# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:10:39 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: N~5~-D-ornithyl-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCC[C@@H](N)C(=O)NCCC[C@H](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
 2YH  2YH  N~5~-D-ornithyl-L-ornithine  L-peptide  39  17  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_2YH
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
 2YH  O3   O  O     0  -0.504   1.6196  -2.2100   1.2340
 2YH  C6   C  C     0   0.531   1.6810  -1.4533   0.2726
 2YH  C7   C  CH1   0  -0.222   3.0163  -1.0887  -0.3813
 2YH  N3   N  NH2   0  -0.776   3.9626  -2.1835  -0.3929
 2YH  C8   C  CH2   0  -0.418   3.6008   0.1224   0.3543
 2YH  C9   C  CH2   0  -0.424   4.8480   0.6879  -0.3095
 2YH  C10  C  CH2   0  -0.272   5.4177   1.8725   0.4555
 2YH  N2   N  NH2   0  -0.801   6.5980   2.4068  -0.2099
 2YH  N1   N  NH1   0  -0.639   0.6019  -0.8589  -0.2548
 2YH  C5   C  CH2   0  -0.231  -0.7437  -1.0586   0.2404
 2YH  C4   C  CH2   0  -0.480  -1.6850  -0.0135  -0.3367
 2YH  C3   C  CH2   0  -0.441  -3.1127  -0.2186   0.1495
 2YH  C2   C  CH1   0  -0.216  -4.0928   0.8000  -0.4656
 2YH  N4   N  NH2   0  -0.785  -3.7950   2.1911  -0.2039
 2YH  C1   C  C     0   0.547  -5.4921   0.4926   0.0289
 2YH  O2   O  OH1   0  -0.595  -5.9698  -0.6288  -0.4993
 2YH  O1   O  O     0  -0.439  -6.0995   1.1585   0.8282
 2YH  H1   H  HCH1  0   0.245   2.8289  -0.7971  -1.4204
 2YH  H2   H  HNH2  0   0.339   4.0588  -2.5532   0.5460
 2YH  H3   H  HNH2  0   0.350   3.6037  -2.9458  -0.9549
 2YH  H5   H  HCH2  0   0.230   2.8360   0.9028   0.4145
 2YH  H6   H  HCH2  0   0.223   3.8251  -0.1680   1.3868
 2YH  H7   H  HCH2  0   0.221   5.6059  -0.0960  -0.3888
 2YH  H8   H  HCH2  0   0.212   4.6126   1.0019  -1.3313
 2YH  H9   H  HCH2  0   0.210   4.6656   2.6656   0.5020
 2YH  H10  H  HCH2  0   0.186   5.6031   1.5665   1.4959
 2YH  H11  H  HNH2  0   0.345   6.9464   3.1999   0.3133
 2YH  H12  H  HNH2  0   0.336   7.3388   1.7167  -0.1757
 2YH  H14  H  HNH1  0   0.399   0.7179  -0.3043  -1.0883
 2YH  H15  H  HCH2  0   0.230  -1.0981  -2.0623  -0.0171
 2YH  H16  H  HCH2  0   0.236  -0.7421  -0.9928   1.3305
 2YH  H17  H  HCH2  0   0.234  -1.3277   0.9806  -0.0548
 2YH  H18  H  HCH2  0   0.236  -1.6611  -0.0633  -1.4309
 2YH  H19  H  HCH2  0   0.241  -3.4352  -1.2332  -0.0972
 2YH  H20  H  HCH2  0   0.235  -3.1466  -0.1325   1.2412
 2YH  H21  H  HCH1  0   0.272  -4.0872   0.6566  -1.5511
 2YH  H22  H  HNH2  0   0.345  -3.6323   2.3376   0.7854
 2YH  H23  H  HNH2  0   0.360  -2.9377   2.4479  -0.6748
 2YH  H25  H  HOH1  0   0.481  -6.8442  -0.8253  -0.1304

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
 2YH  N3   C7   single  1.447  0.020  1.447
 2YH  N4   C2   single  1.447  0.020  1.447
 2YH  C10  N2   single  1.456  0.020  1.456
 2YH  C10  C9   single  1.521  0.020  1.521
 2YH  C7   C8   single  1.533  0.020  1.533
 2YH  C7   C6   single  1.531  0.020  1.531
 2YH  C8   C9   single  1.522  0.020  1.522
 2YH  N1   C6   single  1.340  0.020  1.340
 2YH  N1   C5   single  1.448  0.020  1.448
 2YH  C4   C3   single  1.522  0.020  1.522
 2YH  C4   C5   single  1.520  0.020  1.520
 2YH  C2   C3   single  1.542  0.020  1.542
 2YH  C2   C1   single  1.516  0.020  1.516
 2YH  C6   O3   double  1.225  0.020  1.225
 2YH  O1   C1   double  1.205  0.020  1.205
 2YH  C1   O2   single  1.329  0.020  1.329
 2YH  C7   H1   single  0.970  0.020  1.090
 2YH  N3   H2   single  0.890  0.020  1.040
 2YH  N3   H3   single  0.890  0.020  1.040
 2YH  C8   H5   single  0.970  0.020  1.090
 2YH  C8   H6   single  0.970  0.020  1.090
 2YH  C9   H7   single  0.970  0.020  1.090
 2YH  C9   H8   single  0.970  0.020  1.090
 2YH  C10  H9   single  0.970  0.020  1.090
 2YH  C10  H10  single  0.970  0.020  1.090
 2YH  N2   H11  single  0.890  0.020  1.040
 2YH  N2   H12  single  0.890  0.020  1.040
 2YH  N1   H14  single  0.860  0.020  1.020
 2YH  C5   H15  single  0.970  0.020  1.090
 2YH  C5   H16  single  0.970  0.020  1.090
 2YH  C4   H17  single  0.970  0.020  1.090
 2YH  C4   H18  single  0.970  0.020  1.090
 2YH  C3   H19  single  0.970  0.020  1.090
 2YH  C3   H20  single  0.970  0.020  1.090
 2YH  C2   H21  single  0.970  0.020  1.090
 2YH  N4   H22  single  0.890  0.020  1.040
 2YH  N4   H23  single  0.890  0.020  1.040
 2YH  O2   H25  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
 2YH  N1   C6   C7   115.38  3.000
 2YH  N1   C6   O3   122.85  3.000
 2YH  C7   C6   O3   121.74  3.000
 2YH  H1   C7   C8   108.07  3.000
 2YH  H1   C7   N3   107.80  3.000
 2YH  C8   C7   N3   110.62  3.000
 2YH  H1   C7   C6   108.63  3.000
 2YH  C8   C7   C6   108.41  3.000
 2YH  N3   C7   C6   113.18  3.000
 2YH  H3   N3   H2   105.85  3.000
 2YH  H3   N3   C7   110.01  3.000
 2YH  H2   N3   C7   109.30  3.000
 2YH  H6   C8   H5   106.28  3.000
 2YH  H6   C8   C9   109.98  3.000
 2YH  H5   C8   C9   109.37  3.000
 2YH  H6   C8   C7   108.72  3.000
 2YH  H5   C8   C7   108.87  3.000
 2YH  C9   C8   C7   113.37  3.000
 2YH  H8   C9   H7   106.69  3.000
 2YH  H8   C9   C10  109.06  3.000
 2YH  H7   C9   C10  109.59  3.000
 2YH  H8   C9   C8   109.73  3.000
 2YH  H7   C9   C8   109.47  3.000
 2YH  C10  C9   C8   112.15  3.000
 2YH  H10  C10  H9   106.10  3.000
 2YH  H10  C10  N2   113.42  3.000
 2YH  H9   C10  N2   108.10  3.000
 2YH  H10  C10  C9   108.79  3.000
 2YH  H9   C10  C9   109.18  3.000
 2YH  N2   C10  C9   111.06  3.000
 2YH  H12  N2   H11  105.35  3.000
 2YH  H12  N2   C10  109.11  3.000
 2YH  H11  N2   C10  109.28  3.000
 2YH  H14  N1   C5   117.76  3.000
 2YH  H14  N1   C6   118.49  3.000
 2YH  C5   N1   C6   123.55  3.000
 2YH  H16  C5   H15  106.88  3.000
 2YH  H16  C5   C4   109.78  3.000
 2YH  H15  C5   C4   109.90  3.000
 2YH  H16  C5   N1   109.38  3.000
 2YH  H15  C5   N1   110.29  3.000
 2YH  C4   C5   N1   110.54  3.000
 2YH  H18  C4   H17  106.96  3.000
 2YH  H18  C4   C3   109.48  3.000
 2YH  H17  C4   C3   110.29  3.000
 2YH  H18  C4   C5   109.53  3.000
 2YH  H17  C4   C5   108.95  3.000
 2YH  C3   C4   C5   111.52  3.000
 2YH  H20  C3   H19  106.79  3.000
 2YH  H20  C3   C2   109.03  3.000
 2YH  H19  C3   C2   109.61  3.000
 2YH  H20  C3   C4   109.68  3.000
 2YH  H19  C3   C4   109.26  3.000
 2YH  C2   C3   C4   112.32  3.000
 2YH  H21  C2   C1   107.56  3.000
 2YH  H21  C2   N4   107.71  3.000
 2YH  C1   C2   N4   109.03  3.000
 2YH  H21  C2   C3   107.81  3.000
 2YH  C1   C2   C3   108.83  3.000
 2YH  N4   C2   C3   115.62  3.000
 2YH  H23  N4   H22  106.37  3.000
 2YH  H23  N4   C2   109.54  3.000
 2YH  H22  N4   C2   110.41  3.000
 2YH  O1   C1   O2   123.31  3.000
 2YH  O2   C1   C2   111.93  3.000
 2YH  O1   C1   C2   124.74  3.000
 2YH  H25  O2   C1   110.14  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
 2YH  CONST_01  C5   N1   C6   O3     0.00   0.0  0
 2YH  CONST_02  C5   N1   C6   C7   180.00   0.0  0
 2YH  CONST_03  H14  N1   C6   O3   180.00   0.0  0
 2YH  CONST_04  H25  O2   C1   C2   180.00   0.0  0
 2YH  Var_01    C4   C5   N1   C6   166.53  30.0  3
 2YH  Var_02    C10  C9   C8   C7  -179.03  30.0  3
 2YH  Var_03    N2   C10  C9   C8  -179.18  30.0  1
 2YH  Var_04    C3   C4   C5   N1   178.94  30.0  1
 2YH  Var_05    C2   C3   C4   C5  -177.89  30.0  3
 2YH  Var_06    H11  N2   C10  C9   179.20  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
 2YH  chir_01  C7  N3  C8  C6  positiv
 2YH  chir_02  C2  N4  C3  C1  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
 2YH  plan-1  O3   0.020
 2YH  plan-1  C6   0.020
 2YH  plan-1  C7   0.020
 2YH  plan-1  N1   0.020
 2YH  plan-1  C5   0.020
 2YH  plan-1  H14  0.020
 2YH  plan-2  C2   0.020
 2YH  plan-2  C1   0.020
 2YH  plan-2  O2   0.020
 2YH  plan-2  O1   0.020
 2YH  plan-2  H25  0.020

