# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 17:26:21 2021
#   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  22  12  .  2022-08-10  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (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  -0.773  12.3218  -8.1470   -8.5302
 N9P  CA   C  CH1   0  -0.196  11.6885  -7.4384   -7.4494
 N9P  C    C  C     0   0.521  11.9801  -7.9222   -6.0316
 N9P  O    O  O     0  -0.451  11.7512  -7.2599   -5.0487
 N9P  CB   C  CH2   0  -0.541  10.1597  -7.4371   -7.6351
 N9P  CG   C  CR6   0   0.246   9.7660  -6.7919   -8.9290
 N9P  CD1  C  CR16  0  -0.379   9.4089  -7.5391  -10.0444
 N9P  CD2  C  CR16  0  -0.371   9.7556  -5.4073   -9.0637
 N9P  CE1  C  CR16  0  -0.064   9.0630  -6.8844  -11.2168
 N9P  CE2  C  CR16  0  -0.061   9.3992  -4.8471  -10.2799
 N9P  NZ   N  N     0  -0.412   9.0555  -5.5625  -11.3458
 N9P  O1   O  OH1   0  -0.583  12.4870  -9.1446   -5.9857
 N9P  H1   H  HNH2  0   0.359  13.3286  -8.1252   -8.4377
 N9P  H2   H  HNH2  0   0.347  12.0466  -9.1209   -8.5427
 N9P  H4   H  HCH1  0   0.284  12.0277  -6.3982   -7.4763
 N9P  H5   H  HCH2  0   0.277   9.6965  -6.9050   -6.8028
 N9P  H6   H  HCH2  0   0.269   9.7940  -8.4668   -7.6030
 N9P  H7   H  HCR6  0   0.260   9.3926  -8.6207  -10.0058
 N9P  H8   H  HCR6  0   0.263  10.0195  -4.7659   -8.2318
 N9P  H9   H  HCR6  0   0.261   8.7792  -7.4580  -12.0925
 N9P  H10  H  HCR6  0   0.261   9.3871  -3.7688  -10.3959
 N9P  H11  H  HOH1  0   0.483  12.6293  -9.4103   -5.0646

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  1.329  0.020  1.329
 N9P  CE1  CD1  aromatic  1.387  0.020  1.387
 N9P  CE2  CD2  aromatic  1.386  0.020  1.386
 N9P  CD1  CG   aromatic  1.389  0.020  1.389
 N9P  CD2  CG   aromatic  1.391  0.020  1.391
 N9P  CG   CB   single    1.498  0.020  1.498
 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    double    1.231  0.020  1.231
 N9P  C    O1   single    1.324  0.020  1.324
 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
 N9P  O1   H11  single    0.850  0.020  0.980

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   107.01  3.000
 N9P  H2   N    CA   111.31  3.000
 N9P  H1   N    CA   111.02  3.000
 N9P  H4   CA   CB   107.69  3.000
 N9P  H4   CA   C    105.36  3.000
 N9P  CB   CA   C    110.50  1.500
 N9P  H4   CA   N    108.25  3.000
 N9P  C    CA   N    111.00  2.800
 N9P  CB   CA   N    110.40  1.500
 N9P  O1   C    O    123.43  3.000
 N9P  O1   C    CA   113.45  3.000
 N9P  O    C    CA   120.80  1.700
 N9P  H6   CB   H5   107.15  3.000
 N9P  H6   CB   CG   110.06  3.000
 N9P  H5   CB   CG   109.70  3.000
 N9P  H6   CB   CA   109.13  3.000
 N9P  H5   CB   CA   109.26  3.000
 N9P  CG   CB   CA   111.43  3.000
 N9P  CD2  CG   CD1  117.11  3.000
 N9P  CD2  CG   CB   120.94  3.000
 N9P  CD1  CG   CB   121.95  3.000
 N9P  H7   CD1  CE1  119.88  3.000
 N9P  H7   CD1  CG   120.85  3.000
 N9P  CE1  CD1  CG   119.28  3.000
 N9P  H8   CD2  CE2  119.83  3.000
 N9P  H8   CD2  CG   120.88  3.000
 N9P  CE2  CD2  CG   119.29  3.000
 N9P  H9   CE1  NZ   116.52  3.000
 N9P  H9   CE1  CD1  119.88  3.000
 N9P  NZ   CE1  CD1  123.60  3.000
 N9P  H10  CE2  NZ   116.52  3.000
 N9P  H10  CE2  CD2  119.91  3.000
 N9P  NZ   CE2  CD2  123.57  3.000
 N9P  CE2  NZ   CE1  117.15  3.000
 N9P  H11  O1   C    110.01  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  CONST_13  H11  O1   C    CA   180.00   0.0  0
 N9P  Var_01    CD1  CG   CB   CA   101.55  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
 N9P  plan-2  H11  0.020

