# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 14:25:30 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N~2~-acetyl-N-methyl-N~5~-[N-(methylcarbamoyl)carbamimidoyl]-L-ornithinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)NC(=N)NCCC[C@H](NC(C)=O)C(=O)NC
#
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
 ZRG  ZRG  N~2~-acetyl-N-methyl-N~5~-[N-(methylcarbamoyl)carbamimidoyl]-L-ornithinamide  peptide  42  20  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZRG
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
 ZRG  CAC   C  CH3   0  -0.776  -3.2627   3.4676   0.9699
 ZRG  CAP   C  C     0   0.529  -3.4102   2.2141   0.1471
 ZRG  OAE   O  O     0  -0.504  -4.1996   2.1326  -0.7845
 ZRG  N     N  NH1   0  -0.629  -2.6016   1.1952   0.4840
 ZRG  CA    C  CH1   0  -0.184  -2.6603  -0.0762  -0.1868
 ZRG  C     C  C     0   0.549  -4.0066  -0.7575   0.0672
 ZRG  O     O  O     0  -0.494  -4.6072  -0.6292   1.1228
 ZRG  NAL   N  NH1   0  -0.624  -4.4295  -1.5456  -0.9271
 ZRG  CAB   C  CH3   0  -0.512  -5.6296  -2.3427  -0.8316
 ZRG  CB    C  CH2   0  -0.462  -1.5317  -0.9824   0.3090
 ZRG  CG    C  CH2   0  -0.469  -0.1486  -0.4748  -0.0754
 ZRG  CD    C  CH2   0  -0.220   0.9476  -1.4015   0.4270
 ZRG  NE    N  NH1   0  -0.669   2.2398  -0.8632   0.0794
 ZRG  CZ    C  C     0   0.624   3.3753  -1.5436   0.3498
 ZRG  NH1   N  N     0  -0.723   3.3429  -2.7550   0.7629
 ZRG  NH2   N  NH1   0  -0.765   4.5775  -0.8636   0.1203
 ZRG  CAR   C  C     0   0.754   4.7714   0.4630  -0.2062
 ZRG  OAF   O  O     0  -0.533   3.8558   1.2709  -0.3314
 ZRG  NAK   N  NH1   0  -0.663   6.0592   0.8050  -0.3775
 ZRG  CAA   C  CH3   0  -0.506   6.4454   2.1575  -0.7028
 ZRG  H1AC  H  HCH3  0   0.268  -2.8886   4.2716   0.3354
 ZRG  H2AC  H  HCH3  0   0.265  -4.2385   3.7765   1.3428
 ZRG  H3AC  H  HCH3  0   0.249  -2.5853   3.3575   1.8144
 ZRG  HN    H  HNH1  0   0.403  -2.0324   1.2750   1.3109
 ZRG  HA    H  HCH1  0   0.268  -2.5336   0.0789  -1.2638
 ZRG  HNAL  H  HNH1  0   0.405  -3.9106  -1.5701  -1.7889
 ZRG  H1AB  H  HCH3  0   0.237  -6.5248  -1.7229  -0.7637
 ZRG  H2AB  H  HCH3  0   0.251  -5.7058  -2.9566  -1.7243
 ZRG  H3AB  H  HCH3  0   0.239  -5.6016  -2.9998   0.0372
 ZRG  H1B   H  HCH2  0   0.245  -1.6101  -1.0910   1.3955
 ZRG  H2B   H  HCH2  0   0.257  -1.6816  -1.9795  -0.1114
 ZRG  H1G   H  HCH2  0   0.239  -0.0807  -0.3863  -1.1634
 ZRG  H2G   H  HCH2  0   0.233   0.0137   0.5279   0.3314
 ZRG  H1D   H  HCH2  0   0.215   0.8512  -1.5376   1.5116
 ZRG  H2D   H  HCH2  0   0.226   0.8303  -2.3914  -0.0199
 ZRG  HNE   H  HNH1  0   0.405   2.3275   0.1342  -0.0523
 ZRG  HH1   H  H     0   0.324   4.2732  -3.1326   0.8921
 ZRG  HNH2  H  HNH1  0   0.412   5.4024  -1.4281   0.2569
 ZRG  HNAK  H  HNH1  0   0.407   6.7873   0.1217  -0.2583
 ZRG  H1AA  H  HCH3  0   0.240   5.9400   2.5141  -1.5997
 ZRG  H2AA  H  HCH3  0   0.237   6.2347   2.8532   0.1106
 ZRG  H3AA  H  HCH3  0   0.252   7.5154   2.1668  -0.8889

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
 ZRG  CAB  NAL   single  1.444  0.020  1.444
 ZRG  CAC  CAP   single  1.507  0.020  1.507
 ZRG  NAL  C     single  1.337  0.020  1.337
 ZRG  C    O     double  1.231  0.020  1.231
 ZRG  C    CA    single  1.525  0.021  1.525
 ZRG  CAP  OAE   double  1.224  0.020  1.224
 ZRG  CAP  N     single  1.344  0.020  1.344
 ZRG  CA   N     single  1.458  0.019  1.458
 ZRG  CA   CB    single  1.521  0.033  1.521
 ZRG  CG   CB    single  1.523  0.020  1.523
 ZRG  CG   CD    single  1.521  0.020  1.521
 ZRG  CD   NE    single  1.442  0.020  1.442
 ZRG  NE   CZ    single  1.351  0.020  1.351
 ZRG  CZ   NH1   double  1.280  0.020  1.280
 ZRG  CZ   NH2   single  1.400  0.020  1.400
 ZRG  NH2  CAR   single  1.380  0.020  1.380
 ZRG  CAR  NAK   single  1.343  0.020  1.343
 ZRG  CAR  OAF   double  1.227  0.020  1.227
 ZRG  NAK  CAA   single  1.444  0.020  1.444
 ZRG  CAC  H1AC  single  0.970  0.020  1.090
 ZRG  CAC  H2AC  single  0.970  0.020  1.090
 ZRG  CAC  H3AC  single  0.970  0.020  1.090
 ZRG  N    HN    single  0.860  0.020  1.020
 ZRG  CA   HA    single  0.970  0.020  0.970
 ZRG  NAL  HNAL  single  0.860  0.020  1.020
 ZRG  CAB  H1AB  single  0.970  0.020  1.090
 ZRG  CAB  H2AB  single  0.970  0.020  1.090
 ZRG  CAB  H3AB  single  0.970  0.020  1.090
 ZRG  CB   H1B   single  0.970  0.020  1.090
 ZRG  CB   H2B   single  0.970  0.020  1.090
 ZRG  CG   H1G   single  0.970  0.020  1.090
 ZRG  CG   H2G   single  0.970  0.020  1.090
 ZRG  CD   H1D   single  0.970  0.020  1.090
 ZRG  CD   H2D   single  0.970  0.020  1.090
 ZRG  NE   HNE   single  0.890  0.020  1.040
 ZRG  NH1  HH1   single  0.890  0.020  1.040
 ZRG  NH2  HNH2  single  0.860  0.020  1.020
 ZRG  NAK  HNAK  single  0.860  0.020  1.020
 ZRG  CAA  H1AA  single  0.970  0.020  1.090
 ZRG  CAA  H2AA  single  0.970  0.020  1.090
 ZRG  CAA  H3AA  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
 ZRG  H3AC  CAC  H2AC  108.70  3.000
 ZRG  H3AC  CAC  H1AC  108.22  3.000
 ZRG  H2AC  CAC  H1AC  107.30  3.000
 ZRG  H3AC  CAC  CAP   113.61  3.000
 ZRG  H2AC  CAC  CAP   109.58  3.000
 ZRG  H1AC  CAC  CAP   109.22  3.000
 ZRG  N     CAP  OAE   121.90  3.000
 ZRG  N     CAP  CAC   115.79  3.000
 ZRG  OAE   CAP  CAC   122.30  3.000
 ZRG  HN    N    CA    118.42  3.000
 ZRG  HN    N    CAP   119.07  3.000
 ZRG  CA    N    CAP   121.92  3.000
 ZRG  HA    CA   CB    109.00  3.000
 ZRG  HA    CA   C     110.00  3.000
 ZRG  CB    CA   C     110.50  1.500
 ZRG  HA    CA   N     110.00  3.000
 ZRG  CB    CA   N     110.40  1.500
 ZRG  C     CA   N     111.00  2.800
 ZRG  NAL   C    O     123.30  3.000
 ZRG  O     C    CA    120.80  1.700
 ZRG  NAL   C    CA    114.66  3.000
 ZRG  HNAL  NAL  CAB   118.15  3.000
 ZRG  HNAL  NAL  C     119.21  3.000
 ZRG  CAB   NAL  C     122.62  3.000
 ZRG  H3AB  CAB  H2AB  108.44  3.000
 ZRG  H3AB  CAB  H1AB  108.30  3.000
 ZRG  H2AB  CAB  H1AB  108.35  3.000
 ZRG  H3AB  CAB  NAL   111.36  3.000
 ZRG  H2AB  CAB  NAL   108.42  3.000
 ZRG  H1AB  CAB  NAL   111.87  3.000
 ZRG  H2B   CB   H1B   106.35  3.000
 ZRG  H2B   CB   CG    109.38  3.000
 ZRG  H1B   CB   CG    110.40  3.000
 ZRG  H2B   CB   CA    108.34  3.000
 ZRG  H1B   CB   CA    109.12  3.000
 ZRG  CG    CB   CA    113.01  3.000
 ZRG  H2G   CG   H1G   106.65  3.000
 ZRG  H2G   CG   CD    109.19  3.000
 ZRG  H1G   CG   CD    109.46  3.000
 ZRG  H2G   CG   CB    110.26  3.000
 ZRG  H1G   CG   CB    109.54  3.000
 ZRG  CD    CG   CB    111.61  3.000
 ZRG  H2D   CD   H1D   106.41  3.000
 ZRG  H2D   CD   NE    109.62  3.000
 ZRG  H1D   CD   NE    111.29  3.000
 ZRG  H2D   CD   CG    109.86  3.000
 ZRG  H1D   CD   CG    109.80  3.000
 ZRG  NE    CD   CG    109.80  3.000
 ZRG  HNE   NE   CZ    116.77  3.000
 ZRG  HNE   NE   CD    118.55  3.000
 ZRG  CZ    NE   CD    121.11  3.000
 ZRG  NH2   CZ   NH1   122.28  3.000
 ZRG  NH2   CZ   NE    116.37  3.000
 ZRG  NH1   CZ   NE    121.32  3.000
 ZRG  HH1   NH1  CZ    111.77  3.000
 ZRG  HNH2  NH2  CAR   117.08  3.000
 ZRG  HNH2  NH2  CZ    114.09  3.000
 ZRG  CAR   NH2  CZ    128.78  3.000
 ZRG  NAK   CAR  OAF   122.31  3.000
 ZRG  OAF   CAR  NH2   123.51  3.000
 ZRG  NAK   CAR  NH2   114.18  3.000
 ZRG  HNAK  NAK  CAA   118.01  3.000
 ZRG  HNAK  NAK  CAR   120.39  3.000
 ZRG  CAA   NAK  CAR   121.58  3.000
 ZRG  H3AA  CAA  H2AA  108.21  3.000
 ZRG  H3AA  CAA  H1AA  108.25  3.000
 ZRG  H2AA  CAA  H1AA  108.39  3.000
 ZRG  H3AA  CAA  NAK   108.07  3.000
 ZRG  H2AA  CAA  NAK   112.20  3.000
 ZRG  H1AA  CAA  NAK   111.60  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
 ZRG  CONST_01  CA    N    CAP  CAC   180.00   0.0  0
 ZRG  CONST_02  CA    N    CAP  OAE     0.00   0.0  0
 ZRG  CONST_03  CAB   NAL  C    CA    180.00   0.0  0
 ZRG  CONST_04  CAB   NAL  C    O       0.00   0.0  0
 ZRG  CONST_05  OAF   CAR  NH2  CZ      0.00   0.0  0
 ZRG  CONST_06  CAA   NAK  CAR  OAF     0.00   0.0  0
 ZRG  CONST_07  NH1   CZ   NE   CD      0.00   0.0  0
 ZRG  CONST_08  NH2   CZ   NE   CD    180.00   0.0  0
 ZRG  CONST_09  CAR   NH2  CZ   NE      0.00   0.0  0
 ZRG  CONST_10  NAK   CAR  NH2  CZ    180.00   0.0  0
 ZRG  CONST_11  CAR   NH2  CZ   NH1   180.00   0.0  0
 ZRG  CONST_12  CAA   NAK  CAR  NH2   180.00   0.0  0
 ZRG  CONST_13  HN    N    CAP  CAC     0.00   0.0  0
 ZRG  CONST_14  HNAL  NAL  C    CA      0.00   0.0  0
 ZRG  CONST_15  HNH2  NH2  CAR  OAF   180.00   0.0  0
 ZRG  CONST_16  HNAK  NAK  CAR  OAF   180.00   0.0  0
 ZRG  CONST_17  HH1   NH1  CZ   NE    180.00   0.0  0
 ZRG  CONST_18  HNE   NE   CZ   NH1   180.00   0.0  0
 ZRG  Var_01    CD    CG   CB   CA   -179.73  30.0  1
 ZRG  Var_02    NE    CD   CG   CB   -178.18  30.0  3
 ZRG  Var_03    CZ    NE   CD   CG   -176.18  30.0  3
 ZRG  Var_04    H1AC  CAC  CAP  OAE   -64.11  30.0  3
 ZRG  Var_05    H1AB  CAB  NAL  C      65.64  30.0  3
 ZRG  Var_06    H1AA  CAA  NAK  CAR   -55.46  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
 ZRG  chir_01  CA  C  N  CB  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
 ZRG  plan-1  CAC   0.020
 ZRG  plan-1  CAP   0.020
 ZRG  plan-1  OAE   0.020
 ZRG  plan-1  N     0.020
 ZRG  plan-1  CA    0.020
 ZRG  plan-1  HN    0.020
 ZRG  plan-2  CA    0.020
 ZRG  plan-2  C     0.020
 ZRG  plan-2  O     0.020
 ZRG  plan-2  NAL   0.020
 ZRG  plan-2  CAB   0.020
 ZRG  plan-2  HNAL  0.020
 ZRG  plan-3  CD    0.020
 ZRG  plan-3  NE    0.020
 ZRG  plan-3  CZ    0.020
 ZRG  plan-3  NH1   0.020
 ZRG  plan-3  NH2   0.020
 ZRG  plan-3  CAR   0.020
 ZRG  plan-3  OAF   0.020
 ZRG  plan-3  NAK   0.020
 ZRG  plan-3  CAA   0.020
 ZRG  plan-3  HNE   0.020
 ZRG  plan-3  HH1   0.020
 ZRG  plan-3  HNH2  0.020
 ZRG  plan-3  HNAK  0.020

