# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 10:04:16 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2~{S})-5-carbamimidamido-2-(carboxyamino)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NCCC[C@H](NC(O)=O)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
 73N  73N  '(2~{S})-5-carbamimidamido-2-(carboxyamino)pentanoic acid'  L-peptide  27  15  .  2022-09-22  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_73N
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
 73N  C2   C  C      0   0.524  -4.7380   0.1582   0.0481
 73N  C9   C  CH2    0  -0.442   0.1460  -0.9207   0.0213
 73N  C12  C  CH1    0  -0.169   1.5248  -0.3280   0.3248
 73N  C20  C  C      0   0.390   2.5971  -1.4419   0.2641
 73N  N23  N  NH1    0  -0.648   1.7774   0.7929  -0.5450
 73N  N1   N  NH2    0  -0.813  -4.9940  -0.6656  -1.0228
 73N  N3   N  N      0  -0.722  -5.7192   0.6365   0.7248
 73N  N4   N  NH1    0  -0.650  -3.4088   0.3907   0.2988
 73N  C5   C  CH2    0  -0.253  -2.3473  -0.5181  -0.1014
 73N  C6   C  CH2    0  -0.448  -0.9975   0.0389   0.3196
 73N  O21  O  OC    -1  -0.632   2.5538  -2.2845   1.1882
 73N  O22  O  O      0  -0.609   3.3944  -1.4363  -0.6923
 73N  C25  C  C      0   0.500   2.9124   1.5944  -0.3337
 73N  O26  O  O      0  -0.657   3.3909   1.6168   0.8209
 73N  H1   H  HCH2   0   0.208   0.1079  -1.2303  -1.0307
 73N  H2   H  HCH2   0   0.224   0.0183  -1.8297   0.6131
 73N  H3   H  HCH1   0   0.200   1.5038   0.0409   1.3540
 73N  H4   H  HNH1   0   0.327   1.6413   0.5731  -1.5211
 73N  H5   H  HNH2   0   0.382  -4.3544  -0.6216  -1.7999
 73N  H6   H  HNH2   0   0.380  -5.9555  -0.6389  -1.3221
 73N  H7   H  H      0   0.310  -5.3856   1.1340   1.5426
 73N  H9   H  HNH1   0   0.378  -3.2419   0.8403   1.1864
 73N  H10  H  HCH2   0   0.217  -2.4905  -1.5191   0.3250
 73N  H11  H  HCH2   0   0.223  -2.3488  -0.6357  -1.1877
 73N  H12  H  HCH2   0   0.217  -1.0103   0.2482   1.3951
 73N  H13  H  HCH2   0   0.230  -0.8261   0.9940  -0.1822
 73N  OXT  O  OC    -1  -0.669   3.3109   2.2581  -1.3182

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
 73N  N3   C2   double  1.284  0.020  1.284
 73N  C2   N1   single  1.375  0.020  1.375
 73N  C2   N4   single  1.372  0.020  1.372
 73N  N4   C5   single  1.454  0.020  1.454
 73N  C5   C6   single  1.520  0.020  1.520
 73N  O22  C20  deloc   1.245  0.020  1.245
 73N  C6   C9   single  1.522  0.020  1.522
 73N  C20  O21  deloc   1.251  0.020  1.251
 73N  C20  C12  single  1.547  0.020  1.547
 73N  C9   C12  single  1.531  0.020  1.531
 73N  C12  N23  single  1.441  0.020  1.441
 73N  O26  C25  deloc   1.250  0.020  1.250
 73N  N23  C25  single  1.405  0.020  1.405
 73N  C9   H1   single  0.970  0.020  1.090
 73N  C9   H2   single  0.970  0.020  1.090
 73N  C12  H3   single  0.970  0.020  1.090
 73N  N23  H4   single  0.890  0.020  1.040
 73N  N1   H5   single  0.890  0.020  1.040
 73N  N1   H6   single  0.890  0.020  1.040
 73N  N3   H7   single  0.890  0.020  1.040
 73N  N4   H9   single  0.890  0.020  1.040
 73N  C5   H10  single  0.970  0.020  1.090
 73N  C5   H11  single  0.970  0.020  1.090
 73N  C6   H12  single  0.970  0.020  1.090
 73N  C6   H13  single  0.970  0.020  1.090
 73N  C25  OXT  deloc   1.252  0.020  1.252

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
 73N  N4   C2   N3   125.49  3.000
 73N  N4   C2   N1   115.09  3.000
 73N  N3   C2   N1   119.42  3.000
 73N  H2   C9   H1   106.29  3.000
 73N  H2   C9   C6   109.31  3.000
 73N  H1   C9   C6   109.85  3.000
 73N  H2   C9   C12  108.66  3.000
 73N  H1   C9   C12  109.31  3.000
 73N  C6   C9   C12  113.18  3.000
 73N  H3   C12  N23  108.00  3.000
 73N  H3   C12  C20  107.04  3.000
 73N  N23  C12  C20  114.51  3.000
 73N  H3   C12  C9   107.45  3.000
 73N  N23  C12  C9   109.83  3.000
 73N  C20  C12  C9   109.73  3.000
 73N  O22  C20  O21  126.33  3.000
 73N  O21  C20  C12  115.58  3.000
 73N  O22  C20  C12  118.07  3.000
 73N  H4   N23  C25  112.23  3.000
 73N  H4   N23  C12  112.98  3.000
 73N  C25  N23  C12  119.63  3.000
 73N  H6   N1   H5   112.06  3.000
 73N  H6   N1   C2   113.15  3.000
 73N  H5   N1   C2   117.15  3.000
 73N  H7   N3   C2   110.88  3.000
 73N  H9   N4   C5   113.58  3.000
 73N  H9   N4   C2   113.35  3.000
 73N  C5   N4   C2   123.44  3.000
 73N  H11  C5   H10  106.74  3.000
 73N  H11  C5   C6   108.43  3.000
 73N  H10  C5   C6   110.03  3.000
 73N  H11  C5   N4   109.88  3.000
 73N  H10  C5   N4   111.59  3.000
 73N  C6   C5   N4   110.07  3.000
 73N  H13  C6   H12  106.60  3.000
 73N  H13  C6   C5   109.43  3.000
 73N  H12  C6   C5   109.37  3.000
 73N  H13  C6   C9   110.07  3.000
 73N  H12  C6   C9   108.75  3.000
 73N  C5   C6   C9   112.45  3.000
 73N  OXT  C25  O26  126.49  3.000
 73N  OXT  C25  N23  116.17  3.000
 73N  O26  C25  N23  117.27  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
 73N  CONST_03  H7   N3   C2   N1   180.00   0.0  0
 73N  CONST_04  H9   N4   C2   N1   180.00   0.0  0
 73N  CONST_06  H6   N1   C2   N3     0.00   0.0  0
 73N  Var_01    C6   C5   N4   C2   179.66  30.0  3
 73N  Var_02    N4   C5   C6   C9   175.63  30.0  1
 73N  Var_03    C5   C6   C9   C12  174.94  30.0  1
 73N  Var_04    O26  C25  N23  C12  -24.51  30.0  2

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
 73N  chir_01  C12  C20  C9  N23  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
 73N  plan-1  C2   0.020
 73N  plan-1  N1   0.020
 73N  plan-1  N3   0.020
 73N  plan-1  N4   0.020
 73N  plan-1  C5   0.020
 73N  plan-1  H5   0.020
 73N  plan-1  H6   0.020
 73N  plan-1  H7   0.020
 73N  plan-1  H9   0.020
 73N  plan-2  C12  0.020
 73N  plan-2  C20  0.020
 73N  plan-2  O21  0.020
 73N  plan-2  O22  0.020
 73N  plan-3  N23  0.020
 73N  plan-3  C25  0.020
 73N  plan-3  O26  0.020
 73N  plan-3  OXT  0.020

