# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:17:46 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[6-(1-hydroxycyclohexyl)pyridin-2-yl]-1H-indole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2[nH]c(cc2c1)c3cccc(n3)C4(O)CCCCC4
#
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
 50K  50K  2-[6-(1-hydroxycyclohexyl)pyridin-2-yl]-1H-indole-5-carboximidamide  ligand  47  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_50K
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
 50K  N1   N  NH2   0  -0.806   6.8942   1.1746  -1.2252
 50K  N3   N  NR15  0  -0.762   1.6226  -1.9820   0.3156
 50K  C4   C  CR16  0  -0.308   5.0590  -0.7152  -0.0969
 50K  C5   C  C     0   0.330   5.7798   1.6471  -0.5948
 50K  C6   C  CR56  0   0.097   2.3939   0.0717  -0.1215
 50K  C7   C  CR56  0   0.345   2.7650  -1.2692   0.1275
 50K  C8   C  CR5   0   0.341   0.5353  -1.1519   0.1898
 50K  C10  C  CR6   0   0.183  -0.8419  -1.6184   0.3253
 50K  C13  C  CR16  0  -0.145  -2.5027  -3.2809   0.7161
 50K  C15  C  CT    0   0.172  -4.0543   0.1238   0.0256
 50K  C17  C  CH2   0  -0.435  -4.8866   2.3022   1.0364
 50K  C20  C  CH2   0  -0.461  -3.7202   0.8894  -1.2625
 50K  O1   O  OH1   0  -0.671  -5.3731  -0.3803  -0.0255
 50K  C19  C  CH2   0  -0.431  -4.6275   2.0990  -1.4591
 50K  C18  C  CH2   0  -0.432  -4.5600   3.0376  -0.2592
 50K  C16  C  CH2   0  -0.429  -3.9969   1.0770   1.2257
 50K  C11  C  CR6   0   0.254  -3.0587  -1.0090   0.2406
 50K  N4   N  N     0  -0.439  -1.7771  -0.6876   0.1507
 50K  C12  C  CR16  0  -0.354  -3.4717  -2.3083   0.5322
 50K  C14  C  CR16  0  -0.331  -1.1642  -2.9438   0.6097
 50K  C1   C  CR16  0  -0.298   4.0984  -1.6737   0.1463
 50K  C9   C  CR15  0  -0.425   0.9722   0.1199  -0.0780
 50K  C2   C  CR16  0  -0.402   3.3900   1.0228  -0.3545
 50K  C3   C  CR6   0  -0.004   4.7188   0.6324  -0.3457
 50K  N2   N  N     0  -0.649   5.7172   2.8736  -0.2373
 50K  H1   H  HNH2  0   0.390   6.7909   0.3971  -1.8557
 50K  H2   H  HNH2  0   0.382   7.5541   1.8705  -1.5348
 50K  H3   H  HNR5  0   0.416   1.5924  -2.9732   0.4870
 50K  H4   H  HCR6  0   0.259   6.1013  -1.0055  -0.0732
 50K  H5   H  HCR6  0   0.273  -2.7882  -4.2999   0.9415
 50K  H6   H  HCH2  0   0.228  -4.7635   2.9712   1.8915
 50K  H7   H  HCH2  0   0.216  -5.9374   2.0004   1.0318
 50K  H8   H  HCH2  0   0.238  -2.6798   1.2164  -1.2138
 50K  H9   H  HCH2  0   0.235  -3.7897   0.2109  -2.1198
 50K  H10  H  HOH1  0   0.447  -5.5007  -0.8286  -0.8690
 50K  H11  H  HCH2  0   0.228  -4.3316   2.6253  -2.3695
 50K  H12  H  HCH2  0   0.212  -5.6597   1.7728  -1.6154
 50K  H13  H  HCH2  0   0.228  -5.2439   3.8785  -0.3970
 50K  H14  H  HCH2  0   0.209  -3.5527   3.4634  -0.1901
 50K  H15  H  HCH2  0   0.236  -4.2799   0.5364   2.1339
 50K  H16  H  HCH2  0   0.233  -2.9581   1.3907   1.3588
 50K  H17  H  HCR6  0   0.264  -4.5192  -2.5553   0.6197
 50K  H18  H  HCR6  0   0.260  -0.4064  -3.7029   0.7466
 50K  H19  H  HCR6  0   0.266   4.3749  -2.7002   0.3486
 50K  H20  H  HCR5  0   0.255   0.3387   0.9795  -0.2236
 50K  H21  H  HCR6  0   0.256   3.1170   2.0499  -0.5661
 50K  H22  H  H     0   0.330   4.8822   3.0400   0.3118

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
 50K  N2   C5   double    1.279  0.020  1.279
 50K  C5   N1   single    1.365  0.020  1.365
 50K  C5   C3   single    1.489  0.020  1.489
 50K  C4   C3   aromatic  1.412  0.020  1.412
 50K  C4   C1   aromatic  1.379  0.020  1.379
 50K  C3   C2   aromatic  1.385  0.020  1.385
 50K  C1   C7   aromatic  1.393  0.020  1.393
 50K  C2   C6   aromatic  1.397  0.020  1.397
 50K  C7   C6   aromatic  1.413  0.020  1.413
 50K  C7   N3   aromatic  1.360  0.020  1.360
 50K  C6   C9   aromatic  1.423  0.020  1.423
 50K  N3   C8   aromatic  1.374  0.020  1.374
 50K  C9   C8   aromatic  1.371  0.020  1.371
 50K  C8   C10  single    1.460  0.020  1.460
 50K  C10  N4   aromatic  1.331  0.020  1.331
 50K  C10  C14  aromatic  1.393  0.020  1.393
 50K  N4   C11  aromatic  1.324  0.020  1.324
 50K  C20  C19  single    1.525  0.020  1.525
 50K  C20  C15  single    1.535  0.020  1.535
 50K  C19  C18  single    1.525  0.020  1.525
 50K  C14  C13  aromatic  1.384  0.020  1.384
 50K  O1   C15  single    1.413  0.020  1.413
 50K  C11  C15  single    1.523  0.020  1.523
 50K  C11  C12  aromatic  1.394  0.020  1.394
 50K  C15  C16  single    1.534  0.020  1.534
 50K  C13  C12  aromatic  1.385  0.020  1.385
 50K  C18  C17  single    1.525  0.020  1.525
 50K  C16  C17  single    1.526  0.020  1.526
 50K  N1   H1   single    0.890  0.020  1.040
 50K  N1   H2   single    0.890  0.020  1.040
 50K  N3   H3   single    0.860  0.020  1.020
 50K  C4   H4   single    0.930  0.020  1.080
 50K  C13  H5   single    0.930  0.020  1.080
 50K  C17  H6   single    0.970  0.020  1.090
 50K  C17  H7   single    0.970  0.020  1.090
 50K  C20  H8   single    0.970  0.020  1.090
 50K  C20  H9   single    0.970  0.020  1.090
 50K  O1   H10  single    0.850  0.020  0.980
 50K  C19  H11  single    0.970  0.020  1.090
 50K  C19  H12  single    0.970  0.020  1.090
 50K  C18  H13  single    0.970  0.020  1.090
 50K  C18  H14  single    0.970  0.020  1.090
 50K  C16  H15  single    0.970  0.020  1.090
 50K  C16  H16  single    0.970  0.020  1.090
 50K  C12  H17  single    0.930  0.020  1.080
 50K  C14  H18  single    0.930  0.020  1.080
 50K  C1   H19  single    0.930  0.020  1.080
 50K  C9   H20  single    0.930  0.020  1.080
 50K  C2   H21  single    0.930  0.020  1.080
 50K  N2   H22  single    0.890  0.020  1.040

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
 50K  H2   N1   H1   114.10  3.000
 50K  H2   N1   C5   115.95  3.000
 50K  H1   N1   C5   118.23  3.000
 50K  H3   N3   C8   125.95  3.000
 50K  H3   N3   C7   124.41  3.000
 50K  C8   N3   C7   109.61  3.000
 50K  H4   C4   C3   119.46  3.000
 50K  H4   C4   C1   118.74  3.000
 50K  C3   C4   C1   121.79  3.000
 50K  N2   C5   C3   124.87  3.000
 50K  C3   C5   N1   115.04  3.000
 50K  N2   C5   N1   120.07  3.000
 50K  C2   C6   C9   133.98  3.000
 50K  C9   C6   C7   106.80  3.000
 50K  C2   C6   C7   119.21  3.000
 50K  C1   C7   C6   121.94  3.000
 50K  C6   C7   N3   107.52  3.000
 50K  C1   C7   N3   130.54  3.000
 50K  C9   C8   C10  127.95  3.000
 50K  C10  C8   N3   123.02  3.000
 50K  C9   C8   N3   109.03  3.000
 50K  C14  C10  N4   121.97  3.000
 50K  C14  C10  C8   122.75  3.000
 50K  N4   C10  C8   115.28  3.000
 50K  H5   C13  C14  120.03  3.000
 50K  H5   C13  C12  120.29  3.000
 50K  C14  C13  C12  119.68  3.000
 50K  C11  C15  C16  109.10  3.000
 50K  C16  C15  O1   106.56  3.000
 50K  C11  C15  O1   110.48  3.000
 50K  C16  C15  C20  109.78  3.000
 50K  C11  C15  C20  110.31  3.000
 50K  O1   C15  C20  110.53  3.000
 50K  H7   C17  H6   106.30  3.000
 50K  H7   C17  C16  109.83  3.000
 50K  H6   C17  C16  109.20  3.000
 50K  H7   C17  C18  109.59  3.000
 50K  H6   C17  C18  110.21  3.000
 50K  C16  C17  C18  111.57  3.000
 50K  H9   C20  H8   106.31  3.000
 50K  H9   C20  C19  110.64  3.000
 50K  H8   C20  C19  109.59  3.000
 50K  H9   C20  C15  109.51  3.000
 50K  H8   C20  C15  108.62  3.000
 50K  C19  C20  C15  111.98  3.000
 50K  H10  O1   C15  108.74  3.000
 50K  H12  C19  H11  106.28  3.000
 50K  H12  C19  C18  109.74  3.000
 50K  H11  C19  C18  110.32  3.000
 50K  H12  C19  C20  110.09  3.000
 50K  H11  C19  C20  109.18  3.000
 50K  C18  C19  C20  111.13  3.000
 50K  H14  C18  H13  106.52  3.000
 50K  H14  C18  C19  109.24  3.000
 50K  H13  C18  C19  110.29  3.000
 50K  H14  C18  C17  109.31  3.000
 50K  H13  C18  C17  110.13  3.000
 50K  C19  C18  C17  111.23  3.000
 50K  H16  C16  H15  106.65  3.000
 50K  H16  C16  C17  109.80  3.000
 50K  H15  C16  C17  110.42  3.000
 50K  H16  C16  C15  108.01  3.000
 50K  H15  C16  C15  109.43  3.000
 50K  C17  C16  C15  112.34  3.000
 50K  C12  C11  N4   121.80  3.000
 50K  C12  C11  C15  121.93  3.000
 50K  N4   C11  C15  116.26  3.000
 50K  C11  N4   C10  120.09  3.000
 50K  H17  C12  C11  121.16  3.000
 50K  H17  C12  C13  120.48  3.000
 50K  C11  C12  C13  118.35  3.000
 50K  H18  C14  C13  119.80  3.000
 50K  H18  C14  C10  122.11  3.000
 50K  C13  C14  C10  118.10  3.000
 50K  H19  C1   C7   121.49  3.000
 50K  H19  C1   C4   120.95  3.000
 50K  C7   C1   C4   117.55  3.000
 50K  H20  C9   C8   125.37  3.000
 50K  H20  C9   C6   127.60  3.000
 50K  C8   C9   C6   107.03  3.000
 50K  H21  C2   C3   120.67  3.000
 50K  H21  C2   C6   119.89  3.000
 50K  C3   C2   C6   119.42  3.000
 50K  C2   C3   C5   119.37  3.000
 50K  C2   C3   C4   120.08  3.000
 50K  C5   C3   C4   120.54  3.000
 50K  H22  N2   C5   110.44  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
 50K  CONST_01  C4   C1   C7   N3   180.00   0.0  0
 50K  CONST_02  C2   C6   C7   N3   180.00   0.0  0
 50K  CONST_03  C9   C6   C7   N3     0.00   0.0  0
 50K  CONST_04  C6   C9   C8   N3     0.00   0.0  0
 50K  CONST_05  N4   C10  C8   N3   180.00   0.0  0
 50K  CONST_06  C14  C10  C8   N3     0.00   0.0  0
 50K  CONST_07  C6   C2   C3   C4     0.00   0.0  0
 50K  CONST_08  C6   C7   C1   C4     0.00   0.0  0
 50K  CONST_09  C8   N3   C7   C6     0.00   0.0  0
 50K  CONST_10  C10  C8   C9   C6   180.00   0.0  0
 50K  CONST_11  C3   C4   C1   C7     0.00   0.0  0
 50K  CONST_12  C3   C2   C6   C7     0.00   0.0  0
 50K  CONST_13  C8   C9   C6   C7     0.00   0.0  0
 50K  CONST_14  C9   C8   N3   C7     0.00   0.0  0
 50K  CONST_15  C10  C8   N3   C7   180.00   0.0  0
 50K  CONST_16  C1   C7   N3   C8   180.00   0.0  0
 50K  CONST_17  C2   C6   C9   C8   180.00   0.0  0
 50K  CONST_18  C11  N4   C10  C8   180.00   0.0  0
 50K  CONST_19  C13  C14  C10  C8   180.00   0.0  0
 50K  CONST_20  C12  C11  N4   C10    0.00   0.0  0
 50K  CONST_21  C12  C13  C14  C10    0.00   0.0  0
 50K  CONST_22  N4   C10  C14  C13    0.00   0.0  0
 50K  CONST_23  N4   C11  C12  C13    0.00   0.0  0
 50K  CONST_24  C14  C10  N4   C11    0.00   0.0  0
 50K  CONST_25  C14  C13  C12  C11    0.00   0.0  0
 50K  CONST_26  C9   C8   C10  N4     0.00   0.0  0
 50K  CONST_27  C9   C8   C10  C14  180.00   0.0  0
 50K  CONST_28  C2   C3   C4   C1     0.00   0.0  0
 50K  CONST_29  C2   C6   C7   C1     0.00   0.0  0
 50K  CONST_30  C9   C6   C7   C1   180.00   0.0  0
 50K  CONST_31  C3   C2   C6   C9   180.00   0.0  0
 50K  CONST_32  C15  C11  N4   C10  180.00   0.0  0
 50K  CONST_33  C15  C11  C12  C13  180.00   0.0  0
 50K  CONST_34  C1   C4   C3   C5   180.00   0.0  0
 50K  CONST_35  C6   C2   C3   C5   180.00   0.0  0
 50K  CONST_36  H19  C1   C7   N3     0.00   0.0  0
 50K  CONST_37  H20  C9   C8   N3   180.00   0.0  0
 50K  CONST_38  H21  C2   C3   C4   180.00   0.0  0
 50K  CONST_39  H3   N3   C7   C6   180.00   0.0  0
 50K  CONST_40  H4   C4   C1   C7   180.00   0.0  0
 50K  CONST_41  H18  C14  C10  C8     0.00   0.0  0
 50K  CONST_42  H5   C13  C14  C10  180.00   0.0  0
 50K  CONST_43  H17  C12  C11  C15    0.00   0.0  0
 50K  CONST_44  H22  N2   C5   C3     0.00   0.0  0
 50K  CONST_46  H2   N1   C5   C3   180.00   0.0  0
 50K  Var_01    C18  C19  C20  C15   56.41  30.0  1
 50K  Var_02    C18  C17  C16  C15  -54.72  30.0  1
 50K  Var_03    C20  C19  C18  C17  -55.28  30.0  1
 50K  Var_04    C16  C17  C18  C19   54.45  30.0  1
 50K  Var_05    C4   C3   C5   N1    32.14  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
 50K  chir_01  C15  C20  C11  C16  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
 50K  plan-1  C8   0.020
 50K  plan-1  C10  0.020
 50K  plan-1  C13  0.020
 50K  plan-1  C15  0.020
 50K  plan-1  C11  0.020
 50K  plan-1  N4   0.020
 50K  plan-1  C12  0.020
 50K  plan-1  C14  0.020
 50K  plan-1  H5   0.020
 50K  plan-1  H17  0.020
 50K  plan-1  H18  0.020
 50K  plan-2  N3   0.020
 50K  plan-2  C4   0.020
 50K  plan-2  C5   0.020
 50K  plan-2  C6   0.020
 50K  plan-2  C7   0.020
 50K  plan-2  C8   0.020
 50K  plan-2  C10  0.020
 50K  plan-2  C1   0.020
 50K  plan-2  C9   0.020
 50K  plan-2  C2   0.020
 50K  plan-2  C3   0.020
 50K  plan-2  H3   0.020
 50K  plan-2  H4   0.020
 50K  plan-2  H19  0.020
 50K  plan-2  H20  0.020
 50K  plan-2  H21  0.020
 50K  plan-3  N1   0.020
 50K  plan-3  C5   0.020
 50K  plan-3  C3   0.020
 50K  plan-3  N2   0.020
 50K  plan-3  H1   0.020
 50K  plan-3  H2   0.020
 50K  plan-3  H22  0.020

