# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:00:42 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (5R)-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
 5ND  5ND  (5R)-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_5ND
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
 5ND  N10   N  NR15  0  -0.655   2.0150   0.7149  -0.6827
 5ND  CA    C  CR15  0  -0.189   2.1180  -0.6516  -0.2417
 5ND  CB    C  CH2   0  -0.519   1.1772  -0.9960   0.9165
 5ND  CG    C  CR6   0   0.122  -0.2617  -0.8567   0.5120
 5ND  CD1   C  CR16  0  -0.292  -0.8616  -1.8482  -0.3028
 5ND  CE1   C  CR16  0  -0.297  -2.1616  -1.7355  -0.7070
 5ND  CZ    C  CR66  0   0.099  -2.9451  -0.6210  -0.3231
 5ND  CE2   C  CR66  0   0.138  -2.3529   0.3796   0.4891
 5ND  CD2   C  CR16  0  -0.388  -1.0028   0.2331   0.8874
 5ND  C     C  CR5   0   0.560   3.5757  -0.7305   0.1839
 5ND  N11   N  NR15  0  -0.698   4.1083   0.4942  -0.0685
 5ND  C2    C  CR5   0   0.673   3.1833   1.3840  -0.6163
 5ND  O2    O  O     0  -0.477   3.4227   2.5228  -0.9494
 5ND  O3    O  O     0  -0.432   4.1348  -1.6859   0.6661
 5ND  C1    C  CR16  0  -0.313  -3.1307   1.4948   0.8796
 5ND  C3    C  CR16  0  -0.257  -4.4359   1.6078   0.4834
 5ND  C5    C  CR16  0  -0.260  -5.0243   0.6123  -0.3249
 5ND  C6    C  CR16  0  -0.309  -4.2950  -0.4769  -0.7189
 5ND  H10   H  HNR5  0   0.417   1.2126   1.0895  -1.1618
 5ND  HA    H  HCR5  0   0.316   1.9578  -1.3505  -1.0701
 5ND  HB1C  H  HCH2  0   0.274   1.3870  -2.0215   1.2274
 5ND  HB2C  H  HCH2  0   0.271   1.3986  -0.3435   1.7635
 5ND  HD1   H  HCR6  0   0.255  -0.2788  -2.7112  -0.6041
 5ND  HD2   H  HCR6  0   0.251  -0.5569   1.0016   1.5096
 5ND  HE1   H  HCR6  0   0.255  -2.6092  -2.5058  -1.3235
 5ND  H6    H  HCR6  0   0.255  -4.7462  -1.2427  -1.3384
 5ND  H1    H  HCR6  0   0.254  -2.6779   2.2601   1.4986
 5ND  H11   H  HNR5  0   0.429   5.0649   0.7531   0.1280
 5ND  H3    H  HCR6  0   0.259  -5.0235   2.4630   0.7909
 5ND  H5    H  HCR6  0   0.258  -6.0567   0.7150  -0.6324

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
 5ND  N10  CA    single    1.440  0.020  1.440
 5ND  N10  C2    single    1.348  0.020  1.348
 5ND  CA   CB    single    1.531  0.020  1.531
 5ND  CA   C     single    1.521  0.020  1.521
 5ND  CB   CG    single    1.501  0.020  1.501
 5ND  CG   CD1   aromatic  1.417  0.020  1.417
 5ND  CG   CD2   aromatic  1.370  0.020  1.370
 5ND  CD1  CE1   aromatic  1.366  0.020  1.366
 5ND  CE1  CZ    aromatic  1.415  0.020  1.415
 5ND  CZ   CE2   aromatic  1.418  0.020  1.418
 5ND  CZ   C6    aromatic  1.414  0.020  1.414
 5ND  CE2  CD2   aromatic  1.415  0.020  1.415
 5ND  CE2  C1    aromatic  1.415  0.020  1.415
 5ND  C    N11   single    1.359  0.020  1.359
 5ND  C    O3    double    1.207  0.020  1.207
 5ND  N11  C2    single    1.396  0.020  1.396
 5ND  C2   O2    double    1.210  0.020  1.210
 5ND  C1   C3    aromatic  1.369  0.020  1.369
 5ND  C3   C5    aromatic  1.411  0.020  1.411
 5ND  C5   C6    aromatic  1.369  0.020  1.369
 5ND  N10  H10   single    0.860  0.020  1.020
 5ND  CA   HA    single    0.970  0.020  1.090
 5ND  CB   HB1C  single    0.970  0.020  1.090
 5ND  CB   HB2C  single    0.970  0.020  1.090
 5ND  CD1  HD1   single    0.930  0.020  1.080
 5ND  CD2  HD2   single    0.930  0.020  1.080
 5ND  CE1  HE1   single    0.930  0.020  1.080
 5ND  C6   H6    single    0.930  0.020  1.080
 5ND  C1   H1    single    0.930  0.020  1.080
 5ND  N11  H11   single    0.860  0.020  1.020
 5ND  C3   H3    single    0.930  0.020  1.080
 5ND  C5   H5    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
 5ND  H10   N10  C2    121.97  3.000
 5ND  H10   N10  CA    123.78  3.000
 5ND  C2    N10  CA    113.21  3.000
 5ND  HA    CA   C     108.59  3.000
 5ND  HA    CA   CB    109.79  3.000
 5ND  C     CA   CB    111.44  3.000
 5ND  HA    CA   N10   111.31  3.000
 5ND  C     CA   N10   101.75  3.000
 5ND  CB    CA   N10   113.65  3.000
 5ND  HB2C  CB   HB1C  107.55  3.000
 5ND  HB2C  CB   CG    110.36  3.000
 5ND  HB1C  CB   CG    110.37  3.000
 5ND  HB2C  CB   CA    109.13  3.000
 5ND  HB1C  CB   CA    107.96  3.000
 5ND  CG    CB   CA    111.36  3.000
 5ND  CD2   CG   CD1   119.02  3.000
 5ND  CD2   CG   CB    121.23  3.000
 5ND  CD1   CG   CB    119.73  3.000
 5ND  HD1   CD1  CE1   119.68  3.000
 5ND  HD1   CD1  CG    119.30  3.000
 5ND  CE1   CD1  CG    121.03  3.000
 5ND  HE1   CE1  CZ    119.04  3.000
 5ND  HE1   CE1  CD1   120.19  3.000
 5ND  CZ    CE1  CD1   120.76  3.000
 5ND  C6    CZ   CE2   119.14  3.000
 5ND  C6    CZ   CE1   122.19  3.000
 5ND  CE2   CZ   CE1   118.67  3.000
 5ND  C1    CE2  CD2   121.90  3.000
 5ND  C1    CE2  CZ    118.99  3.000
 5ND  CD2   CE2  CZ    119.11  3.000
 5ND  HD2   CD2  CE2   118.70  3.000
 5ND  HD2   CD2  CG    119.89  3.000
 5ND  CE2   CD2  CG    121.41  3.000
 5ND  O3    C    N11   127.28  3.000
 5ND  O3    C    CA    126.64  3.000
 5ND  N11   C    CA    106.08  3.000
 5ND  H11   N11  C2    122.72  3.000
 5ND  H11   N11  C     124.46  3.000
 5ND  C2    N11  C     112.81  3.000
 5ND  O2    C2   N11   125.23  3.000
 5ND  O2    C2   N10   128.67  3.000
 5ND  N11   C2   N10   106.10  3.000
 5ND  H1    C1   C3    120.37  3.000
 5ND  H1    C1   CE2   119.00  3.000
 5ND  C3    C1   CE2   120.63  3.000
 5ND  H3    C3   C5    119.60  3.000
 5ND  H3    C3   C1    120.05  3.000
 5ND  C5    C3   C1    120.35  3.000
 5ND  H5    C5   C6    120.14  3.000
 5ND  H5    C5   C3    119.59  3.000
 5ND  C6    C5   C3    120.28  3.000
 5ND  H6    C6   C5    120.34  3.000
 5ND  H6    C6   CZ    119.05  3.000
 5ND  C5    C6   CZ    120.61  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
 5ND  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 5ND  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 5ND  CONST_03  C1   CE2  CD2  CG   180.00   0.0  0
 5ND  CONST_04  CE2  CD2  CG   CD1    0.00   0.0  0
 5ND  CONST_05  CE2  CZ   CE1  CD1    0.00   0.0  0
 5ND  CONST_06  C6   CZ   CE1  CD1  180.00   0.0  0
 5ND  CONST_07  CD2  CG   CD1  CE1    0.00   0.0  0
 5ND  CONST_08  CD2  CE2  CZ   CE1    0.00   0.0  0
 5ND  CONST_09  C1   CE2  CZ   CE1  180.00   0.0  0
 5ND  CONST_10  C5   C6   CZ   CE1  180.00   0.0  0
 5ND  CONST_11  C3   C1   CE2  CZ     0.00   0.0  0
 5ND  CONST_12  C3   C5   C6   CZ     0.00   0.0  0
 5ND  CONST_13  C5   C6   CZ   CE2    0.00   0.0  0
 5ND  CONST_14  C5   C3   C1   CE2    0.00   0.0  0
 5ND  CONST_15  C6   CZ   CE2  CD2  180.00   0.0  0
 5ND  CONST_16  C3   C1   CE2  CD2  180.00   0.0  0
 5ND  CONST_17  C6   CZ   CE2  C1     0.00   0.0  0
 5ND  CONST_18  C6   C5   C3   C1     0.00   0.0  0
 5ND  CONST_19  C    N11  C2   N10    0.00   0.0  0
 5ND  CONST_20  N11  C2   N10  CA     0.00   0.0  0
 5ND  CONST_21  C2   N11  C    CA     0.00   0.0  0
 5ND  CONST_22  CE1  CD1  CG   CB   180.00   0.0  0
 5ND  CONST_23  CE2  CD2  CG   CB   180.00   0.0  0
 5ND  CONST_24  O2   C2   N10  CA   180.00   0.0  0
 5ND  CONST_25  O2   C2   N11  C    180.00   0.0  0
 5ND  CONST_26  O3   C    N11  C2   180.00   0.0  0
 5ND  CONST_27  HE1  CE1  CD1  CG   180.00   0.0  0
 5ND  CONST_28  HD2  CD2  CG   CD1  180.00   0.0  0
 5ND  CONST_29  H6   C6   CZ   CE1    0.00   0.0  0
 5ND  CONST_30  HD1  CD1  CE1  CZ   180.00   0.0  0
 5ND  CONST_31  H1   C1   CE2  CZ   180.00   0.0  0
 5ND  CONST_32  H5   C5   C6   CZ   180.00   0.0  0
 5ND  CONST_33  H3   C3   C1   CE2  180.00   0.0  0
 5ND  CONST_34  H11  N11  C2   N10  180.00   0.0  0
 5ND  CONST_35  H10  N10  C2   N11  180.00   0.0  0
 5ND  Var_01    CD1  CG   CB   CA    75.82  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
 5ND  chir_01  CA  N10  CB  C  positiv

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
 5ND  plan-1  CB   0.020
 5ND  plan-1  CG   0.020
 5ND  plan-1  CD1  0.020
 5ND  plan-1  CE1  0.020
 5ND  plan-1  CZ   0.020
 5ND  plan-1  CE2  0.020
 5ND  plan-1  CD2  0.020
 5ND  plan-1  C1   0.020
 5ND  plan-1  C3   0.020
 5ND  plan-1  C5   0.020
 5ND  plan-1  C6   0.020
 5ND  plan-1  HD1  0.020
 5ND  plan-1  HD2  0.020
 5ND  plan-1  HE1  0.020
 5ND  plan-1  H6   0.020
 5ND  plan-1  H1   0.020
 5ND  plan-1  H3   0.020
 5ND  plan-1  H5   0.020
 5ND  plan-2  N10  0.020
 5ND  plan-2  CA   0.020
 5ND  plan-2  C    0.020
 5ND  plan-2  N11  0.020
 5ND  plan-2  C2   0.020
 5ND  plan-2  O2   0.020
 5ND  plan-2  O3   0.020
 5ND  plan-2  H10  0.020
 5ND  plan-2  H11  0.020

