# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 13:16:10 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2S)-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
 NPS  NPS  '(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid'  ligand  31  17  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPS
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
 NPS  C1    C  CR6   0   0.393  15.3854  -5.2023  27.9718
 NPS  O2    O  O2    0  -0.473  16.2640  -6.2209  27.9110
 NPS  C2    C  CR16  0  -0.377  15.3885  -4.1188  27.0620
 NPS  C14   C  CH1   0  -0.426  10.6111  -1.0056  29.5915
 NPS  C3    C  CR16  0  -0.298  14.4674  -3.1137  27.1903
 NPS  C4    C  CR66  0   0.131  13.5014  -3.1255  28.2179
 NPS  C5    C  CR66  0   0.124  13.4995  -4.2153  29.1250
 NPS  C6    C  CR16  0  -0.428  14.4500  -5.2436  28.9816
 NPS  C7    C  CR16  0  -0.390  12.5524  -2.0862  28.3678
 NPS  C8    C  CR6   0   0.121  11.6242  -2.1103  29.3727
 NPS  C10   C  CH3   0  -0.674  10.3804  -0.1001  28.3845
 NPS  C13   C  CR16  0  -0.308  12.5259  -4.2254  30.1553
 NPS  C11   C  CR16  0  -0.281  11.6235  -3.2080  30.2714
 NPS  C12   C  CH3   0  -0.439  17.2503  -6.2184  26.8972
 NPS  C15   C  C     0   0.556  11.0314  -0.1996  30.8045
 NPS  H     H  HOH1  0   0.482  12.3962   0.9770  31.3813
 NPS  H14   H  HCH1  0   0.286   9.6578  -1.4692  29.8551
 NPS  H101  H  HCH3  0   0.255   9.6203   0.6477  28.6102
 NPS  H102  H  HCH3  0   0.238  11.2813   0.4264  28.0728
 NPS  H103  H  HCH3  0   0.251  10.0224  -0.6903  27.5414
 NPS  H7    H  HCR6  0   0.250  12.5805  -1.2680  27.6589
 NPS  H11   H  HCR6  0   0.255  10.8874  -3.2402  31.0665
 NPS  H3    H  HCR6  0   0.261  14.4802  -2.2892  26.4879
 NPS  H2    H  HCR6  0   0.283  16.1095  -4.0642  26.2581
 NPS  H13   H  HCR6  0   0.254  12.5040  -5.0537  30.8529
 NPS  H6    H  HCR6  0   0.259  14.4488  -6.0753  29.6767
 NPS  H121  H  HCH3  0   0.230  16.8112  -6.2566  25.8973
 NPS  H122  H  HCH3  0   0.230  17.9042  -5.3453  26.9625
 NPS  H123  H  HCH3  0   0.261  17.8481  -7.1138  27.0482
 NPS  OXT   O  OH1   0  -0.585  12.1527   0.4752  30.5891
 NPS  O     O  O     0  -0.441  10.4333  -0.1716  31.8514

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
 NPS  OXT  C15   single    1.326  0.020  1.326
 NPS  C15  O     double    1.206  0.020  1.206
 NPS  C15  C14   single    1.516  0.020  1.516
 NPS  C14  C10   single    1.526  0.020  1.526
 NPS  C14  C8    single    1.515  0.020  1.515
 NPS  C8   C7    aromatic  1.368  0.020  1.368
 NPS  C8   C11   aromatic  1.419  0.020  1.419
 NPS  C7   C4    aromatic  1.415  0.020  1.415
 NPS  C4   C3    aromatic  1.410  0.020  1.410
 NPS  C4   C5    aromatic  1.418  0.020  1.418
 NPS  C3   C2    aromatic  1.369  0.020  1.369
 NPS  C2   C1    aromatic  1.415  0.020  1.415
 NPS  C11  C13   aromatic  1.365  0.020  1.365
 NPS  C13  C5    aromatic  1.418  0.020  1.418
 NPS  C5   C6    aromatic  1.408  0.020  1.408
 NPS  C6   C1    aromatic  1.377  0.020  1.377
 NPS  C1   O2    single    1.347  0.020  1.347
 NPS  O2   C12   single    1.414  0.020  1.414
 NPS  OXT  H     single    0.850  0.020  0.980
 NPS  C14  H14   single    0.970  0.020  1.090
 NPS  C10  H101  single    0.970  0.020  1.090
 NPS  C10  H102  single    0.970  0.020  1.090
 NPS  C10  H103  single    0.970  0.020  1.090
 NPS  C7   H7    single    0.930  0.020  1.080
 NPS  C11  H11   single    0.930  0.020  1.080
 NPS  C3   H3    single    0.930  0.020  1.080
 NPS  C2   H2    single    0.930  0.020  1.080
 NPS  C13  H13   single    0.930  0.020  1.080
 NPS  C6   H6    single    0.930  0.020  1.080
 NPS  C12  H121  single    0.970  0.020  1.090
 NPS  C12  H122  single    0.970  0.020  1.090
 NPS  C12  H123  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
 NPS  C6    C1   C2    119.74  3.000
 NPS  C6    C1   O2    116.97  3.000
 NPS  C2    C1   O2    123.28  3.000
 NPS  C12   O2   C1    119.08  3.000
 NPS  H2    C2   C3    118.76  3.000
 NPS  H2    C2   C1    121.22  3.000
 NPS  C3    C2   C1    120.02  3.000
 NPS  H14   C14  C15   105.94  3.000
 NPS  H14   C14  C10   108.10  3.000
 NPS  C15   C14  C10   111.05  3.000
 NPS  H14   C14  C8    108.00  3.000
 NPS  C10   C14  C8    114.81  3.000
 NPS  C15   C14  C8    108.54  3.000
 NPS  H3    C3   C4    119.14  3.000
 NPS  H3    C3   C2    119.34  3.000
 NPS  C4    C3   C2    121.52  3.000
 NPS  C7    C4   C5    119.72  3.000
 NPS  C5    C4   C3    118.26  3.000
 NPS  C7    C4   C3    122.03  3.000
 NPS  C13   C5   C6    122.18  3.000
 NPS  C6    C5   C4    119.70  3.000
 NPS  C13   C5   C4    118.12  3.000
 NPS  H6    C6   C5    119.63  3.000
 NPS  H6    C6   C1    119.61  3.000
 NPS  C5    C6   C1    120.76  3.000
 NPS  H7    C7   C8    120.78  3.000
 NPS  H7    C7   C4    117.91  3.000
 NPS  C8    C7   C4    121.32  3.000
 NPS  C11   C8   C7    118.64  3.000
 NPS  C11   C8   C14   118.19  3.000
 NPS  C7    C8   C14   123.16  3.000
 NPS  H103  C10  H102  108.18  3.000
 NPS  H103  C10  H101  107.62  3.000
 NPS  H102  C10  H101  107.73  3.000
 NPS  H103  C10  C14   109.89  3.000
 NPS  H102  C10  C14   112.84  3.000
 NPS  H101  C10  C14   110.41  3.000
 NPS  H13   C13  C11   120.12  3.000
 NPS  H13   C13  C5    119.17  3.000
 NPS  C11   C13  C5    120.71  3.000
 NPS  H11   C11  C13   119.29  3.000
 NPS  H11   C11  C8    119.21  3.000
 NPS  C13   C11  C8    121.50  3.000
 NPS  H123  C12  H122  108.71  3.000
 NPS  H123  C12  H121  108.62  3.000
 NPS  H122  C12  H121  108.84  3.000
 NPS  H123  C12  O2    106.41  3.000
 NPS  H122  C12  O2    112.08  3.000
 NPS  H121  C12  O2    112.06  3.000
 NPS  O     C15  OXT   123.26  3.000
 NPS  O     C15  C14   124.71  3.000
 NPS  OXT   C15  C14   112.02  3.000
 NPS  H     OXT  C15   110.07  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
 NPS  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 NPS  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 NPS  CONST_03  C13   C5   C6   C1   180.00   0.0  0
 NPS  CONST_04  C7    C4   C3   C2   180.00   0.0  0
 NPS  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 NPS  CONST_06  C5    C6   C1   C2     0.00   0.0  0
 NPS  CONST_07  C8    C7   C4   C3   180.00   0.0  0
 NPS  CONST_08  C13   C5   C4   C3   180.00   0.0  0
 NPS  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 NPS  CONST_10  C6    C1   C2   C3     0.00   0.0  0
 NPS  CONST_11  C11   C8   C7   C4     0.00   0.0  0
 NPS  CONST_12  C11   C13  C5   C4     0.00   0.0  0
 NPS  CONST_13  C8    C7   C4   C5     0.00   0.0  0
 NPS  CONST_14  C8    C11  C13  C5     0.00   0.0  0
 NPS  CONST_15  C7    C4   C5   C6   180.00   0.0  0
 NPS  CONST_16  C11   C13  C5   C6   180.00   0.0  0
 NPS  CONST_17  C13   C11  C8   C7     0.00   0.0  0
 NPS  CONST_18  C13   C5   C4   C7     0.00   0.0  0
 NPS  CONST_19  C3    C2   C1   O2   180.00   0.0  0
 NPS  CONST_20  C5    C6   C1   O2   180.00   0.0  0
 NPS  CONST_21  C4    C7   C8   C14  180.00   0.0  0
 NPS  CONST_22  C13   C11  C8   C14  180.00   0.0  0
 NPS  CONST_23  H3    C3   C2   C1   180.00   0.0  0
 NPS  CONST_24  H6    C6   C1   C2   180.00   0.0  0
 NPS  CONST_25  H7    C7   C4   C3     0.00   0.0  0
 NPS  CONST_26  H2    C2   C3   C4   180.00   0.0  0
 NPS  CONST_27  H13   C13  C5   C4   180.00   0.0  0
 NPS  CONST_28  H11   C11  C13  C5   180.00   0.0  0
 NPS  CONST_29  H     OXT  C15  C14  180.00   0.0  0
 NPS  Var_01    H121  C12  O2   C1   -62.26  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
 NPS  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
 NPS  plan-1  C1   0.020
 NPS  plan-1  O2   0.020
 NPS  plan-1  C2   0.020
 NPS  plan-1  C14  0.020
 NPS  plan-1  C3   0.020
 NPS  plan-1  C4   0.020
 NPS  plan-1  C5   0.020
 NPS  plan-1  C6   0.020
 NPS  plan-1  C7   0.020
 NPS  plan-1  C8   0.020
 NPS  plan-1  C13  0.020
 NPS  plan-1  C11  0.020
 NPS  plan-1  H7   0.020
 NPS  plan-1  H11  0.020
 NPS  plan-1  H3   0.020
 NPS  plan-1  H2   0.020
 NPS  plan-1  H13  0.020
 NPS  plan-1  H6   0.020
 NPS  plan-2  C14  0.020
 NPS  plan-2  C15  0.020
 NPS  plan-2  H    0.020
 NPS  plan-2  OXT  0.020
 NPS  plan-2  O    0.020

