# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:31:27 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (2S)-1-(4-cyclohexylphenoxy)-3-(4-pyridin-2-ylpiperazin-1-yl)propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](COc1ccc(cc1)C2CCCCC2)CN3CCN(CC3)c4ccccn4
#
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
 SDZ  SDZ  (2S)-1-(4-cyclohexylphenoxy)-3-(4-pyridin-2-ylpiperazin-1-yl)propan-2-ol  ligand  62  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SDZ
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
 SDZ  N1    N  N     0  -0.478   1.0414   0.5411   -7.6580
 SDZ  C2    C  CR16  0  -0.063   1.2658   0.5556   -8.9660
 SDZ  C3    C  CR16  0  -0.366   0.4713  -0.0866   -9.8953
 SDZ  C4    C  CR16  0  -0.150  -0.6264  -0.7872   -9.4035
 SDZ  C5    C  CR16  0  -0.410  -0.8806  -0.8149   -8.0491
 SDZ  C6    C  CR6   0   0.538  -0.0145  -0.1185   -7.1798
 SDZ  N2    N  NT    0  -0.508  -0.2219  -0.0592   -5.8233
 SDZ  C7    C  CH2   0  -0.293   0.8398   0.4356   -4.9650
 SDZ  C8    C  CH2   0  -0.301   0.2805   0.9592   -3.6586
 SDZ  N3    N  NT    0  -0.461  -0.5043  -0.0604   -2.9860
 SDZ  C9    C  CH2   0  -0.302  -1.0969  -1.0083   -5.1633
 SDZ  C10   C  CH2   0  -0.278  -1.6027  -0.4616   -3.8417
 SDZ  C11   C  CH2   0  -0.306  -0.9358   0.3356   -1.6590
 SDZ  C12   C  CH1   0   0.002   0.2269   0.1840   -0.6736
 SDZ  O1    O  OH1   0  -0.682   0.8900  -1.0323   -0.9119
 SDZ  C13   C  CH2   0  -0.176  -0.3024   0.2119    0.7418
 SDZ  O2    O  O2    0  -0.479   0.7986   0.2467    1.6274
 SDZ  C14   C  CR6   0   0.368   0.5687   0.2231    2.9570
 SDZ  C15   C  CR16  0  -0.332   1.6913   0.2899    3.7815
 SDZ  C16   C  CR16  0  -0.322   1.5450   0.2656    5.1576
 SDZ  C17   C  CR6   0   0.176   0.2920   0.1725    5.7628
 SDZ  C18   C  CR16  0  -0.309  -0.8156   0.1077    4.9245
 SDZ  C19   C  CR16  0  -0.366  -0.6933   0.1359    3.5397
 SDZ  C20   C  CH1   0  -0.330   0.1618   0.1215    7.2637
 SDZ  C21   C  CH2   0  -0.411  -0.7571   1.2152    7.8180
 SDZ  C22   C  CH2   0  -0.434  -0.8379   1.1564    9.3406
 SDZ  C23   C  CH2   0  -0.429  -1.2929  -0.2188    9.8184
 SDZ  C24   C  CH2   0  -0.434  -0.3924  -1.3193    9.2678
 SDZ  C25   C  CH2   0  -0.407  -0.3008  -1.2591    7.7462
 SDZ  H2    H  HCR6  0   0.254   2.1401   1.1123   -9.2876
 SDZ  H3    H  HCR6  0   0.258   0.7029  -0.0484  -10.9501
 SDZ  H4    H  HCR6  0   0.266  -1.2875  -1.3174  -10.0771
 SDZ  H5    H  HCR6  0   0.268  -1.7377  -1.3623   -7.6876
 SDZ  H71   H  HCH2  0   0.264   1.3688   1.2381   -5.4705
 SDZ  H72   H  HCH2  0   0.220   1.5711  -0.3586   -4.7598
 SDZ  H81   H  HCH2  0   0.213  -0.3243   1.8601   -3.8507
 SDZ  H82   H  HCH2  0   0.254   1.1213   1.2636   -3.0326
 SDZ  H91   H  HCH2  0   0.260  -1.9712  -1.2169   -5.7749
 SDZ  H92   H  HCH2  0   0.227  -0.5785  -1.9617   -4.9934
 SDZ  H101  H  HCH2  0   0.251  -2.1789  -1.2459   -3.3475
 SDZ  H102  H  HCH2  0   0.208  -2.2902   0.3776   -4.0344
 SDZ  H111  H  HCH2  0   0.243  -1.7495  -0.3305   -1.3565
 SDZ  H112  H  HCH2  0   0.226  -1.3314   1.3605   -1.6280
 SDZ  H12   H  HCH1  0   0.211   0.9168   1.0326   -0.7998
 SDZ  HO1   H  HOH1  0   0.437   0.7369  -1.2095   -1.8559
 SDZ  H131  H  HCH2  0   0.226  -0.9398   1.0938    0.8810
 SDZ  H132  H  HCH2  0   0.224  -0.9219  -0.6764    0.9164
 SDZ  H15   H  HCR6  0   0.256   2.6770   0.3621    3.3379
 SDZ  H16   H  HCR6  0   0.246   2.4317   0.3203    5.7791
 SDZ  H18   H  HCR6  0   0.246  -1.8114   0.0317    5.3464
 SDZ  H19   H  HCR6  0   0.275  -1.5901   0.0883    2.9366
 SDZ  H20   H  HCH1  0   0.226   1.1613   0.2959    7.6817
 SDZ  H211  H  HCH2  0   0.230  -0.4023   2.1966    7.4928
 SDZ  H212  H  HCH2  0   0.210  -1.7646   1.0955    7.4047
 SDZ  H221  H  HCH2  0   0.210   0.1461   1.3827    9.7662
 SDZ  H222  H  HCH2  0   0.227  -1.5180   1.9293    9.7073
 SDZ  H231  H  HCH2  0   0.226  -1.3090  -0.2546   10.9106
 SDZ  H232  H  HCH2  0   0.208  -2.3224  -0.3932    9.4868
 SDZ  H241  H  HCH2  0   0.209   0.6123  -1.2098    9.6907
 SDZ  H242  H  HCH2  0   0.227  -0.7551  -2.3010    9.5819
 SDZ  H251  H  HCH2  0   0.211  -1.2799  -1.4854    7.3090
 SDZ  H252  H  HCH2  0   0.229   0.3865  -2.0259    7.3785

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
 SDZ  N1   C2    aromatic  1.327  0.020  1.327
 SDZ  N1   C6    aromatic  1.334  0.020  1.334
 SDZ  C2   C3    aromatic  1.381  0.020  1.381
 SDZ  C2   H2    single    0.930  0.020  1.080
 SDZ  C3   C4    aromatic  1.392  0.020  1.392
 SDZ  C3   H3    single    0.930  0.020  1.080
 SDZ  C4   C5    aromatic  1.378  0.020  1.378
 SDZ  C4   H4    single    0.930  0.020  1.080
 SDZ  C5   C6    aromatic  1.411  0.020  1.411
 SDZ  C5   H5    single    0.930  0.020  1.080
 SDZ  C6   N2    single    1.374  0.020  1.374
 SDZ  N2   C7    single    1.452  0.020  1.452
 SDZ  N2   C9    single    1.450  0.020  1.450
 SDZ  C7   C8    single    1.515  0.020  1.515
 SDZ  C7   H71   single    0.970  0.020  1.090
 SDZ  C7   H72   single    0.970  0.020  1.090
 SDZ  C8   N3    single    1.452  0.020  1.452
 SDZ  C8   H81   single    0.970  0.020  1.090
 SDZ  C8   H82   single    0.970  0.020  1.090
 SDZ  N3   C10   single    1.449  0.020  1.449
 SDZ  N3   C11   single    1.451  0.020  1.451
 SDZ  C9   C10   single    1.517  0.020  1.517
 SDZ  C9   H91   single    0.970  0.020  1.090
 SDZ  C9   H92   single    0.970  0.020  1.090
 SDZ  C10  H101  single    0.970  0.020  1.090
 SDZ  C10  H102  single    0.970  0.020  1.090
 SDZ  C11  C12   single    1.532  0.020  1.532
 SDZ  C11  H111  single    0.970  0.020  1.090
 SDZ  C11  H112  single    0.970  0.020  1.090
 SDZ  C12  O1    single    1.406  0.020  1.406
 SDZ  C12  C13   single    1.511  0.020  1.511
 SDZ  C12  H12   single    0.970  0.020  1.090
 SDZ  O1   HO1   single    0.850  0.020  0.980
 SDZ  C13  O2    single    1.413  0.020  1.413
 SDZ  C13  H131  single    0.970  0.020  1.090
 SDZ  C13  H132  single    0.970  0.020  1.090
 SDZ  O2   C14   single    1.350  0.020  1.350
 SDZ  C14  C15   aromatic  1.394  0.020  1.394
 SDZ  C14  C19   aromatic  1.393  0.020  1.393
 SDZ  C15  C16   aromatic  1.384  0.020  1.384
 SDZ  C15  H15   single    0.930  0.020  1.080
 SDZ  C16  C17   aromatic  1.395  0.020  1.395
 SDZ  C16  H16   single    0.930  0.020  1.080
 SDZ  C17  C18   aromatic  1.391  0.020  1.391
 SDZ  C17  C20   single    1.507  0.020  1.507
 SDZ  C18  C19   aromatic  1.390  0.020  1.390
 SDZ  C18  H18   single    0.930  0.020  1.080
 SDZ  C19  H19   single    0.930  0.020  1.080
 SDZ  C20  C21   single    1.532  0.020  1.532
 SDZ  C20  C25   single    1.534  0.020  1.534
 SDZ  C20  H20   single    0.970  0.020  1.090
 SDZ  C21  C22   single    1.526  0.020  1.526
 SDZ  C21  H211  single    0.970  0.020  1.090
 SDZ  C21  H212  single    0.970  0.020  1.090
 SDZ  C22  C23   single    1.525  0.020  1.525
 SDZ  C22  H221  single    0.970  0.020  1.090
 SDZ  C22  H222  single    0.970  0.020  1.090
 SDZ  C23  C24   single    1.525  0.020  1.525
 SDZ  C23  H231  single    0.970  0.020  1.090
 SDZ  C23  H232  single    0.970  0.020  1.090
 SDZ  C24  C25   single    1.526  0.020  1.526
 SDZ  C24  H241  single    0.970  0.020  1.090
 SDZ  C24  H242  single    0.970  0.020  1.090
 SDZ  C25  H251  single    0.970  0.020  1.090
 SDZ  C25  H252  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
 SDZ  C6    N1   C2    119.51  3.000
 SDZ  H2    C2   C3    120.17  3.000
 SDZ  H2    C2   N1    115.71  3.000
 SDZ  C3    C2   N1    124.12  3.000
 SDZ  H3    C3   C4    122.12  3.000
 SDZ  H3    C3   C2    121.14  3.000
 SDZ  C4    C3   C2    116.74  3.000
 SDZ  H4    C4   C5    119.27  3.000
 SDZ  H4    C4   C3    120.55  3.000
 SDZ  C5    C4   C3    120.18  3.000
 SDZ  H5    C5   C6    122.10  3.000
 SDZ  H5    C5   C4    119.06  3.000
 SDZ  C6    C5   C4    118.83  3.000
 SDZ  N2    C6   C5    122.48  3.000
 SDZ  N2    C6   N1    116.89  3.000
 SDZ  C5    C6   N1    120.61  3.000
 SDZ  C9    N2   C7    113.28  3.000
 SDZ  C9    N2   C6    120.83  3.000
 SDZ  C7    N2   C6    119.21  3.000
 SDZ  H72   C7   H71   107.27  3.000
 SDZ  H72   C7   C8    109.54  3.000
 SDZ  H71   C7   C8    109.02  3.000
 SDZ  H72   C7   N2    110.53  3.000
 SDZ  H71   C7   N2    109.44  3.000
 SDZ  C8    C7   N2    110.95  3.000
 SDZ  H82   C8   H81   107.14  3.000
 SDZ  H82   C8   N3    110.28  3.000
 SDZ  H81   C8   N3    111.00  3.000
 SDZ  H82   C8   C7    107.85  3.000
 SDZ  H81   C8   C7    109.57  3.000
 SDZ  N3    C8   C7    110.88  3.000
 SDZ  C11   N3   C10   112.97  3.000
 SDZ  C11   N3   C8    113.13  3.000
 SDZ  C10   N3   C8    109.31  3.000
 SDZ  H92   C9   H91   107.46  3.000
 SDZ  H92   C9   C10   109.60  3.000
 SDZ  H91   C9   C10   106.92  3.000
 SDZ  H92   C9   N2    110.72  3.000
 SDZ  H91   C9   N2    110.79  3.000
 SDZ  C10   C9   N2    111.21  3.000
 SDZ  H102  C10  H101  107.28  3.000
 SDZ  H102  C10  C9    109.28  3.000
 SDZ  H101  C10  C9    108.15  3.000
 SDZ  H102  C10  N3    111.43  3.000
 SDZ  H101  C10  N3    109.37  3.000
 SDZ  C9    C10  N3    111.19  3.000
 SDZ  H112  C11  H111  106.99  3.000
 SDZ  H112  C11  C12   110.33  3.000
 SDZ  H111  C11  C12   109.05  3.000
 SDZ  H112  C11  N3    112.79  3.000
 SDZ  H111  C11  N3    107.94  3.000
 SDZ  C12   C11  N3    109.61  3.000
 SDZ  H12   C12  C13   108.21  3.000
 SDZ  H12   C12  O1    110.61  3.000
 SDZ  C13   C12  O1    109.88  3.000
 SDZ  H12   C12  C11   109.01  3.000
 SDZ  C13   C12  C11   109.56  3.000
 SDZ  O1    C12  C11   109.55  3.000
 SDZ  HO1   O1   C12   104.36  3.000
 SDZ  H132  C13  H131  107.62  3.000
 SDZ  H132  C13  O2    111.10  3.000
 SDZ  H131  C13  O2    110.69  3.000
 SDZ  H132  C13  C12   109.39  3.000
 SDZ  H131  C13  C12   109.70  3.000
 SDZ  O2    C13  C12   108.33  3.000
 SDZ  C14   O2   C13   118.96  3.000
 SDZ  C19   C14  C15   119.02  3.000
 SDZ  C19   C14  O2    124.58  3.000
 SDZ  C15   C14  O2    116.40  3.000
 SDZ  H15   C15  C16   120.30  3.000
 SDZ  H15   C15  C14   119.57  3.000
 SDZ  C16   C15  C14   120.13  3.000
 SDZ  H16   C16  C17   119.30  3.000
 SDZ  H16   C16  C15   118.85  3.000
 SDZ  C17   C16  C15   121.85  3.000
 SDZ  C20   C17  C18   122.00  3.000
 SDZ  C20   C17  C16   120.80  3.000
 SDZ  C18   C17  C16   117.20  3.000
 SDZ  H18   C18  C19   118.01  3.000
 SDZ  H18   C18  C17   120.02  3.000
 SDZ  C19   C18  C17   121.97  3.000
 SDZ  H19   C19  C18   118.79  3.000
 SDZ  H19   C19  C14   121.38  3.000
 SDZ  C18   C19  C14   119.84  3.000
 SDZ  H20   C20  C25   107.34  3.000
 SDZ  H20   C20  C21   107.15  3.000
 SDZ  C25   C20  C21   110.35  3.000
 SDZ  H20   C20  C17   107.17  3.000
 SDZ  C25   C20  C17   111.70  3.000
 SDZ  C21   C20  C17   112.82  3.000
 SDZ  H212  C21  H211  106.52  3.000
 SDZ  H212  C21  C22   108.88  3.000
 SDZ  H211  C21  C22   110.41  3.000
 SDZ  H212  C21  C20   109.70  3.000
 SDZ  H211  C21  C20   109.79  3.000
 SDZ  C22   C21  C20   111.43  3.000
 SDZ  H222  C22  H221  106.41  3.000
 SDZ  H222  C22  C23   110.29  3.000
 SDZ  H221  C22  C23   109.41  3.000
 SDZ  H222  C22  C21   109.91  3.000
 SDZ  H221  C22  C21   109.40  3.000
 SDZ  C23   C22  C21   111.29  3.000
 SDZ  H232  C23  H231  106.47  3.000
 SDZ  H232  C23  C24   109.31  3.000
 SDZ  H231  C23  C24   110.24  3.000
 SDZ  H232  C23  C22   109.21  3.000
 SDZ  H231  C23  C22   110.31  3.000
 SDZ  C24   C23  C22   111.19  3.000
 SDZ  H242  C24  H241  106.45  3.000
 SDZ  H242  C24  C25   110.01  3.000
 SDZ  H241  C24  C25   109.02  3.000
 SDZ  H242  C24  C23   110.40  3.000
 SDZ  H241  C24  C23   109.27  3.000
 SDZ  C25   C24  C23   111.54  3.000
 SDZ  H252  C25  H251  106.42  3.000
 SDZ  H252  C25  C24   110.21  3.000
 SDZ  H251  C25  C24   109.64  3.000
 SDZ  H252  C25  C20   109.63  3.000
 SDZ  H251  C25  C20   109.26  3.000
 SDZ  C24   C25  C20   111.55  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
 SDZ  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 SDZ  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 SDZ  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 SDZ  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 SDZ  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 SDZ  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 SDZ  CONST_07  C17   C16  C15  C14     0.00   0.0  0
 SDZ  CONST_08  C17   C18  C19  C14     0.00   0.0  0
 SDZ  CONST_09  C18   C19  C14  C15     0.00   0.0  0
 SDZ  CONST_10  C18   C17  C16  C15     0.00   0.0  0
 SDZ  CONST_11  C19   C14  C15  C16     0.00   0.0  0
 SDZ  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 SDZ  CONST_13  N2    C6   N1   C2    180.00   0.0  0
 SDZ  CONST_14  N2    C6   C5   C4    180.00   0.0  0
 SDZ  CONST_15  C20   C17  C16  C15   180.00   0.0  0
 SDZ  CONST_16  C20   C17  C18  C19   180.00   0.0  0
 SDZ  CONST_17  C16   C15  C14  O2    180.00   0.0  0
 SDZ  CONST_18  C18   C19  C14  O2    180.00   0.0  0
 SDZ  CONST_19  H3    C3   C2   N1    180.00   0.0  0
 SDZ  CONST_20  H5    C5   C6   N1    180.00   0.0  0
 SDZ  CONST_21  H4    C4   C3   C2    180.00   0.0  0
 SDZ  CONST_22  H2    C2   C3   C4    180.00   0.0  0
 SDZ  CONST_23  H16   C16  C15  C14   180.00   0.0  0
 SDZ  CONST_24  H18   C18  C19  C14   180.00   0.0  0
 SDZ  CONST_25  H19   C19  C14  C15   180.00   0.0  0
 SDZ  CONST_26  H15   C15  C16  C17   180.00   0.0  0
 SDZ  Var_01    C7    N2   C6   N1    -13.73  30.0  2
 SDZ  Var_02    C8    C7   N2   C6    156.60  30.0  1
 SDZ  Var_03    C10   C9   N2   C6   -157.73  30.0  1
 SDZ  Var_04    N3    C8   C7   N2     55.98  30.0  1
 SDZ  Var_05    N3    C10  C9   N2    -54.83  30.0  1
 SDZ  Var_06    C10   N3   C8   C7    -59.84  30.0  1
 SDZ  Var_07    C9    C10  N3   C8     59.23  30.0  1
 SDZ  Var_08    C23   C22  C21  C20   -56.09  30.0  1
 SDZ  Var_09    C23   C24  C25  C20    55.28  30.0  1
 SDZ  Var_10    C24   C23  C22  C21    55.26  30.0  1
 SDZ  Var_11    C25   C24  C23  C22   -54.90  30.0  1
 SDZ  Var_12    C12   C11  N3   C8    -78.37  30.0  3
 SDZ  Var_13    C15   C14  O2   C13  -178.60  30.0  2
 SDZ  Var_14    H131  C13  O2   C14    62.26  30.0  1

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
 SDZ  chir_01  C12  C11  O1   C13  positiv
 SDZ  chir_02  C20  C17  C21  C25  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
 SDZ  plan-1  N1   0.020
 SDZ  plan-1  C2   0.020
 SDZ  plan-1  C3   0.020
 SDZ  plan-1  C4   0.020
 SDZ  plan-1  C5   0.020
 SDZ  plan-1  C6   0.020
 SDZ  plan-1  N2   0.020
 SDZ  plan-1  H2   0.020
 SDZ  plan-1  H3   0.020
 SDZ  plan-1  H4   0.020
 SDZ  plan-1  H5   0.020
 SDZ  plan-2  O2   0.020
 SDZ  plan-2  C14  0.020
 SDZ  plan-2  C15  0.020
 SDZ  plan-2  C16  0.020
 SDZ  plan-2  C17  0.020
 SDZ  plan-2  C18  0.020
 SDZ  plan-2  C19  0.020
 SDZ  plan-2  C20  0.020
 SDZ  plan-2  H15  0.020
 SDZ  plan-2  H16  0.020
 SDZ  plan-2  H18  0.020
 SDZ  plan-2  H19  0.020

