# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 02:08:27 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-methyl-2-[4-(naphthalen-1-yl)phenoxy]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Oc1ccc(cc1)c2cccc3ccccc23)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
 65W  65W  '2-methyl-2-[4-(naphthalen-1-yl)phenoxy]propanoic acid'  ligand  40  23  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_65W
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
 65W  OAC  O  O      0  -0.592  -3.4450   1.5719  -1.0323
 65W  CAQ  C  C      0   0.400  -3.9433   1.3019   0.0728
 65W  OAD  O  OC    -1  -0.593  -4.2618   2.0974   0.9761
 65W  CAW  C  CT     0   0.082  -4.2749  -0.1987   0.3287
 65W  CAA  C  CH3    0  -0.661  -4.4019  -0.5706   1.8012
 65W  CAB  C  CH3    0  -0.672  -5.5956  -0.4929  -0.3789
 65W  OAP  O  O2     0  -0.493  -3.3321  -1.0582  -0.3297
 65W  CAR  C  CR6    0   0.394  -2.0079  -0.9380  -0.1665
 65W  CAJ  C  CR16   0  -0.354  -1.2250  -1.7819  -0.9601
 65W  CAL  C  CR16   0  -0.283   0.1550  -1.7563  -0.8767
 65W  CAI  C  CR16   0  -0.355  -1.3618  -0.0783   0.7234
 65W  CAK  C  CR16   0  -0.298   0.0233  -0.0642   0.7947
 65W  CAS  C  CR6    0   0.010   0.8125  -0.8912  -0.0014
 65W  CAT  C  CR6    0   0.068   2.2876  -0.9009   0.1059
 65W  CAV  C  CR66   0   0.092   3.0636   0.2884  -0.0527
 65W  CAO  C  CR16   0  -0.345   2.4930   1.5394  -0.3954
 65W  CAF  C  CR16   0  -0.253   3.2696   2.6576  -0.5366
 65W  CAE  C  CR16   0  -0.261   4.6643   2.5896  -0.3468
 65W  CAM  C  CR16   0  -0.311   5.2511   1.3937  -0.0395
 65W  CAU  C  CR66   0   0.115   4.4758   0.2185   0.1054
 65W  CAN  C  CR16   0  -0.330   5.0886  -1.0242   0.3871
 65W  CAG  C  CR16   0  -0.244   4.3316  -2.1559   0.5014
 65W  CAH  C  CR16   0  -0.323   2.9324  -2.0880   0.3646
 65W  H2   H  HCH3   0   0.232  -5.2145  -0.0075   2.2559
 65W  H3   H  HCH3   0   0.221  -4.6362  -1.6320   1.9036
 65W  H4   H  HCH3   0   0.232  -3.5033  -0.3683   2.3826
 65W  H5   H  HCH3   0   0.236  -5.5322  -0.2644  -1.4429
 65W  H6   H  HCH3   0   0.231  -5.8777  -1.5418  -0.2645
 65W  H7   H  HCH3   0   0.230  -6.3924   0.1135   0.0519
 65W  H8   H  HCR6   0   0.255  -1.7119  -2.4540  -1.6565
 65W  H9   H  HCR6   0   0.248   0.7323  -2.4137  -1.5159
 65W  H10  H  HCR6   0   0.270  -1.9114   0.5868   1.3729
 65W  H11  H  HCR6   0   0.259   0.4938   0.6045   1.5057
 65W  H12  H  HCR6   0   0.261   1.4270   1.6129  -0.5607
 65W  H13  H  HCR6   0   0.258   2.8106   3.6004  -0.8043
 65W  H14  H  HCR6   0   0.258   5.2679   3.4811  -0.4570
 65W  H15  H  HCR6   0   0.255   6.3248   1.3270   0.0893
 65W  H16  H  HCR6   0   0.254   6.1649  -1.0656   0.5030
 65W  H17  H  HCR6   0   0.257   4.7994  -3.1083   0.7136
 65W  H18  H  HCR6   0   0.253   2.3473  -2.9909   0.4897

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
 65W  CAN  CAG  aromatic  1.366  0.020  1.366
 65W  CAN  CAU  aromatic  1.414  0.020  1.414
 65W  CAG  CAH  aromatic  1.408  0.020  1.408
 65W  CAM  CAU  aromatic  1.415  0.020  1.415
 65W  CAM  CAE  aromatic  1.367  0.020  1.367
 65W  CAU  CAV  aromatic  1.423  0.020  1.423
 65W  CAH  CAT  aromatic  1.376  0.020  1.376
 65W  CAE  CAF  aromatic  1.409  0.020  1.409
 65W  CAV  CAT  aromatic  1.429  0.020  1.429
 65W  CAV  CAO  aromatic  1.417  0.020  1.417
 65W  CAT  CAS  single    1.479  0.020  1.479
 65W  CAF  CAO  aromatic  1.369  0.020  1.369
 65W  CAS  CAL  aromatic  1.395  0.020  1.395
 65W  CAS  CAK  aromatic  1.393  0.020  1.393
 65W  CAL  CAJ  aromatic  1.383  0.020  1.383
 65W  CAK  CAI  aromatic  1.387  0.020  1.387
 65W  CAJ  CAR  aromatic  1.398  0.020  1.398
 65W  CAI  CAR  aromatic  1.396  0.020  1.396
 65W  CAR  OAP  single    1.340  0.020  1.340
 65W  CAB  CAW  single    1.527  0.020  1.527
 65W  OAP  CAW  single    1.436  0.020  1.436
 65W  OAC  CAQ  deloc     1.242  0.020  1.242
 65W  CAQ  CAW  single    1.558  0.020  1.558
 65W  CAQ  OAD  deloc     1.245  0.020  1.245
 65W  CAW  CAA  single    1.524  0.020  1.524
 65W  CAA  H2   single    0.970  0.020  1.090
 65W  CAA  H3   single    0.970  0.020  1.090
 65W  CAA  H4   single    0.970  0.020  1.090
 65W  CAB  H5   single    0.970  0.020  1.090
 65W  CAB  H6   single    0.970  0.020  1.090
 65W  CAB  H7   single    0.970  0.020  1.090
 65W  CAJ  H8   single    0.930  0.020  1.080
 65W  CAL  H9   single    0.930  0.020  1.080
 65W  CAI  H10  single    0.930  0.020  1.080
 65W  CAK  H11  single    0.930  0.020  1.080
 65W  CAO  H12  single    0.930  0.020  1.080
 65W  CAF  H13  single    0.930  0.020  1.080
 65W  CAE  H14  single    0.930  0.020  1.080
 65W  CAM  H15  single    0.930  0.020  1.080
 65W  CAN  H16  single    0.930  0.020  1.080
 65W  CAG  H17  single    0.930  0.020  1.080
 65W  CAH  H18  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
 65W  CAW  CAQ  OAD  116.22  3.000
 65W  OAD  CAQ  OAC  127.54  3.000
 65W  CAW  CAQ  OAC  116.16  3.000
 65W  OAP  CAW  CAB  103.90  3.000
 65W  OAP  CAW  CAA  110.59  3.000
 65W  CAB  CAW  CAA  109.19  3.000
 65W  CAA  CAW  CAQ  114.30  3.000
 65W  OAP  CAW  CAQ  111.19  3.000
 65W  CAB  CAW  CAQ  107.07  3.000
 65W  H4   CAA  H3   107.91  3.000
 65W  H4   CAA  H2   107.27  3.000
 65W  H3   CAA  H2   107.67  3.000
 65W  H4   CAA  CAW  113.68  3.000
 65W  H3   CAA  CAW  110.23  3.000
 65W  H2   CAA  CAW  109.86  3.000
 65W  H7   CAB  H6   107.70  3.000
 65W  H7   CAB  H5   108.16  3.000
 65W  H6   CAB  H5   108.57  3.000
 65W  H7   CAB  CAW  110.00  3.000
 65W  H6   CAB  CAW  111.09  3.000
 65W  H5   CAB  CAW  111.20  3.000
 65W  CAR  OAP  CAW  122.66  3.000
 65W  CAI  CAR  CAJ  118.32  3.000
 65W  CAI  CAR  OAP  126.19  3.000
 65W  CAJ  CAR  OAP  115.49  3.000
 65W  H8   CAJ  CAL  119.92  3.000
 65W  H8   CAJ  CAR  119.18  3.000
 65W  CAL  CAJ  CAR  120.89  3.000
 65W  H9   CAL  CAS  119.68  3.000
 65W  H9   CAL  CAJ  119.01  3.000
 65W  CAS  CAL  CAJ  121.31  3.000
 65W  H10  CAI  CAK  118.10  3.000
 65W  H10  CAI  CAR  121.81  3.000
 65W  CAK  CAI  CAR  120.09  3.000
 65W  H11  CAK  CAS  119.70  3.000
 65W  H11  CAK  CAI  118.27  3.000
 65W  CAS  CAK  CAI  122.03  3.000
 65W  CAT  CAS  CAK  121.83  3.000
 65W  CAK  CAS  CAL  117.36  3.000
 65W  CAT  CAS  CAL  120.76  3.000
 65W  CAH  CAT  CAV  118.99  3.000
 65W  CAV  CAT  CAS  121.88  3.000
 65W  CAH  CAT  CAS  119.13  3.000
 65W  CAU  CAV  CAO  118.03  3.000
 65W  CAO  CAV  CAT  122.88  3.000
 65W  CAU  CAV  CAT  119.07  3.000
 65W  H12  CAO  CAF  119.21  3.000
 65W  H12  CAO  CAV  119.61  3.000
 65W  CAF  CAO  CAV  121.18  3.000
 65W  H13  CAF  CAE  119.68  3.000
 65W  H13  CAF  CAO  119.78  3.000
 65W  CAE  CAF  CAO  120.54  3.000
 65W  H14  CAE  CAM  120.27  3.000
 65W  H14  CAE  CAF  119.90  3.000
 65W  CAM  CAE  CAF  119.83  3.000
 65W  H15  CAM  CAU  118.65  3.000
 65W  H15  CAM  CAE  120.40  3.000
 65W  CAU  CAM  CAE  120.95  3.000
 65W  CAN  CAU  CAM  120.85  3.000
 65W  CAM  CAU  CAV  119.44  3.000
 65W  CAN  CAU  CAV  119.70  3.000
 65W  H16  CAN  CAG  120.66  3.000
 65W  H16  CAN  CAU  119.04  3.000
 65W  CAG  CAN  CAU  120.30  3.000
 65W  H17  CAG  CAH  119.42  3.000
 65W  H17  CAG  CAN  120.39  3.000
 65W  CAH  CAG  CAN  120.18  3.000
 65W  H18  CAH  CAG  119.06  3.000
 65W  H18  CAH  CAT  119.20  3.000
 65W  CAG  CAH  CAT  121.73  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
 65W  CONST_01  CAS  CAL  CAJ  CAR     0.00   0.0  0
 65W  CONST_02  CAS  CAK  CAI  CAR     0.00   0.0  0
 65W  CONST_03  CAT  CAS  CAL  CAJ   180.00   0.0  0
 65W  CONST_04  CAK  CAS  CAL  CAJ     0.00   0.0  0
 65W  CONST_05  CAK  CAI  CAR  CAJ     0.00   0.0  0
 65W  CONST_08  CAI  CAK  CAS  CAL     0.00   0.0  0
 65W  CONST_09  CAI  CAR  CAJ  CAL     0.00   0.0  0
 65W  CONST_10  CAT  CAS  CAK  CAI   180.00   0.0  0
 65W  CONST_13  CAG  CAH  CAT  CAS   180.00   0.0  0
 65W  CONST_14  CAU  CAV  CAT  CAS   180.00   0.0  0
 65W  CONST_15  CAO  CAV  CAT  CAS     0.00   0.0  0
 65W  CONST_16  CAN  CAG  CAH  CAT     0.00   0.0  0
 65W  CONST_17  CAN  CAU  CAV  CAT     0.00   0.0  0
 65W  CONST_18  CAM  CAU  CAV  CAT   180.00   0.0  0
 65W  CONST_19  CAF  CAO  CAV  CAT   180.00   0.0  0
 65W  CONST_20  CAG  CAN  CAU  CAV     0.00   0.0  0
 65W  CONST_21  CAE  CAM  CAU  CAV     0.00   0.0  0
 65W  CONST_22  CAG  CAH  CAT  CAV     0.00   0.0  0
 65W  CONST_23  CAE  CAF  CAO  CAV     0.00   0.0  0
 65W  CONST_24  CAN  CAU  CAV  CAO   180.00   0.0  0
 65W  CONST_25  CAM  CAU  CAV  CAO     0.00   0.0  0
 65W  CONST_26  CAH  CAT  CAV  CAO   180.00   0.0  0
 65W  CONST_27  CAM  CAE  CAF  CAO     0.00   0.0  0
 65W  CONST_28  CAU  CAM  CAE  CAF     0.00   0.0  0
 65W  CONST_29  CAU  CAV  CAO  CAF     0.00   0.0  0
 65W  CONST_30  CAN  CAU  CAM  CAE   180.00   0.0  0
 65W  CONST_31  CAG  CAN  CAU  CAM   180.00   0.0  0
 65W  CONST_32  CAH  CAG  CAN  CAU     0.00   0.0  0
 65W  CONST_33  CAH  CAT  CAV  CAU     0.00   0.0  0
 65W  CONST_34  CAL  CAJ  CAR  OAP   180.00   0.0  0
 65W  CONST_35  CAK  CAI  CAR  OAP   180.00   0.0  0
 65W  CONST_36  H9   CAL  CAJ  CAR   180.00   0.0  0
 65W  CONST_37  H11  CAK  CAI  CAR   180.00   0.0  0
 65W  CONST_38  H10  CAI  CAR  CAJ   180.00   0.0  0
 65W  CONST_39  H8   CAJ  CAR  CAI   180.00   0.0  0
 65W  CONST_40  H18  CAH  CAT  CAS     0.00   0.0  0
 65W  CONST_41  H17  CAG  CAH  CAT   180.00   0.0  0
 65W  CONST_42  H12  CAO  CAV  CAT     0.00   0.0  0
 65W  CONST_43  H16  CAN  CAU  CAV   180.00   0.0  0
 65W  CONST_44  H15  CAM  CAU  CAV   180.00   0.0  0
 65W  CONST_45  H13  CAF  CAO  CAV   180.00   0.0  0
 65W  CONST_46  H14  CAE  CAF  CAO   180.00   0.0  0
 65W  Var_01    CAJ  CAR  OAP  CAW  -175.08  30.0  2
 65W  Var_02    CAB  CAW  CAQ  OAC   -79.74  30.0  3
 65W  Var_03    H5   CAB  CAW  CAQ    57.36  30.0  3
 65W  Var_04    H2   CAA  CAW  CAQ    61.38  30.0  3

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
 65W  plan-1  OAP  0.020
 65W  plan-1  CAR  0.020
 65W  plan-1  CAJ  0.020
 65W  plan-1  CAL  0.020
 65W  plan-1  CAI  0.020
 65W  plan-1  CAK  0.020
 65W  plan-1  CAS  0.020
 65W  plan-1  CAT  0.020
 65W  plan-1  H8   0.020
 65W  plan-1  H9   0.020
 65W  plan-1  H10  0.020
 65W  plan-1  H11  0.020
 65W  plan-2  CAS  0.020
 65W  plan-2  CAT  0.020
 65W  plan-2  CAV  0.020
 65W  plan-2  CAO  0.020
 65W  plan-2  CAF  0.020
 65W  plan-2  CAE  0.020
 65W  plan-2  CAM  0.020
 65W  plan-2  CAU  0.020
 65W  plan-2  CAN  0.020
 65W  plan-2  CAG  0.020
 65W  plan-2  CAH  0.020
 65W  plan-2  H12  0.020
 65W  plan-2  H13  0.020
 65W  plan-2  H14  0.020
 65W  plan-2  H15  0.020
 65W  plan-2  H16  0.020
 65W  plan-2  H17  0.020
 65W  plan-2  H18  0.020
 65W  plan-3  OAC  0.020
 65W  plan-3  CAQ  0.020
 65W  plan-3  OAD  0.020
 65W  plan-3  CAW  0.020

