# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:09:11 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CC=N[C@@H]1C(=O)NCCCC[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
 2YC  2YC  N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine  L-peptide  38  18  .  2022-07-22  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_2YC
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
 2YC  O2   O  OC    -1  -0.625  -6.0456  -0.1974  -1.6656
 2YC  C6   C  C      0   0.383  -5.9064  -0.3803  -0.4375
 2YC  O1   O  O      0  -0.609  -6.5970  -1.1303   0.2809
 2YC  C5   C  CH1    0  -0.211  -4.7440   0.3917   0.2354
 2YC  N1   N  NH2    0  -0.786  -4.7492   0.3858   1.6905
 2YC  C4   C  CH2    0  -0.418  -3.4096  -0.1456  -0.2883
 2YC  C3   C  CH2    0  -0.406  -2.1958   0.6415   0.1857
 2YC  C2   C  CH2    0  -0.475  -0.8884   0.0695  -0.3459
 2YC  C1   C  CH2    0  -0.232   0.3176   0.8669   0.1222
 2YC  N    N  NH1    0  -0.644   1.5472   0.2625  -0.3501
 2YC  C    C  C      0   0.551   2.7604   0.7444  -0.0544
 2YC  O    O  O      0  -0.497   2.9339   1.7591   0.6063
 2YC  C7   C  CH1    0  -0.227   3.9263  -0.0971  -0.5385
 2YC  C10  C  CH1    0  -0.270   4.4839  -0.9933   0.5967
 2YC  C11  C  CH3    0  -0.661   3.9024  -2.3950   0.6214
 2YC  C9   C  CH2    0  -0.509   5.9952  -0.9167   0.3522
 2YC  C8   C  C1     0  -0.040   6.1014   0.3053  -0.5049
 2YC  N2   N  N      0  -0.336   5.0198   0.7576  -0.9816
 2YC  H2   H  HCH1   0   0.206  -4.8216   1.4380  -0.0856
 2YC  H3   H  HNH2   0   0.333  -5.6052   0.8213   2.0130
 2YC  H4   H  HNH2   0   0.321  -4.8283  -0.5769   2.0000
 2YC  H6   H  HCH2   0   0.203  -3.3014  -1.1954   0.0137
 2YC  H7   H  HCH2   0   0.217  -3.4389  -0.1450  -1.3804
 2YC  H8   H  HCH2   0   0.207  -2.2960   1.6851  -0.1329
 2YC  H9   H  HCH2   0   0.218  -2.1741   0.6567   1.2777
 2YC  H10  H  HCH2   0   0.225  -0.7849  -0.9703  -0.0183
 2YC  H11  H  HCH2   0   0.227  -0.9105   0.0514  -1.4404
 2YC  H12  H  HCH2   0   0.231   0.2441   1.8966  -0.2390
 2YC  H13  H  HCH2   0   0.230   0.3291   0.9156   1.2148
 2YC  H14  H  HNH1   0   0.402   1.4798  -0.5596  -0.9284
 2YC  H15  H  HCH1   0   0.264   3.6127  -0.7121  -1.3918
 2YC  H16  H  HCH1   0   0.257   4.2719  -0.5085   1.5544
 2YC  H17  H  HCH3   0   0.237   4.3350  -2.9831   1.4316
 2YC  H18  H  HCH3   0   0.229   2.8224  -2.3748   0.7765
 2YC  H19  H  HCH3   0   0.225   4.0981  -2.9205  -0.3152
 2YC  H20  H  HCH2   0   0.264   6.5867  -0.8426   1.2658
 2YC  H21  H  HCH2   0   0.260   6.3726  -1.7858  -0.1984
 2YC  H22  H  H      0   0.258   7.0506   0.7782  -0.7425

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
 2YC  C11  C10  single  1.518  0.020  1.518
 2YC  C10  C9   single  1.533  0.020  1.533
 2YC  C10  C7   single  1.550  0.020  1.550
 2YC  C9   C8   single  1.496  0.020  1.496
 2YC  O    C    double  1.231  0.020  1.231
 2YC  C7   C    single  1.517  0.020  1.517
 2YC  C7   N2   single  1.457  0.020  1.457
 2YC  O1   C6   deloc   1.247  0.020  1.247
 2YC  C    N    single  1.338  0.020  1.338
 2YC  C8   N2   double  1.266  0.020  1.266
 2YC  C6   O2   deloc   1.249  0.020  1.249
 2YC  C6   C5   single  1.549  0.020  1.549
 2YC  N    C1   single  1.449  0.020  1.449
 2YC  C2   C1   single  1.520  0.020  1.520
 2YC  C2   C3   single  1.523  0.020  1.523
 2YC  C4   C5   single  1.531  0.020  1.531
 2YC  C4   C3   single  1.522  0.020  1.522
 2YC  C5   N1   single  1.455  0.020  1.455
 2YC  C5   H2   single  0.970  0.020  1.090
 2YC  N1   H3   single  0.890  0.020  1.040
 2YC  N1   H4   single  0.890  0.020  1.040
 2YC  C4   H6   single  0.970  0.020  1.090
 2YC  C4   H7   single  0.970  0.020  1.090
 2YC  C3   H8   single  0.970  0.020  1.090
 2YC  C3   H9   single  0.970  0.020  1.090
 2YC  C2   H10  single  0.970  0.020  1.090
 2YC  C2   H11  single  0.970  0.020  1.090
 2YC  C1   H12  single  0.970  0.020  1.090
 2YC  C1   H13  single  0.970  0.020  1.090
 2YC  N    H14  single  0.860  0.020  1.020
 2YC  C7   H15  single  0.970  0.020  1.090
 2YC  C10  H16  single  0.970  0.020  1.090
 2YC  C11  H17  single  0.970  0.020  1.090
 2YC  C11  H18  single  0.970  0.020  1.090
 2YC  C11  H19  single  0.970  0.020  1.090
 2YC  C9   H20  single  0.970  0.020  1.090
 2YC  C9   H21  single  0.970  0.020  1.090
 2YC  C8   H22  single  0.930  0.020  1.080

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
 2YC  C5   C6   O1   117.71  3.000
 2YC  C5   C6   O2   115.95  3.000
 2YC  O1   C6   O2   126.34  3.000
 2YC  H2   C5   C4   107.23  3.000
 2YC  H2   C5   N1   107.23  3.000
 2YC  C4   C5   N1   110.11  3.000
 2YC  H2   C5   C6   107.16  3.000
 2YC  N1   C5   C6   115.44  3.000
 2YC  C4   C5   C6   109.30  3.000
 2YC  H4   N1   H3   104.18  3.000
 2YC  H4   N1   C5   108.01  3.000
 2YC  H3   N1   C5   108.64  3.000
 2YC  H7   C4   H6   106.15  3.000
 2YC  H7   C4   C3   109.42  3.000
 2YC  H6   C4   C3   109.28  3.000
 2YC  H7   C4   C5   108.57  3.000
 2YC  H6   C4   C5   109.11  3.000
 2YC  C3   C4   C5   114.02  3.000
 2YC  H9   C3   H8   106.21  3.000
 2YC  H9   C3   C2   109.70  3.000
 2YC  H8   C3   C2   109.56  3.000
 2YC  H9   C3   C4   109.53  3.000
 2YC  H8   C3   C4   109.20  3.000
 2YC  C2   C3   C4   112.43  3.000
 2YC  H11  C2   H10  106.57  3.000
 2YC  H11  C2   C1   109.43  3.000
 2YC  H10  C2   C1   109.34  3.000
 2YC  H11  C2   C3   109.74  3.000
 2YC  H10  C2   C3   109.47  3.000
 2YC  C1   C2   C3   112.13  3.000
 2YC  H13  C1   H12  106.78  3.000
 2YC  H13  C1   N    109.59  3.000
 2YC  H12  C1   N    110.00  3.000
 2YC  H13  C1   C2   109.84  3.000
 2YC  H12  C1   C2   109.81  3.000
 2YC  N    C1   C2   110.74  3.000
 2YC  H14  N    C    118.78  3.000
 2YC  H14  N    C1   118.07  3.000
 2YC  C    N    C1   123.15  3.000
 2YC  C7   C    O    121.56  3.000
 2YC  C7   C    N    115.23  3.000
 2YC  O    C    N    123.13  3.000
 2YC  H15  C7   N2   107.87  3.000
 2YC  H15  C7   C10  110.38  3.000
 2YC  N2   C7   C10  106.97  3.000
 2YC  H15  C7   C    109.83  3.000
 2YC  N2   C7   C    110.39  3.000
 2YC  C10  C7   C    111.31  3.000
 2YC  H16  C10  C9   107.97  3.000
 2YC  H16  C10  C11  108.71  3.000
 2YC  C9   C10  C11  115.24  3.000
 2YC  H16  C10  C7   108.37  3.000
 2YC  C9   C10  C7   102.06  3.000
 2YC  C11  C10  C7   114.08  3.000
 2YC  H19  C11  H18  107.96  3.000
 2YC  H19  C11  H17  107.87  3.000
 2YC  H18  C11  H17  107.27  3.000
 2YC  H19  C11  C10  111.22  3.000
 2YC  H18  C11  C10  111.36  3.000
 2YC  H17  C11  C10  110.98  3.000
 2YC  H21  C9   H20  106.73  3.000
 2YC  H21  C9   C8   109.60  3.000
 2YC  H20  C9   C8   112.69  3.000
 2YC  H21  C9   C10  112.34  3.000
 2YC  H20  C9   C10  113.85  3.000
 2YC  C8   C9   C10  101.66  3.000
 2YC  H22  C8   N2   120.57  3.000
 2YC  H22  C8   C9   122.86  3.000
 2YC  N2   C8   C9   116.54  3.000
 2YC  C8   N2   C7   108.50  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
 2YC  CONST_01  C7   C   N   C1    180.00   0.0  0
 2YC  CONST_02  H14  N   C   C7      0.00   0.0  0
 2YC  CONST_03  O    C   N   C1      0.00   0.0  0
 2YC  Var_01    C9   C8  N2  C7     -0.38  30.0  1
 2YC  Var_02    N2   C8  C9  C10   -12.60  30.0  1
 2YC  Var_03    C2   C3  C4  C5    179.50  30.0  3
 2YC  Var_04    C1   C2  C3  C4    179.53  30.0  2
 2YC  Var_05    N    C1  C2  C3    177.41  30.0  3
 2YC  Var_06    C    N   C1  C2   -178.33  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
 2YC  chir_01  C5   C6   C4  N1   positiv
 2YC  chir_02  C7   C10  C   N2   negativ
 2YC  chir_03  C10  C7   C9  C11  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
 2YC  plan-1  C1   0.020
 2YC  plan-1  N    0.020
 2YC  plan-1  C    0.020
 2YC  plan-1  O    0.020
 2YC  plan-1  C7   0.020
 2YC  plan-1  H14  0.020
 2YC  plan-2  O2   0.020
 2YC  plan-2  C6   0.020
 2YC  plan-2  O1   0.020
 2YC  plan-2  C5   0.020

