# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 07:52:20 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  33  16  .  2022-03-23  2022-03-23
;
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  -0.778   0.0416   2.9279   0.2848
 OPR  CA    C  CH1    0  -0.197   0.4642   1.5463   0.3769
 OPR  CB    C  CH2    0  -0.427  -0.5627   0.6282  -0.2995
 OPR  CG    C  CH2    0  -0.449  -1.9241   0.6743   0.3798
 OPR  CD    C  CH2    0  -0.271  -2.9221  -0.2543  -0.2935
 OPR  NE    N  NH1    0  -0.630  -4.2050  -0.1753   0.3717
 OPR  CZ    C  C      0   0.532  -5.3097  -0.8967   0.0061
 OPR  NH1   N  N      0  -0.731  -6.2870  -1.0013   0.8352
 OPR  NH2   N  NH2    0  -0.840  -5.3018  -1.3771  -1.2817
 OPR  C     C  C      0   0.392   1.8353   1.2658  -0.2388
 OPR  O     O  O      0  -0.409   2.2431   1.9296  -1.1669
 OPR  C1    C  CH2    0  -0.561   2.6192   0.1412   0.3765
 OPR  C2    C  CH2    0  -0.584   3.8782  -0.2607  -0.3657
 OPR  C3    C  C      0   0.418   4.7026  -1.3682   0.3167
 OPR  O3    O  O      0  -0.608   4.3863  -1.7003   1.4759
 OPR  H     H  HNH2   0   0.350   0.6708   3.5170   0.8161
 OPR  H2    H  HNH2   0   0.339   0.1157   3.2397  -0.6769
 OPR  HA    H  HCH1   0   0.247   0.5111   1.2730   1.4370
 OPR  HB2   H  HCH2   0   0.231  -0.6612   0.9198  -1.3511
 OPR  HB3   H  HCH2   0   0.237  -0.1920  -0.4008  -0.2984
 OPR  HG2   H  HCH2   0   0.226  -1.8122   0.3845   1.4301
 OPR  HG3   H  HCH2   0   0.239  -2.3073   1.6956   0.3707
 OPR  HD2   H  HCH2   0   0.230  -3.0327   0.0465  -1.3397
 OPR  HD3   H  HCH2   0   0.220  -2.5210  -1.2769  -0.2947
 OPR  HE    H  HNH1   0   0.375  -4.1711   0.0079   1.3621
 OPR  HH1   H  H      0   0.311  -7.0476  -1.5318   0.4276
 OPR  HH21  H  HNH2   0   0.399  -4.4166  -1.5952  -1.7100
 OPR  HH22  H  HNH2   0   0.388  -6.0022  -2.0705  -1.4860
 OPR  H11   H  HCH2   0   0.266   2.8553   0.4544   1.3998
 OPR  H12   H  HCH2   0   0.254   1.9483  -0.7140   0.5086
 OPR  H21   H  HCH2   0   0.226   3.6311  -0.5844  -1.3809
 OPR  H22   H  HCH2   0   0.233   4.5295   0.6103  -0.4920
 OPR  O31   O  OC    -1  -0.630   5.6445  -1.8357  -0.3565

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  1.520  0.020  1.520
 OPR  CG   HG2   single  0.970  0.020  1.090
 OPR  CG   HG3   single  0.970  0.020  1.090
 OPR  CD   NE    single  1.447  0.020  1.447
 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  1.375  0.020  1.375
 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  1.503  0.020  1.503
 OPR  C1   C2    single  1.516  0.020  1.516
 OPR  C1   H11   single  0.970  0.020  1.090
 OPR  C1   H12   single  0.970  0.020  1.090
 OPR  C2   C3    single  1.540  0.020  1.540
 OPR  C2   H21   single  0.970  0.020  1.090
 OPR  C2   H22   single  0.970  0.020  1.090
 OPR  C3   O3    deloc   1.247  0.020  1.247
 OPR  C3   O31   deloc   1.249  0.020  1.249

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     105.87  3.000
 OPR  H2    N    CA    109.42  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   106.37  3.000
 OPR  HB3   CB   CG    109.34  3.000
 OPR  HB2   CB   CG    109.87  3.000
 OPR  HB3   CB   CA    109.61  3.000
 OPR  HB2   CB   CA    108.90  3.000
 OPR  CG    CB   CA    112.56  3.000
 OPR  HG3   CG   HG2   106.95  3.000
 OPR  HG3   CG   CD    109.72  3.000
 OPR  HG2   CG   CD    109.28  3.000
 OPR  HG3   CG   CB    109.80  3.000
 OPR  HG2   CG   CB    109.18  3.000
 OPR  CD    CG   CB    111.78  3.000
 OPR  HD3   CD   HD2   106.97  3.000
 OPR  HD3   CD   NE    112.02  3.000
 OPR  HD2   CD   NE    109.56  3.000
 OPR  HD3   CD   CG    109.23  3.000
 OPR  HD2   CD   CG    108.78  3.000
 OPR  NE    CD   CG    110.19  3.000
 OPR  HE    NE   CZ    112.67  3.000
 OPR  HE    NE   CD    115.58  3.000
 OPR  CZ    NE   CD    124.32  3.000
 OPR  NH2   CZ   NH1   125.46  3.000
 OPR  NH2   CZ   NE    115.45  3.000
 OPR  NH1   CZ   NE    118.94  3.000
 OPR  HH1   NH1  CZ    110.72  3.000
 OPR  HH22  NH2  HH21  112.09  3.000
 OPR  HH22  NH2  CZ    115.27  3.000
 OPR  HH21  NH2  CZ    118.63  3.000
 OPR  C1    C    O     123.24  3.000
 OPR  C1    C    CA    116.12  3.000
 OPR  O     C    CA    120.80  1.700
 OPR  H12   C1   H11   104.04  3.000
 OPR  H12   C1   C2    111.16  3.000
 OPR  H11   C1   C2    110.73  3.000
 OPR  H12   C1   C     108.32  3.000
 OPR  H11   C1   C     106.31  3.000
 OPR  C2    C1   C     115.55  3.000
 OPR  H22   C2   H21   105.24  3.000
 OPR  H22   C2   C3    107.75  3.000
 OPR  H21   C2   C3    108.63  3.000
 OPR  H22   C2   C1    109.85  3.000
 OPR  H21   C2   C1    110.19  3.000
 OPR  C3    C2   C1    114.73  3.000
 OPR  O31   C3   O3    126.38  3.000
 OPR  O31   C3   C2    115.73  3.000
 OPR  O3    C3   C2    117.89  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  Var_01    CD    CG   CB  CA  -179.29  30.0  3
 OPR  Var_02    C2    C1   C   CA   171.33  30.0  3
 OPR  Var_03    NE    CD   CG  CB  -179.53  30.0  3
 OPR  Var_04    CZ    NE   CD  CG  -179.65  30.0  3
 OPR  Var_05    C3    C2   C1  C    177.18  30.0  3
 OPR  Var_06    O3    C3   C2  C1    -9.79  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

