# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:23:06 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (3S)-N~6~-carbamimidoyl-3-hydroxy-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H](O)CCCNC(N)=N)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
 G3M  G3M  (3S)-N~6~-carbamimidoyl-3-hydroxy-L-lysine  L-peptide  30  14  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G3M
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
 G3M  O1   O  O     0  -0.452  -4.3263   0.0526  -1.2584
 G3M  C9   C  C     0   0.544   4.7621  -0.0363  -0.0311
 G3M  C2   C  C     0   0.557  -3.9507   0.1113  -0.1136
 G3M  C3   C  CH1   0  -0.238  -2.6902  -0.5722   0.3831
 G3M  C4   C  CH1   0   0.035  -1.4806   0.1744  -0.2136
 G3M  C7   C  CH2   0  -0.229   2.3492  -0.2440   0.3058
 G3M  C5   C  CH2   0  -0.469  -0.1650  -0.3390   0.3540
 G3M  N8   N  NH1   0  -0.646   3.4928   0.4104  -0.2871
 G3M  O10  O  OH1   0  -0.585  -4.5989   0.7697   0.8355
 G3M  N11  N  NH2   0  -0.788  -2.7831  -1.9788   0.0414
 G3M  O12  O  OH1   0  -0.664  -1.6365   1.5682  -0.0440
 G3M  N13  N  N     0  -0.714   4.9560  -1.1410   0.5893
 G3M  N14  N  NH2   0  -0.839   5.7435   0.8265  -0.4788
 G3M  H1   H  HCH1  0   0.264  -2.6472  -0.4935   1.4735
 G3M  H2   H  HCH1  0   0.232  -1.4872   0.0079  -1.2972
 G3M  H3   H  HCH2  0   0.208   2.3437  -0.1408   1.3990
 G3M  H4   H  HCH2  0   0.227   2.4130  -1.3131   0.0988
 G3M  H5   H  HCH2  0   0.226   1.0250   1.3997  -0.0997
 G3M  H6   H  HCH2  0   0.228   1.0480   0.1700  -1.3523
 G3M  H7   H  HCH2  0   0.230  -0.1567  -0.1917   1.4411
 G3M  H8   H  HCH2  0   0.230  -0.1076  -1.4196   0.1935
 G3M  H9   H  HNH1  0   0.376   3.4017   1.4105  -0.3833
 G3M  H10  H  HOH1  0   0.479  -5.3899   1.1919   0.4661
 G3M  H11  H  HNH2  0   0.350  -2.6265  -2.1120  -0.9506
 G3M  H12  H  HNH2  0   0.364  -2.0613  -2.4986   0.5214
 G3M  H14  H  HOH1  0   0.447  -1.5197   1.7806   0.8889
 G3M  H15  H  H     0   0.315   5.9439  -1.3656   0.6160
 G3M  H16  H  HNH2  0   0.383   6.6664   0.4261  -0.5352
 G3M  H17  H  HNH2  0   0.381   5.5197   1.3572  -1.3072
 G3M  C6   C  CH2   0  -0.452   1.0591   0.3195  -0.2684

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
 G3M  N11  C3   single  1.450  0.020  1.450
 G3M  C3   C4   single  1.542  0.020  1.542
 G3M  C3   C2   single  1.517  0.020  1.517
 G3M  C4   O12  single  1.413  0.020  1.413
 G3M  C4   C5   single  1.522  0.020  1.522
 G3M  O1   C2   double  1.206  0.020  1.206
 G3M  C2   O10  single  1.325  0.020  1.325
 G3M  C6   C5   single  1.523  0.020  1.523
 G3M  C6   C7   single  1.520  0.020  1.520
 G3M  C7   N8   single  1.445  0.020  1.445
 G3M  N8   C9   single  1.370  0.020  1.370
 G3M  C9   N13  double  1.282  0.020  1.282
 G3M  C9   N14  single  1.381  0.020  1.381
 G3M  C3   H1   single  0.970  0.020  1.090
 G3M  C4   H2   single  0.970  0.020  1.090
 G3M  C7   H3   single  0.970  0.020  1.090
 G3M  C7   H4   single  0.970  0.020  1.090
 G3M  C6   H5   single  0.970  0.020  1.090
 G3M  C6   H6   single  0.970  0.020  1.090
 G3M  C5   H7   single  0.970  0.020  1.090
 G3M  C5   H8   single  0.970  0.020  1.090
 G3M  N8   H9   single  0.890  0.020  1.040
 G3M  O10  H10  single  0.850  0.020  0.980
 G3M  N11  H11  single  0.890  0.020  1.040
 G3M  N11  H12  single  0.890  0.020  1.040
 G3M  O12  H14  single  0.850  0.020  0.980
 G3M  N13  H15  single  0.890  0.020  1.040
 G3M  N14  H16  single  0.890  0.020  1.040
 G3M  N14  H17  single  0.890  0.020  1.040

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
 G3M  N14  C9   N13  126.00  3.000
 G3M  N14  C9   N8   113.21  3.000
 G3M  N13  C9   N8   120.78  3.000
 G3M  O10  C2   C3   113.32  3.000
 G3M  O10  C2   O1   123.49  3.000
 G3M  C3   C2   O1   123.19  3.000
 G3M  H1   C3   N11  107.88  3.000
 G3M  H1   C3   C4   108.67  3.000
 G3M  N11  C3   C4   115.39  3.000
 G3M  H1   C3   C2   109.06  3.000
 G3M  C4   C3   C2   107.88  3.000
 G3M  N11  C3   C2   107.85  3.000
 G3M  H2   C4   O12  105.54  3.000
 G3M  H2   C4   C5   108.82  3.000
 G3M  O12  C4   C5   112.55  3.000
 G3M  H2   C4   C3   107.71  3.000
 G3M  C5   C4   C3   111.75  3.000
 G3M  O12  C4   C3   110.17  3.000
 G3M  H4   C7   H3   106.34  3.000
 G3M  H4   C7   N8   108.65  3.000
 G3M  H3   C7   N8   111.71  3.000
 G3M  H4   C7   C6   109.95  3.000
 G3M  H3   C7   C6   109.69  3.000
 G3M  N8   C7   C6   110.41  3.000
 G3M  H8   C5   H7   106.11  3.000
 G3M  H8   C5   C6   108.96  3.000
 G3M  H7   C5   C6   109.93  3.000
 G3M  H8   C5   C4   108.89  3.000
 G3M  H7   C5   C4   109.32  3.000
 G3M  C6   C5   C4   113.36  3.000
 G3M  H9   N8   C7   114.62  3.000
 G3M  H9   N8   C9   115.14  3.000
 G3M  C7   N8   C9   120.60  3.000
 G3M  H10  O10  C2   110.04  3.000
 G3M  H12  N11  H11  106.68  3.000
 G3M  H12  N11  C3   109.95  3.000
 G3M  H11  N11  C3   110.38  3.000
 G3M  H14  O12  C4   108.68  3.000
 G3M  H15  N13  C9   110.56  3.000
 G3M  H17  N14  H16  111.48  3.000
 G3M  H17  N14  C9   115.92  3.000
 G3M  H16  N14  C9   114.88  3.000
 G3M  H6   C6   H5   106.71  3.000
 G3M  H6   C6   C5   109.73  3.000
 G3M  H5   C6   C5   109.81  3.000
 G3M  H6   C6   C7   109.40  3.000
 G3M  H5   C6   C7   109.52  3.000
 G3M  C5   C6   C7   111.55  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
 G3M  CONST_01  N13  C9   N8  C7     0.00   0.0  0
 G3M  CONST_02  N14  C9   N8  C7   180.00   0.0  0
 G3M  CONST_03  H10  O10  C2  O1     0.00   0.0  0
 G3M  CONST_04  H15  N13  C9  N8   180.00   0.0  0
 G3M  Var_01    C6   C7   N8  C9  -172.74  30.0  1
 G3M  Var_02    C7   C6   C5  C4  -178.77  30.0  1
 G3M  Var_03    N8   C7   C6  C5  -179.18  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
 G3M  chir_01  C3  N11  C4  C2  negativ
 G3M  chir_02  C4  O12  C3  C5  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
 G3M  plan-1  C9   0.020
 G3M  plan-1  C7   0.020
 G3M  plan-1  N8   0.020
 G3M  plan-1  N13  0.020
 G3M  plan-1  N14  0.020
 G3M  plan-1  H9   0.020
 G3M  plan-1  H15  0.020
 G3M  plan-1  H16  0.020
 G3M  plan-1  H17  0.020
 G3M  plan-2  O1   0.020
 G3M  plan-2  C2   0.020
 G3M  plan-2  C3   0.020
 G3M  plan-2  O10  0.020
 G3M  plan-2  H10  0.020

