# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:19:00 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 1-[5-(2-methoxyethyl)-4-methyl-thiophen-2-yl]sulfonyl-3-[4-methoxy-6-(methylcarbamoylamino)pyridin-2-yl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)Nc1cc(OC)cc(NC(=O)N[S](=O)(=O)c2sc(CCOC)c(C)c2)n1
#
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
 YCU  YCU  1-[5-(2-methoxyethyl)-4-methyl-thiophen-2-yl]sulfonyl-3-[4-methoxy-6-(methylcarbamoylamino)pyridin-2-yl]urea  ligand  53  30  .  2021-08-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YCU
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
 YCU  S1    S  S     0   1.386  -1.3799   3.6971   0.2249
 YCU  C2    C  CR5   0  -0.464  -2.1702   2.2168   0.6889
 YCU  N3    N  NC1   0  -0.820   0.2397   3.4632   0.5918
 YCU  S4    S  S2    0   0.338  -1.9574   0.7233  -0.1291
 YCU  C5    C  C     0   0.764   0.9707   2.4609  -0.0412
 YCU  C6    C  CR6   0   0.502   2.9440   1.0747   0.3297
 YCU  C7    C  CR6   0   0.523   2.9953  -1.1455  -0.1003
 YCU  C8    C  CR15  0  -0.169  -3.0098   2.1010   1.7617
 YCU  N9    N  N     0  -0.431   2.2881  -0.0445   0.0648
 YCU  C10   C  CR5   0  -0.220  -3.0071  -0.0680   0.9708
 YCU  N11   N  NH1   0  -0.763   2.1690   2.2178   0.5580
 YCU  N12   N  NH1   0  -0.776   2.3335  -2.3166  -0.4189
 YCU  C13   C  CR5   0   0.162  -3.5050   0.7845   1.9250
 YCU  C14   C  C     0   0.717   0.9958  -2.6208  -0.1896
 YCU  C15   C  CR16  0  -0.493   4.3177   1.1702   0.4406
 YCU  C16   C  CR16  0  -0.545   4.3912  -1.1922  -0.0006
 YCU  O17   O  OS    0  -0.623  -1.5025   3.8950  -1.2004
 YCU  O18   O  OS    0  -0.637  -1.8074   4.7302   1.1473
 YCU  C19   C  CR6   0   0.491   5.0557  -0.0055   0.2754
 YCU  O20   O  O     0  -0.450   0.5458   1.8949  -1.0201
 YCU  O21   O  O     0  -0.475   0.2556  -1.9619   0.5152
 YCU  N22   N  NH1   0  -0.668   0.6114  -3.7607  -0.8070
 YCU  C23   C  CH2   0  -0.571  -3.2651  -1.5303   0.8187
 YCU  O24   O  O2    0  -0.460   6.3796   0.1052   0.3946
 YCU  C25   C  CH3   0  -0.741  -4.4360   0.3746   3.0240
 YCU  O26   O  O2    0  -0.479  -4.4478  -3.2075  -0.3724
 YCU  C27   C  CH2   0  -0.112  -4.3006  -1.8171  -0.2608
 YCU  C28   C  CH3   0  -0.510  -0.7347  -4.2646  -0.6871
 YCU  C29   C  CH3   0  -0.443   7.1814  -1.0493   0.2077
 YCU  C30   C  CH3   0  -0.396  -5.3839  -3.5754  -1.3527
 YCU  H3    H  HNC1  0   0.439   0.4863   3.7386   1.5364
 YCU  H8    H  HCR5  0   0.288  -3.2688   2.9221   2.4153
 YCU  H11   H  HNH1  0   0.425   2.5530   2.9117   1.1817
 YCU  H15   H  HCR6  0   0.283   4.8101   2.1122   0.6419
 YCU  H12   H  HNH1  0   0.412   2.9223  -3.0720  -0.7344
 YCU  H16   H  HCR6  0   0.295   4.9129  -2.1311  -0.1261
 YCU  H231  H  HCH2  0   0.291  -2.3314  -2.0412   0.5751
 YCU  H232  H  HCH2  0   0.263  -3.6097  -1.9301   1.7748
 YCU  H251  H  HCH3  0   0.249  -5.3041  -0.1627   2.6417
 YCU  H252  H  HCH3  0   0.253  -3.9404  -0.2773   3.7452
 YCU  H253  H  HCH3  0   0.256  -4.8009   1.2455   3.5659
 YCU  H22   H  HNH1  0   0.399   1.1995  -4.1678  -1.5147
 YCU  H281  H  HCH3  0   0.232  -1.4688  -3.6368  -1.1962
 YCU  H282  H  HCH3  0   0.251  -0.7681  -5.2555  -1.1324
 YCU  H283  H  HCH3  0   0.237  -1.0315  -4.3529   0.3570
 YCU  H271  H  HCH2  0   0.207  -5.2553  -1.3363  -0.0013
 YCU  H272  H  HCH2  0   0.200  -3.9760  -1.3803  -1.2166
 YCU  H291  H  HCH3  0   0.237   6.9623  -1.8180   0.9519
 YCU  H292  H  HCH3  0   0.236   7.0548  -1.4719  -0.7914
 YCU  H293  H  HCH3  0   0.266   8.2124  -0.7275   0.3266
 YCU  H301  H  HCH3  0   0.204  -6.3869  -3.1931  -1.1281
 YCU  H302  H  HCH3  0   0.204  -5.1018  -3.2108  -2.3475
 YCU  H303  H  HCH3  0   0.234  -5.4292  -4.6633  -1.3845

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
 YCU  S1   C2    single    1.741  0.020  1.741
 YCU  S1   N3    single    1.677  0.020  1.677
 YCU  S1   O17   double    1.444  0.020  1.444
 YCU  S1   O18   double    1.449  0.020  1.449
 YCU  C2   S4    aromatic  1.716  0.020  1.716
 YCU  C2   C8    aromatic  1.367  0.020  1.367
 YCU  N3   C5    single    1.393  0.020  1.393
 YCU  S4   C10   aromatic  1.714  0.020  1.714
 YCU  C5   N11   single    1.362  0.020  1.362
 YCU  C5   O20   double    1.208  0.020  1.208
 YCU  C6   N9    aromatic  1.324  0.020  1.324
 YCU  C6   N11   single    1.400  0.020  1.400
 YCU  C6   C15   aromatic  1.382  0.020  1.382
 YCU  C7   N9    aromatic  1.319  0.020  1.319
 YCU  C7   N12   single    1.382  0.020  1.382
 YCU  C7   C16   aromatic  1.400  0.020  1.400
 YCU  C8   C13   aromatic  1.416  0.020  1.416
 YCU  C10  C13   aromatic  1.373  0.020  1.373
 YCU  C10  C23   single    1.493  0.020  1.493
 YCU  N12  C14   single    1.391  0.020  1.391
 YCU  C13  C25   single    1.498  0.020  1.498
 YCU  C14  O21   double    1.216  0.020  1.216
 YCU  C14  N22   single    1.352  0.020  1.352
 YCU  C15  C19   aromatic  1.398  0.020  1.398
 YCU  C16  C19   aromatic  1.388  0.020  1.388
 YCU  C19  O24   single    1.334  0.020  1.334
 YCU  N22  C28   single    1.442  0.020  1.442
 YCU  C23  C27   single    1.523  0.020  1.523
 YCU  O24  C29   single    1.418  0.020  1.418
 YCU  O26  C27   single    1.403  0.020  1.403
 YCU  O26  C30   single    1.405  0.020  1.405
 YCU  N3   H3    single    0.890  0.020  1.040
 YCU  C8   H8    single    0.930  0.020  1.080
 YCU  N11  H11   single    0.860  0.020  1.020
 YCU  C15  H15   single    0.930  0.020  1.080
 YCU  N12  H12   single    0.860  0.020  1.020
 YCU  C16  H16   single    0.930  0.020  1.080
 YCU  C23  H231  single    0.970  0.020  1.090
 YCU  C23  H232  single    0.970  0.020  1.090
 YCU  C25  H251  single    0.970  0.020  1.090
 YCU  C25  H252  single    0.970  0.020  1.090
 YCU  C25  H253  single    0.970  0.020  1.090
 YCU  N22  H22   single    0.860  0.020  1.020
 YCU  C28  H281  single    0.970  0.020  1.090
 YCU  C28  H282  single    0.970  0.020  1.090
 YCU  C28  H283  single    0.970  0.020  1.090
 YCU  C27  H271  single    0.970  0.020  1.090
 YCU  C27  H272  single    0.970  0.020  1.090
 YCU  C29  H291  single    0.970  0.020  1.090
 YCU  C29  H292  single    0.970  0.020  1.090
 YCU  C29  H293  single    0.970  0.020  1.090
 YCU  C30  H301  single    0.970  0.020  1.090
 YCU  C30  H302  single    0.970  0.020  1.090
 YCU  C30  H303  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
 YCU  O18   S1   O17   120.35  3.000
 YCU  O18   S1   N3    104.18  3.000
 YCU  O17   S1   N3    108.48  3.000
 YCU  O18   S1   C2    107.61  3.000
 YCU  O17   S1   C2    109.94  3.000
 YCU  N3    S1   C2    105.16  3.000
 YCU  C8    C2   S4    112.12  3.000
 YCU  C8    C2   S1    124.05  3.000
 YCU  S4    C2   S1    123.82  3.000
 YCU  H3    N3   C5    119.41  3.000
 YCU  H3    N3   S1    113.62  3.000
 YCU  C5    N3   S1    120.51  3.000
 YCU  C10   S4   C2     91.14  3.000
 YCU  O20   C5   N11   125.63  3.000
 YCU  O20   C5   N3    121.40  3.000
 YCU  N11   C5   N3    112.97  3.000
 YCU  C15   C6   N11   118.75  3.000
 YCU  C15   C6   N9    124.54  3.000
 YCU  N11   C6   N9    116.66  3.000
 YCU  C16   C7   N12   117.74  3.000
 YCU  C16   C7   N9    123.60  3.000
 YCU  N12   C7   N9    118.65  3.000
 YCU  H8    C8   C13   123.55  3.000
 YCU  H8    C8   C2    123.87  3.000
 YCU  C13   C8   C2    112.58  3.000
 YCU  C7    N9   C6    117.72  3.000
 YCU  C23   C10  C13   128.06  3.000
 YCU  C23   C10  S4    119.52  3.000
 YCU  C13   C10  S4    112.42  3.000
 YCU  H11   N11  C6    116.85  3.000
 YCU  H11   N11  C5    118.97  3.000
 YCU  C6    N11  C5    124.14  3.000
 YCU  H12   N12  C14   116.70  3.000
 YCU  H12   N12  C7    115.29  3.000
 YCU  C14   N12  C7    127.42  3.000
 YCU  C25   C13  C10   124.43  3.000
 YCU  C25   C13  C8    123.82  3.000
 YCU  C10   C13  C8    111.74  3.000
 YCU  N22   C14  O21   123.25  3.000
 YCU  N22   C14  N12   112.49  3.000
 YCU  O21   C14  N12   124.23  3.000
 YCU  H15   C15  C19   120.93  3.000
 YCU  H15   C15  C6    121.85  3.000
 YCU  C19   C15  C6    117.22  3.000
 YCU  H16   C16  C19   122.30  3.000
 YCU  H16   C16  C7    120.11  3.000
 YCU  C19   C16  C7    117.58  3.000
 YCU  O24   C19  C16   124.34  3.000
 YCU  O24   C19  C15   116.33  3.000
 YCU  C16   C19  C15   119.33  3.000
 YCU  H22   N22  C28   117.56  3.000
 YCU  H22   N22  C14   119.74  3.000
 YCU  C28   N22  C14   121.46  3.000
 YCU  H232  C23  H231  107.08  3.000
 YCU  H232  C23  C27   109.69  3.000
 YCU  H231  C23  C27   109.58  3.000
 YCU  H232  C23  C10   108.90  3.000
 YCU  H231  C23  C10   109.47  3.000
 YCU  C27   C23  C10   111.98  3.000
 YCU  C29   O24  C19   118.81  3.000
 YCU  H253  C25  H252  107.53  3.000
 YCU  H253  C25  H251  107.57  3.000
 YCU  H252  C25  H251  107.40  3.000
 YCU  H253  C25  C13   110.77  3.000
 YCU  H252  C25  C13   111.48  3.000
 YCU  H251  C25  C13   111.87  3.000
 YCU  C30   O26  C27   112.65  3.000
 YCU  H272  C27  H271  106.71  3.000
 YCU  H272  C27  O26   110.83  3.000
 YCU  H271  C27  O26   111.16  3.000
 YCU  H272  C27  C23   109.91  3.000
 YCU  H271  C27  C23   109.91  3.000
 YCU  O26   C27  C23   108.33  3.000
 YCU  H283  C28  H282  108.09  3.000
 YCU  H283  C28  H281  108.09  3.000
 YCU  H282  C28  H281  108.21  3.000
 YCU  H283  C28  N22   111.25  3.000
 YCU  H282  C28  N22   108.25  3.000
 YCU  H281  C28  N22   112.82  3.000
 YCU  H293  C29  H292  108.95  3.000
 YCU  H293  C29  H291  108.92  3.000
 YCU  H292  C29  H291  109.13  3.000
 YCU  H293  C29  O24   106.32  3.000
 YCU  H292  C29  O24   111.72  3.000
 YCU  H291  C29  O24   111.71  3.000
 YCU  H303  C30  H302  108.44  3.000
 YCU  H303  C30  H301  108.43  3.000
 YCU  H302  C30  H301  107.77  3.000
 YCU  H303  C30  O26   108.04  3.000
 YCU  H302  C30  O26   112.00  3.000
 YCU  H301  C30  O26   112.04  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
 YCU  CONST_01  C13   C10  S4   C2     0.00   0.0  0
 YCU  CONST_02  C10   C13  C8   C2     0.00   0.0  0
 YCU  CONST_03  C13   C8   C2   S4     0.00   0.0  0
 YCU  CONST_04  C8    C13  C10  S4     0.00   0.0  0
 YCU  CONST_05  C16   C7   N9   C6     0.00   0.0  0
 YCU  CONST_06  C16   C19  C15  C6     0.00   0.0  0
 YCU  CONST_07  C15   C6   N9   C7     0.00   0.0  0
 YCU  CONST_08  C15   C19  C16  C7     0.00   0.0  0
 YCU  CONST_09  C10   S4   C2   C8     0.00   0.0  0
 YCU  CONST_10  C19   C15  C6   N9     0.00   0.0  0
 YCU  CONST_11  C19   C16  C7   N9     0.00   0.0  0
 YCU  CONST_12  C10   S4   C2   S1   180.00   0.0  0
 YCU  CONST_13  C13   C8   C2   S1   180.00   0.0  0
 YCU  CONST_14  C23   C10  S4   C2   180.00   0.0  0
 YCU  CONST_15  C25   C13  C8   C2   180.00   0.0  0
 YCU  CONST_16  C25   C13  C10  S4   180.00   0.0  0
 YCU  CONST_17  N12   C7   N9   C6   180.00   0.0  0
 YCU  CONST_18  O24   C19  C15  C6   180.00   0.0  0
 YCU  CONST_19  N11   C6   N9   C7   180.00   0.0  0
 YCU  CONST_20  O24   C19  C16  C7   180.00   0.0  0
 YCU  CONST_21  C23   C10  C13  C8   180.00   0.0  0
 YCU  CONST_22  C19   C15  C6   N11  180.00   0.0  0
 YCU  CONST_23  C19   C16  C7   N12  180.00   0.0  0
 YCU  CONST_24  H8    C8   C2   S4   180.00   0.0  0
 YCU  CONST_25  H15   C15  C6   N9   180.00   0.0  0
 YCU  CONST_26  H16   C16  C7   N9   180.00   0.0  0
 YCU  CONST_32  H12   N12  C7   N9   180.00   0.0  0
 YCU  CONST_34  O21   C14  N12  C7     0.00   0.0  0
 YCU  CONST_36  N22   C14  N12  C7   180.00   0.0  0
 YCU  CONST_37  O20   C5   N3   S1     0.00   0.0  0
 YCU  CONST_38  C28   N22  C14  O21    0.00   0.0  0
 YCU  CONST_39  N11   C5   N3   S1   180.00   0.0  0
 YCU  CONST_40  C28   N22  C14  N12  180.00   0.0  0
 YCU  CONST_42  H22   N22  C14  O21  180.00   0.0  0
 YCU  Var_01    S4    C2   S1   N3   -69.38  30.0  2
 YCU  Var_02    C27   C23  C10  S4   -80.30  30.0  2
 YCU  Var_03    H251  C25  C13  C8   129.35  30.0  2
 YCU  Var_04    C5    N3   S1   C2    62.39  30.0  3
 YCU  Var_05    O26   C27  C23  C10  177.90  30.0  3
 YCU  Var_06    H291  C29  O24  C19  -62.58  30.0  3
 YCU  Var_07    H281  C28  N22  C14   68.90  30.0  3
 YCU  Var_08    H301  C30  O26  C27  -61.33  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
 YCU  plan-1  S1   0.020
 YCU  plan-1  C2   0.020
 YCU  plan-1  S4   0.020
 YCU  plan-1  C8   0.020
 YCU  plan-1  C10  0.020
 YCU  plan-1  C13  0.020
 YCU  plan-1  C23  0.020
 YCU  plan-1  C25  0.020
 YCU  plan-1  H8   0.020
 YCU  plan-2  C6   0.020
 YCU  plan-2  C7   0.020
 YCU  plan-2  N9   0.020
 YCU  plan-2  N11  0.020
 YCU  plan-2  N12  0.020
 YCU  plan-2  C15  0.020
 YCU  plan-2  C16  0.020
 YCU  plan-2  C19  0.020
 YCU  plan-2  O24  0.020
 YCU  plan-2  H15  0.020
 YCU  plan-2  H16  0.020
 YCU  plan-3  S1   0.020
 YCU  plan-3  N3   0.020
 YCU  plan-3  C5   0.020
 YCU  plan-3  C6   0.020
 YCU  plan-3  N11  0.020
 YCU  plan-3  O20  0.020
 YCU  plan-3  H3   0.020
 YCU  plan-3  H11  0.020
 YCU  plan-4  C7   0.020
 YCU  plan-4  N12  0.020
 YCU  plan-4  C14  0.020
 YCU  plan-4  O21  0.020
 YCU  plan-4  N22  0.020
 YCU  plan-4  C28  0.020
 YCU  plan-4  H12  0.020
 YCU  plan-4  H22  0.020

