# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 06:00:04 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-6-(4-methylpiperazin-1-yl)-2-(propylsulfanyl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCSc1nc(ccc1C(=O)NC2[C@H]3CC4C[C@@H]2CC(O)(C4)C3)N5CCN(C)CC5
#
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
 HD1  HD1  N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-6-(4-methylpiperazin-1-yl)-2-(propylsulfanyl)pyridine-3-carboxamide  ligand  67  31  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HD1
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
 HD1  O1    O  O     0  -0.494   1.4092  -1.7142  -1.0203
 HD1  C14   C  C     0   0.527   1.1856  -0.5339  -0.7684
 HD1  N4    N  NH1   0  -0.675   2.1721   0.3518  -0.5327
 HD1  C15   C  CR16  0  -0.025   3.5794   0.0211  -0.6282
 HD1  C20   C  CR16  0  -0.278   4.3974   1.2697  -0.9826
 HD1  C19   C  C     0  -0.451   4.3720   2.2825   0.1663
 HD1  C21   C  CH2   0  -0.446   5.8434   0.8434  -1.2478
 HD1  C22   C  CT    0   0.254   6.4389   0.2036   0.0042
 HD1  C23   C  CH2   0  -0.455   6.3955   1.2156   1.1528
 HD1  C18   C  CR16  0  -0.248   4.9504   1.6413   1.4278
 HD1  C17   C  C     0  -0.436   4.1163   0.4135   1.8013
 HD1  O2    O  OH1   0  -0.686   7.7691  -0.1648  -0.3092
 HD1  C24   C  CH2   0  -0.464   5.5966  -1.0180   0.3833
 HD1  C16   C  CR16  0  -0.258   4.1493  -0.6000   0.6569
 HD1  C5    C  CR6   0  -0.131  -0.1970  -0.0141  -0.7143
 HD1  C6    C  CR16  0  -0.165  -0.5066   1.3338  -0.9164
 HD1  C7    C  CR16  0  -0.423  -1.7954   1.8019  -0.8768
 HD1  C8    C  CR6   0   0.563  -2.8265   0.8768  -0.6098
 HD1  N2    N  NT    0  -0.503  -4.1318   1.2343  -0.4928
 HD1  C12   C  CH2   0  -0.308  -5.1740   0.2221  -0.4384
 HD1  C11   C  CH2   0  -0.286  -6.3538   0.7088   0.3805
 HD1  N3    N  NT    0  -0.414  -6.8574   1.9645  -0.1317
 HD1  C13   C  CH3   0  -0.519  -8.0483   2.3959   0.5633
 HD1  C10   C  CH2   0  -0.278  -5.8135   2.9633  -0.0803
 HD1  C9    C  CH2   0  -0.306  -4.6102   2.5414  -0.9037
 HD1  N1    N  N     0  -0.489  -2.5392  -0.4173  -0.4528
 HD1  C4    C  CR6   0   0.081  -1.2992  -0.8605  -0.5079
 HD1  S1    S  S2    0   0.063  -1.0844  -2.5995  -0.2938
 HD1  C3    C  CH2   0  -0.542  -2.7600  -3.1180   0.1771
 HD1  C2    C  CH2   0  -0.432  -2.7316  -4.6111   0.4799
 HD1  C1    C  CH3   0  -0.658  -4.1116  -5.1142   0.8826
 HD1  H4    H  HNH1  0   0.396   1.9299   1.2677  -0.1941
 HD1  H15   H  HCR6  0   0.250   3.6854  -0.7041  -1.4397
 HD1  H20   H  HCR6  0   0.248   3.9846   1.7213  -1.8894
 HD1  H16   H  HCR6  0   0.242   3.5622  -1.4838   0.9199
 HD1  H191  H  H     0   0.241   4.9551   3.1638  -0.1166
 HD1  H192  H  H     0   0.231   3.3584   2.6515   0.3584
 HD1  H211  H  HCH2  0   0.236   5.8809   0.1340  -2.0818
 HD1  H212  H  HCH2  0   0.236   6.4381   1.7144  -1.5415
 HD1  H18   H  HCR6  0   0.235   4.9338   2.3632   2.2485
 HD1  H231  H  HCH2  0   0.227   6.8333   0.7706   2.0543
 HD1  H232  H  HCH2  0   0.230   7.0047   2.0880   0.8942
 HD1  H2    H  HOH1  0   0.439   8.1670  -0.5497   0.4794
 HD1  H241  H  HCH2  0   0.234   5.6356  -1.7578  -0.4235
 HD1  H242  H  HCH2  0   0.231   6.0171  -1.4984   1.2744
 HD1  H171  H  H     0   0.233   4.5094  -0.0472   2.7126
 HD1  H172  H  H     0   0.231   3.0871   0.7075   2.0278
 HD1  H6    H  HCR6  0   0.258   0.2769   2.0473  -1.1394
 HD1  H7    H  HCR6  0   0.275  -1.9793   2.8489  -1.0564
 HD1  H121  H  HCH2  0   0.226  -5.5083  -0.0247  -1.4541
 HD1  H122  H  HCH2  0   0.276  -4.7764  -0.6855   0.0056
 HD1  H91C  H  HCH2  0   0.264  -3.8387   3.2943  -0.7681
 HD1  H92C  H  HCH2  0   0.234  -4.8767   2.5279  -1.9678
 HD1  H111  H  HCH2  0   0.244  -7.1420  -0.0455   0.3281
 HD1  H112  H  HCH2  0   0.196  -6.0514   0.7896   1.4394
 HD1  H131  H  HCH3  0   0.194  -7.8837   2.5866   1.6351
 HD1  H132  H  HCH3  0   0.234  -8.4277   3.3158   0.1159
 HD1  H133  H  HCH3  0   0.235  -8.8261   1.6359   0.4764
 HD1  H101  H  HCH2  0   0.246  -6.1903   3.9047  -0.4862
 HD1  H102  H  HCH2  0   0.197  -5.4881   3.1636   0.9555
 HD1  H31C  H  HCH2  0   0.260  -3.0881  -2.5542   1.0512
 HD1  H32C  H  HCH2  0   0.261  -3.4559  -2.9060  -0.6348
 HD1  H21C  H  HCH2  0   0.231  -2.3806  -5.1623  -0.3964
 HD1  H22C  H  HCH2  0   0.231  -2.0178  -4.8137   1.2823
 HD1  H11C  H  HCH3  0   0.222  -4.4789  -4.5884   1.7651
 HD1  H12C  H  HCH3  0   0.223  -4.8360  -4.9642   0.0809
 HD1  H13C  H  HCH3  0   0.234  -4.0884  -6.1788   1.1150

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
 HD1  O1   C14   double    1.227  0.020  1.227
 HD1  C14  N4    single    1.347  0.020  1.347
 HD1  C14  C5    single    1.478  0.020  1.478
 HD1  N4   C15   single    1.449  0.020  1.449
 HD1  C15  C20   single    1.534  0.020  1.534
 HD1  C15  C16   single    1.537  0.020  1.537
 HD1  C20  C19   single    1.532  0.020  1.532
 HD1  C20  C21   single    1.531  0.020  1.531
 HD1  C19  C18   single    1.529  0.020  1.529
 HD1  C21  C22   single    1.527  0.020  1.527
 HD1  C22  C23   single    1.531  0.020  1.531
 HD1  C22  O2    single    1.415  0.020  1.415
 HD1  C22  C24   single    1.532  0.020  1.532
 HD1  C23  C18   single    1.531  0.020  1.531
 HD1  C18  C17   single    1.531  0.020  1.531
 HD1  C17  C16   single    1.529  0.020  1.529
 HD1  C24  C16   single    1.531  0.020  1.531
 HD1  C5   C6    aromatic  1.398  0.020  1.398
 HD1  C5   C4    aromatic  1.405  0.020  1.405
 HD1  C6   C7    aromatic  1.372  0.020  1.372
 HD1  C7   C8    aromatic  1.411  0.020  1.411
 HD1  C8   N2    single    1.358  0.020  1.358
 HD1  C8   N1    aromatic  1.335  0.020  1.335
 HD1  N2   C12   single    1.454  0.020  1.454
 HD1  N2   C9    single    1.451  0.020  1.451
 HD1  C12  C11   single    1.516  0.020  1.516
 HD1  C11  N3    single    1.447  0.020  1.447
 HD1  N3   C13   single    1.445  0.020  1.445
 HD1  N3   C10   single    1.446  0.020  1.446
 HD1  C10  C9    single    1.518  0.020  1.518
 HD1  N1   C4    aromatic  1.318  0.020  1.318
 HD1  C4   S1    single    1.765  0.020  1.765
 HD1  S1   C3    single    1.816  0.020  1.816
 HD1  C3   C2    single    1.524  0.020  1.524
 HD1  C2   C1    single    1.523  0.020  1.523
 HD1  N4   H4    single    0.860  0.020  1.020
 HD1  C15  H15   single    0.970  0.020  1.090
 HD1  C20  H20   single    0.970  0.020  1.090
 HD1  C16  H16   single    0.970  0.020  1.090
 HD1  C19  H191  single    0.970  0.020  1.090
 HD1  C19  H192  single    0.970  0.020  1.090
 HD1  C21  H211  single    0.970  0.020  1.090
 HD1  C21  H212  single    0.970  0.020  1.090
 HD1  C18  H18   single    0.970  0.020  1.090
 HD1  C23  H231  single    0.970  0.020  1.090
 HD1  C23  H232  single    0.970  0.020  1.090
 HD1  O2   H2    single    0.850  0.020  0.980
 HD1  C24  H241  single    0.970  0.020  1.090
 HD1  C24  H242  single    0.970  0.020  1.090
 HD1  C17  H171  single    0.970  0.020  1.090
 HD1  C17  H172  single    0.970  0.020  1.090
 HD1  C6   H6    single    0.930  0.020  1.080
 HD1  C7   H7    single    0.930  0.020  1.080
 HD1  C12  H121  single    0.970  0.020  1.090
 HD1  C12  H122  single    0.970  0.020  1.090
 HD1  C9   H91C  single    0.970  0.020  1.090
 HD1  C9   H92C  single    0.970  0.020  1.090
 HD1  C11  H111  single    0.970  0.020  1.090
 HD1  C11  H112  single    0.970  0.020  1.090
 HD1  C13  H131  single    0.970  0.020  1.090
 HD1  C13  H132  single    0.970  0.020  1.090
 HD1  C13  H133  single    0.970  0.020  1.090
 HD1  C10  H101  single    0.970  0.020  1.090
 HD1  C10  H102  single    0.970  0.020  1.090
 HD1  C3   H31C  single    0.970  0.020  1.090
 HD1  C3   H32C  single    0.970  0.020  1.090
 HD1  C2   H21C  single    0.970  0.020  1.090
 HD1  C2   H22C  single    0.970  0.020  1.090
 HD1  C1   H11C  single    0.970  0.020  1.090
 HD1  C1   H12C  single    0.970  0.020  1.090
 HD1  C1   H13C  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
 HD1  C5    C14  N4    116.58  3.000
 HD1  C5    C14  O1    121.08  3.000
 HD1  N4    C14  O1    122.34  3.000
 HD1  H4    N4   C15   117.63  3.000
 HD1  H4    N4   C14   118.78  3.000
 HD1  C15   N4   C14   123.36  3.000
 HD1  H15   C15  C16   108.45  3.000
 HD1  H15   C15  C20   108.46  3.000
 HD1  C16   C15  C20   108.93  3.000
 HD1  H15   C15  N4    107.13  3.000
 HD1  C16   C15  N4    113.41  3.000
 HD1  C20   C15  N4    110.33  3.000
 HD1  H20   C20  C21   109.14  3.000
 HD1  H20   C20  C19   110.03  3.000
 HD1  C21   C20  C19   109.26  3.000
 HD1  H20   C20  C15   109.04  3.000
 HD1  C21   C20  C15   108.48  3.000
 HD1  C19   C20  C15   110.85  3.000
 HD1  H192  C19  H191  105.50  3.000
 HD1  H192  C19  C18   110.28  3.000
 HD1  H191  C19  C18   110.46  3.000
 HD1  H192  C19  C20   111.69  3.000
 HD1  H191  C19  C20   109.26  3.000
 HD1  C18   C19  C20   109.59  3.000
 HD1  H212  C21  H211  107.00  3.000
 HD1  H212  C21  C22   109.97  3.000
 HD1  H211  C21  C22   109.85  3.000
 HD1  H212  C21  C20   109.75  3.000
 HD1  H211  C21  C20   110.16  3.000
 HD1  C22   C21  C20   110.06  3.000
 HD1  C24   C22  O2    111.34  3.000
 HD1  C24   C22  C23   109.02  3.000
 HD1  O2    C22  C23   111.39  3.000
 HD1  C24   C22  C21   108.83  3.000
 HD1  O2    C22  C21   107.10  3.000
 HD1  C23   C22  C21   109.09  3.000
 HD1  H232  C23  H231  107.18  3.000
 HD1  H232  C23  C18   110.24  3.000
 HD1  H231  C23  C18   110.00  3.000
 HD1  H232  C23  C22   109.49  3.000
 HD1  H231  C23  C22   109.70  3.000
 HD1  C18   C23  C22   110.19  3.000
 HD1  H18   C18  C17   109.76  3.000
 HD1  H18   C18  C23   109.44  3.000
 HD1  C17   C18  C23   109.58  3.000
 HD1  H18   C18  C19   109.68  3.000
 HD1  C17   C18  C19   109.37  3.000
 HD1  C23   C18  C19   109.00  3.000
 HD1  H172  C17  H171  106.18  3.000
 HD1  H172  C17  C16   110.69  3.000
 HD1  H171  C17  C16   109.66  3.000
 HD1  H172  C17  C18   110.35  3.000
 HD1  H171  C17  C18   110.20  3.000
 HD1  C16   C17  C18   109.71  3.000
 HD1  H2    O2   C22   108.11  3.000
 HD1  H242  C24  H241  106.81  3.000
 HD1  H242  C24  C16   109.69  3.000
 HD1  H241  C24  C16   110.47  3.000
 HD1  H242  C24  C22   109.87  3.000
 HD1  H241  C24  C22   109.69  3.000
 HD1  C16   C24  C22   110.26  3.000
 HD1  H16   C16  C24   109.26  3.000
 HD1  H16   C16  C17   110.14  3.000
 HD1  C24   C16  C17   109.58  3.000
 HD1  H16   C16  C15   109.20  3.000
 HD1  C24   C16  C15   108.15  3.000
 HD1  C17   C16  C15   110.48  3.000
 HD1  C4    C5   C6    115.37  3.000
 HD1  C4    C5   C14   121.82  3.000
 HD1  C6    C5   C14   122.76  3.000
 HD1  H6    C6   C7    117.44  3.000
 HD1  H6    C6   C5    120.33  3.000
 HD1  C7    C6   C5    122.21  3.000
 HD1  H7    C7   C8    122.93  3.000
 HD1  H7    C7   C6    119.14  3.000
 HD1  C8    C7   C6    117.93  3.000
 HD1  N1    C8   N2    116.86  3.000
 HD1  N1    C8   C7    120.04  3.000
 HD1  N2    C8   C7    123.10  3.000
 HD1  C9    N2   C12   113.66  3.000
 HD1  C9    N2   C8    121.96  3.000
 HD1  C12   N2   C8    120.58  3.000
 HD1  H122  C12  H121  107.58  3.000
 HD1  H122  C12  C11   109.42  3.000
 HD1  H121  C12  C11   109.57  3.000
 HD1  H122  C12  N2    109.56  3.000
 HD1  H121  C12  N2    109.89  3.000
 HD1  C11   C12  N2    110.76  3.000
 HD1  H112  C11  H111  107.11  3.000
 HD1  H112  C11  N3    111.80  3.000
 HD1  H111  C11  N3    109.34  3.000
 HD1  H112  C11  C12   109.16  3.000
 HD1  H111  C11  C12   108.30  3.000
 HD1  N3    C11  C12   110.99  3.000
 HD1  C10   N3   C13   111.83  3.000
 HD1  C10   N3   C11   109.62  3.000
 HD1  C13   N3   C11   112.07  3.000
 HD1  H133  C13  H132  107.87  3.000
 HD1  H133  C13  H131  107.75  3.000
 HD1  H132  C13  H131  107.76  3.000
 HD1  H133  C13  N3    109.96  3.000
 HD1  H132  C13  N3    109.95  3.000
 HD1  H131  C13  N3    113.37  3.000
 HD1  H102  C10  H101  107.09  3.000
 HD1  H102  C10  C9    109.01  3.000
 HD1  H101  C10  C9    108.14  3.000
 HD1  H102  C10  N3    111.82  3.000
 HD1  H101  C10  N3    109.46  3.000
 HD1  C9    C10  N3    111.17  3.000
 HD1  H92C  C9   H91C  107.58  3.000
 HD1  H92C  C9   C10   109.70  3.000
 HD1  H91C  C9   C10   107.62  3.000
 HD1  H92C  C9   N2    110.09  3.000
 HD1  H91C  C9   N2    110.78  3.000
 HD1  C10   C9   N2    110.98  3.000
 HD1  C4    N1   C8    121.57  3.000
 HD1  S1    C4   N1    116.15  3.000
 HD1  S1    C4   C5    121.06  3.000
 HD1  N1    C4   C5    122.80  3.000
 HD1  C3    S1   C4    101.57  3.000
 HD1  H32C  C3   H31C  107.72  3.000
 HD1  H32C  C3   C2    110.52  3.000
 HD1  H31C  C3   C2    110.67  3.000
 HD1  H32C  C3   S1    109.89  3.000
 HD1  H31C  C3   S1    109.74  3.000
 HD1  C2    C3   S1    108.31  3.000
 HD1  H22C  C2   H21C  106.58  3.000
 HD1  H22C  C2   C1    109.66  3.000
 HD1  H21C  C2   C1    109.66  3.000
 HD1  H22C  C2   C3    109.86  3.000
 HD1  H21C  C2   C3    109.92  3.000
 HD1  C1    C2   C3    111.06  3.000
 HD1  H13C  C1   H12C  107.76  3.000
 HD1  H13C  C1   H11C  107.78  3.000
 HD1  H12C  C1   H11C  107.74  3.000
 HD1  H13C  C1   C2    111.08  3.000
 HD1  H12C  C1   C2    111.22  3.000
 HD1  H11C  C1   C2    111.09  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
 HD1  CONST_01  C8    C7   C6   C5      0.00   0.0  0
 HD1  CONST_02  C8    N1   C4   C5      0.00   0.0  0
 HD1  CONST_03  N1    C4   C5   C6      0.00   0.0  0
 HD1  CONST_04  N1    C8   C7   C6      0.00   0.0  0
 HD1  CONST_05  C4    C5   C6   C7      0.00   0.0  0
 HD1  CONST_06  C4    N1   C8   C7      0.00   0.0  0
 HD1  CONST_07  N2    C8   C7   C6    180.00   0.0  0
 HD1  CONST_08  C4    N1   C8   N2    180.00   0.0  0
 HD1  CONST_09  C7    C6   C5   C14   180.00   0.0  0
 HD1  CONST_10  N1    C4   C5   C14   180.00   0.0  0
 HD1  CONST_11  S1    C4   C5   C6    180.00   0.0  0
 HD1  CONST_12  S1    C4   N1   C8    180.00   0.0  0
 HD1  CONST_13  H7    C7   C6   C5    180.00   0.0  0
 HD1  CONST_14  H6    C6   C7   C8    180.00   0.0  0
 HD1  CONST_15  C5    C14  N4   C15   180.00   0.0  0
 HD1  CONST_16  C15   N4   C14  O1      0.00   0.0  0
 HD1  CONST_17  H4    N4   C14  C5      0.00   0.0  0
 HD1  Var_01    C12   N2   C8   C7    169.76  30.0  2
 HD1  Var_02    C11   C12  N2   C8    150.16  30.0  1
 HD1  Var_03    C10   C9   N2   C8   -150.89  30.0  1
 HD1  Var_04    N3    C11  C12  N2     55.45  30.0  1
 HD1  Var_05    N3    C10  C9   N2    -54.67  30.0  1
 HD1  Var_06    C10   N3   C11  C12   -59.90  30.0  1
 HD1  Var_07    C9    C10  N3   C11    59.46  30.0  1
 HD1  Var_08    C6    C5   C14  O1   -156.15  30.0  2
 HD1  Var_09    H131  C13  N3   C11    62.30  30.0  3
 HD1  Var_10    C2    C3   S1   C4   -176.85  30.0  3
 HD1  Var_11    C1    C2   C3   S1   -179.97  30.0  3
 HD1  Var_12    H11C  C1   C2   C3    -59.11  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
 HD1  chir_01  C15  N4   C20  C16  negativ
 HD1  chir_02  C20  C15  C19  C21  negativ
 HD1  chir_03  C22  C21  C23  C24  negativ
 HD1  chir_04  C18  C19  C23  C17  positiv
 HD1  chir_05  C16  C15  C17  C24  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
 HD1  plan-1  C14  0.020
 HD1  plan-1  C5   0.020
 HD1  plan-1  C6   0.020
 HD1  plan-1  C7   0.020
 HD1  plan-1  C8   0.020
 HD1  plan-1  N2   0.020
 HD1  plan-1  N1   0.020
 HD1  plan-1  C4   0.020
 HD1  plan-1  S1   0.020
 HD1  plan-1  H6   0.020
 HD1  plan-1  H7   0.020
 HD1  plan-2  O1   0.020
 HD1  plan-2  C14  0.020
 HD1  plan-2  N4   0.020
 HD1  plan-2  C15  0.020
 HD1  plan-2  C5   0.020
 HD1  plan-2  H4   0.020

