# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 07:30:52 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2R)-3-(naphthalen-1-yloxy)propane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[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
 RN1  RN1  (2R)-3-(naphthalen-1-yloxy)propane-1,2-diol  ligand  30  16  .  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_RN1
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
 RN1  C01  C  CR16  0  -0.257   2.7395   2.2839  -0.1722
 RN1  C02  C  CR16  0  -0.251   3.9858   1.6394  -0.0511
 RN1  C03  C  CR16  0  -0.317   4.0451   0.2775   0.0688
 RN1  C04  C  CR66  0   0.126   2.8669  -0.5050   0.0691
 RN1  C05  C  CR66  0  -0.021   1.6133   0.1477  -0.0541
 RN1  C06  C  CR16  0  -0.287   1.5788   1.5564  -0.1731
 RN1  C07  C  CR16  0  -0.345   2.9162  -1.9152   0.1907
 RN1  C08  C  CR16  0  -0.244   1.7592  -2.6387   0.1837
 RN1  C09  C  CR16  0  -0.409   0.5019  -2.0105   0.0608
 RN1  C10  C  CR6   0   0.369   0.4244  -0.6439  -0.0532
 RN1  O11  O  O2    0  -0.461  -0.7204   0.0480  -0.1697
 RN1  C12  C  CH2   0  -0.193  -1.9484  -0.6495  -0.1350
 RN1  C13  C  CH1   0  -0.042  -3.0719   0.3737  -0.1612
 RN1  C14  C  CH2   0  -0.163  -4.4072  -0.3489  -0.2544
 RN1  O15  O  OH1   0  -0.654  -3.0075   1.2556   0.9318
 RN1  O16  O  OH1   0  -0.667  -5.4320   0.6068  -0.3673
 RN1  H1   H  HCR6  0   0.257   2.6995   3.3613  -0.2639
 RN1  H2   H  HCR6  0   0.258   4.8954   2.2259  -0.0521
 RN1  H3   H  HCR6  0   0.254   5.0015  -0.2220   0.1674
 RN1  H4   H  HCR6  0   0.255   0.6304   2.0676  -0.2654
 RN1  H5   H  HCR6  0   0.250   3.8763  -2.4066   0.2884
 RN1  H6   H  HCR6  0   0.259   1.7916  -3.7166   0.2725
 RN1  H7   H  HCR6  0   0.282  -0.3849  -2.6291   0.0580
 RN1  H8   H  HCH2  0   0.232  -2.0326  -1.3228  -0.9953
 RN1  H9   H  HCH2  0   0.227  -2.0179  -1.2623   0.7729
 RN1  H10  H  HCH1  0   0.240  -2.9535   0.9969  -1.0542
 RN1  H11  H  HCH2  0   0.203  -4.3822  -1.0234  -1.1202
 RN1  H12  H  HCH2  0   0.198  -4.5380  -0.9825   0.6356
 RN1  H13  H  HOH1  0   0.444  -3.1514   0.7544   1.7423
 RN1  H14  H  HOH1  0   0.457  -6.2726   0.1410  -0.3806

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
 RN1  C02  C01  aromatic  1.408  0.020  1.408
 RN1  C02  C03  aromatic  1.368  0.020  1.368
 RN1  C01  C06  aromatic  1.370  0.020  1.370
 RN1  C03  C04  aromatic  1.414  0.020  1.414
 RN1  C06  C05  aromatic  1.414  0.020  1.414
 RN1  C04  C05  aromatic  1.419  0.020  1.419
 RN1  C04  C07  aromatic  1.416  0.020  1.416
 RN1  C05  C10  aromatic  1.428  0.020  1.428
 RN1  C07  C08  aromatic  1.365  0.020  1.365
 RN1  C10  O11  single    1.343  0.020  1.343
 RN1  C10  C09  aromatic  1.374  0.020  1.374
 RN1  C08  C09  aromatic  1.411  0.020  1.411
 RN1  O11  C12  single    1.413  0.020  1.413
 RN1  C14  O16  single    1.406  0.020  1.406
 RN1  C14  C13  single    1.521  0.020  1.521
 RN1  C12  C13  single    1.520  0.020  1.520
 RN1  O15  C13  single    1.406  0.020  1.406
 RN1  C01  H1   single    0.930  0.020  1.080
 RN1  C02  H2   single    0.930  0.020  1.080
 RN1  C03  H3   single    0.930  0.020  1.080
 RN1  C06  H4   single    0.930  0.020  1.080
 RN1  C07  H5   single    0.930  0.020  1.080
 RN1  C08  H6   single    0.930  0.020  1.080
 RN1  C09  H7   single    0.930  0.020  1.080
 RN1  C12  H8   single    0.970  0.020  1.090
 RN1  C12  H9   single    0.970  0.020  1.090
 RN1  C13  H10  single    0.970  0.020  1.090
 RN1  C14  H11  single    0.970  0.020  1.090
 RN1  C14  H12  single    0.970  0.020  1.090
 RN1  O15  H13  single    0.850  0.020  0.980
 RN1  O16  H14  single    0.850  0.020  0.980

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
 RN1  H1   C01  C06  119.83  3.000
 RN1  H1   C01  C02  119.72  3.000
 RN1  C06  C01  C02  120.45  3.000
 RN1  H2   C02  C03  120.20  3.000
 RN1  H2   C02  C01  119.71  3.000
 RN1  C03  C02  C01  120.09  3.000
 RN1  H3   C03  C04  118.71  3.000
 RN1  H3   C03  C02  120.33  3.000
 RN1  C04  C03  C02  120.96  3.000
 RN1  C07  C04  C05  119.76  3.000
 RN1  C07  C04  C03  121.45  3.000
 RN1  C05  C04  C03  118.79  3.000
 RN1  C10  C05  C06  122.13  3.000
 RN1  C10  C05  C04  118.72  3.000
 RN1  C06  C05  C04  119.15  3.000
 RN1  H4   C06  C05  119.97  3.000
 RN1  H4   C06  C01  119.48  3.000
 RN1  C05  C06  C01  120.55  3.000
 RN1  H5   C07  C08  120.77  3.000
 RN1  H5   C07  C04  119.37  3.000
 RN1  C08  C07  C04  119.86  3.000
 RN1  H6   C08  C09  118.51  3.000
 RN1  H6   C08  C07  120.15  3.000
 RN1  C09  C08  C07  121.33  3.000
 RN1  H7   C09  C10  121.52  3.000
 RN1  H7   C09  C08  118.45  3.000
 RN1  C10  C09  C08  120.03  3.000
 RN1  O11  C10  C09  124.61  3.000
 RN1  C09  C10  C05  120.30  3.000
 RN1  O11  C10  C05  115.09  3.000
 RN1  C12  O11  C10  118.98  3.000
 RN1  H9   C12  H8   107.55  3.000
 RN1  H9   C12  C13  110.09  3.000
 RN1  H8   C12  C13  110.08  3.000
 RN1  H9   C12  O11  110.55  3.000
 RN1  H8   C12  O11  110.54  3.000
 RN1  C13  C12  O11  108.04  3.000
 RN1  H10  C13  O15  105.79  3.000
 RN1  H10  C13  C14  108.37  3.000
 RN1  O15  C13  C14  112.70  3.000
 RN1  H10  C13  C12  108.50  3.000
 RN1  O15  C13  C12  112.03  3.000
 RN1  C14  C13  C12  109.28  3.000
 RN1  H12  C14  H11  106.67  3.000
 RN1  H12  C14  O16  111.70  3.000
 RN1  H11  C14  O16  111.78  3.000
 RN1  H12  C14  C13  109.17  3.000
 RN1  H11  C14  C13  108.68  3.000
 RN1  O16  C14  C13  108.77  3.000
 RN1  H13  O15  C13  108.71  3.000
 RN1  H14  O16  C14  108.01  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
 RN1  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 RN1  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 RN1  CONST_03  C10  C05  C06  C01  180.00   0.0  0
 RN1  CONST_04  C05  C06  C01  C02    0.00   0.0  0
 RN1  CONST_05  C05  C04  C03  C02    0.00   0.0  0
 RN1  CONST_06  C07  C04  C03  C02  180.00   0.0  0
 RN1  CONST_07  C06  C01  C02  C03    0.00   0.0  0
 RN1  CONST_08  C06  C05  C04  C03    0.00   0.0  0
 RN1  CONST_09  C10  C05  C04  C03  180.00   0.0  0
 RN1  CONST_10  C08  C07  C04  C03  180.00   0.0  0
 RN1  CONST_11  C09  C10  C05  C04    0.00   0.0  0
 RN1  CONST_12  C09  C08  C07  C04    0.00   0.0  0
 RN1  CONST_13  C08  C07  C04  C05    0.00   0.0  0
 RN1  CONST_14  C08  C09  C10  C05    0.00   0.0  0
 RN1  CONST_15  C07  C04  C05  C06  180.00   0.0  0
 RN1  CONST_16  C09  C10  C05  C06  180.00   0.0  0
 RN1  CONST_17  C10  C05  C04  C07    0.00   0.0  0
 RN1  CONST_18  C10  C09  C08  C07    0.00   0.0  0
 RN1  CONST_19  O11  C10  C05  C04  180.00   0.0  0
 RN1  CONST_20  O11  C10  C05  C06    0.00   0.0  0
 RN1  CONST_21  O11  C10  C09  C08  180.00   0.0  0
 RN1  CONST_22  H3   C03  C02  C01  180.00   0.0  0
 RN1  CONST_23  H4   C06  C01  C02  180.00   0.0  0
 RN1  CONST_24  H1   C01  C02  C03  180.00   0.0  0
 RN1  CONST_25  H5   C07  C04  C03    0.00   0.0  0
 RN1  CONST_26  H2   C02  C03  C04  180.00   0.0  0
 RN1  CONST_27  H6   C08  C07  C04  180.00   0.0  0
 RN1  CONST_28  H7   C09  C10  C05  180.00   0.0  0
 RN1  Var_01    C13  C12  O11  C10  175.02  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
 RN1  chir_01  C13  C14  C12  O15  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
 RN1  plan-1  C01  0.020
 RN1  plan-1  C02  0.020
 RN1  plan-1  C03  0.020
 RN1  plan-1  C04  0.020
 RN1  plan-1  C05  0.020
 RN1  plan-1  C06  0.020
 RN1  plan-1  C07  0.020
 RN1  plan-1  C08  0.020
 RN1  plan-1  C09  0.020
 RN1  plan-1  C10  0.020
 RN1  plan-1  O11  0.020
 RN1  plan-1  H1   0.020
 RN1  plan-1  H2   0.020
 RN1  plan-1  H3   0.020
 RN1  plan-1  H4   0.020
 RN1  plan-1  H5   0.020
 RN1  plan-1  H6   0.020
 RN1  plan-1  H7   0.020

