# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 00:52:45 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[(3R)-1-(3-fluorophenyl)piperidin-3-yl]-6-(morpholin-4-yl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(c1)N2CCC[C@H](C2)Nc3cc(ncn3)N4CCOCC4
#
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
 B1I  B1I  "N-[(3R)-1-(3-fluorophenyl)piperidin-3-yl]-6-(morpholin-4-yl)pyrimidin-4-amine"
  ligand  50  26  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B1I
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
 B1I  F    F  F     0  -0.321   -2.1137   -9.8946  39.1635
 B1I  C9   C  CR6   0   0.543   -1.2119  -10.7773  38.6963
 B1I  C8   C  CR16  0  -0.441    0.0961  -10.6829  39.1346
 B1I  C7   C  CR16  0  -0.227    0.9967  -11.6032  38.6217
 B1I  C6   C  CR16  0  -0.369    0.6045  -12.5800  37.7171
 B1I  C10  C  CR16  0  -0.497   -1.6379  -11.7215  37.7892
 B1I  C5   C  CR6   0   0.391   -0.7242  -12.6577  37.2780
 B1I  N    N  NT    0  -0.517   -1.1482  -13.5980  36.3440
 B1I  C4   C  CH2   0  -0.306   -0.1453  -14.4064  35.6742
 B1I  C    C  CH2   0  -0.445   -0.7081  -15.0042  34.3933
 B1I  C3   C  CH2   0  -0.293   -2.3637  -14.3381  36.6490
 B1I  C2   C  CH1   0  -0.076   -2.9901  -14.9271  35.3878
 B1I  C1   C  CH2   0  -0.437   -1.9796  -15.7984  34.6526
 B1I  N1   N  NH1   0  -0.686   -4.1832  -15.6531  35.7562
 B1I  C11  C  CR6   0   0.568   -5.3870  -15.5377  35.1619
 B1I  N3   N  N     0  -0.494   -5.4937  -14.7216  34.1012
 B1I  C14  C  CR16  0   0.061   -6.6952  -14.6477  33.5600
 B1I  N2   N  N     0  -0.500   -7.8001  -15.2554  33.9322
 B1I  C13  C  CR6   0   0.574   -7.7127  -16.0648  35.0079
 B1I  C12  C  CR16  0  -0.533   -6.4876  -16.2555  35.6455
 B1I  N4   N  NT    0  -0.512   -8.8703  -16.6407  35.4301
 B1I  C18  C  CH2   0  -0.317  -10.0448  -16.6823  34.5744
 B1I  C17  C  CH2   0  -0.188  -11.3044  -16.6229  35.4171
 B1I  O    O  O2    0  -0.476  -11.3307  -17.6422  36.3897
 B1I  C16  C  CH2   0  -0.180  -10.2199  -17.5356  37.2456
 B1I  C15  C  CH2   0  -0.319   -8.9010  -17.6223  36.4946
 B1I  H1   H  HCR6  0   0.269    0.3958   -9.9259  39.8464
 B1I  H2   H  HCR6  0   0.262    2.0291  -11.5719  38.9450
 B1I  H3   H  HCR6  0   0.268    1.3434  -13.2899  37.3748
 B1I  H4   H  HCR6  0   0.278   -2.6696  -11.7072  37.4636
 B1I  H5   H  HCH2  0   0.212    0.2242  -15.2119  36.3277
 B1I  H6   H  HCH2  0   0.253    0.7090  -13.7786  35.4208
 B1I  H7   H  HCH2  0   0.242    0.0535  -15.6408  33.9387
 B1I  H8   H  HCH2  0   0.226   -0.9134  -14.1984  33.6828
 B1I  H9   H  HCH2  0   0.263   -3.0924  -13.6866  37.1263
 B1I  H10  H  HCH2  0   0.218   -2.1464  -15.1517  37.3611
 B1I  H11  H  HCH1  0   0.255   -3.2908  -14.1036  34.7392
 B1I  H12  H  HCH2  0   0.242   -2.4085  -16.1605  33.7160
 B1I  H13  H  HCH2  0   0.218   -1.7493  -16.6779  35.2640
 B1I  H14  H  HNH1  0   0.392   -4.1042  -16.3110  36.5165
 B1I  H15  H  HCR6  0   0.240   -6.7819  -13.9997  32.6918
 B1I  H16  H  HCR6  0   0.266   -6.3585  -16.9164  36.4897
 B1I  H17  H  HCH2  0   0.229  -10.0410  -17.6023  33.9752
 B1I  H18  H  HCH2  0   0.270  -10.0282  -15.8401  33.8886
 B1I  H19  H  HCH2  0   0.205  -11.3767  -15.6348  35.8933
 B1I  H20  H  HCH2  0   0.240  -12.1787  -16.7547  34.7783
 B1I  H21  H  HCH2  0   0.206  -10.2511  -16.5881  37.8025
 B1I  H22  H  HCH2  0   0.243  -10.2793  -18.3507  37.9681
 B1I  H23  H  HCH2  0   0.235   -8.7539  -18.6334  36.0937
 B1I  H24  H  HCH2  0   0.262   -8.1062  -17.4361  37.2142

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
 B1I  C14  N2   aromatic  1.315  0.020  1.315
 B1I  C14  N3   aromatic  1.320  0.020  1.320
 B1I  N2   C13  aromatic  1.349  0.020  1.349
 B1I  N3   C11  aromatic  1.343  0.020  1.343
 B1I  C18  C17  single    1.517  0.020  1.517
 B1I  C18  N4   single    1.454  0.020  1.454
 B1I  C    C1   single    1.521  0.020  1.521
 B1I  C    C4   single    1.521  0.020  1.521
 B1I  C17  O    single    1.409  0.020  1.409
 B1I  C1   C2   single    1.523  0.020  1.523
 B1I  C13  N4   single    1.360  0.020  1.360
 B1I  C13  C12  aromatic  1.394  0.020  1.394
 B1I  N4   C15  single    1.448  0.020  1.448
 B1I  C11  C12  aromatic  1.400  0.020  1.400
 B1I  C11  N1   single    1.347  0.020  1.347
 B1I  C4   N    single    1.452  0.020  1.452
 B1I  C2   N1   single    1.444  0.020  1.444
 B1I  C2   C3   single    1.526  0.020  1.526
 B1I  O    C16  single    1.406  0.020  1.406
 B1I  N    C3   single    1.455  0.020  1.455
 B1I  N    C5   single    1.391  0.020  1.391
 B1I  C15  C16  single    1.520  0.020  1.520
 B1I  C6   C5   aromatic  1.402  0.020  1.402
 B1I  C6   C7   aromatic  1.388  0.020  1.388
 B1I  C5   C10  aromatic  1.404  0.020  1.404
 B1I  C7   C8   aromatic  1.386  0.020  1.386
 B1I  C10  C9   aromatic  1.377  0.020  1.377
 B1I  C9   C8   aromatic  1.383  0.020  1.383
 B1I  C9   F    single    1.346  0.020  1.346
 B1I  C8   H1   single    0.930  0.020  1.080
 B1I  C7   H2   single    0.930  0.020  1.080
 B1I  C6   H3   single    0.930  0.020  1.080
 B1I  C10  H4   single    0.930  0.020  1.080
 B1I  C4   H5   single    0.970  0.020  1.090
 B1I  C4   H6   single    0.970  0.020  1.090
 B1I  C    H7   single    0.970  0.020  1.090
 B1I  C    H8   single    0.970  0.020  1.090
 B1I  C3   H9   single    0.970  0.020  1.090
 B1I  C3   H10  single    0.970  0.020  1.090
 B1I  C2   H11  single    0.970  0.020  1.090
 B1I  C1   H12  single    0.970  0.020  1.090
 B1I  C1   H13  single    0.970  0.020  1.090
 B1I  N1   H14  single    0.860  0.020  1.020
 B1I  C14  H15  single    0.930  0.020  1.080
 B1I  C12  H16  single    0.930  0.020  1.080
 B1I  C18  H17  single    0.970  0.020  1.090
 B1I  C18  H18  single    0.970  0.020  1.090
 B1I  C17  H19  single    0.970  0.020  1.090
 B1I  C17  H20  single    0.970  0.020  1.090
 B1I  C16  H21  single    0.970  0.020  1.090
 B1I  C16  H22  single    0.970  0.020  1.090
 B1I  C15  H23  single    0.970  0.020  1.090
 B1I  C15  H24  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
 B1I  C10  C9   C8   123.25  3.000
 B1I  C8   C9   F    118.63  3.000
 B1I  C10  C9   F    118.11  3.000
 B1I  H1   C8   C7   121.88  3.000
 B1I  H1   C8   C9   121.24  3.000
 B1I  C7   C8   C9   116.87  3.000
 B1I  H2   C7   C6   118.98  3.000
 B1I  H2   C7   C8   119.34  3.000
 B1I  C6   C7   C8   121.66  3.000
 B1I  H3   C6   C5   120.84  3.000
 B1I  H3   C6   C7   118.41  3.000
 B1I  C5   C6   C7   120.74  3.000
 B1I  H4   C10  C5   121.30  3.000
 B1I  H4   C10  C9   118.96  3.000
 B1I  C5   C10  C9   119.71  3.000
 B1I  N    C5   C10  119.77  3.000
 B1I  C10  C5   C6   117.75  3.000
 B1I  N    C5   C6   122.45  3.000
 B1I  C3   N    C4   112.98  3.000
 B1I  C3   N    C5   117.22  3.000
 B1I  C4   N    C5   118.39  3.000
 B1I  H6   C4   H5   107.24  3.000
 B1I  H6   C4   C    108.69  3.000
 B1I  H5   C4   C    109.65  3.000
 B1I  H6   C4   N    109.14  3.000
 B1I  H5   C4   N    111.43  3.000
 B1I  C    C4   N    110.59  3.000
 B1I  H8   C    H7   106.86  3.000
 B1I  H8   C    C1   109.78  3.000
 B1I  H7   C    C1   110.47  3.000
 B1I  H8   C    C4   109.08  3.000
 B1I  H7   C    C4   108.76  3.000
 B1I  C1   C    C4   111.76  3.000
 B1I  H10  C3   H9   106.89  3.000
 B1I  H10  C3   C2   109.25  3.000
 B1I  H9   C3   C2   108.59  3.000
 B1I  H10  C3   N    110.24  3.000
 B1I  H9   C3   N    110.29  3.000
 B1I  C2   C3   N    111.46  3.000
 B1I  H11  C2   N1   107.67  3.000
 B1I  H11  C2   C1   109.13  3.000
 B1I  N1   C2   C1   112.55  3.000
 B1I  H11  C2   C3   108.25  3.000
 B1I  N1   C2   C3   108.80  3.000
 B1I  C1   C2   C3   110.32  3.000
 B1I  H13  C1   H12  107.15  3.000
 B1I  H13  C1   C2   109.23  3.000
 B1I  H12  C1   C2   110.07  3.000
 B1I  H13  C1   C    109.78  3.000
 B1I  H12  C1   C    110.80  3.000
 B1I  C2   C1   C    109.76  3.000
 B1I  H14  N1   C11  117.28  3.000
 B1I  H14  N1   C2   117.10  3.000
 B1I  C11  N1   C2   125.62  3.000
 B1I  C12  C11  N3   121.47  3.000
 B1I  C12  C11  N1   120.40  3.000
 B1I  N3   C11  N1   118.14  3.000
 B1I  C14  N3   C11  115.49  3.000
 B1I  H15  C14  N2   115.76  3.000
 B1I  H15  C14  N3   115.69  3.000
 B1I  N2   C14  N3   128.54  3.000
 B1I  C13  N2   C14  116.65  3.000
 B1I  N4   C13  C12  123.23  3.000
 B1I  C12  C13  N2   120.24  3.000
 B1I  N4   C13  N2   116.52  3.000
 B1I  H16  C12  C13  123.11  3.000
 B1I  H16  C12  C11  119.33  3.000
 B1I  C13  C12  C11  117.56  3.000
 B1I  C15  N4   C18  113.34  3.000
 B1I  C15  N4   C13  122.22  3.000
 B1I  C18  N4   C13  121.13  3.000
 B1I  H18  C18  H17  107.76  3.000
 B1I  H18  C18  C17  109.46  3.000
 B1I  H17  C18  C17  109.81  3.000
 B1I  H18  C18  N4   109.70  3.000
 B1I  H17  C18  N4   110.03  3.000
 B1I  C17  C18  N4   110.05  3.000
 B1I  H20  C17  H19  108.03  3.000
 B1I  H20  C17  O    107.57  3.000
 B1I  H19  C17  O    110.49  3.000
 B1I  H20  C17  C18  109.60  3.000
 B1I  H19  C17  C18  109.31  3.000
 B1I  O    C17  C18  111.76  3.000
 B1I  C16  O    C17  110.51  3.000
 B1I  H22  C16  H21  107.88  3.000
 B1I  H22  C16  C15  109.38  3.000
 B1I  H21  C16  C15  108.90  3.000
 B1I  H22  C16  O    107.66  3.000
 B1I  H21  C16  O    110.56  3.000
 B1I  C15  C16  O    112.35  3.000
 B1I  H24  C15  H23  107.54  3.000
 B1I  H24  C15  C16  107.29  3.000
 B1I  H23  C15  C16  110.44  3.000
 B1I  H24  C15  N4   110.77  3.000
 B1I  H23  C15  N4   110.67  3.000
 B1I  C16  C15  N4   110.05  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
 B1I  CONST_01  C6   C5   C10  C9      0.00   0.0  0
 B1I  CONST_02  C6   C7   C8   C9      0.00   0.0  0
 B1I  CONST_03  C5   C6   C7   C8      0.00   0.0  0
 B1I  CONST_04  C5   C10  C9   C8      0.00   0.0  0
 B1I  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 B1I  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 B1I  CONST_07  N2   C14  N3   C11     0.00   0.0  0
 B1I  CONST_08  N2   C13  C12  C11     0.00   0.0  0
 B1I  CONST_09  C13  N2   C14  N3      0.00   0.0  0
 B1I  CONST_10  C13  C12  C11  N3      0.00   0.0  0
 B1I  CONST_11  C12  C13  N2   C14     0.00   0.0  0
 B1I  CONST_12  C12  C11  N3   C14     0.00   0.0  0
 B1I  CONST_13  N    C5   C10  C9    180.00   0.0  0
 B1I  CONST_14  N    C5   C6   C7    180.00   0.0  0
 B1I  CONST_15  N4   C13  C12  C11   180.00   0.0  0
 B1I  CONST_16  N4   C13  N2   C14   180.00   0.0  0
 B1I  CONST_17  C5   C10  C9   F     180.00   0.0  0
 B1I  CONST_18  C7   C8   C9   F     180.00   0.0  0
 B1I  CONST_19  C14  N3   C11  N1    180.00   0.0  0
 B1I  CONST_20  C13  C12  C11  N1    180.00   0.0  0
 B1I  CONST_21  N3   C11  N1   C2      0.00   0.0  0
 B1I  CONST_22  C12  C11  N1   C2    180.00   0.0  0
 B1I  CONST_23  H2   C7   C8   C9    180.00   0.0  0
 B1I  CONST_24  H3   C6   C7   C8    180.00   0.0  0
 B1I  CONST_25  H4   C10  C9   C8    180.00   0.0  0
 B1I  CONST_26  H4   C10  C5   C6    180.00   0.0  0
 B1I  CONST_27  H1   C8   C7   C6    180.00   0.0  0
 B1I  CONST_28  H3   C6   C5   C10   180.00   0.0  0
 B1I  CONST_29  H1   C8   C9   C10   180.00   0.0  0
 B1I  CONST_30  H2   C7   C6   C5    180.00   0.0  0
 B1I  CONST_31  H3   C6   C5   N       0.00   0.0  0
 B1I  CONST_32  H4   C10  C5   N       0.00   0.0  0
 B1I  CONST_33  H15  C14  N3   C11   180.00   0.0  0
 B1I  CONST_34  H16  C12  C11  N3    180.00   0.0  0
 B1I  CONST_35  H16  C12  C13  N2    180.00   0.0  0
 B1I  CONST_36  H15  C14  N2   C13   180.00   0.0  0
 B1I  CONST_37  H16  C12  C13  N4      0.00   0.0  0
 B1I  CONST_38  H14  N1   C11  N3    180.00   0.0  0
 B1I  CONST_39  H14  N1   C11  C12     0.00   0.0  0
 B1I  Var_01    C4   N    C5   C6     -8.30  30.0  2
 B1I  Var_02    C3   N    C5   C6    132.69  30.0  2
 B1I  Var_03    C4   N    C5   C10   170.14  30.0  2
 B1I  Var_04    C3   N    C5   C10   -48.86  30.0  2
 B1I  Var_05    C    C4   N    C5   -160.46  30.0  1
 B1I  Var_06    C2   C3   N    C5    159.08  30.0  1
 B1I  Var_07    C1   C    C4   N     -55.24  30.0  1
 B1I  Var_08    C2   C1   C    C4     54.22  30.0  1
 B1I  Var_09    C2   C3   N    C4    -57.90  30.0  1
 B1I  Var_10    C3   N    C4   C      56.98  30.0  1
 B1I  Var_11    C18  N4   C13  N2     16.26  30.0  2
 B1I  Var_12    C15  N4   C13  N2    174.32  30.0  2
 B1I  Var_13    C17  C18  N4   C13  -148.48  30.0  1
 B1I  Var_14    C16  C15  N4   C13   149.50  30.0  1
 B1I  Var_15    C18  N4   C13  C12  -165.08  30.0  2
 B1I  Var_16    C15  N4   C13  C12    -7.01  30.0  2
 B1I  Var_17    O    C17  C18  N4    -55.23  30.0  1
 B1I  Var_18    O    C16  C15  N4     54.09  30.0  1
 B1I  Var_19    C16  O    C17  C18    59.25  30.0  1
 B1I  Var_20    C16  C15  N4   C18   -50.87  30.0  1
 B1I  Var_21    C15  N4   C18  C17    51.65  30.0  1
 B1I  Var_22    C15  C16  O    C17   -58.76  30.0  1
 B1I  Var_23    H5   C4   N    C5     77.31  30.0  1
 B1I  Var_24    H6   C4   N    C5    -40.94  30.0  1
 B1I  Var_25    H9   C3   N    C5     38.38  30.0  1
 B1I  Var_26    H10  C3   N    C5    -79.42  30.0  1
 B1I  Var_27    H7   C    C4   N    -177.46  30.0  1
 B1I  Var_28    H8   C    C4   N      66.33  30.0  1
 B1I  Var_29    H12  C1   C    C4    175.99  30.0  1
 B1I  Var_30    H13  C1   C    C4    -65.85  30.0  1
 B1I  Var_31    H9   C3   N    C4   -178.60  30.0  1
 B1I  Var_32    H10  C3   N    C4     63.60  30.0  1
 B1I  Var_33    H5   C4   N    C3    -65.25  30.0  1
 B1I  Var_34    H6   C4   N    C3    176.50  30.0  1
 B1I  Var_35    H7   C    C1   C2    175.46  30.0  1
 B1I  Var_36    H8   C    C1   C2    -66.95  30.0  1
 B1I  Var_37    H5   C4   C    C1     68.03  30.0  1
 B1I  Var_38    H6   C4   C    C1   -175.04  30.0  1
 B1I  Var_39    H17  C18  N4   C13    90.39  30.0  1
 B1I  Var_40    H18  C18  N4   C13   -28.00  30.0  1
 B1I  Var_41    H23  C15  N4   C13   -88.15  30.0  1
 B1I  Var_42    H24  C15  N4   C13    31.03  30.0  1
 B1I  Var_43    H19  C17  C18  N4     67.39  30.0  1
 B1I  Var_44    H20  C17  C18  N4   -174.39  30.0  1
 B1I  Var_45    H21  C16  C15  N4    -68.74  30.0  1
 B1I  Var_46    H22  C16  C15  N4    173.59  30.0  1
 B1I  Var_47    H23  C15  N4   C18    71.47  30.0  1
 B1I  Var_48    H24  C15  N4   C18  -169.35  30.0  1
 B1I  Var_49    H21  C16  O    C17    63.13  30.0  1
 B1I  Var_50    H22  C16  O    C17  -179.26  30.0  1
 B1I  Var_51    H17  C18  C17  O      66.03  30.0  1
 B1I  Var_52    H18  C18  C17  O    -175.86  30.0  1
 B1I  Var_53    H23  C15  C16  O     -68.39  30.0  1
 B1I  Var_54    H24  C15  C16  O     174.68  30.0  1
 B1I  Var_55    H19  C17  O    C16   -62.70  30.0  1
 B1I  Var_56    H20  C17  O    C16   179.60  30.0  1
 B1I  Var_57    H17  C18  N4   C15   -69.48  30.0  1
 B1I  Var_58    H18  C18  N4   C15   172.13  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
 B1I  chir_01  C2  C1  N1  C3  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
 B1I  plan-1  F    0.020
 B1I  plan-1  C9   0.020
 B1I  plan-1  C8   0.020
 B1I  plan-1  C7   0.020
 B1I  plan-1  C6   0.020
 B1I  plan-1  C10  0.020
 B1I  plan-1  C5   0.020
 B1I  plan-1  N    0.020
 B1I  plan-1  H1   0.020
 B1I  plan-1  H2   0.020
 B1I  plan-1  H3   0.020
 B1I  plan-1  H4   0.020
 B1I  plan-2  N1   0.020
 B1I  plan-2  C11  0.020
 B1I  plan-2  N3   0.020
 B1I  plan-2  C14  0.020
 B1I  plan-2  N2   0.020
 B1I  plan-2  C13  0.020
 B1I  plan-2  C12  0.020
 B1I  plan-2  N4   0.020
 B1I  plan-2  H15  0.020
 B1I  plan-2  H16  0.020
 B1I  plan-3  C2   0.020
 B1I  plan-3  N1   0.020
 B1I  plan-3  C11  0.020
 B1I  plan-3  H14  0.020

