# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:36:03 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2cc(ccc2c1)[C@@H](C)C(O)=O
#
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
 NPX  NPX  '(2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid'  ligand  30  17  .  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_NPX
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
 NPX  C1    C  CR6    0   0.386  -3.4420  -0.1700  -0.0606
 NPX  O2    O  O2     0  -0.476  -4.7036  -0.6462  -0.1052
 NPX  C2    C  CR16   0  -0.380  -3.1224   1.2012  -0.1858
 NPX  C3    C  CR16   0  -0.303  -1.8146   1.6088  -0.1292
 NPX  C4    C  CR66   0   0.124  -0.7614   0.6899   0.0534
 NPX  C5    C  CR66   0   0.115  -1.0877  -0.6841   0.1783
 NPX  C6    C  CR16   0  -0.428  -2.4340  -1.0910   0.1172
 NPX  C7    C  CR16   0  -0.417   0.5959   1.0936   0.1226
 NPX  C8    C  CR6    0   0.211   1.6101   0.1930   0.3028
 NPX  C9    C  CH1    0  -0.493   3.0434   0.6237   0.4372
 NPX  C10   C  CH3    0  -0.644   3.5402   0.4211   1.8682
 NPX  C13   C  CR16   0  -0.315  -0.0262  -1.6066   0.3668
 NPX  C11   C  CR16   0  -0.289   1.2687  -1.1807   0.4236
 NPX  C12   C  CH3    0  -0.436  -5.7761   0.2614  -0.2545
 NPX  C15   C  C      0   0.429   3.9663  -0.0421  -0.6174
 NPX  H2    H  HCR6   0   0.279  -3.8959   1.9439  -0.3239
 NPX  H6    H  HCR6   0   0.254  -2.6783  -2.1429   0.2151
 NPX  H121  H  HCH3   0   0.259  -6.6854  -0.3351  -0.2546
 NPX  H122  H  HCH3   0   0.227  -5.8301   0.9764   0.5707
 NPX  H123  H  HCH3   0   0.227  -5.7233   0.8125  -1.1970
 NPX  H3    H  HCR6   0   0.255  -1.5854   2.6635  -0.2255
 NPX  H7    H  HCR6   0   0.237   0.8210   2.1514   0.0304
 NPX  H13   H  HCR6   0   0.244  -0.2562  -2.6615   0.4617
 NPX  H9    H  HCH1   0   0.246   3.0836   1.7016   0.2294
 NPX  H11   H  HCR6   0   0.241   2.0566  -1.9105   0.5670
 NPX  H101  H  HCH3   0   0.226   4.5592   0.7869   1.9805
 NPX  H102  H  HCH3   0   0.215   2.9104   0.9563   2.5805
 NPX  H103  H  HCH3   0   0.214   3.5351  -0.6338   2.1510
 NPX  OXT   O  OC     0  -0.607   5.1837  -0.0745  -0.3528
 NPX  O     O  O     -1  -0.601   3.4234  -0.4560  -1.6596

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
 NPX  C1   O2    single    1.349  0.020  1.349
 NPX  C1   C2    aromatic  1.413  0.020  1.413
 NPX  C1   C6    aromatic  1.377  0.020  1.377
 NPX  O2   C12   single    1.413  0.020  1.413
 NPX  C2   C3    aromatic  1.371  0.020  1.371
 NPX  C3   C4    aromatic  1.410  0.020  1.410
 NPX  C4   C5    aromatic  1.418  0.020  1.418
 NPX  C4   C7    aromatic  1.418  0.020  1.418
 NPX  C5   C6    aromatic  1.408  0.020  1.408
 NPX  C5   C13   aromatic  1.419  0.020  1.419
 NPX  C7   C8    aromatic  1.368  0.020  1.368
 NPX  C8   C9    single    1.503  0.020  1.503
 NPX  C8   C11   aromatic  1.421  0.020  1.421
 NPX  C9   C10   single    1.528  0.020  1.528
 NPX  C9   C15   single    1.552  0.020  1.552
 NPX  C13  C11   aromatic  1.364  0.020  1.364
 NPX  OXT  C15   deloc     1.246  0.020  1.246
 NPX  O    C15   deloc     1.246  0.020  1.246
 NPX  C2   H2    single    0.930  0.020  1.080
 NPX  C6   H6    single    0.930  0.020  1.080
 NPX  C12  H121  single    0.970  0.020  1.090
 NPX  C12  H122  single    0.970  0.020  1.090
 NPX  C12  H123  single    0.970  0.020  1.090
 NPX  C3   H3    single    0.930  0.020  1.080
 NPX  C7   H7    single    0.930  0.020  1.080
 NPX  C13  H13   single    0.930  0.020  1.080
 NPX  C9   H9    single    0.970  0.020  1.090
 NPX  C11  H11   single    0.930  0.020  1.080
 NPX  C10  H101  single    0.970  0.020  1.090
 NPX  C10  H102  single    0.970  0.020  1.090
 NPX  C10  H103  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
 NPX  C6    C1   C2    119.66  3.000
 NPX  C6    C1   O2    116.92  3.000
 NPX  C2    C1   O2    123.43  3.000
 NPX  C12   O2   C1    119.11  3.000
 NPX  H2    C2   C3    118.91  3.000
 NPX  H2    C2   C1    121.06  3.000
 NPX  C3    C2   C1    120.03  3.000
 NPX  H3    C3   C4    119.21  3.000
 NPX  H3    C3   C2    119.17  3.000
 NPX  C4    C3   C2    121.62  3.000
 NPX  C7    C4   C5    119.48  3.000
 NPX  C7    C4   C3    122.41  3.000
 NPX  C5    C4   C3    118.11  3.000
 NPX  C13   C5   C6    122.23  3.000
 NPX  C13   C5   C4    118.01  3.000
 NPX  C6    C5   C4    119.77  3.000
 NPX  H6    C6   C5    119.47  3.000
 NPX  H6    C6   C1    119.71  3.000
 NPX  C5    C6   C1    120.82  3.000
 NPX  H7    C7   C8    119.93  3.000
 NPX  H7    C7   C4    118.16  3.000
 NPX  C8    C7   C4    121.91  3.000
 NPX  C11   C8   C9    119.92  3.000
 NPX  C11   C8   C7    118.00  3.000
 NPX  C9    C8   C7    122.02  3.000
 NPX  H9    C9   C15   105.71  3.000
 NPX  H9    C9   C10   107.18  3.000
 NPX  C15   C9   C10   112.72  3.000
 NPX  H9    C9   C8    107.41  3.000
 NPX  C15   C9   C8    112.55  3.000
 NPX  C10   C9   C8    110.85  3.000
 NPX  H103  C10  H102  107.58  3.000
 NPX  H103  C10  H101  107.60  3.000
 NPX  H102  C10  H101  107.95  3.000
 NPX  H103  C10  C9    111.65  3.000
 NPX  H102  C10  C9    111.01  3.000
 NPX  H101  C10  C9    110.88  3.000
 NPX  H13   C13  C11   120.11  3.000
 NPX  H13   C13  C5    119.05  3.000
 NPX  C11   C13  C5    120.84  3.000
 NPX  H11   C11  C13   119.04  3.000
 NPX  H11   C11  C8    119.19  3.000
 NPX  C13   C11  C8    121.77  3.000
 NPX  H123  C12  H122  108.87  3.000
 NPX  H123  C12  H121  108.48  3.000
 NPX  H122  C12  H121  108.52  3.000
 NPX  H123  C12  O2    112.23  3.000
 NPX  H122  C12  O2    112.20  3.000
 NPX  H121  C12  O2    106.40  3.000
 NPX  O     C15  OXT   126.49  3.000
 NPX  O     C15  C9    116.87  3.000
 NPX  OXT   C15  C9    116.61  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
 NPX  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 NPX  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 NPX  CONST_03  C13   C5   C6   C1   180.00   0.0  0
 NPX  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 NPX  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 NPX  CONST_06  C7    C4   C3   C2   180.00   0.0  0
 NPX  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 NPX  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 NPX  CONST_09  C13   C5   C4   C3   180.00   0.0  0
 NPX  CONST_10  C8    C7   C4   C3   180.00   0.0  0
 NPX  CONST_11  C11   C13  C5   C4     0.00   0.0  0
 NPX  CONST_12  C11   C8   C7   C4     0.00   0.0  0
 NPX  CONST_13  C8    C7   C4   C5     0.00   0.0  0
 NPX  CONST_14  C8    C11  C13  C5     0.00   0.0  0
 NPX  CONST_15  C7    C4   C5   C6   180.00   0.0  0
 NPX  CONST_16  C11   C13  C5   C6   180.00   0.0  0
 NPX  CONST_17  C13   C5   C4   C7     0.00   0.0  0
 NPX  CONST_18  C13   C11  C8   C7     0.00   0.0  0
 NPX  CONST_19  C3    C2   C1   O2   180.00   0.0  0
 NPX  CONST_20  C5    C6   C1   O2   180.00   0.0  0
 NPX  CONST_21  C9    C8   C7   C4   180.00   0.0  0
 NPX  CONST_22  C13   C11  C8   C9   180.00   0.0  0
 NPX  CONST_23  H3    C3   C2   C1   180.00   0.0  0
 NPX  CONST_24  H6    C6   C1   C2   180.00   0.0  0
 NPX  CONST_25  H7    C7   C4   C3     0.00   0.0  0
 NPX  CONST_26  H2    C2   C3   C4   180.00   0.0  0
 NPX  CONST_27  H13   C13  C5   C4   180.00   0.0  0
 NPX  CONST_28  H11   C11  C13  C5   180.00   0.0  0
 NPX  Var_01    H121  C12  O2   C1  -179.42  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
 NPX  chir_01  C9  C8  C10  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
 NPX  plan-1  C1   0.020
 NPX  plan-1  O2   0.020
 NPX  plan-1  C2   0.020
 NPX  plan-1  C3   0.020
 NPX  plan-1  C4   0.020
 NPX  plan-1  C5   0.020
 NPX  plan-1  C6   0.020
 NPX  plan-1  C7   0.020
 NPX  plan-1  C8   0.020
 NPX  plan-1  C9   0.020
 NPX  plan-1  C13  0.020
 NPX  plan-1  C11  0.020
 NPX  plan-1  H2   0.020
 NPX  plan-1  H6   0.020
 NPX  plan-1  H3   0.020
 NPX  plan-1  H7   0.020
 NPX  plan-1  H13  0.020
 NPX  plan-1  H11  0.020
 NPX  plan-2  C9   0.020
 NPX  plan-2  C15  0.020
 NPX  plan-2  OXT  0.020
 NPX  plan-2  O    0.020

