# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 08:16:31 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (5R,6S)-6-phenyl-5-[4-(2-pyrrolidin-1-ylethoxy)phenyl]-5,6,7,8-tetrahydronaphthalen-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2[C@H]([C@H](CCc2c1)c3ccccc3)c4ccc(OCCN5CCCC5)cc4
#
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
 C3D  C3D  (5R,6S)-6-phenyl-5-[4-(2-pyrrolidin-1-ylethoxy)phenyl]-5,6,7,8-tetrahydronaphthalen-2-ol  ligand  62  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C3D
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
 C3D  C1    C  CH1   0  -0.373   2.6430   4.4534   0.1929
 C3D  C2    C  CH1   0  -0.300   3.9245   4.7000  -0.6445
 C3D  C3    C  CH2   0  -0.452   4.1526   3.5277  -1.5900
 C3D  C4    C  CH2   0  -0.508   3.0286   3.4731  -2.6132
 C3D  C5    C  CR6   0   0.069   1.6575   3.6059  -2.0007
 C3D  C6    C  CR16  0  -0.387   0.5459   3.2553  -2.7651
 C3D  C7    C  CR6   0   0.350  -0.7411   3.3846  -2.2628
 C3D  C8    C  CR16  0  -0.389  -0.9242   3.8753  -0.9708
 C3D  C9    C  CR16  0  -0.278   0.1821   4.2178  -0.2147
 C3D  C10   C  CR6   0   0.095   1.4805   4.0925  -0.7050
 C3D  C11   C  CR6   0   0.160   5.0991   5.0538   0.2289
 C3D  C12   C  CR16  0  -0.312   5.2561   6.3724   0.6534
 C3D  C13   C  CR16  0  -0.244   6.2947   6.7370   1.4982
 C3D  C14   C  CR16  0  -0.274   7.2047   5.7814   1.9318
 C3D  C15   C  CR16  0  -0.238   7.0626   4.4658   1.5125
 C3D  C16   C  CR16  0  -0.295   6.0187   4.1064   0.6703
 C3D  C17   C  CR6   0   0.137   2.8517   3.4226   1.2822
 C3D  C18   C  CR16  0  -0.273   3.3060   3.8075   2.5374
 C3D  C19   C  CR16  0  -0.369   3.5553   2.8864   3.5475
 C3D  C20   C  CR6   0   0.369   3.3505   1.5307   3.3090
 C3D  C21   C  CR16  0  -0.342   2.8826   1.1259   2.0587
 C3D  C22   C  CR16  0  -0.280   2.6352   2.0610   1.0700
 C3D  C24   C  CH2   0  -0.187   4.0355   0.9068   5.5016
 C3D  C25   C  CH2   0  -0.296   4.1505  -0.3765   6.3050
 C3D  C27   C  CH2   0  -0.273   5.0467  -1.3533   8.3245
 C3D  C28   C  CH2   0  -0.466   5.3576  -0.8714   9.7395
 C3D  O7    O  OH1   0  -0.637  -1.7716   3.0260  -3.0581
 C3D  O23   O  O2    0  -0.480   3.5641   0.5536   4.2145
 C3D  N26   N  NT    0  -0.434   4.7237  -0.1317   7.6067
 C3D  C29   C  CH2   0  -0.465   4.5311   0.4233   9.8867
 C3D  C30   C  CH2   0  -0.285   3.8711   0.6158   8.5180
 C3D  H1    H  HCH1  0   0.262   2.3988   5.4001   0.6866
 C3D  H2    H  HCH1  0   0.246   3.7117   5.5798  -1.2646
 C3D  H31   H  HCH2  0   0.235   4.1954   2.5892  -1.0312
 C3D  H32   H  HCH2  0   0.246   5.1104   3.6283  -2.1045
 C3D  H41   H  HCH2  0   0.251   3.0830   2.5480  -3.1919
 C3D  H42   H  HCH2  0   0.247   3.1641   4.2844  -3.3367
 C3D  H6    H  HCR6  0   0.250   0.6868   2.8743  -3.7710
 C3D  H8    H  HCR6  0   0.265  -1.9208   3.9913  -0.5598
 C3D  H9    H  HCR6  0   0.246   0.0303   4.5916   0.7918
 C3D  H12   H  HCR6  0   0.242   4.5510   7.1253   0.3172
 C3D  H13   H  HCR6  0   0.250   6.3971   7.7678   1.8136
 C3D  H14   H  HCR6  0   0.250   8.0204   6.0605   2.5867
 C3D  H15   H  HCR6  0   0.248   7.7671   3.7132   1.8436
 C3D  H16   H  HCR6  0   0.241   5.9235   3.0716   0.3655
 C3D  H18   H  HCR6  0   0.246   3.4779   4.8570   2.7443
 C3D  H19   H  HCR6  0   0.272   3.9087   3.2463   4.5041
 C3D  H21   H  HCR6  0   0.254   2.7085   0.0737   1.8689
 C3D  H22   H  HCR6  0   0.248   2.2520   1.7168   0.1175
 C3D  H241  H  HCH2  0   0.223   5.0152   1.3947   5.4402
 C3D  H242  H  HCH2  0   0.225   3.3431   1.6077   5.9808
 C3D  H251  H  HCH2  0   0.200   3.1579  -0.8548   6.3785
 C3D  H252  H  HCH2  0   0.241   4.8020  -1.0697   5.7657
 C3D  H272  H  HCH2  0   0.192   4.1924  -2.0508   8.3406
 C3D  H281  H  HCH2  0   0.234   6.4223  -0.6646   9.8510
 C3D  H282  H  HCH2  0   0.234   5.0965  -1.6238  10.4832
 C3D  HO7   H  HOH1  0   0.472  -2.6070   3.1368  -2.5913
 C3D  H291  H  HCH2  0   0.235   3.7837   0.3530  10.6758
 C3D  H292  H  HCH2  0   0.235   5.1760   1.2680  10.1295
 C3D  H301  H  HCH2  0   0.194   2.8446   0.2113   8.5262
 C3D  H302  H  HCH2  0   0.236   3.8008   1.6673   8.2333
 C3D  H271  H  HCH2  0   0.234   5.8819  -1.8734   7.8507

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
 C3D  C1   C17   single    1.514  0.020  1.514
 C3D  C1   C10   single    1.513  0.020  1.513
 C3D  C1   C2    single    1.550  0.020  1.550
 C3D  C1   H1    single    0.970  0.020  1.090
 C3D  C2   C3    single    1.523  0.020  1.523
 C3D  C2   C11   single    1.506  0.020  1.506
 C3D  C2   H2    single    0.970  0.020  1.090
 C3D  C3   C4    single    1.521  0.020  1.521
 C3D  C3   H31   single    0.970  0.020  1.090
 C3D  C3   H32   single    0.970  0.020  1.090
 C3D  C4   C5    single    1.507  0.020  1.507
 C3D  C4   H41   single    0.970  0.020  1.090
 C3D  C4   H42   single    0.970  0.020  1.090
 C3D  C5   C6    aromatic  1.394  0.020  1.394
 C3D  C5   C10   aromatic  1.395  0.020  1.395
 C3D  C6   C7    aromatic  1.388  0.020  1.388
 C3D  C6   H6    single    0.930  0.020  1.080
 C3D  C7   O7    single    1.350  0.020  1.350
 C3D  C7   C8    aromatic  1.394  0.020  1.394
 C3D  C8   C9    aromatic  1.383  0.020  1.383
 C3D  C8   H8    single    0.930  0.020  1.080
 C3D  C9   C10   aromatic  1.393  0.020  1.393
 C3D  C9   H9    single    0.930  0.020  1.080
 C3D  C11  C16   aromatic  1.392  0.020  1.392
 C3D  C11  C12   aromatic  1.394  0.020  1.394
 C3D  C12  C13   aromatic  1.388  0.020  1.388
 C3D  C12  H12   single    0.930  0.020  1.080
 C3D  C13  C14   aromatic  1.389  0.020  1.389
 C3D  C13  H13   single    0.930  0.020  1.080
 C3D  C14  C15   aromatic  1.388  0.020  1.388
 C3D  C14  H14   single    0.930  0.020  1.080
 C3D  C15  C16   aromatic  1.389  0.020  1.389
 C3D  C15  H15   single    0.930  0.020  1.080
 C3D  C16  H16   single    0.930  0.020  1.080
 C3D  C17  C18   aromatic  1.389  0.020  1.389
 C3D  C17  C22   aromatic  1.395  0.020  1.395
 C3D  C18  C19   aromatic  1.390  0.020  1.390
 C3D  C18  H18   single    0.930  0.020  1.080
 C3D  C19  C20   aromatic  1.392  0.020  1.392
 C3D  C19  H19   single    0.930  0.020  1.080
 C3D  C20  O23   single    1.349  0.020  1.349
 C3D  C20  C21   aromatic  1.395  0.020  1.395
 C3D  C21  C22   aromatic  1.383  0.020  1.383
 C3D  C21  H21   single    0.930  0.020  1.080
 C3D  C22  H22   single    0.930  0.020  1.080
 C3D  C24  C25   single    1.518  0.020  1.518
 C3D  C24  O23   single    1.415  0.020  1.415
 C3D  C24  H241  single    0.970  0.020  1.090
 C3D  C24  H242  single    0.970  0.020  1.090
 C3D  C25  N26   single    1.443  0.020  1.443
 C3D  C25  H251  single    0.970  0.020  1.090
 C3D  C25  H252  single    0.970  0.020  1.090
 C3D  C27  C28   single    1.527  0.020  1.527
 C3D  C27  N26   single    1.453  0.020  1.453
 C3D  C27  H271  single    0.970  0.020  1.090
 C3D  C27  H272  single    0.970  0.020  1.090
 C3D  C28  C29   single    1.543  0.020  1.543
 C3D  C28  H281  single    0.970  0.020  1.090
 C3D  C28  H282  single    0.970  0.020  1.090
 C3D  O7   HO7   single    0.850  0.020  0.980
 C3D  N26  C30   single    1.455  0.020  1.455
 C3D  C29  C30   single    1.532  0.020  1.532
 C3D  C29  H291  single    0.970  0.020  1.090
 C3D  C29  H292  single    0.970  0.020  1.090
 C3D  C30  H301  single    0.970  0.020  1.090
 C3D  C30  H302  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
 C3D  H1    C1   C17   107.15  3.000
 C3D  H1    C1   C10   107.60  3.000
 C3D  C17   C1   C10   111.75  3.000
 C3D  H1    C1   C2    106.87  3.000
 C3D  C10   C1   C2    110.65  3.000
 C3D  C17   C1   C2    112.51  3.000
 C3D  H2    C2   C11   106.90  3.000
 C3D  H2    C2   C3    107.18  3.000
 C3D  C11   C2   C3    115.09  3.000
 C3D  H2    C2   C1    105.81  3.000
 C3D  C11   C2   C1    111.64  3.000
 C3D  C3    C2   C1    109.67  3.000
 C3D  H32   C3   H31   106.60  3.000
 C3D  H32   C3   C4    109.55  3.000
 C3D  H31   C3   C4    110.00  3.000
 C3D  H32   C3   C2    110.67  3.000
 C3D  H31   C3   C2    110.45  3.000
 C3D  C4    C3   C2    109.54  3.000
 C3D  H42   C4   H41   105.73  3.000
 C3D  H42   C4   C5    108.40  3.000
 C3D  H41   C4   C5    109.58  3.000
 C3D  H42   C4   C3    109.04  3.000
 C3D  H41   C4   C3    110.48  3.000
 C3D  C5    C4   C3    113.31  3.000
 C3D  C10   C5   C6    119.72  3.000
 C3D  C10   C5   C4    121.56  3.000
 C3D  C6    C5   C4    118.71  3.000
 C3D  H6    C6   C7    119.27  3.000
 C3D  H6    C6   C5    119.55  3.000
 C3D  C7    C6   C5    121.18  3.000
 C3D  O7    C7   C8    122.62  3.000
 C3D  C8    C7   C6    119.35  3.000
 C3D  O7    C7   C6    118.03  3.000
 C3D  H8    C8   C9    120.10  3.000
 C3D  H8    C8   C7    120.64  3.000
 C3D  C9    C8   C7    119.26  3.000
 C3D  H9    C9   C10   119.21  3.000
 C3D  H9    C9   C8    118.74  3.000
 C3D  C10   C9   C8    122.05  3.000
 C3D  C9    C10  C5    118.44  3.000
 C3D  C9    C10  C1    119.07  3.000
 C3D  C5    C10  C1    122.47  3.000
 C3D  C16   C11  C12   118.22  3.000
 C3D  C12   C11  C2    119.12  3.000
 C3D  C16   C11  C2    122.63  3.000
 C3D  H12   C12  C13   119.52  3.000
 C3D  H12   C12  C11   119.27  3.000
 C3D  C13   C12  C11   121.21  3.000
 C3D  H13   C13  C14   120.13  3.000
 C3D  H13   C13  C12   119.89  3.000
 C3D  C14   C13  C12   119.98  3.000
 C3D  H14   C14  C15   120.28  3.000
 C3D  H14   C14  C13   120.33  3.000
 C3D  C15   C14  C13   119.39  3.000
 C3D  H15   C15  C16   119.65  3.000
 C3D  H15   C15  C14   119.99  3.000
 C3D  C16   C15  C14   120.36  3.000
 C3D  H16   C16  C15   118.95  3.000
 C3D  H16   C16  C11   120.20  3.000
 C3D  C15   C16  C11   120.84  3.000
 C3D  C22   C17  C18   117.30  3.000
 C3D  C22   C17  C1    122.25  3.000
 C3D  C18   C17  C1    120.43  3.000
 C3D  H18   C18  C19   118.34  3.000
 C3D  H18   C18  C17   119.53  3.000
 C3D  C19   C18  C17   122.13  3.000
 C3D  H19   C19  C20   121.59  3.000
 C3D  H19   C19  C18   118.76  3.000
 C3D  C20   C19  C18   119.65  3.000
 C3D  O23   C20  C21   116.38  3.000
 C3D  C21   C20  C19   119.06  3.000
 C3D  O23   C20  C19   124.56  3.000
 C3D  H21   C21  C22   120.18  3.000
 C3D  H21   C21  C20   119.53  3.000
 C3D  C22   C21  C20   120.29  3.000
 C3D  H22   C22  C21   118.49  3.000
 C3D  H22   C22  C17   119.94  3.000
 C3D  C21   C22  C17   121.56  3.000
 C3D  H242  C24  H241  107.73  3.000
 C3D  H242  C24  O23   110.29  3.000
 C3D  H241  C24  O23   110.96  3.000
 C3D  H242  C24  C25   110.92  3.000
 C3D  H241  C24  C25   109.76  3.000
 C3D  O23   C24  C25   107.19  3.000
 C3D  H252  C25  H251  107.08  3.000
 C3D  H252  C25  N26   108.40  3.000
 C3D  H251  C25  N26   111.74  3.000
 C3D  H252  C25  C24   108.66  3.000
 C3D  H251  C25  C24   109.46  3.000
 C3D  N26   C25  C24   111.35  3.000
 C3D  H272  C27  H271  107.31  3.000
 C3D  H272  C27  N26   111.51  3.000
 C3D  H271  C27  N26   110.86  3.000
 C3D  H272  C27  C28   110.11  3.000
 C3D  H271  C27  C28   113.37  3.000
 C3D  N26   C27  C28   103.75  3.000
 C3D  H282  C28  H281  107.17  3.000
 C3D  H282  C28  C29   112.70  3.000
 C3D  H281  C28  C29   110.74  3.000
 C3D  H282  C28  C27   111.46  3.000
 C3D  H281  C28  C27   110.70  3.000
 C3D  C29   C28  C27   104.13  3.000
 C3D  HO7   O7   C7    110.24  3.000
 C3D  C24   O23  C20   118.83  3.000
 C3D  C30   N26  C27   104.64  3.000
 C3D  C30   N26  C25   114.79  3.000
 C3D  C27   N26  C25   113.03  3.000
 C3D  H292  C29  H291  107.14  3.000
 C3D  H292  C29  C30   110.89  3.000
 C3D  H291  C29  C30   111.08  3.000
 C3D  H292  C29  C28   110.77  3.000
 C3D  H291  C29  C28   112.49  3.000
 C3D  C30   C29  C28   104.54  3.000
 C3D  H302  C30  H301  107.18  3.000
 C3D  H302  C30  C29   112.45  3.000
 C3D  H301  C30  C29   110.37  3.000
 C3D  H302  C30  N26   111.67  3.000
 C3D  H301  C30  N26   111.19  3.000
 C3D  C29   C30  N26   104.04  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
 C3D  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 C3D  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 C3D  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 C3D  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 C3D  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 C3D  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 C3D  CONST_07  C14  C15  C16  C11     0.00   0.0  0
 C3D  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 C3D  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 C3D  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 C3D  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 C3D  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 C3D  CONST_13  C20  C19  C18  C17     0.00   0.0  0
 C3D  CONST_14  C20  C21  C22  C17     0.00   0.0  0
 C3D  CONST_15  C21  C22  C17  C18     0.00   0.0  0
 C3D  CONST_16  C21  C20  C19  C18     0.00   0.0  0
 C3D  CONST_17  C22  C17  C18  C19     0.00   0.0  0
 C3D  CONST_18  C22  C21  C20  C19     0.00   0.0  0
 C3D  CONST_19  C19  C18  C17  C1    180.00   0.0  0
 C3D  CONST_20  C21  C22  C17  C1    180.00   0.0  0
 C3D  CONST_21  C15  C16  C11  C2    180.00   0.0  0
 C3D  CONST_22  C13  C12  C11  C2    180.00   0.0  0
 C3D  CONST_23  O7   C7   C6   C5    180.00   0.0  0
 C3D  CONST_24  O7   C7   C8   C9    180.00   0.0  0
 C3D  CONST_25  O23  C20  C19  C18   180.00   0.0  0
 C3D  CONST_26  O23  C20  C21  C22   180.00   0.0  0
 C3D  CONST_27  H18  C18  C17  C1      0.00   0.0  0
 C3D  CONST_28  H22  C22  C17  C1      0.00   0.0  0
 C3D  CONST_29  H9   C9   C10  C1      0.00   0.0  0
 C3D  CONST_30  H16  C16  C11  C2      0.00   0.0  0
 C3D  CONST_31  H12  C12  C11  C2      0.00   0.0  0
 C3D  CONST_32  H6   C6   C5   C4      0.00   0.0  0
 C3D  CONST_33  H8   C8   C7   C6    180.00   0.0  0
 C3D  CONST_34  H15  C15  C16  C11   180.00   0.0  0
 C3D  CONST_35  H13  C13  C12  C11   180.00   0.0  0
 C3D  CONST_36  H14  C14  C13  C12   180.00   0.0  0
 C3D  CONST_37  H19  C19  C18  C17   180.00   0.0  0
 C3D  CONST_38  H21  C21  C22  C17   180.00   0.0  0
 C3D  Var_01    C5   C4   C3   C2    -47.16  30.0  1
 C3D  Var_02    C6   C5   C4   C3   -164.78  30.0  1
 C3D  Var_03    C30  C29  C28  C27    -2.84  30.0  1
 C3D  Var_04    C29  C30  N26  C27    41.39  30.0  1
 C3D  Var_05    C30  N26  C27  C28   -43.34  30.0  1
 C3D  Var_06    N26  C30  C29  C28   -22.79  30.0  1
 C3D  Var_07    C29  C28  C27  N26    27.53  30.0  1
 C3D  Var_08    C27  N26  C25  C24  -170.84  30.0  3
 C3D  Var_09    C25  C24  O23  C20   178.71  30.0  1
 C3D  Var_10    N26  C25  C24  O23   175.58  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
 C3D  chir_01  C1  C17  C10  C2   positiv
 C3D  chir_02  C2  C1   C3   C11  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
 C3D  plan-1  C2   0.020
 C3D  plan-1  C11  0.020
 C3D  plan-1  C12  0.020
 C3D  plan-1  C13  0.020
 C3D  plan-1  C14  0.020
 C3D  plan-1  C15  0.020
 C3D  plan-1  C16  0.020
 C3D  plan-1  H12  0.020
 C3D  plan-1  H13  0.020
 C3D  plan-1  H14  0.020
 C3D  plan-1  H15  0.020
 C3D  plan-1  H16  0.020
 C3D  plan-2  C1   0.020
 C3D  plan-2  C4   0.020
 C3D  plan-2  C5   0.020
 C3D  plan-2  C6   0.020
 C3D  plan-2  C7   0.020
 C3D  plan-2  C8   0.020
 C3D  plan-2  C9   0.020
 C3D  plan-2  C10  0.020
 C3D  plan-2  O7   0.020
 C3D  plan-2  H6   0.020
 C3D  plan-2  H8   0.020
 C3D  plan-2  H9   0.020
 C3D  plan-3  C1   0.020
 C3D  plan-3  C17  0.020
 C3D  plan-3  C18  0.020
 C3D  plan-3  C19  0.020
 C3D  plan-3  C20  0.020
 C3D  plan-3  C21  0.020
 C3D  plan-3  C22  0.020
 C3D  plan-3  O23  0.020
 C3D  plan-3  H18  0.020
 C3D  plan-3  H19  0.020
 C3D  plan-3  H21  0.020
 C3D  plan-3  H22  0.020

