# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:55:28 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: (3R)-3-[(2S)-2-amino-3-oxopropyl]piperidine-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@H]1CCCN(C1)C(N)=N)C=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
 1PI  1PI  (3R)-3-[(2S)-2-amino-3-oxopropyl]piperidine-1-carboximidamide  L-peptide  32  14  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1PI
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
 1PI  C     C  C1    0   0.182  15.2759  -11.1682  18.6010
 1PI  N     N  NH2   0  -0.819  15.8261  -10.9010  20.9078
 1PI  O     O  O     0  -0.372  14.5539  -11.1031  17.6400
 1PI  C1    C  CH2   0  -0.432  12.1680  -13.1483  20.7162
 1PI  C2    C  CH2   0  -0.429  11.3315  -13.9455  21.7121
 1PI  C3    C  CH2   0  -0.323  12.0444  -14.0535  23.0553
 1PI  CA    C  CH1   0  -0.196  14.8320  -11.4850  20.0140
 1PI  CB    C  CH2   0  -0.455  13.4230  -10.9686  20.3143
 1PI  CD    C  CH2   0  -0.301  13.2533  -12.0086  22.6537
 1PI  NE    N  NT    0  -0.454  12.3972  -12.7381  23.5708
 1PI  CG    C  CH1   0  -0.237  12.5865  -11.7957  21.2944
 1PI  NH1   N  N     0  -0.711  11.4991  -10.7335  24.2921
 1PI  NH2   N  NH2   0  -0.837  10.6995  -12.7810  25.1573
 1PI  H4    H  H     0   0.195  16.3680  -11.0175  18.4980
 1PI  H     H  HNH2  0   0.366  15.5024  -10.9385  21.8645
 1PI  H2    H  HNH2  0   0.352  16.6788  -11.4473  20.8858
 1PI  H1    H  HCH2  0   0.232  11.6128  -12.9997  19.7861
 1PI  H1A   H  HCH2  0   0.215  13.0573  -13.7337  20.4544
 1PI  H2B   H  HCH2  0   0.220  10.3616  -13.4599  21.8599
 1PI  H2A   H  HCH2  0   0.233  11.1285  -14.9469  21.3249
 1PI  H3    H  HCH2  0   0.251  11.4338  -14.6026  23.7675
 1PI  H3A   H  HCH2  0   0.234  12.9706  -14.6246  22.9366
 1PI  HA    H  HCH1  0   0.258  14.8235  -12.5888  20.0550
 1PI  HB    H  HCH2  0   0.241  13.5148   -9.9421  20.6834
 1PI  HBA   H  HCH2  0   0.245  12.8578  -10.9082  19.3817
 1PI  HD    H  HCH2  0   0.231  14.1694  -12.5994  22.5315
 1PI  HDA   H  HCH2  0   0.250  13.5268  -11.0576  23.1086
 1PI  HG    H  HCH1  0   0.231  11.6735  -11.2174  21.4769
 1PI  HNH1  H  H     0   0.315  10.8938  -10.3553  25.0114
 1PI  HNH2  H  HNH2  0   0.384  10.2003  -12.2508  25.8541
 1PI  HNHA  H  HNH2  0   0.384  11.1107  -13.6097  25.5593
 1PI  CZ    C  C     0   0.550  11.5218  -12.0155  24.3517

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
 1PI  O    C     double  1.231  0.020  1.231
 1PI  C    CA    single  1.525  0.021  1.525
 1PI  C    H4    single  0.930  0.020  1.080
 1PI  CA   N     single  1.458  0.019  1.458
 1PI  N    H     single  0.860  0.020  0.860
 1PI  N    H2    single  0.890  0.020  1.040
 1PI  C1   CG    single  1.529  0.020  1.529
 1PI  C1   C2    single  1.525  0.020  1.525
 1PI  C1   H1    single  0.970  0.020  1.090
 1PI  C1   H1A   single  0.970  0.020  1.090
 1PI  C2   C3    single  1.525  0.020  1.525
 1PI  C2   H2B   single  0.970  0.020  1.090
 1PI  C2   H2A   single  0.970  0.020  1.090
 1PI  C3   NE    single  1.456  0.020  1.456
 1PI  C3   H3    single  0.970  0.020  1.090
 1PI  C3   H3A   single  0.970  0.020  1.090
 1PI  CA   CB    single  1.521  0.033  1.521
 1PI  CA   HA    single  0.970  0.020  0.970
 1PI  CB   CG    single  1.531  0.020  1.531
 1PI  CB   HB    single  0.970  0.020  1.090
 1PI  CB   HBA   single  0.970  0.020  1.090
 1PI  CG   CD    single  1.529  0.020  1.529
 1PI  CD   NE    single  1.451  0.020  1.451
 1PI  CD   HD    single  0.970  0.020  1.090
 1PI  CD   HDA   single  0.970  0.020  1.090
 1PI  NE   CZ    single  1.378  0.020  1.378
 1PI  CG   HG    single  0.970  0.020  1.090
 1PI  CZ   NH1   double  1.284  0.020  1.284
 1PI  CZ   NH2   single  1.382  0.020  1.382
 1PI  NH1  HNH1  single  0.890  0.020  1.040
 1PI  NH2  HNH2  single  0.890  0.020  1.040
 1PI  NH2  HNHA  single  0.890  0.020  1.040

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
 1PI  H4    C    CA    113.85  3.000
 1PI  H4    C    O     120.66  3.000
 1PI  CA    C    O     120.80  1.700
 1PI  H2    N    H     105.68  3.000
 1PI  H2    N    CA    110.15  3.000
 1PI  H     N    CA    114.00  3.000
 1PI  H1A   C1   H1    106.34  3.000
 1PI  H1A   C1   CG    109.91  3.000
 1PI  H1    C1   CG    109.90  3.000
 1PI  H1A   C1   C2    108.76  3.000
 1PI  H1    C1   C2    110.36  3.000
 1PI  CG    C1   C2    111.43  3.000
 1PI  H2A   C2   H2B   106.85  3.000
 1PI  H2A   C2   C3    109.52  3.000
 1PI  H2B   C2   C3    109.07  3.000
 1PI  H2A   C2   C1    110.45  3.000
 1PI  H2B   C2   C1    110.01  3.000
 1PI  C3    C2   C1    110.84  3.000
 1PI  H3A   C3   H3    106.43  3.000
 1PI  H3A   C3   NE    107.74  3.000
 1PI  H3    C3   NE    111.13  3.000
 1PI  H3A   C3   C2    109.70  3.000
 1PI  H3    C3   C2    110.51  3.000
 1PI  NE    C3   C2    111.18  3.000
 1PI  HA    CA   CB    109.00  3.000
 1PI  HA    CA   N     110.00  3.000
 1PI  CB    CA   N     110.40  1.500
 1PI  HA    CA   C     109.00  3.000
 1PI  CB    CA   C     110.50  1.500
 1PI  N     CA   C     111.00  2.800
 1PI  HBA   CB   HB    106.23  3.000
 1PI  HBA   CB   CG    107.08  3.000
 1PI  HB    CB   CG    109.67  3.000
 1PI  HBA   CB   CA    109.12  3.000
 1PI  HB    CB   CA    107.77  3.000
 1PI  CG    CB   CA    116.51  3.000
 1PI  HDA   CD   HD    107.89  3.000
 1PI  HDA   CD   CG    111.05  3.000
 1PI  HD    CD   CG    109.89  3.000
 1PI  HDA   CD   NE    108.85  3.000
 1PI  HD    CD   NE    107.00  3.000
 1PI  CG    CD   NE    112.00  3.000
 1PI  CZ    NE   CD    117.99  3.000
 1PI  CZ    NE   C3    121.37  3.000
 1PI  CD    NE   C3    111.92  3.000
 1PI  HG    CG   CD    106.78  3.000
 1PI  HG    CG   CB    106.06  3.000
 1PI  CD    CG   CB    113.96  3.000
 1PI  HG    CG   C1    107.56  3.000
 1PI  CD    CG   C1    109.40  3.000
 1PI  CB    CG   C1    112.66  3.000
 1PI  HNH1  NH1  CZ    110.52  3.000
 1PI  HNHA  NH2  HNH2  111.01  3.000
 1PI  HNHA  NH2  CZ    116.40  3.000
 1PI  HNH2  NH2  CZ    113.97  3.000
 1PI  NH2   CZ   NH1   124.72  3.000
 1PI  NH2   CZ   NE    114.69  3.000
 1PI  NH1   CZ   NE    120.58  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
 1PI  CONST_03  NH1   CZ   NE  CD    0.00   0.0  0
 1PI  CONST_04  NH2   CZ   NE  CD  180.00   0.0  0
 1PI  CONST_05  HNH1  NH1  CZ  NE  180.00   0.0  0
 1PI  CONST_06  HNH2  NH2  CZ  NE  180.00   0.0  0
 1PI  Var_01    NE    C3   C2  C1   54.80  30.0  1
 1PI  Var_02    CD    NE   C3  C2  -58.55  30.0  1
 1PI  Var_03    CG    C1   C2  C3  -52.60  30.0  1
 1PI  Var_04    CG    CD   NE  C3   59.67  30.0  1

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
 1PI  chir_01  CA  C   N   CB  negativ
 1PI  chir_02  CG  CD  CB  C1  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
 1PI  plan-1  C3    0.020
 1PI  plan-1  CD    0.020
 1PI  plan-1  NE    0.020
 1PI  plan-1  NH1   0.020
 1PI  plan-1  NH2   0.020
 1PI  plan-1  HNH1  0.020
 1PI  plan-1  HNH2  0.020
 1PI  plan-1  HNHA  0.020
 1PI  plan-1  CZ    0.020
 1PI  plan-2  C     0.020
 1PI  plan-2  O     0.020
 1PI  plan-2  CA    0.020
 1PI  plan-2  H4    0.020

