  C3B  C4B   110.35  3.000
 134  H3'1  C3B  C4B   109.46  3.000
 134  H3'2  C3B  C2B   109.93  3.000
 134  H3'1  C3B  C2B   109.62  3.000
 134  C4B   C3B  C2B   110.79  3.000
 134  H4'2  C4B  H4'1  106.47  3.000
 134  H4'2  C4B  C5B   109.52  3.000
 134  H4'1  C4B  C5B   109.73  3.000
 134  H4'2  C4B  C3B   109.38  3.000
 134  H4'1  C4B  C3B   110.83  3.000
 134  C5B   C4B  C3B   110.81  3.000
 134  H5'2  C5B  H5'1  106.91  3.000
 134  H5'2  C5B  C6B   110.78  3.000
 134  H5'1  C5B  C6B   108.66  3.000
 134  H5'2  C5B  C4B   110.11  3.000
 134  H5'1  C5B  C4B   109.60  3.000
 134  C6B   C5B  C4B   110.69  3.000
 134  H6'   C6B  C5B   109.85  3.000
 134  H6'   C6B  C1B   108.10  3.000
 134  C5B   C6B  C1B   111.73  3.000
 134  H6'   C6B  O5'   109.15  3.000
 134  C5B   C6B  O5'   110.77  3.000
 134  C1B   C6B  O5'   107.15  3.000
 134  HM3   CM   HM2   107.98  3.000
 134  HM3   CM   HM1   107.48  3.000
 134  HM2   CM   HM1   107.51  3.000
 134  HM3   CM   C1B   110.91  3.000
 134  HM2   CM   C1B   112.44  3.000
 134  HM1   CM   C1B   110.32  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
 134  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 134  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 134  CONST_03  CN4   C5   C6   C1   180.00   0.0  0
 134  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 134  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 134  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 134  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 134  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 134  CONST_09  CN4   C5   C4   C3   180.00   0.0  0
 134  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 134  CONST_11  C8    CN4  C5   C4     0.00   0.0  0
 134  CONST_12  CN4   C8   N3   C4     0.00   0.0  0
 134  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 134  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 134  CONST_15  N3    C8   CN4  C5     0.00   0.0  0
 134  CONST_16  C1'   C8   CN4  C5   180.00   0.0  0
 134  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 134  CONST_18  C8    CN4  C5   C6   180.00   0.0  0
 134  CONST_19  CN4   C5   C4   N3     0.00   0.0  0
 134  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 134  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 134  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 134  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 134  CONST_28  C5'   C6'  C1'  C2'    0.00   0.0  0
 134  CONST_29  C5'   C4'  C3'  C2'    0.00   0.0  0
 134  CONST_30  C6'   C1'  C2'  C3'    0.00   0.0  0
 134  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 134  CONST_32  C6    C1   C2   F2   180.00   0.0  0
 134  CONST_33  C4    C3   C2   F2   180.00   0.0  0
 134  CONST_34  C7    C1   C2   C3   180.00   0.0  0
 134  CONST_35  C7    C1   C6   C5   180.00   0.0  0
 134  CONST_36  O6'   C6'  C1'  C8     0.00   0.0  0
 134  CONST_37  O5'   C5'  C6'  C1'  180.00   0.0  0
 134  CONST_38  O6'   C6'  C1'  C2'  180.00   0.0  0
 134  CONST_39  O5'   C5'  C4'  C3'  180.00   0.0  0
 134  CONST_40  O6'   C6'  C5'  C4'  180.00   0.0  0
 134  CONST_41  HC3   C3   C2   C1   180.00   0.0  0
 134  CONST_42  HC6   C6   C1   C2   180.00   0.0  0
 134  CONST_43  HN3   N3   C4   C3     0.00   0.0  0
 134  CONST_44  HN4   CN4  C5   C4   180.00   0.0  0
 134  CONST_45  HC'2  C2'  C1'  C8     0.00   0.0  0
 134  CONST_46  HC'3  C3'  C2'  C1'  180.00   0.0  0
 134  CONST_47  HC'4  C4'  C3'  C2'  180.00   0.0  0
 134  CONST_49  HH12  N1   C7   C1   180.00   0.0  0
 134  CONST_50  HH21  N2   C7   C1   180.00   0.0  0
 134  Var_01    C4B   C3B  C2B  C1B  -55.39  30.0  1
 134  Var_02    C5B   C4B  C3B  C2B   55.14  30.0  1
 134  Var_03    C6B   C5B  C4B  C3B  -56.63  30.0  1
 134  Var_04    N1    C7   C1   C2   136.71  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
 134  chir_01  C1B  C2B  C6B  CM   negativ
 134  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
 134  plan-1  C8    0.020
 134  plan-1  C1'   0.020
 134  plan-1  C2'   0.020
 134  plan-1  C3'   0.020
 134  plan-1  C4'   0.020
 134  plan-1  C5'   0.020
 134  plan-1  C6'   0.020
 134  plan-1  O6'   0.020
 134  plan-1  O5'   0.020
 134  plan-1  HC'2  0.020
 134  plan-1  HC'3  0.020
 134  plan-1  HC'4  0.020
 134  plan-2  C1    0.020
 134  plan-2  C2    0.020
 134  plan-2  F2    0.020
 134  plan-2  C3    0.020
 134  plan-2  C4    0.020
 134  plan-2  C5    0.020
 134  plan-2  C6    0.020
 134  plan-2  C7    0.020
 134  plan-2  N3    0.020
 134  plan-2  CN4   0.020
 134  plan-2  C8    0.020
 134  plan-2  C1'   0.020
 134  plan-2  HC3   0.020
 134  plan-2  HC6   0.020
 134  plan-2  HN3   0.020
 134  plan-2  HN4   0.020
 134  plan-3  C1    0.020
 134  plan-3  C7    0.020
 134  plan-3  N1    0.020
 134  plan-3  N2    0.020
 134  plan-3  HH11  0.020
 134  plan-3  HH12  0.020
 134  plan-3  HH21  0.020

