# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 11:09:11 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  29  15  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (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   0.526  -4.7022   0.2294  -0.0029
 73N  C9   C  CH2   0  -0.466   0.1467  -0.9062  -0.2230
 73N  C12  C  CH1   0  -0.186   1.5284  -0.4486   0.2553
 73N  C20  C  C     0   0.548   2.5970  -1.4560  -0.1487
 73N  N23  N  NH1   0  -0.638   1.8303   0.8514  -0.2719
 73N  N1   N  NH2   0  -0.814  -5.0717  -1.0568  -0.3170
 73N  N3   N  N     0  -0.719  -5.5851   1.1612  -0.0133
 73N  N4   N  NH1   0  -0.652  -3.3720   0.3966   0.2969
 73N  C5   C  CH2   0  -0.251  -2.3315  -0.4915  -0.1903
 73N  C6   C  CH2   0  -0.458  -0.9717  -0.0068   0.2867
 73N  O21  O  OH1   0  -0.591   2.4762  -2.5844   0.5352
 73N  O22  O  O     0  -0.431   3.4346  -1.2621  -0.9897
 73N  C25  C  C     0   0.683   2.8529   1.5793   0.2173
 73N  O26  O  O     0  -0.513   3.5045   1.2814   1.1977
 73N  H1   H  HCH2  0   0.250   0.1345  -0.9432  -1.3171
 73N  H2   H  HCH2  0   0.265  -0.0229  -1.9265   0.1244
 73N  H3   H  HCH1  0   0.293   1.5136  -0.3988   1.3478
 73N  H4   H  HNH1  0   0.408   1.4425   1.1026  -1.1685
 73N  H5   H  HNH2  0   0.383  -4.5848  -1.8049   0.1501
 73N  H6   H  HNH2  0   0.382  -6.0695  -1.1949  -0.3169
 73N  H7   H  H     0   0.311  -5.1566   2.0685   0.1291
 73N  H9   H  HNH1  0   0.380  -3.0926   1.3650   0.3427
 73N  H10  H  HCH2  0   0.229  -2.4934  -1.5021   0.1919
 73N  H11  H  HCH2  0   0.225  -2.3355  -0.5596  -1.2847
 73N  H12  H  HCH2  0   0.241  -0.9551   0.0145   1.3799
 73N  H13  H  HCH2  0   0.240  -0.8156   1.0213  -0.0521
 73N  H14  H  HOH1  0   0.486   3.1388  -3.2288   0.2438
 73N  OXT  O  OH1   0  -0.618   3.0489   2.6890  -0.4981
 73N  H8   H  HOH1  0   0.485   3.7708   3.1957  -0.1040

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  1.374  0.020  1.374
 73N  N4   C5   single  1.452  0.020  1.452
 73N  C5   C6   single  1.520  0.020  1.520
 73N  O22  C20  double  1.203  0.020  1.203
 73N  C6   C9   single  1.523  0.020  1.523
 73N  C20  O21  single  1.325  0.020  1.325
 73N  C20  C12  single  1.523  0.020  1.523
 73N  C9   C12  single  1.532  0.020  1.532
 73N  C12  N23  single  1.435  0.020  1.435
 73N  O26  C25  double  1.214  0.020  1.214
 73N  N23  C25  single  1.347  0.020  1.347
 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  0.860  0.020  1.020
 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  O21  H14  single  0.850  0.020  0.980
 73N  C25  OXT  single  1.335  0.020  1.335
 73N  OXT  H8   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
 73N  N4   C2   N3   125.41  3.000
 73N  N4   C2   N1   115.08  3.000
 73N  N3   C2   N1   119.50  3.000
 73N  H2   C9   H1   106.55  3.000
 73N  H2   C9   C6   109.36  3.000
 73N  H1   C9   C6   110.26  3.000
 73N  H2   C9   C12  108.66  3.000
 73N  H1   C9   C12  109.40  3.000
 73N  C6   C9   C12  112.42  3.000
 73N  H3   C12  N23  109.18  3.000
 73N  H3   C12  C20  107.73  3.000
 73N  N23  C12  C20  110.74  3.000
 73N  H3   C12  C9   108.26  3.000
 73N  N23  C12  C9   110.22  3.000
 73N  C20  C12  C9   110.64  3.000
 73N  O22  C20  O21  124.17  3.000
 73N  O21  C20  C12  111.25  3.000
 73N  O22  C20  C12  124.58  3.000
 73N  H4   N23  C25  118.69  3.000
 73N  H4   N23  C12  118.12  3.000
 73N  C25  N23  C12  121.05  3.000
 73N  H6   N1   H5   112.14  3.000
 73N  H6   N1   C2   113.23  3.000
 73N  H5   N1   C2   117.32  3.000
 73N  H7   N3   C2   110.97  3.000
 73N  H9   N4   C5   113.81  3.000
 73N  H9   N4   C2   113.26  3.000
 73N  C5   N4   C2   123.10  3.000
 73N  H11  C5   H10  106.93  3.000
 73N  H11  C5   C6   109.64  3.000
 73N  H10  C5   C6   108.53  3.000
 73N  H11  C5   N4   111.73  3.000
 73N  H10  C5   N4   110.01  3.000
 73N  C6   C5   N4   109.91  3.000
 73N  H13  C6   H12  106.82  3.000
 73N  H13  C6   C5   109.28  3.000
 73N  H12  C6   C5   109.47  3.000
 73N  H13  C6   C9   110.28  3.000
 73N  H12  C6   C9   109.57  3.000
 73N  C5   C6   C9   111.32  3.000
 73N  H14  O21  C20  110.41  3.000
 73N  OXT  C25  O26  123.91  3.000
 73N  OXT  C25  N23  111.47  3.000
 73N  O26  C25  N23  124.60  3.000
 73N  H8   OXT  C25  109.09  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  H14  O21  C20  C12   180.00   0.0  0
 73N  CONST_04  H8   OXT  C25  N23   180.00   0.0  0
 73N  CONST_05  H7   N3   C2   N1    180.00   0.0  0
 73N  CONST_06  H9   N4   C2   N1    180.00   0.0  0
 73N  CONST_08  H6   N1   C2   N3      0.00   0.0  0
 73N  Var_01    C6   C5   N4   C2    178.32  30.0  3
 73N  Var_02    N4   C5   C6   C9   -179.22  30.0  1
 73N  Var_03    C5   C6   C9   C12  -179.40  30.0  1
 73N  Var_04    O26  C25  N23  C12    -7.59  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-2  H14  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
 73N  plan-3  H8   0.020

