# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 02:54:12 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: 2-({3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-(1,3-thiazol-5-yl)-2,3-dihydropyridazin-4-yl]-1,1-dioxido-2H-1,2,4-benzothiadiazin-7-yl}oxy)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCN1N=C(C(=C(C1=O)C2=Nc3ccc(OCC(N)=O)cc3[S](=O)(=O)N2)O)c4scnc4
#
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
 1PD  1PD  2-({3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-(1,3-thiazol-5-yl)-2,3-dihydropyridazin-4-yl]-1,1-dioxido-2H-1,2,4-benzothiadiazin-7-yl}oxy)acetamide  ligand  57  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1PD
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
 1PD  O31   O  OS    0  -0.640   2.1717  -3.1126  -1.4593
 1PD  S35   S  S     0   1.399   1.8371  -1.7124  -1.6362
 1PD  O30   O  OS    0  -0.632   1.8068  -1.1819  -2.9872
 1PD  C8    C  CR6   0  -0.241   2.8190  -0.6659  -0.6442
 1PD  C3    C  CR16  0  -0.349   4.1677  -0.9304  -0.4950
 1PD  C7    C  CR6   0   0.397   4.9586  -0.0260   0.2060
 1PD  O33   O  O2    0  -0.458   6.2593  -0.3409   0.3155
 1PD  C18   C  CH2   0  -0.304   7.1029   0.5228   1.0325
 1PD  C15   C  C     0   0.482   8.5171  -0.0281   0.9354
 1PD  O29   O  O     0  -0.471   8.8406  -0.8401   0.0882
 1PD  N27   N  NH2   0  -0.800   9.3543   0.4963   1.8379
 1PD  C2    C  CR16  0  -0.353   4.3740   1.1293   0.7341
 1PD  N25   N  NC1   0  -0.867   0.3935  -1.4424  -0.8785
 1PD  C13   C  C     0   0.524   0.0095  -0.1703  -0.5048
 1PD  N23   N  N     0  -0.438   0.8466   0.7409  -0.1709
 1PD  C6    C  CR6   0   0.295   2.1964   0.4722  -0.1118
 1PD  C1    C  CR16  0  -0.304   3.0227   1.3666   0.5713
 1PD  C11   C  CR6   0  -0.255  -1.4409   0.0920  -0.4479
 1PD  C12   C  CR6   0   0.355  -1.9521   1.3718  -0.3985
 1PD  O32   O  OH1   0  -0.541  -1.1785   2.4320  -0.4774
 1PD  C14   C  CR6   0   0.640  -2.3678  -1.0187  -0.4639
 1PD  O28   O  O     0  -0.512  -2.0414  -2.2067  -0.5161
 1PD  N26   N  NR6   0  -0.362  -3.7078  -0.6954  -0.4343
 1PD  C20   C  CH2   0  -0.294  -4.7187  -1.7550  -0.4251
 1PD  C19   C  CH2   0  -0.422  -5.0543  -2.1954   0.9925
 1PD  C21   C  CH1   0  -0.244  -6.1383  -3.2736   1.0453
 1PD  C17   C  CH3   0  -0.660  -5.6695  -4.5857   0.4216
 1PD  C16   C  CH3   0  -0.650  -6.5710  -3.5019   2.4902
 1PD  N24   N  N     0  -0.185  -4.1797   0.5186  -0.3117
 1PD  C10   C  CR6   0   0.130  -3.3760   1.5302  -0.2806
 1PD  C9    C  CR5   0  -0.347  -3.9855   2.8536  -0.1558
 1PD  S34   S  S2    0   0.282  -5.3618   3.3000  -1.0840
 1PD  C5    C  CR15  0  -0.199  -5.3805   4.8141  -0.2833
 1PD  N22   N  N     0  -0.347  -4.4477   4.9842   0.5987
 1PD  C4    C  CR15  0  -0.029  -3.6561   3.8822   0.6821
 1PD  H3    H  HCR6  0   0.296   4.6155  -1.8212  -0.9179
 1PD  H18   H  HCH2  0   0.274   7.1007   1.5342   0.6074
 1PD  H18A  H  HCH2  0   0.265   6.7929   0.6058   2.0801
 1PD  HN27  H  HNH2  0   0.413   9.0447   1.1365   2.5492
 1PD  HN2A  H  HNH2  0   0.409  10.3309   0.2508   1.8308
 1PD  H2    H  HCR6  0   0.299   4.9584   1.8530   1.2853
 1PD  HN25  H  HNC1  0   0.465  -0.3520  -2.1484  -0.9479
 1PD  H1    H  HCR6  0   0.280   2.5788   2.2578   0.9946
 1PD  HO32  H  HOH1  0   0.493  -1.7020   3.2417  -0.5801
 1PD  H20   H  HCH2  0   0.273  -5.5973  -1.3454  -0.9210
 1PD  H20A  H  HCH2  0   0.271  -4.3493  -2.5785  -1.0308
 1PD  H19   H  HCH2  0   0.232  -4.1519  -2.5662   1.4890
 1PD  H19A  H  HCH2  0   0.238  -5.3901  -1.3192   1.5552
 1PD  H21   H  HCH1  0   0.221  -7.0074  -2.9119   0.4830
 1PD  H17   H  HCH3  0   0.231  -6.4455  -5.3490   0.4902
 1PD  H17A  H  HCH3  0   0.229  -5.4120  -4.4811  -0.6330
 1PD  H17B  H  HCH3  0   0.217  -4.7857  -4.9611   0.9430
 1PD  H16   H  HCH3  0   0.227  -6.9331  -2.5816   2.9515
 1PD  H16A  H  HCH3  0   0.228  -7.3721  -4.2402   2.5511
 1PD  H16B  H  HCH3  0   0.215  -5.7358  -3.8690   3.0920
 1PD  H5    H  HCR5  0   0.316  -6.1322   5.5546  -0.5196
 1PD  H4    H  HCR5  0   0.304  -2.8508   3.8558   1.4041

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
 1PD  O31  S35   double    1.450  0.020  1.450
 1PD  S35  O30   double    1.452  0.020  1.452
 1PD  S35  C8    single    1.745  0.020  1.745
 1PD  S35  N25   single    1.653  0.020  1.653
 1PD  C8   C3    aromatic  1.382  0.020  1.382
 1PD  C8   C6    aromatic  1.402  0.020  1.402
 1PD  C3   C7    aromatic  1.391  0.020  1.391
 1PD  C7   O33   single    1.343  0.020  1.343
 1PD  C7   C2    aromatic  1.398  0.020  1.398
 1PD  O33  C18   single    1.404  0.020  1.404
 1PD  C18  C15   single    1.521  0.020  1.521
 1PD  C15  O29   double    1.217  0.020  1.217
 1PD  C15  N27   single    1.338  0.020  1.338
 1PD  C2   C1    aromatic  1.382  0.020  1.382
 1PD  N25  C13   single    1.380  0.020  1.380
 1PD  C13  N23   double    1.282  0.020  1.282
 1PD  C13  C11   single    1.475  0.020  1.475
 1PD  N23  C6    single    1.377  0.020  1.377
 1PD  C6   C1    aromatic  1.396  0.020  1.396
 1PD  C11  C12   double    1.379  0.020  1.379
 1PD  C11  C14   single    1.447  0.020  1.447
 1PD  C12  O32   single    1.315  0.020  1.315
 1PD  C12  C10   single    1.438  0.020  1.438
 1PD  C14  O28   double    1.233  0.020  1.233
 1PD  C14  N26   single    1.379  0.020  1.379
 1PD  N26  C20   single    1.464  0.020  1.464
 1PD  N26  N24   single    1.308  0.020  1.308
 1PD  C20  C19   single    1.522  0.020  1.522
 1PD  C19  C21   single    1.530  0.020  1.530
 1PD  C21  C17   single    1.527  0.020  1.527
 1PD  C21  C16   single    1.525  0.020  1.525
 1PD  N24  C10   double    1.292  0.020  1.292
 1PD  C10  C9    single    1.462  0.020  1.462
 1PD  C9   S34   aromatic  1.719  0.020  1.719
 1PD  C9   C4    aromatic  1.367  0.020  1.367
 1PD  S34  C5    aromatic  1.713  0.020  1.713
 1PD  C5   N22   aromatic  1.295  0.020  1.295
 1PD  N22  C4    aromatic  1.359  0.020  1.359
 1PD  C3   H3    single    0.930  0.020  1.080
 1PD  C18  H18   single    0.970  0.020  1.090
 1PD  C18  H18A  single    0.970  0.020  1.090
 1PD  N27  HN27  single    0.860  0.020  1.020
 1PD  N27  HN2A  single    0.860  0.020  1.020
 1PD  C2   H2    single    0.930  0.020  1.080
 1PD  N25  HN25  single    0.890  0.020  1.040
 1PD  C1   H1    single    0.930  0.020  1.080
 1PD  O32  HO32  single    0.850  0.020  0.980
 1PD  C20  H20   single    0.970  0.020  1.090
 1PD  C20  H20A  single    0.970  0.020  1.090
 1PD  C19  H19   single    0.970  0.020  1.090
 1PD  C19  H19A  single    0.970  0.020  1.090
 1PD  C21  H21   single    0.970  0.020  1.090
 1PD  C17  H17   single    0.970  0.020  1.090
 1PD  C17  H17A  single    0.970  0.020  1.090
 1PD  C17  H17B  single    0.970  0.020  1.090
 1PD  C16  H16   single    0.970  0.020  1.090
 1PD  C16  H16A  single    0.970  0.020  1.090
 1PD  C16  H16B  single    0.970  0.020  1.090
 1PD  C5   H5    single    0.930  0.020  1.080
 1PD  C4   H4    single    0.930  0.020  1.080

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
 1PD  N25   S35  C8     97.64  3.000
 1PD  N25   S35  O30   110.41  3.000
 1PD  C8    S35  O30   108.76  3.000
 1PD  N25   S35  O31   107.66  3.000
 1PD  C8    S35  O31   112.33  3.000
 1PD  O30   S35  O31   118.11  3.000
 1PD  C6    C8   C3    123.19  3.000
 1PD  C6    C8   S35   116.93  3.000
 1PD  C3    C8   S35   119.71  3.000
 1PD  H3    C3   C7    119.76  3.000
 1PD  H3    C3   C8    121.24  3.000
 1PD  C7    C3   C8    118.99  3.000
 1PD  C2    C7   O33   124.61  3.000
 1PD  C2    C7   C3    119.32  3.000
 1PD  O33   C7   C3    116.07  3.000
 1PD  C18   O33  C7    118.65  3.000
 1PD  H18A  C18  H18   107.46  3.000
 1PD  H18A  C18  C15   110.59  3.000
 1PD  H18   C18  C15   108.13  3.000
 1PD  H18A  C18  O33   111.39  3.000
 1PD  H18   C18  O33   111.59  3.000
 1PD  C15   C18  O33   107.65  3.000
 1PD  N27   C15  O29   124.37  3.000
 1PD  N27   C15  C18   113.38  3.000
 1PD  O29   C15  C18   122.22  3.000
 1PD  HN2A  N27  HN27  117.30  3.000
 1PD  HN2A  N27  C15   120.43  3.000
 1PD  HN27  N27  C15   122.27  3.000
 1PD  H2    C2   C1    118.28  3.000
 1PD  H2    C2   C7    121.30  3.000
 1PD  C1    C2   C7    120.42  3.000
 1PD  HN25  N25  C13   116.68  3.000
 1PD  HN25  N25  S35   119.33  3.000
 1PD  C13   N25  S35   121.18  3.000
 1PD  C11   C13  N23   120.38  3.000
 1PD  C11   C13  N25   116.61  3.000
 1PD  N23   C13  N25   122.96  3.000
 1PD  C6    N23  C13   120.83  3.000
 1PD  C1    C6   N23   118.42  3.000
 1PD  C1    C6   C8    116.29  3.000
 1PD  N23   C6   C8    125.25  3.000
 1PD  H1    C1   C6    118.44  3.000
 1PD  H1    C1   C2    119.79  3.000
 1PD  C6    C1   C2    121.77  3.000
 1PD  C14   C11  C12   118.39  3.000
 1PD  C14   C11  C13   119.54  3.000
 1PD  C12   C11  C13   122.07  3.000
 1PD  C10   C12  O32   119.92  3.000
 1PD  C10   C12  C11   118.19  3.000
 1PD  O32   C12  C11   121.87  3.000
 1PD  HO32  O32  C12   111.22  3.000
 1PD  N26   C14  O28   118.95  3.000
 1PD  N26   C14  C11   116.26  3.000
 1PD  O28   C14  C11   124.79  3.000
 1PD  N24   N26  C20   114.95  3.000
 1PD  N24   N26  C14   124.76  3.000
 1PD  C20   N26  C14   120.09  3.000
 1PD  H20A  C20  H20   107.78  3.000
 1PD  H20A  C20  C19   112.01  3.000
 1PD  H20   C20  C19   110.80  3.000
 1PD  H20A  C20  N26   108.07  3.000
 1PD  H20   C20  N26   106.37  3.000
 1PD  C19   C20  N26   111.56  3.000
 1PD  H19A  C19  H19   106.92  3.000
 1PD  H19A  C19  C21   109.22  3.000
 1PD  H19   C19  C21   109.25  3.000
 1PD  H19A  C19  C20   108.36  3.000
 1PD  H19   C19  C20   109.79  3.000
 1PD  C21   C19  C20   113.10  3.000
 1PD  H21   C21  C16   108.07  3.000
 1PD  H21   C21  C17   108.50  3.000
 1PD  C16   C21  C17   110.22  3.000
 1PD  H21   C21  C19   108.14  3.000
 1PD  C16   C21  C19   109.83  3.000
 1PD  C17   C21  C19   111.97  3.000
 1PD  H17B  C17  H17A  107.66  3.000
 1PD  H17B  C17  H17   107.75  3.000
 1PD  H17A  C17  H17   107.21  3.000
 1PD  H17B  C17  C21   110.41  3.000
 1PD  H17A  C17  C21   112.66  3.000
 1PD  H17   C17  C21   110.94  3.000
 1PD  H16B  C16  H16A  107.64  3.000
 1PD  H16B  C16  H16   107.70  3.000
 1PD  H16A  C16  H16   107.66  3.000
 1PD  H16B  C16  C21   110.79  3.000
 1PD  H16A  C16  C21   111.25  3.000
 1PD  H16   C16  C21   111.62  3.000
 1PD  C10   N24  N26   120.28  3.000
 1PD  C9    C10  N24   116.82  3.000
 1PD  C9    C10  C12   121.31  3.000
 1PD  N24   C10  C12   121.85  3.000
 1PD  C4    C9   S34   109.17  3.000
 1PD  C4    C9   C10   129.26  3.000
 1PD  S34   C9   C10   121.51  3.000
 1PD  C5    S34  C9     89.19  3.000
 1PD  H5    C5   N22   124.03  3.000
 1PD  H5    C5   S34   120.72  3.000
 1PD  N22   C5   S34   115.25  3.000
 1PD  C4    N22  C5    110.78  3.000
 1PD  H4    C4   N22   119.61  3.000
 1PD  H4    C4   C9    124.75  3.000
 1PD  N22   C4   C9    115.60  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
 1PD  CONST_01  C2    C7   C3   C8      0.00   0.0  0
 1PD  CONST_02  C2    C1   C6   C8      0.00   0.0  0
 1PD  CONST_03  C1    C6   C8   C3      0.00   0.0  0
 1PD  CONST_04  C1    C2   C7   C3      0.00   0.0  0
 1PD  CONST_05  C6    C8   C3   C7      0.00   0.0  0
 1PD  CONST_06  C6    C1   C2   C7      0.00   0.0  0
 1PD  CONST_07  N22   C5   S34  C9      0.00   0.0  0
 1PD  CONST_08  C5    N22  C4   C9      0.00   0.0  0
 1PD  CONST_09  N22   C4   C9   S34     0.00   0.0  0
 1PD  CONST_10  C4    N22  C5   S34     0.00   0.0  0
 1PD  CONST_11  C4    C9   S34  C5      0.00   0.0  0
 1PD  CONST_12  C5    S34  C9   C10   180.00   0.0  0
 1PD  CONST_13  N22   C4   C9   C10   180.00   0.0  0
 1PD  CONST_16  C6    N23  C13  N25     0.00   0.0  0
 1PD  CONST_17  C11   C13  N23  C6    180.00   0.0  0
 1PD  CONST_18  N24   N26  C14  C11     0.00   0.0  0
 1PD  CONST_19  O33   C7   C3   C8    180.00   0.0  0
 1PD  CONST_20  C1    C2   C7   O33   180.00   0.0  0
 1PD  CONST_21  C20   N26  C14  C11   180.00   0.0  0
 1PD  CONST_22  N24   N26  C14  O28   180.00   0.0  0
 1PD  CONST_23  H3    C3   C8   S35     0.00   0.0  0
 1PD  CONST_24  H1    C1   C6   C8    180.00   0.0  0
 1PD  CONST_25  H2    C2   C7   C3    180.00   0.0  0
 1PD  CONST_26  H4    C4   C9   C10     0.00   0.0  0
 1PD  CONST_27  H5    C5   S34  C9    180.00   0.0  0
 1PD  CONST_28  HN25  N25  C13  N23   180.00   0.0  0
 1PD  CONST_29  C20   N26  C14  O28     0.00   0.0  0
 1PD  CONST_30  HN27  N27  C15  C18     0.00   0.0  0
 1PD  CONST_31  HN2A  N27  C15  C18   180.00   0.0  0
 1PD  Var_01    C12   C11  C13  N25  -164.56  30.0  2
 1PD  Var_02    S34   C9   C10  C12   133.98  30.0  2
 1PD  Var_03    C3    C8   S35  O31    40.46  30.0  1
 1PD  Var_04    C13   N25  S35  O31   159.53  30.0  1
 1PD  Var_05    C2    C7   O33  C18     1.51  30.0  1
 1PD  Var_06    C19   C20  N26  C14    88.74  30.0  3
 1PD  Var_07    C15   C18  O33  C7   -177.01  30.0  3
 1PD  Var_08    C21   C19  C20  N26   178.29  30.0  3
 1PD  Var_09    O29   C15  C18  O33    17.76  30.0  3
 1PD  Var_10    C17   C21  C19  C20    66.04  30.0  3
 1PD  Var_11    H17   C17  C21  C19   178.60  30.0  3
 1PD  Var_12    H16   C16  C21  C19    57.52  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
 1PD  plan-1  C10   0.020
 1PD  plan-1  C9    0.020
 1PD  plan-1  S34   0.020
 1PD  plan-1  C5    0.020
 1PD  plan-1  N22   0.020
 1PD  plan-1  C4    0.020
 1PD  plan-1  H5    0.020
 1PD  plan-1  H4    0.020
 1PD  plan-2  C13   0.020
 1PD  plan-2  C11   0.020
 1PD  plan-2  C12   0.020
 1PD  plan-2  O32   0.020
 1PD  plan-2  C14   0.020
 1PD  plan-2  O28   0.020
 1PD  plan-2  N26   0.020
 1PD  plan-2  C20   0.020
 1PD  plan-2  N24   0.020
 1PD  plan-2  C10   0.020
 1PD  plan-2  C9    0.020
 1PD  plan-3  C18   0.020
 1PD  plan-3  C15   0.020
 1PD  plan-3  O29   0.020
 1PD  plan-3  N27   0.020
 1PD  plan-3  HN27  0.020
 1PD  plan-3  HN2A  0.020
 1PD  plan-4  S35   0.020
 1PD  plan-4  C8    0.020
 1PD  plan-4  C3    0.020
 1PD  plan-4  C7    0.020
 1PD  plan-4  O33   0.020
 1PD  plan-4  C2    0.020
 1PD  plan-4  N25   0.020
 1PD  plan-4  C13   0.020
 1PD  plan-4  N23   0.020
 1PD  plan-4  C6    0.020
 1PD  plan-4  C1    0.020
 1PD  plan-4  C11   0.020
 1PD  plan-4  H3    0.020
 1PD  plan-4  H2    0.020
 1PD  plan-4  HN25  0.020
 1PD  plan-4  H1    0.020

