# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 01:17:48 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: 3-fluoro-N-hydroxy-4-[(methyl{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]methyl}amino)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1ccc(cc1F)C(=O)NO)CC23CC4CC(CC(C4)C2)C3
#
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
 HBV  HBV  3-fluoro-N-hydroxy-4-[(methyl{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]methyl}amino)methyl]benzamide  ligand  52  25  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HBV
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
 HBV  C10  C  CH2   0  -0.267  -2.2149  -1.6554  -0.3403
 HBV  C13  C  CH1   0  -0.244  -5.5055   0.3532  -0.2423
 HBV  C01  C  CH3   0  -0.528  -0.3295  -2.2038   1.0804
 HBV  C02  C  CH2   0  -0.347   0.0481  -1.5348  -1.2001
 HBV  C03  C  CR6   0  -0.109   1.4166  -0.9647  -0.9324
 HBV  C04  C  CR6   0   0.542   2.5731  -1.7281  -0.9397
 HBV  C05  C  CR16  0  -0.428   3.8260  -1.2041  -0.6925
 HBV  C06  C  CR6   0  -0.059   3.9461   0.1485  -0.4003
 HBV  C07  C  C     0   0.509   5.3195   0.6794  -0.1492
 HBV  C08  C  CR16  0  -0.282   2.8040   0.9485  -0.3864
 HBV  C11  C  CT    0  -0.067  -3.1155  -0.4383  -0.1254
 HBV  C09  C  CR16  0  -0.252   1.5647   0.3895  -0.6439
 HBV  C12  C  CH2   0  -0.406  -4.5623  -0.8344  -0.4452
 HBV  C14  C  CH2   0  -0.418  -5.0903   1.4936  -1.1739
 HBV  C15  C  CH1   0  -0.240  -3.6540   1.9120  -0.8554
 HBV  C16  C  CH2   0  -0.418  -3.5720   2.3862   0.5977
 HBV  C17  C  CH1   0  -0.244  -3.9868   1.2464   1.5308
 HBV  C18  C  CH2   0  -0.403  -3.0452   0.0572   1.3241
 HBV  C19  C  CH2   0  -0.417  -5.4222   0.8231   1.2119
 HBV  C20  C  CH2   0  -0.423  -2.7168   0.7176  -1.0509
 HBV  F01  F  F     0  -0.309   2.4863  -3.0447  -1.1929
 HBV  N01  N  NT    0  -0.401  -0.8081  -1.4178  -0.0359
 HBV  N02  N  NH1   0  -0.385   5.3506   1.8083   0.5918
 HBV  O01  O  OH1   0  -0.538   6.5580   2.2836   1.0074
 HBV  O02  O  O     0  -0.457   6.3150   0.1430  -0.5994
 HBV  H1   H  HCH2  0   0.222  -2.5950  -2.4817   0.2740
 HBV  H2   H  HCH2  0   0.220  -2.3302  -1.9905  -1.3792
 HBV  H3   H  HCH1  0   0.219  -6.5308   0.0467  -0.4717
 HBV  H4   H  HCH3  0   0.195  -0.2901  -3.2844   0.8715
 HBV  H5   H  HCH3  0   0.232   0.6716  -1.8855   1.3755
 HBV  H6   H  HCH3  0   0.237  -0.9788  -2.0558   1.9426
 HBV  H7   H  HCH2  0   0.260  -0.3997  -0.9568  -2.0121
 HBV  H8   H  HCH2  0   0.226   0.1245  -2.5700  -1.5636
 HBV  H9   H  HCR6  0   0.282   4.6946  -1.8491  -0.7162
 HBV  H10  H  HCR6  0   0.266   2.8697   2.0125  -0.2019
 HBV  H11  H  HCR6  0   0.274   0.6847   1.0193  -0.6317
 HBV  H12  H  HCH2  0   0.217  -4.8708  -1.6726   0.1910
 HBV  H13  H  HCH2  0   0.216  -4.6261  -1.1897  -1.4808
 HBV  H14  H  HCH2  0   0.218  -5.1701   1.1733  -2.2182
 HBV  H15  H  HCH2  0   0.219  -5.7682   2.3451  -1.0540
 HBV  H16  H  HCH1  0   0.218  -3.3506   2.7240  -1.5239
 HBV  H17  H  HCH2  0   0.217  -2.5505   2.7070   0.8293
 HBV  H18  H  HCH2  0   0.218  -4.2205   3.2555   0.7504
 HBV  H19  H  HCH1  0   0.217  -3.9244   1.5819   2.5707
 HBV  H20  H  HCH2  0   0.210  -3.3085  -0.7544   2.0135
 HBV  H21  H  HCH2  0   0.224  -2.0162   0.3501   1.5551
 HBV  H22  H  HCH2  0   0.219  -6.1112   1.6576   1.3800
 HBV  H23  H  HCH2  0   0.217  -5.7343   0.0164   1.8835
 HBV  H24  H  HCH2  0   0.236  -1.6849   1.0164  -0.8380
 HBV  H25  H  HCH2  0   0.211  -2.7464   0.3838  -2.0954
 HBV  H27  H  HNH1  0   0.419   4.5822   2.0644   1.1957
 HBV  H28  H  HOH1  0   0.480   6.7687   3.0212   0.4208

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
 HBV  C19  C17  single    1.530  0.020  1.530
 HBV  C19  C13  single    1.530  0.020  1.530
 HBV  C01  N01  single    1.447  0.020  1.447
 HBV  C18  C17  single    1.531  0.020  1.531
 HBV  C18  C11  single    1.533  0.020  1.533
 HBV  C12  C13  single    1.530  0.020  1.530
 HBV  C12  C11  single    1.534  0.020  1.534
 HBV  C17  C16  single    1.530  0.020  1.530
 HBV  C13  C14  single    1.530  0.020  1.530
 HBV  C10  C11  single    1.529  0.020  1.529
 HBV  C10  N01  single    1.459  0.020  1.459
 HBV  C11  C20  single    1.533  0.020  1.533
 HBV  N01  C02  single    1.450  0.020  1.450
 HBV  C16  C15  single    1.531  0.020  1.531
 HBV  C14  C15  single    1.530  0.020  1.530
 HBV  C02  C03  single    1.507  0.020  1.507
 HBV  C20  C15  single    1.531  0.020  1.531
 HBV  C09  C03  aromatic  1.392  0.020  1.392
 HBV  C09  C08  aromatic  1.384  0.020  1.384
 HBV  C03  C04  aromatic  1.386  0.020  1.386
 HBV  C08  C06  aromatic  1.394  0.020  1.394
 HBV  C04  F01  single    1.343  0.020  1.343
 HBV  C04  C05  aromatic  1.380  0.020  1.380
 HBV  C06  C05  aromatic  1.389  0.020  1.389
 HBV  C06  C07  single    1.494  0.020  1.494
 HBV  C07  O02  double    1.217  0.020  1.217
 HBV  C07  N02  single    1.351  0.020  1.351
 HBV  N02  O01  single    1.362  0.020  1.362
 HBV  C10  H1   single    0.970  0.020  1.090
 HBV  C10  H2   single    0.970  0.020  1.090
 HBV  C13  H3   single    0.970  0.020  1.090
 HBV  C01  H4   single    0.970  0.020  1.090
 HBV  C01  H5   single    0.970  0.020  1.090
 HBV  C01  H6   single    0.970  0.020  1.090
 HBV  C02  H7   single    0.970  0.020  1.090
 HBV  C02  H8   single    0.970  0.020  1.090
 HBV  C05  H9   single    0.930  0.020  1.080
 HBV  C08  H10  single    0.930  0.020  1.080
 HBV  C09  H11  single    0.930  0.020  1.080
 HBV  C12  H12  single    0.970  0.020  1.090
 HBV  C12  H13  single    0.970  0.020  1.090
 HBV  C14  H14  single    0.970  0.020  1.090
 HBV  C14  H15  single    0.970  0.020  1.090
 HBV  C15  H16  single    0.970  0.020  1.090
 HBV  C16  H17  single    0.970  0.020  1.090
 HBV  C16  H18  single    0.970  0.020  1.090
 HBV  C17  H19  single    0.970  0.020  1.090
 HBV  C18  H20  single    0.970  0.020  1.090
 HBV  C18  H21  single    0.970  0.020  1.090
 HBV  C19  H22  single    0.970  0.020  1.090
 HBV  C19  H23  single    0.970  0.020  1.090
 HBV  C20  H24  single    0.970  0.020  1.090
 HBV  C20  H25  single    0.970  0.020  1.090
 HBV  N02  H27  single    0.890  0.020  1.040
 HBV  O01  H28  single    0.850  0.020  0.980

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
 HBV  H2   C10  H1   105.28  3.000
 HBV  H2   C10  N01  110.40  3.000
 HBV  H1   C10  N01  109.86  3.000
 HBV  H2   C10  C11  108.31  3.000
 HBV  H1   C10  C11  108.46  3.000
 HBV  N01  C10  C11  114.14  3.000
 HBV  H3   C13  C19  109.64  3.000
 HBV  H3   C13  C14  109.60  3.000
 HBV  C19  C13  C14  109.57  3.000
 HBV  H3   C13  C12  109.41  3.000
 HBV  C14  C13  C12  109.30  3.000
 HBV  C19  C13  C12  109.31  3.000
 HBV  H6   C01  H5   107.04  3.000
 HBV  H6   C01  H4   107.74  3.000
 HBV  H5   C01  H4   107.74  3.000
 HBV  H6   C01  N01  109.86  3.000
 HBV  H5   C01  N01  110.71  3.000
 HBV  H4   C01  N01  113.49  3.000
 HBV  H8   C02  H7   106.30  3.000
 HBV  H8   C02  N01  112.48  3.000
 HBV  H7   C02  N01  108.18  3.000
 HBV  H8   C02  C03  110.60  3.000
 HBV  H7   C02  C03  107.71  3.000
 HBV  N01  C02  C03  111.30  3.000
 HBV  C09  C03  C04  116.62  3.000
 HBV  C04  C03  C02  123.27  3.000
 HBV  C09  C03  C02  120.10  3.000
 HBV  F01  C04  C05  117.67  3.000
 HBV  C05  C04  C03  123.19  3.000
 HBV  F01  C04  C03  119.14  3.000
 HBV  H9   C05  C06  121.04  3.000
 HBV  H9   C05  C04  119.89  3.000
 HBV  C06  C05  C04  119.06  3.000
 HBV  C08  C06  C07  123.19  3.000
 HBV  C07  C06  C05  117.45  3.000
 HBV  C08  C06  C05  119.34  3.000
 HBV  O02  C07  N02  123.53  3.000
 HBV  N02  C07  C06  114.23  3.000
 HBV  O02  C07  C06  122.22  3.000
 HBV  H10  C08  C09  118.91  3.000
 HBV  H10  C08  C06  121.08  3.000
 HBV  C09  C08  C06  119.99  3.000
 HBV  C20  C11  C18  108.36  3.000
 HBV  C20  C11  C12  108.30  3.000
 HBV  C18  C11  C12  108.89  3.000
 HBV  C20  C11  C10  111.22  3.000
 HBV  C12  C11  C10  108.70  3.000
 HBV  C18  C11  C10  111.29  3.000
 HBV  H11  C09  C08  119.41  3.000
 HBV  H11  C09  C03  118.80  3.000
 HBV  C08  C09  C03  121.78  3.000
 HBV  H13  C12  H12  106.49  3.000
 HBV  H13  C12  C11  109.60  3.000
 HBV  H12  C12  C11  109.99  3.000
 HBV  H13  C12  C13  109.92  3.000
 HBV  H12  C12  C13  110.05  3.000
 HBV  C11  C12  C13  110.70  3.000
 HBV  H15  C14  H14  106.66  3.000
 HBV  H15  C14  C15  110.23  3.000
 HBV  H14  C14  C15  110.30  3.000
 HBV  H15  C14  C13  110.18  3.000
 HBV  H14  C14  C13  110.05  3.000
 HBV  C15  C14  C13  109.39  3.000
 HBV  H16  C15  C20  109.33  3.000
 HBV  H16  C15  C16  109.58  3.000
 HBV  C20  C15  C16  109.28  3.000
 HBV  H16  C15  C14  109.64  3.000
 HBV  C20  C15  C14  109.56  3.000
 HBV  C16  C15  C14  109.44  3.000
 HBV  H18  C16  H17  106.87  3.000
 HBV  H18  C16  C17  110.23  3.000
 HBV  H17  C16  C17  110.00  3.000
 HBV  H18  C16  C15  110.27  3.000
 HBV  H17  C16  C15  109.96  3.000
 HBV  C17  C16  C15  109.48  3.000
 HBV  H19  C17  C19  109.65  3.000
 HBV  H19  C17  C18  109.35  3.000
 HBV  C19  C17  C18  109.51  3.000
 HBV  H19  C17  C16  109.61  3.000
 HBV  C18  C17  C16  109.24  3.000
 HBV  C19  C17  C16  109.47  3.000
 HBV  H21  C18  H20  106.92  3.000
 HBV  H21  C18  C17  109.99  3.000
 HBV  H20  C18  C17  110.02  3.000
 HBV  H21  C18  C11  109.21  3.000
 HBV  H20  C18  C11  110.12  3.000
 HBV  C17  C18  C11  110.52  3.000
 HBV  H23  C19  H22  106.73  3.000
 HBV  H23  C19  C17  110.08  3.000
 HBV  H22  C19  C17  110.33  3.000
 HBV  H23  C19  C13  109.95  3.000
 HBV  H22  C19  C13  110.21  3.000
 HBV  C17  C19  C13  109.51  3.000
 HBV  H25  C20  H24  107.07  3.000
 HBV  H25  C20  C15  110.04  3.000
 HBV  H24  C20  C15  109.82  3.000
 HBV  H25  C20  C11  109.78  3.000
 HBV  H24  C20  C11  109.46  3.000
 HBV  C15  C20  C11  110.60  3.000
 HBV  C02  N01  C01  112.35  3.000
 HBV  C02  N01  C10  112.88  3.000
 HBV  C01  N01  C10  113.05  3.000
 HBV  H27  N02  O01  113.78  3.000
 HBV  H27  N02  C07  121.48  3.000
 HBV  O01  N02  C07  118.64  3.000
 HBV  H28  O01  N02  105.93  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
 HBV  CONST_01  C06  C08  C09  C03    0.00   0.0  0
 HBV  CONST_02  C06  C05  C04  C03    0.00   0.0  0
 HBV  CONST_03  C08  C09  C03  C04    0.00   0.0  0
 HBV  CONST_04  C08  C06  C05  C04    0.00   0.0  0
 HBV  CONST_05  C09  C03  C04  C05    0.00   0.0  0
 HBV  CONST_06  C09  C08  C06  C05    0.00   0.0  0
 HBV  CONST_07  C08  C09  C03  C02  180.00   0.0  0
 HBV  CONST_08  C05  C04  C03  C02  180.00   0.0  0
 HBV  CONST_09  C07  C06  C05  C04  180.00   0.0  0
 HBV  CONST_10  F01  C04  C05  C06  180.00   0.0  0
 HBV  CONST_11  C09  C08  C06  C07  180.00   0.0  0
 HBV  CONST_12  F01  C04  C03  C09  180.00   0.0  0
 HBV  CONST_13  H10  C08  C09  C03  180.00   0.0  0
 HBV  CONST_14  H9   C05  C04  C03  180.00   0.0  0
 HBV  CONST_15  H11  C09  C03  C04  180.00   0.0  0
 HBV  CONST_16  O01  N02  C07  C06  180.00   0.0  0
 HBV  CONST_18  O02  C07  N02  O01    0.00   0.0  0
 HBV  Var_01    N01  C02  C03  C04  116.06  30.0  2
 HBV  Var_02    O02  C07  C06  C05   24.70  30.0  2
 HBV  Var_03    C03  C02  N01  C10  166.16  30.0  3
 HBV  Var_04    C11  C10  N01  C01  115.29  30.0  3
 HBV  Var_05    H4   C01  N01  C10   67.65  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
 HBV  chir_01  C13  C19  C12  C14  positiv
 HBV  chir_02  C11  C12  C10  C20  negativ
 HBV  chir_03  C15  C20  C14  C16  negativ
 HBV  chir_04  C17  C19  C18  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
 HBV  plan-1  C02  0.020
 HBV  plan-1  C03  0.020
 HBV  plan-1  C04  0.020
 HBV  plan-1  C05  0.020
 HBV  plan-1  C06  0.020
 HBV  plan-1  C07  0.020
 HBV  plan-1  C08  0.020
 HBV  plan-1  C09  0.020
 HBV  plan-1  F01  0.020
 HBV  plan-1  H9   0.020
 HBV  plan-1  H10  0.020
 HBV  plan-1  H11  0.020
 HBV  plan-2  C06  0.020
 HBV  plan-2  C07  0.020
 HBV  plan-2  N02  0.020
 HBV  plan-2  O01  0.020
 HBV  plan-2  O02  0.020
 HBV  plan-2  H27  0.020

