# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 09:32:53 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 1-(1,2,3-benzothiadiazol-6-yl)-3-(2-oxidanylidene-2-piperidin-1-yl-ethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC(=O)N1CCCCC1)Nc2ccc3nnsc3c2
#
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
 RV5  RV5  1-(1,2,3-benzothiadiazol-6-yl)-3-(2-oxidanylidene-2-piperidin-1-yl-ethyl)urea  ligand  39  22  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RV5
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
 RV5  C10   C  CH2   0  -0.426   8.5182  -4.5069  26.3367
 RV5  C13   C  CH2   0  -0.324   7.2560  -4.3950  25.4901
 RV5  C15   C  CH2   0  -0.439   6.3311  -1.8264  24.5664
 RV5  C17   C  CR6   0   0.401   7.3543   2.6325  22.8697
 RV5  C20   C  CR16  0  -0.356   6.7663   3.5254  21.9347
 RV5  C21   C  CR56  0   0.285   8.5365   5.0785  22.2519
 RV5  C22   C  CR16  0  -0.256   7.3374   4.7287  21.6232
 RV5  C09   C  CH2   0  -0.445   9.5591  -5.3761  25.6379
 RV5  C11   C  CH2   0  -0.431   9.8165  -4.8864  24.2161
 RV5  C12   C  CH2   0  -0.311   8.5102  -4.7573  23.4416
 RV5  C16   C  C     0   0.746   6.9960   0.3989  23.9015
 RV5  C18   C  CR16  0  -0.358   8.5485   2.9702  23.4970
 RV5  C19   C  CR56  0  -0.228   9.1174   4.1985  23.1727
 RV5  N04   N  NT    0  -0.448   7.5766  -3.9037  24.1599
 RV5  N05   N  NH1   0  -0.663   6.0398  -0.5614  23.9623
 RV5  N06   N  NH1   0  -0.790   6.6548   1.4607  23.0916
 RV5  N07   N  N     0  -0.228   9.2412   6.2360  22.0698
 RV5  N08   N  N     0  -0.317  10.2874   6.3235  22.7539
 RV5  O02   O  O     0  -0.490   7.5899  -2.2815  22.5861
 RV5  O03   O  O     0  -0.500   8.0363   0.3400  24.5345
 RV5  S01   S  S2    0   0.380  10.5485   4.9457  23.7384
 RV5  H102  H  HCH2  0   0.225   8.9207  -3.5049  26.5131
 RV5  H101  H  HCH2  0   0.238   8.2599  -4.9248  27.3119
 RV5  H132  H  HCH2  0   0.273   6.5200  -3.7591  25.9735
 RV5  H131  H  HCH2  0   0.244   6.7948  -5.3825  25.3852
 RV5  H151  H  HCH2  0   0.282   6.7911  -1.6714  25.5432
 RV5  H152  H  HCH2  0   0.297   5.3835  -2.3364  24.7466
 RV5  H201  H  HCR6  0   0.284   5.8358   3.2424  21.4576
 RV5  H221  H  HCR6  0   0.284   6.8744   5.3960  20.9088
 RV5  H092  H  HCH2  0   0.218   9.1968  -6.4089  25.6014
 RV5  H091  H  HCH2  0   0.238  10.4887  -5.3912  26.2101
 RV5  H111  H  HCH2  0   0.237  10.4803  -5.5742  23.6878
 RV5  H112  H  HCH2  0   0.224  10.3173  -3.9139  24.2390
 RV5  H122  H  HCH2  0   0.261   8.6770  -4.3551  22.4463
 RV5  H121  H  HCH2  0   0.236   8.0501  -5.7443  23.3240
 RV5  H181  H  HCR6  0   0.300   9.0179   2.3150  24.2108
 RV5  H051  H  HNH1  0   0.402   5.2744  -0.5439  23.3070
 RV5  H061  H  HNH1  0   0.418   5.7856   1.3889  22.5843
 RV5  C14   C  C     0   0.535   7.2334  -2.6935  23.6798

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
 RV5  C20  C22   aromatic  1.368  0.020  1.368
 RV5  C20  C17   aromatic  1.420  0.020  1.420
 RV5  C22  C21   aromatic  1.398  0.020  1.398
 RV5  O02  C14   double    1.222  0.020  1.222
 RV5  N06  C17   single    1.383  0.020  1.383
 RV5  N06  C16   single    1.378  0.020  1.378
 RV5  C17  C18   aromatic  1.391  0.020  1.391
 RV5  C21  N07   aromatic  1.367  0.020  1.367
 RV5  C21  C19   aromatic  1.400  0.020  1.400
 RV5  N07  N08   aromatic  1.253  0.020  1.253
 RV5  N05  C16   single    1.357  0.020  1.357
 RV5  N05  C15   single    1.432  0.020  1.432
 RV5  C18  C19   aromatic  1.392  0.020  1.392
 RV5  C19  S01   aromatic  1.711  0.020  1.711
 RV5  N08  S01   aromatic  1.713  0.020  1.713
 RV5  C16  O03   double    1.219  0.020  1.219
 RV5  C14  C15   single    1.534  0.020  1.534
 RV5  C14  N04   single    1.346  0.020  1.346
 RV5  C12  C11   single    1.524  0.020  1.524
 RV5  C12  N04   single    1.455  0.020  1.455
 RV5  C11  C09   single    1.526  0.020  1.526
 RV5  N04  C13   single    1.454  0.020  1.454
 RV5  C13  C10   single    1.524  0.020  1.524
 RV5  C09  C10   single    1.526  0.020  1.526
 RV5  C10  H102  single    0.970  0.020  1.090
 RV5  C10  H101  single    0.970  0.020  1.090
 RV5  C13  H132  single    0.970  0.020  1.090
 RV5  C13  H131  single    0.970  0.020  1.090
 RV5  C15  H151  single    0.970  0.020  1.090
 RV5  C15  H152  single    0.970  0.020  1.090
 RV5  C20  H201  single    0.930  0.020  1.080
 RV5  C22  H221  single    0.930  0.020  1.080
 RV5  C09  H092  single    0.970  0.020  1.090
 RV5  C09  H091  single    0.970  0.020  1.090
 RV5  C11  H111  single    0.970  0.020  1.090
 RV5  C11  H112  single    0.970  0.020  1.090
 RV5  C12  H122  single    0.970  0.020  1.090
 RV5  C12  H121  single    0.970  0.020  1.090
 RV5  C18  H181  single    0.930  0.020  1.080
 RV5  N05  H051  single    0.890  0.020  1.040
 RV5  N06  H061  single    0.860  0.020  1.020

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
 RV5  H101  C10  H102  107.07  3.000
 RV5  H101  C10  C09   110.63  3.000
 RV5  H102  C10  C09   110.16  3.000
 RV5  H101  C10  C13   109.17  3.000
 RV5  H102  C10  C13   109.08  3.000
 RV5  C09   C10  C13   110.64  3.000
 RV5  H131  C13  H132  106.57  3.000
 RV5  H131  C13  N04   108.06  3.000
 RV5  H132  C13  N04   111.03  3.000
 RV5  H131  C13  C10   109.62  3.000
 RV5  H132  C13  C10   110.91  3.000
 RV5  N04   C13  C10   110.52  3.000
 RV5  H152  C15  H151  106.54  3.000
 RV5  H152  C15  N05   107.82  3.000
 RV5  H151  C15  N05   109.76  3.000
 RV5  H152  C15  C14   110.01  3.000
 RV5  H151  C15  C14   110.49  3.000
 RV5  N05   C15  C14   112.05  3.000
 RV5  N06   C17  C18   124.60  3.000
 RV5  C18   C17  C20   119.99  3.000
 RV5  N06   C17  C20   115.41  3.000
 RV5  H201  C20  C22   119.22  3.000
 RV5  H201  C20  C17   118.77  3.000
 RV5  C22   C20  C17   122.02  3.000
 RV5  N07   C21  C19   113.95  3.000
 RV5  C19   C21  C22   119.62  3.000
 RV5  N07   C21  C22   126.43  3.000
 RV5  H221  C22  C21   120.64  3.000
 RV5  H221  C22  C20   120.96  3.000
 RV5  C21   C22  C20   118.40  3.000
 RV5  H091  C09  H092  106.63  3.000
 RV5  H091  C09  C11   110.44  3.000
 RV5  H092  C09  C11   109.11  3.000
 RV5  H091  C09  C10   110.42  3.000
 RV5  H092  C09  C10   109.08  3.000
 RV5  C11   C09  C10   111.05  3.000
 RV5  H112  C11  H111  106.95  3.000
 RV5  H112  C11  C12   109.13  3.000
 RV5  H111  C11  C12   109.18  3.000
 RV5  H112  C11  C09   110.06  3.000
 RV5  H111  C11  C09   110.56  3.000
 RV5  C12   C11  C09   110.86  3.000
 RV5  H121  C12  H122  107.44  3.000
 RV5  H121  C12  N04   108.19  3.000
 RV5  H122  C12  N04   109.50  3.000
 RV5  H121  C12  C11   109.77  3.000
 RV5  H122  C12  C11   111.43  3.000
 RV5  N04   C12  C11   110.42  3.000
 RV5  O03   C16  N06   123.61  3.000
 RV5  O03   C16  N05   122.95  3.000
 RV5  N06   C16  N05   113.41  3.000
 RV5  H181  C18  C19   120.89  3.000
 RV5  H181  C18  C17   121.72  3.000
 RV5  C19   C18  C17   117.40  3.000
 RV5  S01   C19  C18   130.56  3.000
 RV5  S01   C19  C21   106.86  3.000
 RV5  C18   C19  C21   122.57  3.000
 RV5  C14   N04  C12   120.99  3.000
 RV5  C12   N04  C13   113.27  3.000
 RV5  C14   N04  C13   125.01  3.000
 RV5  H051  N05  C16   119.60  3.000
 RV5  H051  N05  C15   116.37  3.000
 RV5  C16   N05  C15   120.07  3.000
 RV5  H061  N06  C16   116.99  3.000
 RV5  H061  N06  C17   114.54  3.000
 RV5  C16   N06  C17   128.47  3.000
 RV5  N08   N07  C21   114.63  3.000
 RV5  S01   N08  N07   112.63  3.000
 RV5  N08   S01  C19    91.93  3.000
 RV5  O02   C14  N04   123.22  3.000
 RV5  N04   C14  C15   116.87  3.000
 RV5  O02   C14  C15   119.90  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
 RV5  CONST_01  C21   C22  C20  C17    0.00   0.0  0
 RV5  CONST_02  C21   C19  C18  C17    0.00   0.0  0
 RV5  CONST_03  S01   C19  C18  C17  180.00   0.0  0
 RV5  CONST_04  N07   C21  C22  C20  180.00   0.0  0
 RV5  CONST_05  C19   C21  C22  C20    0.00   0.0  0
 RV5  CONST_06  C19   C18  C17  C20    0.00   0.0  0
 RV5  CONST_07  S01   N08  N07  C21    0.00   0.0  0
 RV5  CONST_08  N08   S01  C19  C21    0.00   0.0  0
 RV5  CONST_09  C18   C17  C20  C22    0.00   0.0  0
 RV5  CONST_10  N08   N07  C21  C22  180.00   0.0  0
 RV5  CONST_11  C18   C19  C21  C22    0.00   0.0  0
 RV5  CONST_12  S01   C19  C21  C22  180.00   0.0  0
 RV5  CONST_13  N07   C21  C19  C18  180.00   0.0  0
 RV5  CONST_14  N08   S01  C19  C18  180.00   0.0  0
 RV5  CONST_15  N08   N07  C21  C19    0.00   0.0  0
 RV5  CONST_16  N07   N08  S01  C19    0.00   0.0  0
 RV5  CONST_17  S01   C19  C21  N07    0.00   0.0  0
 RV5  CONST_18  N06   C17  C20  C22  180.00   0.0  0
 RV5  CONST_19  N06   C17  C18  C19  180.00   0.0  0
 RV5  CONST_20  H221  C22  C20  C17  180.00   0.0  0
 RV5  CONST_21  H181  C18  C17  C20  180.00   0.0  0
 RV5  CONST_22  H201  C20  C22  C21  180.00   0.0  0
 RV5  CONST_23  O02   C14  N04  C13  180.00   0.0  0
 RV5  CONST_24  C15   C14  N04  C13    0.00   0.0  0
 RV5  CONST_25  C12   N04  C14  C15  180.00   0.0  0
 RV5  CONST_26  O02   C14  N04  C12    0.00   0.0  0
 RV5  CONST_27  C16   N06  C17  C20  180.00   0.0  0
 RV5  CONST_28  C18   C17  N06  C16    0.00   0.0  0
 RV5  CONST_29  H061  N06  C17  C20    0.00   0.0  0
 RV5  CONST_30  O03   C16  N06  C17    0.00   0.0  0
 RV5  CONST_31  N05   C16  N06  C17  180.00   0.0  0
 RV5  CONST_32  O03   C16  N05  C15    0.00   0.0  0
 RV5  CONST_33  N06   C16  N05  C15  180.00   0.0  0
 RV5  CONST_34  H051  N05  C16  O03  180.00   0.0  0
 RV5  Var_01    C12   N04  C13  C10   59.34  30.0  1
 RV5  Var_02    C12   C11  C09  C10  -52.72  30.0  1
 RV5  Var_03    C11   C12  N04  C13  -59.08  30.0  1
 RV5  Var_04    C11   C09  C10  C13   52.79  30.0  1
 RV5  Var_05    N04   C12  C11  C09   54.83  30.0  1
 RV5  Var_06    N04   C13  C10  C09  -55.17  30.0  1
 RV5  Var_07    N05   C15  C14  N04  179.55  30.0  3
 RV5  Var_08    C16   N05  C15  C14  -73.46  30.0  2

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
 RV5  plan-1  C17   0.020
 RV5  plan-1  C20   0.020
 RV5  plan-1  C21   0.020
 RV5  plan-1  C22   0.020
 RV5  plan-1  C18   0.020
 RV5  plan-1  C19   0.020
 RV5  plan-1  N06   0.020
 RV5  plan-1  N07   0.020
 RV5  plan-1  N08   0.020
 RV5  plan-1  S01   0.020
 RV5  plan-1  H201  0.020
 RV5  plan-1  H221  0.020
 RV5  plan-1  H181  0.020
 RV5  plan-2  C13   0.020
 RV5  plan-2  C15   0.020
 RV5  plan-2  C12   0.020
 RV5  plan-2  N04   0.020
 RV5  plan-2  O02   0.020
 RV5  plan-2  C14   0.020
 RV5  plan-3  C15   0.020
 RV5  plan-3  C17   0.020
 RV5  plan-3  C16   0.020
 RV5  plan-3  N05   0.020
 RV5  plan-3  N06   0.020
 RV5  plan-3  O03   0.020
 RV5  plan-3  H051  0.020
 RV5  plan-3  H061  0.020

