# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 13:40:47 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (3-amino-1H-indazol-5-yl)[(2S)-2-(4-fluorophenyl)piperidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1n[nH]c2ccc(cc12)C(=O)N3CCCC[C@H]3c4ccc(F)cc4
#
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
 6A6  6A6  (3-amino-1H-indazol-5-yl)[(2S)-2-(4-fluorophenyl)piperidin-1-yl]methanone  ligand  44  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6A6
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
 6A6  C2   C  CR6   0   0.506   4.4026  -2.0376  -0.9989
 6A6  C3   C  CR16  0  -0.401   3.6369  -1.3633  -1.9305
 6A6  C4   C  CR16  0  -0.274   2.9492  -0.2306  -1.5229
 6A6  C5   C  CR6   0   0.136   3.0080   0.2217  -0.2068
 6A6  C6   C  CR16  0  -0.296   3.7908  -0.4827   0.6984
 6A6  C7   C  CR16  0  -0.400   4.4971  -1.6140   0.3110
 6A6  C8   C  CH1   0  -0.140   2.2689   1.4873   0.1583
 6A6  C11  C  CH2   0  -0.442   1.8248   3.4086   1.6832
 6A6  C12  C  CH2   0  -0.427   0.3650   3.3749   1.2412
 6A6  C17  C  CR6   0  -0.076  -1.2864   0.2112  -0.1810
 6A6  C18  C  CR16  0  -0.335  -2.2232  -0.3174   0.6863
 6A6  C19  C  CR56  0  -0.104  -3.5347  -0.4671   0.2405
 6A6  C21  C  CR16  0  -0.287  -2.9372   0.3976  -1.9721
 6A6  F1   F  F     0  -0.320   5.0782  -3.1362  -1.3812
 6A6  C10  C  CH2   0  -0.442   2.4914   2.0387   1.5643
 6A6  C13  C  CH2   0  -0.339   0.2120   2.7291  -0.1320
 6A6  N14  N  NT    0  -0.468   0.8336   1.4051  -0.1330
 6A6  O16  O  O     0  -0.461   0.6250  -0.5891   0.9364
 6A6  C20  C  CR56  0   0.430  -3.8853  -0.1152  -1.0761
 6A6  C22  C  CR16  0  -0.274  -1.6558   0.5567  -1.5031
 6A6  N23  N  NR15  0  -0.565  -5.1957  -0.3800  -1.1993
 6A6  N24  N  N     0  -0.286  -5.7277  -0.8875  -0.0616
 6A6  C25  C  CR5   0   0.360  -4.7570  -0.9444   0.8135
 6A6  N26  N  NH2   0  -0.847  -4.9463  -1.3466   2.1132
 6A6  H1   H  HCR6  0   0.275   3.5828  -1.7086  -2.9546
 6A6  H2   H  HCR6  0   0.257   2.3503   0.3062  -2.2487
 6A6  H3   H  HCR6  0   0.257   3.8560  -0.1646   1.7300
 6A6  H4   H  HCR6  0   0.275   5.1067  -2.1576   1.0211
 6A6  H5   H  HCH1  0   0.259   2.6378   2.2536  -0.5359
 6A6  H6   H  HCH2  0   0.221   2.3716   4.1246   1.0609
 6A6  H7   H  HCH2  0   0.240   1.8995   3.7721   2.7099
 6A6  H8   H  HCH2  0   0.223  -0.2312   2.8098   1.9650
 6A6  H9   H  HCH2  0   0.242  -0.0476   4.3857   1.2108
 6A6  H10  H  HCR6  0   0.258  -1.9408  -0.5995   1.6932
 6A6  H11  H  HCR6  0   0.273  -3.1971   0.6535  -2.9904
 6A6  H12  H  HCH2  0   0.235   2.0829   1.3470   2.3055
 6A6  H13  H  HCH2  0   0.241   3.5612   2.1348   1.7630
 6A6  H14  H  HCH2  0   0.273  -0.8384   2.6574  -0.4016
 6A6  H15  H  HCH2  0   0.246   0.6990   3.3365  -0.8992
 6A6  H16  H  HCR6  0   0.268  -0.8988   0.9422  -2.1749
 6A6  H17  H  HNR5  0   0.413  -5.7832  -0.2498  -2.0049
 6A6  H18  H  HNH2  0   0.381  -5.7701  -1.9112   2.2552
 6A6  H19  H  HNH2  0   0.385  -4.1399  -1.7725   2.5425
 6A6  C15  C  C     0   0.527   0.1302   0.3101   0.2750

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
 6A6  F1   C2   single    1.345  0.020  1.345
 6A6  C2   C3   aromatic  1.382  0.020  1.382
 6A6  C2   C7   aromatic  1.380  0.020  1.380
 6A6  C3   C4   aromatic  1.386  0.020  1.386
 6A6  C7   C6   aromatic  1.389  0.020  1.389
 6A6  C4   C5   aromatic  1.393  0.020  1.393
 6A6  N26  C25  single    1.374  0.020  1.374
 6A6  C6   C5   aromatic  1.389  0.020  1.389
 6A6  C5   C8   single    1.510  0.020  1.510
 6A6  C25  N24  aromatic  1.308  0.020  1.308
 6A6  C25  C19  aromatic  1.432  0.020  1.432
 6A6  N24  N23  aromatic  1.355  0.020  1.355
 6A6  C8   N14  single    1.467  0.020  1.467
 6A6  C8   C10  single    1.527  0.020  1.527
 6A6  C18  C19  aromatic  1.393  0.020  1.393
 6A6  C18  C17  aromatic  1.382  0.020  1.382
 6A6  C19  C20  aromatic  1.407  0.020  1.407
 6A6  C13  N14  single    1.463  0.020  1.463
 6A6  C13  C12  single    1.525  0.020  1.525
 6A6  N14  C15  single    1.364  0.020  1.364
 6A6  C10  C11  single    1.528  0.020  1.528
 6A6  N23  C20  aromatic  1.343  0.020  1.343
 6A6  C15  C17  single    1.491  0.020  1.491
 6A6  C15  O16  double    1.221  0.020  1.221
 6A6  C12  C11  single    1.526  0.020  1.526
 6A6  C17  C22  aromatic  1.416  0.020  1.416
 6A6  C20  C21  aromatic  1.402  0.020  1.402
 6A6  C22  C21  aromatic  1.374  0.020  1.374
 6A6  C3   H1   single    0.930  0.020  1.080
 6A6  C4   H2   single    0.930  0.020  1.080
 6A6  C6   H3   single    0.930  0.020  1.080
 6A6  C7   H4   single    0.930  0.020  1.080
 6A6  C8   H5   single    0.970  0.020  1.090
 6A6  C11  H6   single    0.970  0.020  1.090
 6A6  C11  H7   single    0.970  0.020  1.090
 6A6  C12  H8   single    0.970  0.020  1.090
 6A6  C12  H9   single    0.970  0.020  1.090
 6A6  C18  H10  single    0.930  0.020  1.080
 6A6  C21  H11  single    0.930  0.020  1.080
 6A6  C10  H12  single    0.970  0.020  1.090
 6A6  C10  H13  single    0.970  0.020  1.090
 6A6  C13  H14  single    0.970  0.020  1.090
 6A6  C13  H15  single    0.970  0.020  1.090
 6A6  C22  H16  single    0.930  0.020  1.080
 6A6  N23  H17  single    0.860  0.020  1.020
 6A6  N26  H18  single    0.890  0.020  1.040
 6A6  N26  H19  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
 6A6  F1   C2   C7   119.09  3.000
 6A6  C7   C2   C3   121.88  3.000
 6A6  F1   C2   C3   119.03  3.000
 6A6  H1   C3   C4   120.94  3.000
 6A6  H1   C3   C2   120.67  3.000
 6A6  C4   C3   C2   118.39  3.000
 6A6  H2   C4   C5   119.69  3.000
 6A6  H2   C4   C3   118.83  3.000
 6A6  C5   C4   C3   121.48  3.000
 6A6  C8   C5   C6   122.91  3.000
 6A6  C8   C5   C4   118.68  3.000
 6A6  C6   C5   C4   118.35  3.000
 6A6  H3   C6   C7   118.36  3.000
 6A6  H3   C6   C5   120.43  3.000
 6A6  C7   C6   C5   121.20  3.000
 6A6  H4   C7   C6   120.83  3.000
 6A6  H4   C7   C2   120.48  3.000
 6A6  C6   C7   C2   118.69  3.000
 6A6  H5   C8   N14  104.03  3.000
 6A6  H5   C8   C10  106.34  3.000
 6A6  N14  C8   C10  110.23  3.000
 6A6  H5   C8   C5   105.52  3.000
 6A6  C10  C8   C5   117.00  3.000
 6A6  N14  C8   C5   112.57  3.000
 6A6  H7   C11  H6   106.41  3.000
 6A6  H7   C11  C10  109.99  3.000
 6A6  H6   C11  C10  108.91  3.000
 6A6  H7   C11  C12  110.20  3.000
 6A6  H6   C11  C12  109.12  3.000
 6A6  C10  C11  C12  112.03  3.000
 6A6  H9   C12  H8   106.88  3.000
 6A6  H9   C12  C13  109.20  3.000
 6A6  H8   C12  C13  108.79  3.000
 6A6  H9   C12  C11  110.44  3.000
 6A6  H8   C12  C11  109.93  3.000
 6A6  C13  C12  C11  111.48  3.000
 6A6  C22  C17  C18  120.18  3.000
 6A6  C22  C17  C15  121.15  3.000
 6A6  C18  C17  C15  118.52  3.000
 6A6  H10  C18  C19  120.99  3.000
 6A6  H10  C18  C17  120.42  3.000
 6A6  C19  C18  C17  118.58  3.000
 6A6  C25  C19  C20  104.19  3.000
 6A6  C20  C19  C18  120.47  3.000
 6A6  C25  C19  C18  135.34  3.000
 6A6  H11  C21  C22  121.21  3.000
 6A6  H11  C21  C20  121.73  3.000
 6A6  C22  C21  C20  117.07  3.000
 6A6  H13  C10  H12  107.35  3.000
 6A6  H13  C10  C11  109.53  3.000
 6A6  H12  C10  C11  110.58  3.000
 6A6  H13  C10  C8   110.01  3.000
 6A6  H12  C10  C8   109.97  3.000
 6A6  C11  C10  C8   109.38  3.000
 6A6  H15  C13  H14  107.05  3.000
 6A6  H15  C13  N14  108.25  3.000
 6A6  H14  C13  N14  110.54  3.000
 6A6  H15  C13  C12  110.61  3.000
 6A6  H14  C13  C12  110.38  3.000
 6A6  N14  C13  C12  109.96  3.000
 6A6  C13  N14  C15  120.49  3.000
 6A6  C15  N14  C8   119.36  3.000
 6A6  C13  N14  C8   111.40  3.000
 6A6  N23  C20  C21  132.35  3.000
 6A6  C21  C20  C19  121.40  3.000
 6A6  N23  C20  C19  106.24  3.000
 6A6  H16  C22  C21  118.78  3.000
 6A6  H16  C22  C17  118.93  3.000
 6A6  C21  C22  C17  122.28  3.000
 6A6  H17  N23  N24  119.47  3.000
 6A6  H17  N23  C20  128.19  3.000
 6A6  N24  N23  C20  112.34  3.000
 6A6  C25  N24  N23  106.66  3.000
 6A6  N26  C25  N24  122.92  3.000
 6A6  N24  C25  C19  110.56  3.000
 6A6  N26  C25  C19  126.43  3.000
 6A6  H19  N26  H18  110.91  3.000
 6A6  H19  N26  C25  114.61  3.000
 6A6  H18  N26  C25  114.18  3.000
 6A6  O16  C15  N14  122.98  3.000
 6A6  O16  C15  C17  120.11  3.000
 6A6  N14  C15  C17  116.85  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
 6A6  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 6A6  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 6A6  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 6A6  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 6A6  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 6A6  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 6A6  CONST_07  C25  C19  C18  C17   180.00   0.0  0
 6A6  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 6A6  CONST_09  C20  C21  C22  C17     0.00   0.0  0
 6A6  CONST_10  N24  C25  C19  C18   180.00   0.0  0
 6A6  CONST_11  N23  C20  C19  C18   180.00   0.0  0
 6A6  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 6A6  CONST_13  C21  C22  C17  C18     0.00   0.0  0
 6A6  CONST_14  N23  N24  C25  C19     0.00   0.0  0
 6A6  CONST_15  C22  C17  C18  C19     0.00   0.0  0
 6A6  CONST_16  N24  N23  C20  C19     0.00   0.0  0
 6A6  CONST_17  C22  C21  C20  C19     0.00   0.0  0
 6A6  CONST_18  C25  C19  C20  C21   180.00   0.0  0
 6A6  CONST_19  N24  N23  C20  C21   180.00   0.0  0
 6A6  CONST_20  N24  C25  C19  C20     0.00   0.0  0
 6A6  CONST_21  C25  N24  N23  C20     0.00   0.0  0
 6A6  CONST_22  N23  C20  C21  C22   180.00   0.0  0
 6A6  CONST_23  C25  C19  C20  N23     0.00   0.0  0
 6A6  CONST_24  C8   C5   C4   C3    180.00   0.0  0
 6A6  CONST_25  C8   C5   C6   C7    180.00   0.0  0
 6A6  CONST_26  F1   C2   C3   C4    180.00   0.0  0
 6A6  CONST_27  F1   C2   C7   C6    180.00   0.0  0
 6A6  CONST_28  C19  C18  C17  C15   180.00   0.0  0
 6A6  CONST_29  C21  C22  C17  C15   180.00   0.0  0
 6A6  CONST_30  N26  C25  C19  C18     0.00   0.0  0
 6A6  CONST_31  N26  C25  C19  C20   180.00   0.0  0
 6A6  CONST_32  N26  C25  N24  N23   180.00   0.0  0
 6A6  CONST_33  C17  C15  N14  C8    180.00   0.0  0
 6A6  CONST_35  H2   C4   C3   C2    180.00   0.0  0
 6A6  CONST_36  H3   C6   C7   C2    180.00   0.0  0
 6A6  CONST_37  H4   C7   C2   C3    180.00   0.0  0
 6A6  CONST_38  H1   C3   C4   C5    180.00   0.0  0
 6A6  CONST_39  H11  C21  C22  C17   180.00   0.0  0
 6A6  CONST_40  H16  C22  C17  C18   180.00   0.0  0
 6A6  CONST_41  H17  N23  C20  C19   180.00   0.0  0
 6A6  CONST_42  H10  C18  C19  C20   180.00   0.0  0
 6A6  CONST_43  O16  C15  N14  C8      0.00   0.0  0
 6A6  Var_01    C12  C13  N14  C8    -60.93  30.0  1
 6A6  Var_02    C12  C11  C10  C8     51.96  30.0  1
 6A6  Var_03    N14  C13  C12  C11    54.22  30.0  1
 6A6  Var_04    C13  C12  C11  C10   -50.97  30.0  1
 6A6  Var_05    N14  C15  C17  C18  -143.34  30.0  1

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
 6A6  chir_01  C8  C5  N14  C10  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
 6A6  plan-1  C2   0.020
 6A6  plan-1  C3   0.020
 6A6  plan-1  C4   0.020
 6A6  plan-1  C5   0.020
 6A6  plan-1  C6   0.020
 6A6  plan-1  C7   0.020
 6A6  plan-1  C8   0.020
 6A6  plan-1  F1   0.020
 6A6  plan-1  H1   0.020
 6A6  plan-1  H2   0.020
 6A6  plan-1  H3   0.020
 6A6  plan-1  H4   0.020
 6A6  plan-2  C17  0.020
 6A6  plan-2  C18  0.020
 6A6  plan-2  C19  0.020
 6A6  plan-2  C21  0.020
 6A6  plan-2  C20  0.020
 6A6  plan-2  C22  0.020
 6A6  plan-2  N23  0.020
 6A6  plan-2  N24  0.020
 6A6  plan-2  C25  0.020
 6A6  plan-2  N26  0.020
 6A6  plan-2  H10  0.020
 6A6  plan-2  H11  0.020
 6A6  plan-2  H16  0.020
 6A6  plan-2  H17  0.020
 6A6  plan-2  C15  0.020
 6A6  plan-3  C25  0.020
 6A6  plan-3  N26  0.020
 6A6  plan-3  H18  0.020
 6A6  plan-3  H19  0.020
 6A6  plan-4  C8   0.020
 6A6  plan-4  C17  0.020
 6A6  plan-4  C13  0.020
 6A6  plan-4  N14  0.020
 6A6  plan-4  O16  0.020
 6A6  plan-4  C15  0.020

