# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:01:29 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 1-[(1S)-1-(4-chloro-3-fluorophenyl)-2-hydroxyethyl]-4-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](N1C=CC(=CC1=O)c2ccnc(NC3CCOCC3)n2)c4ccc(Cl)c(F)c4
#
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
 41B  41B  1-[(1S)-1-(4-chloro-3-fluorophenyl)-2-hydroxyethyl]-4-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]pyridin-2(1H)-one  ligand  53  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_41B
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
 41B  C4   C   CR6   0   0.634  -6.3101   0.3275  -0.2306
 41B  C5   C   CR16  0  -0.468  -5.4732  -0.6941   0.1663
 41B  C6   C   CR6   0   0.180  -4.1518  -0.7075  -0.2617
 41B  C7   C   CH1   0  -0.200  -3.2716  -1.8683   0.1391
 41B  C13  C   CR16  0  -0.431   0.3881  -1.2308  -0.2068
 41B  C15  C   CR16  0  -0.562  -0.3630  -0.3285   1.8781
 41B  C20  C   CR16  0  -0.010   3.7260   0.8664   2.6379
 41B  C22  C   CR6   0   0.606   4.2176   0.0036   0.6122
 41B  C26  C   CH2   0  -0.471   7.3281  -0.7975  -1.2243
 41B  C1   C   CR16  0  -0.312  -3.6933   0.3164  -1.0820
 41B  C2   C   CR16  0  -0.193  -4.5394   1.3440  -1.4694
 41B  C3   C   CR6   0  -0.247  -5.8585   1.3513  -1.0458
 41B  C9   C   CH2   0  -0.194  -3.3858  -3.0193  -0.8523
 41B  O10  O   OH1   0  -0.657  -3.1878  -2.5703  -2.1684
 41B  N11  N   NR6   0  -0.542  -1.8997  -1.4240   0.4069
 41B  C12  C   CR16  0   0.066  -0.8775  -1.6391  -0.4625
 41B  C14  C   CR6   0   0.201   0.6625  -0.5537   1.0092
 41B  C16  C   CR6   0   0.611  -1.7109  -0.7456   1.6092
 41B  O17  O   O     0  -0.507  -2.6584  -0.5417   2.3627
 41B  C18  C   CR6   0   0.315   2.0488  -0.1127   1.3063
 41B  C19  C   CR16  0  -0.404   2.3926   0.5264   2.4959
 41B  N21  N   N     0  -0.460   4.6448   0.6198   1.7199
 41B  N23  N   N     0  -0.496   2.9529  -0.3676   0.3754
 41B  C25  C   CH1   0  -0.059   6.5089   0.0992  -0.3036
 41B  C27  C   CH2   0  -0.183   8.7822  -0.3488  -1.2258
 41B  O28  O   O2    0  -0.483   8.9218   1.0049  -1.5945
 41B  C29  C   CH2   0  -0.186   8.2239   1.8659  -0.7207
 41B  C30  C   CH2   0  -0.457   6.7339   1.5604  -0.6909
 41B  F31  F   F     0  -0.295  -7.5780   0.3384   0.1863
 41B  CL1  CL  CL    0  -0.093  -6.9390   2.6103  -1.5097
 41B  H1   H   HCR6  0   0.286  -5.8583  -1.4737   0.8128
 41B  H2   H   HCH1  0   0.303  -3.6439  -2.2707   1.0828
 41B  H3   H   HCR6  0   0.272   1.1661  -1.4217  -0.9284
 41B  H4   H   HCR6  0   0.270  -0.2178   0.1824   2.8197
 41B  H5   H   HCR6  0   0.274   4.0671   1.3648   3.5387
 41B  H7   H   HCH2  0   0.232   6.9281  -0.7530  -2.2429
 41B  H8   H   HCR6  0   0.266  -2.6675   0.3361  -1.4249
 41B  H9   H   HCR6  0   0.290  -4.1754   2.1393  -2.1054
 41B  H10  H   HCH2  0   0.238  -2.6798  -3.8099  -0.5679
 41B  H11  H   HCH2  0   0.249  -4.3926  -3.4310  -0.7184
 41B  H12  H   HOH1  0   0.468  -3.2545  -3.3276  -2.7579
 41B  H13  H   HCR6  0   0.321  -1.1249  -2.1415  -1.3843
 41B  H14  H   HCR6  0   0.273   1.6844   0.7533   3.2768
 41B  H16  H   HCH1  0   0.241   6.8670  -0.0443   0.7203
 41B  H17  H   HCH2  0   0.199   9.2158  -0.5209  -0.2293
 41B  H18  H   HCH2  0   0.240   9.3611  -0.9370  -1.9392
 41B  H19  H   HCH2  0   0.199   8.6335   1.7889   0.2978
 41B  H20  H   HCH2  0   0.239   8.4016   2.8854  -1.0660
 41B  H21  H   HCH2  0   0.226   6.2947   1.7504  -1.6751
 41B  H22  H   HCH2  0   0.243   6.2423   2.2252   0.0228
 41B  N24  N   NH1   0  -0.669   5.1177  -0.2906  -0.3420
 41B  H6   H   HCH2  0   0.249   7.2728  -1.8385  -0.8971
 41B  H15  H   HNH1  0   0.390   4.7496  -0.6647  -1.2026

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
 41B  C26  C27  single    1.522  0.020  1.522
 41B  C26  C25  single    1.524  0.020  1.524
 41B  O28  C27  single    1.410  0.020  1.410
 41B  O28  C29  single    1.411  0.020  1.411
 41B  N24  C25  single    1.445  0.020  1.445
 41B  N24  C22  single    1.344  0.020  1.344
 41B  C30  C25  single    1.528  0.020  1.528
 41B  C30  C29  single    1.521  0.020  1.521
 41B  N21  C22  aromatic  1.338  0.020  1.338
 41B  N21  C20  aromatic  1.322  0.020  1.322
 41B  C22  N23  aromatic  1.339  0.020  1.339
 41B  C20  C19  aromatic  1.383  0.020  1.383
 41B  N23  C18  aromatic  1.322  0.020  1.322
 41B  C19  C18  aromatic  1.393  0.020  1.393
 41B  C18  C14  single    1.485  0.020  1.485
 41B  C14  C13  single    1.419  0.020  1.419
 41B  C14  C15  double    1.363  0.020  1.363
 41B  C13  C12  double    1.354  0.020  1.354
 41B  C15  C16  single    1.436  0.020  1.436
 41B  C12  N11  single    1.359  0.020  1.359
 41B  C16  N11  single    1.393  0.020  1.393
 41B  C16  O17  double    1.228  0.020  1.228
 41B  N11  C7   single    1.467  0.020  1.467
 41B  C9   C7   single    1.523  0.020  1.523
 41B  C9   O10  single    1.405  0.020  1.405
 41B  C7   C6   single    1.511  0.020  1.511
 41B  C1   C6   aromatic  1.390  0.020  1.390
 41B  C1   C2   aromatic  1.386  0.020  1.386
 41B  C6   C5   aromatic  1.389  0.020  1.389
 41B  C2   C3   aromatic  1.386  0.020  1.386
 41B  C5   C4   aromatic  1.379  0.020  1.379
 41B  C3   C4   aromatic  1.385  0.020  1.385
 41B  C3   CL1  single    1.723  0.020  1.723
 41B  C4   F31  single    1.335  0.020  1.335
 41B  C5   H1   single    0.930  0.020  1.080
 41B  C7   H2   single    0.970  0.020  1.090
 41B  C13  H3   single    0.930  0.020  1.080
 41B  C15  H4   single    0.930  0.020  1.080
 41B  C20  H5   single    0.930  0.020  1.080
 41B  C26  H6   single    0.970  0.020  1.090
 41B  C26  H7   single    0.970  0.020  1.090
 41B  C1   H8   single    0.930  0.020  1.080
 41B  C2   H9   single    0.930  0.020  1.080
 41B  C9   H10  single    0.970  0.020  1.090
 41B  C9   H11  single    0.970  0.020  1.090
 41B  O10  H12  single    0.850  0.020  0.980
 41B  C12  H13  single    0.930  0.020  1.080
 41B  C19  H14  single    0.930  0.020  1.080
 41B  N24  H15  single    0.860  0.020  1.020
 41B  C25  H16  single    0.970  0.020  1.090
 41B  C27  H17  single    0.970  0.020  1.090
 41B  C27  H18  single    0.970  0.020  1.090
 41B  C29  H19  single    0.970  0.020  1.090
 41B  C29  H20  single    0.970  0.020  1.090
 41B  C30  H21  single    0.970  0.020  1.090
 41B  C30  H22  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
 41B  F31  C4   C3   119.19  3.000
 41B  F31  C4   C5   119.52  3.000
 41B  C3   C4   C5   121.29  3.000
 41B  H1   C5   C6   121.00  3.000
 41B  H1   C5   C4   119.28  3.000
 41B  C6   C5   C4   119.73  3.000
 41B  C1   C6   C7   122.03  3.000
 41B  C1   C6   C5   119.25  3.000
 41B  C7   C6   C5   118.68  3.000
 41B  H2   C7   N11  105.83  3.000
 41B  H2   C7   C9   104.99  3.000
 41B  N11  C7   C9   114.69  3.000
 41B  H2   C7   C6   108.30  3.000
 41B  C9   C7   C6   111.36  3.000
 41B  N11  C7   C6   111.14  3.000
 41B  H3   C13  C14  121.25  3.000
 41B  H3   C13  C12  119.64  3.000
 41B  C14  C13  C12  119.11  3.000
 41B  H4   C15  C16  115.23  3.000
 41B  H4   C15  C14  122.17  3.000
 41B  C16  C15  C14  122.60  3.000
 41B  H5   C20  N21  116.35  3.000
 41B  H5   C20  C19  120.09  3.000
 41B  N21  C20  C19  123.56  3.000
 41B  N24  C22  N23  116.50  3.000
 41B  N23  C22  N21  125.16  3.000
 41B  N24  C22  N21  118.34  3.000
 41B  H7   C26  H6   107.38  3.000
 41B  H7   C26  C27  109.64  3.000
 41B  H6   C26  C27  109.24  3.000
 41B  H7   C26  C25  109.97  3.000
 41B  H6   C26  C25  110.63  3.000
 41B  C27  C26  C25  109.92  3.000
 41B  H8   C1   C2   118.47  3.000
 41B  H8   C1   C6   120.89  3.000
 41B  C2   C1   C6   120.64  3.000
 41B  H9   C2   C3   119.76  3.000
 41B  H9   C2   C1   120.27  3.000
 41B  C3   C2   C1   119.97  3.000
 41B  CL1  C3   C2   121.25  3.000
 41B  CL1  C3   C4   119.63  3.000
 41B  C2   C3   C4   119.12  3.000
 41B  H11  C9   H10  106.78  3.000
 41B  H11  C9   O10  111.35  3.000
 41B  H10  C9   O10  112.49  3.000
 41B  H11  C9   C7   105.85  3.000
 41B  H10  C9   C7   109.11  3.000
 41B  O10  C9   C7   110.96  3.000
 41B  H12  O10  C9   108.22  3.000
 41B  C16  N11  C12  121.82  3.000
 41B  C16  N11  C7   115.58  3.000
 41B  C12  N11  C7   122.60  3.000
 41B  H13  C12  N11  116.61  3.000
 41B  H13  C12  C13  121.07  3.000
 41B  N11  C12  C13  122.30  3.000
 41B  C18  C14  C15  121.73  3.000
 41B  C15  C14  C13  118.68  3.000
 41B  C18  C14  C13  119.60  3.000
 41B  O17  C16  N11  120.39  3.000
 41B  O17  C16  C15  124.13  3.000
 41B  N11  C16  C15  115.47  3.000
 41B  N23  C18  C19  121.38  3.000
 41B  C19  C18  C14  122.51  3.000
 41B  N23  C18  C14  116.11  3.000
 41B  H14  C19  C18  123.55  3.000
 41B  H14  C19  C20  120.47  3.000
 41B  C18  C19  C20  115.98  3.000
 41B  C22  N21  C20  116.03  3.000
 41B  C18  N23  C22  117.88  3.000
 41B  H16  C25  C30  108.32  3.000
 41B  H16  C25  N24  107.73  3.000
 41B  C30  C25  N24  113.14  3.000
 41B  H16  C25  C26  108.19  3.000
 41B  C30  C25  C26  109.28  3.000
 41B  N24  C25  C26  110.04  3.000
 41B  H18  C27  H17  107.38  3.000
 41B  H18  C27  O28  107.10  3.000
 41B  H17  C27  O28  110.37  3.000
 41B  H18  C27  C26  110.41  3.000
 41B  H17  C27  C26  109.25  3.000
 41B  O28  C27  C26  112.21  3.000
 41B  C29  O28  C27  112.01  3.000
 41B  H20  C29  H19  107.32  3.000
 41B  H20  C29  C30  110.69  3.000
 41B  H19  C29  C30  109.42  3.000
 41B  H20  C29  O28  107.07  3.000
 41B  H19  C29  O28  110.26  3.000
 41B  C30  C29  O28  111.96  3.000
 41B  H22  C30  H21  107.54  3.000
 41B  H22  C30  C29  109.35  3.000
 41B  H21  C30  C29  109.92  3.000
 41B  H22  C30  C25  110.49  3.000
 41B  H21  C30  C25  109.56  3.000
 41B  C29  C30  C25  109.95  3.000
 41B  H15  N24  C25  118.32  3.000
 41B  H15  N24  C22  116.27  3.000
 41B  C25  N24  C22  124.52  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
 41B  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 41B  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 41B  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 41B  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 41B  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 41B  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 41B  CONST_07  N23  C22  N21  C20    0.00   0.0  0
 41B  CONST_08  N23  C18  C19  C20    0.00   0.0  0
 41B  CONST_09  C19  C20  N21  C22    0.00   0.0  0
 41B  CONST_10  C19  C18  N23  C22    0.00   0.0  0
 41B  CONST_11  N21  C22  N23  C18    0.00   0.0  0
 41B  CONST_12  N21  C20  C19  C18    0.00   0.0  0
 41B  CONST_13  C14  C18  C19  C20  180.00   0.0  0
 41B  CONST_14  C14  C18  N23  C22  180.00   0.0  0
 41B  CONST_15  C12  N11  C16  C15    0.00   0.0  0
 41B  CONST_16  C7   C6   C5   C4   180.00   0.0  0
 41B  CONST_17  CL1  C3   C4   C5   180.00   0.0  0
 41B  CONST_18  F31  C4   C5   C6   180.00   0.0  0
 41B  CONST_19  C2   C1   C6   C7   180.00   0.0  0
 41B  CONST_20  N24  C22  N21  C20  180.00   0.0  0
 41B  CONST_21  CL1  C3   C2   C1   180.00   0.0  0
 41B  CONST_22  F31  C4   C3   C2   180.00   0.0  0
 41B  CONST_23  N24  C22  N23  C18  180.00   0.0  0
 41B  CONST_24  C25  N24  C22  N21    0.00   0.0  0
 41B  CONST_25  C25  N24  C22  N23  180.00   0.0  0
 41B  CONST_26  C15  C16  N11  C7   180.00   0.0  0
 41B  CONST_27  O17  C16  N11  C12  180.00   0.0  0
 41B  CONST_28  H9   C2   C3   C4   180.00   0.0  0
 41B  CONST_29  H8   C1   C6   C5   180.00   0.0  0
 41B  CONST_30  H5   C20  N21  C22  180.00   0.0  0
 41B  CONST_31  H1   C5   C6   C1   180.00   0.0  0
 41B  CONST_32  H14  C19  C18  C14    0.00   0.0  0
 41B  CONST_33  O17  C16  N11  C7     0.00   0.0  0
 41B  CONST_34  H15  N24  C22  N21  180.00   0.0  0
 41B  Var_01    N23  C18  C14  C13    1.29  30.0  2
 41B  Var_02    O28  C27  C26  C25  -56.34  30.0  1
 41B  Var_03    O28  C29  C30  C25   56.51  30.0  1
 41B  Var_04    C30  C29  O28  C27  -59.61  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
 41B  chir_01  C7   N11  C9   C6   positiv
 41B  chir_02  C25  C26  N24  C30  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
 41B  plan-1  C4   0.020
 41B  plan-1  C5   0.020
 41B  plan-1  C6   0.020
 41B  plan-1  C7   0.020
 41B  plan-1  C1   0.020
 41B  plan-1  C2   0.020
 41B  plan-1  C3   0.020
 41B  plan-1  F31  0.020
 41B  plan-1  CL1  0.020
 41B  plan-1  H1   0.020
 41B  plan-1  H8   0.020
 41B  plan-1  H9   0.020
 41B  plan-2  C7   0.020
 41B  plan-2  C13  0.020
 41B  plan-2  C15  0.020
 41B  plan-2  N11  0.020
 41B  plan-2  C12  0.020
 41B  plan-2  C14  0.020
 41B  plan-2  C16  0.020
 41B  plan-2  O17  0.020
 41B  plan-2  C18  0.020
 41B  plan-2  H3   0.020
 41B  plan-2  H4   0.020
 41B  plan-2  H13  0.020
 41B  plan-3  C20  0.020
 41B  plan-3  C22  0.020
 41B  plan-3  C14  0.020
 41B  plan-3  C18  0.020
 41B  plan-3  C19  0.020
 41B  plan-3  N21  0.020
 41B  plan-3  N23  0.020
 41B  plan-3  H5   0.020
 41B  plan-3  H14  0.020
 41B  plan-3  N24  0.020
 41B  plan-4  C22  0.020
 41B  plan-4  C25  0.020
 41B  plan-4  N24  0.020
 41B  plan-4  H15  0.020

