# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:26:56 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N~2~-[(1S)-1-(5-fluoropyrimidin-2-yl)ethyl]-7-methyl-N~4~-(1-methyl-1H-imidazol-4-yl)thieno[3,2-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1nc(Nc2cn(C)cn2)c3scc(C)c3n1)c4ncc(F)cn4
#
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
 LMM  LMM  N~2~-[(1S)-1-(5-fluoropyrimidin-2-yl)ethyl]-7-methyl-N~4~-(1-methyl-1H-imidazol-4-yl)thieno[3,2-d]pyrimidine-2,4-diamine  ligand  44  27  .  2022-07-25  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_LMM
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
 LMM  F28   F  F     0  -0.288  -6.9445  -2.0650   0.5847
 LMM  C25   C  CR6   0   0.398  -5.7126  -1.6309   0.3200
 LMM  C26   C  CR16  0  -0.155  -5.4147  -0.2829   0.3725
 LMM  N27   N  N     0  -0.389  -4.1894   0.1443   0.1168
 LMM  C22   C  CR6   0   0.399  -3.2711  -0.7648  -0.1878
 LMM  N23   N  N     0  -0.411  -3.4849  -2.0687  -0.2641
 LMM  C24   C  CR16  0  -0.147  -4.7076  -2.5141  -0.0086
 LMM  C19   C  CH1   0  -0.148  -1.8948  -0.2384  -0.5151
 LMM  C21   C  CH3   0  -0.665  -1.9037   0.3902  -1.9126
 LMM  N18   N  NH1   0  -0.674  -0.9287  -1.2967  -0.3859
 LMM  C8    C  CR6   0   0.593   0.3993  -1.1094  -0.2344
 LMM  N7    N  N     0  -0.519   1.1555  -2.2017  -0.2286
 LMM  C6    C  CR56  0   0.283   2.4615  -1.9822  -0.0447
 LMM  C2    C  CR5   0   0.157   3.4647  -3.0143   0.0047
 LMM  C1    C  CH3   0  -0.721   3.1466  -4.4622  -0.1521
 LMM  N9    N  N     0  -0.533   0.8219   0.1584  -0.0916
 LMM  C10   C  CR6   0   0.585   2.1131   0.3779   0.0837
 LMM  C5    C  CR56  0  -0.385   3.0050  -0.7119   0.1236
 LMM  S4    S  S2    0   0.199   4.7201  -0.7629   0.3397
 LMM  C3    C  CR15  0  -0.520   4.6958  -2.4853   0.2049
 LMM  N11   N  NH1   0  -0.752   2.5552   1.6449   0.2183
 LMM  C12   C  CR5   0   0.310   1.8058   2.8116   0.1652
 LMM  N16   N  N     0  -0.486   2.4674   3.9921   0.2894
 LMM  C15   C  CR15  0   0.097   1.5404   4.9165   0.2011
 LMM  N14   N  NR5   0  -0.403   0.3201   4.3887   0.0286
 LMM  C17   C  CH3   0  -0.518  -0.9223   5.1101  -0.1222
 LMM  C13   C  CR15  0  -0.111   0.4617   3.0239   0.0005
 LMM  H26   H  HCR6  0   0.303  -6.1712   0.4516   0.6267
 LMM  H24   H  HCR6  0   0.304  -4.8867  -3.5820  -0.0659
 LMM  H19   H  HCH1  0   0.272  -1.6676   0.5379   0.2187
 LMM  H211  H  HCH3  0   0.236  -2.1688  -0.3532  -2.6655
 LMM  H212  H  HCH3  0   0.237  -2.6202   1.2097  -1.9670
 LMM  H213  H  HCH3  0   0.247  -0.9165   0.7841  -2.1505
 LMM  H18   H  HNH1  0   0.390  -1.2399  -2.2392  -0.5608
 LMM  H11C  H  HCH3  0   0.246   2.7463  -4.6700  -1.1457
 LMM  H12C  H  HCH3  0   0.247   4.0306  -5.0807  -0.0087
 LMM  H13C  H  HCH3  0   0.245   2.3899  -4.7763   0.5679
 LMM  H3    H  HCR5  0   0.299   5.6275  -3.0264   0.2866
 LMM  H11   H  HNH1  0   0.409   3.5445   1.7976   0.3425
 LMM  H13   H  HCR5  0   0.301  -0.3689   2.3560  -0.1195
 LMM  H15   H  HCR5  0   0.284   1.7071   5.9817   0.2552
 LMM  H171  H  HCH3  0   0.259  -1.3638   4.9120  -1.0971
 LMM  H172  H  HCH3  0   0.261  -1.6291   4.8197   0.6526
 LMM  H173  H  HCH3  0   0.264  -0.7276   6.1756  -0.0366

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
 LMM  F28  C25   single    1.333  0.020  1.333
 LMM  C25  C26   aromatic  1.382  0.020  1.382
 LMM  C25  C24   aromatic  1.378  0.020  1.378
 LMM  C26  N27   aromatic  1.323  0.020  1.323
 LMM  N27  C22   aromatic  1.328  0.020  1.328
 LMM  C22  N23   aromatic  1.323  0.020  1.323
 LMM  C22  C19   single    1.509  0.020  1.509
 LMM  N23  C24   aromatic  1.326  0.020  1.326
 LMM  C19  C21   single    1.532  0.020  1.532
 LMM  C19  N18   single    1.439  0.020  1.439
 LMM  N18  C8    single    1.350  0.020  1.350
 LMM  C8   N7    aromatic  1.329  0.020  1.329
 LMM  C8   N9    aromatic  1.344  0.020  1.344
 LMM  N7   C6    aromatic  1.337  0.020  1.337
 LMM  C6   C2    aromatic  1.440  0.020  1.440
 LMM  C6   C5    aromatic  1.392  0.020  1.392
 LMM  C2   C1    single    1.491  0.020  1.491
 LMM  C2   C3    aromatic  1.355  0.020  1.355
 LMM  N9   C10   aromatic  1.321  0.020  1.321
 LMM  C10  C5    aromatic  1.409  0.020  1.409
 LMM  C10  N11   single    1.349  0.020  1.349
 LMM  C5   S4    aromatic  1.729  0.020  1.729
 LMM  S4   C3    aromatic  1.728  0.020  1.728
 LMM  N11  C12   single    1.388  0.020  1.388
 LMM  C12  N16   aromatic  1.359  0.020  1.359
 LMM  C12  C13   aromatic  1.371  0.020  1.371
 LMM  N16  C15   aromatic  1.312  0.020  1.312
 LMM  C15  N14   aromatic  1.341  0.020  1.341
 LMM  N14  C17   single    1.444  0.020  1.444
 LMM  N14  C13   aromatic  1.372  0.020  1.372
 LMM  C26  H26   single    0.930  0.020  1.080
 LMM  C24  H24   single    0.930  0.020  1.080
 LMM  C19  H19   single    0.970  0.020  1.090
 LMM  C21  H211  single    0.970  0.020  1.090
 LMM  C21  H212  single    0.970  0.020  1.090
 LMM  C21  H213  single    0.970  0.020  1.090
 LMM  N18  H18   single    0.860  0.020  1.020
 LMM  C1   H11C  single    0.970  0.020  1.090
 LMM  C1   H12C  single    0.970  0.020  1.090
 LMM  C1   H13C  single    0.970  0.020  1.090
 LMM  C3   H3    single    0.930  0.020  1.080
 LMM  N11  H11   single    0.860  0.020  1.020
 LMM  C13  H13   single    0.930  0.020  1.080
 LMM  C15  H15   single    0.930  0.020  1.080
 LMM  C17  H171  single    0.970  0.020  1.090
 LMM  C17  H172  single    0.970  0.020  1.090
 LMM  C17  H173  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
 LMM  C24   C25  C26   118.50  3.000
 LMM  C24   C25  F28   120.85  3.000
 LMM  C26   C25  F28   120.64  3.000
 LMM  H26   C26  N27   118.21  3.000
 LMM  H26   C26  C25   121.28  3.000
 LMM  N27   C26  C25   120.50  3.000
 LMM  C22   N27  C26   117.65  3.000
 LMM  C19   C22  N23   118.58  3.000
 LMM  C19   C22  N27   116.21  3.000
 LMM  N23   C22  N27   125.18  3.000
 LMM  C24   N23  C22   117.95  3.000
 LMM  H24   C24  N23   118.23  3.000
 LMM  H24   C24  C25   121.56  3.000
 LMM  N23   C24  C25   120.21  3.000
 LMM  H19   C19  N18   108.83  3.000
 LMM  H19   C19  C21   108.81  3.000
 LMM  N18   C19  C21   112.81  3.000
 LMM  H19   C19  C22   106.97  3.000
 LMM  N18   C19  C22   109.65  3.000
 LMM  C21   C19  C22   109.60  3.000
 LMM  H213  C21  H212  108.24  3.000
 LMM  H213  C21  H211  108.42  3.000
 LMM  H212  C21  H211  108.56  3.000
 LMM  H213  C21  C19   110.02  3.000
 LMM  H212  C21  C19   110.97  3.000
 LMM  H211  C21  C19   110.57  3.000
 LMM  H18   N18  C8    116.94  3.000
 LMM  H18   N18  C19   117.70  3.000
 LMM  C8    N18  C19   124.66  3.000
 LMM  N9    C8   N7    126.59  3.000
 LMM  N9    C8   N18   116.89  3.000
 LMM  N7    C8   N18   116.52  3.000
 LMM  C6    N7   C8    114.94  3.000
 LMM  C5    C6   C2    112.20  3.000
 LMM  C5    C6   N7    123.22  3.000
 LMM  C2    C6   N7    124.58  3.000
 LMM  C3    C2   C1    126.06  3.000
 LMM  C3    C2   C6    110.99  3.000
 LMM  C1    C2   C6    122.95  3.000
 LMM  H13C  C1   H12C  108.23  3.000
 LMM  H13C  C1   H11C  106.96  3.000
 LMM  H12C  C1   H11C  108.04  3.000
 LMM  H13C  C1   C2    110.99  3.000
 LMM  H12C  C1   C2    111.40  3.000
 LMM  H11C  C1   C2    111.04  3.000
 LMM  C10   N9   C8    118.56  3.000
 LMM  N11   C10  C5    121.09  3.000
 LMM  N11   C10  N9    119.32  3.000
 LMM  C5    C10  N9    119.59  3.000
 LMM  S4    C5   C10   130.86  3.000
 LMM  S4    C5   C6    112.05  3.000
 LMM  C10   C5   C6    117.09  3.000
 LMM  C3    S4   C5     90.33  3.000
 LMM  H3    C3   S4    118.76  3.000
 LMM  H3    C3   C2    126.81  3.000
 LMM  S4    C3   C2    114.42  3.000
 LMM  H11   N11  C12   114.02  3.000
 LMM  H11   N11  C10   118.43  3.000
 LMM  C12   N11  C10   127.51  3.000
 LMM  C13   C12  N16   110.72  3.000
 LMM  C13   C12  N11   131.64  3.000
 LMM  N16   C12  N11   117.64  3.000
 LMM  C15   N16  C12   105.18  3.000
 LMM  H15   C15  N14   122.38  3.000
 LMM  H15   C15  N16   125.64  3.000
 LMM  N14   C15  N16   111.98  3.000
 LMM  C13   N14  C17   125.68  3.000
 LMM  C13   N14  C15   107.47  3.000
 LMM  C17   N14  C15   126.84  3.000
 LMM  H173  C17  H172  108.79  3.000
 LMM  H173  C17  H171  108.76  3.000
 LMM  H172  C17  H171  109.01  3.000
 LMM  H173  C17  N14   109.11  3.000
 LMM  H172  C17  N14   110.56  3.000
 LMM  H171  C17  N14   110.58  3.000
 LMM  H13   C13  N14   122.80  3.000
 LMM  H13   C13  C12   132.56  3.000
 LMM  N14   C13  C12   104.64  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
 LMM  CONST_01  C22   N27  C26  C25     0.00   0.0  0
 LMM  CONST_02  C22   N23  C24  C25     0.00   0.0  0
 LMM  CONST_03  N23   C24  C25  C26     0.00   0.0  0
 LMM  CONST_04  N23   C22  N27  C26     0.00   0.0  0
 LMM  CONST_05  C24   C25  C26  N27     0.00   0.0  0
 LMM  CONST_06  C24   N23  C22  N27     0.00   0.0  0
 LMM  CONST_07  C2    C6   N7   C8    180.00   0.0  0
 LMM  CONST_08  C5    C6   N7   C8      0.00   0.0  0
 LMM  CONST_09  C5    C10  N9   C8      0.00   0.0  0
 LMM  CONST_10  C10   N9   C8   N7      0.00   0.0  0
 LMM  CONST_11  C3    C2   C6   N7    180.00   0.0  0
 LMM  CONST_12  C10   C5   C6   N7      0.00   0.0  0
 LMM  CONST_13  S4    C5   C6   N7    180.00   0.0  0
 LMM  CONST_14  N9    C8   N7   C6      0.00   0.0  0
 LMM  CONST_15  S4    C3   C2   C6      0.00   0.0  0
 LMM  CONST_16  N9    C10  C5   C6      0.00   0.0  0
 LMM  CONST_17  C3    S4   C5   C6      0.00   0.0  0
 LMM  CONST_18  C10   C5   C6   C2    180.00   0.0  0
 LMM  CONST_19  S4    C5   C6   C2      0.00   0.0  0
 LMM  CONST_20  C5    S4   C3   C2      0.00   0.0  0
 LMM  CONST_21  S4    C5   C10  N9    180.00   0.0  0
 LMM  CONST_22  C3    S4   C5   C10   180.00   0.0  0
 LMM  CONST_23  C3    C2   C6   C5      0.00   0.0  0
 LMM  CONST_24  N14   C15  N16  C12     0.00   0.0  0
 LMM  CONST_25  C15   N14  C13  C12     0.00   0.0  0
 LMM  CONST_26  N14   C13  C12  N16     0.00   0.0  0
 LMM  CONST_27  C13   N14  C15  N16     0.00   0.0  0
 LMM  CONST_28  C13   C12  N16  C15     0.00   0.0  0
 LMM  CONST_29  N27   C26  C25  F28   180.00   0.0  0
 LMM  CONST_30  N23   C24  C25  F28   180.00   0.0  0
 LMM  CONST_31  C19   C22  N27  C26   180.00   0.0  0
 LMM  CONST_32  C19   C22  N23  C24   180.00   0.0  0
 LMM  CONST_33  C6    N7   C8   N18   180.00   0.0  0
 LMM  CONST_34  C10   N9   C8   N18   180.00   0.0  0
 LMM  CONST_35  N11   C10  N9   C8    180.00   0.0  0
 LMM  CONST_36  C1    C2   C6   N7      0.00   0.0  0
 LMM  CONST_37  N11   C10  C5   C6    180.00   0.0  0
 LMM  CONST_38  C5    C6   C2   C1    180.00   0.0  0
 LMM  CONST_39  S4    C3   C2   C1    180.00   0.0  0
 LMM  CONST_40  N11   C10  C5   S4      0.00   0.0  0
 LMM  CONST_41  C15   N16  C12  N11   180.00   0.0  0
 LMM  CONST_42  N14   C13  C12  N11   180.00   0.0  0
 LMM  CONST_43  C17   N14  C13  C12   180.00   0.0  0
 LMM  CONST_44  C17   N14  C15  N16   180.00   0.0  0
 LMM  CONST_45  H24   C24  C25  C26   180.00   0.0  0
 LMM  CONST_46  H26   C26  N27  C22   180.00   0.0  0
 LMM  CONST_47  H3    C3   C2   C6    180.00   0.0  0
 LMM  CONST_48  H15   C15  N16  C12   180.00   0.0  0
 LMM  CONST_49  H13   C13  C12  N16   180.00   0.0  0
 LMM  CONST_50  N7    C8   N18  C19   180.00   0.0  0
 LMM  CONST_51  N9    C8   N18  C19     0.00   0.0  0
 LMM  CONST_52  H18   N18  C8   N7      0.00   0.0  0
 LMM  Var_01    C12   N11  C10  N9     -1.67  30.0  2
 LMM  Var_02    N16   C12  N11  C10  -178.15  30.0  2
 LMM  Var_03    H11C  C1   C2   C6     63.82  30.0  2
 LMM  Var_04    H171  C17  N14  C15   117.45  30.0  2

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
 LMM  chir_01  C19  C22  C21  N18  positiv

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
 LMM  plan-1  N11  0.020
 LMM  plan-1  C12  0.020
 LMM  plan-1  N16  0.020
 LMM  plan-1  C15  0.020
 LMM  plan-1  N14  0.020
 LMM  plan-1  C17  0.020
 LMM  plan-1  C13  0.020
 LMM  plan-1  H13  0.020
 LMM  plan-1  H15  0.020
 LMM  plan-2  F28  0.020
 LMM  plan-2  C25  0.020
 LMM  plan-2  C26  0.020
 LMM  plan-2  N27  0.020
 LMM  plan-2  C22  0.020
 LMM  plan-2  N23  0.020
 LMM  plan-2  C24  0.020
 LMM  plan-2  C19  0.020
 LMM  plan-2  H26  0.020
 LMM  plan-2  H24  0.020
 LMM  plan-3  N18  0.020
 LMM  plan-3  C8   0.020
 LMM  plan-3  N7   0.020
 LMM  plan-3  C6   0.020
 LMM  plan-3  C2   0.020
 LMM  plan-3  C1   0.020
 LMM  plan-3  N9   0.020
 LMM  plan-3  C10  0.020
 LMM  plan-3  C5   0.020
 LMM  plan-3  S4   0.020
 LMM  plan-3  C3   0.020
 LMM  plan-3  N11  0.020
 LMM  plan-3  H3   0.020
 LMM  plan-4  C19  0.020
 LMM  plan-4  N18  0.020
 LMM  plan-4  C8   0.020
 LMM  plan-4  H18  0.020

