# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 07:16:59 2022
#   Inital geometry file: a 152 line input string
#   Ligand name: N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(C#N)c(SCc2ccc(cc2)N(C)[S](C)(=O)=O)nc(N(C)CCNC)c1C#N
#
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
 X52  X52  N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide  ligand  60  32  .  2023-02-15  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_X52
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
 X52  C01  C  CH3   0  -0.659  -44.0896   -7.2732  31.3961
 X52  C02  C  CH2   0  -0.549  -44.7258   -7.7214  30.0790
 X52  C03  C  CR6   0   0.336  -44.0213   -8.9167  29.5105
 X52  C04  C  CR6   0  -0.193  -44.4127  -10.2171  29.8404
 X52  C05  C  CSP   0   0.009  -45.4184  -10.3511  30.8324
 X52  C07  C  CR6   0   0.589  -43.7068  -11.3282  29.2777
 X52  C09  C  CH2   0  -0.336  -43.1608  -13.6680  28.9818
 X52  C10  C  CH2   0  -0.292  -43.2512  -14.0076  27.4982
 X52  C12  C  CH3   0  -0.527  -44.7291  -15.9279  27.4327
 X52  C13  C  CH3   0  -0.564  -45.3825  -13.0236  29.8683
 X52  C15  C  CR6   0   0.113  -42.1974   -9.8980  28.2842
 X52  C17  C  CH2   0  -0.642  -40.2645  -11.3835  26.9360
 X52  C18  C  CR6   0   0.103  -39.2077  -11.3010  25.8769
 X52  C19  C  CR16  0  -0.286  -37.8617  -11.2016  26.2149
 X52  C20  C  CR16  0  -0.250  -36.8920  -11.1086  25.2292
 X52  C21  C  CR6   0   0.306  -37.2592  -11.0980  23.8899
 X52  C24  C  CH3   0  -0.784  -33.9257   -9.6860  22.6984
 X52  C27  C  CH3   0  -0.532  -36.2656  -12.0425  21.8366
 X52  C28  C  CR16  0  -0.247  -38.6020  -11.1922  23.5432
 X52  C29  C  CR16  0  -0.283  -39.5662  -11.2963  24.5323
 X52  C30  C  CR6   0  -0.109  -42.9078   -8.7480  28.6896
 X52  C31  C  CSP   0  -0.030  -42.4573   -7.4612  28.3067
 X52  N06  N  NS    0  -0.250  -46.2112  -10.3909  31.6706
 X52  N08  N  NT    0  -0.457  -44.0716  -12.6075  29.4051
 X52  N11  N  NH1   0  -0.588  -44.5465  -14.5268  27.1120
 X52  N14  N  N     0  -0.495  -42.5873  -11.1077  28.5719
 X52  N22  N  N     0  -0.688  -36.2487  -11.0333  22.8909
 X52  N32  N  NS    0  -0.239  -42.0737   -6.4209  27.9859
 X52  O25  O  OS    0  -0.650  -36.1902   -8.5760  23.4539
 X52  O26  O  OS    0  -0.653  -35.9292   -9.2772  21.0604
 X52  S16  S  S2    0   0.109  -40.7476   -9.6714  27.3358
 X52  S23  S  S     0   1.325  -35.6790   -9.5207  22.4744
 X52  H1   H  HCH3  0   0.249  -44.6123   -6.3983  31.7800
 X52  H2   H  HCH3  0   0.240  -44.1438   -8.0554  32.1525
 X52  H3   H  HCH3  0   0.239  -43.0416   -7.0062  31.2607
 X52  H4   H  HCH2  0   0.276  -44.6901   -6.9020  29.3596
 X52  H5   H  HCH2  0   0.275  -45.7816   -7.9438  30.2343
 X52  H6   H  HCH2  0   0.266  -43.3886  -14.5421  29.5934
 X52  H7   H  HCH2  0   0.266  -42.1373  -13.3819  29.2163
 X52  H8   H  HCH2  0   0.201  -42.4286  -14.7062  27.2751
 X52  H9   H  HCH2  0   0.247  -43.0568  -13.1014  26.9242
 X52  H10  H  HCH3  0   0.234  -45.6821  -16.2752  27.0346
 X52  H11  H  HCH3  0   0.199  -43.9375  -16.5806  27.0385
 X52  H12  H  HCH3  0   0.222  -44.7613  -16.0742  28.5140
 X52  H13  H  HCH3  0   0.260  -46.1610  -12.3625  29.4924
 X52  H14  H  HCH3  0   0.287  -45.5847  -14.0105  29.4657
 X52  H15  H  HCH3  0   0.256  -45.4447  -13.0758  30.9554
 X52  H16  H  HCH2  0   0.318  -41.1449  -11.9132  26.5771
 X52  H17  H  HCH2  0   0.305  -39.9044  -11.8746  27.8388
 X52  H18  H  HCR6  0   0.262  -37.5655  -11.2096  27.2570
 X52  H19  H  HCR6  0   0.267  -35.8452  -11.0529  25.4986
 X52  H20  H  HCH3  0   0.299  -33.4624   -8.7415  22.4172
 X52  H21  H  HCH3  0   0.293  -33.7230   -9.9110  23.7422
 X52  H22  H  HCH3  0   0.292  -33.5468  -10.4825  22.0616
 X52  H23  H  HCH3  0   0.265  -36.3965  -13.0150  22.3053
 X52  H24  H  HCH3  0   0.247  -37.0611  -11.8910  21.1055
 X52  H25  H  HCH3  0   0.262  -35.3115  -12.0604  21.3124
 X52  H26  H  HCR6  0   0.270  -38.9010  -11.1854  22.5024
 X52  H27  H  HCR6  0   0.262  -40.6105  -11.3702  24.2535
 X52  H28  H  HNH1  0   0.354  -44.6694  -14.3967  26.1177

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
 X52  C24  S23  single    1.775  0.020  1.775
 X52  C27  N22  single    1.460  0.020  1.460
 X52  N22  S23  single    1.669  0.020  1.669
 X52  N22  C21  single    1.422  0.020  1.422
 X52  S23  O26  double    1.456  0.020  1.456
 X52  S23  O25  double    1.454  0.020  1.454
 X52  C28  C21  aromatic  1.390  0.020  1.390
 X52  C28  C29  aromatic  1.385  0.020  1.385
 X52  C21  C20  aromatic  1.389  0.020  1.389
 X52  C29  C18  aromatic  1.392  0.020  1.392
 X52  C20  C19  aromatic  1.386  0.020  1.386
 X52  C18  C19  aromatic  1.391  0.020  1.391
 X52  C18  C17  single    1.498  0.020  1.498
 X52  C17  S16  single    1.823  0.020  1.823
 X52  S16  C15  single    1.747  0.020  1.747
 X52  N11  C12  single    1.449  0.020  1.449
 X52  N11  C10  single    1.448  0.020  1.448
 X52  C10  C09  single    1.525  0.020  1.525
 X52  N32  C31  triple    1.154  0.020  1.154
 X52  C15  N14  aromatic  1.303  0.020  1.303
 X52  C15  C30  aromatic  1.411  0.020  1.411
 X52  C31  C30  single    1.416  0.020  1.416
 X52  N14  C07  aromatic  1.342  0.020  1.342
 X52  C30  C03  aromatic  1.394  0.020  1.394
 X52  C09  N08  single    1.461  0.020  1.461
 X52  C07  N08  single    1.336  0.020  1.336
 X52  C07  C04  aromatic  1.432  0.020  1.432
 X52  C03  C04  aromatic  1.398  0.020  1.398
 X52  C03  C02  single    1.499  0.020  1.499
 X52  N08  C13  single    1.451  0.020  1.451
 X52  C04  C05  single    1.419  0.020  1.419
 X52  C02  C01  single    1.530  0.020  1.530
 X52  C05  N06  triple    1.154  0.020  1.154
 X52  C01  H1   single    0.970  0.020  1.090
 X52  C01  H2   single    0.970  0.020  1.090
 X52  C01  H3   single    0.970  0.020  1.090
 X52  C02  H4   single    0.970  0.020  1.090
 X52  C02  H5   single    0.970  0.020  1.090
 X52  C09  H6   single    0.970  0.020  1.090
 X52  C09  H7   single    0.970  0.020  1.090
 X52  C10  H8   single    0.970  0.020  1.090
 X52  C10  H9   single    0.970  0.020  1.090
 X52  C12  H10  single    0.970  0.020  1.090
 X52  C12  H11  single    0.970  0.020  1.090
 X52  C12  H12  single    0.970  0.020  1.090
 X52  C13  H13  single    0.970  0.020  1.090
 X52  C13  H14  single    0.970  0.020  1.090
 X52  C13  H15  single    0.970  0.020  1.090
 X52  C17  H16  single    0.970  0.020  1.090
 X52  C17  H17  single    0.970  0.020  1.090
 X52  C19  H18  single    0.930  0.020  1.080
 X52  C20  H19  single    0.930  0.020  1.080
 X52  C24  H20  single    0.970  0.020  1.090
 X52  C24  H21  single    0.970  0.020  1.090
 X52  C24  H22  single    0.970  0.020  1.090
 X52  C27  H23  single    0.970  0.020  1.090
 X52  C27  H24  single    0.970  0.020  1.090
 X52  C27  H25  single    0.970  0.020  1.090
 X52  C28  H26  single    0.930  0.020  1.080
 X52  C29  H27  single    0.930  0.020  1.080
 X52  N11  H28  single    0.890  0.020  1.040

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
 X52  H3   C01  H2   108.06  3.000
 X52  H3   C01  H1   107.97  3.000
 X52  H2   C01  H1   107.95  3.000
 X52  H3   C01  C02  111.39  3.000
 X52  H2   C01  C02  111.51  3.000
 X52  H1   C01  C02  109.83  3.000
 X52  H5   C02  H4   106.19  3.000
 X52  H5   C02  C03  110.28  3.000
 X52  H4   C02  C03  109.48  3.000
 X52  H5   C02  C01  109.87  3.000
 X52  H4   C02  C01  109.51  3.000
 X52  C03  C02  C01  111.38  3.000
 X52  C30  C03  C04  118.38  3.000
 X52  C04  C03  C02  121.38  3.000
 X52  C30  C03  C02  120.15  3.000
 X52  C07  C04  C05  123.43  3.000
 X52  C05  C04  C03  116.83  3.000
 X52  C07  C04  C03  119.43  3.000
 X52  N06  C05  C04  180.00  3.000
 X52  N14  C07  N08  115.80  3.000
 X52  N08  C07  C04  124.82  3.000
 X52  N14  C07  C04  119.38  3.000
 X52  H7   C09  H6   106.64  3.000
 X52  H7   C09  N08  109.46  3.000
 X52  H6   C09  N08  106.80  3.000
 X52  H7   C09  C10  108.91  3.000
 X52  H6   C09  C10  110.78  3.000
 X52  N08  C09  C10  114.00  3.000
 X52  H9   C10  H8   106.69  3.000
 X52  H9   C10  N11  108.49  3.000
 X52  H8   C10  N11  112.73  3.000
 X52  H9   C10  C09  108.46  3.000
 X52  H8   C10  C09  107.09  3.000
 X52  N11  C10  C09  113.11  3.000
 X52  H12  C12  H11  107.28  3.000
 X52  H12  C12  H10  107.06  3.000
 X52  H11  C12  H10  108.03  3.000
 X52  H12  C12  N11  110.64  3.000
 X52  H11  C12  N11  113.84  3.000
 X52  H10  C12  N11  109.72  3.000
 X52  H15  C13  H14  108.41  3.000
 X52  H15  C13  H13  109.44  3.000
 X52  H14  C13  H13  106.93  3.000
 X52  H15  C13  N08  112.55  3.000
 X52  H14  C13  N08  108.10  3.000
 X52  H13  C13  N08  111.21  3.000
 X52  S16  C15  N14  119.25  3.000
 X52  N14  C15  C30  122.85  3.000
 X52  S16  C15  C30  117.90  3.000
 X52  H17  C17  H16  108.74  3.000
 X52  H17  C17  S16  109.22  3.000
 X52  H16  C17  S16  108.36  3.000
 X52  H17  C17  C18  112.19  3.000
 X52  H16  C17  C18  111.36  3.000
 X52  S16  C17  C18  106.87  3.000
 X52  C29  C18  C19  118.93  3.000
 X52  C19  C18  C17  120.96  3.000
 X52  C29  C18  C17  120.10  3.000
 X52  H18  C19  C20  119.56  3.000
 X52  H18  C19  C18  119.84  3.000
 X52  C20  C19  C18  120.59  3.000
 X52  H19  C20  C21  119.69  3.000
 X52  H19  C20  C19  120.21  3.000
 X52  C21  C20  C19  120.10  3.000
 X52  N22  C21  C28  120.94  3.000
 X52  C28  C21  C20  119.70  3.000
 X52  N22  C21  C20  119.33  3.000
 X52  H22  C24  H21  110.22  3.000
 X52  H22  C24  H20  109.62  3.000
 X52  H21  C24  H20  110.38  3.000
 X52  H22  C24  S23  109.77  3.000
 X52  H21  C24  S23  108.94  3.000
 X52  H20  C24  S23  107.87  3.000
 X52  H25  C27  H24  108.58  3.000
 X52  H25  C27  H23  107.36  3.000
 X52  H24  C27  H23  108.98  3.000
 X52  H25  C27  N22  110.43  3.000
 X52  H24  C27  N22  113.36  3.000
 X52  H23  C27  N22  107.96  3.000
 X52  H26  C28  C29  119.64  3.000
 X52  H26  C28  C21  120.40  3.000
 X52  C29  C28  C21  119.96  3.000
 X52  H27  C29  C28  119.50  3.000
 X52  H27  C29  C18  119.78  3.000
 X52  C28  C29  C18  120.72  3.000
 X52  C31  C30  C15  120.18  3.000
 X52  C31  C30  C03  121.56  3.000
 X52  C15  C30  C03  118.22  3.000
 X52  N32  C31  C30  180.00  3.000
 X52  C13  N08  C09  116.59  3.000
 X52  C13  N08  C07  123.46  3.000
 X52  C09  N08  C07  119.81  3.000
 X52  H28  N11  C12  109.09  3.000
 X52  H28  N11  C10  108.97  3.000
 X52  C12  N11  C10  113.61  3.000
 X52  C15  N14  C07  121.23  3.000
 X52  S23  N22  C27  116.76  3.000
 X52  S23  N22  C21  117.32  3.000
 X52  C27  N22  C21  117.88  3.000
 X52  C17  S16  C15  102.54  3.000
 X52  O26  S23  O25  119.02  3.000
 X52  O25  S23  N22  107.50  3.000
 X52  O26  S23  N22  109.58  3.000
 X52  O25  S23  C24  108.83  3.000
 X52  O26  S23  C24  107.92  3.000
 X52  N22  S23  C24  102.78  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
 X52  CONST_01  N14  C15  C30  C03     0.00   0.0  0
 X52  CONST_02  N14  C07  C04  C03     0.00   0.0  0
 X52  CONST_03  C15  N14  C07  C04     0.00   0.0  0
 X52  CONST_04  C15  C30  C03  C04     0.00   0.0  0
 X52  CONST_05  C30  C15  N14  C07     0.00   0.0  0
 X52  CONST_06  C30  C03  C04  C07     0.00   0.0  0
 X52  CONST_07  C21  C28  C29  C18     0.00   0.0  0
 X52  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 X52  CONST_09  C28  C21  C20  C19     0.00   0.0  0
 X52  CONST_10  C28  C29  C18  C19     0.00   0.0  0
 X52  CONST_11  C29  C28  C21  C20     0.00   0.0  0
 X52  CONST_12  C29  C18  C19  C20     0.00   0.0  0
 X52  CONST_13  C15  C30  C03  C02   180.00   0.0  0
 X52  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 X52  CONST_15  S16  C15  C30  C03   180.00   0.0  0
 X52  CONST_16  N08  C07  C04  C03   180.00   0.0  0
 X52  CONST_17  C31  C30  C03  C04   180.00   0.0  0
 X52  CONST_18  N14  C07  C04  C05   180.00   0.0  0
 X52  CONST_19  C30  C03  C04  C05   180.00   0.0  0
 X52  CONST_20  S16  C15  N14  C07   180.00   0.0  0
 X52  CONST_21  N08  C07  N14  C15   180.00   0.0  0
 X52  CONST_22  C28  C29  C18  C17   180.00   0.0  0
 X52  CONST_23  C20  C19  C18  C17   180.00   0.0  0
 X52  CONST_24  N22  C21  C20  C19   180.00   0.0  0
 X52  CONST_25  N22  C21  C28  C29   180.00   0.0  0
 X52  CONST_26  N14  C15  C30  C31   180.00   0.0  0
 X52  CONST_27  H26  C28  C29  C18   180.00   0.0  0
 X52  CONST_28  H19  C20  C19  C18   180.00   0.0  0
 X52  CONST_29  H27  C29  C18  C19   180.00   0.0  0
 X52  CONST_30  H18  C19  C20  C21   180.00   0.0  0
 X52  CONST_31  C09  N08  C07  C04   180.00   0.0  0
 X52  CONST_32  C13  N08  C07  C04     0.00   0.0  0
 X52  CONST_33  N14  C07  N08  C09     0.00   0.0  0
 X52  CONST_34  N14  C07  N08  C13   180.00   0.0  0
 X52  Var_01    C30  C03  C02  C01   -86.88  30.0  2
 X52  Var_02    C18  C17  S16  C15   167.79  30.0  1
 X52  Var_03    N14  C15  S16  C17     3.63  30.0  2
 X52  Var_04    S16  C17  C18  C19    89.07  30.0  2
 X52  Var_05    C10  C09  N08  C07   -85.25  30.0  1
 X52  Var_06    C24  S23  N22  C21   125.83  30.0  3
 X52  Var_07    H1   C01  C02  C03   179.34  30.0  3
 X52  Var_08    H13  C13  N08  C07    37.29  30.0  3
 X52  Var_09    H23  C27  N22  C21   -47.03  30.0  3
 X52  Var_10    C12  N11  C10  C09   -79.77  30.0  1
 X52  Var_11    N11  C10  C09  N08   -63.13  30.0  1
 X52  Var_12    H10  C12  N11  C10  -174.79  30.0  3
 X52  Var_13    H20  C24  S23  N22   178.34  30.0  3

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
 X52  plan-1  C02  0.020
 X52  plan-1  C03  0.020
 X52  plan-1  C04  0.020
 X52  plan-1  C05  0.020
 X52  plan-1  C07  0.020
 X52  plan-1  C15  0.020
 X52  plan-1  C30  0.020
 X52  plan-1  C31  0.020
 X52  plan-1  N06  0.020
 X52  plan-1  N08  0.020
 X52  plan-1  N14  0.020
 X52  plan-1  N32  0.020
 X52  plan-1  S16  0.020
 X52  plan-2  C17  0.020
 X52  plan-2  C18  0.020
 X52  plan-2  C19  0.020
 X52  plan-2  C20  0.020
 X52  plan-2  C21  0.020
 X52  plan-2  C28  0.020
 X52  plan-2  C29  0.020
 X52  plan-2  N22  0.020
 X52  plan-2  H18  0.020
 X52  plan-2  H19  0.020
 X52  plan-2  H26  0.020
 X52  plan-2  H27  0.020
 X52  plan-3  C07  0.020
 X52  plan-3  C09  0.020
 X52  plan-3  C13  0.020
 X52  plan-3  N08  0.020
 X52  plan-4  C21  0.020
 X52  plan-4  C27  0.020
 X52  plan-4  N22  0.020
 X52  plan-4  S23  0.020

