# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:39:34 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (1S)-1-carboxy-2-naphthalen-2-ylethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@@H](Cc1ccc2ccccc2c1)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
 NA8  NA8  (1S)-1-carboxy-2-naphthalen-2-ylethanaminium  L-peptide  29  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NA8
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
 NA8  C11   C  C      0   0.453  -4.0159  -0.1581  -0.0774
 NA8  N     N  NT3    1  -0.781  -2.0990  -1.1505   1.1251
 NA8  O2    O  O      0  -0.584  -4.4820  -1.3010   0.0760
 NA8  C1    C  CR16   0  -0.388   0.7110  -0.6389  -0.7584
 NA8  C2    C  CR6    0   0.093  -0.1950   0.3706  -0.5579
 NA8  C3    C  CR16   0  -0.285   0.2477   1.5868   0.0206
 NA8  C4    C  CR16   0  -0.298   1.5559   1.7643   0.3682
 NA8  C4A   C  CR66   0   0.102   2.5065   0.7343   0.1655
 NA8  C5    C  CR16   0  -0.309   3.8682   0.8885   0.5124
 NA8  C6    C  CR16   0  -0.258   4.7605  -0.1278   0.3001
 NA8  C7    C  CR16   0  -0.257   4.3310  -1.3446  -0.2694
 NA8  C8    C  CR16   0  -0.314   3.0182  -1.5208  -0.6153
 NA8  C8A   C  CR66   0   0.137   2.0748  -0.4882  -0.4077
 NA8  C9    C  CH2    0  -0.532  -1.6470   0.1958  -0.9014
 NA8  C10   C  CH1    0  -0.248  -2.5332   0.0333   0.3352
 NA8  OXT   O  OC    -1  -0.580  -4.5574   0.8487  -0.5498
 NA8  H10   H  HCH1   0   0.303  -2.4295   0.9015   0.9862
 NA8  HN1   H  HNT3   0   0.450  -2.5655  -1.9831   0.7538
 NA8  HN2   H  HNT3   0   0.459  -1.0880  -1.2957   1.1161
 NA8  HN3   H  HNT3   0   0.470  -2.3783  -1.0743   2.1018
 NA8  H3    H  HCR6   0   0.257  -0.4652   2.3873   0.1800
 NA8  H91C  H  HCH2   0   0.286  -2.0182   1.0692  -1.4384
 NA8  H92C  H  HCH2   0   0.273  -1.7780  -0.6657  -1.5611
 NA8  H4    H  HCR6   0   0.258   1.8826   2.7020   0.8018
 NA8  H5    H  HCR6   0   0.257   4.1972   1.8238   0.9487
 NA8  H6    H  HCR6   0   0.260   5.8012  -0.0010   0.5685
 NA8  H7    H  HCR6   0   0.260   5.0468  -2.1395  -0.4330
 NA8  H8    H  HCR6   0   0.256   2.6867  -2.4549  -1.0531
 NA8  H1    H  HCR6   0   0.260   0.3906  -1.5733  -1.2078

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
 NA8  C11  O2    deloc     1.244  0.020  1.244
 NA8  C11  C10   single    1.551  0.020  1.551
 NA8  C11  OXT   deloc     1.237  0.020  1.237
 NA8  N    C10   single    1.488  0.020  1.488
 NA8  C1   C2    aromatic  1.371  0.020  1.371
 NA8  C1   C8A   aromatic  1.416  0.020  1.416
 NA8  C2   C3    aromatic  1.418  0.020  1.418
 NA8  C2   C9    single    1.502  0.020  1.502
 NA8  C3   C4    aromatic  1.365  0.020  1.365
 NA8  C4   C4A   aromatic  1.416  0.020  1.416
 NA8  C4A  C5    aromatic  1.414  0.020  1.414
 NA8  C4A  C8A   aromatic  1.418  0.020  1.418
 NA8  C5   C6    aromatic  1.369  0.020  1.369
 NA8  C6   C7    aromatic  1.410  0.020  1.410
 NA8  C7   C8    aromatic  1.369  0.020  1.369
 NA8  C8   C8A   aromatic  1.414  0.020  1.414
 NA8  C9   C10   single    1.530  0.020  1.530
 NA8  C10  H10   single    0.970  0.020  1.090
 NA8  N    HN1   single    0.890  0.020  1.040
 NA8  N    HN2   single    0.890  0.020  1.040
 NA8  N    HN3   single    0.890  0.020  1.040
 NA8  C1   H1    single    0.930  0.020  1.080
 NA8  C3   H3    single    0.930  0.020  1.080
 NA8  C9   H91C  single    0.970  0.020  1.090
 NA8  C9   H92C  single    0.970  0.020  1.090
 NA8  C4   H4    single    0.930  0.020  1.080
 NA8  C5   H5    single    0.930  0.020  1.080
 NA8  C6   H6    single    0.930  0.020  1.080
 NA8  C7   H7    single    0.930  0.020  1.080
 NA8  C8   H8    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
 NA8  OXT   C11  C10   114.82  3.000
 NA8  OXT   C11  O2    129.12  3.000
 NA8  C10   C11  O2    116.03  3.000
 NA8  HN3   N    HN2   106.88  3.000
 NA8  HN3   N    HN1   106.47  3.000
 NA8  HN2   N    HN1   109.39  3.000
 NA8  HN3   N    C10   111.68  3.000
 NA8  HN2   N    C10   113.41  3.000
 NA8  HN1   N    C10   108.75  3.000
 NA8  H1    C1   C8A   118.58  3.000
 NA8  H1    C1   C2    119.96  3.000
 NA8  C8A   C1   C2    121.45  3.000
 NA8  C9    C2   C3    119.67  3.000
 NA8  C9    C2   C1    121.30  3.000
 NA8  C3    C2   C1    119.01  3.000
 NA8  H3    C3   C4    119.80  3.000
 NA8  H3    C3   C2    119.23  3.000
 NA8  C4    C3   C2    120.97  3.000
 NA8  H4    C4   C4A   118.97  3.000
 NA8  H4    C4   C3    120.22  3.000
 NA8  C4A   C4   C3    120.81  3.000
 NA8  C8A   C4A  C5    119.12  3.000
 NA8  C8A   C4A  C4    118.73  3.000
 NA8  C5    C4A  C4    122.15  3.000
 NA8  H5    C5   C6    120.36  3.000
 NA8  H5    C5   C4A   119.05  3.000
 NA8  C6    C5   C4A   120.59  3.000
 NA8  H6    C6   C7    119.61  3.000
 NA8  H6    C6   C5    120.09  3.000
 NA8  C7    C6   C5    120.30  3.000
 NA8  H7    C7   C8    120.10  3.000
 NA8  H7    C7   C6    119.56  3.000
 NA8  C8    C7   C6    120.34  3.000
 NA8  H8    C8   C8A   118.99  3.000
 NA8  H8    C8   C7    120.43  3.000
 NA8  C8A   C8   C7    120.58  3.000
 NA8  C8    C8A  C4A   119.07  3.000
 NA8  C8    C8A  C1    121.90  3.000
 NA8  C4A   C8A  C1    119.03  3.000
 NA8  H92C  C9   H91C  107.05  3.000
 NA8  H92C  C9   C10   109.55  3.000
 NA8  H91C  C9   C10   106.62  3.000
 NA8  H92C  C9   C2    110.22  3.000
 NA8  H91C  C9   C2    110.39  3.000
 NA8  C10   C9   C2    112.80  3.000
 NA8  H10   C10  C9    110.06  3.000
 NA8  H10   C10  N     106.79  3.000
 NA8  C9    C10  N     110.15  3.000
 NA8  H10   C10  C11   110.37  3.000
 NA8  C9    C10  C11   110.60  3.000
 NA8  N     C10  C11   108.79  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
 NA8  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 NA8  CONST_02  C4   C4A  C8A  C1     0.00   0.0  0
 NA8  CONST_03  C5   C4A  C8A  C1   180.00   0.0  0
 NA8  CONST_04  C7   C8   C8A  C1   180.00   0.0  0
 NA8  CONST_05  C4A  C8A  C1   C2     0.00   0.0  0
 NA8  CONST_06  C8   C8A  C1   C2   180.00   0.0  0
 NA8  CONST_07  C4A  C4   C3   C2     0.00   0.0  0
 NA8  CONST_08  C8A  C1   C2   C3     0.00   0.0  0
 NA8  CONST_09  C5   C4A  C4   C3   180.00   0.0  0
 NA8  CONST_10  C8A  C4A  C4   C3     0.00   0.0  0
 NA8  CONST_11  C6   C5   C4A  C4   180.00   0.0  0
 NA8  CONST_12  C8   C8A  C4A  C4   180.00   0.0  0
 NA8  CONST_13  C7   C6   C5   C4A    0.00   0.0  0
 NA8  CONST_14  C7   C8   C8A  C4A    0.00   0.0  0
 NA8  CONST_15  C8   C8A  C4A  C5     0.00   0.0  0
 NA8  CONST_16  C8   C7   C6   C5     0.00   0.0  0
 NA8  CONST_17  C8A  C4A  C5   C6     0.00   0.0  0
 NA8  CONST_18  C8A  C8   C7   C6     0.00   0.0  0
 NA8  CONST_19  C9   C2   C3   C4   180.00   0.0  0
 NA8  CONST_20  C9   C2   C1   C8A  180.00   0.0  0
 NA8  CONST_21  H3   C3   C2   C1   180.00   0.0  0
 NA8  CONST_22  H8   C8   C8A  C1     0.00   0.0  0
 NA8  CONST_23  H4   C4   C3   C2   180.00   0.0  0
 NA8  CONST_24  H1   C1   C2   C3   180.00   0.0  0
 NA8  CONST_25  H5   C5   C4A  C4     0.00   0.0  0
 NA8  CONST_26  H6   C6   C5   C4A  180.00   0.0  0
 NA8  CONST_27  H7   C7   C6   C5   180.00   0.0  0
 NA8  Var_01    C10  C9   C2   C1   106.32  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
 NA8  chir_01  C10  C11  N  C9  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
 NA8  plan-1  C1   0.020
 NA8  plan-1  C2   0.020
 NA8  plan-1  C3   0.020
 NA8  plan-1  C4   0.020
 NA8  plan-1  C4A  0.020
 NA8  plan-1  C5   0.020
 NA8  plan-1  C6   0.020
 NA8  plan-1  C7   0.020
 NA8  plan-1  C8   0.020
 NA8  plan-1  C8A  0.020
 NA8  plan-1  C9   0.020
 NA8  plan-1  H3   0.020
 NA8  plan-1  H4   0.020
 NA8  plan-1  H5   0.020
 NA8  plan-1  H6   0.020
 NA8  plan-1  H7   0.020
 NA8  plan-1  H8   0.020
 NA8  plan-1  H1   0.020
 NA8  plan-2  C11  0.020
 NA8  plan-2  O2   0.020
 NA8  plan-2  C10  0.020
 NA8  plan-2  OXT  0.020

