# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 20:38:19 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: N~5~-(pyrazin-2-ylcarbonyl)-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=O)c1cnccn1)C(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
 08M  08M  N~5~-(pyrazin-2-ylcarbonyl)-L-ornithine  L-peptide  30  17  .  2022-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_08M
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
 08M  C21  C  C      0   0.402   5.2730   0.1004   0.1973
 08M  O22  O  O      0  -0.609   5.8010  -0.3389  -0.8466
 08M  C23  C  CH1    0  -0.230   3.8859   0.7678   0.0391
 08M  N24  N  NH2    0  -0.795   3.7101   1.5078  -1.2049
 08M  C31  C  CH2    0  -0.417   2.8113  -0.3179   0.1438
 08M  C32  C  CH2    0  -0.462   1.3949   0.2372   0.2013
 08M  C33  C  CH2    0  -0.236   0.3565  -0.8717   0.1809
 08M  N34  N  NH1    0  -0.636  -0.9881  -0.3374   0.2242
 08M  C35  C  C      0   0.540  -2.0379  -0.9316  -0.3425
 08M  O36  O  O      0  -0.515  -1.9893  -1.9726  -0.9850
 08M  C37  C  CR6    0   0.078  -3.3443  -0.2184  -0.1429
 08M  N38  N  N      0  -0.346  -3.3607   0.8845   0.5943
 08M  C39  C  CR16   0  -0.101  -4.5226   1.4900   0.7591
 08M  C40  C  CR16   0  -0.107  -5.6840   0.9890   0.1817
 08M  N41  N  N      0  -0.375  -5.6751  -0.1107  -0.5559
 08M  C42  C  CR16   0  -0.038  -4.5070  -0.7168  -0.7193
 08M  H18  H  HCH1   0   0.214   3.7375   1.4669   0.8693
 08M  H19  H  HNH2   0   0.351   4.3034   2.3293  -1.1841
 08M  H24  H  HCH2   0   0.238   2.9101  -0.9951  -0.7128
 08M  H25  H  HCH2   0   0.196   3.0003  -0.9233   1.0358
 08M  H26  H  HCH2   0   0.209   1.2813   0.8343   1.1129
 08M  H27  H  HCH2   0   0.239   1.2311   0.9135  -0.6398
 08M  H28  H  HCH2   0   0.224   0.4640  -1.4677  -0.7267
 08M  H29  H  HCH2   0   0.262   0.5108  -1.5521   1.0249
 08M  H30  H  HNH1   0   0.416  -1.1610   0.5015   0.7579
 08M  H31  H  HCR6   0   0.267  -4.5428   2.3886   1.3635
 08M  H32  H  HCR6   0   0.302  -6.6319   1.4935   0.3226
 08M  H33  H  HCR6   0   0.269  -4.4914  -1.6167  -1.3204
 08M  H2   H  HNH2   0   0.344   4.0970   0.9349  -1.9479
 08M  OXT  O  OC    -1  -0.685   5.7424   0.0341   1.3506

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
 08M  N24  C23  single    1.458  0.020  1.458
 08M  O22  C21  deloc     1.250  0.020  1.250
 08M  C21  C23  single    1.547  0.020  1.547
 08M  C23  C31  single    1.531  0.020  1.531
 08M  C31  C32  single    1.522  0.020  1.522
 08M  C32  C33  single    1.519  0.020  1.519
 08M  C33  N34  single    1.447  0.020  1.447
 08M  N34  C35  single    1.333  0.020  1.333
 08M  N38  C39  aromatic  1.321  0.020  1.321
 08M  N38  C37  aromatic  1.327  0.020  1.327
 08M  C39  C40  aromatic  1.390  0.020  1.390
 08M  C35  C37  single    1.502  0.020  1.502
 08M  C35  O36  double    1.224  0.020  1.224
 08M  C37  C42  aromatic  1.390  0.020  1.390
 08M  C40  N41  aromatic  1.324  0.020  1.324
 08M  C42  N41  aromatic  1.326  0.020  1.326
 08M  C23  H18  single    0.970  0.020  1.090
 08M  N24  H19  single    0.890  0.020  1.040
 08M  C31  H24  single    0.970  0.020  1.090
 08M  C31  H25  single    0.970  0.020  1.090
 08M  C32  H26  single    0.970  0.020  1.090
 08M  C32  H27  single    0.970  0.020  1.090
 08M  C33  H28  single    0.970  0.020  1.090
 08M  C33  H29  single    0.970  0.020  1.090
 08M  N34  H30  single    0.860  0.020  1.020
 08M  C39  H31  single    0.930  0.020  1.080
 08M  C40  H32  single    0.930  0.020  1.080
 08M  C42  H33  single    0.930  0.020  1.080
 08M  N24  H2   single    0.890  0.020  1.040
 08M  C21  OXT  deloc     1.247  0.020  1.247

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
 08M  OXT  C21  C23  117.06  3.000
 08M  OXT  C21  O22  126.51  3.000
 08M  C23  C21  O22  116.42  3.000
 08M  H18  C23  C31  107.80  3.000
 08M  H18  C23  N24  107.84  3.000
 08M  C31  C23  N24  109.49  3.000
 08M  H18  C23  C21  108.62  3.000
 08M  C31  C23  C21  108.44  3.000
 08M  N24  C23  C21  114.47  3.000
 08M  H2   N24  H19  104.45  3.000
 08M  H2   N24  C23  106.99  3.000
 08M  H19  N24  C23  108.86  3.000
 08M  H25  C31  H24  106.23  3.000
 08M  H25  C31  C32  109.36  3.000
 08M  H24  C31  C32  109.79  3.000
 08M  H25  C31  C23  109.07  3.000
 08M  H24  C31  C23  108.74  3.000
 08M  C32  C31  C23  113.39  3.000
 08M  H27  C32  H26  106.73  3.000
 08M  H27  C32  C33  109.83  3.000
 08M  H26  C32  C33  109.76  3.000
 08M  H27  C32  C31  109.66  3.000
 08M  H26  C32  C31  109.06  3.000
 08M  C33  C32  C31  111.67  3.000
 08M  H29  C33  H28  106.73  3.000
 08M  H29  C33  N34  109.70  3.000
 08M  H28  C33  N34  108.55  3.000
 08M  H29  C33  C32  110.29  3.000
 08M  H28  C33  C32  110.03  3.000
 08M  N34  C33  C32  111.41  3.000
 08M  H30  N34  C35  117.42  3.000
 08M  H30  N34  C33  118.81  3.000
 08M  C35  N34  C33  123.67  3.000
 08M  C37  C35  O36  120.54  3.000
 08M  O36  C35  N34  124.82  3.000
 08M  C37  C35  N34  114.64  3.000
 08M  C42  C37  N38  121.21  3.000
 08M  C42  C37  C35  120.15  3.000
 08M  N38  C37  C35  118.65  3.000
 08M  C39  N38  C37  117.48  3.000
 08M  H31  C39  C40  121.01  3.000
 08M  H31  C39  N38  117.80  3.000
 08M  C40  C39  N38  121.19  3.000
 08M  H32  C40  N41  117.72  3.000
 08M  H32  C40  C39  120.61  3.000
 08M  N41  C40  C39  121.67  3.000
 08M  C42  N41  C40  117.01  3.000
 08M  H33  C42  N41  117.46  3.000
 08M  H33  C42  C37  121.09  3.000
 08M  N41  C42  C37  121.45  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
 08M  CONST_01  C40  C39  N38  C37     0.00   0.0  0
 08M  CONST_02  C40  N41  C42  C37     0.00   0.0  0
 08M  CONST_03  N41  C40  C39  N38     0.00   0.0  0
 08M  CONST_04  N41  C42  C37  N38     0.00   0.0  0
 08M  CONST_05  C42  C37  N38  C39     0.00   0.0  0
 08M  CONST_06  C42  N41  C40  C39     0.00   0.0  0
 08M  CONST_07  C39  N38  C37  C35   180.00   0.0  0
 08M  CONST_08  N41  C42  C37  C35   180.00   0.0  0
 08M  CONST_09  H31  C39  N38  C37   180.00   0.0  0
 08M  CONST_10  H32  C40  C39  N38   180.00   0.0  0
 08M  CONST_11  H33  C42  C37  N38   180.00   0.0  0
 08M  CONST_12  C37  C35  N34  C33   180.00   0.0  0
 08M  CONST_13  H30  N34  C35  C37     0.00   0.0  0
 08M  CONST_14  O36  C35  N34  C33     0.00   0.0  0
 08M  Var_01    N38  C37  C35  N34    -2.20  30.0  2
 08M  Var_02    C33  C32  C31  C23   174.97  30.0  3
 08M  Var_03    N34  C33  C32  C31  -179.51  30.0  3
 08M  Var_04    C35  N34  C33  C32   149.43  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
 08M  chir_01  C23  N24  C21  C31  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
 08M  plan-1  C35  0.020
 08M  plan-1  C37  0.020
 08M  plan-1  N38  0.020
 08M  plan-1  C39  0.020
 08M  plan-1  C40  0.020
 08M  plan-1  N41  0.020
 08M  plan-1  C42  0.020
 08M  plan-1  H31  0.020
 08M  plan-1  H32  0.020
 08M  plan-1  H33  0.020
 08M  plan-2  C33  0.020
 08M  plan-2  N34  0.020
 08M  plan-2  C35  0.020
 08M  plan-2  O36  0.020
 08M  plan-2  C37  0.020
 08M  plan-2  H30  0.020
 08M  plan-3  C21  0.020
 08M  plan-3  O22  0.020
 08M  plan-3  C23  0.020
 08M  plan-3  OXT  0.020

