# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 02:04:54 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-{[4-{[(1R,2R)-2-(dimethylamino)cyclopentyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-N-methylbenzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[S](=O)(=O)c1ccc(Nc2ncc(c(N[C@@H]3CCC[C@H]3N(C)C)n2)C(F)(F)F)cc1
#
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
 P1E  P1E  4-{[4-{[(1R,2R)-2-(dimethylamino)cyclopentyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-N-methylbenzenesulfonamide  ligand  56  31  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1E
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
 P1E  C4    C  CR6   0   0.388   2.2239   0.4854   0.4096
 P1E  C6    C  CR16  0  -0.224   4.3060  -0.6494  -0.0209
 P1E  C9    C  CR6   0   0.621  -0.1362  -0.3492   0.3771
 P1E  C13   C  CR16  0  -0.004  -0.8395  -2.4746   0.2688
 P1E  F22   F  F     0  -0.298  -2.8104  -4.3340   0.1932
 P1E  F16   F  F     0  -0.320  -4.0241  -2.9222  -0.8863
 P1E  F21   F  F     0  -0.321  -4.0953  -2.9762   1.2591
 P1E  C12   C  CR6   0  -0.438  -2.1585  -2.0840   0.2726
 P1E  N14   N  N     0  -0.495   0.1876  -1.6343   0.3155
 P1E  C11   C  CR6   0   0.596  -2.3950  -0.6776   0.3211
 P1E  N8    N  NH1   0  -0.680  -3.6158  -0.1359   0.2879
 P1E  C25   C  CR15  0  -0.088  -3.8556   1.2964   0.2979
 P1E  C28   C  CH2   0  -0.440  -3.8222   1.9121   1.7125
 P1E  C31   C  CH2   0  -0.448  -5.2799   2.2170   2.0416
 P1E  C27   C  CH2   0  -0.472  -5.8400   2.6465   0.6920
 P1E  C24   C  CR15  0  -0.049  -5.2592   1.6128  -0.2772
 P1E  N26   N  NT    0  -0.414  -5.2074   2.0548  -1.6593
 P1E  C30   C  CH3   0  -0.531  -4.6899   1.0263  -2.5398
 P1E  C29   C  CH3   0  -0.529  -6.5019   2.5034  -2.1333
 P1E  N10   N  N     0  -0.524  -1.3632   0.1572   0.3860
 P1E  N7    N  NH1   0  -0.766   0.8469   0.5933   0.4568
 P1E  C5    C  CR16  0  -0.295   2.9240  -0.6664   0.0319
 P1E  C3    C  CR16  0  -0.344   2.9503   1.6372   0.7409
 P1E  C2    C  CR16  0  -0.220   4.3285   1.6481   0.6957
 P1E  C1    C  CR6   0  -0.233   5.0117   0.5002   0.3086
 P1E  S18   S  S     0   1.367   6.7706   0.5187   0.1768
 P1E  O19   O  OS    0  -0.661   7.2682   1.5791   1.0389
 P1E  O20   O  OS    0  -0.661   7.2576  -0.8422   0.3380
 P1E  N17   N  NC1   0  -0.706   7.1433   0.9503  -1.3686
 P1E  C23   C  CH3   0  -0.531   6.7290   2.2629  -1.8441
 P1E  H6    H  HCR6  0   0.282   4.8234  -1.5505  -0.3219
 P1E  H13   H  HCR6  0   0.283  -0.5773  -3.5250   0.2254
 P1E  HN8   H  HNH1  0   0.397  -4.4286  -0.7284   0.2875
 P1E  H25   H  HCR5  0   0.266  -3.0969   1.7664  -0.3278
 P1E  H28   H  HCH2  0   0.244  -3.3315   1.2585   2.4337
 P1E  H28A  H  HCH2  0   0.233  -3.2501   2.8418   1.6833
 P1E  H31   H  HCH2  0   0.224  -5.7940   1.3171   2.3912
 P1E  H31A  H  HCH2  0   0.240  -5.3947   2.9777   2.8143
 P1E  H27   H  HCH2  0   0.247  -6.9293   2.6798   0.6700
 P1E  H27A  H  HCH2  0   0.227  -5.4683   3.6428   0.4323
 P1E  H24   H  HCR5  0   0.202  -5.8872   0.7016  -0.1932
 P1E  H30   H  HCH3  0   0.192  -5.3105   0.1157  -2.5532
 P1E  H30A  H  HCH3  0   0.237  -4.6428   1.4088  -3.5600
 P1E  H30B  H  HCH3  0   0.241  -3.6798   0.7341  -2.2559
 P1E  H29   H  HCH3  0   0.243  -6.8510   3.3624  -1.5623
 P1E  H29A  H  HCH3  0   0.235  -6.4193   2.8165  -3.1747
 P1E  H29B  H  HCH3  0   0.193  -7.2773   1.7232  -2.0800
 P1E  HN7   H  HNH1  0   0.415   0.4883   1.5275   0.5916
 P1E  H5    H  HCR6  0   0.295   2.3957  -1.5706  -0.2196
 P1E  H3    H  HCR6  0   0.284   2.4254   2.5339   1.0457
 P1E  H2    H  HCR6  0   0.286   4.8575   2.5491   0.9747
 P1E  HN17  H  HNC1  0   0.412   6.9469   0.1998  -2.0214
 P1E  H23   H  HCH3  0   0.238   5.6459   2.4114  -1.8268
 P1E  H23A  H  HCH3  0   0.258   7.2055   3.0437  -1.2569
 P1E  H23B  H  HCH3  0   0.272   7.0681   2.3611  -2.8719
 P1E  C15   C  CT    0   1.076  -3.2582  -3.0772   0.2095

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
 P1E  C4   N7    single    1.382  0.020  1.382
 P1E  C4   C5    aromatic  1.400  0.020  1.400
 P1E  C4   C3    aromatic  1.401  0.020  1.401
 P1E  C6   C5    aromatic  1.383  0.020  1.383
 P1E  C6   C1    aromatic  1.389  0.020  1.389
 P1E  C9   N14   aromatic  1.327  0.020  1.327
 P1E  C9   N10   aromatic  1.327  0.020  1.327
 P1E  C9   N7    single    1.364  0.020  1.364
 P1E  C13  C12   aromatic  1.376  0.020  1.376
 P1E  C13  N14   aromatic  1.328  0.020  1.328
 P1E  F22  C15   single    1.334  0.020  1.334
 P1E  C15  F16   single    1.346  0.020  1.346
 P1E  C15  F21   single    1.346  0.020  1.346
 P1E  C15  C12   single    1.483  0.020  1.483
 P1E  C12  C11   aromatic  1.427  0.020  1.427
 P1E  C11  N8    single    1.336  0.020  1.336
 P1E  C11  N10   aromatic  1.329  0.020  1.329
 P1E  N8   C25   single    1.452  0.020  1.452
 P1E  C25  C28   single    1.543  0.020  1.543
 P1E  C25  C24   single    1.550  0.020  1.550
 P1E  C28  C31   single    1.525  0.020  1.525
 P1E  C31  C27   single    1.523  0.020  1.523
 P1E  C27  C24   single    1.531  0.020  1.531
 P1E  C24  N26   single    1.452  0.020  1.452
 P1E  N26  C30   single    1.449  0.020  1.449
 P1E  N26  C29   single    1.450  0.020  1.450
 P1E  C3   C2    aromatic  1.379  0.020  1.379
 P1E  C2   C1    aromatic  1.391  0.020  1.391
 P1E  C1   S18   single    1.764  0.020  1.764
 P1E  S18  O19   double    1.454  0.020  1.454
 P1E  S18  O20   double    1.454  0.020  1.454
 P1E  S18  N17   single    1.647  0.020  1.647
 P1E  N17  C23   single    1.456  0.020  1.456
 P1E  C6   H6    single    0.930  0.020  1.080
 P1E  C13  H13   single    0.930  0.020  1.080
 P1E  N8   HN8   single    0.860  0.020  1.020
 P1E  C25  H25   single    0.970  0.020  1.090
 P1E  C28  H28   single    0.970  0.020  1.090
 P1E  C28  H28A  single    0.970  0.020  1.090
 P1E  C31  H31   single    0.970  0.020  1.090
 P1E  C31  H31A  single    0.970  0.020  1.090
 P1E  C27  H27   single    0.970  0.020  1.090
 P1E  C27  H27A  single    0.970  0.020  1.090
 P1E  C24  H24   single    0.970  0.020  1.090
 P1E  C30  H30   single    0.970  0.020  1.090
 P1E  C30  H30A  single    0.970  0.020  1.090
 P1E  C30  H30B  single    0.970  0.020  1.090
 P1E  C29  H29   single    0.970  0.020  1.090
 P1E  C29  H29A  single    0.970  0.020  1.090
 P1E  C29  H29B  single    0.970  0.020  1.090
 P1E  N7   HN7   single    0.860  0.020  1.020
 P1E  C5   H5    single    0.930  0.020  1.080
 P1E  C3   H3    single    0.930  0.020  1.080
 P1E  C2   H2    single    0.930  0.020  1.080
 P1E  N17  HN17  single    0.890  0.020  1.040
 P1E  C23  H23   single    0.970  0.020  1.090
 P1E  C23  H23A  single    0.970  0.020  1.090
 P1E  C23  H23B  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
 P1E  C3    C4   C5    118.74  3.000
 P1E  C3    C4   N7    116.37  3.000
 P1E  C5    C4   N7    124.88  3.000
 P1E  H6    C6   C1    120.83  3.000
 P1E  H6    C6   C5    118.58  3.000
 P1E  C1    C6   C5    120.59  3.000
 P1E  N7    C9   N10   113.71  3.000
 P1E  N7    C9   N14   119.74  3.000
 P1E  N10   C9   N14   126.54  3.000
 P1E  H13   C13  N14   115.32  3.000
 P1E  H13   C13  C12   120.50  3.000
 P1E  N14   C13  C12   124.19  3.000
 P1E  C11   C12  C15   122.59  3.000
 P1E  C11   C12  C13   116.03  3.000
 P1E  C15   C12  C13   121.38  3.000
 P1E  C13   N14  C9    115.20  3.000
 P1E  N10   C11  N8    117.13  3.000
 P1E  N10   C11  C12   119.48  3.000
 P1E  N8    C11  C12   123.38  3.000
 P1E  HN8   N8   C25   116.59  3.000
 P1E  HN8   N8   C11   119.97  3.000
 P1E  C25   N8   C11   123.41  3.000
 P1E  H25   C25  C24   109.23  3.000
 P1E  H25   C25  C28   109.82  3.000
 P1E  C24   C25  C28   106.16  3.000
 P1E  H25   C25  N8    107.85  3.000
 P1E  C24   C25  N8    110.39  3.000
 P1E  C28   C25  N8    113.34  3.000
 P1E  H28A  C28  H28   107.00  3.000
 P1E  H28A  C28  C31   109.65  3.000
 P1E  H28   C28  C31   114.04  3.000
 P1E  H28A  C28  C25   109.06  3.000
 P1E  H28   C28  C25   112.15  3.000
 P1E  C31   C28  C25   104.89  3.000
 P1E  H31A  C31  H31   107.34  3.000
 P1E  H31A  C31  C27   113.11  3.000
 P1E  H31   C31  C27   110.02  3.000
 P1E  H31A  C31  C28   113.15  3.000
 P1E  H31   C31  C28   110.72  3.000
 P1E  C27   C31  C28   102.51  3.000
 P1E  H27A  C27  H27   107.86  3.000
 P1E  H27A  C27  C24   109.60  3.000
 P1E  H27   C27  C24   112.77  3.000
 P1E  H27A  C27  C31   110.00  3.000
 P1E  H27   C27  C31   113.21  3.000
 P1E  C24   C27  C31   103.35  3.000
 P1E  H24   C24  N26   110.01  3.000
 P1E  H24   C24  C27   106.96  3.000
 P1E  N26   C24  C27   114.23  3.000
 P1E  H24   C24  C25   108.47  3.000
 P1E  N26   C24  C25   112.53  3.000
 P1E  C27   C24  C25   104.27  3.000
 P1E  C29   N26  C30   109.86  3.000
 P1E  C29   N26  C24   111.93  3.000
 P1E  C30   N26  C24   112.02  3.000
 P1E  H30B  C30  H30A  107.33  3.000
 P1E  H30B  C30  H30   107.68  3.000
 P1E  H30A  C30  H30   107.62  3.000
 P1E  H30B  C30  N26   111.29  3.000
 P1E  H30A  C30  N26   109.56  3.000
 P1E  H30   C30  N26   113.12  3.000
 P1E  H29B  C29  H29A  107.63  3.000
 P1E  H29B  C29  H29   107.92  3.000
 P1E  H29A  C29  H29   107.37  3.000
 P1E  H29B  C29  N26   113.19  3.000
 P1E  H29A  C29  N26   109.48  3.000
 P1E  H29   C29  N26   111.03  3.000
 P1E  C11   N10  C9    118.54  3.000
 P1E  HN7   N7   C9    113.02  3.000
 P1E  HN7   N7   C4    115.51  3.000
 P1E  C9    N7   C4    131.46  3.000
 P1E  H5    C5   C6    119.44  3.000
 P1E  H5    C5   C4    120.56  3.000
 P1E  C6    C5   C4    120.00  3.000
 P1E  H3    C3   C2    119.16  3.000
 P1E  H3    C3   C4    119.73  3.000
 P1E  C2    C3   C4    121.12  3.000
 P1E  H2    C2   C1    121.27  3.000
 P1E  H2    C2   C3    119.15  3.000
 P1E  C1    C2   C3    119.58  3.000
 P1E  S18   C1   C2    120.14  3.000
 P1E  S18   C1   C6    119.85  3.000
 P1E  C2    C1   C6    119.98  3.000
 P1E  N17   S18  O20   105.87  3.000
 P1E  N17   S18  O19   106.72  3.000
 P1E  O20   S18  O19   120.14  3.000
 P1E  N17   S18  C1    107.36  3.000
 P1E  O20   S18  C1    108.41  3.000
 P1E  O19   S18  C1    107.73  3.000
 P1E  HN17  N17  C23   113.69  3.000
 P1E  HN17  N17  S18   111.49  3.000
 P1E  C23   N17  S18   118.56  3.000
 P1E  H23B  C23  H23A  108.00  3.000
 P1E  H23B  C23  H23   108.17  3.000
 P1E  H23A  C23  H23   109.16  3.000
 P1E  H23B  C23  N17   107.55  3.000
 P1E  H23A  C23  N17   110.27  3.000
 P1E  H23   C23  N17   113.52  3.000
 P1E  C12   C15  F21   112.19  3.000
 P1E  C12   C15  F16   112.30  3.000
 P1E  F21   C15  F16   105.80  3.000
 P1E  C12   C15  F22   112.49  3.000
 P1E  F21   C15  F22   106.79  3.000
 P1E  F16   C15  F22   106.83  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
 P1E  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 P1E  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 P1E  CONST_03  C3   C4   C5   C6      0.00   0.0  0
 P1E  CONST_04  C3   C2   C1   C6      0.00   0.0  0
 P1E  CONST_05  C12  C13  N14  C9      0.00   0.0  0
 P1E  CONST_06  C12  C11  N10  C9      0.00   0.0  0
 P1E  CONST_07  N10  C11  C12  C13     0.00   0.0  0
 P1E  CONST_08  N10  C9   N14  C13     0.00   0.0  0
 P1E  CONST_09  C11  N10  C9   N14     0.00   0.0  0
 P1E  CONST_10  C11  C12  C13  N14     0.00   0.0  0
 P1E  CONST_11  C2   C3   C4   C5      0.00   0.0  0
 P1E  CONST_12  C2   C1   C6   C5      0.00   0.0  0
 P1E  CONST_13  N7   C4   C5   C6    180.00   0.0  0
 P1E  CONST_14  N8   C11  N10  C9    180.00   0.0  0
 P1E  CONST_15  N8   C11  C12  C13   180.00   0.0  0
 P1E  CONST_16  N7   C9   N14  C13   180.00   0.0  0
 P1E  CONST_17  N14  C13  C12  C15   180.00   0.0  0
 P1E  CONST_18  N10  C11  C12  C15   180.00   0.0  0
 P1E  CONST_19  N7   C9   N10  C11   180.00   0.0  0
 P1E  CONST_20  C2   C3   C4   N7    180.00   0.0  0
 P1E  CONST_21  S18  C1   C6   C5    180.00   0.0  0
 P1E  CONST_22  S18  C1   C2   C3    180.00   0.0  0
 P1E  CONST_23  C25  N8   C11  C12   180.00   0.0  0
 P1E  CONST_24  N10  C11  N8   C25     0.00   0.0  0
 P1E  CONST_25  H6   C6   C5   C4    180.00   0.0  0
 P1E  CONST_26  H2   C2   C3   C4    180.00   0.0  0
 P1E  CONST_27  H13  C13  N14  C9    180.00   0.0  0
 P1E  CONST_28  H3   C3   C4   C5    180.00   0.0  0
 P1E  CONST_29  H5   C5   C4   C3    180.00   0.0  0
 P1E  CONST_30  HN8  N8   C11  C12     0.00   0.0  0
 P1E  Var_01    C27  C31  C28  C25   -35.98  30.0  1
 P1E  Var_02    C24  C27  C31  C28    43.93  30.0  1
 P1E  Var_03    N14  C9   N7   C4      4.44  30.0  1
 P1E  Var_04    C5   C4   N7   C9     11.56  30.0  1
 P1E  Var_05    O19  S18  C1   C6   -158.11  30.0  2
 P1E  Var_06    F22  C15  C12  C13     1.92  30.0  2
 P1E  Var_07    C23  N17  S18  C1     62.08  30.0  3
 P1E  Var_08    H30  C30  N26  C24    61.46  30.0  3
 P1E  Var_09    H29  C29  N26  C24    62.15  30.0  3
 P1E  Var_10    H23  C23  N17  S18   -60.70  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
 P1E  chir_01  C25  N8   C28  C24  positiv
 P1E  chir_02  C24  N26  C25  C27  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
 P1E  plan-1  C4   0.020
 P1E  plan-1  C6   0.020
 P1E  plan-1  N7   0.020
 P1E  plan-1  C5   0.020
 P1E  plan-1  C3   0.020
 P1E  plan-1  C2   0.020
 P1E  plan-1  C1   0.020
 P1E  plan-1  S18  0.020
 P1E  plan-1  H6   0.020
 P1E  plan-1  H5   0.020
 P1E  plan-1  H3   0.020
 P1E  plan-1  H2   0.020
 P1E  plan-2  C9   0.020
 P1E  plan-2  C13  0.020
 P1E  plan-2  C12  0.020
 P1E  plan-2  N14  0.020
 P1E  plan-2  C11  0.020
 P1E  plan-2  N8   0.020
 P1E  plan-2  N10  0.020
 P1E  plan-2  N7   0.020
 P1E  plan-2  H13  0.020
 P1E  plan-2  C15  0.020
 P1E  plan-3  C11  0.020
 P1E  plan-3  N8   0.020
 P1E  plan-3  C25  0.020
 P1E  plan-3  HN8  0.020

