# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 13:11:38 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-(naphthalen-1-yl)-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)c1cccc2ccccc12
#
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
 Q5M  Q5M  '4-(naphthalen-1-yl)-4-oxobutanoic acid'  ligand  29  17  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q5M
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
 Q5M  C10  C  CR6   0  -0.030   0.5565   0.4657  -0.3178
 Q5M  C13  C  CH2   0  -0.578  -1.9964   0.2948  -0.0890
 Q5M  C15  C  C     0   0.557  -4.4410  -0.0928   0.3342
 Q5M  C01  C  CR16  0  -0.259   4.3751  -1.3027   0.3368
 Q5M  C02  C  CR16  0  -0.241   3.2338  -2.1192   0.2297
 Q5M  C03  C  CR16  0  -0.331   1.9958  -1.5776   0.0073
 Q5M  C04  C  CR66  0   0.120   1.8221  -0.1757  -0.1177
 Q5M  C05  C  CR66  0   0.101   2.9769   0.6450   0.0218
 Q5M  C06  C  CR16  0  -0.303   4.2434   0.0534   0.2389
 Q5M  C07  C  CR16  0  -0.306   2.8555   2.0520  -0.0402
 Q5M  C08  C  CR16  0  -0.245   1.6359   2.6405  -0.2115
 Q5M  C09  C  CR16  0  -0.304   0.4882   1.8405  -0.3400
 Q5M  C11  C  C     0   0.365  -0.6948  -0.3060  -0.5710
 Q5M  O12  O  O     0  -0.399  -0.6751  -1.3709  -1.1504
 Q5M  C14  C  CH2   0  -0.583  -3.1439  -0.6974  -0.1289
 Q5M  O16  O  O     0  -0.443  -4.5972   1.0558   0.6663
 Q5M  O17  O  OH1   0  -0.596  -5.4230  -0.9882   0.3344
 Q5M  H1   H  HCH2  0   0.281  -1.8520   0.6820   0.9219
 Q5M  H2   H  HCH2  0   0.289  -2.2315   1.1644  -0.7094
 Q5M  H3   H  HCR6  0   0.261   5.3459  -1.7493   0.5067
 Q5M  H4   H  HCR6  0   0.262   3.3344  -3.1925   0.3273
 Q5M  H5   H  HCR6  0   0.258   1.1494  -2.2414  -0.0632
 Q5M  H6   H  HCR6  0   0.260   5.1074   0.6999   0.3354
 Q5M  H7   H  HCR6  0   0.265   3.7481   2.6579   0.0569
 Q5M  H8   H  HCR6  0   0.267   1.5434   3.7171  -0.2469
 Q5M  H9   H  HCR6  0   0.272  -0.4611   2.3378  -0.4861
 Q5M  H10  H  HCH2  0   0.290  -3.2938  -1.0884  -1.1382
 Q5M  H11  H  HCH2  0   0.289  -2.9296  -1.5648   0.5007
 Q5M  H12  H  HOH1  0   0.480  -6.2454  -0.5795   0.6439

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
 Q5M  C01  C02  aromatic  1.407  0.020  1.407
 Q5M  C01  C06  aromatic  1.366  0.020  1.366
 Q5M  C02  C03  aromatic  1.369  0.020  1.369
 Q5M  C06  C05  aromatic  1.415  0.020  1.415
 Q5M  C03  C04  aromatic  1.418  0.020  1.418
 Q5M  C05  C04  aromatic  1.424  0.020  1.424
 Q5M  C05  C07  aromatic  1.414  0.020  1.414
 Q5M  C04  C10  aromatic  1.433  0.020  1.433
 Q5M  O12  C11  double    1.213  0.020  1.213
 Q5M  C07  C08  aromatic  1.365  0.020  1.365
 Q5M  C10  C11  single    1.492  0.020  1.492
 Q5M  C10  C09  aromatic  1.377  0.020  1.377
 Q5M  C11  C13  single    1.512  0.020  1.512
 Q5M  C08  C09  aromatic  1.405  0.020  1.405
 Q5M  C13  C14  single    1.518  0.020  1.518
 Q5M  C14  C15  single    1.504  0.020  1.504
 Q5M  O16  C15  double    1.206  0.020  1.206
 Q5M  C15  O17  single    1.329  0.020  1.329
 Q5M  C13  H1   single    0.970  0.020  1.090
 Q5M  C13  H2   single    0.970  0.020  1.090
 Q5M  C01  H3   single    0.930  0.020  1.080
 Q5M  C02  H4   single    0.930  0.020  1.080
 Q5M  C03  H5   single    0.930  0.020  1.080
 Q5M  C06  H6   single    0.930  0.020  1.080
 Q5M  C07  H7   single    0.930  0.020  1.080
 Q5M  C08  H8   single    0.930  0.020  1.080
 Q5M  C09  H9   single    0.930  0.020  1.080
 Q5M  C14  H10  single    0.970  0.020  1.090
 Q5M  C14  H11  single    0.970  0.020  1.090
 Q5M  O17  H12  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
 Q5M  C11  C10  C09  118.18  3.000
 Q5M  C09  C10  C04  119.55  3.000
 Q5M  C11  C10  C04  122.21  3.000
 Q5M  H2   C13  H1   105.75  3.000
 Q5M  H2   C13  C14  110.02  3.000
 Q5M  H1   C13  C14  110.86  3.000
 Q5M  H2   C13  C11  108.67  3.000
 Q5M  H1   C13  C11  108.79  3.000
 Q5M  C14  C13  C11  112.50  3.000
 Q5M  O17  C15  O16  123.10  3.000
 Q5M  O17  C15  C14  111.50  3.000
 Q5M  O16  C15  C14  125.41  3.000
 Q5M  H3   C01  C06  120.50  3.000
 Q5M  H3   C01  C02  120.01  3.000
 Q5M  C06  C01  C02  119.49  3.000
 Q5M  H4   C02  C03  119.40  3.000
 Q5M  H4   C02  C01  119.54  3.000
 Q5M  C03  C02  C01  121.06  3.000
 Q5M  H5   C03  C04  120.45  3.000
 Q5M  H5   C03  C02  118.48  3.000
 Q5M  C04  C03  C02  121.07  3.000
 Q5M  C05  C04  C03  117.51  3.000
 Q5M  C05  C04  C10  118.17  3.000
 Q5M  C03  C04  C10  124.27  3.000
 Q5M  C07  C05  C06  119.99  3.000
 Q5M  C07  C05  C04  119.99  3.000
 Q5M  C06  C05  C04  120.01  3.000
 Q5M  H6   C06  C05  118.55  3.000
 Q5M  H6   C06  C01  120.61  3.000
 Q5M  C05  C06  C01  120.83  3.000
 Q5M  H7   C07  C08  120.43  3.000
 Q5M  H7   C07  C05  118.82  3.000
 Q5M  C08  C07  C05  120.75  3.000
 Q5M  H8   C08  C09  119.62  3.000
 Q5M  H8   C08  C07  120.65  3.000
 Q5M  C09  C08  C07  119.73  3.000
 Q5M  H9   C09  C08  117.88  3.000
 Q5M  H9   C09  C10  120.32  3.000
 Q5M  C08  C09  C10  121.78  3.000
 Q5M  O12  C11  C13  121.01  3.000
 Q5M  C13  C11  C10  117.54  3.000
 Q5M  O12  C11  C10  121.45  3.000
 Q5M  H11  C14  H10  105.96  3.000
 Q5M  H11  C14  C15  108.10  3.000
 Q5M  H10  C14  C15  108.06  3.000
 Q5M  H11  C14  C13  110.82  3.000
 Q5M  H10  C14  C13  111.22  3.000
 Q5M  C15  C14  C13  112.41  3.000
 Q5M  H12  O17  C15  110.06  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
 Q5M  CONST_01  C02  C03  C04  C10   180.00   0.0  0
 Q5M  CONST_02  C06  C05  C04  C10   180.00   0.0  0
 Q5M  CONST_03  C07  C05  C04  C10     0.00   0.0  0
 Q5M  CONST_04  C07  C08  C09  C10     0.00   0.0  0
 Q5M  CONST_05  C04  C03  C02  C01     0.00   0.0  0
 Q5M  CONST_06  C04  C05  C06  C01     0.00   0.0  0
 Q5M  CONST_07  C07  C05  C06  C01   180.00   0.0  0
 Q5M  CONST_08  C05  C06  C01  C02     0.00   0.0  0
 Q5M  CONST_09  C05  C04  C03  C02     0.00   0.0  0
 Q5M  CONST_10  C06  C01  C02  C03     0.00   0.0  0
 Q5M  CONST_11  C06  C05  C04  C03     0.00   0.0  0
 Q5M  CONST_12  C07  C05  C04  C03   180.00   0.0  0
 Q5M  CONST_13  C09  C10  C04  C03   180.00   0.0  0
 Q5M  CONST_14  C08  C07  C05  C04     0.00   0.0  0
 Q5M  CONST_15  C08  C09  C10  C04     0.00   0.0  0
 Q5M  CONST_16  C09  C10  C04  C05     0.00   0.0  0
 Q5M  CONST_17  C09  C08  C07  C05     0.00   0.0  0
 Q5M  CONST_18  C08  C07  C05  C06   180.00   0.0  0
 Q5M  CONST_19  C11  C10  C04  C03     0.00   0.0  0
 Q5M  CONST_20  C11  C10  C04  C05   180.00   0.0  0
 Q5M  CONST_21  C11  C10  C09  C08   180.00   0.0  0
 Q5M  CONST_22  H5   C03  C04  C10     0.00   0.0  0
 Q5M  CONST_23  H8   C08  C09  C10   180.00   0.0  0
 Q5M  CONST_24  H6   C06  C01  C02   180.00   0.0  0
 Q5M  CONST_25  H3   C01  C02  C03   180.00   0.0  0
 Q5M  CONST_26  H4   C02  C03  C04   180.00   0.0  0
 Q5M  CONST_27  H7   C07  C05  C04   180.00   0.0  0
 Q5M  CONST_28  H9   C09  C10  C04   180.00   0.0  0
 Q5M  CONST_29  H12  O17  C15  C14   180.00   0.0  0
 Q5M  Var_01    C04  C10  C11  C13   149.59  30.0  3
 Q5M  Var_02    C14  C13  C11  C10  -167.59  30.0  3
 Q5M  Var_03    O16  C15  C14  C13     2.21  30.0  3
 Q5M  Var_04    C11  C13  C14  C15  -179.27  30.0  1

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
 Q5M  plan-1  C10  0.020
 Q5M  plan-1  C01  0.020
 Q5M  plan-1  C02  0.020
 Q5M  plan-1  C03  0.020
 Q5M  plan-1  C04  0.020
 Q5M  plan-1  C05  0.020
 Q5M  plan-1  C06  0.020
 Q5M  plan-1  C07  0.020
 Q5M  plan-1  C08  0.020
 Q5M  plan-1  C09  0.020
 Q5M  plan-1  C11  0.020
 Q5M  plan-1  H3   0.020
 Q5M  plan-1  H4   0.020
 Q5M  plan-1  H5   0.020
 Q5M  plan-1  H6   0.020
 Q5M  plan-1  H7   0.020
 Q5M  plan-1  H8   0.020
 Q5M  plan-1  H9   0.020
 Q5M  plan-2  C10  0.020
 Q5M  plan-2  C13  0.020
 Q5M  plan-2  C11  0.020
 Q5M  plan-2  O12  0.020
 Q5M  plan-3  C15  0.020
 Q5M  plan-3  C14  0.020
 Q5M  plan-3  O16  0.020
 Q5M  plan-3  O17  0.020
 Q5M  plan-3  H12  0.020

