# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:28:10 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (4-amino-2-{[1-(methylsulfonyl)piperidin-4-yl]amino}pyrimidin-5-yl)(2,3-difluoro-6-methoxyphenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(F)c(F)c1C(=O)c2cnc(NC3CCN(CC3)[S](C)(=O)=O)nc2N
#
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
 LIA  LIA  (4-amino-2-{[1-(methylsulfonyl)piperidin-4-yl]amino}pyrimidin-5-yl)(2,3-difluoro-6-methoxyphenyl)methanone  ligand  51  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LIA
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
 LIA  N1    N  N     0  -0.567  -5.7281   0.5834   0.5819
 LIA  C2    C  CH2   0  -0.330  -5.1886   1.8623   0.1255
 LIA  C3    C  CH2   0  -0.459  -3.9083   1.7015  -0.6836
 LIA  C4    C  CH1   0  -0.056  -2.8785   0.8841   0.0880
 LIA  C5    C  CH2   0  -0.442  -3.4744  -0.4549   0.5203
 LIA  C6    C  CH2   0  -0.330  -4.7636  -0.2454   1.3035
 LIA  N7    N  NH1   0  -0.654  -1.6901   0.7216  -0.7203
 LIA  C8    C  CR6   0   0.619  -0.4542   0.5272  -0.2494
 LIA  N9    N  N     0  -0.480  -0.2911   0.5119   1.0888
 LIA  C10   C  CR16  0   0.006   0.9371   0.3021   1.4966
 LIA  C11   C  CR6   0  -0.246   2.0437   0.1002   0.6661
 LIA  C12   C  CR6   0   0.482   1.7572   0.1851  -0.7318
 LIA  N13   N  N     0  -0.514   0.5112   0.3820  -1.1522
 LIA  C14   C  C     0   0.406   3.3201  -0.1829   1.3027
 LIA  O15   O  O     0  -0.401   3.4999  -0.0431   2.4992
 LIA  C16   C  CR6   0  -0.470   4.4658  -0.7137   0.4878
 LIA  C17   C  CR6   0   0.472   4.4207  -1.9979  -0.0145
 LIA  C18   C  CR6   0   0.379   5.4974  -2.5458  -0.6886
 LIA  C19   C  CR16  0  -0.391   6.6385  -1.7985  -0.8681
 LIA  C20   C  CR16  0  -0.388   6.7122  -0.5028  -0.3726
 LIA  C21   C  CR6   0   0.421   5.6333   0.0440   0.3159
 LIA  O22   O  O2    0  -0.457   5.5997   1.2849   0.8180
 LIA  C23   C  CH3   0  -0.441   6.7340   2.1169   0.6470
 LIA  F24   F  F     0  -0.291   3.3127  -2.7237   0.1503
 LIA  F25   F  F     0  -0.306   5.4124  -3.7969  -1.1554
 LIA  N26   N  NH2   0  -0.819   2.6746   0.0882  -1.6995
 LIA  S27   S  S     0   1.349  -6.9781  -0.1117  -0.2258
 LIA  C28   C  CH3   0  -0.809  -6.3548  -0.7763  -1.7565
 LIA  O29   O  OS    0  -0.669  -7.4446  -1.2291   0.5829
 LIA  O30   O  OS    0  -0.670  -7.9150   0.9494  -0.5675
 LIA  H21   H  HCH2  0   0.263  -4.9885   2.4625   1.0173
 LIA  H22   H  HCH2  0   0.282  -5.9403   2.4015  -0.4466
 LIA  H31   H  HCH2  0   0.267  -3.5078   2.6916  -0.9111
 LIA  H32   H  HCH2  0   0.237  -4.1275   1.2191  -1.6418
 LIA  H4    H  HCH1  0   0.252  -2.5985   1.4410   0.9861
 LIA  H51   H  HCH2  0   0.232  -3.6570  -1.0820  -0.3574
 LIA  H52   H  HCH2  0   0.259  -2.7631  -0.9922   1.1508
 LIA  H61   H  HCH2  0   0.260  -4.5445   0.2684   2.2437
 LIA  H62   H  HCH2  0   0.281  -5.2176  -1.1974   1.5679
 LIA  HN7   H  HNH1  0   0.396  -1.7960   0.6822  -1.7228
 LIA  H10   H  HCR6  0   0.275   1.0811   0.2686   2.5711
 LIA  H19   H  HCR6  0   0.302   7.4797  -2.2241  -1.3988
 LIA  H20   H  HCR6  0   0.301   7.6200   0.0608  -0.5331
 LIA  H231  H  HCH3  0   0.237   7.6169   1.7033   1.1396
 LIA  H232  H  HCH3  0   0.236   6.9583   2.2837  -0.4088
 LIA  H233  H  HCH3  0   0.267   6.4860   3.0679   1.1100
 LIA  H261  H  HNH2  0   0.404   2.3771   0.2547  -2.6465
 LIA  H262  H  HNH2  0   0.417   3.6608   0.1224  -1.5205
 LIA  H281  H  HCH3  0   0.289  -5.6044  -1.5359  -1.5508
 LIA  H282  H  HCH3  0   0.309  -7.1910  -1.2224  -2.2928
 LIA  H283  H  HCH3  0   0.288  -5.9245   0.0249  -2.3532

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
 LIA  N1   C2    single    1.461  0.020  1.461
 LIA  N1   C6    single    1.462  0.020  1.462
 LIA  N1   S27   single    1.643  0.020  1.643
 LIA  C2   C3    single    1.523  0.020  1.523
 LIA  C2   H21   single    0.970  0.020  1.090
 LIA  C2   H22   single    0.970  0.020  1.090
 LIA  C3   C4    single    1.524  0.020  1.524
 LIA  C3   H31   single    0.970  0.020  1.090
 LIA  C3   H32   single    0.970  0.020  1.090
 LIA  C4   C5    single    1.528  0.020  1.528
 LIA  C4   N7    single    1.446  0.020  1.446
 LIA  C4   H4    single    0.970  0.020  1.090
 LIA  C5   C6    single    1.523  0.020  1.523
 LIA  C5   H51   single    0.970  0.020  1.090
 LIA  C5   H52   single    0.970  0.020  1.090
 LIA  C6   H61   single    0.970  0.020  1.090
 LIA  C6   H62   single    0.970  0.020  1.090
 LIA  N7   C8    single    1.337  0.020  1.337
 LIA  N7   HN7   single    0.860  0.020  1.020
 LIA  C8   N9    aromatic  1.348  0.020  1.348
 LIA  C8   N13   aromatic  1.330  0.020  1.330
 LIA  N9   C10   aromatic  1.311  0.020  1.311
 LIA  C10  C11   aromatic  1.398  0.020  1.398
 LIA  C10  H10   single    0.930  0.020  1.080
 LIA  C11  C12   aromatic  1.429  0.020  1.429
 LIA  C11  C14   single    1.454  0.020  1.454
 LIA  C12  N13   aromatic  1.330  0.020  1.330
 LIA  C12  N26   single    1.337  0.020  1.337
 LIA  C14  O15   double    1.218  0.020  1.218
 LIA  C14  C16   single    1.503  0.020  1.503
 LIA  C16  C17   aromatic  1.380  0.020  1.380
 LIA  C16  C21   aromatic  1.402  0.020  1.402
 LIA  C17  C18   aromatic  1.383  0.020  1.383
 LIA  C17  F24   single    1.335  0.020  1.335
 LIA  C18  C19   aromatic  1.376  0.020  1.376
 LIA  C18  F25   single    1.338  0.020  1.338
 LIA  C19  C20   aromatic  1.389  0.020  1.389
 LIA  C19  H19   single    0.930  0.020  1.080
 LIA  C20  C21   aromatic  1.392  0.020  1.392
 LIA  C20  H20   single    0.930  0.020  1.080
 LIA  C21  O22   single    1.339  0.020  1.339
 LIA  O22  C23   single    1.417  0.020  1.417
 LIA  C23  H231  single    0.970  0.020  1.090
 LIA  C23  H232  single    0.970  0.020  1.090
 LIA  C23  H233  single    0.970  0.020  1.090
 LIA  N26  H261  single    0.860  0.020  1.020
 LIA  N26  H262  single    0.860  0.020  1.020
 LIA  S27  C28   single    1.781  0.020  1.781
 LIA  S27  O29   double    1.456  0.020  1.456
 LIA  S27  O30   double    1.456  0.020  1.456
 LIA  C28  H281  single    0.970  0.020  1.090
 LIA  C28  H282  single    0.970  0.020  1.090
 LIA  C28  H283  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
 LIA  S27   N1   C6    120.32  3.000
 LIA  S27   N1   C2    119.85  3.000
 LIA  C6    N1   C2    114.00  3.000
 LIA  H22   C2   H21   106.46  3.000
 LIA  H22   C2   C3    110.72  3.000
 LIA  H21   C2   C3    109.72  3.000
 LIA  H22   C2   N1    110.06  3.000
 LIA  H21   C2   N1    107.05  3.000
 LIA  C3    C2   N1    112.58  3.000
 LIA  H32   C3   H31   106.89  3.000
 LIA  H32   C3   C4    109.99  3.000
 LIA  H31   C3   C4    110.11  3.000
 LIA  H32   C3   C2    110.07  3.000
 LIA  H31   C3   C2    108.86  3.000
 LIA  C4    C3   C2    110.83  3.000
 LIA  H4    C4   N7    107.81  3.000
 LIA  H4    C4   C5    108.29  3.000
 LIA  N7    C4   C5    112.33  3.000
 LIA  H4    C4   C3    108.40  3.000
 LIA  N7    C4   C3    109.41  3.000
 LIA  C5    C4   C3    110.46  3.000
 LIA  H52   C5   H51   106.86  3.000
 LIA  H52   C5   C6    108.80  3.000
 LIA  H51   C5   C6    110.49  3.000
 LIA  H52   C5   C4    109.91  3.000
 LIA  H51   C5   C4    109.90  3.000
 LIA  C6    C5   C4    110.79  3.000
 LIA  H62   C6   H61   106.61  3.000
 LIA  H62   C6   C5    110.98  3.000
 LIA  H61   C6   C5    109.70  3.000
 LIA  H62   C6   N1    109.94  3.000
 LIA  H61   C6   N1    106.87  3.000
 LIA  C5    C6   N1    112.50  3.000
 LIA  HN7   N7   C8    116.20  3.000
 LIA  HN7   N7   C4    118.26  3.000
 LIA  C8    N7   C4    125.38  3.000
 LIA  N13   C8   N9    125.79  3.000
 LIA  N13   C8   N7    116.61  3.000
 LIA  N9    C8   N7    117.59  3.000
 LIA  C10   N9   C8    115.08  3.000
 LIA  H10   C10  C11   118.61  3.000
 LIA  H10   C10  N9    115.95  3.000
 LIA  C11   C10  N9    125.43  3.000
 LIA  C14   C11  C12   128.00  3.000
 LIA  C14   C11  C10   117.57  3.000
 LIA  C12   C11  C10   114.43  3.000
 LIA  N26   C12  N13   115.14  3.000
 LIA  N26   C12  C11   124.47  3.000
 LIA  N13   C12  C11   120.38  3.000
 LIA  C12   N13  C8    118.81  3.000
 LIA  C16   C14  O15   117.43  3.000
 LIA  C16   C14  C11   120.04  3.000
 LIA  O15   C14  C11   122.50  3.000
 LIA  C21   C16  C17   119.05  3.000
 LIA  C21   C16  C14   120.68  3.000
 LIA  C17   C16  C14   120.09  3.000
 LIA  F24   C17  C18   119.40  3.000
 LIA  F24   C17  C16   119.23  3.000
 LIA  C18   C17  C16   121.37  3.000
 LIA  F25   C18  C19   121.00  3.000
 LIA  F25   C18  C17   119.39  3.000
 LIA  C19   C18  C17   119.61  3.000
 LIA  H19   C19  C20   120.04  3.000
 LIA  H19   C19  C18   119.69  3.000
 LIA  C20   C19  C18   120.27  3.000
 LIA  H20   C20  C21   121.32  3.000
 LIA  H20   C20  C19   118.56  3.000
 LIA  C21   C20  C19   120.12  3.000
 LIA  O22   C21  C20   124.68  3.000
 LIA  O22   C21  C16   115.72  3.000
 LIA  C20   C21  C16   119.58  3.000
 LIA  C23   O22  C21   118.60  3.000
 LIA  H233  C23  H232  108.97  3.000
 LIA  H233  C23  H231  108.89  3.000
 LIA  H232  C23  H231  109.14  3.000
 LIA  H233  C23  O22   106.25  3.000
 LIA  H232  C23  O22   111.76  3.000
 LIA  H231  C23  O22   111.73  3.000
 LIA  H262  N26  H261  116.93  3.000
 LIA  H262  N26  C12   122.89  3.000
 LIA  H261  N26  C12   117.79  3.000
 LIA  O30   S27  O29   118.91  3.000
 LIA  O30   S27  C28   107.18  3.000
 LIA  O29   S27  C28   107.64  3.000
 LIA  O30   S27  N1    107.26  3.000
 LIA  O29   S27  N1    107.18  3.000
 LIA  C28   S27  N1    108.31  3.000
 LIA  H283  C28  H282  109.59  3.000
 LIA  H283  C28  H281  110.20  3.000
 LIA  H282  C28  H281  109.69  3.000
 LIA  H283  C28  S27   109.58  3.000
 LIA  H282  C28  S27   107.90  3.000
 LIA  H281  C28  S27   109.85  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
 LIA  CONST_01  C11   C10  N9   C8     0.00   0.0  0
 LIA  CONST_02  C11   C12  N13  C8     0.00   0.0  0
 LIA  CONST_03  C12   N13  C8   N9     0.00   0.0  0
 LIA  CONST_04  C12   C11  C10  N9     0.00   0.0  0
 LIA  CONST_05  N13   C8   N9   C10    0.00   0.0  0
 LIA  CONST_06  N13   C12  C11  C10    0.00   0.0  0
 LIA  CONST_07  C19   C18  C17  C16    0.00   0.0  0
 LIA  CONST_08  C19   C20  C21  C16    0.00   0.0  0
 LIA  CONST_09  C20   C21  C16  C17    0.00   0.0  0
 LIA  CONST_10  C20   C19  C18  C17    0.00   0.0  0
 LIA  CONST_11  C21   C16  C17  C18    0.00   0.0  0
 LIA  CONST_12  C21   C20  C19  C18    0.00   0.0  0
 LIA  CONST_13  C10   N9   C8   N7   180.00   0.0  0
 LIA  CONST_14  C12   N13  C8   N7   180.00   0.0  0
 LIA  CONST_15  N26   C12  N13  C8   180.00   0.0  0
 LIA  CONST_16  C14   C11  C10  N9   180.00   0.0  0
 LIA  CONST_17  N26   C12  C11  C10  180.00   0.0  0
 LIA  CONST_18  C14   C11  C12  N13  180.00   0.0  0
 LIA  CONST_19  C18   C17  C16  C14  180.00   0.0  0
 LIA  CONST_20  C20   C21  C16  C14  180.00   0.0  0
 LIA  CONST_21  F25   C18  C17  C16  180.00   0.0  0
 LIA  CONST_22  O22   C21  C16  C17  180.00   0.0  0
 LIA  CONST_23  F24   C17  C18  C19  180.00   0.0  0
 LIA  CONST_24  O22   C21  C20  C19  180.00   0.0  0
 LIA  CONST_25  F25   C18  C19  C20  180.00   0.0  0
 LIA  CONST_26  F24   C17  C16  C21  180.00   0.0  0
 LIA  CONST_27  N9    C8   N7   C4     0.00   0.0  0
 LIA  CONST_28  N13   C8   N7   C4   180.00   0.0  0
 LIA  CONST_29  H10   C10  N9   C8   180.00   0.0  0
 LIA  CONST_30  H20   C20  C21  C16  180.00   0.0  0
 LIA  CONST_31  H19   C19  C18  C17  180.00   0.0  0
 LIA  CONST_32  HN7   N7   C8   N9   180.00   0.0  0
 LIA  CONST_33  H261  N26  C12  C11  180.00   0.0  0
 LIA  CONST_34  H262  N26  C12  C11    0.00   0.0  0
 LIA  Var_01    C4    C3   C2   N1   -53.40  30.0  1
 LIA  Var_02    C4    C5   C6   N1    53.40  30.0  1
 LIA  Var_03    C5    C6   N1   C2   -52.96  30.0  1
 LIA  Var_04    C6    N1   C2   C3    52.94  30.0  1
 LIA  Var_05    C16   C14  C11  C10  166.05  30.0  2
 LIA  Var_06    C17   C16  C14  C11  -69.87  30.0  2
 LIA  Var_07    C28   S27  N1   C2    73.97  30.0  3
 LIA  Var_08    H281  C28  S27  N1    61.27  30.0  3
 LIA  Var_09    H231  C23  O22  C21  -62.28  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
 LIA  chir_01  C4  C3  C5  N7  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
 LIA  plan-1  N7    0.020
 LIA  plan-1  C8    0.020
 LIA  plan-1  N9    0.020
 LIA  plan-1  C10   0.020
 LIA  plan-1  C11   0.020
 LIA  plan-1  C12   0.020
 LIA  plan-1  N13   0.020
 LIA  plan-1  C14   0.020
 LIA  plan-1  N26   0.020
 LIA  plan-1  H10   0.020
 LIA  plan-2  C14   0.020
 LIA  plan-2  C16   0.020
 LIA  plan-2  C17   0.020
 LIA  plan-2  C18   0.020
 LIA  plan-2  C19   0.020
 LIA  plan-2  C20   0.020
 LIA  plan-2  C21   0.020
 LIA  plan-2  O22   0.020
 LIA  plan-2  F24   0.020
 LIA  plan-2  F25   0.020
 LIA  plan-2  H19   0.020
 LIA  plan-2  H20   0.020
 LIA  plan-3  C4    0.020
 LIA  plan-3  N7    0.020
 LIA  plan-3  C8    0.020
 LIA  plan-3  HN7   0.020
 LIA  plan-4  C12   0.020
 LIA  plan-4  N26   0.020
 LIA  plan-4  H261  0.020
 LIA  plan-4  H262  0.020
 LIA  plan-5  C11   0.020
 LIA  plan-5  C14   0.020
 LIA  plan-5  O15   0.020
 LIA  plan-5  C16   0.020

