# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 20:52:26 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 1-[(2S)-pyrrolidin-2-yl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1CCCN1
#
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
 P2Y  P2Y  1-[(2S)-pyrrolidin-2-yl]methanamine  L-peptide  19  7  .  2022-09-22  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_P2Y
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
 P2Y  NA    N  NH2   0  -0.807  -0.4450  -0.0326   2.6117
 P2Y  C     C  CH2   0  -0.290   0.5854   0.2313   1.6179
 P2Y  CA    C  CH1   0  -0.055   0.2140  -0.3503   0.2662
 P2Y  N     N  NH1   0  -0.620  -1.0090   0.2388  -0.2686
 P2Y  CD    C  CH2   0  -0.287  -1.0167  -0.1116  -1.6806
 P2Y  CG    C  CH2   0  -0.455   0.4238   0.1680  -2.1124
 P2Y  CB    C  CH2   0  -0.455   1.2490  -0.0543  -0.8290
 P2Y  HNA1  H  HNH2  0   0.349  -0.1043   0.2232   3.5293
 P2Y  HNA2  H  HNH2  0   0.339  -1.2372   0.5742   2.4405
 P2Y  H1    H  HCH2  0   0.218   1.5128  -0.2418   1.9506
 P2Y  H2    H  HCH2  0   0.186   0.8069   1.3008   1.4854
 P2Y  HA    H  HCH1  0   0.196   0.1133  -1.4424   0.3798
 P2Y  H     H  HNH1  0   0.344  -1.8266  -0.1336   0.1984
 P2Y  HD3   H  HCH2  0   0.224  -1.7501   0.4806  -2.2316
 P2Y  HD2   H  HCH2  0   0.194  -1.2564  -1.1714  -1.8505
 P2Y  HG3   H  HCH2  0   0.230   0.5265   1.1959  -2.4624
 P2Y  HG2   H  HCH2  0   0.231   0.7326  -0.4818  -2.9311
 P2Y  HB2   H  HCH2  0   0.226   1.8252   0.8394  -0.5791
 P2Y  HB3   H  HCH2  0   0.233   1.9603  -0.8738  -0.9258

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
 P2Y  NA  C     single  1.456  0.020  1.456
 P2Y  NA  HNA1  single  0.890  0.020  1.040
 P2Y  NA  HNA2  single  0.890  0.020  1.040
 P2Y  C   CA    single  1.525  0.021  1.525
 P2Y  C   H1    single  0.970  0.020  1.090
 P2Y  C   H2    single  0.970  0.020  1.090
 P2Y  CA  N     single  1.466  0.015  1.466
 P2Y  CA  CB    single  1.530  0.020  1.530
 P2Y  CA  HA    single  0.970  0.020  0.970
 P2Y  N   CD    single  1.473  0.014  1.473
 P2Y  N   H     single  0.860  0.020  1.020
 P2Y  CD  CG    single  1.530  0.020  1.530
 P2Y  CD  HD3   single  0.970  0.020  1.090
 P2Y  CD  HD2   single  0.970  0.020  1.090
 P2Y  CG  CB    single  1.542  0.020  1.542
 P2Y  CG  HG3   single  0.970  0.020  1.090
 P2Y  CG  HG2   single  0.970  0.020  1.090
 P2Y  CB  HB2   single  0.970  0.020  1.090
 P2Y  CB  HB3   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
 P2Y  HNA2  NA  HNA1  105.39  3.000
 P2Y  HNA2  NA  C     109.25  3.000
 P2Y  HNA1  NA  C     109.57  3.000
 P2Y  H2    C   H1    106.66  3.000
 P2Y  H2    C   CA    108.33  3.000
 P2Y  H1    C   CA    108.24  3.000
 P2Y  H2    C   NA    113.64  3.000
 P2Y  H1    C   NA    108.32  3.000
 P2Y  CA    C   NA    111.43  3.000
 P2Y  HA    CA  CB    109.00  3.000
 P2Y  HA    CA  N     110.00  3.000
 P2Y  CB    CA  N     103.00  1.100
 P2Y  HA    CA  C     109.00  3.000
 P2Y  CB    CA  C     110.10  1.900
 P2Y  N     CA  C     112.10  2.500
 P2Y  H     N   CD    110.78  3.000
 P2Y  H     N   CA    111.06  3.000
 P2Y  CD    N   CA    105.24  3.000
 P2Y  HD2   CD  HD3   107.36  3.000
 P2Y  HD2   CD  CG    109.75  3.000
 P2Y  HD3   CD  CG    113.01  3.000
 P2Y  HD2   CD  N     112.53  3.000
 P2Y  HD3   CD  N     111.26  3.000
 P2Y  CG    CD  N     103.20  1.500
 P2Y  HG2   CG  HG3   107.11  3.000
 P2Y  HG2   CG  CB    112.81  3.000
 P2Y  HG3   CG  CB    110.65  3.000
 P2Y  HG2   CG  CD    111.70  3.000
 P2Y  HG3   CG  CD    110.58  3.000
 P2Y  CB    CG  CD    104.04  3.000
 P2Y  HB3   CB  HB2   106.94  3.000
 P2Y  HB3   CB  CG    112.58  3.000
 P2Y  HB2   CB  CG    110.78  3.000
 P2Y  HB3   CB  CA    111.01  3.000
 P2Y  HB2   CB  CA    110.49  3.000
 P2Y  CG    CB  CA    105.11  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
 P2Y  Var_01  CG    CD  N   CA  -44.43  30.0  1
 P2Y  Var_02  CD    CG  CB  CA   -3.77  30.0  1
 P2Y  Var_03  CB    CG  CD  N    28.52  30.0  1
 P2Y  Var_04  HNA1  NA  C   CA  170.38  30.0  3

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
 P2Y  chir_01  CA  C  N  CB  negativ

