# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 00:23:47 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 4-(6-ethoxynaphthalen-2-yl)-6-(piperazin-1-ylmethyl)-2H-indazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc2cc(ccc2c1)c3cc(CN4CCNCC4)cc5n[nH]c(N)c35
#
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
 BK8  BK8  4-(6-ethoxynaphthalen-2-yl)-6-(piperazin-1-ylmethyl)-2H-indazol-3-amine  ligand  57  30  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BK8
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
 BK8  N2   N  NH2   0  -0.847   0.4166   4.1879  -0.0313
 BK8  C21  C  CR5   0   0.467  -0.8495   3.8001   0.3097
 BK8  C20  C  CR56  0  -0.179  -1.4310   2.5324   0.4783
 BK8  C10  C  CR6   0   0.139  -0.9643   1.1924   0.4418
 BK8  C9   C  CR6   0   0.004   0.4215   0.8494   0.0641
 BK8  C22  C  CR16  0  -0.310   0.9578   1.3033  -1.1699
 BK8  C23  C  CR16  0  -0.302   2.2209   0.9621  -1.5604
 BK8  C4   C  CR66  0   0.131   3.0396   0.1442  -0.7420
 BK8  C3   C  CR16  0  -0.437   4.3435  -0.2261  -1.1210
 BK8  C8   C  CR16  0  -0.366   1.1988   0.0542   0.8688
 BK8  C5   C  CR66  0   0.121   2.5108  -0.3128   0.4929
 BK8  C6   C  CR16  0  -0.300   3.3249  -1.1275   1.3079
 BK8  C7   C  CR16  0  -0.379   4.5912  -1.4814   0.9269
 BK8  C2   C  CR6   0   0.404   5.1137  -1.0275  -0.3079
 BK8  O    O  O2    0  -0.473   6.3463  -1.3388  -0.7475
 BK8  C1   C  CH2   0  -0.190   7.1842  -2.1743   0.0418
 BK8  C    C  CH3   0  -0.681   8.4799  -2.3737  -0.7078
 BK8  N3   N  NR15  0  -0.478  -1.8451   4.6712   0.5015
 BK8  N4   N  N     0  -0.352  -3.0390   4.1246   0.8035
 BK8  C19  C  CR56  0   0.273  -2.7908   2.8212   0.7966
 BK8  C18  C  CR16  0  -0.393  -3.6906   1.7663   1.0869
 BK8  C12  C  CR6   0   0.107  -3.2241   0.4834   1.0753
 BK8  C11  C  CR16  0  -0.385  -1.8647   0.2049   0.7480
 BK8  C13  C  CH2   0  -0.332  -4.1275  -0.6729   1.4134
 BK8  N    N  NT    0  -0.417  -4.0978  -1.7078   0.4024
 BK8  C17  C  CH2   0  -0.275  -4.7475  -2.9240   0.8553
 BK8  C16  C  CH2   0  -0.301  -4.6275  -4.0111  -0.1965
 BK8  N1   N  NH1   0  -0.599  -5.2162  -3.5487  -1.4389
 BK8  C15  C  CH2   0  -0.299  -4.5394  -2.3540  -1.9075
 BK8  C14  C  CH2   0  -0.271  -4.6542  -1.2611  -0.8616
 BK8  H1   H  HNH2  0   0.396   0.6826   5.1142   0.2672
 BK8  H2   H  HNH2  0   0.399   1.1340   3.5143   0.1853
 BK8  H3   H  HCR6  0   0.260   0.3441   1.9128  -1.8212
 BK8  H4   H  HCR6  0   0.255   2.6049   1.3104  -2.5114
 BK8  H5   H  HCR6  0   0.258   4.7454   0.1221  -2.0656
 BK8  H6   H  HCR6  0   0.252   0.8110  -0.2959   1.8188
 BK8  H7   H  HCR6  0   0.261   2.9372  -1.4830   2.2547
 BK8  H8   H  HCR6  0   0.284   5.1761  -2.1108   1.5830
 BK8  H9   H  HCH2  0   0.226   7.3754  -1.7108   1.0152
 BK8  H10  H  HCH2  0   0.226   6.6988  -3.1387   0.2230
 BK8  H11  H  HCH3  0   0.235   8.9904  -1.4262  -0.8808
 BK8  H12  H  HCH3  0   0.238   9.1422  -3.0092  -0.1210
 BK8  H13  H  HCH3  0   0.235   8.3134  -2.8601  -1.6691
 BK8  H14  H  HNR5  0   0.420  -1.7655   5.6757   0.4538
 BK8  H15  H  HCR6  0   0.244  -4.7272   1.9818   1.3185
 BK8  H16  H  HCR6  0   0.234  -1.5536  -0.8316   0.6998
 BK8  H17  H  HCH2  0   0.246  -3.7884  -1.1177   2.3551
 BK8  H18  H  HCH2  0   0.211  -5.1484  -0.2986   1.5999
 BK8  H20  H  HCH2  0   0.233  -4.2681  -3.2583   1.7786
 BK8  H21  H  HCH2  0   0.187  -5.8147  -2.7587   1.0832
 BK8  H22  H  HCH2  0   0.190  -3.5646  -4.2808  -0.3030
 BK8  H23  H  HCH2  0   0.232  -5.1557  -4.9031   0.1460
 BK8  H24  H  HNH1  0   0.353  -5.1541  -4.2756  -2.1393
 BK8  H26  H  HCH2  0   0.190  -3.4716  -2.5246  -2.1180
 BK8  H27  H  HCH2  0   0.231  -5.0034  -2.0143  -2.8353
 BK8  H28  H  HCH2  0   0.187  -5.7128  -0.9653  -0.7551
 BK8  H29  H  HCH2  0   0.238  -4.1081  -0.3799  -1.2035

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
 BK8  C    C1   single    1.510  0.020  1.510
 BK8  C1   O    single    1.422  0.020  1.422
 BK8  O    C2   single    1.345  0.020  1.345
 BK8  C2   C7   aromatic  1.416  0.020  1.416
 BK8  C2   C3   aromatic  1.377  0.020  1.377
 BK8  C7   C6   aromatic  1.369  0.020  1.369
 BK8  C3   C4   aromatic  1.408  0.020  1.408
 BK8  C6   C5   aromatic  1.411  0.020  1.411
 BK8  C4   C5   aromatic  1.419  0.020  1.419
 BK8  C4   C23  aromatic  1.417  0.020  1.417
 BK8  C5   C8   aromatic  1.413  0.020  1.413
 BK8  C23  C22  aromatic  1.365  0.020  1.365
 BK8  C8   C9   aromatic  1.373  0.020  1.373
 BK8  N2   C21  single    1.367  0.020  1.367
 BK8  C22  C9   aromatic  1.420  0.020  1.420
 BK8  C9   C10  single    1.477  0.020  1.477
 BK8  C21  N3   aromatic  1.337  0.020  1.337
 BK8  C21  C20  aromatic  1.405  0.020  1.405
 BK8  N3   N4   aromatic  1.347  0.020  1.347
 BK8  C10  C20  aromatic  1.419  0.020  1.419
 BK8  C10  C11  aromatic  1.371  0.020  1.371
 BK8  C20  C19  aromatic  1.426  0.020  1.426
 BK8  N4   C19  aromatic  1.327  0.020  1.327
 BK8  C11  C12  aromatic  1.426  0.020  1.426
 BK8  C19  C18  aromatic  1.417  0.020  1.417
 BK8  C12  C18  aromatic  1.365  0.020  1.365
 BK8  C12  C13  single    1.506  0.020  1.506
 BK8  C16  C17  single    1.517  0.020  1.517
 BK8  C16  N1   single    1.451  0.020  1.451
 BK8  N    C13  single    1.447  0.020  1.447
 BK8  N    C17  single    1.451  0.020  1.451
 BK8  N    C14  single    1.451  0.020  1.451
 BK8  C15  N1   single    1.451  0.020  1.451
 BK8  C15  C14  single    1.517  0.020  1.517
 BK8  N2   H1   single    0.890  0.020  1.040
 BK8  N2   H2   single    0.890  0.020  1.040
 BK8  C22  H3   single    0.930  0.020  1.080
 BK8  C23  H4   single    0.930  0.020  1.080
 BK8  C3   H5   single    0.930  0.020  1.080
 BK8  C8   H6   single    0.930  0.020  1.080
 BK8  C6   H7   single    0.930  0.020  1.080
 BK8  C7   H8   single    0.930  0.020  1.080
 BK8  C1   H9   single    0.970  0.020  1.090
 BK8  C1   H10  single    0.970  0.020  1.090
 BK8  C    H11  single    0.970  0.020  1.090
 BK8  C    H12  single    0.970  0.020  1.090
 BK8  C    H13  single    0.970  0.020  1.090
 BK8  N3   H14  single    0.860  0.020  1.020
 BK8  C18  H15  single    0.930  0.020  1.080
 BK8  C11  H16  single    0.930  0.020  1.080
 BK8  C13  H17  single    0.970  0.020  1.090
 BK8  C13  H18  single    0.970  0.020  1.090
 BK8  C17  H20  single    0.970  0.020  1.090
 BK8  C17  H21  single    0.970  0.020  1.090
 BK8  C16  H22  single    0.970  0.020  1.090
 BK8  C16  H23  single    0.970  0.020  1.090
 BK8  N1   H24  single    0.890  0.020  1.040
 BK8  C15  H26  single    0.970  0.020  1.090
 BK8  C15  H27  single    0.970  0.020  1.090
 BK8  C14  H28  single    0.970  0.020  1.090
 BK8  C14  H29  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
 BK8  H2   N2   H1   111.25  3.000
 BK8  H2   N2   C21  114.59  3.000
 BK8  H1   N2   C21  115.52  3.000
 BK8  N3   C21  C20  105.21  3.000
 BK8  C20  C21  N2   132.00  3.000
 BK8  N3   C21  N2   122.73  3.000
 BK8  C19  C20  C10  120.70  3.000
 BK8  C19  C20  C21  103.81  3.000
 BK8  C10  C20  C21  135.45  3.000
 BK8  C11  C10  C9   120.40  3.000
 BK8  C11  C10  C20  117.28  3.000
 BK8  C9   C10  C20  122.31  3.000
 BK8  C8   C9   C22  118.73  3.000
 BK8  C22  C9   C10  120.16  3.000
 BK8  C8   C9   C10  121.07  3.000
 BK8  H3   C22  C23  119.53  3.000
 BK8  H3   C22  C9   119.25  3.000
 BK8  C23  C22  C9   121.21  3.000
 BK8  H4   C23  C4   119.19  3.000
 BK8  H4   C23  C22  119.92  3.000
 BK8  C4   C23  C22  120.89  3.000
 BK8  C5   C4   C3   119.66  3.000
 BK8  C5   C4   C23  118.24  3.000
 BK8  C3   C4   C23  122.10  3.000
 BK8  H5   C3   C2   119.61  3.000
 BK8  H5   C3   C4   119.57  3.000
 BK8  C2   C3   C4   120.81  3.000
 BK8  H6   C8   C5   118.77  3.000
 BK8  H6   C8   C9   119.88  3.000
 BK8  C5   C8   C9   121.35  3.000
 BK8  C6   C5   C8   122.14  3.000
 BK8  C8   C5   C4   119.59  3.000
 BK8  C6   C5   C4   118.27  3.000
 BK8  H7   C6   C7   119.31  3.000
 BK8  H7   C6   C5   119.20  3.000
 BK8  C7   C6   C5   121.49  3.000
 BK8  H8   C7   C2   121.09  3.000
 BK8  H8   C7   C6   118.82  3.000
 BK8  C2   C7   C6   120.09  3.000
 BK8  O    C2   C7   123.30  3.000
 BK8  C7   C2   C3   119.68  3.000
 BK8  O    C2   C3   117.01  3.000
 BK8  C1   O    C2   119.63  3.000
 BK8  H10  C1   H9   107.64  3.000
 BK8  H10  C1   C    110.26  3.000
 BK8  H9   C1   C    110.33  3.000
 BK8  H10  C1   O    110.37  3.000
 BK8  H9   C1   O    110.33  3.000
 BK8  C    C1   O    107.91  3.000
 BK8  H13  C    H12  107.91  3.000
 BK8  H13  C    H11  108.63  3.000
 BK8  H12  C    H11  107.93  3.000
 BK8  H13  C    C1   111.44  3.000
 BK8  H12  C    C1   109.34  3.000
 BK8  H11  C    C1   111.46  3.000
 BK8  H14  N3   N4   118.98  3.000
 BK8  H14  N3   C21  125.68  3.000
 BK8  N4   N3   C21  115.33  3.000
 BK8  C19  N4   N3   103.39  3.000
 BK8  C18  C19  N4   127.71  3.000
 BK8  C18  C19  C20  120.04  3.000
 BK8  N4   C19  C20  112.24  3.000
 BK8  H15  C18  C12  121.03  3.000
 BK8  H15  C18  C19  120.21  3.000
 BK8  C12  C18  C19  118.76  3.000
 BK8  C13  C12  C11  118.27  3.000
 BK8  C13  C12  C18  120.98  3.000
 BK8  C11  C12  C18  120.75  3.000
 BK8  H16  C11  C12  118.10  3.000
 BK8  H16  C11  C10  119.39  3.000
 BK8  C12  C11  C10  122.46  3.000
 BK8  H18  C13  H17  106.20  3.000
 BK8  H18  C13  N    112.32  3.000
 BK8  H17  C13  N    107.69  3.000
 BK8  H18  C13  C12  109.43  3.000
 BK8  H17  C13  C12  108.61  3.000
 BK8  N    C13  C12  112.33  3.000
 BK8  C14  N    C17  110.98  3.000
 BK8  C14  N    C13  112.36  3.000
 BK8  C17  N    C13  111.84  3.000
 BK8  H21  C17  H20  107.19  3.000
 BK8  H21  C17  C16  109.08  3.000
 BK8  H20  C17  C16  109.38  3.000
 BK8  H21  C17  N    111.83  3.000
 BK8  H20  C17  N    108.88  3.000
 BK8  C16  C17  N    110.41  3.000
 BK8  H23  C16  H22  107.28  3.000
 BK8  H23  C16  N1   109.44  3.000
 BK8  H22  C16  N1   112.75  3.000
 BK8  H23  C16  C17  109.25  3.000
 BK8  H22  C16  C17  108.58  3.000
 BK8  N1   C16  C17  109.46  3.000
 BK8  H24  N1   C15  109.85  3.000
 BK8  H24  N1   C16  109.82  3.000
 BK8  C15  N1   C16  110.48  3.000
 BK8  H27  C15  H26  107.32  3.000
 BK8  H27  C15  C14  109.25  3.000
 BK8  H26  C15  C14  108.46  3.000
 BK8  H27  C15  N1   109.42  3.000
 BK8  H26  C15  N1   112.73  3.000
 BK8  C14  C15  N1   109.59  3.000
 BK8  H29  C14  H28  107.07  3.000
 BK8  H29  C14  C15  109.13  3.000
 BK8  H28  C14  C15  109.39  3.000
 BK8  H29  C14  N    109.23  3.000
 BK8  H28  C14  N    111.47  3.000
 BK8  C15  C14  N    110.47  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
 BK8  CONST_01  C19  N4   N3   C21    0.00   0.0  0
 BK8  CONST_02  C9   C10  C20  C21    0.00   0.0  0
 BK8  CONST_03  C11  C10  C20  C21  180.00   0.0  0
 BK8  CONST_04  N4   C19  C20  C21    0.00   0.0  0
 BK8  CONST_05  C18  C19  C20  C21  180.00   0.0  0
 BK8  CONST_06  N4   N3   C21  C20    0.00   0.0  0
 BK8  CONST_09  C12  C11  C10  C20    0.00   0.0  0
 BK8  CONST_10  N3   N4   C19  C20    0.00   0.0  0
 BK8  CONST_11  C12  C18  C19  C20    0.00   0.0  0
 BK8  CONST_12  C5   C8   C9   C10  180.00   0.0  0
 BK8  CONST_13  C23  C22  C9   C10  180.00   0.0  0
 BK8  CONST_14  N3   C21  C20  C10  180.00   0.0  0
 BK8  CONST_15  N4   C19  C20  C10  180.00   0.0  0
 BK8  CONST_16  C18  C19  C20  C10    0.00   0.0  0
 BK8  CONST_17  C18  C12  C11  C10    0.00   0.0  0
 BK8  CONST_18  C6   C5   C8   C9   180.00   0.0  0
 BK8  CONST_19  C4   C5   C8   C9     0.00   0.0  0
 BK8  CONST_20  C4   C23  C22  C9     0.00   0.0  0
 BK8  CONST_21  C19  C20  C10  C9   180.00   0.0  0
 BK8  CONST_22  C12  C11  C10  C9   180.00   0.0  0
 BK8  CONST_23  C3   C4   C23  C22  180.00   0.0  0
 BK8  CONST_24  C5   C4   C23  C22    0.00   0.0  0
 BK8  CONST_25  C5   C8   C9   C22    0.00   0.0  0
 BK8  CONST_27  C2   C3   C4   C23  180.00   0.0  0
 BK8  CONST_28  C6   C5   C4   C23  180.00   0.0  0
 BK8  CONST_29  C8   C5   C4   C23    0.00   0.0  0
 BK8  CONST_30  C8   C9   C22  C23    0.00   0.0  0
 BK8  CONST_31  C7   C2   C3   C4     0.00   0.0  0
 BK8  CONST_32  C7   C6   C5   C4     0.00   0.0  0
 BK8  CONST_33  C6   C7   C2   C3     0.00   0.0  0
 BK8  CONST_34  C6   C5   C4   C3     0.00   0.0  0
 BK8  CONST_35  C8   C5   C4   C3   180.00   0.0  0
 BK8  CONST_36  C7   C6   C5   C8   180.00   0.0  0
 BK8  CONST_38  C2   C7   C6   C5     0.00   0.0  0
 BK8  CONST_39  C2   C3   C4   C5     0.00   0.0  0
 BK8  CONST_40  C19  C20  C21  N3     0.00   0.0  0
 BK8  CONST_41  C18  C19  N4   N3   180.00   0.0  0
 BK8  CONST_42  C12  C18  C19  N4   180.00   0.0  0
 BK8  CONST_43  C11  C10  C20  C19    0.00   0.0  0
 BK8  CONST_44  C11  C12  C18  C19    0.00   0.0  0
 BK8  CONST_45  N4   N3   C21  N2   180.00   0.0  0
 BK8  CONST_46  C10  C20  C21  N2     0.00   0.0  0
 BK8  CONST_47  C19  C20  C21  N2   180.00   0.0  0
 BK8  CONST_48  C13  C12  C11  C10  180.00   0.0  0
 BK8  CONST_49  O    C2   C3   C4   180.00   0.0  0
 BK8  CONST_50  O    C2   C7   C6   180.00   0.0  0
 BK8  CONST_51  C13  C12  C18  C19  180.00   0.0  0
 BK8  CONST_52  H14  N3   C21  C20  180.00   0.0  0
 BK8  CONST_53  H16  C11  C10  C20  180.00   0.0  0
 BK8  CONST_54  H15  C18  C19  C20  180.00   0.0  0
 BK8  CONST_55  H6   C8   C9   C10    0.00   0.0  0
 BK8  CONST_56  H3   C22  C9   C10    0.00   0.0  0
 BK8  CONST_57  H4   C23  C22  C9   180.00   0.0  0
 BK8  CONST_58  H5   C3   C4   C23    0.00   0.0  0
 BK8  CONST_59  H7   C6   C5   C4   180.00   0.0  0
 BK8  CONST_60  H8   C7   C2   C3   180.00   0.0  0
 BK8  Var_01    N1   C16  C17  N    -57.95  30.0  1
 BK8  Var_02    N1   C15  C14  N     57.59  30.0  1
 BK8  Var_03    C15  N1   C16  C17   59.69  30.0  1
 BK8  Var_04    C15  C14  N    C17  -56.73  30.0  1
 BK8  Var_05    C14  N    C17  C16   56.92  30.0  1
 BK8  Var_06    C14  C15  N1   C16  -59.54  30.0  1
 BK8  Var_07    N    C13  C12  C18  128.11  30.0  2
 BK8  Var_08    C17  N    C13  C12  168.30  30.0  1
 BK8  Var_09    C    C1   O    C2   178.81  30.0  1
 BK8  Var_10    H11  C    C1   O     60.57  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
 BK8  plan-1  N2   0.020
 BK8  plan-1  C21  0.020
 BK8  plan-1  C20  0.020
 BK8  plan-1  C10  0.020
 BK8  plan-1  C9   0.020
 BK8  plan-1  N3   0.020
 BK8  plan-1  N4   0.020
 BK8  plan-1  C19  0.020
 BK8  plan-1  C18  0.020
 BK8  plan-1  C12  0.020
 BK8  plan-1  C11  0.020
 BK8  plan-1  C13  0.020
 BK8  plan-1  H14  0.020
 BK8  plan-1  H15  0.020
 BK8  plan-1  H16  0.020
 BK8  plan-2  C10  0.020
 BK8  plan-2  C9   0.020
 BK8  plan-2  C22  0.020
 BK8  plan-2  C23  0.020
 BK8  plan-2  C4   0.020
 BK8  plan-2  C3   0.020
 BK8  plan-2  C8   0.020
 BK8  plan-2  C5   0.020
 BK8  plan-2  C6   0.020
 BK8  plan-2  C7   0.020
 BK8  plan-2  C2   0.020
 BK8  plan-2  O    0.020
 BK8  plan-2  H3   0.020
 BK8  plan-2  H4   0.020
 BK8  plan-2  H5   0.020
 BK8  plan-2  H6   0.020
 BK8  plan-2  H7   0.020
 BK8  plan-2  H8   0.020
 BK8  plan-3  N2   0.020
 BK8  plan-3  C21  0.020
 BK8  plan-3  H1   0.020
 BK8  plan-3  H2   0.020

