# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 11:50:18 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  30  16  .  2022-03-23  2022-11-17
;
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   0.578  -4.0047  -0.1343   0.0368
 NA8  N     N  NT3   1  -0.780  -2.0931  -1.1022   1.1757
 NA8  O2    O  O     0  -0.415  -4.6090  -1.1451   0.2779
 NA8  C1    C  CR16  0  -0.376   0.6803  -0.6303  -0.7540
 NA8  C2    C  CR6   0   0.074  -0.2129   0.3821  -0.5182
 NA8  C3    C  CR16  0  -0.281   0.2415   1.5814   0.0842
 NA8  C4    C  CR16  0  -0.296   1.5550   1.7391   0.4224
 NA8  C4A   C  CR66  0   0.105   2.4949   0.7079   0.1821
 NA8  C5    C  CR16  0  -0.308   3.8619   0.8439   0.5159
 NA8  C6    C  CR16  0  -0.256   4.7438  -0.1727   0.2658
 NA8  C7    C  CR16  0  -0.256   4.2991  -1.3717  -0.3297
 NA8  C8    C  CR16  0  -0.311   2.9811  -1.5308  -0.6629
 NA8  C8A   C  CR66  0   0.138   2.0483  -0.4970  -0.4166
 NA8  C9    C  CH2   0  -0.533  -1.6669   0.2290  -0.8684
 NA8  C10   C  CH1   0  -0.242  -2.5406   0.0652   0.3804
 NA8  OXT   O  OH1   0  -0.573  -4.4943   0.9316  -0.5560
 NA8  H10   H  HCH1  0   0.362  -2.4402   0.9376   1.0292
 NA8  HXT   H  HOH1  0   0.501  -5.4242   0.7966  -0.7981
 NA8  HN1   H  HNT3  0   0.475  -2.2219  -1.9875   0.6832
 NA8  HN2   H  HNT3  0   0.481  -1.1004  -1.0271   1.4080
 NA8  HN3   H  HNT3  0   0.485  -2.5926  -1.1790   2.0628
 NA8  H3    H  HCR6  0   0.263  -0.4625   2.3844   0.2686
 NA8  H91C  H  HCH2  0   0.308  -2.0197   1.1130  -1.4000
 NA8  H92C  H  HCH2  0   0.296  -1.8130  -0.6266  -1.5313
 NA8  H4    H  HCR6  0   0.260   1.8934   2.6630   0.8756
 NA8  H5    H  HCR6  0   0.258   4.2030   1.7654   0.9719
 NA8  H6    H  HCR6  0   0.262   5.7886  -0.0601   0.5239
 NA8  H7    H  HCR6  0   0.262   5.0076  -2.1663  -0.5234
 NA8  H8    H  HCR6  0   0.258   2.6377  -2.4508  -1.1202
 NA8  H1    H  HCR6  0   0.262   0.3456  -1.5526  -1.2170

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    double    1.202  0.020  1.202
 NA8  C11  C10   single    1.517  0.020  1.517
 NA8  C11  OXT   single    1.314  0.020  1.314
 NA8  N    C10   single    1.482  0.020  1.482
 NA8  C1   C2    aromatic  1.371  0.020  1.371
 NA8  C1   C8A   aromatic  1.415  0.020  1.415
 NA8  C2   C3    aromatic  1.417  0.020  1.417
 NA8  C2   C9    single    1.503  0.020  1.503
 NA8  C3   C4    aromatic  1.366  0.020  1.366
 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  1.411  0.020  1.411
 NA8  C7   C8    aromatic  1.369  0.020  1.369
 NA8  C8   C8A   aromatic  1.414  0.020  1.414
 NA8  C9   C10   single    1.533  0.020  1.533
 NA8  C10  H10   single    0.970  0.020  1.090
 NA8  OXT  HXT   single    0.850  0.020  0.980
 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   110.79  3.000
 NA8  OXT   C11  O2    125.82  3.000
 NA8  C10   C11  O2    123.39  3.000
 NA8  HN3   N    HN2   106.45  3.000
 NA8  HN3   N    HN1   106.98  3.000
 NA8  HN2   N    HN1   107.20  3.000
 NA8  HN3   N    C10   112.21  3.000
 NA8  HN2   N    C10   110.94  3.000
 NA8  HN1   N    C10   112.71  3.000
 NA8  H1    C1   C8A   118.68  3.000
 NA8  H1    C1   C2    120.02  3.000
 NA8  C8A   C1   C2    121.29  3.000
 NA8  C9    C2   C3    119.70  3.000
 NA8  C9    C2   C1    121.00  3.000
 NA8  C3    C2   C1    119.29  3.000
 NA8  H3    C3   C4    119.81  3.000
 NA8  H3    C3   C2    119.42  3.000
 NA8  C4    C3   C2    120.77  3.000
 NA8  H4    C4   C4A   119.01  3.000
 NA8  H4    C4   C3    120.17  3.000
 NA8  C4A   C4   C3    120.82  3.000
 NA8  C8A   C4A  C5    119.09  3.000
 NA8  C8A   C4A  C4    118.79  3.000
 NA8  C5    C4A  C4    122.12  3.000
 NA8  H5    C5   C6    120.39  3.000
 NA8  H5    C5   C4A   119.06  3.000
 NA8  C6    C5   C4A   120.55  3.000
 NA8  H6    C6   C7    119.58  3.000
 NA8  H6    C6   C5    120.07  3.000
 NA8  C7    C6   C5    120.35  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   119.03  3.000
 NA8  H8    C8   C7    120.45  3.000
 NA8  C8A   C8   C7    120.52  3.000
 NA8  C8    C8A  C4A   119.15  3.000
 NA8  C8    C8A  C1    121.83  3.000
 NA8  C4A   C8A  C1    119.03  3.000
 NA8  H92C  C9   H91C  107.21  3.000
 NA8  H92C  C9   C10   109.54  3.000
 NA8  H91C  C9   C10   107.43  3.000
 NA8  H92C  C9   C2    110.52  3.000
 NA8  H91C  C9   C2    110.12  3.000
 NA8  C10   C9   C2    111.86  3.000
 NA8  H10   C10  C9    110.26  3.000
 NA8  H10   C10  N     106.42  3.000
 NA8  C9    C10  N     110.44  3.000
 NA8  H10   C10  C11   109.18  3.000
 NA8  C9    C10  C11   112.31  3.000
 NA8  N     C10  C11   108.03  3.000
 NA8  HXT   OXT  C11   110.90  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  CONST_28  HXT  OXT  C11  O2     0.00   0.0  0
 NA8  Var_01    C10  C9   C2   C1   107.63  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
 NA8  plan-2  HXT  0.020

