# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:15:51 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-{[(2S)-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
 XX7  XX7  2-{[(2S)-2-hydroxy-3-(phenanthren-9-yloxy)propyl]amino}propane-1,3-diol  ligand  48  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XX7
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
 XX7  O4    O  OH1   0  -0.667   6.0359  -0.8672  -1.9303
 XX7  C19   C  CH2   0  -0.167   5.9941  -1.5522  -0.6998
 XX7  C18   C  CH1   0  -0.134   5.7031  -0.5795   0.4439
 XX7  C20   C  CH2   0  -0.157   6.8793   0.3143   0.8068
 XX7  O3    O  OH1   0  -0.668   7.1426   1.2401  -0.2243
 XX7  N     N  NH1   0  -0.593   4.5127   0.2323   0.2725
 XX7  C17   C  CH2   0  -0.295   3.2800  -0.5080   0.1305
 XX7  O2    O  OH1   0  -0.654   2.0413   1.2099   1.3533
 XX7  C15   C  CH2   0  -0.181   0.7968  -0.3815   0.0215
 XX7  O1    O  O2    0  -0.463  -0.2841   0.5283  -0.0317
 XX7  C10   C  CR6   0   0.373  -1.5382   0.0579  -0.0591
 XX7  C5    C  CR66  0  -0.058  -2.5561   1.0823  -0.0470
 XX7  C6    C  CR16  0  -0.280  -2.2042   2.4443  -0.0077
 XX7  C1    C  CR16  0  -0.259  -3.1718   3.4201   0.0017
 XX7  C2    C  CR16  0  -0.235  -4.5226   3.0594  -0.0272
 XX7  C3    C  CR16  0  -0.356  -4.8831   1.7334  -0.0628
 XX7  C4    C  CR66  0   0.145  -3.9182   0.7093  -0.0734
 XX7  C7    C  CR66  0   0.083  -4.2801  -0.6946  -0.1070
 XX7  C11   C  CR16  0  -0.349  -5.6137  -1.1414  -0.1287
 XX7  C12   C  CR16  0  -0.252  -5.9185  -2.4828  -0.1592
 XX7  C13   C  CR16  0  -0.261  -4.8922  -3.4354  -0.1704
 XX7  C14   C  CR16  0  -0.324  -3.5812  -3.0255  -0.1500
 XX7  C8    C  CR66  0   0.121  -3.2492  -1.6577  -0.1175
 XX7  C9    C  CR16  0  -0.510  -1.8781  -1.2557  -0.0944
 XX7  C16   C  CH1   0  -0.022   2.0741   0.4257   0.1869
 XX7  H4    H  HOH1  0   0.451   5.9777  -1.5182  -2.6343
 XX7  H191  H  HCH2  0   0.204   5.2163  -2.3260  -0.7082
 XX7  H192  H  HCH2  0   0.194   6.9399  -2.0702  -0.4864
 XX7  H18   H  HCH1  0   0.235   5.5473  -1.2124   1.3267
 XX7  H201  H  HCH2  0   0.204   6.6330   0.8262   1.7449
 XX7  H202  H  HCH2  0   0.189   7.7526  -0.3213   1.0084
 XX7  H     H  HNH1  0   0.340   4.6356   0.8406  -0.5278
 XX7  H3    H  HOH1  0   0.453   7.7032   1.9311   0.1378
 XX7  H171  H  HCH2  0   0.210   3.2170  -1.0969  -0.7965
 XX7  H172  H  HCH2  0   0.222   3.2111  -1.2293   0.9543
 XX7  H16   H  HCH1  0   0.233   2.1430   1.1318  -0.6488
 XX7  H2    H  HOH1  0   0.443   2.2332   0.6430   2.1080
 XX7  H151  H  HCH2  0   0.225   0.6744  -1.0750   0.8636
 XX7  H152  H  HCH2  0   0.229   0.8404  -0.9788  -0.8964
 XX7  H9    H  HCR6  0   0.279  -1.1276  -2.0349  -0.1087
 XX7  H6    H  HCR6  0   0.258  -1.1619   2.7295   0.0190
 XX7  H1    H  HCR6  0   0.260  -2.8888   4.4641   0.0317
 XX7  HA    H  HCR6  0   0.262  -5.2884   3.8235  -0.0207
 XX7  HB    H  HCR6  0   0.255  -5.9357   1.4890  -0.0832
 XX7  H11   H  HCR6  0   0.254  -6.4281  -0.4301  -0.1207
 XX7  H12   H  HCR6  0   0.257  -6.9533  -2.7987  -0.1746
 XX7  H13   H  HCR6  0   0.256  -5.1300  -4.4912  -0.1939
 XX7  H14   H  HCR6  0   0.254  -2.7828  -3.7576  -0.1574

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
 XX7  O4   C19   single    1.409  0.020  1.409
 XX7  O4   H4    single    0.850  0.020  0.980
 XX7  C19  C18   single    1.529  0.020  1.529
 XX7  C19  H191  single    0.970  0.020  1.090
 XX7  C19  H192  single    0.970  0.020  1.090
 XX7  C18  C20   single    1.521  0.020  1.521
 XX7  C18  N     single    1.451  0.020  1.451
 XX7  C18  H18   single    0.970  0.020  1.090
 XX7  C20  O3    single    1.411  0.020  1.411
 XX7  C20  H201  single    0.970  0.020  1.090
 XX7  C20  H202  single    0.970  0.020  1.090
 XX7  O3   H3    single    0.850  0.020  0.980
 XX7  N    C17   single    1.445  0.020  1.445
 XX7  N    H     single    0.860  0.020  1.020
 XX7  C17  C16   single    1.526  0.020  1.526
 XX7  C17  H171  single    0.970  0.020  1.090
 XX7  C17  H172  single    0.970  0.020  1.090
 XX7  O2   C16   single    1.406  0.020  1.406
 XX7  O2   H2    single    0.850  0.020  0.980
 XX7  C15  O1    single    1.414  0.020  1.414
 XX7  C15  C16   single    1.520  0.020  1.520
 XX7  C15  H151  single    0.970  0.020  1.090
 XX7  C15  H152  single    0.970  0.020  1.090
 XX7  O1   C10   single    1.340  0.020  1.340
 XX7  C10  C5    aromatic  1.444  0.020  1.444
 XX7  C10  C9    aromatic  1.357  0.020  1.357
 XX7  C5   C6    aromatic  1.407  0.020  1.407
 XX7  C5   C4    aromatic  1.412  0.020  1.412
 XX7  C6   C1    aromatic  1.374  0.020  1.374
 XX7  C6   H6    single    0.930  0.020  1.080
 XX7  C1   C2    aromatic  1.398  0.020  1.398
 XX7  C1   H1    single    0.930  0.020  1.080
 XX7  C2   C3    aromatic  1.375  0.020  1.375
 XX7  C2   HA    single    0.930  0.020  1.080
 XX7  C3   C4    aromatic  1.407  0.020  1.407
 XX7  C3   HB    single    0.930  0.020  1.080
 XX7  C4   C7    aromatic  1.450  0.020  1.450
 XX7  C7   C11   aromatic  1.407  0.020  1.407
 XX7  C7   C8    aromatic  1.411  0.020  1.411
 XX7  C11  C12   aromatic  1.376  0.020  1.376
 XX7  C11  H11   single    0.930  0.020  1.080
 XX7  C12  C13   aromatic  1.400  0.020  1.400
 XX7  C12  H12   single    0.930  0.020  1.080
 XX7  C13  C14   aromatic  1.374  0.020  1.374
 XX7  C13  H13   single    0.930  0.020  1.080
 XX7  C14  C8    aromatic  1.408  0.020  1.408
 XX7  C14  H14   single    0.930  0.020  1.080
 XX7  C8   C9    aromatic  1.429  0.020  1.429
 XX7  C9   H9    single    0.930  0.020  1.080
 XX7  C16  H16   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
 XX7  H4    O4   C19   107.99  3.000
 XX7  H192  C19  H191  106.20  3.000
 XX7  H192  C19  C18   108.56  3.000
 XX7  H191  C19  C18   108.63  3.000
 XX7  H192  C19  O4    111.91  3.000
 XX7  H191  C19  O4    110.93  3.000
 XX7  C18   C19  O4    110.46  3.000
 XX7  H18   C18  N     107.53  3.000
 XX7  H18   C18  C20   104.88  3.000
 XX7  N     C18  C20   109.50  3.000
 XX7  H18   C18  C19   105.18  3.000
 XX7  N     C18  C19   115.06  3.000
 XX7  C20   C18  C19   113.89  3.000
 XX7  H202  C20  H201  106.96  3.000
 XX7  H202  C20  O3    111.43  3.000
 XX7  H201  C20  O3    111.14  3.000
 XX7  H202  C20  C18   108.57  3.000
 XX7  H201  C20  C18   107.74  3.000
 XX7  O3    C20  C18   110.83  3.000
 XX7  H3    O3   C20   107.79  3.000
 XX7  H     N    C17   109.50  3.000
 XX7  H     N    C18   109.26  3.000
 XX7  C17   N    C18   115.14  3.000
 XX7  H172  C17  H171  106.10  3.000
 XX7  H172  C17  C16   108.96  3.000
 XX7  H171  C17  C16   108.26  3.000
 XX7  H172  C17  N     108.46  3.000
 XX7  H171  C17  N     113.95  3.000
 XX7  C16   C17  N     110.92  3.000
 XX7  H2    O2   C16   108.49  3.000
 XX7  H152  C15  H151  107.61  3.000
 XX7  H152  C15  C16   110.31  3.000
 XX7  H151  C15  C16   110.23  3.000
 XX7  H152  C15  O1    110.46  3.000
 XX7  H151  C15  O1    110.50  3.000
 XX7  C16   C15  O1    107.75  3.000
 XX7  C10   O1   C15   119.37  3.000
 XX7  C9    C10  C5    120.68  3.000
 XX7  C9    C10  O1    125.09  3.000
 XX7  C5    C10  O1    114.24  3.000
 XX7  C4    C5   C6    119.82  3.000
 XX7  C4    C5   C10   119.49  3.000
 XX7  C6    C5   C10   120.70  3.000
 XX7  H6    C6   C1    119.43  3.000
 XX7  H6    C6   C5    119.81  3.000
 XX7  C1    C6   C5    120.76  3.000
 XX7  H1    C1   C2    120.13  3.000
 XX7  H1    C1   C6    120.07  3.000
 XX7  C2    C1   C6    119.79  3.000
 XX7  HA    C2   C3    119.72  3.000
 XX7  HA    C2   C1    120.10  3.000
 XX7  C3    C2   C1    120.18  3.000
 XX7  HB    C3   C4    120.21  3.000
 XX7  HB    C3   C2    118.30  3.000
 XX7  C4    C3   C2    121.50  3.000
 XX7  C7    C4   C3    122.25  3.000
 XX7  C7    C4   C5    119.79  3.000
 XX7  C3    C4   C5    117.97  3.000
 XX7  C8    C7   C11   118.42  3.000
 XX7  C8    C7   C4    118.59  3.000
 XX7  C11   C7   C4    122.99  3.000
 XX7  H11   C11  C12   118.33  3.000
 XX7  H11   C11  C7    120.33  3.000
 XX7  C12   C11  C7    121.33  3.000
 XX7  H12   C12  C13   120.14  3.000
 XX7  H12   C12  C11   119.79  3.000
 XX7  C13   C12  C11   120.07  3.000
 XX7  H13   C13  C14   120.07  3.000
 XX7  H13   C13  C12   120.18  3.000
 XX7  C14   C13  C12   119.76  3.000
 XX7  H14   C14  C8    118.87  3.000
 XX7  H14   C14  C13   120.11  3.000
 XX7  C8    C14  C13   121.02  3.000
 XX7  C9    C8   C14   119.99  3.000
 XX7  C9    C8   C7    120.60  3.000
 XX7  C14   C8   C7    119.41  3.000
 XX7  H9    C9   C8    117.56  3.000
 XX7  H9    C9   C10   121.58  3.000
 XX7  C8    C9   C10   120.86  3.000
 XX7  H16   C16  C15   108.17  3.000
 XX7  H16   C16  O2    105.94  3.000
 XX7  C15   C16  O2    111.52  3.000
 XX7  H16   C16  C17   108.44  3.000
 XX7  C15   C16  C17   109.58  3.000
 XX7  O2    C16  C17   112.98  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
 XX7  CONST_01  C1   C6   C5   C10   180.00   0.0  0
 XX7  CONST_02  C3   C4   C5   C10   180.00   0.0  0
 XX7  CONST_03  C7   C4   C5   C10     0.00   0.0  0
 XX7  CONST_04  C7   C8   C9   C10     0.00   0.0  0
 XX7  CONST_05  C14  C8   C9   C10   180.00   0.0  0
 XX7  CONST_06  C8   C9   C10  C5      0.00   0.0  0
 XX7  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 XX7  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 XX7  CONST_09  C11  C7   C4   C5    180.00   0.0  0
 XX7  CONST_10  C8   C7   C4   C5      0.00   0.0  0
 XX7  CONST_11  C9   C10  C5   C6    180.00   0.0  0
 XX7  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 XX7  CONST_13  C7   C4   C5   C6    180.00   0.0  0
 XX7  CONST_14  C3   C2   C1   C6      0.00   0.0  0
 XX7  CONST_15  C4   C5   C6   C1      0.00   0.0  0
 XX7  CONST_16  C4   C3   C2   C1      0.00   0.0  0
 XX7  CONST_17  C7   C4   C3   C2    180.00   0.0  0
 XX7  CONST_18  C11  C7   C4   C3      0.00   0.0  0
 XX7  CONST_19  C8   C7   C4   C3    180.00   0.0  0
 XX7  CONST_20  C9   C10  C5   C4      0.00   0.0  0
 XX7  CONST_21  C12  C11  C7   C4    180.00   0.0  0
 XX7  CONST_22  C14  C8   C7   C4    180.00   0.0  0
 XX7  CONST_23  C9   C8   C7   C4      0.00   0.0  0
 XX7  CONST_24  C13  C12  C11  C7      0.00   0.0  0
 XX7  CONST_25  C13  C14  C8   C7      0.00   0.0  0
 XX7  CONST_26  C14  C8   C7   C11     0.00   0.0  0
 XX7  CONST_27  C9   C8   C7   C11   180.00   0.0  0
 XX7  CONST_28  C14  C13  C12  C11     0.00   0.0  0
 XX7  CONST_29  C8   C7   C11  C12     0.00   0.0  0
 XX7  CONST_30  C8   C14  C13  C12     0.00   0.0  0
 XX7  CONST_31  C9   C8   C14  C13   180.00   0.0  0
 XX7  CONST_32  C6   C5   C10  O1      0.00   0.0  0
 XX7  CONST_33  C4   C5   C10  O1    180.00   0.0  0
 XX7  CONST_34  C8   C9   C10  O1    180.00   0.0  0
 XX7  CONST_35  H6   C6   C5   C10     0.00   0.0  0
 XX7  CONST_36  H9   C9   C10  C5    180.00   0.0  0
 XX7  CONST_37  H1   C1   C6   C5    180.00   0.0  0
 XX7  CONST_38  HB   C3   C4   C5    180.00   0.0  0
 XX7  CONST_39  HA   C2   C1   C6    180.00   0.0  0
 XX7  CONST_40  H11  C11  C7   C4      0.00   0.0  0
 XX7  CONST_41  H12  C12  C11  C7    180.00   0.0  0
 XX7  CONST_42  H14  C14  C8   C7    180.00   0.0  0
 XX7  CONST_43  H13  C13  C12  C11   180.00   0.0  0
 XX7  Var_01    C5   C10  O1   C15   177.13  30.0  2
 XX7  Var_02    C16  C15  O1   C10  -174.26  30.0  1
 XX7  Var_03    C20  C18  C19  O4    -73.61  30.0  3
 XX7  Var_04    O3   C20  C18  C19    68.83  30.0  3
 XX7  Var_05    C17  N    C18  C19    59.44  30.0  3
 XX7  Var_06    C16  C17  N    C18   170.69  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
 XX7  chir_01  C16  C17  O2  C15  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
 XX7  plan-1  O1   0.020
 XX7  plan-1  C10  0.020
 XX7  plan-1  C5   0.020
 XX7  plan-1  C6   0.020
 XX7  plan-1  C1   0.020
 XX7  plan-1  C2   0.020
 XX7  plan-1  C3   0.020
 XX7  plan-1  C4   0.020
 XX7  plan-1  C7   0.020
 XX7  plan-1  C11  0.020
 XX7  plan-1  C12  0.020
 XX7  plan-1  C13  0.020
 XX7  plan-1  C14  0.020
 XX7  plan-1  C8   0.020
 XX7  plan-1  C9   0.020
 XX7  plan-1  H9   0.020
 XX7  plan-1  H6   0.020
 XX7  plan-1  H1   0.020
 XX7  plan-1  HA   0.020
 XX7  plan-1  HB   0.020
 XX7  plan-1  H11  0.020
 XX7  plan-1  H12  0.020
 XX7  plan-1  H13  0.020
 XX7  plan-1  H14  0.020

