# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 06:56:05 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (4S,6R)-4-[2,4-difluoro-5-({[1-(trifluoromethyl)cyclopropyl]amino}methyl)phenyl]-4,6-dimethyl-5,6-dihydro-4H-1,3-thiazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@](C)(N=C(N)S1)c2cc(CNC3(CC3)C(F)(F)F)c(F)cc2F
#
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
 P6M  P6M  (4S,6R)-4-[2,4-difluoro-5-({[1-(trifluoromethyl)cyclopropyl]amino}methyl)phenyl]-4,6-dimethyl-5,6-dihydro-4H-1,3-thiazin-2-amine  ligand  46  26  .  2022-07-22  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_P6M
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
 P6M  F1   F  F     0  -0.311  -2.4733  -3.0661   0.1000
 P6M  C7   C  CR6   0   0.531  -1.4433  -2.2063   0.0067
 P6M  C6   C  CR6   0  -0.074  -1.6338  -0.8528   0.2533
 P6M  C8   C  CR16  0  -0.558  -0.2239  -2.7525  -0.3486
 P6M  C9   C  CR6   0   0.535   0.8587  -1.9063  -0.4560
 P6M  F    F  F     0  -0.301   2.0384  -2.4272  -0.8161
 P6M  C4   C  CR6   0  -0.094   0.7571  -0.5451  -0.2225
 P6M  C5   C  CR16  0  -0.342  -0.4955  -0.0580   0.1317
 P6M  C3   C  CH2   0  -0.325   1.9496   0.3645  -0.3120
 P6M  N    N  NH1   0  -0.623   2.8857   0.0694   0.7590
 P6M  C1   C  CT    0  -0.085   4.1641   0.6976   0.6874
 P6M  C16  C  CT    0   1.036   5.2047  -0.2364   0.1407
 P6M  F2   F  F     0  -0.313   5.3381  -1.3304   0.9025
 P6M  F3   F  F     0  -0.312   4.8970  -0.6652  -1.0934
 P6M  F4   F  F     0  -0.311   6.4210   0.3250   0.0570
 P6M  C2   C  CH2   0  -0.485   4.3147   2.1695   0.4104
 P6M  C    C  CH2   0  -0.497   4.5907   1.6328   1.7771
 P6M  C10  C  CT    0   0.053  -2.9964  -0.2490   0.6355
 P6M  C11  C  CH2   0  -0.436  -4.0012  -0.5889  -0.4885
 P6M  C12  C  CH1   0  -0.391  -5.2097   0.3275  -0.6275
 P6M  S    S  S2    0   0.005  -4.6404   2.0213  -0.9674
 P6M  C13  C  C     0   0.278  -3.3632   2.1165   0.2649
 P6M  N1   N  N     0  -0.416  -2.7889   1.1617   0.8644
 P6M  N2   N  NH2   0  -0.803  -3.0511   3.4094   0.5661
 P6M  C15  C  CH3   0  -0.644  -3.4232  -0.8398   1.9919
 P6M  C14  C  CH3   0  -0.640  -6.2226   0.3009   0.5064
 P6M  H1   H  HCR6  0   0.295  -0.1279  -3.8138  -0.5387
 P6M  H2   H  HCR6  0   0.271  -0.5959   1.0016   0.3240
 P6M  H3   H  HCH2  0   0.251   2.4534   0.2290  -1.2695
 P6M  H4   H  HCH2  0   0.229   1.5920   1.4019  -0.2989
 P6M  H5   H  HNH1  0   0.365   2.4569   0.2123   1.6620
 P6M  H7   H  HCH2  0   0.271   5.1463   2.5202  -0.1865
 P6M  H8   H  HCH2  0   0.273   3.3979   2.7245   0.2595
 P6M  H9   H  HCH2  0   0.276   3.8613   1.8174   2.5557
 P6M  H10  H  HCH2  0   0.272   5.6135   1.6061   2.1295
 P6M  H11  H  HCH2  0   0.257  -3.4827  -0.5847  -1.4500
 P6M  H12  H  HCH2  0   0.259  -4.3781  -1.6016  -0.3412
 P6M  H13  H  HCH1  0   0.299  -5.7178   0.0362  -1.5486
 P6M  H14  H  HNH2  0   0.394  -3.3380   4.1387  -0.0659
 P6M  H15  H  HNH2  0   0.388  -2.1492   3.5570   0.9916
 P6M  H16  H  HCH3  0   0.235  -2.6345  -0.6851   2.7286
 P6M  H17  H  HCH3  0   0.240  -4.3207  -0.3453   2.3590
 P6M  H18  H  HCH3  0   0.228  -3.6318  -1.9059   1.9303
 P6M  H19  H  HCH3  0   0.236  -5.8423   0.7522   1.4210
 P6M  H20  H  HCH3  0   0.247  -7.1233   0.8434   0.2213
 P6M  H21  H  HCH3  0   0.238  -6.5089  -0.7281   0.7313

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
 P6M  C14  C12  single    1.521  0.020  1.521
 P6M  C12  C11  single    1.523  0.020  1.523
 P6M  C12  S    single    1.819  0.020  1.819
 P6M  C11  C10  single    1.546  0.020  1.546
 P6M  F1   C7   single    1.345  0.020  1.345
 P6M  S    C13  single    1.777  0.020  1.777
 P6M  C7   C8   aromatic  1.383  0.020  1.383
 P6M  C7   C6   aromatic  1.389  0.020  1.389
 P6M  C8   C9   aromatic  1.378  0.020  1.378
 P6M  C10  C6   single    1.539  0.020  1.539
 P6M  C10  C15  single    1.540  0.020  1.540
 P6M  C10  N1   single    1.444  0.020  1.444
 P6M  C6   C5   aromatic  1.394  0.020  1.394
 P6M  C13  N1   double    1.265  0.020  1.265
 P6M  C13  N2   single    1.364  0.020  1.364
 P6M  C9   F    single    1.339  0.020  1.339
 P6M  C9   C4   aromatic  1.385  0.020  1.385
 P6M  C5   C4   aromatic  1.390  0.020  1.390
 P6M  C4   C3   single    1.502  0.020  1.502
 P6M  F2   C16  single    1.340  0.020  1.340
 P6M  N    C3   single    1.453  0.020  1.453
 P6M  N    C1   single    1.426  0.020  1.426
 P6M  C    C1   single    1.498  0.020  1.498
 P6M  C    C2   single    1.494  0.020  1.494
 P6M  C1   C16  single    1.501  0.020  1.501
 P6M  C1   C2   single    1.505  0.020  1.505
 P6M  C16  F3   single    1.342  0.020  1.342
 P6M  C16  F4   single    1.342  0.020  1.342
 P6M  C8   H1   single    0.930  0.020  1.080
 P6M  C5   H2   single    0.930  0.020  1.080
 P6M  C3   H3   single    0.970  0.020  1.090
 P6M  C3   H4   single    0.970  0.020  1.090
 P6M  N    H5   single    0.890  0.020  1.040
 P6M  C2   H7   single    0.970  0.020  1.090
 P6M  C2   H8   single    0.970  0.020  1.090
 P6M  C    H9   single    0.970  0.020  1.090
 P6M  C    H10  single    0.970  0.020  1.090
 P6M  C11  H11  single    0.970  0.020  1.090
 P6M  C11  H12  single    0.970  0.020  1.090
 P6M  C12  H13  single    0.970  0.020  1.090
 P6M  N2   H14  single    0.890  0.020  1.040
 P6M  N2   H15  single    0.890  0.020  1.040
 P6M  C15  H16  single    0.970  0.020  1.090
 P6M  C15  H17  single    0.970  0.020  1.090
 P6M  C15  H18  single    0.970  0.020  1.090
 P6M  C14  H19  single    0.970  0.020  1.090
 P6M  C14  H20  single    0.970  0.020  1.090
 P6M  C14  H21  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
 P6M  C8   C7   C6   123.47  3.000
 P6M  C6   C7   F1   120.37  3.000
 P6M  C8   C7   F1   116.15  3.000
 P6M  C10  C6   C5   121.41  3.000
 P6M  C5   C6   C7   115.36  3.000
 P6M  C10  C6   C7   123.23  3.000
 P6M  H1   C8   C9   121.24  3.000
 P6M  H1   C8   C7   120.71  3.000
 P6M  C9   C8   C7   118.05  3.000
 P6M  C4   C9   F    119.50  3.000
 P6M  C4   C9   C8   122.19  3.000
 P6M  F    C9   C8   118.30  3.000
 P6M  C3   C4   C5   121.22  3.000
 P6M  C3   C4   C9   121.79  3.000
 P6M  C5   C4   C9   116.97  3.000
 P6M  H2   C5   C4   118.18  3.000
 P6M  H2   C5   C6   117.86  3.000
 P6M  C4   C5   C6   123.95  3.000
 P6M  H4   C3   H3   106.17  3.000
 P6M  H4   C3   N    113.16  3.000
 P6M  H3   C3   N    108.93  3.000
 P6M  H4   C3   C4   108.24  3.000
 P6M  H3   C3   C4   110.11  3.000
 P6M  N    C3   C4   110.16  3.000
 P6M  H5   N    C1   111.30  3.000
 P6M  H5   N    C3   110.91  3.000
 P6M  C1   N    C3   116.82  3.000
 P6M  C    C1   C2    59.66  3.000
 P6M  C2   C1   C16  118.17  3.000
 P6M  C    C1   C16  117.12  3.000
 P6M  C2   C1   N    121.98  3.000
 P6M  C16  C1   N    111.44  3.000
 P6M  C    C1   N    119.59  3.000
 P6M  F4   C16  F3   106.50  3.000
 P6M  F4   C16  F2   106.66  3.000
 P6M  F3   C16  F2   106.55  3.000
 P6M  F4   C16  C1   112.99  3.000
 P6M  F3   C16  C1   112.00  3.000
 P6M  F2   C16  C1   111.72  3.000
 P6M  H8   C2   H7   114.07  3.000
 P6M  H8   C2   C    117.92  3.000
 P6M  H7   C2   C    118.63  3.000
 P6M  H8   C2   C1   116.25  3.000
 P6M  H7   C2   C1   119.69  3.000
 P6M  C    C2   C1    59.93  3.000
 P6M  H10  C    H9   114.00  3.000
 P6M  H10  C    C2   118.78  3.000
 P6M  H9   C    C2   118.17  3.000
 P6M  H10  C    C1   119.39  3.000
 P6M  H9   C    C1   115.96  3.000
 P6M  C2   C    C1    60.41  3.000
 P6M  C15  C10  N1   105.96  3.000
 P6M  N1   C10  C11  115.06  3.000
 P6M  C15  C10  C11  112.09  3.000
 P6M  N1   C10  C6   107.19  3.000
 P6M  C15  C10  C6   108.28  3.000
 P6M  C11  C10  C6   107.99  3.000
 P6M  H12  C11  H11  106.65  3.000
 P6M  H12  C11  C12  107.27  3.000
 P6M  H11  C11  C12  107.10  3.000
 P6M  H12  C11  C10  109.31  3.000
 P6M  H11  C11  C10  109.31  3.000
 P6M  C12  C11  C10  116.74  3.000
 P6M  H13  C12  C14  108.33  3.000
 P6M  H13  C12  S    103.68  3.000
 P6M  C14  C12  S    111.35  3.000
 P6M  H13  C12  C11  106.61  3.000
 P6M  S    C12  C11  109.21  3.000
 P6M  C14  C12  C11  116.74  3.000
 P6M  C13  S    C12   98.35  3.000
 P6M  N2   C13  N1   120.46  3.000
 P6M  N2   C13  S    111.61  3.000
 P6M  N1   C13  S    127.90  3.000
 P6M  C13  N1   C10  126.64  3.000
 P6M  H15  N2   H14  114.45  3.000
 P6M  H15  N2   C13  115.89  3.000
 P6M  H14  N2   C13  118.87  3.000
 P6M  H18  C15  H17  107.82  3.000
 P6M  H18  C15  H16  108.42  3.000
 P6M  H17  C15  H16  107.70  3.000
 P6M  H18  C15  C10  112.29  3.000
 P6M  H17  C15  C10  110.57  3.000
 P6M  H16  C15  C10  109.90  3.000
 P6M  H21  C14  H20  107.85  3.000
 P6M  H21  C14  H19  108.03  3.000
 P6M  H20  C14  H19  107.59  3.000
 P6M  H21  C14  C12  110.18  3.000
 P6M  H20  C14  C12  110.29  3.000
 P6M  H19  C14  C12  112.74  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
 P6M  CONST_01  C4   C9   C8  C7      0.00   0.0  0
 P6M  CONST_02  C4   C5   C6  C7      0.00   0.0  0
 P6M  CONST_03  C9   C8   C7  C6      0.00   0.0  0
 P6M  CONST_04  C9   C4   C5  C6      0.00   0.0  0
 P6M  CONST_05  C5   C6   C7  C8      0.00   0.0  0
 P6M  CONST_06  C5   C4   C9  C8      0.00   0.0  0
 P6M  CONST_07  C10  C6   C7  C8    180.00   0.0  0
 P6M  CONST_08  C10  C6   C5  C4    180.00   0.0  0
 P6M  CONST_09  S    C13  N1  C10     0.00   0.0  0
 P6M  CONST_10  C9   C8   C7  F1    180.00   0.0  0
 P6M  CONST_11  C10  C6   C7  F1      0.00   0.0  0
 P6M  CONST_12  C5   C6   C7  F1    180.00   0.0  0
 P6M  CONST_13  F    C9   C8  C7    180.00   0.0  0
 P6M  CONST_14  C3   C4   C5  C6    180.00   0.0  0
 P6M  CONST_15  C3   C4   C9  C8    180.00   0.0  0
 P6M  CONST_16  C5   C4   C9  F     180.00   0.0  0
 P6M  CONST_17  N2   C13  N1  C10   180.00   0.0  0
 P6M  CONST_18  H2   C5   C6  C7    180.00   0.0  0
 P6M  CONST_19  H1   C8   C7  C6    180.00   0.0  0
 P6M  Var_01    N1   C13  S   C12    18.95  30.0  1
 P6M  Var_02    C2   C    C1  N    -111.92  30.0  1
 P6M  Var_03    H7   C2   C   C1   -109.63  30.0  1
 P6M  Var_04    N    C3   C4  C9    -67.59  30.0  2
 P6M  Var_05    C1   N    C3  C4    170.22  30.0  2
 P6M  Var_06    C    C1   N   C3    118.50  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
 P6M  chir_02  C10  C6  C11  N1   positiv
 P6M  chir_03  C12  S   C11  C14  negativ
 P6M  chir_04  C1   C   C16  C2   both

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
 P6M  plan-1  F1   0.020
 P6M  plan-1  C7   0.020
 P6M  plan-1  C6   0.020
 P6M  plan-1  C8   0.020
 P6M  plan-1  C9   0.020
 P6M  plan-1  F    0.020
 P6M  plan-1  C4   0.020
 P6M  plan-1  C5   0.020
 P6M  plan-1  C3   0.020
 P6M  plan-1  C10  0.020
 P6M  plan-1  H1   0.020
 P6M  plan-1  H2   0.020
 P6M  plan-2  C10  0.020
 P6M  plan-2  S    0.020
 P6M  plan-2  C13  0.020
 P6M  plan-2  N1   0.020
 P6M  plan-2  N2   0.020
 P6M  plan-2  H14  0.020
 P6M  plan-2  H15  0.020

