# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 06:24:53 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-(1-methylpyridinium-3-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1cccc(C[C@H](N)C(O)=O)c1
#
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
 PRR  PRR  3-(1-methylpyridinium-3-yl)-L-alanine  L-peptide  25  13  .  2012-08-28  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_PRR
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
 PRR  N     N  NH2    0  -0.816  16.8898  -17.3686  23.3616
 PRR  CA    C  CH1    0  -0.208  17.1773  -18.1238  24.5667
 PRR  C     C  C      0   0.414  15.9906  -19.0429  24.9784
 PRR  O     O  O      0  -0.588  15.0688  -19.1752  24.1507
 PRR  N1    N  NR6    1  -0.410  20.9726  -15.8055  25.2237
 PRR  C2    C  CR16   0   0.077  20.7565  -14.6521  24.5759
 PRR  C3    C  CR16   0  -0.340  19.4742  -14.2502  24.2920
 PRR  C4    C  CR16   0  -0.120  18.4095  -15.0497  24.6785
 PRR  C5    C  CH2    0  -0.503  17.5314  -17.1753  25.7290
 PRR  C8    C  CR6    0   0.020  18.6397  -16.2485  25.3481
 PRR  C9    C  CR16   0   0.046  19.9548  -16.5898  25.6019
 PRR  OXT   O  OC    -1  -0.598  16.0837  -19.5791  26.0975
 PRR  H     H  HNH2   0   0.338  17.6663  -17.4060  22.7170
 PRR  H2    H  HNH2   0   0.342  16.0979  -17.8095  22.9098
 PRR  HA    H  HCH1   0   0.223  18.0406  -18.7913  24.4258
 PRR  H3    H  HCR6   0   0.309  19.3187  -13.3164  23.7722
 PRR  H4    H  HCR6   0   0.293  17.3954  -14.7395  24.4692
 PRR  H51   H  HCH2   0   0.249  16.6506  -16.5864  25.9947
 PRR  H52   H  HCH2   0   0.252  17.8156  -17.7572  26.6050
 PRR  H9    H  HCR6   0   0.338  20.2181  -17.5026  26.1179
 PRR  H101  H  HCH3   0   0.287  22.3614  -17.1694  25.9970
 PRR  H102  H  HCH3   0   0.293  22.9205  -16.2400  24.5934
 PRR  H103  H  HCH3   0   0.293  22.7997  -15.4612  26.1877
 PRR  C10   C  CH3    0  -0.534  22.3562  -16.1954  25.5206
 PRR  HC2   H  HCR6   0   0.343  21.6276  -14.0743  24.3039

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
 PRR  N    CA    single    1.458  0.019  1.458
 PRR  N    H     single    0.860  0.020  0.860
 PRR  N    H2    single    0.890  0.020  1.040
 PRR  CA   C     single    1.525  0.021  1.525
 PRR  CA   C5    single    1.541  0.020  1.541
 PRR  CA   HA    single    0.970  0.020  0.970
 PRR  C    O     deloc     1.231  0.020  1.231
 PRR  C    OXT   deloc     1.244  0.020  1.244
 PRR  N1   C2    aromatic  1.340  0.020  1.340
 PRR  N1   C9    aromatic  1.339  0.020  1.339
 PRR  N1   C10   single    1.468  0.020  1.468
 PRR  C2   C3    aromatic  1.373  0.020  1.373
 PRR  C2   HC2   single    0.930  0.020  1.080
 PRR  C3   C4    aromatic  1.386  0.020  1.386
 PRR  C3   H3    single    0.930  0.020  1.080
 PRR  C4   C8    aromatic  1.392  0.020  1.392
 PRR  C4   H4    single    0.930  0.020  1.080
 PRR  C5   C8    single    1.494  0.020  1.494
 PRR  C5   H51   single    0.970  0.020  1.090
 PRR  C5   H52   single    0.970  0.020  1.090
 PRR  C8   C9    aromatic  1.382  0.020  1.382
 PRR  C9   H9    single    0.930  0.020  1.080
 PRR  C10  H101  single    0.970  0.020  1.090
 PRR  C10  H102  single    0.970  0.020  1.090
 PRR  C10  H103  single    0.970  0.020  1.090

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
 PRR  H2    N    H     107.48  3.000
 PRR  H2    N    CA    107.39  3.000
 PRR  H     N    CA    114.00  3.000
 PRR  HA    CA   C5    106.84  3.000
 PRR  HA    CA   C     110.00  3.000
 PRR  C5    CA   C     109.82  3.000
 PRR  HA    CA   N     110.00  3.000
 PRR  C5    CA   N     110.58  3.000
 PRR  C     CA   N     111.00  2.800
 PRR  OXT   C    O     127.38  3.000
 PRR  OXT   C    CA    120.80  1.700
 PRR  O     C    CA    120.80  1.700
 PRR  C10   N1   C9    120.23  3.000
 PRR  C10   N1   C2    118.57  3.000
 PRR  C9    N1   C2    121.19  3.000
 PRR  HC2   C2   C3    122.98  3.000
 PRR  HC2   C2   N1    116.87  3.000
 PRR  C3    C2   N1    120.15  3.000
 PRR  H3    C3   C4    121.48  3.000
 PRR  H3    C3   C2    119.14  3.000
 PRR  C4    C3   C2    119.38  3.000
 PRR  H4    C4   C8    119.69  3.000
 PRR  H4    C4   C3    120.07  3.000
 PRR  C8    C4   C3    120.24  3.000
 PRR  H52   C5   H51   107.62  3.000
 PRR  H52   C5   C8    110.05  3.000
 PRR  H51   C5   C8    109.01  3.000
 PRR  H52   C5   CA    109.73  3.000
 PRR  H51   C5   CA    109.26  3.000
 PRR  C8    C5   CA    111.09  3.000
 PRR  C9    C8   C5    120.39  3.000
 PRR  C9    C8   C4    117.27  3.000
 PRR  C5    C8   C4    122.28  3.000
 PRR  H9    C9   C8    121.86  3.000
 PRR  H9    C9   N1    116.37  3.000
 PRR  C8    C9   N1    121.77  3.000
 PRR  H103  C10  H102  109.86  3.000
 PRR  H103  C10  H101  109.58  3.000
 PRR  H102  C10  H101  109.61  3.000
 PRR  H103  C10  N1    109.24  3.000
 PRR  H102  C10  N1    109.14  3.000
 PRR  H101  C10  N1    109.39  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
 PRR  CONST_01  C4    C3   C2  N1     0.00   0.0  0
 PRR  CONST_02  C4    C8   C9  N1     0.00   0.0  0
 PRR  CONST_03  C8    C9   N1  C2     0.00   0.0  0
 PRR  CONST_04  C8    C4   C3  C2     0.00   0.0  0
 PRR  CONST_05  C9    N1   C2  C3     0.00   0.0  0
 PRR  CONST_06  C9    C8   C4  C3     0.00   0.0  0
 PRR  CONST_07  C5    C8   C9  N1   180.00   0.0  0
 PRR  CONST_08  C10   N1   C2  C3   180.00   0.0  0
 PRR  CONST_09  C5    C8   C4  C3   180.00   0.0  0
 PRR  CONST_10  C10   N1   C9  C8   180.00   0.0  0
 PRR  CONST_11  H3    C3   C2  N1   180.00   0.0  0
 PRR  CONST_12  H9    C9   N1  C2   180.00   0.0  0
 PRR  CONST_13  H4    C4   C3  C2   180.00   0.0  0
 PRR  CONST_14  HC2   C2   C3  C4   180.00   0.0  0
 PRR  Var_01    C4    C8   C5  CA    85.42  30.0  2
 PRR  Var_02    H101  C10  N1  C2  -177.06  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
 PRR  chir_01  CA  N  C  C5  positiv

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
 PRR  plan-1  N1   0.020
 PRR  plan-1  C2   0.020
 PRR  plan-1  C3   0.020
 PRR  plan-1  C4   0.020
 PRR  plan-1  C5   0.020
 PRR  plan-1  C8   0.020
 PRR  plan-1  C9   0.020
 PRR  plan-1  H3   0.020
 PRR  plan-1  H4   0.020
 PRR  plan-1  H9   0.020
 PRR  plan-1  C10  0.020
 PRR  plan-1  HC2  0.020
 PRR  plan-2  CA   0.020
 PRR  plan-2  C    0.020
 PRR  plan-2  O    0.020
 PRR  plan-2  OXT  0.020

