# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 15:23:08 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-[2-chloro-6-(4,4,4-trifluorobutoxy)phenyl]-6-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nc(N)n1)c2c(Cl)cccc2OCCCC(F)(F)F
#
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
 FU5  FU5  4-[2-chloro-6-(4,4,4-trifluorobutoxy)phenyl]-6-methylpyrimidin-2-amine  ligand  38  23  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FU5
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
 FU5  C1    C   CR6   0  -0.011   1.7889  -1.0526  -0.1981
 FU5  C2    C   CR6   0   0.277   1.8719   0.4290  -0.1499
 FU5  C3    C   CR6   0   0.380   0.5410  -1.6810  -0.0942
 FU5  C4    C   CR6   0  -0.072   2.9173  -1.8436  -0.3409
 FU5  C5    C   CR16  0  -0.359   1.5552   1.1874  -1.2654
 FU5  N6    N   N     0  -0.447   2.2684   0.9720   0.9888
 FU5  C7    C   CR16  0  -0.356   0.4462  -3.0676  -0.1449
 FU5  O8    O   O2    0  -0.455  -0.5030  -0.8523   0.0614
 FU5  C9    C   CR16  0  -0.218   2.8440  -3.2284  -0.3914
 FU5  CL10  CL  CL    0  -0.114   4.4654  -1.0843  -0.4864
 FU5  C11   C   CR6   0   0.294   1.6674   2.5665  -1.1390
 FU5  C12   C   CR6   0   0.528   2.3528   2.3043   1.0085
 FU5  C13   C   CR16  0  -0.231   1.6001  -3.8246  -0.2917
 FU5  C14   C   CH2   0  -0.142  -1.8098  -1.3839   0.1277
 FU5  N15   N   N     0  -0.469   2.0677   3.1233  -0.0028
 FU5  C16   C   CH3   0  -0.693   1.3274   3.4881  -2.2652
 FU5  N17   N   NH2   0  -0.808   2.8050   2.8720   2.1520
 FU5  C18   C   CH2   0  -0.474  -2.7563  -0.2168   0.3247
 FU5  C19   C   CH2   0  -0.630  -4.1992  -0.7047   0.3828
 FU5  C20   C   CT    0   1.000  -5.1858   0.3997   0.6418
 FU5  F21   F   F     0  -0.317  -5.1436   1.3556  -0.3008
 FU5  F22   F   F     0  -0.312  -6.4484  -0.0538   0.6712
 FU5  F23   F   F     0  -0.315  -4.9714   1.0144   1.8157
 FU5  H5    H   HCR6  0   0.238   1.2313   0.7266  -2.1866
 FU5  H7    H   HCR6  0   0.264  -0.5061  -3.5730  -0.0678
 FU5  H9    H   HCR6  0   0.257   3.7376  -3.8238  -0.5087
 FU5  H13   H   HCR6  0   0.251   1.5224  -4.9022  -0.3292
 FU5  H14   H   HCH2  0   0.216  -2.0515  -1.9258  -0.7940
 FU5  H14A  H   HCH2  0   0.214  -1.9002  -2.0891   0.9617
 FU5  H16   H   HCH3  0   0.249   0.3975   4.0159  -2.0493
 FU5  H16A  H   HCH3  0   0.247   2.1033   4.2411  -2.3958
 FU5  H16B  H   HCH3  0   0.233   1.1987   2.9526  -3.2030
 FU5  HN17  H   HNH2  0   0.373   2.7922   2.3183   2.9895
 FU5  HN1A  H   HNH2  0   0.370   2.6510   3.8561   2.2785
 FU5  H18   H   HCH2  0   0.249  -2.4881   0.2964   1.2497
 FU5  H18A  H   HCH2  0   0.251  -2.6254   0.4895  -0.4969
 FU5  H19   H   HCH2  0   0.267  -4.4785  -1.1866  -0.5568
 FU5  H19A  H   HCH2  0   0.267  -4.3233  -1.4512   1.1709

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
 FU5  C2    C1    single    1.485  0.020  1.485
 FU5  C4    C1    aromatic  1.385  0.020  1.385
 FU5  C1    C3    aromatic  1.401  0.020  1.401
 FU5  N6    C2    aromatic  1.322  0.020  1.322
 FU5  C2    C5    aromatic  1.386  0.020  1.386
 FU5  C3    O8    single    1.342  0.020  1.342
 FU5  C3    C7    aromatic  1.391  0.020  1.391
 FU5  CL10  C4    single    1.730  0.020  1.730
 FU5  C4    C9    aromatic  1.388  0.020  1.388
 FU5  C11   C5    aromatic  1.389  0.020  1.389
 FU5  C5    H5    single    0.930  0.020  1.080
 FU5  C12   N6    aromatic  1.335  0.020  1.335
 FU5  C13   C7    aromatic  1.388  0.020  1.388
 FU5  C7    H7    single    0.930  0.020  1.080
 FU5  O8    C14   single    1.412  0.020  1.412
 FU5  C9    C13   aromatic  1.383  0.020  1.383
 FU5  C9    H9    single    0.930  0.020  1.080
 FU5  N15   C11   aromatic  1.327  0.020  1.327
 FU5  C16   C11   single    1.494  0.020  1.494
 FU5  N17   C12   single    1.354  0.020  1.354
 FU5  N15   C12   aromatic  1.332  0.020  1.332
 FU5  C13   H13   single    0.930  0.020  1.080
 FU5  C14   C18   single    1.515  0.020  1.515
 FU5  C14   H14   single    0.970  0.020  1.090
 FU5  C14   H14A  single    0.970  0.020  1.090
 FU5  C16   H16   single    0.970  0.020  1.090
 FU5  C16   H16A  single    0.970  0.020  1.090
 FU5  C16   H16B  single    0.970  0.020  1.090
 FU5  N17   HN17  single    0.890  0.020  1.040
 FU5  N17   HN1A  single    0.890  0.020  1.040
 FU5  C19   C18   single    1.524  0.020  1.524
 FU5  C18   H18   single    0.970  0.020  1.090
 FU5  C18   H18A  single    0.970  0.020  1.090
 FU5  C19   C20   single    1.503  0.020  1.503
 FU5  C19   H19   single    0.970  0.020  1.090
 FU5  C19   H19A  single    0.970  0.020  1.090
 FU5  F22   C20   single    1.342  0.020  1.342
 FU5  F23   C20   single    1.342  0.020  1.342
 FU5  C20   F21   single    1.343  0.020  1.343

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
 FU5  C4    C1   C3    118.49  3.000
 FU5  C3    C1   C2    119.67  3.000
 FU5  C4    C1   C2    121.84  3.000
 FU5  N6    C2   C5    122.48  3.000
 FU5  C5    C2   C1    120.49  3.000
 FU5  N6    C2   C1    117.03  3.000
 FU5  O8    C3   C7    124.53  3.000
 FU5  C7    C3   C1    120.34  3.000
 FU5  O8    C3   C1    115.12  3.000
 FU5  CL10  C4   C9    118.82  3.000
 FU5  C9    C4   C1    122.04  3.000
 FU5  CL10  C4   C1    119.13  3.000
 FU5  H5    C5   C11   121.70  3.000
 FU5  H5    C5   C2    121.45  3.000
 FU5  C11   C5   C2    116.85  3.000
 FU5  C12   N6   C2    116.19  3.000
 FU5  H7    C7   C13   119.02  3.000
 FU5  H7    C7   C3    121.58  3.000
 FU5  C13   C7   C3    119.40  3.000
 FU5  C14   O8   C3    119.52  3.000
 FU5  H9    C9   C13   120.95  3.000
 FU5  H9    C9   C4    120.68  3.000
 FU5  C13   C9   C4    118.37  3.000
 FU5  C16   C11  N15   117.07  3.000
 FU5  C16   C11  C5    121.68  3.000
 FU5  N15   C11  C5    121.25  3.000
 FU5  N17   C12  N15   117.04  3.000
 FU5  N15   C12  N6    126.07  3.000
 FU5  N17   C12  N6    116.86  3.000
 FU5  H13   C13  C9    119.46  3.000
 FU5  H13   C13  C7    119.18  3.000
 FU5  C9    C13  C7    121.35  3.000
 FU5  H14A  C14  H14   107.67  3.000
 FU5  H14A  C14  C18   110.18  3.000
 FU5  H14   C14  C18   110.63  3.000
 FU5  H14A  C14  O8    110.75  3.000
 FU5  H14   C14  O8    110.53  3.000
 FU5  C18   C14  O8    107.10  3.000
 FU5  C12   N15  C11   117.16  3.000
 FU5  H16B  C16  H16A  108.75  3.000
 FU5  H16B  C16  H16   107.94  3.000
 FU5  H16A  C16  H16   107.24  3.000
 FU5  H16B  C16  C11   111.91  3.000
 FU5  H16A  C16  C11   110.77  3.000
 FU5  H16   C16  C11   110.07  3.000
 FU5  HN1A  N17  HN17  115.69  3.000
 FU5  HN1A  N17  C12   117.77  3.000
 FU5  HN17  N17  C12   117.95  3.000
 FU5  H18A  C18  H18   107.72  3.000
 FU5  H18A  C18  C19   110.45  3.000
 FU5  H18   C18  C19   110.54  3.000
 FU5  H18A  C18  C14   109.00  3.000
 FU5  H18   C18  C14   108.59  3.000
 FU5  C19   C18  C14   110.47  3.000
 FU5  H19A  C19  H19   106.86  3.000
 FU5  H19A  C19  C20   107.64  3.000
 FU5  H19   C19  C20   107.73  3.000
 FU5  H19A  C19  C18   110.72  3.000
 FU5  H19   C19  C18   110.52  3.000
 FU5  C20   C19  C18   113.12  3.000
 FU5  F23   C20  F22   106.61  3.000
 FU5  F23   C20  F21   106.43  3.000
 FU5  F22   C20  F21   106.58  3.000
 FU5  F21   C20  C19   112.42  3.000
 FU5  F23   C20  C19   112.47  3.000
 FU5  F22   C20  C19   111.90  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
 FU5  CONST_01  C12   N6   C2   C1    180.00   0.0  0
 FU5  CONST_02  C11   C5   C2   C1    180.00   0.0  0
 FU5  CONST_03  C13   C9   C4   C1      0.00   0.0  0
 FU5  CONST_04  C13   C7   C3   C1      0.00   0.0  0
 FU5  CONST_05  C9    C4   C1   C2    180.00   0.0  0
 FU5  CONST_06  C7    C3   C1   C2    180.00   0.0  0
 FU5  CONST_07  N15   C12  N6   C2      0.00   0.0  0
 FU5  CONST_08  N15   C11  C5   C2      0.00   0.0  0
 FU5  CONST_11  C9    C4   C1   C3      0.00   0.0  0
 FU5  CONST_12  C9    C13  C7   C3      0.00   0.0  0
 FU5  CONST_15  C7    C3   C1   C4      0.00   0.0  0
 FU5  CONST_16  C7    C13  C9   C4      0.00   0.0  0
 FU5  CONST_17  C12   N6   C2   C5      0.00   0.0  0
 FU5  CONST_18  C12   N15  C11  C5      0.00   0.0  0
 FU5  CONST_19  C11   C5   C2   N6      0.00   0.0  0
 FU5  CONST_20  C11   N15  C12  N6      0.00   0.0  0
 FU5  CONST_21  CL10  C4   C1   C2      0.00   0.0  0
 FU5  CONST_22  O8    C3   C1   C2      0.00   0.0  0
 FU5  CONST_23  N17   C12  N6   C2    180.00   0.0  0
 FU5  CONST_24  C16   C11  C5   C2    180.00   0.0  0
 FU5  CONST_25  CL10  C4   C1   C3    180.00   0.0  0
 FU5  CONST_26  O8    C3   C1   C4    180.00   0.0  0
 FU5  CONST_27  C13   C7   C3   O8    180.00   0.0  0
 FU5  CONST_28  C13   C9   C4   CL10  180.00   0.0  0
 FU5  CONST_29  N17   C12  N15  C11   180.00   0.0  0
 FU5  CONST_30  C16   C11  N15  C12   180.00   0.0  0
 FU5  CONST_31  H5    C5   C2   C1      0.00   0.0  0
 FU5  CONST_32  H9    C9   C4   C1    180.00   0.0  0
 FU5  CONST_33  H7    C7   C3   C1    180.00   0.0  0
 FU5  CONST_34  H13   C13  C7   C3    180.00   0.0  0
 FU5  Var_01    H16   C16  C11  C5    108.16  30.0  2
 FU5  Var_02    C18   C14  O8   C3    179.14  30.0  3
 FU5  Var_03    C19   C18  C14  O8    179.02  30.0  3
 FU5  Var_04    C20   C19  C18  C14   177.30  30.0  1
 FU5  Var_05    F22   C20  C19  C18   179.21  30.0  3

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
 FU5  plan-1  C1    0.020
 FU5  plan-1  C2    0.020
 FU5  plan-1  C3    0.020
 FU5  plan-1  C4    0.020
 FU5  plan-1  C7    0.020
 FU5  plan-1  O8    0.020
 FU5  plan-1  C9    0.020
 FU5  plan-1  CL10  0.020
 FU5  plan-1  C13   0.020
 FU5  plan-1  H7    0.020
 FU5  plan-1  H9    0.020
 FU5  plan-1  H13   0.020
 FU5  plan-2  C1    0.020
 FU5  plan-2  C2    0.020
 FU5  plan-2  C5    0.020
 FU5  plan-2  N6    0.020
 FU5  plan-2  C11   0.020
 FU5  plan-2  C12   0.020
 FU5  plan-2  N15   0.020
 FU5  plan-2  C16   0.020
 FU5  plan-2  N17   0.020
 FU5  plan-2  H5    0.020
 FU5  plan-3  C12   0.020
 FU5  plan-3  N17   0.020
 FU5  plan-3  HN17  0.020
 FU5  plan-3  HN1A  0.020

