# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:27:54 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2~{S},5~{R})-1-[2-[[1-(hydroxymethyl)cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1(CCCC1)NCC(=O)N2[C@H](CC[C@H]2C#N)C#N
#
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
 8YC  8YC  (2~{S},5~{R})-1-[2-[[1-(hydroxymethyl)cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile  ligand  40  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8YC
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
 8YC  O1   O  O     0  -0.458   0.7075  -1.9143  -0.4958
 8YC  C5   C  C     0   0.576   0.7672  -0.8065   0.0005
 8YC  N1   N  NT    0  -0.499   1.9648  -0.2967   0.3940
 8YC  C1   C  CH1   0  -0.134   3.1776  -1.0979   0.2996
 8YC  C6   C  CSP   0   0.139   3.4784  -1.4684  -1.0842
 8YC  N2   N  NS    0  -0.255   3.7601  -1.7563  -2.1607
 8YC  C3   C  CH2   0  -0.486   4.2667  -0.2009   0.9076
 8YC  C4   C  CH2   0  -0.471   3.4852   0.6747   1.8753
 8YC  C2   C  CH1   0  -0.209   2.1804   0.9411   1.1194
 8YC  C7   C  CSP   0   0.156   2.3090   2.0745   0.1906
 8YC  N3   N  NS    0  -0.247   2.4117   2.9567  -0.5392
 8YC  C8   C  CH2   0  -0.412  -0.4424   0.0742   0.2265
 8YC  N4   N  NH1   0  -0.608  -1.6111  -0.5009  -0.3801
 8YC  C9   C  CT    0   0.120  -2.8717   0.1840  -0.0973
 8YC  C14  C  CH2   0  -0.164  -2.8514   1.5900  -0.6820
 8YC  O2   O  OH1   0  -0.667  -2.6197   1.5341  -2.0672
 8YC  C10  C  CH2   0  -0.472  -3.2232   0.2768   1.4186
 8YC  C11  C  CH2   0  -0.437  -4.6501  -0.2522   1.5544
 8YC  C12  C  CH2   0  -0.446  -4.7176  -1.3276   0.4765
 8YC  C13  C  CH2   0  -0.462  -4.0221  -0.6583  -0.7065
 8YC  H1   H  HCH1  0   0.343   3.0716  -2.0237   0.8725
 8YC  H2   H  HCH2  0   0.300   5.0364  -0.7943   1.3947
 8YC  H3   H  HCH2  0   0.280   4.7454   0.4058   0.1381
 8YC  H4   H  HCH2  0   0.292   3.2395   0.1302   2.7871
 8YC  H5   H  HCH2  0   0.299   4.0077   1.5881   2.1503
 8YC  H6   H  HCH1  0   0.357   1.3606   1.1571   1.8066
 8YC  H9   H  HCH2  0   0.252  -0.5288   0.2480   1.3128
 8YC  H10  H  HCH2  0   0.266  -0.2394   1.0546  -0.2159
 8YC  H11  H  HNH1  0   0.347  -1.6956  -1.4689  -0.0936
 8YC  H13  H  HCH2  0   0.207  -3.8183   2.0555  -0.4467
 8YC  H14  H  HCH2  0   0.201  -2.0916   2.1998  -0.1719
 8YC  H15  H  HOH1  0   0.452  -2.7029   2.4258  -2.4161
 8YC  H16  H  HCH2  0   0.234  -2.5476  -0.3669   1.9897
 8YC  H17  H  HCH2  0   0.237  -3.1023   1.2861   1.8197
 8YC  H18  H  HCH2  0   0.232  -4.8675  -0.6234   2.5571
 8YC  H19  H  HCH2  0   0.219  -5.3765   0.5367   1.3380
 8YC  H20  H  HCH2  0   0.218  -4.1628  -2.2137   0.7998
 8YC  H21  H  HCH2  0   0.232  -5.7335  -1.6497   0.2431
 8YC  H22  H  HCH2  0   0.235  -4.7342  -0.0075  -1.2193
 8YC  H23  H  HCH2  0   0.237  -3.6494  -1.3631  -1.4507

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
 8YC  C12  C11  single  1.524  0.020  1.524
 8YC  C12  C13  single  1.527  0.020  1.527
 8YC  C11  C10  single  1.528  0.020  1.528
 8YC  C13  C9   single  1.551  0.020  1.551
 8YC  C10  C9   single  1.559  0.020  1.559
 8YC  C9   C14  single  1.523  0.020  1.523
 8YC  C9   N4   single  1.462  0.020  1.462
 8YC  C14  O2   single  1.406  0.020  1.406
 8YC  N4   C8   single  1.437  0.020  1.437
 8YC  C8   C5   single  1.513  0.020  1.513
 8YC  N2   C6   triple  1.149  0.020  1.149
 8YC  C6   C1   single  1.464  0.020  1.464
 8YC  C5   O1   double  1.215  0.020  1.215
 8YC  C5   N1   single  1.360  0.020  1.360
 8YC  N3   C7   triple  1.150  0.020  1.150
 8YC  N1   C1   single  1.457  0.020  1.457
 8YC  N1   C2   single  1.451  0.020  1.451
 8YC  C1   C3   single  1.536  0.020  1.536
 8YC  C7   C2   single  1.471  0.020  1.471
 8YC  C2   C4   single  1.531  0.020  1.531
 8YC  C3   C4   single  1.521  0.020  1.521
 8YC  C1   H1   single  0.970  0.020  1.090
 8YC  C3   H2   single  0.970  0.020  1.090
 8YC  C3   H3   single  0.970  0.020  1.090
 8YC  C4   H4   single  0.970  0.020  1.090
 8YC  C4   H5   single  0.970  0.020  1.090
 8YC  C2   H6   single  0.970  0.020  1.090
 8YC  C8   H9   single  0.970  0.020  1.090
 8YC  C8   H10  single  0.970  0.020  1.090
 8YC  N4   H11  single  0.890  0.020  1.040
 8YC  C14  H13  single  0.970  0.020  1.090
 8YC  C14  H14  single  0.970  0.020  1.090
 8YC  O2   H15  single  0.850  0.020  0.980
 8YC  C10  H16  single  0.970  0.020  1.090
 8YC  C10  H17  single  0.970  0.020  1.090
 8YC  C11  H18  single  0.970  0.020  1.090
 8YC  C11  H19  single  0.970  0.020  1.090
 8YC  C12  H20  single  0.970  0.020  1.090
 8YC  C12  H21  single  0.970  0.020  1.090
 8YC  C13  H22  single  0.970  0.020  1.090
 8YC  C13  H23  single  0.970  0.020  1.090

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
 8YC  C8   C5   N1   116.27  3.000
 8YC  N1   C5   O1   120.21  3.000
 8YC  C8   C5   O1   123.52  3.000
 8YC  C2   N1   C1   112.21  3.000
 8YC  C2   N1   C5   126.55  3.000
 8YC  C1   N1   C5   120.55  3.000
 8YC  H1   C1   C3   110.83  3.000
 8YC  H1   C1   C6   107.51  3.000
 8YC  C3   C1   C6   112.10  3.000
 8YC  H1   C1   N1   110.55  3.000
 8YC  C3   C1   N1   104.09  3.000
 8YC  C6   C1   N1   111.81  3.000
 8YC  N2   C6   C1   180.00  3.000
 8YC  H3   C3   H2   108.01  3.000
 8YC  H3   C3   C4   110.74  3.000
 8YC  H2   C3   C4   113.13  3.000
 8YC  H3   C3   C1   110.90  3.000
 8YC  H2   C3   C1   111.13  3.000
 8YC  C4   C3   C1   102.92  3.000
 8YC  H5   C4   H4   108.44  3.000
 8YC  H5   C4   C2   112.83  3.000
 8YC  H4   C4   C2   107.92  3.000
 8YC  H5   C4   C3   113.42  3.000
 8YC  H4   C4   C3   111.13  3.000
 8YC  C2   C4   C3   102.94  3.000
 8YC  H6   C2   C7   108.10  3.000
 8YC  H6   C2   C4   111.33  3.000
 8YC  C7   C2   C4   111.80  3.000
 8YC  H6   C2   N1   111.84  3.000
 8YC  C4   C2   N1   103.00  3.000
 8YC  C7   C2   N1   110.78  3.000
 8YC  N3   C7   C2   180.00  3.000
 8YC  H10  C8   H9   105.74  3.000
 8YC  H10  C8   N4   109.80  3.000
 8YC  H9   C8   N4   114.51  3.000
 8YC  H10  C8   C5   108.22  3.000
 8YC  H9   C8   C5   107.53  3.000
 8YC  N4   C8   C5   110.74  3.000
 8YC  H11  N4   C9   108.72  3.000
 8YC  H11  N4   C8   109.33  3.000
 8YC  C9   N4   C8   115.60  3.000
 8YC  C13  C9   C10  104.31  3.000
 8YC  C10  C9   C14  108.75  3.000
 8YC  C13  C9   C14  111.13  3.000
 8YC  C14  C9   N4   110.28  3.000
 8YC  C10  C9   N4   114.23  3.000
 8YC  C13  C9   N4   108.01  3.000
 8YC  H14  C14  H13  105.89  3.000
 8YC  H14  C14  O2   111.43  3.000
 8YC  H13  C14  O2   111.91  3.000
 8YC  H14  C14  C9   110.06  3.000
 8YC  H13  C14  C9   107.29  3.000
 8YC  O2   C14  C9   110.11  3.000
 8YC  H15  O2   C14  107.85  3.000
 8YC  H17  C10  H16  106.47  3.000
 8YC  H17  C10  C11  112.98  3.000
 8YC  H16  C10  C11  109.07  3.000
 8YC  H17  C10  C9   112.77  3.000
 8YC  H16  C10  C9   109.47  3.000
 8YC  C11  C10  C9   106.05  3.000
 8YC  H19  C11  H18  107.14  3.000
 8YC  H19  C11  C12  109.85  3.000
 8YC  H18  C11  C12  113.65  3.000
 8YC  H19  C11  C10  110.67  3.000
 8YC  H18  C11  C10  112.68  3.000
 8YC  C12  C11  C10  102.87  3.000
 8YC  H21  C12  H20  107.23  3.000
 8YC  H21  C12  C13  112.81  3.000
 8YC  H20  C12  C13  110.66  3.000
 8YC  H21  C12  C11  113.63  3.000
 8YC  H20  C12  C11  109.88  3.000
 8YC  C13  C12  C11  102.62  3.000
 8YC  H23  C13  H22  106.71  3.000
 8YC  H23  C13  C12  113.65  3.000
 8YC  H22  C13  C12  109.14  3.000
 8YC  H23  C13  C9   111.45  3.000
 8YC  H22  C13  C9   110.14  3.000
 8YC  C12  C13  C9   105.76  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
 8YC  CONST_01  C1   N1   C5   O1     0.00   0.0  0
 8YC  CONST_02  C2   N1   C5   O1   180.00   0.0  0
 8YC  CONST_03  C8   C5   N1   C1   180.00   0.0  0
 8YC  CONST_04  C8   C5   N1   C2     0.00   0.0  0
 8YC  Var_01    C2   C4   C3   C1   -38.07  30.0  1
 8YC  Var_02    C11  C12  C13  C9    36.65  30.0  1
 8YC  Var_03    C12  C11  C10  C9    33.49  30.0  1
 8YC  Var_04    C13  C12  C11  C10  -43.09  30.0  1
 8YC  Var_05    C9   N4   C8   C5   173.28  30.0  1
 8YC  Var_06    N4   C8   C5   N1   172.73  30.0  1

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
 8YC  chir_01  C1  C6   N1   C3   positiv
 8YC  chir_02  C2  N1   C4   C7   negativ
 8YC  chir_03  C9  C14  C10  C13  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
 8YC  plan-1  O1  0.020
 8YC  plan-1  C5  0.020
 8YC  plan-1  N1  0.020
 8YC  plan-1  C1  0.020
 8YC  plan-1  C2  0.020
 8YC  plan-1  C8  0.020

