# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:09:50 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (5S)-5-(naphthalen-2-ylmethyl)imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@@H](Cc2ccc3ccccc3c2)C(=O)N1
#
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
 5NL  5NL  (5S)-5-(naphthalen-2-ylmethyl)imidazolidine-2,4-dione  ligand  30  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5NL
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
 5NL  C     C  CR5   0   0.560   3.4219  -1.0850  -0.0963
 5NL  CA    C  CR15  0  -0.185   1.9942  -0.6323   0.1673
 5NL  CG    C  CR6   0   0.120  -0.2775  -0.2697  -0.8256
 5NL  CD1   C  CR16  0  -0.307  -0.6101   1.0740  -1.1219
 5NL  CE1   C  CR16  0  -0.297  -1.8586   1.5660  -0.8585
 5NL  CZ    C  CR66  0   0.099  -2.8529   0.7434  -0.2807
 5NL  CE2   C  CR66  0   0.139  -2.5306  -0.6060   0.0177
 5NL  CD2   C  CR16  0  -0.373  -1.2306  -1.0822  -0.2665
 5NL  N10   N  NR15  0  -0.658   2.1930   0.7295   0.5938
 5NL  C2    C  CR5   0   0.674   3.4949   1.0723   0.6808
 5NL  N11   N  NR15  0  -0.698   4.2175  -0.0325   0.2312
 5NL  C1    C  CR16  0  -0.314  -3.5231  -1.4367   0.5913
 5NL  C3    C  CR16  0  -0.258  -4.7731  -0.9482   0.8560
 5NL  C5    C  CR16  0  -0.259  -5.0927   0.3948   0.5598
 5NL  C6    C  CR16  0  -0.309  -4.1543   1.2205   0.0034
 5NL  C4    C  CH2   0  -0.522   1.1149  -0.7746  -1.0783
 5NL  O3    O  O     0  -0.432   3.7710  -2.1586  -0.5241
 5NL  O2    O  O     0  -0.476   3.9772   2.1150   1.0618
 5NL  HA    H  HCR5  0   0.317   1.5775  -1.2419   0.9769
 5NL  H11   H  HNR5  0   0.429   5.2245  -0.0303   0.1511
 5NL  H10   H  HNR5  0   0.417   1.4707   1.2946   1.0100
 5NL  H41C  H  HCH2  0   0.271   1.5731  -0.2297  -1.9066
 5NL  H42C  H  HCH2  0   0.275   1.0924  -1.8302  -1.3532
 5NL  HD1   H  HCR6  0   0.255   0.1373   1.7156  -1.5730
 5NL  HD2   H  HCR6  0   0.250  -0.9935  -2.1149  -0.0330
 5NL  HE1   H  HCR6  0   0.256  -2.0989   2.5952  -1.0965
 5NL  H6    H  HCR6  0   0.255  -4.3967   2.2508  -0.2280
 5NL  H1    H  HCR6  0   0.255  -3.2781  -2.4670   0.8196
 5NL  HB    H  HCR6  0   0.259  -5.5250  -1.5911   1.2950
 5NL  HC    H  HCR6  0   0.258  -6.0858   0.7670   0.7752

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
 5NL  C    CA    single    1.521  0.020  1.521
 5NL  C    N11   single    1.359  0.020  1.359
 5NL  C    O3    double    1.207  0.020  1.207
 5NL  CA   N10   single    1.441  0.020  1.441
 5NL  CA   C4    single    1.531  0.020  1.531
 5NL  CG   CD1   aromatic  1.416  0.020  1.416
 5NL  CG   CD2   aromatic  1.372  0.020  1.372
 5NL  CG   C4    single    1.503  0.020  1.503
 5NL  CD1  CE1   aromatic  1.368  0.020  1.368
 5NL  CE1  CZ    aromatic  1.414  0.020  1.414
 5NL  CZ   CE2   aromatic  1.419  0.020  1.419
 5NL  CZ   C6    aromatic  1.415  0.020  1.415
 5NL  CE2  CD2   aromatic  1.413  0.020  1.413
 5NL  CE2  C1    aromatic  1.416  0.020  1.416
 5NL  N10  C2    single    1.349  0.020  1.349
 5NL  C2   N11   single    1.395  0.020  1.395
 5NL  C2   O2    double    1.210  0.020  1.210
 5NL  C1   C3    aromatic  1.368  0.020  1.368
 5NL  C3   C5    aromatic  1.412  0.020  1.412
 5NL  C5   C6    aromatic  1.368  0.020  1.368
 5NL  CA   HA    single    0.970  0.020  1.090
 5NL  N11  H11   single    0.860  0.020  1.020
 5NL  N10  H10   single    0.860  0.020  1.020
 5NL  C4   H41C  single    0.970  0.020  1.090
 5NL  C4   H42C  single    0.970  0.020  1.090
 5NL  CD1  HD1   single    0.930  0.020  1.080
 5NL  CD2  HD2   single    0.930  0.020  1.080
 5NL  CE1  HE1   single    0.930  0.020  1.080
 5NL  C6   H6    single    0.930  0.020  1.080
 5NL  C1   H1    single    0.930  0.020  1.080
 5NL  C3   HB    single    0.930  0.020  1.080
 5NL  C5   HC    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
 5NL  O3    C    N11   127.20  3.000
 5NL  O3    C    CA    126.70  3.000
 5NL  N11   C    CA    106.09  3.000
 5NL  HA    CA   C4    109.33  3.000
 5NL  HA    CA   N10   111.07  3.000
 5NL  C4    CA   N10   114.07  3.000
 5NL  HA    CA   C     108.63  3.000
 5NL  C4    CA   C     111.74  3.000
 5NL  N10   CA   C     101.72  3.000
 5NL  C4    CG   CD2   120.90  3.000
 5NL  C4    CG   CD1   120.10  3.000
 5NL  CD2   CG   CD1   118.97  3.000
 5NL  HD1   CD1  CE1   119.80  3.000
 5NL  HD1   CD1  CG    119.15  3.000
 5NL  CE1   CD1  CG    121.05  3.000
 5NL  HE1   CE1  CZ    119.11  3.000
 5NL  HE1   CE1  CD1   120.13  3.000
 5NL  CZ    CE1  CD1   120.76  3.000
 5NL  C6    CZ   CE2   119.16  3.000
 5NL  C6    CZ   CE1   122.19  3.000
 5NL  CE2   CZ   CE1   118.65  3.000
 5NL  C1    CE2  CD2   121.92  3.000
 5NL  C1    CE2  CZ    118.95  3.000
 5NL  CD2   CE2  CZ    119.14  3.000
 5NL  HD2   CD2  CE2   118.58  3.000
 5NL  HD2   CD2  CG    119.98  3.000
 5NL  CE2   CD2  CG    121.44  3.000
 5NL  H10   N10  C2    121.53  3.000
 5NL  H10   N10  CA    123.62  3.000
 5NL  C2    N10  CA    113.10  3.000
 5NL  O2    C2   N11   125.27  3.000
 5NL  O2    C2   N10   128.59  3.000
 5NL  N11   C2   N10   106.14  3.000
 5NL  H11   N11  C2    122.70  3.000
 5NL  H11   N11  C     124.48  3.000
 5NL  C2    N11  C     112.82  3.000
 5NL  H1    C1   C3    120.36  3.000
 5NL  H1    C1   CE2   119.01  3.000
 5NL  C3    C1   CE2   120.63  3.000
 5NL  HB    C3   C5    119.53  3.000
 5NL  HB    C3   C1    120.08  3.000
 5NL  C5    C3   C1    120.39  3.000
 5NL  HC    C5   C6    120.18  3.000
 5NL  HC    C5   C3    119.55  3.000
 5NL  C6    C5   C3    120.27  3.000
 5NL  H6    C6   C5    120.49  3.000
 5NL  H6    C6   CZ    118.91  3.000
 5NL  C5    C6   CZ    120.60  3.000
 5NL  H42C  C4   H41C  107.48  3.000
 5NL  H42C  C4   CG    110.39  3.000
 5NL  H41C  C4   CG    110.41  3.000
 5NL  H42C  C4   CA    107.86  3.000
 5NL  H41C  C4   CA    109.25  3.000
 5NL  CG    C4   CA    111.35  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
 5NL  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 5NL  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 5NL  CONST_03  C1   CE2  CD2  CG   180.00   0.0  0
 5NL  CONST_04  CE2  CD2  CG   CD1    0.00   0.0  0
 5NL  CONST_05  CE2  CZ   CE1  CD1    0.00   0.0  0
 5NL  CONST_06  C6   CZ   CE1  CD1  180.00   0.0  0
 5NL  CONST_07  CD2  CG   CD1  CE1    0.00   0.0  0
 5NL  CONST_08  CD2  CE2  CZ   CE1    0.00   0.0  0
 5NL  CONST_09  C1   CE2  CZ   CE1  180.00   0.0  0
 5NL  CONST_10  C5   C6   CZ   CE1  180.00   0.0  0
 5NL  CONST_11  C3   C1   CE2  CZ     0.00   0.0  0
 5NL  CONST_12  C3   C5   C6   CZ     0.00   0.0  0
 5NL  CONST_13  C5   C6   CZ   CE2    0.00   0.0  0
 5NL  CONST_14  C5   C3   C1   CE2    0.00   0.0  0
 5NL  CONST_15  C6   CZ   CE2  CD2  180.00   0.0  0
 5NL  CONST_16  C3   C1   CE2  CD2  180.00   0.0  0
 5NL  CONST_17  C6   CZ   CE2  C1     0.00   0.0  0
 5NL  CONST_18  C6   C5   C3   C1     0.00   0.0  0
 5NL  CONST_19  N10  C2   N11  C      0.00   0.0  0
 5NL  CONST_20  C2   N11  C    CA     0.00   0.0  0
 5NL  CONST_21  N11  C2   N10  CA     0.00   0.0  0
 5NL  CONST_22  C4   CG   CD1  CE1  180.00   0.0  0
 5NL  CONST_23  C4   CG   CD2  CE2  180.00   0.0  0
 5NL  CONST_24  O2   C2   N11  C    180.00   0.0  0
 5NL  CONST_25  O2   C2   N10  CA   180.00   0.0  0
 5NL  CONST_26  O3   C    N11  C2   180.00   0.0  0
 5NL  CONST_27  HE1  CE1  CD1  CG   180.00   0.0  0
 5NL  CONST_28  HD2  CD2  CG   CD1  180.00   0.0  0
 5NL  CONST_29  H6   C6   CZ   CE1    0.00   0.0  0
 5NL  CONST_30  HD1  CD1  CE1  CZ   180.00   0.0  0
 5NL  CONST_31  H1   C1   CE2  CZ   180.00   0.0  0
 5NL  CONST_32  HC   C5   C6   CZ   180.00   0.0  0
 5NL  CONST_33  HB   C3   C1   CE2  180.00   0.0  0
 5NL  CONST_34  H11  N11  C    CA   180.00   0.0  0
 5NL  CONST_35  H10  N10  C2   N11  180.00   0.0  0
 5NL  Var_01    CD1  CG   C4   CA    92.44  30.0  2

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
 5NL  chir_01  CA  C  N10  C4  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
 5NL  plan-1  CG   0.020
 5NL  plan-1  CD1  0.020
 5NL  plan-1  CE1  0.020
 5NL  plan-1  CZ   0.020
 5NL  plan-1  CE2  0.020
 5NL  plan-1  CD2  0.020
 5NL  plan-1  C1   0.020
 5NL  plan-1  C3   0.020
 5NL  plan-1  C5   0.020
 5NL  plan-1  C6   0.020
 5NL  plan-1  C4   0.020
 5NL  plan-1  HD1  0.020
 5NL  plan-1  HD2  0.020
 5NL  plan-1  HE1  0.020
 5NL  plan-1  H6   0.020
 5NL  plan-1  H1   0.020
 5NL  plan-1  HB   0.020
 5NL  plan-1  HC   0.020
 5NL  plan-2  C    0.020
 5NL  plan-2  CA   0.020
 5NL  plan-2  N10  0.020
 5NL  plan-2  C2   0.020
 5NL  plan-2  N11  0.020
 5NL  plan-2  O3   0.020
 5NL  plan-2  O2   0.020
 5NL  plan-2  H11  0.020
 5NL  plan-2  H10  0.020

