# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:49:26 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3-(trifluoromethyl)phenyl]amino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCCN(C1)c2ncc(C(N)=O)c(Nc3cccc(c3)C(F)(F)F)n2
#
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
 MMW  MMW  2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3-(trifluoromethyl)phenyl]amino]pyrimidine-5-carboxamide  ligand  46  27  .  2021-08-14  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MMW
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
 MMW  C1   C  CH2   0  -0.441   4.5616   3.1038  -0.0801
 MMW  C2   C  CH2   0  -0.459   3.0347   3.0173  -0.0886
 MMW  C3   C  CH2   0  -0.317   2.5355   2.1809   1.0843
 MMW  C4   C  CH2   0  -0.331   4.6299   0.9723   1.2240
 MMW  C5   C  CR6   0   0.644   2.5678  -0.2457   0.7046
 MMW  C7   C  CR6   0  -0.305   1.3185  -2.5167  -0.0710
 MMW  C9   C  CR6   0   0.573   0.6402  -1.2651   0.0176
 MMW  N    N  NH2   0  -0.792   5.0964   1.0136  -1.2413
 MMW  C    C  CH1   0  -0.105   5.2185   1.7263   0.0217
 MMW  O    O  O     0  -0.517  -0.5760  -3.8332  -0.6052
 MMW  C10  C  CR6   0   0.398  -1.5223  -0.0869  -0.2880
 MMW  C11  C  CR16  0  -0.285  -1.1086   1.2252  -0.5356
 MMW  C12  C  CR16  0  -0.236  -2.0407   2.2485  -0.5618
 MMW  C13  C  CR16  0  -0.309  -3.3913   2.0036  -0.3584
 MMW  C14  C  CR6   0  -0.173  -3.8028   0.6984  -0.1308
 MMW  C15  C  CR16  0  -0.384  -2.8794  -0.3371  -0.0901
 MMW  C16  C  CT    0   1.051  -5.2450   0.3636   0.0896
 MMW  C6   C  CR16  0  -0.021   2.6541  -2.4635   0.3091
 MMW  C8   C  C     0   0.539   0.6528  -3.7603  -0.4937
 MMW  F    F  F     0  -0.314  -5.6847  -0.5411  -0.7976
 MMW  F1   F  F     0  -0.315  -5.4515  -0.1676   1.3042
 MMW  F2   F  F     0  -0.302  -6.0437   1.4290  -0.0107
 MMW  N1   N  NT    0  -0.475   3.1876   0.8821   1.0955
 MMW  N2   N  N     0  -0.486   3.2925  -1.3789   0.6885
 MMW  N3   N  NH2   0  -0.820   1.4262  -4.8288  -0.7422
 MMW  N4   N  NH1   0  -0.794  -0.6758  -1.1913  -0.2812
 MMW  N5   N  N     0  -0.529   1.2737  -0.1680   0.3910
 MMW  H1   H  HCH2  0   0.240   4.9219   3.6184  -0.9735
 MMW  H2   H  HCH2  0   0.227   4.8775   3.7042   0.7783
 MMW  H3   H  HCH2  0   0.246   2.6048   4.0187  -0.0233
 MMW  H4   H  HCH2  0   0.227   2.6701   2.5859  -1.0259
 MMW  H5   H  HCH2  0   0.243   2.7835   2.6820   2.0252
 MMW  H6   H  HCH2  0   0.271   1.4577   2.0521   1.0565
 MMW  H7   H  HCH2  0   0.272   5.0561  -0.0237   1.3073
 MMW  H8   H  HCH2  0   0.240   4.8596   1.5083   2.1506
 MMW  H9   H  HNH2  0   0.346   5.4534   0.0710  -1.1407
 MMW  H10  H  HNH2  0   0.344   4.1224   0.9092  -1.4993
 MMW  H12  H  HCH1  0   0.238   6.2857   1.8632   0.2214
 MMW  H13  H  HCR6  0   0.281  -0.0694   1.4444  -0.7179
 MMW  H14  H  HCR6  0   0.269  -1.7067   3.2589  -0.7559
 MMW  H15  H  HCR6  0   0.270  -4.0957   2.8222  -0.3870
 MMW  H16  H  HCR6  0   0.282  -3.2032  -1.3541   0.0989
 MMW  H17  H  HCR6  0   0.260   3.2543  -3.3677   0.3263
 MMW  H18  H  HNH2  0   0.407   0.9895  -5.6764  -1.0652
 MMW  H19  H  HNH2  0   0.413   2.4253  -4.7805  -0.8298
 MMW  H20  H  HNH1  0   0.429  -1.0974  -2.1048  -0.4425

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
 MMW  F1   C16  single    1.342  0.020  1.342
 MMW  F    C16  single    1.341  0.020  1.341
 MMW  C16  C14  single    1.497  0.020  1.497
 MMW  C16  F2   single    1.335  0.020  1.335
 MMW  C14  C13  aromatic  1.387  0.020  1.387
 MMW  C14  C15  aromatic  1.388  0.020  1.388
 MMW  C13  C12  aromatic  1.388  0.020  1.388
 MMW  C15  C10  aromatic  1.394  0.020  1.394
 MMW  C12  C11  aromatic  1.384  0.020  1.384
 MMW  O    C8   double    1.236  0.020  1.236
 MMW  C10  C11  aromatic  1.398  0.020  1.398
 MMW  C10  N4   single    1.392  0.020  1.392
 MMW  N4   C9   single    1.352  0.020  1.352
 MMW  N3   C8   single    1.342  0.020  1.342
 MMW  C8   C7   single    1.473  0.020  1.473
 MMW  C9   C7   aromatic  1.426  0.020  1.426
 MMW  C9   N5   aromatic  1.321  0.020  1.321
 MMW  C7   C6   aromatic  1.390  0.020  1.390
 MMW  N5   C5   aromatic  1.334  0.020  1.334
 MMW  C2   C3   single    1.525  0.020  1.525
 MMW  C2   C1   single    1.529  0.020  1.529
 MMW  C6   N2   aromatic  1.314  0.020  1.314
 MMW  C5   N2   aromatic  1.345  0.020  1.345
 MMW  C5   N1   single    1.345  0.020  1.345
 MMW  C3   N1   single    1.453  0.020  1.453
 MMW  N1   C4   single    1.451  0.020  1.451
 MMW  C1   C    single    1.530  0.020  1.530
 MMW  C    C4   single    1.536  0.020  1.536
 MMW  C    N    single    1.455  0.020  1.455
 MMW  C1   H1   single    0.970  0.020  1.090
 MMW  C1   H2   single    0.970  0.020  1.090
 MMW  C2   H3   single    0.970  0.020  1.090
 MMW  C2   H4   single    0.970  0.020  1.090
 MMW  C3   H5   single    0.970  0.020  1.090
 MMW  C3   H6   single    0.970  0.020  1.090
 MMW  C4   H7   single    0.970  0.020  1.090
 MMW  C4   H8   single    0.970  0.020  1.090
 MMW  N    H9   single    0.890  0.020  1.040
 MMW  N    H10  single    0.890  0.020  1.040
 MMW  C    H12  single    0.970  0.020  1.090
 MMW  C11  H13  single    0.930  0.020  1.080
 MMW  C12  H14  single    0.930  0.020  1.080
 MMW  C13  H15  single    0.930  0.020  1.080
 MMW  C15  H16  single    0.930  0.020  1.080
 MMW  C6   H17  single    0.930  0.020  1.080
 MMW  N3   H18  single    0.860  0.020  1.020
 MMW  N3   H19  single    0.860  0.020  1.020
 MMW  N4   H20  single    0.860  0.020  1.020

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
 MMW  H2   C1   H1   106.74  3.000
 MMW  H2   C1   C    108.54  3.000
 MMW  H1   C1   C    109.70  3.000
 MMW  H2   C1   C2   108.88  3.000
 MMW  H1   C1   C2   110.57  3.000
 MMW  C    C1   C2   112.22  3.000
 MMW  H4   C2   H3   106.36  3.000
 MMW  H4   C2   C3   109.49  3.000
 MMW  H3   C2   C3   109.16  3.000
 MMW  H4   C2   C1   111.09  3.000
 MMW  H3   C2   C1   109.93  3.000
 MMW  C3   C2   C1   110.71  3.000
 MMW  H6   C3   H5   107.53  3.000
 MMW  H6   C3   N1   109.85  3.000
 MMW  H5   C3   N1   107.51  3.000
 MMW  H6   C3   C2   111.74  3.000
 MMW  H5   C3   C2   109.63  3.000
 MMW  N1   C3   C2   110.44  3.000
 MMW  H8   C4   H7   107.56  3.000
 MMW  H8   C4   N1   108.30  3.000
 MMW  H7   C4   N1   109.86  3.000
 MMW  H8   C4   C    109.98  3.000
 MMW  H7   C4   C    111.07  3.000
 MMW  N1   C4   C    110.00  3.000
 MMW  N5   C5   N2   124.67  3.000
 MMW  N2   C5   N1   117.49  3.000
 MMW  N5   C5   N1   117.82  3.000
 MMW  C8   C7   C6   123.05  3.000
 MMW  C6   C7   C9   113.99  3.000
 MMW  C8   C7   C9   122.95  3.000
 MMW  N5   C9   N4   118.96  3.000
 MMW  N5   C9   C7   121.22  3.000
 MMW  N4   C9   C7   119.82  3.000
 MMW  H10  N    H9   105.57  3.000
 MMW  H10  N    C    110.62  3.000
 MMW  H9   N    C    109.87  3.000
 MMW  H12  C    N    107.55  3.000
 MMW  H12  C    C4   106.99  3.000
 MMW  N    C    C4   114.00  3.000
 MMW  H12  C    C1   108.56  3.000
 MMW  N    C    C1   110.32  3.000
 MMW  C4   C    C1   109.24  3.000
 MMW  N4   C10  C15  116.68  3.000
 MMW  N4   C10  C11  124.46  3.000
 MMW  C15  C10  C11  118.80  3.000
 MMW  H13  C11  C12  119.72  3.000
 MMW  H13  C11  C10  120.42  3.000
 MMW  C12  C11  C10  119.86  3.000
 MMW  H14  C12  C13  119.45  3.000
 MMW  H14  C12  C11  119.07  3.000
 MMW  C13  C12  C11  121.47  3.000
 MMW  H15  C13  C14  121.59  3.000
 MMW  H15  C13  C12  119.80  3.000
 MMW  C14  C13  C12  118.61  3.000
 MMW  C16  C14  C15  118.02  3.000
 MMW  C15  C14  C13  120.62  3.000
 MMW  C16  C14  C13  121.36  3.000
 MMW  H16  C15  C14  120.42  3.000
 MMW  H16  C15  C10  118.94  3.000
 MMW  C14  C15  C10  120.63  3.000
 MMW  F2   C16  F1   106.97  3.000
 MMW  F2   C16  F    107.00  3.000
 MMW  F1   C16  F    106.33  3.000
 MMW  F2   C16  C14  112.75  3.000
 MMW  F    C16  C14  111.68  3.000
 MMW  F1   C16  C14  111.72  3.000
 MMW  H17  C6   N2   114.47  3.000
 MMW  H17  C6   C7   120.26  3.000
 MMW  N2   C6   C7   125.26  3.000
 MMW  N3   C8   O    120.60  3.000
 MMW  N3   C8   C7   117.71  3.000
 MMW  O    C8   C7   121.68  3.000
 MMW  C5   N1   C4   122.41  3.000
 MMW  C4   N1   C3   113.03  3.000
 MMW  C5   N1   C3   122.71  3.000
 MMW  C6   N2   C5   115.91  3.000
 MMW  H19  N3   H18  116.37  3.000
 MMW  H19  N3   C8   123.44  3.000
 MMW  H18  N3   C8   118.67  3.000
 MMW  H20  N4   C10  117.33  3.000
 MMW  H20  N4   C9   112.89  3.000
 MMW  C10  N4   C9   129.55  3.000
 MMW  C9   N5   C5   118.91  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
 MMW  CONST_01  C7   C9   N5   C5      0.00   0.0  0
 MMW  CONST_02  C7   C6   N2   C5      0.00   0.0  0
 MMW  CONST_03  N2   C6   C7   C9      0.00   0.0  0
 MMW  CONST_04  N2   C5   N5   C9      0.00   0.0  0
 MMW  CONST_05  C13  C14  C15  C10     0.00   0.0  0
 MMW  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 MMW  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 MMW  CONST_08  C14  C15  C10  C11     0.00   0.0  0
 MMW  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 MMW  CONST_10  C15  C10  C11  C12     0.00   0.0  0
 MMW  CONST_11  N5   C9   C7   C6      0.00   0.0  0
 MMW  CONST_12  N5   C5   N2   C6      0.00   0.0  0
 MMW  CONST_13  N1   C5   N5   C9    180.00   0.0  0
 MMW  CONST_14  N1   C5   N2   C6    180.00   0.0  0
 MMW  CONST_15  N4   C9   N5   C5    180.00   0.0  0
 MMW  CONST_16  C16  C14  C15  C10   180.00   0.0  0
 MMW  CONST_17  C16  C14  C13  C12   180.00   0.0  0
 MMW  CONST_18  N4   C10  C11  C12   180.00   0.0  0
 MMW  CONST_19  N4   C10  C15  C14   180.00   0.0  0
 MMW  CONST_20  N4   C9   C7   C6    180.00   0.0  0
 MMW  CONST_21  N5   C9   C7   C8    180.00   0.0  0
 MMW  CONST_22  N2   C6   C7   C8    180.00   0.0  0
 MMW  CONST_23  H17  C6   N2   C5    180.00   0.0  0
 MMW  CONST_24  H14  C12  C11  C10   180.00   0.0  0
 MMW  CONST_25  H15  C13  C12  C11   180.00   0.0  0
 MMW  CONST_26  H16  C15  C10  C11   180.00   0.0  0
 MMW  CONST_27  H13  C11  C12  C13   180.00   0.0  0
 MMW  CONST_28  H18  N3   C8   C7    180.00   0.0  0
 MMW  CONST_29  H19  N3   C8   C7      0.00   0.0  0
 MMW  Var_01    N1   C3   C2   C1    -53.53  30.0  1
 MMW  Var_02    C5   N1   C3   C2   -104.58  30.0  1
 MMW  Var_03    C    C1   C2   C3     51.55  30.0  1
 MMW  Var_04    N5   C5   N1   C3     -5.06  30.0  2
 MMW  Var_05    C    C4   N1   C3    -61.96  30.0  1
 MMW  Var_06    C10  N4   C9   C7   -178.68  30.0  2
 MMW  Var_07    C15  C10  N4   C9   -154.29  30.0  2
 MMW  Var_08    O    C8   C7   C9    -10.98  30.0  2
 MMW  Var_09    F1   C16  C14  C13  -118.14  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
 MMW  chir_01  C  C1  C4  N  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
 MMW  plan-1  C5   0.020
 MMW  plan-1  C7   0.020
 MMW  plan-1  C9   0.020
 MMW  plan-1  C6   0.020
 MMW  plan-1  C8   0.020
 MMW  plan-1  N1   0.020
 MMW  plan-1  N2   0.020
 MMW  plan-1  N4   0.020
 MMW  plan-1  N5   0.020
 MMW  plan-1  H17  0.020
 MMW  plan-2  C10  0.020
 MMW  plan-2  C11  0.020
 MMW  plan-2  C12  0.020
 MMW  plan-2  C13  0.020
 MMW  plan-2  C14  0.020
 MMW  plan-2  C15  0.020
 MMW  plan-2  C16  0.020
 MMW  plan-2  N4   0.020
 MMW  plan-2  H13  0.020
 MMW  plan-2  H14  0.020
 MMW  plan-2  H15  0.020
 MMW  plan-2  H16  0.020
 MMW  plan-3  C7   0.020
 MMW  plan-3  O    0.020
 MMW  plan-3  C8   0.020
 MMW  plan-3  N3   0.020
 MMW  plan-3  H18  0.020
 MMW  plan-3  H19  0.020

