# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:21:28 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: 5-[2,3-bis(fluoranyl)phenyl]-~{N}-[[1-(2-methoxyethyl)piperidin-4-yl]methyl]-1~{H}-indazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN1CCC(CC1)CNC(=O)c2n[nH]c3ccc(cc23)c4cccc(F)c4F
#
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
 N1Q  N1Q  5-[2,3-bis(fluoranyl)phenyl]-~{N}-[[1-(2-methoxyethyl)piperidin-4-yl]methyl]-1~{H}-indazole-3-carboxamide  ligand  57  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N1Q
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
 N1Q  C1   C  CH2   0  -0.134  -21.1792  -16.0792   -8.4158
 N1Q  C2   C  CH2   0  -0.304  -20.0218  -17.0583   -8.2981
 N1Q  C3   C  CH2   0  -0.286  -20.4180  -18.0228   -6.1235
 N1Q  C4   C  CH2   0  -0.425  -19.9813  -18.0295   -4.6669
 N1Q  C5   C  CH1   0  -0.251  -18.5297  -18.4731   -4.5281
 N1Q  C6   C  CH2   0  -0.268  -18.0931  -18.4279   -3.0661
 N1Q  C7   C  C     0   0.523  -15.6849  -18.1641   -2.6087
 N1Q  C8   C  CR5   0   0.068  -14.3979  -18.8868   -2.5026
 N1Q  C11  C  CR16  0  -0.294  -10.4286  -18.0841   -1.6046
 N1Q  C12  C  CR6   0   0.086  -11.2806  -16.9531   -1.5432
 N1Q  C15  C  CR6   0  -0.145  -10.7461  -15.6380   -1.1312
 N1Q  C16  C  CR16  0  -0.291  -11.3483  -14.9095   -0.1035
 N1Q  C17  C  CR16  0  -0.241  -10.8619  -13.6702    0.2792
 N1Q  C18  C  CR16  0  -0.412   -9.7547  -13.1226   -0.3548
 N1Q  C19  C  CR6   0   0.409   -9.1581  -13.8350   -1.3730
 N1Q  C21  C  CH2   0  -0.423  -17.6553  -17.6164   -5.4367
 N1Q  C20  C  CR6   0   0.383   -9.6470  -15.0712   -1.7593
 N1Q  F    F  F     0  -0.306   -8.0986  -13.3343   -2.0175
 N1Q  C10  C  CR16  0  -0.276  -10.8957  -19.3334   -1.9307
 N1Q  C13  C  CR16  0  -0.379  -12.6268  -17.0779   -1.8229
 N1Q  C14  C  CR56  0  -0.042  -13.1276  -18.3402   -2.1632
 N1Q  C9   C  CR56  0   0.414  -12.2609  -19.4434   -2.2110
 N1Q  N3   N  NR15  0  -0.530  -13.0285  -20.5066   -2.5537
 N1Q  N2   N  N     0  -0.240  -14.2967  -20.1777   -2.7262
 N1Q  O1   O  O     0  -0.488  -15.7175  -16.9480   -2.4633
 N1Q  N1   N  NH1   0  -0.648  -16.7553  -18.9310   -2.8562
 N1Q  C22  C  CH2   0  -0.276  -18.1774  -17.6333   -6.8651
 N1Q  N    N  NT    0  -0.426  -19.5549  -17.1771   -6.9305
 N1Q  O    O  O2    0  -0.488  -21.5460  -15.9884   -9.7703
 N1Q  C    C  CH3   0  -0.395  -22.6230  -15.1136   -9.9815
 N1Q  H1   H  HCH2  0   0.197  -20.8668  -15.1013   -8.0232
 N1Q  H2   H  HCH2  0   0.196  -22.0367  -16.4056   -7.8105
 N1Q  H3   H  HCH2  0   0.199  -20.3130  -18.0332   -8.7237
 N1Q  H4   H  HCH2  0   0.234  -19.1977  -16.6825   -8.9101
 N1Q  H5   H  HCH2  0   0.236  -21.4455  -17.6600   -6.1865
 N1Q  H6   H  HCH2  0   0.188  -20.4272  -19.0595   -6.5062
 N1Q  H7   H  HCH2  0   0.217  -20.1018  -17.0226   -4.2538
 N1Q  H8   H  HCH2  0   0.233  -20.6419  -18.6895   -4.0987
 N1Q  H9   H  HCH1  0   0.219  -18.4615  -19.5147   -4.8715
 N1Q  H10  H  HCH2  0   0.240  -18.1418  -17.4046   -2.6934
 N1Q  H11  H  HCH2  0   0.250  -18.7817  -19.0234   -2.4618
 N1Q  H12  H  HCR6  0   0.263   -9.3812  -17.9709   -1.3585
 N1Q  H13  H  HCR6  0   0.270  -12.2008  -15.3348    0.4096
 N1Q  H14  H  HCR6  0   0.274  -11.3407  -13.1256    1.0809
 N1Q  H15  H  HCR6  0   0.293   -9.3588  -12.1578   -0.0675
 N1Q  H16  H  HCH2  0   0.231  -16.6235  -17.9751   -5.4353
 N1Q  H17  H  HCH2  0   0.214  -17.6390  -16.5854   -5.0680
 N1Q  H18  H  HCR6  0   0.279  -10.2354  -20.1891   -1.9601
 N1Q  H19  H  HCR6  0   0.263  -13.2827  -16.2192   -1.7888
 N1Q  H20  H  HNR5  0   0.427  -12.7391  -21.4636   -2.6815
 N1Q  H21  H  HNH1  0   0.403  -16.6078  -19.9225   -2.9672
 N1Q  H22  H  HCH2  0   0.184  -18.0658  -18.6538   -7.2743
 N1Q  H23  H  HCH2  0   0.236  -17.5640  -16.9775   -7.4872
 N1Q  H25  H  HCH3  0   0.232  -22.8390  -15.0938  -11.0494
 N1Q  H26  H  HCH3  0   0.203  -23.5275  -15.4379   -9.4526
 N1Q  H27  H  HCH3  0   0.203  -22.3943  -14.0915   -9.6560
 N1Q  F1   F  F     0  -0.297   -9.0488  -15.7036   -2.7752

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
 N1Q  C    O    single    1.403  0.020  1.403
 N1Q  O    C1   single    1.406  0.020  1.406
 N1Q  C2   C1   single    1.521  0.020  1.521
 N1Q  C2   N    single    1.450  0.020  1.450
 N1Q  C22  N    single    1.453  0.020  1.453
 N1Q  C22  C21  single    1.521  0.020  1.521
 N1Q  N    C3   single    1.453  0.020  1.453
 N1Q  C3   C4   single    1.521  0.020  1.521
 N1Q  C21  C5   single    1.524  0.020  1.524
 N1Q  C4   C5   single    1.524  0.020  1.524
 N1Q  C5   C6   single    1.526  0.020  1.526
 N1Q  C6   N1   single    1.445  0.020  1.445
 N1Q  N1   C7   single    1.340  0.020  1.340
 N1Q  O1   C7   double    1.225  0.020  1.225
 N1Q  C7   C8   single    1.480  0.020  1.480
 N1Q  F1   C20  single    1.338  0.020  1.338
 N1Q  C8   N2   aromatic  1.314  0.020  1.314
 N1Q  C8   C14  aromatic  1.424  0.020  1.424
 N1Q  F    C19  single    1.337  0.020  1.337
 N1Q  N2   N3   aromatic  1.321  0.020  1.321
 N1Q  C14  C13  aromatic  1.400  0.020  1.400
 N1Q  C14  C9   aromatic  1.404  0.020  1.404
 N1Q  C13  C12  aromatic  1.381  0.020  1.381
 N1Q  C20  C19  aromatic  1.384  0.020  1.384
 N1Q  C20  C15  aromatic  1.387  0.020  1.387
 N1Q  N3   C9   aromatic  1.355  0.020  1.355
 N1Q  C19  C18  aromatic  1.378  0.020  1.378
 N1Q  C9   C10  aromatic  1.398  0.020  1.398
 N1Q  C12  C15  single    1.478  0.020  1.478
 N1Q  C12  C11  aromatic  1.417  0.020  1.417
 N1Q  C15  C16  aromatic  1.396  0.020  1.396
 N1Q  C10  C11  aromatic  1.373  0.020  1.373
 N1Q  C18  C17  aromatic  1.388  0.020  1.388
 N1Q  C16  C17  aromatic  1.385  0.020  1.385
 N1Q  C1   H1   single    0.970  0.020  1.090
 N1Q  C1   H2   single    0.970  0.020  1.090
 N1Q  C2   H3   single    0.970  0.020  1.090
 N1Q  C2   H4   single    0.970  0.020  1.090
 N1Q  C3   H5   single    0.970  0.020  1.090
 N1Q  C3   H6   single    0.970  0.020  1.090
 N1Q  C4   H7   single    0.970  0.020  1.090
 N1Q  C4   H8   single    0.970  0.020  1.090
 N1Q  C5   H9   single    0.970  0.020  1.090
 N1Q  C6   H10  single    0.970  0.020  1.090
 N1Q  C6   H11  single    0.970  0.020  1.090
 N1Q  C11  H12  single    0.930  0.020  1.080
 N1Q  C16  H13  single    0.930  0.020  1.080
 N1Q  C17  H14  single    0.930  0.020  1.080
 N1Q  C18  H15  single    0.930  0.020  1.080
 N1Q  C21  H16  single    0.970  0.020  1.090
 N1Q  C21  H17  single    0.970  0.020  1.090
 N1Q  C10  H18  single    0.930  0.020  1.080
 N1Q  C13  H19  single    0.930  0.020  1.080
 N1Q  N3   H20  single    0.860  0.020  1.020
 N1Q  N1   H21  single    0.860  0.020  1.020
 N1Q  C22  H22  single    0.970  0.020  1.090
 N1Q  C22  H23  single    0.970  0.020  1.090
 N1Q  C    H25  single    0.970  0.020  1.090
 N1Q  C    H26  single    0.970  0.020  1.090
 N1Q  C    H27  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
 N1Q  H2   C1   H1   106.82  3.000
 N1Q  H2   C1   O    110.24  3.000
 N1Q  H1   C1   O    111.14  3.000
 N1Q  H2   C1   C2   111.10  3.000
 N1Q  H1   C1   C2   109.20  3.000
 N1Q  O    C1   C2   108.34  3.000
 N1Q  H4   C2   H3   106.67  3.000
 N1Q  H4   C2   N    108.27  3.000
 N1Q  H3   C2   N    112.12  3.000
 N1Q  H4   C2   C1   108.01  3.000
 N1Q  H3   C2   C1   109.78  3.000
 N1Q  N    C2   C1   111.77  3.000
 N1Q  H6   C3   H5   106.50  3.000
 N1Q  H6   C3   N    111.01  3.000
 N1Q  H5   C3   N    109.49  3.000
 N1Q  H6   C3   C4   109.27  3.000
 N1Q  H5   C3   C4   109.09  3.000
 N1Q  N    C3   C4   111.34  3.000
 N1Q  H8   C4   H7   107.02  3.000
 N1Q  H8   C4   C5   110.64  3.000
 N1Q  H7   C4   C5   109.75  3.000
 N1Q  H8   C4   C3   109.09  3.000
 N1Q  H7   C4   C3   109.01  3.000
 N1Q  C5   C4   C3   111.22  3.000
 N1Q  H9   C5   C21  108.11  3.000
 N1Q  H9   C5   C6   108.04  3.000
 N1Q  C21  C5   C6   112.96  3.000
 N1Q  H9   C5   C4   107.85  3.000
 N1Q  C6   C5   C4   110.55  3.000
 N1Q  C21  C5   C4   109.17  3.000
 N1Q  H11  C6   H10  107.12  3.000
 N1Q  H11  C6   N1   108.26  3.000
 N1Q  H10  C6   N1   108.58  3.000
 N1Q  H11  C6   C5   109.47  3.000
 N1Q  H10  C6   C5   110.03  3.000
 N1Q  N1   C6   C5   113.19  3.000
 N1Q  N1   C7   O1   124.66  3.000
 N1Q  O1   C7   C8   119.96  3.000
 N1Q  N1   C7   C8   115.37  3.000
 N1Q  N2   C8   C14  110.42  3.000
 N1Q  C14  C8   C7   127.26  3.000
 N1Q  N2   C8   C7   122.32  3.000
 N1Q  H12  C11  C10  118.60  3.000
 N1Q  H12  C11  C12  119.25  3.000
 N1Q  C10  C11  C12  122.13  3.000
 N1Q  C13  C12  C15  119.31  3.000
 N1Q  C15  C12  C11  120.31  3.000
 N1Q  C13  C12  C11  120.35  3.000
 N1Q  C20  C15  C16  117.51  3.000
 N1Q  C16  C15  C12  120.89  3.000
 N1Q  C20  C15  C12  121.60  3.000
 N1Q  H13  C16  C17  119.82  3.000
 N1Q  H13  C16  C15  118.93  3.000
 N1Q  C17  C16  C15  121.24  3.000
 N1Q  H14  C17  C18  119.55  3.000
 N1Q  H14  C17  C16  120.01  3.000
 N1Q  C18  C17  C16  120.44  3.000
 N1Q  H15  C18  C19  119.92  3.000
 N1Q  H15  C18  C17  121.49  3.000
 N1Q  C19  C18  C17  118.59  3.000
 N1Q  F    C19  C20  118.66  3.000
 N1Q  C20  C19  C18  120.98  3.000
 N1Q  F    C19  C18  120.35  3.000
 N1Q  H17  C21  H16  107.14  3.000
 N1Q  H17  C21  C22  109.38  3.000
 N1Q  H16  C21  C22  108.77  3.000
 N1Q  H17  C21  C5   109.69  3.000
 N1Q  H16  C21  C5   110.88  3.000
 N1Q  C22  C21  C5   110.89  3.000
 N1Q  F1   C20  C19  118.43  3.000
 N1Q  C19  C20  C15  121.23  3.000
 N1Q  F1   C20  C15  120.33  3.000
 N1Q  H18  C10  C9   121.91  3.000
 N1Q  H18  C10  C11  121.25  3.000
 N1Q  C9   C10  C11  116.84  3.000
 N1Q  H19  C13  C14  120.45  3.000
 N1Q  H19  C13  C12  120.89  3.000
 N1Q  C14  C13  C12  118.66  3.000
 N1Q  C9   C14  C13  119.74  3.000
 N1Q  C9   C14  C8   103.94  3.000
 N1Q  C13  C14  C8   136.32  3.000
 N1Q  N3   C9   C14  105.99  3.000
 N1Q  N3   C9   C10  131.72  3.000
 N1Q  C14  C9   C10  122.29  3.000
 N1Q  H20  N3   N2   119.69  3.000
 N1Q  H20  N3   C9   127.89  3.000
 N1Q  N2   N3   C9   112.42  3.000
 N1Q  N3   N2   C8   107.23  3.000
 N1Q  H21  N1   C7   117.79  3.000
 N1Q  H21  N1   C6   117.50  3.000
 N1Q  C7   N1   C6   124.57  3.000
 N1Q  H23  C22  H22  106.66  3.000
 N1Q  H23  C22  N    108.56  3.000
 N1Q  H22  C22  N    111.66  3.000
 N1Q  H23  C22  C21  109.60  3.000
 N1Q  H22  C22  C21  108.87  3.000
 N1Q  N    C22  C21  111.37  3.000
 N1Q  C22  N    C3   110.82  3.000
 N1Q  C3   N    C2   112.35  3.000
 N1Q  C22  N    C2   111.94  3.000
 N1Q  C    O    C1   112.67  3.000
 N1Q  H27  C    H26  107.72  3.000
 N1Q  H27  C    H25  108.38  3.000
 N1Q  H26  C    H25  108.33  3.000
 N1Q  H27  C    O    112.10  3.000
 N1Q  H26  C    O    112.08  3.000
 N1Q  H25  C    O    108.11  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
 N1Q  CONST_01  C9   N3   N2   C8      0.00   0.0  0
 N1Q  CONST_02  C12  C13  C14  C8    180.00   0.0  0
 N1Q  CONST_03  N3   C9   C14  C8      0.00   0.0  0
 N1Q  CONST_04  C10  C9   C14  C8    180.00   0.0  0
 N1Q  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 N1Q  CONST_08  C14  C9   C10  C11     0.00   0.0  0
 N1Q  CONST_09  N3   C9   C10  C11   180.00   0.0  0
 N1Q  CONST_10  C9   C14  C13  C12     0.00   0.0  0
 N1Q  CONST_11  C19  C20  C15  C12   180.00   0.0  0
 N1Q  CONST_12  C17  C16  C15  C12   180.00   0.0  0
 N1Q  CONST_13  C9   C10  C11  C12     0.00   0.0  0
 N1Q  CONST_14  C18  C19  C20  C15     0.00   0.0  0
 N1Q  CONST_15  C14  C13  C12  C15   180.00   0.0  0
 N1Q  CONST_16  C10  C11  C12  C15   180.00   0.0  0
 N1Q  CONST_17  C18  C17  C16  C15     0.00   0.0  0
 N1Q  CONST_18  C19  C20  C15  C16     0.00   0.0  0
 N1Q  CONST_20  C19  C18  C17  C16     0.00   0.0  0
 N1Q  CONST_21  C20  C19  C18  C17     0.00   0.0  0
 N1Q  CONST_22  C20  C15  C16  C17     0.00   0.0  0
 N1Q  CONST_24  C13  C14  C9   C10     0.00   0.0  0
 N1Q  CONST_25  N2   N3   C9   C10   180.00   0.0  0
 N1Q  CONST_26  C13  C12  C11  C10     0.00   0.0  0
 N1Q  CONST_27  N2   C8   C14  C13   180.00   0.0  0
 N1Q  CONST_28  N3   C9   C14  C13   180.00   0.0  0
 N1Q  CONST_29  N3   N2   C8   C14     0.00   0.0  0
 N1Q  CONST_30  N2   N3   C9   C14     0.00   0.0  0
 N1Q  CONST_31  N2   C8   C14  C9      0.00   0.0  0
 N1Q  CONST_32  N3   N2   C8   C7    180.00   0.0  0
 N1Q  CONST_33  C13  C14  C8   C7      0.00   0.0  0
 N1Q  CONST_34  C9   C14  C8   C7    180.00   0.0  0
 N1Q  CONST_35  F1   C20  C15  C12     0.00   0.0  0
 N1Q  CONST_36  F    C19  C20  C15   180.00   0.0  0
 N1Q  CONST_37  F1   C20  C15  C16   180.00   0.0  0
 N1Q  CONST_38  F    C19  C18  C17   180.00   0.0  0
 N1Q  CONST_39  F1   C20  C19  C18   180.00   0.0  0
 N1Q  CONST_40  H20  N3   N2   C8    180.00   0.0  0
 N1Q  CONST_41  H19  C13  C14  C8      0.00   0.0  0
 N1Q  CONST_42  H13  C16  C15  C12     0.00   0.0  0
 N1Q  CONST_43  H18  C10  C11  C12   180.00   0.0  0
 N1Q  CONST_44  H12  C11  C12  C15     0.00   0.0  0
 N1Q  CONST_45  H14  C17  C16  C15   180.00   0.0  0
 N1Q  CONST_46  H15  C18  C17  C16   180.00   0.0  0
 N1Q  CONST_47  C8   C7   N1   C6    180.00   0.0  0
 N1Q  CONST_48  H21  N1   C7   C8      0.00   0.0  0
 N1Q  CONST_49  O1   C7   N1   C6      0.00   0.0  0
 N1Q  Var_01    C21  C22  N    C3    -59.58  30.0  1
 N1Q  Var_02    C22  N    C3   C4     59.17  30.0  1
 N1Q  Var_03    N    C22  C21  C5     57.26  30.0  1
 N1Q  Var_04    N    C3   C4   C5    -56.64  30.0  1
 N1Q  Var_05    N1   C7   C8   C14  -175.63  30.0  1
 N1Q  Var_06    C7   N1   C6   C5    105.24  30.0  3
 N1Q  Var_07    O    C1   C2   N     178.20  30.0  3
 N1Q  Var_08    H25  C    O    C1    179.58  30.0  3

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
 N1Q  chir_01  C5  C21  C4  C6  positiv

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
 N1Q  plan-1  C12  0.020
 N1Q  plan-1  C15  0.020
 N1Q  plan-1  C16  0.020
 N1Q  plan-1  C17  0.020
 N1Q  plan-1  C18  0.020
 N1Q  plan-1  C19  0.020
 N1Q  plan-1  C20  0.020
 N1Q  plan-1  F    0.020
 N1Q  plan-1  H13  0.020
 N1Q  plan-1  H14  0.020
 N1Q  plan-1  H15  0.020
 N1Q  plan-1  F1   0.020
 N1Q  plan-2  C7   0.020
 N1Q  plan-2  C8   0.020
 N1Q  plan-2  C11  0.020
 N1Q  plan-2  C12  0.020
 N1Q  plan-2  C15  0.020
 N1Q  plan-2  C10  0.020
 N1Q  plan-2  C13  0.020
 N1Q  plan-2  C14  0.020
 N1Q  plan-2  C9   0.020
 N1Q  plan-2  N3   0.020
 N1Q  plan-2  N2   0.020
 N1Q  plan-2  H12  0.020
 N1Q  plan-2  H18  0.020
 N1Q  plan-2  H19  0.020
 N1Q  plan-2  H20  0.020
 N1Q  plan-3  C6   0.020
 N1Q  plan-3  C7   0.020
 N1Q  plan-3  C8   0.020
 N1Q  plan-3  O1   0.020
 N1Q  plan-3  N1   0.020
 N1Q  plan-3  H21  0.020

