# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 02:36:14 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-{[(2R)-2-hydroxy-3-(phenanthren-9-yloxy)propyl]amino}propane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(CO)NC[C@@H](O)COc1cc2ccccc2c3ccccc13
#
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
 XX6  XX6  2-{[(2R)-2-hydroxy-3-(phenanthren-9-yloxy)propyl]amino}propane-1,3-diol  ligand  48  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XX6
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
 XX6  O4    O  OH1   0  -0.661   7.1516  -1.3012  -0.0806
 XX6  C19   C  CH2   0  -0.176   6.8835  -0.2832   0.8522
 XX6  C18   C  CH1   0  -0.102   5.7059   0.5775   0.4228
 XX6  C20   C  CH2   0  -0.164   5.9669   1.3982  -0.8342
 XX6  O3    O  OH1   0  -0.660   5.9499   0.5941  -1.9873
 XX6  N     N  NH1   0  -0.597   4.5047  -0.2292   0.3109
 XX6  C17   C  CH2   0  -0.284   3.2788   0.5324   0.2330
 XX6  C16   C  CH1   0  -0.033   2.0728  -0.4004   0.2474
 XX6  O2    O  OH1   0  -0.656   2.0531  -1.2279   1.3897
 XX6  C15   C  CH2   0  -0.188   0.7903   0.4003   0.1080
 XX6  O1    O  O2    0  -0.463  -0.2819  -0.5148   0.0070
 XX6  C10   C  CR6   0   0.374  -1.5401  -0.0533  -0.0164
 XX6  C5    C  CR66  0  -0.058  -2.5483  -1.0850  -0.0807
 XX6  C6    C  CR16  0  -0.280  -2.1848  -2.4440  -0.1156
 XX6  C1    C  CR16  0  -0.259  -3.1434  -3.4262  -0.1835
 XX6  C2    C  CR16  0  -0.235  -4.4968  -3.0752  -0.2163
 XX6  C3    C  CR16  0  -0.356  -4.8686  -1.7523  -0.1791
 XX6  C4    C  CR66  0   0.145  -3.9130  -0.7217  -0.1107
 XX6  C7    C  CR66  0   0.084  -4.2868   0.6789  -0.0694
 XX6  C11   C  CR16  0  -0.349  -5.6237   1.1156  -0.0871
 XX6  C12   C  CR16  0  -0.252  -5.9397   2.4539  -0.0442
 XX6  C13   C  CR16  0  -0.261  -4.9220   3.4137   0.0174
 XX6  C14   C  CR16  0  -0.324  -3.6079   3.0138   0.0346
 XX6  C8    C  CR66  0   0.121  -3.2645   1.6491  -0.0076
 XX6  C9    C  CR16  0  -0.509  -1.8903   1.2574   0.0136
 XX6  H4    H  HOH1  0   0.450   7.8498  -1.8503   0.2865
 XX6  H191  H  HCH2  0   0.201   6.6510  -0.7023   1.8422
 XX6  H192  H  HCH2  0   0.197   7.7481   0.3798   0.9923
 XX6  H18   H  HCH1  0   0.204   5.6136   1.3314   1.2268
 XX6  H201  H  HCH2  0   0.201   5.2120   2.1931  -0.8984
 XX6  H202  H  HCH2  0   0.198   6.9306   1.9103  -0.7012
 XX6  H     H  HNH1  0   0.338   4.4496  -0.8368   1.1197
 XX6  H3    H  HOH1  0   0.448   6.0419   1.1773  -2.7455
 XX6  H171  H  HCH2  0   0.191   3.1785   1.2736   1.0471
 XX6  H172  H  HCH2  0   0.232   3.2585   1.0996  -0.7011
 XX6  H16   H  HCH1  0   0.239   2.1593  -1.0799  -0.6061
 XX6  H2    H  HOH1  0   0.446   1.9682  -0.6714   2.1724
 XX6  H151  H  HCH2  0   0.228   0.6556   1.0592   0.9759
 XX6  H152  H  HCH2  0   0.234   0.8402   1.0356  -0.7835
 XX6  H9    H  HCR6  0   0.279  -1.1466   2.0422   0.0505
 XX6  H6    H  HCR6  0   0.258  -1.1406  -2.7220  -0.0886
 XX6  H1    H  HCR6  0   0.260  -2.8514  -4.4677  -0.2115
 XX6  HA    H  HCR6  0   0.262  -5.2556  -3.8444  -0.2701
 XX6  HB    H  HCR6  0   0.255  -5.9229  -1.5159  -0.2036
 XX6  H11   H  HCR6  0   0.254  -6.4320   0.3990  -0.1336
 XX6  H12   H  HCR6  0   0.257  -6.9769   2.7619  -0.0575
 XX6  H13   H  HCR6  0   0.257  -5.1691   4.4667   0.0518
 XX6  H14   H  HCR6  0   0.254  -2.8159   3.7514   0.0818

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
 XX6  O4   C19   single    1.407  0.020  1.407
 XX6  O4   H4    single    0.850  0.020  0.980
 XX6  C19  C18   single    1.520  0.020  1.520
 XX6  C19  H191  single    0.970  0.020  1.090
 XX6  C19  H192  single    0.970  0.020  1.090
 XX6  C18  C20   single    1.524  0.020  1.524
 XX6  C18  N     single    1.451  0.020  1.451
 XX6  C18  H18   single    0.970  0.020  1.090
 XX6  C20  O3    single    1.406  0.020  1.406
 XX6  C20  H201  single    0.970  0.020  1.090
 XX6  C20  H202  single    0.970  0.020  1.090
 XX6  O3   H3    single    0.850  0.020  0.980
 XX6  N    C17   single    1.445  0.020  1.445
 XX6  N    H     single    0.860  0.020  1.020
 XX6  C17  C16   single    1.525  0.020  1.525
 XX6  C17  H171  single    0.970  0.020  1.090
 XX6  C17  H172  single    0.970  0.020  1.090
 XX6  C16  O2    single    1.411  0.020  1.411
 XX6  C16  C15   single    1.518  0.020  1.518
 XX6  C16  H16   single    0.970  0.020  1.090
 XX6  O2   H2    single    0.850  0.020  0.980
 XX6  C15  O1    single    1.413  0.020  1.413
 XX6  C15  H151  single    0.970  0.020  1.090
 XX6  C15  H152  single    0.970  0.020  1.090
 XX6  O1   C10   single    1.340  0.020  1.340
 XX6  C10  C5    aromatic  1.444  0.020  1.444
 XX6  C10  C9    aromatic  1.357  0.020  1.357
 XX6  C5   C6    aromatic  1.407  0.020  1.407
 XX6  C5   C4    aromatic  1.413  0.020  1.413
 XX6  C6   C1    aromatic  1.374  0.020  1.374
 XX6  C6   H6    single    0.930  0.020  1.080
 XX6  C1   C2    aromatic  1.398  0.020  1.398
 XX6  C1   H1    single    0.930  0.020  1.080
 XX6  C2   C3    aromatic  1.375  0.020  1.375
 XX6  C2   HA    single    0.930  0.020  1.080
 XX6  C3   C4    aromatic  1.407  0.020  1.407
 XX6  C3   HB    single    0.930  0.020  1.080
 XX6  C4   C7    aromatic  1.450  0.020  1.450
 XX6  C7   C11   aromatic  1.407  0.020  1.407
 XX6  C7   C8    aromatic  1.411  0.020  1.411
 XX6  C11  H11   single    0.930  0.020  1.080
 XX6  C11  C12   aromatic  1.376  0.020  1.376
 XX6  C12  H12   single    0.930  0.020  1.080
 XX6  C12  C13   aromatic  1.400  0.020  1.400
 XX6  C13  H13   single    0.930  0.020  1.080
 XX6  C13  C14   aromatic  1.374  0.020  1.374
 XX6  C14  H14   single    0.930  0.020  1.080
 XX6  C14  C8    aromatic  1.408  0.020  1.408
 XX6  C8   C9    aromatic  1.429  0.020  1.429
 XX6  C9   H9    single    0.930  0.020  1.080

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
 XX6  H4    O4   C19   107.38  3.000
 XX6  H192  C19  H191  106.35  3.000
 XX6  H192  C19  C18   107.69  3.000
 XX6  H191  C19  C18   107.83  3.000
 XX6  H192  C19  O4    111.80  3.000
 XX6  H191  C19  O4    111.19  3.000
 XX6  C18   C19  O4    111.72  3.000
 XX6  H18   C18  N     111.46  3.000
 XX6  H18   C18  C20   104.29  3.000
 XX6  N     C18  C20   112.18  3.000
 XX6  H18   C18  C19   104.20  3.000
 XX6  N     C18  C19   110.37  3.000
 XX6  C20   C18  C19   113.90  3.000
 XX6  H202  C20  H201  105.81  3.000
 XX6  H202  C20  O3    112.11  3.000
 XX6  H201  C20  O3    110.96  3.000
 XX6  H202  C20  C18   107.53  3.000
 XX6  H201  C20  C18   108.68  3.000
 XX6  O3    C20  C18   111.50  3.000
 XX6  H3    O3   C20   107.39  3.000
 XX6  H     N    C17   108.24  3.000
 XX6  H     N    C18   108.47  3.000
 XX6  C17   N    C18   114.41  3.000
 XX6  H172  C17  H171  106.24  3.000
 XX6  H172  C17  C16   108.11  3.000
 XX6  H171  C17  C16   109.35  3.000
 XX6  H172  C17  N     109.59  3.000
 XX6  H171  C17  N     112.99  3.000
 XX6  C16   C17  N     110.37  3.000
 XX6  H16   C16  C15   108.82  3.000
 XX6  H16   C16  O2    105.56  3.000
 XX6  C15   C16  O2    111.83  3.000
 XX6  H16   C16  C17   108.06  3.000
 XX6  C15   C16  C17   110.16  3.000
 XX6  O2    C16  C17   112.19  3.000
 XX6  H2    O2   C16   108.66  3.000
 XX6  H152  C15  H151  107.50  3.000
 XX6  H152  C15  O1    110.60  3.000
 XX6  H151  C15  O1    110.61  3.000
 XX6  H152  C15  C16   110.00  3.000
 XX6  H151  C15  C16   110.34  3.000
 XX6  O1    C15  C16   107.82  3.000
 XX6  C10   O1   C15   119.38  3.000
 XX6  C9    C10  C5    120.72  3.000
 XX6  C9    C10  O1    125.06  3.000
 XX6  C5    C10  O1    114.22  3.000
 XX6  C4    C5   C6    119.83  3.000
 XX6  C4    C5   C10   119.46  3.000
 XX6  C6    C5   C10   120.72  3.000
 XX6  H6    C6   C1    119.43  3.000
 XX6  H6    C6   C5    119.82  3.000
 XX6  C1    C6   C5    120.75  3.000
 XX6  H1    C1   C2    120.15  3.000
 XX6  H1    C1   C6    120.06  3.000
 XX6  C2    C1   C6    119.79  3.000
 XX6  HA    C2   C3    119.72  3.000
 XX6  HA    C2   C1    120.10  3.000
 XX6  C3    C2   C1    120.18  3.000
 XX6  HB    C3   C4    120.23  3.000
 XX6  HB    C3   C2    118.28  3.000
 XX6  C4    C3   C2    121.50  3.000
 XX6  C7    C4   C3    122.26  3.000
 XX6  C7    C4   C5    119.79  3.000
 XX6  C3    C4   C5    117.95  3.000
 XX6  C8    C7   C11   118.41  3.000
 XX6  C8    C7   C4    118.60  3.000
 XX6  C11   C7   C4    122.99  3.000
 XX6  H11   C11  C12   118.31  3.000
 XX6  C12   C11  C7    121.33  3.000
 XX6  H11   C11  C7    120.36  3.000
 XX6  H12   C12  C13   120.14  3.000
 XX6  C13   C12  C11   120.08  3.000
 XX6  H12   C12  C11   119.78  3.000
 XX6  H13   C13  C14   120.09  3.000
 XX6  C14   C13  C12   119.75  3.000
 XX6  H13   C13  C12   120.16  3.000
 XX6  H14   C14  C8    118.88  3.000
 XX6  C8    C14  C13   121.01  3.000
 XX6  H14   C14  C13   120.11  3.000
 XX6  C9    C8   C14   119.99  3.000
 XX6  C9    C8   C7    120.59  3.000
 XX6  C14   C8   C7    119.42  3.000
 XX6  H9    C9   C8    117.56  3.000
 XX6  H9    C9   C10   121.60  3.000
 XX6  C8    C9   C10   120.84  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
 XX6  CONST_01  C1    C6   C5   C10   180.00   0.0  0
 XX6  CONST_02  C3    C4   C5   C10   180.00   0.0  0
 XX6  CONST_03  C7    C4   C5   C10     0.00   0.0  0
 XX6  CONST_04  C7    C8   C9   C10     0.00   0.0  0
 XX6  CONST_05  C14   C8   C9   C10   180.00   0.0  0
 XX6  CONST_06  C8    C9   C10  C5      0.00   0.0  0
 XX6  CONST_07  C2    C1   C6   C5      0.00   0.0  0
 XX6  CONST_08  C2    C3   C4   C5      0.00   0.0  0
 XX6  CONST_09  C11   C7   C4   C5    180.00   0.0  0
 XX6  CONST_10  C8    C7   C4   C5      0.00   0.0  0
 XX6  CONST_11  C9    C10  C5   C6    180.00   0.0  0
 XX6  CONST_12  C3    C4   C5   C6      0.00   0.0  0
 XX6  CONST_13  C7    C4   C5   C6    180.00   0.0  0
 XX6  CONST_14  C3    C2   C1   C6      0.00   0.0  0
 XX6  CONST_15  C4    C5   C6   C1      0.00   0.0  0
 XX6  CONST_16  C4    C3   C2   C1      0.00   0.0  0
 XX6  CONST_17  C7    C4   C3   C2    180.00   0.0  0
 XX6  CONST_18  C11   C7   C4   C3      0.00   0.0  0
 XX6  CONST_19  C8    C7   C4   C3    180.00   0.0  0
 XX6  CONST_20  C9    C10  C5   C4      0.00   0.0  0
 XX6  CONST_21  C12   C11  C7   C4    180.00   0.0  0
 XX6  CONST_22  C14   C8   C7   C4    180.00   0.0  0
 XX6  CONST_23  C9    C8   C7   C4      0.00   0.0  0
 XX6  CONST_24  C13   C12  C11  C7      0.00   0.0  0
 XX6  CONST_25  C13   C14  C8   C7      0.00   0.0  0
 XX6  CONST_26  C14   C8   C7   C11     0.00   0.0  0
 XX6  CONST_27  C9    C8   C7   C11   180.00   0.0  0
 XX6  CONST_28  C14   C13  C12  C11     0.00   0.0  0
 XX6  CONST_29  C8    C7   C11  C12     0.00   0.0  0
 XX6  CONST_30  C8    C14  C13  C12     0.00   0.0  0
 XX6  CONST_31  C9    C8   C14  C13   180.00   0.0  0
 XX6  CONST_32  C6    C5   C10  O1      0.00   0.0  0
 XX6  CONST_33  C4    C5   C10  O1    180.00   0.0  0
 XX6  CONST_34  C8    C9   C10  O1    180.00   0.0  0
 XX6  CONST_35  H6    C6   C5   C10     0.00   0.0  0
 XX6  CONST_36  H9    C9   C10  C5    180.00   0.0  0
 XX6  CONST_37  H1    C1   C6   C5    180.00   0.0  0
 XX6  CONST_38  HB    C3   C4   C5    180.00   0.0  0
 XX6  CONST_39  HA    C2   C1   C6    180.00   0.0  0
 XX6  CONST_40  H11   C11  C7   C4      0.00   0.0  0
 XX6  CONST_41  H12   C12  C11  C7    180.00   0.0  0
 XX6  CONST_42  H14   C14  C8   C7    180.00   0.0  0
 XX6  CONST_43  H13   C13  C12  C11   180.00   0.0  0
 XX6  Var_01    C5    C10  O1   C15  -178.21  30.0  2
 XX6  Var_02    H151  C15  O1   C10    53.89  30.0  1
 XX6  Var_03    C20   C18  C19  O4    -66.41  30.0  3
 XX6  Var_04    O3    C20  C18  C19    74.22  30.0  3
 XX6  Var_05    C17   N    C18  C19   165.52  30.0  3
 XX6  Var_06    C16   C17  N    C18  -174.81  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
 XX6  chir_01  C16  C17  O2  C15  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
 XX6  plan-1  O1   0.020
 XX6  plan-1  C10  0.020
 XX6  plan-1  C5   0.020
 XX6  plan-1  C6   0.020
 XX6  plan-1  C1   0.020
 XX6  plan-1  C2   0.020
 XX6  plan-1  C3   0.020
 XX6  plan-1  C4   0.020
 XX6  plan-1  C7   0.020
 XX6  plan-1  C11  0.020
 XX6  plan-1  C12  0.020
 XX6  plan-1  C13  0.020
 XX6  plan-1  C14  0.020
 XX6  plan-1  C8   0.020
 XX6  plan-1  C9   0.020
 XX6  plan-1  H9   0.020
 XX6  plan-1  H6   0.020
 XX6  plan-1  H1   0.020
 XX6  plan-1  HA   0.020
 XX6  plan-1  HB   0.020
 XX6  plan-1  H11  0.020
 XX6  plan-1  H12  0.020
 XX6  plan-1  H13  0.020
 XX6  plan-1  H14  0.020

