# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:49:55 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C1=C(CN2CC[C@@H](CC2)C(O)(C#C)C#C)NC(=N[C@H]1c3ccc(F)cc3Cl)c4ccccn4
#
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
 58H  58H  'methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate'  ligand  63  37  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_58H
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
 58H  C14  C   CSP   0   0.382   5.7139  -0.4396   2.2310
 58H  C11  C   CH2   0  -0.429   3.0951  -0.6545   0.8550
 58H  CL3  CL  CL    0  -0.113  -4.3232   2.4033   0.3807
 58H  C01  C   CH3   0  -0.418   0.0043   3.4079  -3.2676
 58H  O02  O   O2    0  -0.463  -0.5995   2.4048  -2.4582
 58H  C04  C   C     0  -0.253  -0.9149   0.2394  -1.7369
 58H  C05  C   C     0   0.407  -0.4964  -1.0272  -1.5006
 58H  C06  C   CH2   0  -0.378   0.8072  -1.6363  -1.9488
 58H  N07  N   NT    0  -0.406   1.9164  -1.0074  -1.2641
 58H  C08  C   CH2   0  -0.274   3.1677  -1.1543  -1.9800
 58H  C09  C   CH2   0  -0.449   4.2655  -0.3320  -1.3217
 58H  C10  C   CH1   0  -0.267   4.4385  -0.7433   0.1383
 58H  C12  C   CH2   0  -0.302   2.0413  -1.4580   0.1093
 58H  C13  C   CT    0  -0.036   5.5428   0.0717   0.8630
 58H  C15  C   CSP1  0  -0.578   5.8535  -0.8718   3.3415
 58H  O16  O   OH1   0  -0.645   5.2210   1.4360   0.9877
 58H  C17  C   CSP   0   0.345   6.8293  -0.0979   0.1596
 58H  C18  C   CSP1  0  -0.569   7.8723  -0.2236  -0.4218
 58H  N19  N   NH1   0  -0.710  -1.2819  -1.8374  -0.7334
 58H  C20  C   C     0   0.441  -2.5839  -1.4897  -0.4710
 58H  C21  C   CR6   0   0.193  -3.4545  -2.5964  -0.0049
 58H  C22  C   CR16  0  -0.299  -4.7673  -2.3525   0.3807
 58H  C23  C   CR16  0  -0.147  -5.5352  -3.4274   0.7920
 58H  C24  C   CR16  0  -0.318  -4.9681  -4.6936   0.8111
 58H  C25  C   CR16  0  -0.062  -3.6447  -4.8294   0.4186
 58H  N26  N   N     0  -0.449  -2.9045  -3.8049   0.0189
 58H  N27  N   N     0  -0.387  -3.0528  -0.3244  -0.6365
 58H  C28  C   CH1   0  -0.199  -2.1292   0.7444  -0.9894
 58H  C29  C   CR6   0   0.229  -1.7637   1.4921   0.2877
 58H  C30  C   CR6   0  -0.085  -2.7072   2.2449   0.9849
 58H  C32  C   CR16  0  -0.363  -2.4020   2.9106   2.1622
 58H  C33  C   CR6   0   0.519  -1.1128   2.8152   2.6479
 58H  C35  C   CR16  0  -0.397  -0.1360   2.0947   1.9936
 58H  C36  C   CR16  0  -0.314  -0.4791   1.4441   0.8182
 58H  O37  O   O     0  -0.459   0.6855   0.8537  -3.4114
 58H  F34  F   F     0  -0.311  -0.8091   3.4543   3.7857
 58H  H1   H   HCH2  0   0.248   3.1748  -1.0366   1.8744
 58H  H2   H   HCH2  0   0.227   2.7742   0.3889   0.9232
 58H  H3   H   HCH3  0   0.249  -0.4587   4.3461  -2.9749
 58H  H4   H   HCH3  0   0.234   1.0790   3.4690  -3.0966
 58H  H5   H   HCH3  0   0.235  -0.1775   3.2336  -4.3283
 58H  H6   H   HCH2  0   0.234   0.7728  -2.7248  -1.7787
 58H  H7   H   HCH2  0   0.279   0.9182  -1.4944  -3.0212
 58H  H9   H   HCH2  0   0.194   3.4892  -2.2096  -2.0351
 58H  H10  H   HCH2  0   0.245   3.0269  -0.8097  -3.0053
 58H  H11  H   HCH2  0   0.252   5.1926  -0.4727  -1.8804
 58H  H12  H   HCH2  0   0.221   3.9911   0.7253  -1.4011
 58H  H13  H   HCH1  0   0.250   4.7712  -1.7880   0.1556
 58H  H14  H   HCH2  0   0.208   2.2942  -2.5327   0.1588
 58H  H15  H   HCH2  0   0.244   1.0843  -1.3426   0.6229
 58H  H16  H   H     0   0.285   5.9763  -1.2582   4.3278
 58H  H17  H   HOH1  0   0.460   5.0864   1.8058   0.1070
 58H  H18  H   H     0   0.286   8.7994  -0.3361  -0.9366
 58H  H19  H   HCR6  0   0.277  -5.1612  -1.3463   0.3575
 58H  H20  H   HCR6  0   0.281  -6.5627  -3.2792   1.0964
 58H  H21  H   HCR6  0   0.279  -5.5337  -5.5597   1.1247
 58H  H22  H   HCR6  0   0.272  -3.1655  -5.8012   0.4243
 58H  H23  H   HCR6  0   0.300  -3.1466   3.4944   2.6866
 58H  H24  H   HCR6  0   0.280   0.8715   2.0440   2.3839
 58H  H25  H   HCR6  0   0.277   0.2879   0.8947   0.2867
 58H  H8   H   HNH1  0   0.414  -1.0300  -2.8087  -0.6074
 58H  H26  H   HCH1  0   0.262  -2.6861   1.4379  -1.6235
 58H  C03  C   C     0   0.572  -0.1810   1.1476  -2.6182

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
 58H  C18  C17  triple    1.201  0.020  1.201
 58H  C15  C14  triple    1.200  0.020  1.200
 58H  C17  C13  single    1.476  0.020  1.476
 58H  C14  C13  single    1.470  0.020  1.470
 58H  O37  C03  double    1.211  0.020  1.211
 58H  C13  C10  single    1.552  0.020  1.552
 58H  C13  O16  single    1.407  0.020  1.407
 58H  N26  C25  aromatic  1.326  0.020  1.326
 58H  N26  C21  aromatic  1.328  0.020  1.328
 58H  C06  C05  single    1.507  0.020  1.507
 58H  C06  N07  single    1.447  0.020  1.447
 58H  N19  C05  single    1.365  0.020  1.365
 58H  N19  C20  single    1.373  0.020  1.373
 58H  C10  C09  single    1.527  0.020  1.527
 58H  C10  C11  single    1.525  0.020  1.525
 58H  C05  C04  double    1.355  0.020  1.355
 58H  C25  C24  aromatic  1.387  0.020  1.387
 58H  C20  N27  double    1.267  0.020  1.267
 58H  C20  C21  single    1.483  0.020  1.483
 58H  C04  C03  single    1.463  0.020  1.463
 58H  C04  C28  single    1.513  0.020  1.513
 58H  N27  C28  single    1.456  0.020  1.456
 58H  C03  O02  single    1.335  0.020  1.335
 58H  C28  C29  single    1.524  0.020  1.524
 58H  C21  C22  aromatic  1.390  0.020  1.390
 58H  C09  C08  single    1.521  0.020  1.521
 58H  C24  C23  aromatic  1.388  0.020  1.388
 58H  C22  C23  aromatic  1.384  0.020  1.384
 58H  C11  C12  single    1.521  0.020  1.521
 58H  N07  C08  single    1.449  0.020  1.449
 58H  N07  C12  single    1.451  0.020  1.451
 58H  O02  C01  single    1.423  0.020  1.423
 58H  C36  C29  aromatic  1.391  0.020  1.391
 58H  C36  C35  aromatic  1.387  0.020  1.387
 58H  C29  C30  aromatic  1.394  0.020  1.394
 58H  C35  C33  aromatic  1.379  0.020  1.379
 58H  C30  CL3  single    1.733  0.020  1.733
 58H  C30  C32  aromatic  1.386  0.020  1.386
 58H  C33  C32  aromatic  1.381  0.020  1.381
 58H  C33  F34  single    1.340  0.020  1.340
 58H  C11  H1   single    0.939  0.020  1.096
 58H  C11  H2   single    0.939  0.020  1.096
 58H  C01  H3   single    0.939  0.020  1.096
 58H  C01  H4   single    0.939  0.020  1.096
 58H  C01  H5   single    0.939  0.020  1.096
 58H  C06  H6   single    0.939  0.020  1.096
 58H  C06  H7   single    0.939  0.020  1.096
 58H  C08  H9   single    0.939  0.020  1.096
 58H  C08  H10  single    0.939  0.020  1.096
 58H  C09  H11  single    0.939  0.020  1.096
 58H  C09  H12  single    0.939  0.020  1.096
 58H  C10  H13  single    0.939  0.020  1.096
 58H  C12  H14  single    0.939  0.020  1.096
 58H  C12  H15  single    0.939  0.020  1.096
 58H  C15  H16  single    0.913  0.020  1.066
 58H  O16  H17  single    0.832  0.020  0.971
 58H  C18  H18  single    0.913  0.020  1.066
 58H  C22  H19  single    0.929  0.020  1.085
 58H  C23  H20  single    0.929  0.020  1.085
 58H  C24  H21  single    0.929  0.020  1.085
 58H  C25  H22  single    0.929  0.020  1.085
 58H  C32  H23  single    0.929  0.020  1.085
 58H  C35  H24  single    0.929  0.020  1.085
 58H  C36  H25  single    0.929  0.020  1.085
 58H  N19  H8   single    0.868  0.020  1.013
 58H  C28  H26  single    0.939  0.020  1.096

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
 58H  C15  C14  C13  180.00  3.000
 58H  H2   C11  H1   107.28  3.000
 58H  H2   C11  C12  109.35  3.000
 58H  H1   C11  C12  108.88  3.000
 58H  H2   C11  C10  110.08  3.000
 58H  H1   C11  C10  110.74  3.000
 58H  C12  C11  C10  110.44  3.000
 58H  H5   C01  H4   109.03  3.000
 58H  H5   C01  H3   109.22  3.000
 58H  H4   C01  H3   109.24  3.000
 58H  H5   C01  O02  111.71  3.000
 58H  H4   C01  O02  111.63  3.000
 58H  H3   C01  O02  105.94  3.000
 58H  C03  O02  C01  117.56  3.000
 58H  C28  C04  C05  118.29  3.000
 58H  C28  C04  C03  119.54  3.000
 58H  C05  C04  C03  122.04  3.000
 58H  N19  C05  C06  115.16  3.000
 58H  N19  C05  C04  118.38  3.000
 58H  C06  C05  C04  126.39  3.000
 58H  H7   C06  H6   106.52  3.000
 58H  H7   C06  N07  109.37  3.000
 58H  H6   C06  N07  112.34  3.000
 58H  H7   C06  C05  109.20  3.000
 58H  H6   C06  C05  109.04  3.000
 58H  N07  C06  C05  110.28  3.000
 58H  C12  N07  C08  111.21  3.000
 58H  C12  N07  C06  112.27  3.000
 58H  C08  N07  C06  112.58  3.000
 58H  H10  C08  H9   107.01  3.000
 58H  H10  C08  C09  109.22  3.000
 58H  H9   C08  C09  109.14  3.000
 58H  H10  C08  N07  108.72  3.000
 58H  H9   C08  N07  111.89  3.000
 58H  C09  C08  N07  110.77  3.000
 58H  H12  C09  H11  107.46  3.000
 58H  H12  C09  C10  110.97  3.000
 58H  H11  C09  C10  111.01  3.000
 58H  H12  C09  C08  108.04  3.000
 58H  H11  C09  C08  108.77  3.000
 58H  C10  C09  C08  110.48  3.000
 58H  H13  C10  C13  106.09  3.000
 58H  H13  C10  C09  107.83  3.000
 58H  C13  C10  C09  112.69  3.000
 58H  H13  C10  C11  108.38  3.000
 58H  C09  C10  C11  109.50  3.000
 58H  C13  C10  C11  112.13  3.000
 58H  H15  C12  H14  106.39  3.000
 58H  H15  C12  N07  109.68  3.000
 58H  H14  C12  N07  111.35  3.000
 58H  H15  C12  C11  108.71  3.000
 58H  H14  C12  C11  109.47  3.000
 58H  N07  C12  C11  111.09  3.000
 58H  C17  C13  O16  110.67  3.000
 58H  O16  C13  C10  112.82  3.000
 58H  C17  C13  C10  109.71  3.000
 58H  O16  C13  C14  106.33  3.000
 58H  C10  C13  C14  109.55  3.000
 58H  C17  C13  C14  107.57  3.000
 58H  H16  C15  C14  180.00  3.000
 58H  H17  O16  C13  108.82  3.000
 58H  C18  C17  C13  180.00  3.000
 58H  H18  C18  C17  180.00  3.000
 58H  H8   N19  C20  117.11  3.000
 58H  H8   N19  C05  119.79  3.000
 58H  C20  N19  C05  120.20  3.000
 58H  N27  C20  C21  120.67  3.000
 58H  C21  C20  N19  115.32  3.000
 58H  N27  C20  N19  123.98  3.000
 58H  N26  C21  C22  123.09  3.000
 58H  C22  C21  C20  120.71  3.000
 58H  N26  C21  C20  116.20  3.000
 58H  H19  C22  C23  121.83  3.000
 58H  H19  C22  C21  120.11  3.000
 58H  C23  C22  C21  118.06  3.000
 58H  H20  C23  C24  120.62  3.000
 58H  H20  C23  C22  120.29  3.000
 58H  C24  C23  C22  119.09  3.000
 58H  H21  C24  C25  120.19  3.000
 58H  H21  C24  C23  121.42  3.000
 58H  C25  C24  C23  118.39  3.000
 58H  H22  C25  N26  116.59  3.000
 58H  H22  C25  C24  120.55  3.000
 58H  N26  C25  C24  122.85  3.000
 58H  C25  N26  C21  118.51  3.000
 58H  C28  N27  C20  118.17  3.000
 58H  H26  C28  C29  107.29  3.000
 58H  H26  C28  N27  106.46  3.000
 58H  C29  C28  N27  108.00  3.000
 58H  H26  C28  C04  109.53  3.000
 58H  C29  C28  C04  112.66  3.000
 58H  N27  C28  C04  112.57  3.000
 58H  C36  C29  C30  116.94  3.000
 58H  C30  C29  C28  121.44  3.000
 58H  C36  C29  C28  121.61  3.000
 58H  C32  C30  C29  122.34  3.000
 58H  C32  C30  CL3  117.23  3.000
 58H  C29  C30  CL3  120.41  3.000
 58H  H23  C32  C33  120.62  3.000
 58H  H23  C32  C30  121.28  3.000
 58H  C33  C32  C30  118.10  3.000
 58H  F34  C33  C35  119.45  3.000
 58H  F34  C33  C32  118.51  3.000
 58H  C35  C33  C32  122.04  3.000
 58H  H24  C35  C36  120.96  3.000
 58H  H24  C35  C33  120.87  3.000
 58H  C36  C35  C33  118.18  3.000
 58H  H25  C36  C35  118.62  3.000
 58H  H25  C36  C29  118.98  3.000
 58H  C35  C36  C29  122.39  3.000
 58H  O37  C03  C04  127.08  3.000
 58H  C04  C03  O02  110.81  3.000
 58H  O37  C03  O02  122.11  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
 58H  CONST_01  C24  C25  N26  C21     0.00   0.0  0
 58H  CONST_02  C24  C23  C22  C21     0.00   0.0  0
 58H  CONST_03  C25  N26  C21  C22     0.00   0.0  0
 58H  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 58H  CONST_05  N26  C25  C24  C23     0.00   0.0  0
 58H  CONST_06  N26  C21  C22  C23     0.00   0.0  0
 58H  CONST_07  C33  C35  C36  C29     0.00   0.0  0
 58H  CONST_08  C33  C32  C30  C29     0.00   0.0  0
 58H  CONST_09  C35  C36  C29  C30     0.00   0.0  0
 58H  CONST_10  C35  C33  C32  C30     0.00   0.0  0
 58H  CONST_11  C36  C29  C30  C32     0.00   0.0  0
 58H  CONST_12  C36  C35  C33  C32     0.00   0.0  0
 58H  CONST_13  C25  N26  C21  C20   180.00   0.0  0
 58H  CONST_14  C23  C22  C21  C20   180.00   0.0  0
 58H  CONST_15  C35  C36  C29  C28   180.00   0.0  0
 58H  CONST_16  C32  C30  C29  C28   180.00   0.0  0
 58H  CONST_19  C28  N27  C20  N19     0.00   0.0  0
 58H  CONST_20  C28  N27  C20  C21   180.00   0.0  0
 58H  CONST_21  C28  C29  C30  CL3     0.00   0.0  0
 58H  CONST_22  C36  C29  C30  CL3   180.00   0.0  0
 58H  CONST_23  C33  C32  C30  CL3   180.00   0.0  0
 58H  CONST_24  F34  C33  C32  C30   180.00   0.0  0
 58H  CONST_25  F34  C33  C35  C36   180.00   0.0  0
 58H  CONST_26  H19  C22  C21  C20     0.00   0.0  0
 58H  CONST_27  H22  C25  N26  C21   180.00   0.0  0
 58H  CONST_28  H20  C23  C22  C21   180.00   0.0  0
 58H  CONST_29  H21  C24  C23  C22   180.00   0.0  0
 58H  CONST_30  H25  C36  C29  C28     0.00   0.0  0
 58H  CONST_31  H24  C35  C36  C29   180.00   0.0  0
 58H  CONST_32  H23  C32  C30  C29   180.00   0.0  0
 58H  CONST_33  H8   N19  C20  C21     0.00   0.0  0
 58H  Var_01    C08  N07  C12  C11    60.16  30.0  1
 58H  Var_02    C20  N19  C05  C04    14.69  30.0  1
 58H  Var_03    C10  C09  C08  N07    57.45  30.0  1
 58H  Var_04    C10  C11  C12  N07   -56.97  30.0  1
 58H  Var_05    C12  N07  C08  C09   -60.28  30.0  1
 58H  Var_06    C28  C04  C05  N19     8.12  30.0  1
 58H  Var_07    N26  C21  C20  N19    -4.37  30.0  2
 58H  Var_08    N07  C06  C05  C04    67.21  30.0  2
 58H  Var_09    C05  C04  C03  O02  -165.80  30.0  2
 58H  Var_10    C04  C03  O02  C01  -178.86  30.0  2
 58H  Var_11    C17  C13  C14  C15   -73.35  30.0  3
 58H  Var_12    H3   C01  O02  C03  -179.13  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
 58H  chir_01  C10  C13  C09  C11  positiv
 58H  chir_02  C28  C04  N27  C29  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
 58H  plan-1  C05  0.020
 58H  plan-1  N19  0.020
 58H  plan-1  C20  0.020
 58H  plan-1  C21  0.020
 58H  plan-1  N27  0.020
 58H  plan-1  C28  0.020
 58H  plan-1  H8   0.020
 58H  plan-2  C20  0.020
 58H  plan-2  C21  0.020
 58H  plan-2  C22  0.020
 58H  plan-2  C23  0.020
 58H  plan-2  C24  0.020
 58H  plan-2  C25  0.020
 58H  plan-2  N26  0.020
 58H  plan-2  H19  0.020
 58H  plan-2  H20  0.020
 58H  plan-2  H21  0.020
 58H  plan-2  H22  0.020
 58H  plan-3  CL3  0.020
 58H  plan-3  C28  0.020
 58H  plan-3  C29  0.020
 58H  plan-3  C30  0.020
 58H  plan-3  C32  0.020
 58H  plan-3  C33  0.020
 58H  plan-3  C35  0.020
 58H  plan-3  C36  0.020
 58H  plan-3  F34  0.020
 58H  plan-3  H23  0.020
 58H  plan-3  H24  0.020
 58H  plan-3  H25  0.020
 58H  plan-4  O02  0.020
 58H  plan-4  C04  0.020
 58H  plan-4  O37  0.020
 58H  plan-4  C03  0.020

