# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 19:32:20 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (5S)-5-amino-8-carbamimidamido-4-oxooctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=N)C(=O)CCC(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
 OPR  OPR  '(5S)-5-amino-8-carbamimidamido-4-oxooctanoic acid'  peptide  34  16  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OPR
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
 OPR  N     N  NH2   0  -0.777   0.0489   2.9057   0.4604
 OPR  CA    C  CH1   0  -0.198   0.4620   1.5192   0.4715
 OPR  CB    C  CH2   0  -0.430  -0.5726   0.6468  -0.2523
 OPR  CG    C  CH2   0  -0.445  -1.9339   0.6670   0.4281
 OPR  CD    C  CH2   0  -0.271  -2.9392  -0.2064  -0.3057
 OPR  NE    N  NH1   0  -0.630  -4.2292  -0.1422   0.3452
 OPR  CZ    C  C     0   0.533  -5.3166  -0.8934  -0.0137
 OPR  NH1   N  N     0  -0.730  -6.4785  -0.5497   0.4171
 OPR  NH2   N  NH2   0  -0.840  -5.0403  -2.0247  -0.7435
 OPR  C     C  C     0   0.396   1.8247   1.2689  -0.1706
 OPR  O     O  O     0  -0.400   2.2392   1.9806  -1.0573
 OPR  C1    C  CH2   0  -0.570   2.6051   0.0973   0.3626
 OPR  C2    C  CH2   0  -0.581   3.8617  -0.2115  -0.4257
 OPR  C3    C  C     0   0.557   4.6440  -1.3576   0.1528
 OPR  O3    O  O     0  -0.444   4.3269  -2.0023   1.1211
 OPR  H     H  HNH2  0   0.352   0.6804   3.4599   1.0250
 OPR  H2    H  HNH2  0   0.341   0.1197   3.2726  -0.4815
 OPR  HA    H  HCH1  0   0.252   0.5152   1.1851   1.5134
 OPR  HB2   H  HCH2  0   0.233  -0.6675   0.9939  -1.2870
 OPR  HB3   H  HCH2  0   0.238  -0.2112  -0.3842  -0.3067
 OPR  HG2   H  HCH2  0   0.230  -1.8353   0.3158   1.4593
 OPR  HG3   H  HCH2  0   0.236  -2.2995   1.6953   0.4756
 OPR  HD2   H  HCH2  0   0.220  -2.9908   0.1046  -1.3582
 OPR  HD3   H  HCH2  0   0.230  -2.5783  -1.2384  -0.2953
 OPR  HE    H  HNH1  0   0.375  -4.4862   0.7603   0.7133
 OPR  HH1   H  H     0   0.311  -7.1840  -1.2052   0.1030
 OPR  HH21  H  HNH2  0   0.398  -4.2466  -2.0182  -1.3634
 OPR  HH22  H  HNH2  0   0.389  -5.8398  -2.4796  -1.1520
 OPR  H11   H  HCH2  0   0.288   2.8442   0.3288   1.4063
 OPR  H12   H  HCH2  0   0.277   1.9433  -0.7720   0.4124
 OPR  H21   H  HCH2  0   0.289   3.6209  -0.4540  -1.4645
 OPR  H22   H  HCH2  0   0.288   4.5185   0.6607  -0.4702
 OPR  O31   O  OH1   0  -0.597   5.7559  -1.5893  -0.5388
 OPR  H18   H  HOH1  0   0.479   6.2426  -2.3275  -0.1430

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
 OPR  N    CA    single  1.458  0.019  1.458
 OPR  N    H     single  0.860  0.020  0.860
 OPR  N    H2    single  0.890  0.020  1.040
 OPR  CA   CB    single  1.521  0.033  1.521
 OPR  CA   C     single  1.525  0.021  1.525
 OPR  CA   HA    single  0.970  0.020  0.970
 OPR  CB   CG    single  1.522  0.020  1.522
 OPR  CB   HB2   single  0.970  0.020  1.090
 OPR  CB   HB3   single  0.970  0.020  1.090
 OPR  CG   CD    single  1.521  0.020  1.521
 OPR  CG   HG2   single  0.970  0.020  1.090
 OPR  CG   HG3   single  0.970  0.020  1.090
 OPR  CD   NE    single  1.446  0.020  1.446
 OPR  CD   HD2   single  0.970  0.020  1.090
 OPR  CD   HD3   single  0.970  0.020  1.090
 OPR  NE   CZ    single  1.369  0.020  1.369
 OPR  NE   HE    single  0.890  0.020  1.040
 OPR  CZ   NH1   double  1.286  0.020  1.286
 OPR  CZ   NH2   single  1.374  0.020  1.374
 OPR  NH1  HH1   single  0.890  0.020  1.040
 OPR  NH2  HH21  single  0.890  0.020  1.040
 OPR  NH2  HH22  single  0.890  0.020  1.040
 OPR  C    O     double  1.231  0.020  1.231
 OPR  C    C1    single  1.505  0.020  1.505
 OPR  C1   C2    single  1.515  0.020  1.515
 OPR  C1   H11   single  0.970  0.020  1.090
 OPR  C1   H12   single  0.970  0.020  1.090
 OPR  C2   C3    single  1.503  0.020  1.503
 OPR  C2   H21   single  0.970  0.020  1.090
 OPR  C2   H22   single  0.970  0.020  1.090
 OPR  C3   O3    double  1.206  0.020  1.206
 OPR  C3   O31   single  1.330  0.020  1.330
 OPR  O31  H18   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
 OPR  H2    N    H     106.06  3.000
 OPR  H2    N    CA    109.52  3.000
 OPR  H     N    CA    114.00  3.000
 OPR  HA    CA   C     110.00  3.000
 OPR  HA    CA   CB    109.00  3.000
 OPR  C     CA   CB    110.50  1.500
 OPR  HA    CA   N     110.00  3.000
 OPR  C     CA   N     111.00  2.800
 OPR  CB    CA   N     110.40  1.500
 OPR  HB3   CB   HB2   106.28  3.000
 OPR  HB3   CB   CG    109.29  3.000
 OPR  HB2   CB   CG    109.91  3.000
 OPR  HB3   CB   CA    109.66  3.000
 OPR  HB2   CB   CA    108.89  3.000
 OPR  CG    CB   CA    112.62  3.000
 OPR  HG3   CG   HG2   106.94  3.000
 OPR  HG3   CG   CD    109.90  3.000
 OPR  HG2   CG   CD    109.28  3.000
 OPR  HG3   CG   CB    109.35  3.000
 OPR  HG2   CG   CB    109.67  3.000
 OPR  CD    CG   CB    111.59  3.000
 OPR  HD3   CD   HD2   106.97  3.000
 OPR  HD3   CD   NE    109.39  3.000
 OPR  HD2   CD   NE    112.12  3.000
 OPR  HD3   CD   CG    108.63  3.000
 OPR  HD2   CD   CG    109.31  3.000
 OPR  NE    CD   CG    110.30  3.000
 OPR  HE    NE   CZ    112.61  3.000
 OPR  HE    NE   CD    115.56  3.000
 OPR  CZ    NE   CD    124.47  3.000
 OPR  NH2   CZ   NH1   125.42  3.000
 OPR  NH2   CZ   NE    115.53  3.000
 OPR  NH1   CZ   NE    118.88  3.000
 OPR  HH1   NH1  CZ    110.64  3.000
 OPR  HH22  NH2  HH21  112.28  3.000
 OPR  HH22  NH2  CZ    115.33  3.000
 OPR  HH21  NH2  CZ    118.69  3.000
 OPR  C1    C    O     122.66  3.000
 OPR  C1    C    CA    116.19  3.000
 OPR  O     C    CA    120.80  1.700
 OPR  H12   C1   H11   104.88  3.000
 OPR  H12   C1   C2    111.31  3.000
 OPR  H11   C1   C2    110.96  3.000
 OPR  H12   C1   C     108.72  3.000
 OPR  H11   C1   C     106.63  3.000
 OPR  C2    C1   C     113.85  3.000
 OPR  H22   C2   H21   105.70  3.000
 OPR  H22   C2   C3    108.14  3.000
 OPR  H21   C2   C3    108.12  3.000
 OPR  H22   C2   C1    110.91  3.000
 OPR  H21   C2   C1    110.91  3.000
 OPR  C3    C2   C1    112.75  3.000
 OPR  O31   C3   O3    122.99  3.000
 OPR  O31   C3   C2    111.58  3.000
 OPR  O3    C3   C2    125.43  3.000
 OPR  H18   O31  C3    109.90  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
 OPR  CONST_03  HH1   NH1  CZ  NE   180.00   0.0  0
 OPR  CONST_05  HH22  NH2  CZ  NE   180.00   0.0  0
 OPR  CONST_07  H18   O31  C3  C2   180.00   0.0  0
 OPR  Var_01    CD    CG   CB  CA  -179.87  30.0  3
 OPR  Var_02    C2    C1   C   CA   172.55  30.0  3
 OPR  Var_03    NE    CD   CG  CB  -178.65  30.0  3
 OPR  Var_04    CZ    NE   CD  CG  -174.87  30.0  3
 OPR  Var_05    C3    C2   C1  C    178.21  30.0  3
 OPR  Var_06    O3    C3   C2  C1     1.36  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
 OPR  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
 OPR  plan-1  CA    0.020
 OPR  plan-1  C     0.020
 OPR  plan-1  O     0.020
 OPR  plan-1  C1    0.020
 OPR  plan-2  CD    0.020
 OPR  plan-2  NE    0.020
 OPR  plan-2  CZ    0.020
 OPR  plan-2  NH1   0.020
 OPR  plan-2  NH2   0.020
 OPR  plan-2  HE    0.020
 OPR  plan-2  HH1   0.020
 OPR  plan-2  HH21  0.020
 OPR  plan-2  HH22  0.020
 OPR  plan-3  C2    0.020
 OPR  plan-3  C3    0.020
 OPR  plan-3  O3    0.020
 OPR  plan-3  O31   0.020
 OPR  plan-3  H18   0.020

