# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 09:32:18 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: methyl (2~{S})-2-(6-methoxynaphthalen-2-yl)propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](C)c1ccc2cc(OC)ccc2c1
#
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
 RXH  RXH  'methyl (2~{S})-2-(6-methoxynaphthalen-2-yl)propanoate'  ligand  34  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RXH
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
 RXH  OXT   O  O2    0  -0.447  25.9315  10.8651  -25.9665
 RXH  O     O  O     0  -0.438  24.6406  12.1549  -24.6819
 RXH  C01   C  CH3   0  -0.423  25.0463   9.7598  -25.7891
 RXH  C1    C  CR6   0   0.387  31.2710  12.0283  -21.0102
 RXH  C2    C  CR16  0  -0.334  30.1599  12.6959  -20.4320
 RXH  O2    O  O2    0  -0.466  32.2845  11.7747  -20.1641
 RXH  C3    C  CR16  0  -0.294  29.0721  13.0115  -21.1897
 RXH  C4    C  CR66  0   0.114  29.0215  12.6870  -22.5682
 RXH  C5    C  CR66  0   0.135  30.1308  12.0191  -23.1411
 RXH  C6    C  CR16  0  -0.464  31.2531  11.6938  -22.3413
 RXH  C7    C  CR16  0  -0.369  27.9102  13.0155  -23.3745
 RXH  C8    C  CR6   0   0.126  27.8850  12.7105  -24.7129
 RXH  C10   C  CH3   0  -0.652  26.1490  14.4590  -25.3588
 RXH  C11   C  CR16  0  -0.300  28.9928  12.0378  -25.2756
 RXH  C12   C  CH3   0  -0.436  33.4288  11.1156  -20.6666
 RXH  C13   C  CR16  0  -0.308  30.0811  11.7019  -24.5172
 RXH  C14   C  CH1   0  -0.445  26.6934  13.0557  -25.5864
 RXH  C15   C  C     0   0.611  25.6275  12.0016  -25.3551
 RXH  H1    H  HCH3  0   0.250  25.4751   8.9391  -26.3564
 RXH  H4    H  HCH3  0   0.237  24.9725   9.4734  -24.7399
 RXH  H5    H  HCH3  0   0.238  24.0499   9.9805  -26.1712
 RXH  H2    H  HCR6  0   0.265  30.1914  12.9507  -19.3802
 RXH  H3    H  HCR6  0   0.257  28.2306  13.5228  -20.7376
 RXH  H6    H  HCR6  0   0.275  32.0845  11.1846  -22.8117
 RXH  H7    H  HCR6  0   0.252  27.0755  13.5253  -22.9066
 RXH  H101  H  HCH3  0   0.242  26.9329  15.1930  -25.5409
 RXH  H102  H  HCH3  0   0.243  25.3283  14.6699  -26.0441
 RXH  H103  H  HCH3  0   0.235  25.7802  14.6053  -24.3450
 RXH  H11   H  HCR6  0   0.252  28.9808  11.7910  -26.3302
 RXH  H121  H  HCH3  0   0.260  34.1192  11.0133  -19.8330
 RXH  H122  H  HCH3  0   0.228  33.1901  10.1204  -21.0507
 RXH  H123  H  HCH3  0   0.228  33.9148  11.6910  -21.4591
 RXH  H13   H  HCR6  0   0.251  30.9220  11.1916  -24.9717
 RXH  H14   H  HCH1  0   0.288  27.0144  12.9736  -26.6285

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
 RXH  OXT  C01   single    1.427  0.020  1.427
 RXH  OXT  C15   single    1.326  0.020  1.326
 RXH  C15  C14   single    1.517  0.020  1.517
 RXH  C15  O     double    1.204  0.020  1.204
 RXH  C14  C10   single    1.522  0.020  1.522
 RXH  C14  C8    single    1.517  0.020  1.517
 RXH  C11  C8    aromatic  1.413  0.020  1.413
 RXH  C11  C13   aromatic  1.368  0.020  1.368
 RXH  C8   C7    aromatic  1.373  0.020  1.373
 RXH  C13  C5    aromatic  1.413  0.020  1.413
 RXH  C7   C4    aromatic  1.412  0.020  1.412
 RXH  C5   C4    aromatic  1.416  0.020  1.416
 RXH  C5   C6    aromatic  1.416  0.020  1.416
 RXH  C4   C3    aromatic  1.417  0.020  1.417
 RXH  C6   C1    aromatic  1.373  0.020  1.373
 RXH  C3   C2    aromatic  1.363  0.020  1.363
 RXH  C1   C2    aromatic  1.419  0.020  1.419
 RXH  C1   O2    single    1.344  0.020  1.344
 RXH  C12  O2    single    1.413  0.020  1.413
 RXH  C01  H1    single    0.970  0.020  1.090
 RXH  C01  H4    single    0.970  0.020  1.090
 RXH  C01  H5    single    0.970  0.020  1.090
 RXH  C2   H2    single    0.930  0.020  1.080
 RXH  C3   H3    single    0.930  0.020  1.080
 RXH  C6   H6    single    0.930  0.020  1.080
 RXH  C7   H7    single    0.930  0.020  1.080
 RXH  C10  H101  single    0.970  0.020  1.090
 RXH  C10  H102  single    0.970  0.020  1.090
 RXH  C10  H103  single    0.970  0.020  1.090
 RXH  C11  H11   single    0.930  0.020  1.080
 RXH  C12  H121  single    0.970  0.020  1.090
 RXH  C12  H122  single    0.970  0.020  1.090
 RXH  C12  H123  single    0.970  0.020  1.090
 RXH  C13  H13   single    0.930  0.020  1.080
 RXH  C14  H14   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
 RXH  C15   OXT  C01   117.67  3.000
 RXH  H5    C01  H4    109.19  3.000
 RXH  H5    C01  H1    109.32  3.000
 RXH  H4    C01  H1    109.33  3.000
 RXH  H5    C01  OXT   111.51  3.000
 RXH  H4    C01  OXT   111.42  3.000
 RXH  H1    C01  OXT   105.99  3.000
 RXH  C6    C1   O2    125.04  3.000
 RXH  O2    C1   C2    115.00  3.000
 RXH  C6    C1   C2    119.96  3.000
 RXH  H2    C2   C3    120.59  3.000
 RXH  H2    C2   C1    118.92  3.000
 RXH  C3    C2   C1    120.49  3.000
 RXH  C12   O2   C1    118.34  3.000
 RXH  H3    C3   C4    119.09  3.000
 RXH  H3    C3   C2    119.82  3.000
 RXH  C4    C3   C2    121.09  3.000
 RXH  C7    C4   C5    119.70  3.000
 RXH  C5    C4   C3    118.27  3.000
 RXH  C7    C4   C3    122.03  3.000
 RXH  C13   C5   C6    121.76  3.000
 RXH  C6    C5   C4    120.05  3.000
 RXH  C13   C5   C4    118.18  3.000
 RXH  H6    C6   C5    118.12  3.000
 RXH  H6    C6   C1    121.74  3.000
 RXH  C5    C6   C1    120.14  3.000
 RXH  H7    C7   C8    120.73  3.000
 RXH  H7    C7   C4    117.97  3.000
 RXH  C8    C7   C4    121.30  3.000
 RXH  C14   C8   C11   119.65  3.000
 RXH  C11   C8   C7    118.66  3.000
 RXH  C14   C8   C7    121.68  3.000
 RXH  H103  C10  H102  107.73  3.000
 RXH  H103  C10  H101  107.99  3.000
 RXH  H102  C10  H101  107.84  3.000
 RXH  H103  C10  C14   112.60  3.000
 RXH  H102  C10  C14   110.72  3.000
 RXH  H101  C10  C14   109.80  3.000
 RXH  H11   C11  C13   119.51  3.000
 RXH  H11   C11  C8    119.18  3.000
 RXH  C13   C11  C8    121.32  3.000
 RXH  H123  C12  H122  108.76  3.000
 RXH  H123  C12  H121  108.85  3.000
 RXH  H122  C12  H121  108.80  3.000
 RXH  H123  C12  O2    111.86  3.000
 RXH  H122  C12  O2    111.89  3.000
 RXH  H121  C12  O2    106.59  3.000
 RXH  H13   C13  C11   120.03  3.000
 RXH  H13   C13  C5    119.13  3.000
 RXH  C11   C13  C5    120.84  3.000
 RXH  H14   C14  C15   107.43  3.000
 RXH  H14   C14  C10   108.46  3.000
 RXH  C15   C14  C10   111.50  3.000
 RXH  H14   C14  C8    107.52  3.000
 RXH  C10   C14  C8    113.86  3.000
 RXH  C15   C14  C8    107.82  3.000
 RXH  C14   C15  O     124.93  3.000
 RXH  O     C15  OXT   123.69  3.000
 RXH  C14   C15  OXT   111.36  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
 RXH  CONST_01  C13   C5   C6   C1    180.00   0.0  0
 RXH  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 RXH  CONST_03  C4    C3   C2   C1      0.00   0.0  0
 RXH  CONST_04  C7    C4   C3   C2    180.00   0.0  0
 RXH  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 RXH  CONST_06  C5    C6   C1   C2      0.00   0.0  0
 RXH  CONST_07  C8    C7   C4   C3    180.00   0.0  0
 RXH  CONST_08  C13   C5   C4   C3    180.00   0.0  0
 RXH  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 RXH  CONST_10  C6    C1   C2   C3      0.00   0.0  0
 RXH  CONST_11  C11   C8   C7   C4      0.00   0.0  0
 RXH  CONST_12  C11   C13  C5   C4      0.00   0.0  0
 RXH  CONST_13  C8    C11  C13  C5      0.00   0.0  0
 RXH  CONST_14  C8    C7   C4   C5      0.00   0.0  0
 RXH  CONST_15  C11   C13  C5   C6    180.00   0.0  0
 RXH  CONST_16  C7    C4   C5   C6    180.00   0.0  0
 RXH  CONST_17  C13   C11  C8   C7      0.00   0.0  0
 RXH  CONST_18  C13   C5   C4   C7      0.00   0.0  0
 RXH  CONST_19  C5    C6   C1   O2    180.00   0.0  0
 RXH  CONST_20  C3    C2   C1   O2    180.00   0.0  0
 RXH  CONST_21  C14   C8   C7   C4    180.00   0.0  0
 RXH  CONST_22  C14   C8   C11  C13   180.00   0.0  0
 RXH  CONST_23  H3    C3   C2   C1    180.00   0.0  0
 RXH  CONST_24  H6    C6   C1   C2    180.00   0.0  0
 RXH  CONST_25  H7    C7   C4   C3      0.00   0.0  0
 RXH  CONST_26  H13   C13  C5   C4    180.00   0.0  0
 RXH  CONST_27  H2    C2   C3   C4    180.00   0.0  0
 RXH  CONST_28  H11   C11  C13  C5    180.00   0.0  0
 RXH  Var_01    H121  C12  O2   C1    179.78  30.0  3
 RXH  Var_02    C14   C15  OXT  C01   177.31  30.0  3
 RXH  Var_03    H1    C01  OXT  C15  -179.52  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
 RXH  chir_01  C14  C15  C10  C8  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
 RXH  plan-1  C1   0.020
 RXH  plan-1  C2   0.020
 RXH  plan-1  O2   0.020
 RXH  plan-1  C3   0.020
 RXH  plan-1  C4   0.020
 RXH  plan-1  C5   0.020
 RXH  plan-1  C6   0.020
 RXH  plan-1  C7   0.020
 RXH  plan-1  C8   0.020
 RXH  plan-1  C11  0.020
 RXH  plan-1  C13  0.020
 RXH  plan-1  C14  0.020
 RXH  plan-1  H2   0.020
 RXH  plan-1  H3   0.020
 RXH  plan-1  H6   0.020
 RXH  plan-1  H7   0.020
 RXH  plan-1  H11  0.020
 RXH  plan-1  H13  0.020
 RXH  plan-2  OXT  0.020
 RXH  plan-2  O    0.020
 RXH  plan-2  C14  0.020
 RXH  plan-2  C15  0.020

