# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 01:56:23 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-[2-(hydroxymethyl)pyrimidin-4-yl]-N,N-dimethylpiperazine-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[S](=O)(=O)N1CCN(CC1)c2ccnc(CO)n2
#
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
 572  572  4-[2-(hydroxymethyl)pyrimidin-4-yl]-N,N-dimethylpiperazine-1-sulfonamide  ligand  39  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_572
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
 572  O30   O  OH1   0  -0.659  -2.6986  -0.5196  -4.0890
 572  C14   C  CH2   0  -0.209  -1.5359  -0.7369  -4.8355
 572  C7    C  CR6   0   0.328  -0.3084  -0.3817  -4.0409
 572  N4    N  N     0  -0.478  -0.4617   0.0746  -2.8161
 572  C2    C  CR6   0   0.572   0.6305   0.3966  -2.1105
 572  C5    C  CR16  0  -0.429   1.9019   0.2452  -2.7008
 572  C6    C  CR16  0  -0.046   1.9292  -0.2430  -3.9841
 572  N3    N  N     0  -0.457   0.8401  -0.5664  -4.6804
 572  N1    N  NT    0  -0.506   0.4397   0.8559  -0.8545
 572  C19   C  CH2   0  -0.314  -0.8789   1.0451  -0.2853
 572  C15   C  CH2   0  -0.315  -0.9884   0.3457   1.0583
 572  N17   N  N     0  -0.574   0.0715   0.8345   1.9419
 572  S28   S  S     0   1.534  -0.0959   0.4546   3.5506
 572  O25   O  OS    0  -0.652  -1.4541   0.8168   3.9109
 572  N22   N  N     0  -0.587   0.0701  -1.1860   3.6754
 572  C13   C  CH3   0  -0.510   1.2888  -1.7080   4.2805
 572  C11   C  CH3   0  -0.511  -1.1282  -1.9818   3.9095
 572  O12   O  OS    0  -0.653   1.0221   1.0829   4.2300
 572  C16   C  CH2   0  -0.309   1.3965   0.5887   1.3735
 572  C18   C  CH2   0  -0.309   1.5004   1.2865   0.0275
 572  H30   H  HOH1  0   0.460  -3.4474  -0.7250  -4.6556
 572  H141  H  HCH2  0   0.225  -1.5135  -0.1382  -5.7561
 572  H142  H  HCH2  0   0.224  -1.4319  -1.7833  -5.1534
 572  H5    H  HCR6  0   0.277   2.8275   0.4873  -2.2039
 572  H6    H  HCR6  0   0.268   2.8831  -0.3816  -4.4818
 572  H191  H  HCH2  0   0.290  -1.6287   0.6481  -0.9626
 572  H192  H  HCH2  0   0.249  -1.0688   2.1155  -0.1531
 572  H151  H  HCH2  0   0.244  -0.9153  -0.7401   0.9174
 572  H152  H  HCH2  0   0.279  -1.9628   0.5776   1.4836
 572  H131  H  HCH3  0   0.240   1.2888  -1.6249   5.3701
 572  H132  H  HCH3  0   0.255   1.3618  -2.7613   4.0158
 572  H133  H  HCH3  0   0.257   2.1718  -1.2116   3.8885
 572  H111  H  HCH3  0   0.239  -1.4452  -1.9677   4.9552
 572  H112  H  HCH3  0   0.258  -1.9551  -1.6520   3.2865
 572  H113  H  HCH3  0   0.255  -0.9019  -3.0095   3.6312
 572  H161  H  HCH2  0   0.281   2.1648   0.9974   2.0265
 572  H162  H  HCH2  0   0.244   1.5788  -0.4858   1.2442
 572  H181  H  HCH2  0   0.280   2.4785   1.0647  -0.3878
 572  H182  H  HCH2  0   0.256   1.4417   2.3699   0.1731

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
 572  O30  C14   single    1.399  0.020  1.399
 572  O30  H30   single    0.850  0.020  0.980
 572  C14  C7    single    1.505  0.020  1.505
 572  C14  H141  single    0.970  0.020  1.090
 572  C14  H142  single    0.970  0.020  1.090
 572  C7   N4    aromatic  1.316  0.020  1.316
 572  C7   N3    aromatic  1.328  0.020  1.328
 572  N4   C2    aromatic  1.340  0.020  1.340
 572  C2   C5    aromatic  1.410  0.020  1.410
 572  C2   N1    single    1.351  0.020  1.351
 572  C5   C6    aromatic  1.373  0.020  1.373
 572  C5   H5    single    0.930  0.020  1.080
 572  C6   N3    aromatic  1.332  0.020  1.332
 572  C6   H6    single    0.930  0.020  1.080
 572  N1   C19   single    1.449  0.020  1.449
 572  N1   C18   single    1.445  0.020  1.445
 572  C19  C15   single    1.519  0.020  1.519
 572  C19  H191  single    0.970  0.020  1.090
 572  C19  H192  single    0.970  0.020  1.090
 572  C15  N17   single    1.464  0.020  1.464
 572  C15  H151  single    0.970  0.020  1.090
 572  C15  H152  single    0.970  0.020  1.090
 572  N17  S28   single    1.661  0.020  1.661
 572  N17  C16   single    1.463  0.020  1.463
 572  S28  O25   double    1.451  0.020  1.451
 572  S28  N22   single    1.654  0.020  1.654
 572  S28  O12   double    1.451  0.020  1.451
 572  N22  C13   single    1.457  0.020  1.457
 572  N22  C11   single    1.457  0.020  1.457
 572  C13  H131  single    0.970  0.020  1.090
 572  C13  H132  single    0.970  0.020  1.090
 572  C13  H133  single    0.970  0.020  1.090
 572  C11  H111  single    0.970  0.020  1.090
 572  C11  H112  single    0.970  0.020  1.090
 572  C11  H113  single    0.970  0.020  1.090
 572  C16  C18   single    1.520  0.020  1.520
 572  C16  H161  single    0.970  0.020  1.090
 572  C16  H162  single    0.970  0.020  1.090
 572  C18  H181  single    0.970  0.020  1.090
 572  C18  H182  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
 572  H30   O30  C14   107.44  3.000
 572  H142  C14  H141  105.95  3.000
 572  H142  C14  C7    107.49  3.000
 572  H141  C14  C7    107.30  3.000
 572  H142  C14  O30   112.40  3.000
 572  H141  C14  O30   112.31  3.000
 572  C7    C14  O30   111.07  3.000
 572  N3    C7   N4    126.68  3.000
 572  N3    C7   C14   114.74  3.000
 572  N4    C7   C14   118.58  3.000
 572  C2    N4   C7    118.60  3.000
 572  N1    C2   C5    123.58  3.000
 572  N1    C2   N4    117.15  3.000
 572  C5    C2   N4    119.27  3.000
 572  H5    C5   C6    119.56  3.000
 572  H5    C5   C2    123.86  3.000
 572  C6    C5   C2    116.57  3.000
 572  H6    C6   N3    116.61  3.000
 572  H6    C6   C5    119.45  3.000
 572  N3    C6   C5    123.94  3.000
 572  C6    N3   C7    114.94  3.000
 572  C18   N1   C19   112.91  3.000
 572  C18   N1   C2    124.41  3.000
 572  C19   N1   C2    122.57  3.000
 572  H192  C19  H191  108.24  3.000
 572  H192  C19  C15   109.32  3.000
 572  H191  C19  C15   109.49  3.000
 572  H192  C19  N1    109.45  3.000
 572  H191  C19  N1    109.62  3.000
 572  C15   C19  N1    110.68  3.000
 572  H152  C15  H151  108.71  3.000
 572  H152  C15  N17   109.95  3.000
 572  H151  C15  N17   111.08  3.000
 572  H152  C15  C19   108.20  3.000
 572  H151  C15  C19   109.71  3.000
 572  N17   C15  C19   109.15  3.000
 572  C16   N17  S28   115.42  3.000
 572  C16   N17  C15   111.42  3.000
 572  S28   N17  C15   115.79  3.000
 572  O12   S28  N22   108.47  3.000
 572  O12   S28  O25   119.78  3.000
 572  N22   S28  O25   108.83  3.000
 572  O12   S28  N17   106.06  3.000
 572  N22   S28  N17   106.85  3.000
 572  O25   S28  N17   106.12  3.000
 572  C11   N22  C13   115.17  3.000
 572  C11   N22  S28   118.12  3.000
 572  C13   N22  S28   118.07  3.000
 572  H133  C13  H132  107.46  3.000
 572  H133  C13  H131  108.97  3.000
 572  H132  C13  H131  108.42  3.000
 572  H133  C13  N22   111.49  3.000
 572  H132  C13  N22   107.56  3.000
 572  H131  C13  N22   112.75  3.000
 572  H113  C11  H112  107.35  3.000
 572  H113  C11  H111  108.49  3.000
 572  H112  C11  H111  108.90  3.000
 572  H113  C11  N22   107.67  3.000
 572  H112  C11  N22   111.58  3.000
 572  H111  C11  N22   112.65  3.000
 572  H162  C16  H161  108.73  3.000
 572  H162  C16  C18   109.50  3.000
 572  H161  C16  C18   108.11  3.000
 572  H162  C16  N17   111.15  3.000
 572  H161  C16  N17   110.08  3.000
 572  C18   C16  N17   109.21  3.000
 572  H182  C18  H181  107.54  3.000
 572  H182  C18  C16   109.44  3.000
 572  H181  C18  C16   107.86  3.000
 572  H182  C18  N1    109.67  3.000
 572  H181  C18  N1    111.53  3.000
 572  C16   C18  N1    110.71  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
 572  CONST_01  C5    C2   N4   C7      0.00   0.0  0
 572  CONST_02  C5    C6   N3   C7      0.00   0.0  0
 572  CONST_03  C6    N3   C7   N4      0.00   0.0  0
 572  CONST_04  C6    C5   C2   N4      0.00   0.0  0
 572  CONST_05  N3    C7   N4   C2      0.00   0.0  0
 572  CONST_06  N3    C6   C5   C2      0.00   0.0  0
 572  CONST_07  N1    C2   N4   C7    180.00   0.0  0
 572  CONST_08  N1    C2   C5   C6    180.00   0.0  0
 572  CONST_09  C2    N4   C7   C14   180.00   0.0  0
 572  CONST_10  C6    N3   C7   C14   180.00   0.0  0
 572  CONST_11  H6    C6   N3   C7    180.00   0.0  0
 572  CONST_12  H5    C5   C2   N4    180.00   0.0  0
 572  Var_01    C19   N1   C2   N4     -2.06  30.0  2
 572  Var_02    C15   C19  N1   C2    128.06  30.0  1
 572  Var_03    C16   C18  N1   C2   -128.20  30.0  1
 572  Var_04    N17   C15  C19  N1     56.01  30.0  1
 572  Var_05    N17   C16  C18  N1    -55.99  30.0  1
 572  Var_06    C16   N17  C15  C19   -59.10  30.0  1
 572  Var_07    C18   C16  N17  C15    59.06  30.0  1
 572  Var_08    N4    C7   C14  O30    -0.54  30.0  2
 572  Var_09    O25   S28  N17  C15   -49.19  30.0  3
 572  Var_10    C13   N22  S28  N17   108.17  30.0  3
 572  Var_11    H131  C13  N22  S28    77.06  30.0  3
 572  Var_12    H111  C11  N22  S28   -79.29  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
 572  plan-1  C14  0.020
 572  plan-1  C7   0.020
 572  plan-1  N4   0.020
 572  plan-1  C2   0.020
 572  plan-1  C5   0.020
 572  plan-1  C6   0.020
 572  plan-1  N3   0.020
 572  plan-1  N1   0.020
 572  plan-1  H5   0.020
 572  plan-1  H6   0.020

