# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:48:08 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (1~{S},2~{R})-2-[[(6-bromanyl-1~{H}-indazol-4-yl)amino]methyl]cyclohexan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCCC[C@@H]1CNc2cc(Br)cc3[nH]ncc23
#
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
 HU3  HU3  (1~{S},2~{R})-2-[[(6-bromanyl-1~{H}-indazol-4-yl)amino]methyl]cyclohexan-1-ol  ligand  37  19  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HU3
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
 HU3  C10  C   CH2   0  -0.449  -10.1291  -25.6089  37.9078
 HU3  C15  C   CR15  0  -0.113  -12.8960  -29.6757  32.4572
 HU3  BR1  BR  BR    0  -0.062   -7.4725  -30.8370  30.0952
 HU3  C02  C   CR6   0  -0.107   -9.1322  -30.4287  30.9131
 HU3  C03  C   CR16  0  -0.382   -9.1035  -29.7104  32.1099
 HU3  C04  C   CR6   0   0.380  -10.2872  -29.3599  32.7728
 HU3  N05  N   NH1   0  -0.703  -10.2221  -28.6493  33.9207
 HU3  C06  C   CH2   0  -0.244  -11.3363  -28.2714  34.7599
 HU3  C07  C   CH1   0  -0.327  -10.8456  -27.4379  35.9381
 HU3  C08  C   CH1   0   0.088  -11.9837  -27.0337  36.8709
 HU3  C09  C   CH2   0  -0.466  -11.4131  -26.4112  38.1542
 HU3  C11  C   CH2   0  -0.451  -10.1213  -25.0371  36.4974
 HU3  C12  C   CH2   0  -0.426  -10.1194  -26.1642  35.4562
 HU3  O13  O   OH1   0  -0.672  -12.7832  -28.1626  37.1561
 HU3  C14  C   CR56  0  -0.172  -11.5028  -29.7771  32.1707
 HU3  N16  N   N     0  -0.234  -13.6116  -30.2650  31.5361
 HU3  N17  N   NR15  0  -0.553  -12.7480  -30.7577  30.6424
 HU3  C18  C   CR56  0   0.432  -11.4621  -30.5025  30.9631
 HU3  C19  C   CR16  0  -0.333  -10.2850  -30.8525  30.2924
 HU3  H1   H   HCH2  0   0.221   -9.2553  -26.2545  38.0328
 HU3  H2   H   HCH2  0   0.233  -10.0310  -24.8147  38.6498
 HU3  H4   H   HCR6  0   0.271   -8.1562  -29.4101  32.5402
 HU3  H5   H   HNH1  0   0.394   -9.2994  -28.5049  34.2978
 HU3  H6   H   HCH2  0   0.224  -12.0511  -27.6734  34.1829
 HU3  H7   H   HCH2  0   0.244  -11.8654  -29.1593  35.1168
 HU3  H8   H   HCH1  0   0.239  -10.1439  -28.0555  36.5157
 HU3  H9   H   HCH1  0   0.194  -12.5881  -26.2779  36.3446
 HU3  H10  H   HCH2  0   0.227  -12.1760  -25.7736  38.6098
 HU3  H11  H   HCH2  0   0.227  -11.2140  -27.2181  38.8645
 HU3  H12  H   HCH2  0   0.234   -9.2528  -24.3935  36.3460
 HU3  H13  H   HCH2  0   0.222  -10.9992  -24.3987  36.3630
 HU3  H14  H   HCH2  0   0.233   -9.0876  -26.4129  35.1996
 HU3  H15  H   HCH2  0   0.228  -10.5894  -25.8106  34.5342
 HU3  H16  H   HOH1  0   0.447  -13.5102  -27.8800  37.7200
 HU3  H18  H   HCR6  0   0.276  -10.2926  -31.4087  29.3661
 HU3  H17  H   HNR5  0   0.414  -13.0889  -31.2628  29.8403
 HU3  H3   H   HCR5  0   0.266  -13.3902  -29.2025  33.2898

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
 HU3  BR1  C02  single    1.895  0.020  1.895
 HU3  C19  C02  aromatic  1.376  0.020  1.376
 HU3  C19  C18  aromatic  1.399  0.020  1.399
 HU3  C02  C03  aromatic  1.396  0.020  1.396
 HU3  N17  C18  aromatic  1.350  0.020  1.350
 HU3  N17  N16  aromatic  1.337  0.020  1.337
 HU3  C18  C14  aromatic  1.409  0.020  1.409
 HU3  C03  C04  aromatic  1.401  0.020  1.401
 HU3  N16  C15  aromatic  1.307  0.020  1.307
 HU3  C14  C04  aromatic  1.419  0.020  1.419
 HU3  C14  C15  aromatic  1.426  0.020  1.426
 HU3  C04  N05  single    1.352  0.020  1.352
 HU3  N05  C06  single    1.445  0.020  1.445
 HU3  C06  C07  single    1.524  0.020  1.524
 HU3  C12  C07  single    1.543  0.020  1.543
 HU3  C12  C11  single    1.534  0.020  1.534
 HU3  C07  C08  single    1.526  0.020  1.526
 HU3  O13  C08  single    1.412  0.020  1.412
 HU3  C11  C10  single    1.522  0.020  1.522
 HU3  C08  C09  single    1.536  0.020  1.536
 HU3  C10  C09  single    1.534  0.020  1.534
 HU3  C10  H1   single    0.970  0.020  1.090
 HU3  C10  H2   single    0.970  0.020  1.090
 HU3  C15  H3   single    0.930  0.020  1.080
 HU3  C03  H4   single    0.930  0.020  1.080
 HU3  N05  H5   single    0.860  0.020  1.020
 HU3  C06  H6   single    0.970  0.020  1.090
 HU3  C06  H7   single    0.970  0.020  1.090
 HU3  C07  H8   single    0.970  0.020  1.090
 HU3  C08  H9   single    0.970  0.020  1.090
 HU3  C09  H10  single    0.970  0.020  1.090
 HU3  C09  H11  single    0.970  0.020  1.090
 HU3  C11  H12  single    0.970  0.020  1.090
 HU3  C11  H13  single    0.970  0.020  1.090
 HU3  C12  H14  single    0.970  0.020  1.090
 HU3  C12  H15  single    0.970  0.020  1.090
 HU3  O13  H16  single    0.850  0.020  0.980
 HU3  C19  H18  single    0.930  0.020  1.080
 HU3  N17  H17  single    0.860  0.020  1.020

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
 HU3  H2   C10  H1   106.26  3.000
 HU3  H2   C10  C11  110.87  3.000
 HU3  H1   C10  C11  108.88  3.000
 HU3  H2   C10  C09  110.28  3.000
 HU3  H1   C10  C09  109.98  3.000
 HU3  C11  C10  C09  110.47  3.000
 HU3  H3   C15  N16  119.44  3.000
 HU3  H3   C15  C14  129.38  3.000
 HU3  N16  C15  C14  111.19  3.000
 HU3  C19  C02  C03  124.21  3.000
 HU3  C03  C02  BR1  117.57  3.000
 HU3  C19  C02  BR1  118.21  3.000
 HU3  H4   C03  C04  118.79  3.000
 HU3  H4   C03  C02  120.08  3.000
 HU3  C04  C03  C02  121.12  3.000
 HU3  C14  C04  N05  123.79  3.000
 HU3  N05  C04  C03  119.51  3.000
 HU3  C14  C04  C03  116.70  3.000
 HU3  H5   N05  C06  116.84  3.000
 HU3  H5   N05  C04  115.95  3.000
 HU3  C06  N05  C04  126.40  3.000
 HU3  H7   C06  H6   107.42  3.000
 HU3  H7   C06  C07  110.33  3.000
 HU3  H6   C06  C07  108.57  3.000
 HU3  H7   C06  N05  110.50  3.000
 HU3  H6   C06  N05  109.87  3.000
 HU3  C07  C06  N05  110.10  3.000
 HU3  H8   C07  C12  109.11  3.000
 HU3  H8   C07  C08  107.69  3.000
 HU3  C12  C07  C08  108.86  3.000
 HU3  H8   C07  C06  107.73  3.000
 HU3  C08  C07  C06  112.16  3.000
 HU3  C12  C07  C06  111.18  3.000
 HU3  H9   C08  O13  109.53  3.000
 HU3  H9   C08  C09  108.96  3.000
 HU3  O13  C08  C09  111.43  3.000
 HU3  H9   C08  C07  107.39  3.000
 HU3  C09  C08  C07  109.93  3.000
 HU3  O13  C08  C07  109.51  3.000
 HU3  H11  C09  H10  106.66  3.000
 HU3  H11  C09  C08  108.14  3.000
 HU3  H10  C09  C08  108.98  3.000
 HU3  H11  C09  C10  109.75  3.000
 HU3  H10  C09  C10  110.24  3.000
 HU3  C08  C09  C10  112.87  3.000
 HU3  H13  C11  H12  106.10  3.000
 HU3  H13  C11  C12  110.27  3.000
 HU3  H12  C11  C12  109.76  3.000
 HU3  H13  C11  C10  109.21  3.000
 HU3  H12  C11  C10  110.74  3.000
 HU3  C12  C11  C10  110.66  3.000
 HU3  H15  C12  H14  106.35  3.000
 HU3  H15  C12  C11  109.51  3.000
 HU3  H14  C12  C11  109.14  3.000
 HU3  H15  C12  C07  109.14  3.000
 HU3  H14  C12  C07  109.28  3.000
 HU3  C11  C12  C07  113.19  3.000
 HU3  H16  O13  C08  108.13  3.000
 HU3  C18  C14  C04  119.35  3.000
 HU3  C04  C14  C15  136.95  3.000
 HU3  C18  C14  C15  103.70  3.000
 HU3  N17  N16  C15  106.48  3.000
 HU3  H17  N17  C18  127.33  3.000
 HU3  H17  N17  N16  119.90  3.000
 HU3  C18  N17  N16  112.76  3.000
 HU3  C19  C18  N17  129.82  3.000
 HU3  N17  C18  C14  105.87  3.000
 HU3  C19  C18  C14  124.32  3.000
 HU3  H18  C19  C18  122.26  3.000
 HU3  H18  C19  C02  123.44  3.000
 HU3  C18  C19  C02  114.30  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
 HU3  CONST_01  C18  N17  N16  C15     0.00   0.0  0
 HU3  CONST_02  C19  C18  C14  C15   180.00   0.0  0
 HU3  CONST_03  N17  C18  C14  C15     0.00   0.0  0
 HU3  CONST_04  C03  C04  C14  C15   180.00   0.0  0
 HU3  CONST_05  N17  C18  C19  C02   180.00   0.0  0
 HU3  CONST_06  C14  C18  C19  C02     0.00   0.0  0
 HU3  CONST_07  C14  C04  C03  C02     0.00   0.0  0
 HU3  CONST_08  C18  C19  C02  C03     0.00   0.0  0
 HU3  CONST_09  C18  C14  C04  C03     0.00   0.0  0
 HU3  CONST_10  C19  C02  C03  C04     0.00   0.0  0
 HU3  CONST_11  C19  C18  C14  C04     0.00   0.0  0
 HU3  CONST_12  N17  C18  C14  C04   180.00   0.0  0
 HU3  CONST_13  N16  C15  C14  C04   180.00   0.0  0
 HU3  CONST_14  N16  N17  C18  C14     0.00   0.0  0
 HU3  CONST_15  N17  N16  C15  C14     0.00   0.0  0
 HU3  CONST_16  C19  C18  N17  N16   180.00   0.0  0
 HU3  CONST_17  C18  C14  C15  N16     0.00   0.0  0
 HU3  CONST_18  N05  C04  C14  C15     0.00   0.0  0
 HU3  CONST_19  C18  C19  C02  BR1   180.00   0.0  0
 HU3  CONST_20  C04  C03  C02  BR1   180.00   0.0  0
 HU3  CONST_21  N05  C04  C03  C02   180.00   0.0  0
 HU3  CONST_22  C18  C14  C04  N05   180.00   0.0  0
 HU3  CONST_23  H17  N17  N16  C15   180.00   0.0  0
 HU3  CONST_24  H18  C19  C02  C03   180.00   0.0  0
 HU3  CONST_25  H3   C15  C14  C04     0.00   0.0  0
 HU3  CONST_26  H4   C03  C04  C14   180.00   0.0  0
 HU3  CONST_27  C06  N05  C04  C03   180.00   0.0  0
 HU3  CONST_28  C14  C04  N05  C06     0.00   0.0  0
 HU3  CONST_29  H5   N05  C04  C03     0.00   0.0  0
 HU3  Var_01    C07  C12  C11  C10    30.54  30.0  1
 HU3  Var_02    C11  C10  C09  C08    28.88  30.0  1
 HU3  Var_03    C12  C11  C10  C09   -63.04  30.0  1
 HU3  Var_04    C07  C06  N05  C04  -178.22  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
 HU3  chir_01  C07  C06  C12  C08  negativ
 HU3  chir_02  C08  O13  C07  C09  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
 HU3  plan-1  C15  0.020
 HU3  plan-1  BR1  0.020
 HU3  plan-1  C02  0.020
 HU3  plan-1  C03  0.020
 HU3  plan-1  C04  0.020
 HU3  plan-1  N05  0.020
 HU3  plan-1  C14  0.020
 HU3  plan-1  N16  0.020
 HU3  plan-1  N17  0.020
 HU3  plan-1  C18  0.020
 HU3  plan-1  C19  0.020
 HU3  plan-1  H4   0.020
 HU3  plan-1  H18  0.020
 HU3  plan-1  H17  0.020
 HU3  plan-1  H3   0.020
 HU3  plan-2  C04  0.020
 HU3  plan-2  N05  0.020
 HU3  plan-2  C06  0.020
 HU3  plan-2  H5   0.020

