# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:45:38 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2S)-2-amino-3-naphthalen-1-ylpropanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cccc2ccccc12)C(N)=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
 NAM  NAM  '(2S)-2-amino-3-naphthalen-1-ylpropanamide (non-preferred name)'  L-peptide  30  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_NAM
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
 NAM  N     N  NH2   0  -0.782   1.1429   1.3297   2.1856
 NAM  CA    C  CH1   0  -0.212   0.0085   0.4503   2.0132
 NAM  CB    C  CH2   0  -0.569   0.3009  -0.8545   1.2288
 NAM  C     C  C     0   0.522  -0.5195   0.0518   3.3851
 NAM  O     O  O     0  -0.491   0.2400  -0.2528   4.2930
 NAM  NXT   N  NH2   0  -0.799  -1.8537   0.0111   3.4927
 NAM  CG    C  CR6   0   0.123   0.7579  -0.5775  -0.1731
 NAM  CD1   C  CR16  0  -0.340   2.1007  -0.5542  -0.4588
 NAM  CE1   C  CR16  0  -0.243   2.5809  -0.2461  -1.7474
 NAM  CZ1   C  CR16  0  -0.333   1.7050   0.0436  -2.7543
 NAM  CE2   C  CR66  0   0.115   0.3112   0.0306  -2.5126
 NAM  CH1   C  CR16  0  -0.310  -0.6101   0.3238  -3.5457
 NAM  CP    C  CR16  0  -0.261  -1.9574   0.3097  -3.3117
 NAM  CH2   C  CR16  0  -0.251  -2.4433  -0.0037  -2.0270
 NAM  CZ2   C  CR16  0  -0.335  -1.5751  -0.2909  -1.0082
 NAM  CD2   C  CR66  0   0.091  -0.1735  -0.2823  -1.2129
 NAM  H     H  HNH2  0   0.355   1.4914   1.6167   1.2800
 NAM  H2    H  HNH2  0   0.343   1.8993   0.8330   2.6409
 NAM  HA    H  HCH1  0   0.262  -0.7638   1.0127   1.4788
 NAM  HB2   H  HCH2  0   0.269   1.0814  -1.4055   1.7597
 NAM  HB3   H  HCH2  0   0.259  -0.5847  -1.4947   1.2362
 NAM  HNX1  H  HNH2  0   0.403  -2.2926  -0.3002   4.3445
 NAM  HNX2  H  HNH2  0   0.408  -2.4575   0.3040   2.7443
 NAM  HD1   H  HCR6  0   0.253   2.8123  -0.7834   0.3259
 NAM  HE1   H  HCR6  0   0.257   3.6475  -0.2394  -1.9304
 NAM  HZ1   H  HCR6  0   0.255   2.0651   0.2860  -3.7469
 NAM  HH1   H  HCR6  0   0.256  -0.2289   0.5624  -4.5313
 NAM  HP    H  HCR6  0   0.258  -2.6523   0.5357  -4.1099
 NAM  HH2   H  HCR6  0   0.259  -3.5101  -0.0196  -1.8461
 NAM  HZ2   H  HCR6  0   0.239  -1.9764  -0.5373  -0.0342

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
 NAM  N    CA    single    1.458  0.019  1.458
 NAM  N    H     single    0.860  0.020  0.860
 NAM  N    H2    single    0.890  0.020  1.040
 NAM  CA   CB    single    1.521  0.033  1.521
 NAM  CA   C     single    1.525  0.021  1.525
 NAM  CA   HA    single    0.970  0.020  0.970
 NAM  CB   CG    single    1.500  0.020  1.500
 NAM  CB   HB2   single    0.970  0.020  1.090
 NAM  CB   HB3   single    0.970  0.020  1.090
 NAM  C    O     double    1.231  0.020  1.231
 NAM  C    NXT   single    1.339  0.020  1.339
 NAM  NXT  HNX1  single    0.860  0.020  1.020
 NAM  NXT  HNX2  single    0.860  0.020  1.020
 NAM  CG   CD1   aromatic  1.373  0.020  1.373
 NAM  CG   CD2   aromatic  1.427  0.020  1.427
 NAM  CD1  CE1   aromatic  1.409  0.020  1.409
 NAM  CD1  HD1   single    0.930  0.020  1.080
 NAM  CE1  CZ1   aromatic  1.366  0.020  1.366
 NAM  CE1  HE1   single    0.930  0.020  1.080
 NAM  CZ1  CE2   aromatic  1.415  0.020  1.415
 NAM  CZ1  HZ1   single    0.930  0.020  1.080
 NAM  CE2  CH1   aromatic  1.415  0.020  1.415
 NAM  CE2  CD2   aromatic  1.422  0.020  1.422
 NAM  CH1  CP    aromatic  1.368  0.020  1.368
 NAM  CH1  HH1   single    0.930  0.020  1.080
 NAM  CP   CH2   aromatic  1.409  0.020  1.409
 NAM  CP   HP    single    0.930  0.020  1.080
 NAM  CH2  CZ2   aromatic  1.369  0.020  1.369
 NAM  CH2  HH2   single    0.930  0.020  1.080
 NAM  CZ2  CD2   aromatic  1.416  0.020  1.416
 NAM  CZ2  HZ2   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
 NAM  H2    N    H     106.51  3.000
 NAM  H2    N    CA    109.95  3.000
 NAM  H     N    CA    114.00  3.000
 NAM  HA    CA   C     109.00  3.000
 NAM  HA    CA   CB    109.00  3.000
 NAM  C     CA   CB    110.50  1.500
 NAM  HA    CA   N     110.00  3.000
 NAM  C     CA   N     111.00  2.800
 NAM  CB    CA   N     110.40  1.500
 NAM  HB3   CB   HB2   106.26  3.000
 NAM  HB3   CB   CG    111.18  3.000
 NAM  HB2   CB   CG    109.24  3.000
 NAM  HB3   CB   CA    109.68  3.000
 NAM  HB2   CB   CA    108.25  3.000
 NAM  CG    CB   CA    112.02  3.000
 NAM  NXT   C    O     123.49  3.000
 NAM  NXT   C    CA    115.20  3.000
 NAM  O     C    CA    120.80  1.700
 NAM  HNX2  NXT  HNX1  117.24  3.000
 NAM  HNX2  NXT  C     121.99  3.000
 NAM  HNX1  NXT  C     120.76  3.000
 NAM  CD2   CG   CD1   118.90  3.000
 NAM  CD2   CG   CB    121.35  3.000
 NAM  CD1   CG   CB    119.70  3.000
 NAM  HD1   CD1  CE1   118.98  3.000
 NAM  HD1   CD1  CG    119.20  3.000
 NAM  CE1   CD1  CG    121.82  3.000
 NAM  HE1   CE1  CZ1   120.41  3.000
 NAM  HE1   CE1  CD1   119.46  3.000
 NAM  CZ1   CE1  CD1   120.13  3.000
 NAM  HZ1   CZ1  CE2   119.08  3.000
 NAM  HZ1   CZ1  CE1   120.66  3.000
 NAM  CE2   CZ1  CE1   120.27  3.000
 NAM  CD2   CE2  CH1   119.41  3.000
 NAM  CD2   CE2  CZ1   119.60  3.000
 NAM  CH1   CE2  CZ1   120.99  3.000
 NAM  HH1   CH1  CP    120.30  3.000
 NAM  HH1   CH1  CE2   118.74  3.000
 NAM  CP    CH1  CE2   120.96  3.000
 NAM  HP    CP   CH2   119.84  3.000
 NAM  HP    CP   CH1   120.29  3.000
 NAM  CH2   CP   CH1   119.87  3.000
 NAM  HH2   CH2  CZ2   119.85  3.000
 NAM  HH2   CH2  CP    119.72  3.000
 NAM  CZ2   CH2  CP    120.44  3.000
 NAM  HZ2   CZ2  CD2   119.90  3.000
 NAM  HZ2   CZ2  CH2   118.85  3.000
 NAM  CD2   CZ2  CH2   121.25  3.000
 NAM  CZ2   CD2  CE2   118.08  3.000
 NAM  CZ2   CD2  CG    122.64  3.000
 NAM  CE2   CD2  CG    119.28  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
 NAM  CONST_01  CZ1   CE1  CD1  CG     0.00   0.0  0
 NAM  CONST_02  CZ1   CE2  CD2  CG     0.00   0.0  0
 NAM  CONST_03  CH1   CE2  CD2  CG   180.00   0.0  0
 NAM  CONST_04  CH2   CZ2  CD2  CG   180.00   0.0  0
 NAM  CONST_05  CE2   CD2  CG   CD1    0.00   0.0  0
 NAM  CONST_06  CZ2   CD2  CG   CD1  180.00   0.0  0
 NAM  CONST_07  CE2   CZ1  CE1  CD1    0.00   0.0  0
 NAM  CONST_08  CD2   CG   CD1  CE1    0.00   0.0  0
 NAM  CONST_09  CH1   CE2  CZ1  CE1  180.00   0.0  0
 NAM  CONST_10  CD2   CE2  CZ1  CE1    0.00   0.0  0
 NAM  CONST_11  CP    CH1  CE2  CZ1  180.00   0.0  0
 NAM  CONST_12  CZ2   CD2  CE2  CZ1  180.00   0.0  0
 NAM  CONST_13  CH2   CP   CH1  CE2    0.00   0.0  0
 NAM  CONST_14  CH2   CZ2  CD2  CE2    0.00   0.0  0
 NAM  CONST_15  CZ2   CD2  CE2  CH1    0.00   0.0  0
 NAM  CONST_16  CZ2   CH2  CP   CH1    0.00   0.0  0
 NAM  CONST_17  CD2   CE2  CH1  CP     0.00   0.0  0
 NAM  CONST_18  CD2   CZ2  CH2  CP     0.00   0.0  0
 NAM  CONST_19  CE1   CD1  CG   CB   180.00   0.0  0
 NAM  CONST_20  CE2   CD2  CG   CB   180.00   0.0  0
 NAM  CONST_21  CZ2   CD2  CG   CB     0.00   0.0  0
 NAM  CONST_22  HE1   CE1  CD1  CG   180.00   0.0  0
 NAM  CONST_23  HZ2   CZ2  CD2  CG     0.00   0.0  0
 NAM  CONST_24  HZ1   CZ1  CE1  CD1  180.00   0.0  0
 NAM  CONST_25  HD1   CD1  CE1  CZ1  180.00   0.0  0
 NAM  CONST_26  HH1   CH1  CE2  CZ1    0.00   0.0  0
 NAM  CONST_27  HP    CP   CH1  CE2  180.00   0.0  0
 NAM  CONST_28  HH2   CH2  CP   CH1  180.00   0.0  0
 NAM  CONST_29  HNX1  NXT  C    CA   180.00   0.0  0
 NAM  CONST_30  HNX2  NXT  C    CA     0.00   0.0  0
 NAM  Var_01    CD1   CG   CB   CA    96.40  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
 NAM  chir_01  CA  N  CB  C  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
 NAM  plan-1  CB    0.020
 NAM  plan-1  CG    0.020
 NAM  plan-1  CD1   0.020
 NAM  plan-1  CE1   0.020
 NAM  plan-1  CZ1   0.020
 NAM  plan-1  CE2   0.020
 NAM  plan-1  CH1   0.020
 NAM  plan-1  CP    0.020
 NAM  plan-1  CH2   0.020
 NAM  plan-1  CZ2   0.020
 NAM  plan-1  CD2   0.020
 NAM  plan-1  HD1   0.020
 NAM  plan-1  HE1   0.020
 NAM  plan-1  HZ1   0.020
 NAM  plan-1  HH1   0.020
 NAM  plan-1  HP    0.020
 NAM  plan-1  HH2   0.020
 NAM  plan-1  HZ2   0.020
 NAM  plan-2  CA    0.020
 NAM  plan-2  C     0.020
 NAM  plan-2  O     0.020
 NAM  plan-2  NXT   0.020
 NAM  plan-2  HNX1  0.020
 NAM  plan-2  HNX2  0.020

