# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 22:13:27 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 3-pyridin-4-yl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccncc1)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
 N9P  N9P  '3-pyridin-4-yl-L-alanine '  L-peptide  21  12  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_N9P
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
 N9P  N    N  NH2    0  -0.779  12.2866  -8.2758   -8.4567
 N9P  CA   C  CH1    0  -0.213  11.6955  -7.4308   -7.4338
 N9P  C    C  C      0   0.383  12.0298  -7.8016   -5.9610
 N9P  O    O  O      0  -0.613  11.6158  -6.9992   -5.0986
 N9P  CB   C  CH2    0  -0.518  10.1700  -7.3912   -7.6187
 N9P  CG   C  CR6    0   0.245   9.7676  -6.7508   -8.9102
 N9P  CD1  C  CR16   0  -0.386   9.4041  -7.4876  -10.0318
 N9P  CD2  C  CR16   0  -0.370   9.7665  -5.3644   -9.0445
 N9P  CE1  C  CR16   0  -0.065   9.0676  -6.8251  -11.2030
 N9P  CE2  C  CR16   0  -0.064   9.4166  -4.7959  -10.2577
 N9P  NZ   N  N      0  -0.414   9.0709  -5.5029  -11.3294
 N9P  O1   O  OC    -1  -0.595  12.6710  -8.8506   -5.7645
 N9P  H1   H  HNH2   0   0.335  13.2951  -8.2127   -8.3866
 N9P  H2   H  HNH2   0   0.324  12.0786  -9.2414   -8.2270
 N9P  H4   H  HCH1   0   0.224  12.0684  -6.4122   -7.5946
 N9P  H5   H  HCH2   0   0.250   9.7306  -6.8362   -6.7896
 N9P  H6   H  HCH2   0   0.239   9.7786  -8.4121   -7.5684
 N9P  H7   H  HCR6   0   0.254   9.3759  -8.5692   -9.9980
 N9P  H8   H  HCR6   0   0.256  10.0337  -4.7293   -8.2085
 N9P  H9   H  HCR6   0   0.254   8.7816  -7.3938  -12.0817
 N9P  H10  H  HCR6   0   0.254   9.4120  -3.7165  -10.3681

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
 N9P  NZ   CE1  aromatic  1.328  0.020  1.328
 N9P  NZ   CE2  aromatic  1.330  0.020  1.330
 N9P  CE1  CD1  aromatic  1.387  0.020  1.387
 N9P  CE2  CD2  aromatic  1.385  0.020  1.385
 N9P  CD1  CG   aromatic  1.390  0.020  1.390
 N9P  CD2  CG   aromatic  1.393  0.020  1.393
 N9P  CG   CB   single    1.497  0.020  1.497
 N9P  N    CA   single    1.458  0.019  1.458
 N9P  CB   CA   single    1.521  0.033  1.521
 N9P  CA   C    single    1.525  0.021  1.525
 N9P  C    O    deloc     1.231  0.020  1.231
 N9P  C    O1   deloc     1.245  0.020  1.245
 N9P  N    H1   single    0.890  0.020  1.040
 N9P  N    H2   single    0.890  0.020  1.040
 N9P  CA   H4   single    0.970  0.020  1.090
 N9P  CB   H5   single    0.970  0.020  1.090
 N9P  CB   H6   single    0.970  0.020  1.090
 N9P  CD1  H7   single    0.930  0.020  1.080
 N9P  CD2  H8   single    0.930  0.020  1.080
 N9P  CE1  H9   single    0.930  0.020  1.080
 N9P  CE2  H10  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
 N9P  H2   N    H1   104.35  3.000
 N9P  H2   N    CA   108.11  3.000
 N9P  H1   N    CA   108.68  3.000
 N9P  H4   CA   CB   107.22  3.000
 N9P  H4   CA   C    106.69  3.000
 N9P  CB   CA   C    110.50  1.500
 N9P  H4   CA   N    107.38  3.000
 N9P  C    CA   N    111.00  2.800
 N9P  CB   CA   N    110.40  1.500
 N9P  O1   C    O    127.10  3.000
 N9P  O1   C    CA   117.46  3.000
 N9P  O    C    CA   120.80  1.700
 N9P  H6   CB   H5   107.21  3.000
 N9P  H6   CB   CG   110.04  3.000
 N9P  H5   CB   CG   109.27  3.000
 N9P  H6   CB   CA   108.99  3.000
 N9P  H5   CB   CA   108.76  3.000
 N9P  CG   CB   CA   112.43  3.000
 N9P  CD2  CG   CD1  116.71  3.000
 N9P  CD2  CG   CB   120.62  3.000
 N9P  CD1  CG   CB   122.66  3.000
 N9P  H7   CD1  CE1  119.82  3.000
 N9P  H7   CD1  CG   120.73  3.000
 N9P  CE1  CD1  CG   119.44  3.000
 N9P  H8   CD2  CE2  119.85  3.000
 N9P  H8   CD2  CG   120.59  3.000
 N9P  CE2  CD2  CG   119.56  3.000
 N9P  H9   CE1  NZ   116.44  3.000
 N9P  H9   CE1  CD1  119.83  3.000
 N9P  NZ   CE1  CD1  123.73  3.000
 N9P  H10  CE2  NZ   116.48  3.000
 N9P  H10  CE2  CD2  119.91  3.000
 N9P  NZ   CE2  CD2  123.61  3.000
 N9P  CE2  NZ   CE1  116.95  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
 N9P  CONST_01  NZ   CE1  CD1  CG     0.00   0.0  0
 N9P  CONST_02  NZ   CE2  CD2  CG     0.00   0.0  0
 N9P  CONST_03  CE2  NZ   CE1  CD1    0.00   0.0  0
 N9P  CONST_04  CE2  CD2  CG   CD1    0.00   0.0  0
 N9P  CONST_05  CE1  NZ   CE2  CD2    0.00   0.0  0
 N9P  CONST_06  CE1  CD1  CG   CD2    0.00   0.0  0
 N9P  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 N9P  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 N9P  CONST_09  H9   CE1  CD1  CG   180.00   0.0  0
 N9P  CONST_10  H10  CE2  CD2  CG   180.00   0.0  0
 N9P  CONST_11  H8   CD2  CG   CD1  180.00   0.0  0
 N9P  CONST_12  H7   CD1  CG   CD2  180.00   0.0  0
 N9P  Var_01    CD1  CG   CB   CA   100.13  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
 N9P  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
 N9P  plan-1  CB   0.020
 N9P  plan-1  CG   0.020
 N9P  plan-1  CD1  0.020
 N9P  plan-1  CD2  0.020
 N9P  plan-1  CE1  0.020
 N9P  plan-1  CE2  0.020
 N9P  plan-1  NZ   0.020
 N9P  plan-1  H7   0.020
 N9P  plan-1  H8   0.020
 N9P  plan-1  H9   0.020
 N9P  plan-1  H10  0.020
 N9P  plan-2  CA   0.020
 N9P  plan-2  C    0.020
 N9P  plan-2  O    0.020
 N9P  plan-2  O1   0.020

