# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:24:38 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: (3S)-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
 3GA  3GA  (3S)-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_3GA
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
 3GA  C2    C  CH2   0  -0.428  12.4181  -14.3723  22.3098
 3GA  C3    C  CH2   0  -0.309  12.6113  -13.7685  23.6984
 3GA  N     N  NH2   0  -0.802  16.0217  -12.0333  20.0755
 3GA  CA    C  CH1   0  -0.198  14.7423  -11.6063  19.5589
 3GA  C     C  C1    0   0.180  14.9012  -10.4926  18.5638
 3GA  O     O  O     0  -0.371  15.9542  -10.0641  18.1653
 3GA  CB    C  CH2   0  -0.418  13.8153  -11.1099  20.6744
 3GA  NE    N  NT    0  -0.475  12.0809  -12.4225  23.7525
 3GA  C1    C  CH2   0  -0.428  12.6636  -13.3249  21.2097
 3GA  CG    C  CH1   0  -0.309  13.4796  -12.1515  21.7400
 3GA  CD    C  CH2   0  -0.238  12.6948  -11.4577  22.8582
 3GA  NH1   N  N     0  -0.741  10.5512  -12.9916  25.3845
 3GA  NH2   N  NH2   0  -0.848  10.8206  -10.7426  24.7443
 3GA  H21   H  HCH2  0   0.225  13.1038  -15.2149  22.1991
 3GA  H22   H  HCH2  0   0.228  11.4083  -14.7764  22.2188
 3GA  H31   H  HCH2  0   0.264  12.1188  -14.3664  24.4586
 3GA  H32   H  HCH2  0   0.227  13.6766  -13.7492  23.9528
 3GA  H     H  HNH2  0   0.356  15.9167  -12.9128  20.5634
 3GA  HA    H  HCH1  0   0.245  14.2002  -12.3884  18.9962
 3GA  HB1   H  HCH2  0   0.241  14.2842  -10.2457  21.1570
 3GA  HB2   H  HCH2  0   0.231  12.8824  -10.7532  20.2247
 3GA  H11   H  HCH2  0   0.243  13.1587  -13.7916  20.3559
 3GA  H12   H  HCH2  0   0.222  11.7114  -12.9377  20.8333
 3GA  HG    H  HCH1  0   0.243  14.4194  -12.5277  22.1594
 3GA  HD1   H  HCH2  0   0.225  11.9237  -10.8490  22.3723
 3GA  HD2   H  HCH2  0   0.235  13.3601  -10.7686  23.3944
 3GA  HN11  H  H     0   0.311   9.8737  -12.5679  26.0064
 3GA  H2    H  HNH2  0   0.350  16.6633  -12.2148  19.3138
 3GA  HN21  H  HNH2  0   0.385   9.9319  -10.5335  25.1700
 3GA  HN22  H  HNH2  0   0.389  10.9945  -10.1492  23.9500
 3GA  H3    H  H     0   0.192  13.9418  -10.0876  18.1920
 3GA  CZ    C  C     0   0.574  11.1032  -12.0900  24.6475

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
 3GA  C2   C3    single  1.527  0.020  1.527
 3GA  C2   C1    single  1.539  0.020  1.539
 3GA  C2   H21   single  0.970  0.020  1.090
 3GA  C2   H22   single  0.970  0.020  1.090
 3GA  C3   NE    single  1.448  0.020  1.448
 3GA  C3   H31   single  0.970  0.020  1.090
 3GA  C3   H32   single  0.970  0.020  1.090
 3GA  N    CA    single  1.458  0.019  1.458
 3GA  N    H     single  0.860  0.020  0.860
 3GA  N    H2    single  0.890  0.020  1.040
 3GA  CA   C     single  1.525  0.021  1.525
 3GA  CA   CB    single  1.521  0.033  1.521
 3GA  CA   HA    single  0.970  0.020  0.970
 3GA  C    O     double  1.231  0.020  1.231
 3GA  C    H3    single  0.930  0.020  1.080
 3GA  CB   CG    single  1.527  0.020  1.527
 3GA  CB   HB1   single  0.970  0.020  1.090
 3GA  CB   HB2   single  0.970  0.020  1.090
 3GA  CZ   NE    single  1.367  0.020  1.367
 3GA  CZ   NH1   double  1.289  0.020  1.289
 3GA  CZ   NH2   single  1.380  0.020  1.380
 3GA  NE   CD    single  1.452  0.020  1.452
 3GA  C1   CG    single  1.525  0.020  1.525
 3GA  C1   H11   single  0.970  0.020  1.090
 3GA  C1   H12   single  0.970  0.020  1.090
 3GA  CG   CD    single  1.532  0.020  1.532
 3GA  CG   HG    single  0.970  0.020  1.090
 3GA  CD   HD1   single  0.970  0.020  1.090
 3GA  CD   HD2   single  0.970  0.020  1.090
 3GA  NH1  HN11  single  0.890  0.020  1.040
 3GA  NH2  HN21  single  0.890  0.020  1.040
 3GA  NH2  HN22  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
 3GA  H22   C2   H21   106.67  3.000
 3GA  H22   C2   C1    109.88  3.000
 3GA  H21   C2   C1    110.65  3.000
 3GA  H22   C2   C3    109.84  3.000
 3GA  H21   C2   C3    108.54  3.000
 3GA  C1    C2   C3    111.16  3.000
 3GA  H32   C3   H31   106.76  3.000
 3GA  H32   C3   NE    109.34  3.000
 3GA  H31   C3   NE    108.65  3.000
 3GA  H32   C3   C2    109.96  3.000
 3GA  H31   C3   C2    111.21  3.000
 3GA  NE    C3   C2    110.82  3.000
 3GA  H2    N    H     105.83  3.000
 3GA  H2    N    CA    110.21  3.000
 3GA  H     N    CA    114.00  3.000
 3GA  HA    CA   CB    109.00  3.000
 3GA  HA    CA   C     109.00  3.000
 3GA  CB    CA   C     110.50  1.500
 3GA  HA    CA   N     110.00  3.000
 3GA  CB    CA   N     110.40  1.500
 3GA  C     CA   N     111.00  2.800
 3GA  H3    C    O     121.13  3.000
 3GA  H3    C    CA    113.73  3.000
 3GA  O     C    CA    120.80  1.700
 3GA  HB2   CB   HB1   106.77  3.000
 3GA  HB2   CB   CG    108.74  3.000
 3GA  HB1   CB   CG    108.95  3.000
 3GA  HB2   CB   CA    108.77  3.000
 3GA  HB1   CB   CA    108.50  3.000
 3GA  CG    CB   CA    114.82  3.000
 3GA  CD    NE   CZ    122.98  3.000
 3GA  CD    NE   C3    116.10  3.000
 3GA  CZ    NE   C3    120.85  3.000
 3GA  H12   C1   H11   106.07  3.000
 3GA  H12   C1   CG    108.24  3.000
 3GA  H11   C1   CG    110.99  3.000
 3GA  H12   C1   C2    110.36  3.000
 3GA  H11   C1   C2    109.91  3.000
 3GA  CG    C1   C2    111.14  3.000
 3GA  HG    CG   CD    108.39  3.000
 3GA  HG    CG   C1    109.15  3.000
 3GA  CD    CG   C1    109.16  3.000
 3GA  HG    CG   CB    108.22  3.000
 3GA  CD    CG   CB    108.24  3.000
 3GA  C1    CG   CB    113.57  3.000
 3GA  HD2   CD   HD1   107.12  3.000
 3GA  HD2   CD   CG    109.29  3.000
 3GA  HD1   CD   CG    106.76  3.000
 3GA  HD2   CD   NE    111.88  3.000
 3GA  HD1   CD   NE    110.16  3.000
 3GA  CG    CD   NE    111.42  3.000
 3GA  HN11  NH1  CZ    110.19  3.000
 3GA  HN22  NH2  HN21  111.32  3.000
 3GA  HN22  NH2  CZ    119.00  3.000
 3GA  HN21  NH2  CZ    114.39  3.000
 3GA  NH2   CZ   NH1   123.72  3.000
 3GA  NH2   CZ   NE    115.47  3.000
 3GA  NH1   CZ   NE    120.72  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
 3GA  CONST_01  NH1   CZ   NE  C3    0.00   0.0  0
 3GA  CONST_02  NH2   CZ   NE  C3  180.00   0.0  0
 3GA  CONST_03  NH1   CZ   NE  CD  180.00   0.0  0
 3GA  CONST_04  NH2   CZ   NE  CD    0.00   0.0  0
 3GA  CONST_05  HN11  NH1  CZ  NE  180.00   0.0  0
 3GA  Var_01    CD    NE   C3  C2  -61.51  30.0  1
 3GA  Var_02    CG    C1   C2  C3   19.72  30.0  1
 3GA  Var_03    CG    CD   NE  C3   17.66  30.0  1
 3GA  Var_04    C1    C2   C3  NE   39.15  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
 3GA  chir_01  CA  N   C   CB  positiv
 3GA  chir_02  CG  CB  C1  CD  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
 3GA  plan-1  C3    0.020
 3GA  plan-1  NE    0.020
 3GA  plan-1  CD    0.020
 3GA  plan-1  NH1   0.020
 3GA  plan-1  NH2   0.020
 3GA  plan-1  HN11  0.020
 3GA  plan-1  HN21  0.020
 3GA  plan-1  HN22  0.020
 3GA  plan-1  CZ    0.020
 3GA  plan-2  CA    0.020
 3GA  plan-2  C     0.020
 3GA  plan-2  O     0.020
 3GA  plan-2  H3    0.020

