# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 07:13:47 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 6-fluoro-2-[2-hydroxy-3-(2-methylpropoxy)phenyl]-1H-benzimidazole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)COc1cccc(c1O)c2[nH]c3cc(F)c(cc3n2)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
 133  133  6-fluoro-2-[2-hydroxy-3-(2-methylpropoxy)phenyl]-1H-benzimidazole-5-carboximidamide  ligand  44  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_133
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
 133  C1    C  CR6   0  -0.188   0.7022   0.0660  -4.5014
 133  C2    C  CR6   0   0.529  -0.6557   0.3483  -4.7181
 133  F2    F  F     0  -0.305  -1.0816   0.5436  -5.9740
 133  C3    C  CR16  0  -0.469  -1.5985   0.3987  -3.7160
 133  C4    C  CR56  0   0.362  -1.1287   0.1579  -2.4316
 133  C5    C  CR56  0   0.146   0.2189  -0.1290  -2.1614
 133  C6    C  CR16  0  -0.350   1.1357  -0.1843  -3.2055
 133  C7    C  C     0   0.341   1.6777   0.0488  -5.6272
 133  N1    N  NH2   0  -0.809   2.5428  -1.0057  -5.5903
 133  N2    N  N     0  -0.649   1.6854   1.0126  -6.4634
 133  N3    N  NR15  0  -0.713  -1.7396   0.1236  -1.2157
 133  N4    N  N     0  -0.461   0.3991  -0.3235  -0.8152
 133  C8    C  CR5   0   0.476  -0.7824  -0.1658  -0.2820
 133  C1'   C  CR6   0  -0.110  -1.1369  -0.3139   1.1286
 133  C2'   C  CR16  0  -0.317  -2.3898  -0.8439   1.4704
 133  C3'   C  CR16  0  -0.259  -2.7533  -0.9985   2.7899
 133  C4'   C  CR16  0  -0.376  -1.8772  -0.6258   3.8080
 133  C5'   C  CR6   0   0.329  -0.6391  -0.1000   3.4877
 133  C6'   C  CR6   0   0.239  -0.2573   0.0598   2.1415
 133  O6'   O  OH1   0  -0.608   0.9374   0.5918   1.8439
 133  O5'   O  O2    0  -0.502   0.2937   0.3094   4.3696
 133  C10   C  CH2   0  -0.150   0.0507   0.1590   5.7600
 133  C20   C  CH1   0  -0.282   1.2751   0.6259   6.5276
 133  C30   C  CH3   0  -0.661   0.9697   0.5639   8.0208
 133  C40   C  CH3   0  -0.654   2.5110  -0.2008   6.1893
 133  HC3   H  HCR6  0   0.290  -2.6379   0.6037  -3.9350
 133  HC6   H  HCR6  0   0.273   2.1776  -0.4017  -3.0086
 133  HH11  H  HNH2  0   0.391   3.1466  -1.1506  -6.3840
 133  HH12  H  HNH2  0   0.397   2.2504  -1.8524  -5.1317
 133  HH21  H  H     0   0.321   2.3952   0.8689  -7.1775
 133  HN3   H  HNR5  0   0.426  -2.7061   0.3403  -1.0278
 133  HC'2  H  HCR6  0   0.259  -3.0709  -1.1569   0.6895
 133  HC'3  H  HCR6  0   0.263  -3.7170  -1.4177   3.0438
 133  HC'4  H  HCR6  0   0.289  -2.1756  -0.7532   4.8398
 133  HO'6  H  HOH1  0   0.475   1.3953   0.8266   2.6617
 133  H101  H  HCH2  0   0.221  -0.1602  -0.8927   5.9920
 133  H102  H  HCH2  0   0.234  -0.8279   0.7477   6.0494
 133  H20   H  HCH1  0   0.235   1.4637   1.6711   6.2595
 133  H301  H  HCH3  0   0.237   1.8216   0.9148   8.6037
 133  H302  H  HCH3  0   0.232   0.1111   1.1836   8.2841
 133  H303  H  HCH3  0   0.221   0.7544  -0.4597   8.3362
 133  H401  H  HCH3  0   0.216   2.3561  -1.2522   6.4435
 133  H402  H  HCH3  0   0.233   2.7685  -0.1469   5.1314
 133  H403  H  HCH3  0   0.231   3.3746   0.1518   6.7548

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
 133  C1   C2    aromatic  1.404  0.020  1.404
 133  C1   C6    aromatic  1.389  0.020  1.389
 133  C1   C7    single    1.490  0.020  1.490
 133  C2   F2    single    1.340  0.020  1.340
 133  C2   C3    aromatic  1.377  0.020  1.377
 133  C3   C4    aromatic  1.389  0.020  1.389
 133  C3   HC3   single    0.930  0.020  1.080
 133  C4   C5    aromatic  1.404  0.020  1.404
 133  C4   N3    aromatic  1.361  0.020  1.361
 133  C5   C6    aromatic  1.391  0.020  1.391
 133  C5   N4    aromatic  1.372  0.020  1.372
 133  C6   HC6   single    0.930  0.020  1.080
 133  C7   N1    single    1.364  0.020  1.364
 133  C7   N2    double    1.276  0.020  1.276
 133  N1   HH11  single    0.890  0.020  1.040
 133  N1   HH12  single    0.890  0.020  1.040
 133  N2   HH21  single    0.890  0.020  1.040
 133  N3   C8    aromatic  1.368  0.020  1.368
 133  N3   HN3   single    0.860  0.020  1.020
 133  N4   C8    aromatic  1.306  0.020  1.306
 133  C8   C1'   single    1.462  0.020  1.462
 133  C1'  C2'   aromatic  1.403  0.020  1.403
 133  C1'  C6'   aromatic  1.393  0.020  1.393
 133  C2'  C3'   aromatic  1.377  0.020  1.377
 133  C2'  HC'2  single    0.930  0.020  1.080
 133  C3'  C4'   aromatic  1.394  0.020  1.394
 133  C3'  HC'3  single    0.930  0.020  1.080
 133  C4'  C5'   aromatic  1.383  0.020  1.383
 133  C4'  HC'4  single    0.930  0.020  1.080
 133  C5'  C6'   aromatic  1.408  0.020  1.408
 133  C5'  O5'   single    1.347  0.020  1.347
 133  C6'  O6'   single    1.341  0.020  1.341
 133  O6'  HO'6  single    0.850  0.020  0.980
 133  O5'  C10   single    1.419  0.020  1.419
 133  C10  C20   single    1.519  0.020  1.519
 133  C10  H101  single    0.970  0.020  1.090
 133  C10  H102  single    0.970  0.020  1.090
 133  C20  C30   single    1.525  0.020  1.525
 133  C20  C40   single    1.525  0.020  1.525
 133  C20  H20   single    0.970  0.020  1.090
 133  C30  H301  single    0.970  0.020  1.090
 133  C30  H302  single    0.970  0.020  1.090
 133  C30  H303  single    0.970  0.020  1.090
 133  C40  H401  single    0.970  0.020  1.090
 133  C40  H402  single    0.970  0.020  1.090
 133  C40  H403  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
 133  C7    C1   C6    119.90  3.000
 133  C7    C1   C2    121.27  3.000
 133  C6    C1   C2    118.83  3.000
 133  C3    C2   F2    117.32  3.000
 133  C3    C2   C1    123.87  3.000
 133  F2    C2   C1    118.77  3.000
 133  HC3   C3   C4    123.03  3.000
 133  HC3   C3   C2    121.17  3.000
 133  C4    C3   C2    115.80  3.000
 133  N3    C4   C5    104.69  3.000
 133  N3    C4   C3    132.75  3.000
 133  C5    C4   C3    122.56  3.000
 133  N4    C5   C6    130.12  3.000
 133  N4    C5   C4    110.11  3.000
 133  C6    C5   C4    119.76  3.000
 133  HC6   C6   C5    120.40  3.000
 133  HC6   C6   C1    120.41  3.000
 133  C5    C6   C1    119.18  3.000
 133  N2    C7   N1    126.70  3.000
 133  N2    C7   C1    119.37  3.000
 133  N1    C7   C1    113.81  3.000
 133  HH12  N1   HH11  114.33  3.000
 133  HH12  N1   C7    118.57  3.000
 133  HH11  N1   C7    118.02  3.000
 133  HH21  N2   C7    110.96  3.000
 133  HN3   N3   C8    126.08  3.000
 133  HN3   N3   C4    126.25  3.000
 133  C8    N3   C4    107.52  3.000
 133  C8    N4   C5    105.35  3.000
 133  C1'   C8   N4    126.95  3.000
 133  C1'   C8   N3    120.68  3.000
 133  N4    C8   N3    112.32  3.000
 133  C6'   C1'  C2'   119.23  3.000
 133  C6'   C1'  C8    121.43  3.000
 133  C2'   C1'  C8    119.34  3.000
 133  HC'2  C2'  C3'   119.51  3.000
 133  HC'2  C2'  C1'   119.70  3.000
 133  C3'   C2'  C1'   120.77  3.000
 133  HC'3  C3'  C4'   119.50  3.000
 133  HC'3  C3'  C2'   120.25  3.000
 133  C4'   C3'  C2'   120.25  3.000
 133  HC'4  C4'  C5'   120.85  3.000
 133  HC'4  C4'  C3'   119.46  3.000
 133  C5'   C4'  C3'   119.69  3.000
 133  O5'   C5'  C6'   113.79  3.000
 133  O5'   C5'  C4'   125.72  3.000
 133  C6'   C5'  C4'   120.49  3.000
 133  O6'   C6'  C5'   119.91  3.000
 133  O6'   C6'  C1'   120.51  3.000
 133  C5'   C6'  C1'   119.57  3.000
 133  HO'6  O6'  C6'   109.31  3.000
 133  C10   O5'  C5'   119.37  3.000
 133  H102  C10  H101  107.74  3.000
 133  H102  C10  C20   110.34  3.000
 133  H101  C10  C20   110.05  3.000
 133  H102  C10  O5'   109.80  3.000
 133  H101  C10  O5'   109.97  3.000
 133  C20   C10  O5'   108.93  3.000
 133  H20   C20  C40   108.87  3.000
 133  H20   C20  C30   108.24  3.000
 133  C40   C20  C30   110.94  3.000
 133  H20   C20  C10   107.97  3.000
 133  C40   C20  C10   112.00  3.000
 133  C30   C20  C10   108.71  3.000
 133  H303  C30  H302  107.91  3.000
 133  H303  C30  H301  107.54  3.000
 133  H302  C30  H301  107.64  3.000
 133  H303  C30  C20   111.11  3.000
 133  H302  C30  C20   111.75  3.000
 133  H301  C30  C20   110.72  3.000
 133  H403  C40  H402  107.47  3.000
 133  H403  C40  H401  107.61  3.000
 133  H402  C40  H401  107.87  3.000
 133  H403  C40  C20   110.57  3.000
 133  H402  C40  C20   112.33  3.000
 133  H401  C40  C20   110.80  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
 133  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 133  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 133  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 133  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 133  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 133  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 133  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 133  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 133  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 133  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 133  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 133  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 133  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 133  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 133  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 133  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 133  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 133  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 133  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 133  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 133  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 133  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 133  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 133  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 133  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 133  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 133  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 133  CONST_32  C6    C1   C2   F2    180.00   0.0  0
 133  CONST_33  C4    C3   C2   F2    180.00   0.0  0
 133  CONST_34  C7    C1   C2   C3    180.00   0.0  0
 133  CONST_35  C7    C1   C6   C5    180.00   0.0  0
 133  CONST_36  O6'   C6'  C1'  C8      0.00   0.0  0
 133  CONST_37  O5'   C5'  C6'  C1'   180.00   0.0  0
 133  CONST_38  O6'   C6'  C1'  C2'   180.00   0.0  0
 133  CONST_39  O5'   C5'  C4'  C3'   180.00   0.0  0
 133  CONST_40  O6'   C6'  C5'  C4'   180.00   0.0  0
 133  CONST_41  HC3   C3   C2   C1    180.00   0.0  0
 133  CONST_42  HC6   C6   C1   C2    180.00   0.0  0
 133  CONST_43  HN3   N3   C4   C3      0.00   0.0  0
 133  CONST_44  HC'2  C2'  C1'  C8      0.00   0.0  0
 133  CONST_45  HC'3  C3'  C2'  C1'   180.00   0.0  0
 133  CONST_46  HC'4  C4'  C3'  C2'   180.00   0.0  0
 133  CONST_47  HH11  N1   C7   C1    180.00   0.0  0
 133  CONST_49  HH21  N2   C7   C1    180.00   0.0  0
 133  Var_01    N1    C7   C1   C2   -136.09  30.0  2
 133  Var_02    C20   C10  O5'  C5'   177.07  30.0  3
 133  Var_03    C30   C20  C10  O5'   175.68  30.0  3
 133  Var_04    H301  C30  C20  C10  -178.71  30.0  3
 133  Var_05    H401  C40  C20  C10   -60.60  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
 133  plan-1  C8    0.020
 133  plan-1  C1'   0.020
 133  plan-1  C2'   0.020
 133  plan-1  C3'   0.020
 133  plan-1  C4'   0.020
 133  plan-1  C5'   0.020
 133  plan-1  C6'   0.020
 133  plan-1  O6'   0.020
 133  plan-1  O5'   0.020
 133  plan-1  HC'2  0.020
 133  plan-1  HC'3  0.020
 133  plan-1  HC'4  0.020
 133  plan-2  C1    0.020
 133  plan-2  C2    0.020
 133  plan-2  F2    0.020
 133  plan-2  C3    0.020
 133  plan-2  C4    0.020
 133  plan-2  C5    0.020
 133  plan-2  C6    0.020
 133  plan-2  C7    0.020
 133  plan-2  N3    0.020
 133  plan-2  N4    0.020
 133  plan-2  C8    0.020
 133  plan-2  C1'   0.020
 133  plan-2  HC3   0.020
 133  plan-2  HC6   0.020
 133  plan-2  HN3   0.020
 133  plan-3  C1    0.020
 133  plan-3  C7    0.020
 133  plan-3  N1    0.020
 133  plan-3  N2    0.020
 133  plan-3  HH11  0.020
 133  plan-3  HH12  0.020
 133  plan-3  HH21  0.020

