# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 07:16:37 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-[[(2~{S})-3-naphthalen-1-yloxy-2-oxidanyl-propyl]amino]propane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(CO)NC[C@H](O)COc1cccc2ccccc12
#
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
 F9B  F9B  2-[[(2~{S})-3-naphthalen-1-yloxy-2-oxidanyl-propyl]amino]propane-1,3-diol  ligand  42  21  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F9B
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
 F9B  N1   N  NH1   0  -0.599   3.6228   0.3190  -0.4558
 F9B  C4   C  CR66  0   0.126  -4.7822  -0.3923   0.0829
 F9B  C5   C  CR66  0  -0.022  -3.5035   0.1994  -0.0838
 F9B  C6   C  CR16  0  -0.287  -3.4114   1.5969  -0.2797
 F9B  C7   C  CR16  0  -0.345  -4.8891  -1.7903   0.2831
 F9B  C8   C  CR16  0  -0.244  -3.7631  -2.5606   0.3119
 F9B  C10  C  CR6   0   0.369  -2.3483  -0.6395  -0.0442
 F9B  C13  C  CH2   0  -0.283   2.5024  -0.5645  -0.2231
 F9B  C15  C  CH2   0  -0.157   5.9324   0.6596  -1.1306
 F9B  O2   O  OH1   0  -0.657   1.1685   1.1977   0.7958
 F9B  C12  C  CH1   0  -0.028   1.1926   0.2150  -0.2156
 F9B  C14  C  CH1   0  -0.134   4.8911  -0.3516  -0.6784
 F9B  O3   O  OH1   0  -0.668   6.1455   1.6359  -0.1358
 F9B  C16  C  CH2   0  -0.166   5.3556  -1.2515   0.4676
 F9B  O4   O  OH1   0  -0.665   5.3874  -0.5330   1.6790
 F9B  C11  C  CH2   0  -0.186   0.0226  -0.7469  -0.1058
 F9B  O1   O  O2    0  -0.463  -1.1762  -0.0046  -0.2060
 F9B  C9   C  CR16  0  -0.409  -2.4818  -1.9930   0.1487
 F9B  C3   C  CR16  0  -0.317  -5.9267   0.4380   0.0459
 F9B  C2   C  CR16  0  -0.252  -5.8116   1.7876  -0.1484
 F9B  C1   C  CR16  0  -0.257  -4.5405   2.3718  -0.3113
 F9B  H1   H  HNH1  0   0.339   3.7159   0.9616   0.3200
 F9B  H4   H  HCR6  0   0.250  -5.8682  -2.2343   0.4123
 F9B  H5   H  HCR6  0   0.259  -3.8396  -3.6298   0.4608
 F9B  H6   H  HCH2  0   0.228   2.4685  -1.2990  -1.0335
 F9B  H7   H  HCH2  0   0.200   2.5736  -1.1425   0.7134
 F9B  H8   H  HCH2  0   0.190   6.8590   0.1224  -1.3739
 F9B  H9   H  HCH2  0   0.203   5.5748   1.1147  -2.0627
 F9B  H10  H  HOH1  0   0.444   1.2437   0.7599   1.6516
 F9B  H11  H  HCH1  0   0.234   1.1151   0.7612  -1.1608
 F9B  H12  H  HCH1  0   0.235   4.7606  -1.0250  -1.5350
 F9B  H13  H  HOH1  0   0.452   6.6572   2.3484  -0.5280
 F9B  H14  H  HCH2  0   0.203   4.6714  -2.1062   0.5370
 F9B  H15  H  HCH2  0   0.193   6.3403  -1.6669   0.2096
 F9B  H16  H  HOH1  0   0.451   5.4550  -1.1679   2.3968
 F9B  H17  H  HCH2  0   0.232   0.0826  -1.4919  -0.9071
 F9B  H18  H  HCH2  0   0.226   0.0610  -1.2853   0.8502
 F9B  H19  H  HCR6  0   0.282  -1.6210  -2.6462   0.1788
 F9B  H20  H  HCR6  0   0.254  -6.9026  -0.0144   0.1756
 F9B  H21  H  HCR6  0   0.258  -6.6958   2.4109  -0.1765
 F9B  H22  H  HCR6  0   0.258  -4.4564   3.4403  -0.4602
 F9B  H3   H  HCR6  0   0.254  -2.4429   2.0612  -0.4052

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
 F9B  O3   C15  single    1.410  0.020  1.410
 F9B  C15  C14  single    1.520  0.020  1.520
 F9B  C1   C2   aromatic  1.408  0.020  1.408
 F9B  C1   C6   aromatic  1.370  0.020  1.370
 F9B  C2   C3   aromatic  1.368  0.020  1.368
 F9B  C6   C5   aromatic  1.414  0.020  1.414
 F9B  C14  C16  single    1.529  0.020  1.529
 F9B  C14  N1   single    1.452  0.020  1.452
 F9B  C16  O4   single    1.409  0.020  1.409
 F9B  C3   C4   aromatic  1.414  0.020  1.414
 F9B  N1   C13  single    1.446  0.020  1.446
 F9B  C5   C4   aromatic  1.419  0.020  1.419
 F9B  C5   C10  aromatic  1.428  0.020  1.428
 F9B  C13  C12  single    1.524  0.020  1.524
 F9B  O2   C12  single    1.410  0.020  1.410
 F9B  C4   C7   aromatic  1.416  0.020  1.416
 F9B  O1   C10  single    1.343  0.020  1.343
 F9B  O1   C11  single    1.414  0.020  1.414
 F9B  C10  C9   aromatic  1.374  0.020  1.374
 F9B  C12  C11  single    1.519  0.020  1.519
 F9B  C7   C8   aromatic  1.365  0.020  1.365
 F9B  C9   C8   aromatic  1.411  0.020  1.411
 F9B  N1   H1   single    0.890  0.020  1.040
 F9B  C6   H3   single    0.930  0.020  1.080
 F9B  C7   H4   single    0.930  0.020  1.080
 F9B  C8   H5   single    0.930  0.020  1.080
 F9B  C13  H6   single    0.970  0.020  1.090
 F9B  C13  H7   single    0.970  0.020  1.090
 F9B  C15  H8   single    0.970  0.020  1.090
 F9B  C15  H9   single    0.970  0.020  1.090
 F9B  O2   H10  single    0.850  0.020  0.980
 F9B  C12  H11  single    0.970  0.020  1.090
 F9B  C14  H12  single    0.970  0.020  1.090
 F9B  O3   H13  single    0.850  0.020  0.980
 F9B  C16  H14  single    0.970  0.020  1.090
 F9B  C16  H15  single    0.970  0.020  1.090
 F9B  O4   H16  single    0.850  0.020  0.980
 F9B  C11  H17  single    0.970  0.020  1.090
 F9B  C11  H18  single    0.970  0.020  1.090
 F9B  C9   H19  single    0.930  0.020  1.080
 F9B  C3   H20  single    0.930  0.020  1.080
 F9B  C2   H21  single    0.930  0.020  1.080
 F9B  C1   H22  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
 F9B  H1   N1   C14  109.31  3.000
 F9B  H1   N1   C13  109.64  3.000
 F9B  C14  N1   C13  114.80  3.000
 F9B  C3   C4   C7   121.47  3.000
 F9B  C7   C4   C5   119.76  3.000
 F9B  C3   C4   C5   118.78  3.000
 F9B  C10  C5   C6   122.11  3.000
 F9B  C10  C5   C4   118.74  3.000
 F9B  C6   C5   C4   119.15  3.000
 F9B  H3   C6   C1   119.52  3.000
 F9B  H3   C6   C5   119.91  3.000
 F9B  C1   C6   C5   120.57  3.000
 F9B  H4   C7   C8   120.81  3.000
 F9B  H4   C7   C4   119.33  3.000
 F9B  C8   C7   C4   119.86  3.000
 F9B  H5   C8   C9   118.53  3.000
 F9B  H5   C8   C7   120.15  3.000
 F9B  C9   C8   C7   121.33  3.000
 F9B  C9   C10  O1   124.58  3.000
 F9B  C9   C10  C5   120.27  3.000
 F9B  O1   C10  C5   115.15  3.000
 F9B  H7   C13  H6   106.21  3.000
 F9B  H7   C13  C12  108.62  3.000
 F9B  H6   C13  C12  108.68  3.000
 F9B  H7   C13  N1   114.01  3.000
 F9B  H6   C13  N1   108.36  3.000
 F9B  C12  C13  N1   110.74  3.000
 F9B  H9   C15  H8   106.84  3.000
 F9B  H9   C15  O3   111.19  3.000
 F9B  H8   C15  O3   111.56  3.000
 F9B  H9   C15  C14  107.77  3.000
 F9B  H8   C15  C14  108.56  3.000
 F9B  O3   C15  C14  110.75  3.000
 F9B  H10  O2   C12  108.59  3.000
 F9B  H11  C12  C11  108.90  3.000
 F9B  H11  C12  O2   105.69  3.000
 F9B  C11  C12  O2   112.11  3.000
 F9B  H11  C12  C13  108.17  3.000
 F9B  C11  C12  C13  109.78  3.000
 F9B  O2   C12  C13  112.00  3.000
 F9B  H12  C14  C16  105.07  3.000
 F9B  H12  C14  C15  104.92  3.000
 F9B  C16  C14  C15  113.96  3.000
 F9B  H12  C14  N1   107.41  3.000
 F9B  C16  C14  N1   114.97  3.000
 F9B  C15  C14  N1   109.68  3.000
 F9B  H13  O3   C15  107.81  3.000
 F9B  H15  C16  H14  106.21  3.000
 F9B  H15  C16  O4   111.98  3.000
 F9B  H14  C16  O4   110.92  3.000
 F9B  H15  C16  C14  108.57  3.000
 F9B  H14  C16  C14  108.44  3.000
 F9B  O4   C16  C14  110.56  3.000
 F9B  H16  O4   C16  107.88  3.000
 F9B  H18  C11  H17  107.55  3.000
 F9B  H18  C11  O1   110.42  3.000
 F9B  H17  C11  O1   110.58  3.000
 F9B  H18  C11  C12  110.28  3.000
 F9B  H17  C11  C12  109.61  3.000
 F9B  O1   C11  C12  108.40  3.000
 F9B  C11  O1   C10  118.91  3.000
 F9B  H19  C9   C10  121.46  3.000
 F9B  H19  C9   C8   118.48  3.000
 F9B  C10  C9   C8   120.06  3.000
 F9B  H20  C3   C2   120.30  3.000
 F9B  H20  C3   C4   118.73  3.000
 F9B  C2   C3   C4   120.97  3.000
 F9B  H21  C2   C1   119.70  3.000
 F9B  H21  C2   C3   120.20  3.000
 F9B  C1   C2   C3   120.10  3.000
 F9B  H22  C1   C2   119.71  3.000
 F9B  H22  C1   C6   119.85  3.000
 F9B  C2   C1   C6   120.44  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
 F9B  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 F9B  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 F9B  CONST_03  C9   C10  C5   C4      0.00   0.0  0
 F9B  CONST_04  C9   C8   C7   C4      0.00   0.0  0
 F9B  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 F9B  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 F9B  CONST_07  C8   C7   C4   C5      0.00   0.0  0
 F9B  CONST_08  C8   C9   C10  C5      0.00   0.0  0
 F9B  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 F9B  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 F9B  CONST_11  C7   C4   C5   C6    180.00   0.0  0
 F9B  CONST_12  C9   C10  C5   C6    180.00   0.0  0
 F9B  CONST_13  C2   C3   C4   C7    180.00   0.0  0
 F9B  CONST_14  C10  C5   C4   C7      0.00   0.0  0
 F9B  CONST_15  C10  C9   C8   C7      0.00   0.0  0
 F9B  CONST_16  C3   C4   C7   C8    180.00   0.0  0
 F9B  CONST_17  C1   C6   C5   C10   180.00   0.0  0
 F9B  CONST_18  C3   C4   C5   C10   180.00   0.0  0
 F9B  CONST_19  O1   C10  C5   C4    180.00   0.0  0
 F9B  CONST_20  O1   C10  C5   C6      0.00   0.0  0
 F9B  CONST_21  O1   C10  C9   C8    180.00   0.0  0
 F9B  CONST_22  H21  C2   C3   C4    180.00   0.0  0
 F9B  CONST_23  H3   C6   C5   C4    180.00   0.0  0
 F9B  CONST_24  H5   C8   C7   C4    180.00   0.0  0
 F9B  CONST_25  H22  C1   C6   C5    180.00   0.0  0
 F9B  CONST_26  H20  C3   C4   C5    180.00   0.0  0
 F9B  CONST_27  H4   C7   C4   C5    180.00   0.0  0
 F9B  CONST_28  H19  C9   C10  C5    180.00   0.0  0
 F9B  Var_01    C9   C10  O1   C11    -3.50  30.0  2
 F9B  Var_02    C12  C11  O1   C10  -175.53  30.0  3
 F9B  Var_03    O3   C15  C14  N1     61.86  30.0  2
 F9B  Var_04    O4   C16  C14  N1    -54.24  30.0  3
 F9B  Var_05    C15  C14  N1   C13   170.87  30.0  1
 F9B  Var_06    C14  N1   C13  C12  -171.27  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
 F9B  chir_01  C12  C13  O2  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
 F9B  plan-1  C4   0.020
 F9B  plan-1  C5   0.020
 F9B  plan-1  C6   0.020
 F9B  plan-1  C7   0.020
 F9B  plan-1  C8   0.020
 F9B  plan-1  C10  0.020
 F9B  plan-1  O1   0.020
 F9B  plan-1  C9   0.020
 F9B  plan-1  C3   0.020
 F9B  plan-1  C2   0.020
 F9B  plan-1  C1   0.020
 F9B  plan-1  H4   0.020
 F9B  plan-1  H5   0.020
 F9B  plan-1  H19  0.020
 F9B  plan-1  H20  0.020
 F9B  plan-1  H21  0.020
 F9B  plan-1  H22  0.020
 F9B  plan-1  H3   0.020

