# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:11:26 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-chloro-4-{[(1R,2R)-2-hydroxy-2-methylcyclopentyl]amino}-3-methylbenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Cl)c(ccc1N[C@@H]2CCC[C@@]2(C)O)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
 51Y  51Y  2-chloro-4-{[(1R,2R)-2-hydroxy-2-methylcyclopentyl]amino}-3-methylbenzonitrile  ligand  35  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_51Y
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
 51Y  C7   C   CR16  0  -0.334   0.4485  -1.3731   0.4309
 51Y  C6   C   CR6   0   0.371   0.0682  -0.0856   0.0138
 51Y  C1   C   CR16  0  -0.271   1.7740  -1.7349   0.4657
 51Y  C4   C   CR6   0   0.109   1.0656   0.8528  -0.3769
 51Y  C3   C   CR6   0  -0.125   2.3838   0.4470  -0.3361
 51Y  C2   C   CR6   0   0.051   2.7677  -0.8369   0.0811
 51Y  N8   N   NH1   0  -0.694  -1.2286   0.2999   0.0028
 51Y  C9   C   CH1   0  -0.112  -2.3417  -0.5676   0.3253
 51Y  C10  C   CT    0   0.197  -3.6101   0.2719   0.5667
 51Y  O11  O   OH1   0  -0.673  -4.5031  -0.6392   1.1842
 51Y  C12  C   CH3   0  -0.663  -3.4200   1.5025   1.4401
 51Y  C13  C   CH2   0  -0.477  -4.0724   0.5733  -0.8612
 51Y  C14  C   CH2   0  -0.439  -3.8282  -0.7319  -1.6315
 51Y  C15  C   CH2   0  -0.437  -2.7398  -1.4937  -0.8392
 51Y  CL1  CL  CL    0  -0.104   3.6494   1.5317  -0.8023
 51Y  C17  C   CSP   0   0.037   4.1299  -1.2274   0.1133
 51Y  N18  N   NS    0  -0.262   5.2307  -1.5727   0.1499
 51Y  H1   H   HCR6  0   0.283  -0.2953  -2.1016   0.7188
 51Y  H2   H   HCR6  0   0.283   2.0509  -2.7296   0.7872
 51Y  H3   H   HCH3  0   0.261   0.0579   2.2000  -1.7218
 51Y  H4   H   HCH3  0   0.257   0.0110   2.6890  -0.0286
 51Y  H5   H   HCH3  0   0.271   1.4779   2.8906  -0.9680
 51Y  H6   H   HNH1  0   0.397  -1.4475   1.1305  -0.5216
 51Y  H7   H   HCH1  0   0.268  -2.0884  -1.1194   1.2335
 51Y  H8   H   HOH1  0   0.448  -5.3836  -0.2491   1.1764
 51Y  H9   H   HCH3  0   0.235  -4.3803   1.9967   1.6019
 51Y  H10  H   HCH3  0   0.236  -3.0098   1.2326   2.4144
 51Y  H11  H   HCH3  0   0.218  -2.7552   2.2378   0.9875
 51Y  H12  H   HCH2  0   0.253  -5.1121   0.9082  -0.8917
 51Y  H13  H   HCH2  0   0.228  -3.4797   1.3913  -1.2819
 51Y  H14  H   HCH2  0   0.235  -4.7418  -1.3235  -1.6861
 51Y  H15  H   HCH2  0   0.234  -3.5203  -0.5337  -2.6580
 51Y  H16  H   HCH2  0   0.240  -1.8734  -1.7407  -1.4540
 51Y  H17  H   HCH2  0   0.242  -3.1270  -2.4360  -0.4526
 51Y  C5   C   CH3   0  -0.762   0.6373   2.2264  -0.7949

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
 51Y  C12  C10  single    1.521  0.020  1.521
 51Y  CL1  C3   single    1.731  0.020  1.731
 51Y  C5   C4   single    1.498  0.020  1.498
 51Y  C10  C13  single    1.531  0.020  1.531
 51Y  C10  O11  single    1.417  0.020  1.417
 51Y  C10  C9   single    1.540  0.020  1.540
 51Y  C13  C14  single    1.535  0.020  1.535
 51Y  C4   C3   aromatic  1.380  0.020  1.380
 51Y  C4   C6   aromatic  1.424  0.020  1.424
 51Y  C3   C2   aromatic  1.404  0.020  1.404
 51Y  N18  C17  triple    1.154  0.020  1.154
 51Y  N8   C6   single    1.353  0.020  1.353
 51Y  N8   C9   single    1.448  0.020  1.448
 51Y  C17  C2   single    1.417  0.020  1.417
 51Y  C2   C1   aromatic  1.393  0.020  1.393
 51Y  C6   C7   aromatic  1.406  0.020  1.406
 51Y  C1   C7   aromatic  1.374  0.020  1.374
 51Y  C9   C15  single    1.540  0.020  1.540
 51Y  C14  C15  single    1.547  0.020  1.547
 51Y  C7   H1   single    0.930  0.020  1.080
 51Y  C1   H2   single    0.930  0.020  1.080
 51Y  C5   H3   single    0.970  0.020  1.090
 51Y  C5   H4   single    0.970  0.020  1.090
 51Y  C5   H5   single    0.970  0.020  1.090
 51Y  N8   H6   single    0.860  0.020  1.020
 51Y  C9   H7   single    0.970  0.020  1.090
 51Y  O11  H8   single    0.850  0.020  0.980
 51Y  C12  H9   single    0.970  0.020  1.090
 51Y  C12  H10  single    0.970  0.020  1.090
 51Y  C12  H11  single    0.970  0.020  1.090
 51Y  C13  H12  single    0.970  0.020  1.090
 51Y  C13  H13  single    0.970  0.020  1.090
 51Y  C14  H14  single    0.970  0.020  1.090
 51Y  C14  H15  single    0.970  0.020  1.090
 51Y  C15  H16  single    0.970  0.020  1.090
 51Y  C15  H17  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
 51Y  H1   C7   C1   118.67  3.000
 51Y  H1   C7   C6   120.70  3.000
 51Y  C1   C7   C6   120.62  3.000
 51Y  N8   C6   C4   118.77  3.000
 51Y  N8   C6   C7   121.51  3.000
 51Y  C4   C6   C7   119.70  3.000
 51Y  H2   C1   C2   119.49  3.000
 51Y  H2   C1   C7   119.77  3.000
 51Y  C2   C1   C7   120.74  3.000
 51Y  C3   C4   C5   123.43  3.000
 51Y  C3   C4   C6   117.85  3.000
 51Y  C5   C4   C6   118.71  3.000
 51Y  CL1  C3   C2   116.96  3.000
 51Y  C2   C3   C4   122.62  3.000
 51Y  CL1  C3   C4   120.42  3.000
 51Y  C17  C2   C3   121.44  3.000
 51Y  C17  C2   C1   120.10  3.000
 51Y  C3   C2   C1   118.46  3.000
 51Y  H6   N8   C9   116.33  3.000
 51Y  H6   N8   C6   116.61  3.000
 51Y  C9   N8   C6   124.36  3.000
 51Y  H7   C9   C15  112.63  3.000
 51Y  H7   C9   C10  109.63  3.000
 51Y  C15  C9   C10  103.50  3.000
 51Y  H7   C9   N8   108.04  3.000
 51Y  C15  C9   N8   112.99  3.000
 51Y  C10  C9   N8   109.97  3.000
 51Y  C13  C10  C12  114.46  3.000
 51Y  C13  C10  O11  110.04  3.000
 51Y  C12  C10  O11  110.41  3.000
 51Y  O11  C10  C9   103.69  3.000
 51Y  C13  C10  C9   102.11  3.000
 51Y  C12  C10  C9   115.35  3.000
 51Y  H8   O11  C10  108.18  3.000
 51Y  H11  C12  H10  107.97  3.000
 51Y  H11  C12  H9   107.01  3.000
 51Y  H10  C12  H9   108.08  3.000
 51Y  H11  C12  C10  112.56  3.000
 51Y  H10  C12  C10  111.08  3.000
 51Y  H9   C12  C10  109.96  3.000
 51Y  H13  C13  H12  105.99  3.000
 51Y  H13  C13  C14  110.89  3.000
 51Y  H12  C13  C14  113.45  3.000
 51Y  H13  C13  C10  110.01  3.000
 51Y  H12  C13  C10  111.94  3.000
 51Y  C14  C13  C10  104.63  3.000
 51Y  H15  C14  H14  106.77  3.000
 51Y  H15  C14  C15  111.91  3.000
 51Y  H14  C14  C15  110.38  3.000
 51Y  H15  C14  C13  111.28  3.000
 51Y  H14  C14  C13  110.69  3.000
 51Y  C15  C14  C13  105.88  3.000
 51Y  H17  C15  H16  106.65  3.000
 51Y  H17  C15  C14  110.95  3.000
 51Y  H16  C15  C14  112.44  3.000
 51Y  H17  C15  C9   110.09  3.000
 51Y  H16  C15  C9   110.92  3.000
 51Y  C14  C15  C9   105.84  3.000
 51Y  N18  C17  C2   180.00  3.000
 51Y  H5   C5   H4   107.26  3.000
 51Y  H5   C5   H3   106.86  3.000
 51Y  H4   C5   H3   107.52  3.000
 51Y  H5   C5   C4   112.59  3.000
 51Y  H4   C5   C4   110.88  3.000
 51Y  H3   C5   C4   111.46  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
 51Y  CONST_01  C3   C4   C6   C7     0.00   0.0  0
 51Y  CONST_02  C3   C2   C1   C7     0.00   0.0  0
 51Y  CONST_03  C2   C3   C4   C6     0.00   0.0  0
 51Y  CONST_04  C2   C1   C7   C6     0.00   0.0  0
 51Y  CONST_05  C4   C3   C2   C1     0.00   0.0  0
 51Y  CONST_06  C4   C6   C7   C1     0.00   0.0  0
 51Y  CONST_07  C5   C4   C6   C7   180.00   0.0  0
 51Y  CONST_08  C17  C2   C1   C7   180.00   0.0  0
 51Y  CONST_09  CL1  C3   C4   C6   180.00   0.0  0
 51Y  CONST_10  CL1  C3   C2   C1   180.00   0.0  0
 51Y  CONST_11  N8   C6   C7   C1   180.00   0.0  0
 51Y  CONST_12  C2   C3   C4   C5   180.00   0.0  0
 51Y  CONST_13  C17  C2   C3   C4   180.00   0.0  0
 51Y  CONST_14  N8   C6   C4   C3   180.00   0.0  0
 51Y  CONST_15  C9   N8   C6   C7     0.00   0.0  0
 51Y  CONST_16  C9   N8   C6   C4   180.00   0.0  0
 51Y  CONST_17  H2   C1   C7   C6   180.00   0.0  0
 51Y  CONST_18  H1   C7   C6   C4   180.00   0.0  0
 51Y  Var_01    C13  C14  C15  C9    -2.76  30.0  1
 51Y  Var_02    C15  C14  C13  C10  -23.05  30.0  1
 51Y  Var_03    H3   C5   C4   C6   -66.14  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
 51Y  chir_01  C9   C10  N8   C15  positiv
 51Y  chir_02  C10  C12  C13  C9   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
 51Y  plan-1  C7   0.020
 51Y  plan-1  C6   0.020
 51Y  plan-1  C1   0.020
 51Y  plan-1  C4   0.020
 51Y  plan-1  C3   0.020
 51Y  plan-1  C2   0.020
 51Y  plan-1  N8   0.020
 51Y  plan-1  CL1  0.020
 51Y  plan-1  C17  0.020
 51Y  plan-1  N18  0.020
 51Y  plan-1  H1   0.020
 51Y  plan-1  H2   0.020
 51Y  plan-1  C5   0.020
 51Y  plan-2  C6   0.020
 51Y  plan-2  N8   0.020
 51Y  plan-2  C9   0.020
 51Y  plan-2  H6   0.020

