# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 07:44:53 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: ~{N}-[5-chloranyl-3-[[(3~{S})-4-cyclopentylcarbonyl-3-methyl-piperazin-1-yl]methyl]-2-methyl-phenyl]-2-methyl-pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN(CCN1C(=O)C2CCCC2)Cc3cc(Cl)cc(NC(=O)c4cnc(C)nc4)c3C
#
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
 98E  98E  ~{N}-[5-chloranyl-3-[[(3~{S})-4-cyclopentylcarbonyl-3-methyl-piperazin-1-yl]methyl]-2-methyl-phenyl]-2-methyl-pyrimidine-5-carboxamide  ligand  65  33  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_98E
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
 98E  C2   C   CH2   0  -0.275   2.3125   1.2748   0.2089
 98E  C3   C   CH2   0  -0.315   3.0482   0.3352   1.1466
 98E  C11  C   CH2   0  -0.448   8.8562  -1.7144   0.4062
 98E  C12  C   C     0   0.586   5.3972  -0.2834   0.9948
 98E  C14  C   CH3   0  -0.657   2.9073  -2.2187  -0.5138
 98E  C15  C   CR6   0   0.319  -2.4808   1.1374  -0.6083
 98E  C16  C   CR16  0  -0.252  -2.7256   2.4385  -0.1782
 98E  C17  C   CR6   0  -0.048  -1.7192   3.3755  -0.2926
 98E  C18  C   CR16  0  -0.270  -0.4922   3.0428  -0.8420
 98E  C19  C   CR6   0   0.076  -0.2525   1.7446  -1.2719
 98E  C20  C   CR6   0   0.031  -1.2437   0.7625  -1.1419
 98E  C21  C   CH3   0  -0.776  -1.0119  -0.6506  -1.5942
 98E  C25  C   CR6   0   0.361  -7.3156  -2.8999   0.1067
 98E  C27  C   CR16  0  -0.005  -5.8905  -1.7364   1.4344
 98E  C28  C   CR6   0  -0.196  -5.3539  -1.0808   0.3322
 98E  C29  C   CR16  0  -0.032  -5.9125  -1.4221  -0.8933
 98E  N1   N   NT    0  -0.409   1.8923   0.5842  -0.9928
 98E  N4   N   NT    0  -0.463   4.1525  -0.3162   0.4616
 98E  C5   C   CH1   0  -0.139   3.7615  -0.9811  -0.7775
 98E  C6   C   CH2   0  -0.259   3.0423   0.0261  -1.6714
 98E  C7   C   CH2   0  -0.422   7.9260  -0.5103   0.6752
 98E  C8   C   CH1   0  -0.427   6.5262  -0.9575   0.2339
 98E  C9   C   CH2   0  -0.440   6.5578  -2.4806   0.4366
 98E  C10  C   CH2   0  -0.463   7.9456  -2.8579  -0.0711
 98E  O13  O   O     0  -0.505   5.6094   0.2553   2.0758
 98E  N24  N   NH1   0  -0.775  -3.5147   0.1831  -0.5514
 98E  N26  N   N     0  -0.406  -6.8493  -2.6392   1.3279
 98E  N30  N   N     0  -0.404  -6.8790  -2.3168  -1.0077
 98E  C32  C   C     0   0.542  -4.2941  -0.0560   0.5301
 98E  O33  O   O     0  -0.452  -4.1557   0.5058   1.6012
 98E  H1   H   HCH2  0   0.249   1.4396   1.6700   0.7319
 98E  H2   H   HCH2  0   0.194   2.9659   2.1327  -0.0290
 98E  H3   H   HCH2  0   0.267   3.4332   0.8953   1.9935
 98E  H4   H   HCH2  0   0.240   2.3565  -0.4145   1.5409
 98E  H5   H   HCH2  0   0.227   9.6267  -1.4840  -0.3303
 98E  H6   H   HCH2  0   0.225   9.3775  -1.9970   1.3223
 98E  H7   H   HCH3  0   0.232   2.6941  -2.7247  -1.4562
 98E  H8   H   HCH3  0   0.237   3.4283  -2.9220   0.1354
 98E  H9   H   HCH3  0   0.239   1.9534  -1.9669  -0.0537
 98E  H10  H   HCR6  0   0.284  -3.6924   2.7193   0.2135
 98E  H11  H   HCR6  0   0.271   0.2831   3.7927  -0.9342
 98E  H12  H   HCH3  0   0.254  -1.3751  -0.8107  -2.6129
 98E  H13  H   HCH3  0   0.280   0.0455  -0.8998  -1.5721
 98E  H14  H   HCH3  0   0.244  -1.5248  -1.3669  -0.9526
 98E  H17  H   HCR6  0   0.284  -5.5223  -1.5273   2.4326
 98E  H18  H   HCR6  0   0.280  -5.5922  -0.9503  -1.8176
 98E  H20  H   HCH1  0   0.265   4.6564  -1.2974  -1.3090
 98E  H21  H   HCH2  0   0.241   2.7119  -0.4841  -2.5792
 98E  H22  H   HCH2  0   0.211   3.7567   0.8092  -1.9799
 98E  H23  H   HCH2  0   0.233   7.9211  -0.2641   1.7358
 98E  H24  H   HCH2  0   0.233   8.2418   0.3879   0.1430
 98E  H25  H   HCH1  0   0.259   6.4292  -0.7568  -0.8368
 98E  H26  H   HCH2  0   0.234   6.4602  -2.7099   1.5022
 98E  H27  H   HCH2  0   0.254   5.7596  -3.0070  -0.0876
 98E  H28  H   HCH2  0   0.237   7.9300  -2.9004  -1.1627
 98E  H29  H   HCH2  0   0.243   8.2721  -3.8358   0.2846
 98E  H30  H   HNH1  0   0.433  -3.6044  -0.4303  -1.3461
 98E  H31  H   HCH3  0   0.274  -9.3827  -3.3626  -0.0210
 98E  H32  H   HCH3  0   0.265  -8.3551  -4.4389  -0.9535
 98E  H33  H   HCH3  0   0.263  -8.4279  -4.5811   0.8189
 98E  C23  C   CH2   0  -0.369   1.0935   1.4181  -1.8687
 98E  CL   CL  CL    0  -0.117  -2.0055   4.9983   0.2377
 98E  C31  C   CH3   0  -0.732  -8.4242  -3.8873  -0.0182
 98E  H15  H   HCH2  0   0.256   0.9520   0.8840  -2.8122
 98E  H16  H   HCH2  0   0.231   1.6103   2.3557  -2.1286

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
 98E  N30  C29  aromatic  1.322  0.020  1.322
 98E  N30  C25  aromatic  1.331  0.020  1.331
 98E  C31  C25  single    1.490  0.020  1.490
 98E  C29  C28  aromatic  1.389  0.020  1.389
 98E  C25  N26  aromatic  1.333  0.020  1.333
 98E  O33  C32  double    1.217  0.020  1.217
 98E  C28  C32  single    1.488  0.020  1.488
 98E  C28  C27  aromatic  1.390  0.020  1.390
 98E  N26  C27  aromatic  1.321  0.020  1.321
 98E  C32  N24  single    1.354  0.020  1.354
 98E  N24  C15  single    1.408  0.020  1.408
 98E  C16  C15  aromatic  1.392  0.020  1.392
 98E  C16  C17  aromatic  1.380  0.020  1.380
 98E  CL   C17  single    1.731  0.020  1.731
 98E  C15  C20  aromatic  1.399  0.020  1.399
 98E  C14  C5   single    1.527  0.020  1.527
 98E  C17  C18  aromatic  1.385  0.020  1.385
 98E  C5   C6   single    1.527  0.020  1.527
 98E  C5   N4   single    1.459  0.020  1.459
 98E  C20  C21  single    1.502  0.020  1.502
 98E  C20  C19  aromatic  1.401  0.020  1.401
 98E  O13  C12  double    1.226  0.020  1.226
 98E  C6   N1   single    1.447  0.020  1.447
 98E  C18  C19  aromatic  1.388  0.020  1.388
 98E  C19  C23  single    1.508  0.020  1.508
 98E  C12  N4   single    1.354  0.020  1.354
 98E  C12  C8   single    1.519  0.020  1.519
 98E  N4   C3   single    1.454  0.020  1.454
 98E  N1   C23  single    1.449  0.020  1.449
 98E  N1   C2   single    1.448  0.020  1.448
 98E  C7   C8   single    1.534  0.020  1.534
 98E  C7   C11  single    1.545  0.020  1.545
 98E  C8   C9   single    1.537  0.020  1.537
 98E  C3   C2   single    1.518  0.020  1.518
 98E  C10  C11  single    1.538  0.020  1.538
 98E  C10  C9   single    1.525  0.020  1.525
 98E  C2   H1   single    0.970  0.020  1.090
 98E  C2   H2   single    0.970  0.020  1.090
 98E  C3   H3   single    0.970  0.020  1.090
 98E  C3   H4   single    0.970  0.020  1.090
 98E  C11  H5   single    0.970  0.020  1.090
 98E  C11  H6   single    0.970  0.020  1.090
 98E  C14  H7   single    0.970  0.020  1.090
 98E  C14  H8   single    0.970  0.020  1.090
 98E  C14  H9   single    0.970  0.020  1.090
 98E  C16  H10  single    0.930  0.020  1.080
 98E  C18  H11  single    0.930  0.020  1.080
 98E  C21  H12  single    0.970  0.020  1.090
 98E  C21  H13  single    0.970  0.020  1.090
 98E  C21  H14  single    0.970  0.020  1.090
 98E  C23  H15  single    0.970  0.020  1.090
 98E  C23  H16  single    0.970  0.020  1.090
 98E  C27  H17  single    0.930  0.020  1.080
 98E  C29  H18  single    0.930  0.020  1.080
 98E  C5   H20  single    0.970  0.020  1.090
 98E  C6   H21  single    0.970  0.020  1.090
 98E  C6   H22  single    0.970  0.020  1.090
 98E  C7   H23  single    0.970  0.020  1.090
 98E  C7   H24  single    0.970  0.020  1.090
 98E  C8   H25  single    0.970  0.020  1.090
 98E  C9   H26  single    0.970  0.020  1.090
 98E  C9   H27  single    0.970  0.020  1.090
 98E  C10  H28  single    0.970  0.020  1.090
 98E  C10  H29  single    0.970  0.020  1.090
 98E  N24  H30  single    0.860  0.020  1.020
 98E  C31  H31  single    0.970  0.020  1.090
 98E  C31  H32  single    0.970  0.020  1.090
 98E  C31  H33  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
 98E  H2   C2   H1   107.16  3.000
 98E  H2   C2   N1   111.31  3.000
 98E  H1   C2   N1   109.76  3.000
 98E  H2   C2   C3   109.10  3.000
 98E  H1   C2   C3   108.41  3.000
 98E  N1   C2   C3   110.98  3.000
 98E  H4   C3   H3   107.25  3.000
 98E  H4   C3   N4   110.07  3.000
 98E  H3   C3   N4   109.23  3.000
 98E  H4   C3   C2   109.92  3.000
 98E  H3   C3   C2   109.53  3.000
 98E  N4   C3   C2   110.77  3.000
 98E  H6   C11  H5   106.52  3.000
 98E  H6   C11  C10  110.54  3.000
 98E  H5   C11  C10  111.46  3.000
 98E  H6   C11  C7   110.08  3.000
 98E  H5   C11  C7   112.23  3.000
 98E  C10  C11  C7   106.08  3.000
 98E  O13  C12  C8   120.52  3.000
 98E  C8   C12  N4   118.36  3.000
 98E  O13  C12  N4   121.11  3.000
 98E  H9   C14  H8   108.45  3.000
 98E  H9   C14  H7   107.53  3.000
 98E  H8   C14  H7   107.99  3.000
 98E  H9   C14  C5   112.07  3.000
 98E  H8   C14  C5   111.01  3.000
 98E  H7   C14  C5   109.65  3.000
 98E  N24  C15  C20  118.89  3.000
 98E  C20  C15  C16  121.60  3.000
 98E  N24  C15  C16  119.46  3.000
 98E  H10  C16  C17  120.42  3.000
 98E  H10  C16  C15  120.82  3.000
 98E  C17  C16  C15  118.74  3.000
 98E  CL   C17  C18  119.56  3.000
 98E  C18  C17  C16  121.06  3.000
 98E  CL   C17  C16  119.38  3.000
 98E  H11  C18  C19  119.85  3.000
 98E  H11  C18  C17  120.12  3.000
 98E  C19  C18  C17  120.03  3.000
 98E  C23  C19  C20  121.08  3.000
 98E  C23  C19  C18  118.62  3.000
 98E  C20  C19  C18  120.30  3.000
 98E  C21  C20  C19  121.49  3.000
 98E  C19  C20  C15  118.24  3.000
 98E  C21  C20  C15  120.25  3.000
 98E  H14  C21  H13  107.17  3.000
 98E  H14  C21  H12  107.22  3.000
 98E  H13  C21  H12  107.98  3.000
 98E  H14  C21  C20  111.62  3.000
 98E  H13  C21  C20  111.09  3.000
 98E  H12  C21  C20  111.54  3.000
 98E  C31  C25  N30  117.65  3.000
 98E  C31  C25  N26  117.82  3.000
 98E  N30  C25  N26  124.51  3.000
 98E  H17  C27  N26  116.90  3.000
 98E  H17  C27  C28  120.52  3.000
 98E  N26  C27  C28  122.58  3.000
 98E  C32  C28  C29  124.96  3.000
 98E  C32  C28  C27  119.63  3.000
 98E  C29  C28  C27  115.36  3.000
 98E  H18  C29  N30  115.84  3.000
 98E  H18  C29  C28  121.70  3.000
 98E  N30  C29  C28  122.44  3.000
 98E  C6   N1   C23  112.12  3.000
 98E  C23  N1   C2   112.76  3.000
 98E  C6   N1   C2   110.02  3.000
 98E  C5   N4   C12  126.26  3.000
 98E  C12  N4   C3   120.11  3.000
 98E  C5   N4   C3   113.62  3.000
 98E  H20  C5   C6   107.05  3.000
 98E  H20  C5   N4   109.08  3.000
 98E  C6   C5   N4   108.83  3.000
 98E  H20  C5   C14  107.99  3.000
 98E  N4   C5   C14  111.88  3.000
 98E  C6   C5   C14  111.86  3.000
 98E  H22  C6   H21  107.14  3.000
 98E  H22  C6   C5   109.07  3.000
 98E  H21  C6   C5   108.72  3.000
 98E  H22  C6   N1   111.82  3.000
 98E  H21  C6   N1   109.23  3.000
 98E  C5   C6   N1   110.74  3.000
 98E  H24  C7   H23  106.87  3.000
 98E  H24  C7   C8   111.33  3.000
 98E  H23  C7   C8   110.00  3.000
 98E  H24  C7   C11  112.49  3.000
 98E  H23  C7   C11  110.39  3.000
 98E  C8   C7   C11  105.79  3.000
 98E  H25  C8   C9   108.23  3.000
 98E  H25  C8   C7   108.00  3.000
 98E  C9   C8   C7   103.42  3.000
 98E  H25  C8   C12  110.06  3.000
 98E  C9   C8   C12  112.89  3.000
 98E  C7   C8   C12  113.87  3.000
 98E  H27  C9   H26  107.56  3.000
 98E  H27  C9   C10  112.75  3.000
 98E  H26  C9   C10  110.70  3.000
 98E  H27  C9   C8   113.57  3.000
 98E  H26  C9   C8   109.52  3.000
 98E  C10  C9   C8   102.71  3.000
 98E  H29  C10  H28  107.17  3.000
 98E  H29  C10  C9   112.68  3.000
 98E  H28  C10  C9   109.23  3.000
 98E  H29  C10  C11  112.84  3.000
 98E  H28  C10  C11  110.34  3.000
 98E  C9   C10  C11  104.57  3.000
 98E  H30  N24  C32  118.10  3.000
 98E  H30  N24  C15  116.49  3.000
 98E  C32  N24  C15  125.05  3.000
 98E  C27  N26  C25  117.47  3.000
 98E  C29  N30  C25  117.63  3.000
 98E  O33  C32  N24  123.76  3.000
 98E  N24  C32  C28  115.17  3.000
 98E  O33  C32  C28  121.07  3.000
 98E  H16  C23  H15  105.83  3.000
 98E  H16  C23  N1   111.94  3.000
 98E  H15  C23  N1   108.16  3.000
 98E  H16  C23  C19  109.14  3.000
 98E  H15  C23  C19  109.37  3.000
 98E  N1   C23  C19  112.17  3.000
 98E  H33  C31  H32  109.79  3.000
 98E  H33  C31  H31  107.78  3.000
 98E  H32  C31  H31  107.27  3.000
 98E  H33  C31  C25  111.16  3.000
 98E  H32  C31  C25  111.15  3.000
 98E  H31  C31  C25  109.55  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
 98E  CONST_01  C18  C17  C16  C15    0.00   0.0  0
 98E  CONST_02  C18  C19  C20  C15    0.00   0.0  0
 98E  CONST_03  C19  C20  C15  C16    0.00   0.0  0
 98E  CONST_04  C19  C18  C17  C16    0.00   0.0  0
 98E  CONST_05  C20  C15  C16  C17    0.00   0.0  0
 98E  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 98E  CONST_07  C28  C29  N30  C25    0.00   0.0  0
 98E  CONST_08  C28  C27  N26  C25    0.00   0.0  0
 98E  CONST_09  N30  C29  C28  C27    0.00   0.0  0
 98E  CONST_10  N30  C25  N26  C27    0.00   0.0  0
 98E  CONST_11  N26  C25  N30  C29    0.00   0.0  0
 98E  CONST_12  N26  C27  C28  C29    0.00   0.0  0
 98E  CONST_13  CL   C17  C16  C15  180.00   0.0  0
 98E  CONST_14  C23  C19  C20  C15  180.00   0.0  0
 98E  CONST_15  C21  C20  C15  C16  180.00   0.0  0
 98E  CONST_16  N24  C15  C16  C17  180.00   0.0  0
 98E  CONST_17  C23  C19  C18  C17  180.00   0.0  0
 98E  CONST_18  C21  C20  C19  C18  180.00   0.0  0
 98E  CONST_19  N24  C15  C20  C19  180.00   0.0  0
 98E  CONST_20  CL   C17  C18  C19  180.00   0.0  0
 98E  CONST_21  C31  C25  N26  C27  180.00   0.0  0
 98E  CONST_22  C31  C25  N30  C29  180.00   0.0  0
 98E  CONST_23  C32  C28  C27  N26  180.00   0.0  0
 98E  CONST_24  C32  C28  C29  N30  180.00   0.0  0
 98E  CONST_25  C8   C12  N4   C3   180.00   0.0  0
 98E  CONST_26  C8   C12  N4   C5     0.00   0.0  0
 98E  CONST_27  H11  C18  C17  C16  180.00   0.0  0
 98E  CONST_28  H10  C16  C17  C18  180.00   0.0  0
 98E  CONST_29  H18  C29  N30  C25  180.00   0.0  0
 98E  CONST_30  H17  C27  N26  C25  180.00   0.0  0
 98E  CONST_31  O13  C12  N4   C3     0.00   0.0  0
 98E  CONST_32  C28  C32  N24  C15  180.00   0.0  0
 98E  CONST_33  O13  C12  N4   C5   180.00   0.0  0
 98E  CONST_37  O33  C32  N24  C15    0.00   0.0  0
 98E  Var_01    C5   C6   N1   C2    60.76  30.0  1
 98E  Var_02    C5   N4   C3   C2   -53.10  30.0  1
 98E  Var_03    C6   N1   C2   C3   -58.62  30.0  1
 98E  Var_04    C8   C9   C10  C11   38.47  30.0  1
 98E  Var_05    N4   C3   C2   N1    54.16  30.0  1
 98E  Var_06    C9   C10  C11  C7   -21.00  30.0  1
 98E  Var_07    C10  C11  C7   C8    -4.61  30.0  1
 98E  Var_08    C19  C23  N1   C2   -68.09  30.0  3
 98E  Var_09    N1   C23  C19  C18  109.05  30.0  2
 98E  Var_10    O33  C32  C28  C27  -21.82  30.0  2
 98E  Var_11    H12  C21  C20  C15   84.00  30.0  2
 98E  Var_12    H31  C31  C25  N26   94.06  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
 98E  chir_01  C5  C14  C6  N4  negativ
 98E  chir_02  C8  C12  C7  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
 98E  plan-1  C15  0.020
 98E  plan-1  C16  0.020
 98E  plan-1  C17  0.020
 98E  plan-1  C18  0.020
 98E  plan-1  C19  0.020
 98E  plan-1  C20  0.020
 98E  plan-1  C21  0.020
 98E  plan-1  N24  0.020
 98E  plan-1  H10  0.020
 98E  plan-1  H11  0.020
 98E  plan-1  C23  0.020
 98E  plan-1  CL   0.020
 98E  plan-2  C3   0.020
 98E  plan-2  C12  0.020
 98E  plan-2  N4   0.020
 98E  plan-2  C5   0.020
 98E  plan-2  C8   0.020
 98E  plan-2  O13  0.020
 98E  plan-3  C25  0.020
 98E  plan-3  C27  0.020
 98E  plan-3  C28  0.020
 98E  plan-3  C29  0.020
 98E  plan-3  N26  0.020
 98E  plan-3  N30  0.020
 98E  plan-3  C32  0.020
 98E  plan-3  H17  0.020
 98E  plan-3  H18  0.020
 98E  plan-3  C31  0.020
 98E  plan-4  C15  0.020
 98E  plan-4  C28  0.020
 98E  plan-4  N24  0.020
 98E  plan-4  C32  0.020
 98E  plan-4  O33  0.020
 98E  plan-4  H30  0.020

