# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:22:24 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 5-[[3-[3-(dimethylamino)-1,2,4-oxadiazol-5-yl]-2-oxidanyl-phenyl]methylamino]-2~{H}-indazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1noc(n1)c2cccc(CNc3ccc4n[nH]c(C(O)=O)c4c3)c2O
#
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
 SL7  SL7  '5-[[3-[3-(dimethylamino)-1,2,4-oxadiazol-5-yl]-2-oxidanyl-phenyl]methylamino]-2~{H}-indazole-3-carboxylic acid'  ligand  46  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SL7
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
 SL7  C1   C  CH3    0  -0.529  5.3147  30.5518  33.4582
 SL7  C2   C  CR5    0   0.620  3.2492  30.5695  32.2060
 SL7  C3   C  CR5    0   0.658  2.7264  31.6662  30.5046
 SL7  C7   C  CR16   0  -0.262  2.7618  34.0888  27.0624
 SL7  C8   C  CR6    0  -0.033  3.9365  33.9158  27.7694
 SL7  C9   C  CH2    0  -0.341  5.2332  34.5713  27.3454
 SL7  C10  C  CR6    0   0.360  5.3660  34.3939  24.9018
 SL7  C11  C  CR16   0  -0.441  5.3128  33.0179  24.9096
 SL7  C12  C  CR56   0  -0.066  5.4936  32.3312  23.6876
 SL7  C13  C  CR56   0   0.203  5.7243  33.0385  22.4782
 SL7  C14  C  CR5    0   0.152  5.5152  30.9870  23.3067
 SL7  C15  C  C      0   0.361  5.3490  29.6991  24.0577
 SL7  C16  C  CR16   0  -0.284  5.7741  34.4511  22.4847
 SL7  O2   O  O      0  -0.596  5.4613  28.6595  23.3791
 SL7  O1   O  OC    -1  -0.577  5.1204  29.8053  25.2762
 SL7  N5   N  NR15   0  -0.449  5.7443  31.0101  21.9814
 SL7  N4   N  N      0  -0.309  5.8752  32.2039  21.4405
 SL7  C17  C  CR16   0  -0.338  5.5943  35.0952  23.6710
 SL7  N3   N  NH1    0  -0.698  5.1754  35.1607  26.0363
 SL7  C6   C  CR16   0  -0.256  1.5681  33.4868  27.4590
 SL7  C5   C  CR16   0  -0.285  1.5479  32.6939  28.5833
 SL7  C18  C  CR6    0   0.334  3.9189  33.1160  28.9210
 SL7  O3   O  OH1    0  -0.622  5.0647  32.9822  29.5907
 SL7  C4   C  CR6    0  -0.178  2.7191  32.4993  29.3250
 SL7  O    O  O      0  -0.342  1.6296  31.0827  30.9376
 SL7  N1   N  N      0  -0.241  1.9599  30.3617  32.0784
 SL7  N2   N  N      0  -0.611  3.7605  31.3957  31.2437
 SL7  N    N  NT     0  -0.512  4.0072  30.0039  33.1617
 SL7  C    C  CH3    0  -0.531  3.3351  29.2693  34.2114
 SL7  H1   H  HCH3   0   0.249  5.9084  29.7876  33.9563
 SL7  H2   H  HCH3   0   0.259  5.8297  30.8317  32.5430
 SL7  H3   H  HCH3   0   0.233  5.2644  31.4278  34.1115
 SL7  H4   H  HCR6   0   0.265  2.7787  34.7079  26.1747
 SL7  H5   H  HCH2   0   0.238  6.0513  33.8427  27.4162
 SL7  H6   H  HCH2   0   0.280  5.4789  35.3638  28.0555
 SL7  H7   H  HCR6   0   0.246  5.1334  32.4576  25.8155
 SL7  H8   H  HCR6   0   0.251  5.9527  35.0076  21.5733
 SL7  H10  H  HNR5   0   0.406  5.8190  30.1829  21.4066
 SL7  H11  H  HCR6   0   0.255  5.6270  36.1788  23.6985
 SL7  H12  H  HNH1   0   0.382  5.5381  36.0977  25.9821
 SL7  H13  H  HCR6   0   0.257  0.6657  33.6383  26.8834
 SL7  H14  H  HCR6   0   0.267  0.6265  32.2190  28.8935
 SL7  H15  H  HOH1   0   0.485  4.9423  32.3801  30.3579
 SL7  H16  H  HCH3   0   0.251  4.0697  28.6750  34.7501
 SL7  H17  H  HCH3   0   0.235  2.8309  29.9272  34.9260
 SL7  H18  H  HCH3   0   0.253  2.5966  28.5902  33.7886

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
 SL7  N4   N5   aromatic  1.317  0.020  1.317
 SL7  N4   C13  aromatic  1.340  0.020  1.340
 SL7  N5   C14  aromatic  1.345  0.020  1.345
 SL7  C13  C16  aromatic  1.413  0.020  1.413
 SL7  C13  C12  aromatic  1.420  0.020  1.420
 SL7  C16  C17  aromatic  1.362  0.020  1.362
 SL7  O2   C15  deloc     1.247  0.020  1.247
 SL7  C14  C12  aromatic  1.397  0.020  1.397
 SL7  C14  C15  single    1.500  0.020  1.500
 SL7  C12  C11  aromatic  1.413  0.020  1.413
 SL7  C15  O1   deloc     1.244  0.020  1.244
 SL7  C17  C10  aromatic  1.435  0.020  1.435
 SL7  C11  C10  aromatic  1.377  0.020  1.377
 SL7  C10  N3   single    1.383  0.020  1.383
 SL7  N3   C9   single    1.437  0.020  1.437
 SL7  C7   C6   aromatic  1.395  0.020  1.395
 SL7  C7   C8   aromatic  1.382  0.020  1.382
 SL7  C6   C5   aromatic  1.376  0.020  1.376
 SL7  C9   C8   single    1.514  0.020  1.514
 SL7  C8   C18  aromatic  1.402  0.020  1.402
 SL7  C5   C4   aromatic  1.400  0.020  1.400
 SL7  C18  C4   aromatic  1.408  0.020  1.408
 SL7  C18  O3   single    1.334  0.020  1.334
 SL7  C4   C3   single    1.444  0.020  1.444
 SL7  C3   O    aromatic  1.316  0.020  1.316
 SL7  C3   N2   aromatic  1.300  0.020  1.300
 SL7  O    N1   aromatic  1.389  0.020  1.389
 SL7  N2   C2   aromatic  1.367  0.020  1.367
 SL7  N1   C2   aromatic  1.312  0.020  1.312
 SL7  C2   N    single    1.345  0.020  1.345
 SL7  C1   N    single    1.448  0.020  1.448
 SL7  N    C    single    1.447  0.020  1.447
 SL7  C1   H1   single    0.970  0.020  1.090
 SL7  C1   H2   single    0.970  0.020  1.090
 SL7  C1   H3   single    0.970  0.020  1.090
 SL7  C7   H4   single    0.930  0.020  1.080
 SL7  C9   H5   single    0.970  0.020  1.090
 SL7  C9   H6   single    0.970  0.020  1.090
 SL7  C11  H7   single    0.930  0.020  1.080
 SL7  C16  H8   single    0.930  0.020  1.080
 SL7  N5   H10  single    0.860  0.020  1.020
 SL7  C17  H11  single    0.930  0.020  1.080
 SL7  N3   H12  single    0.890  0.020  1.040
 SL7  C6   H13  single    0.930  0.020  1.080
 SL7  C5   H14  single    0.930  0.020  1.080
 SL7  O3   H15  single    0.850  0.020  0.980
 SL7  C    H16  single    0.970  0.020  1.090
 SL7  C    H17  single    0.970  0.020  1.090
 SL7  C    H18  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
 SL7  H3   C1   H2   108.58  3.000
 SL7  H3   C1   H1   108.30  3.000
 SL7  H2   C1   H1   107.92  3.000
 SL7  H3   C1   N    112.56  3.000
 SL7  H2   C1   N    110.67  3.000
 SL7  H1   C1   N    108.70  3.000
 SL7  N    C2   N2   122.93  3.000
 SL7  N    C2   N1   123.81  3.000
 SL7  N2   C2   N1   113.24  3.000
 SL7  N2   C3   O    112.57  3.000
 SL7  N2   C3   C4   126.06  3.000
 SL7  O    C3   C4   121.36  3.000
 SL7  H4   C7   C6   119.57  3.000
 SL7  H4   C7   C8   118.55  3.000
 SL7  C6   C7   C8   121.88  3.000
 SL7  C18  C8   C9   119.20  3.000
 SL7  C18  C8   C7   118.74  3.000
 SL7  C9   C8   C7   122.05  3.000
 SL7  H6   C9   H5   105.78  3.000
 SL7  H6   C9   N3   107.68  3.000
 SL7  H5   C9   N3   111.17  3.000
 SL7  H6   C9   C8   108.96  3.000
 SL7  H5   C9   C8   109.45  3.000
 SL7  N3   C9   C8   113.48  3.000
 SL7  N3   C10  C17  117.05  3.000
 SL7  N3   C10  C11  122.97  3.000
 SL7  C17  C10  C11  119.96  3.000
 SL7  H7   C11  C12  119.63  3.000
 SL7  H7   C11  C10  121.97  3.000
 SL7  C12  C11  C10  118.40  3.000
 SL7  C14  C12  C13  104.15  3.000
 SL7  C14  C12  C11  134.83  3.000
 SL7  C13  C12  C11  121.01  3.000
 SL7  N4   C13  C16  128.46  3.000
 SL7  C16  C13  C12  119.98  3.000
 SL7  N4   C13  C12  111.56  3.000
 SL7  N5   C14  C15  121.80  3.000
 SL7  C15  C14  C12  133.45  3.000
 SL7  N5   C14  C12  104.75  3.000
 SL7  O1   C15  O2   128.37  3.000
 SL7  O1   C15  C14  115.94  3.000
 SL7  O2   C15  C14  115.69  3.000
 SL7  H8   C16  C17  120.80  3.000
 SL7  H8   C16  C13  121.04  3.000
 SL7  C17  C16  C13  118.16  3.000
 SL7  H10  N5   N4   120.08  3.000
 SL7  H10  N5   C14  124.00  3.000
 SL7  N4   N5   C14  115.92  3.000
 SL7  N5   N4   C13  103.61  3.000
 SL7  H11  C17  C16  119.38  3.000
 SL7  H11  C17  C10  118.13  3.000
 SL7  C16  C17  C10  122.49  3.000
 SL7  H12  N3   C10  114.99  3.000
 SL7  H12  N3   C9   114.62  3.000
 SL7  C10  N3   C9   120.97  3.000
 SL7  H13  C6   C5   120.24  3.000
 SL7  H13  C6   C7   120.17  3.000
 SL7  C5   C6   C7   119.58  3.000
 SL7  H14  C5   C4   119.97  3.000
 SL7  H14  C5   C6   119.98  3.000
 SL7  C4   C5   C6   120.05  3.000
 SL7  C4   C18  O3   122.95  3.000
 SL7  O3   C18  C8   117.30  3.000
 SL7  C4   C18  C8   119.74  3.000
 SL7  H15  O3   C18  110.26  3.000
 SL7  C18  C4   C5   120.00  3.000
 SL7  C18  C4   C3   118.86  3.000
 SL7  C5   C4   C3   121.14  3.000
 SL7  N1   O    C3   107.59  3.000
 SL7  O    N1   C2   103.37  3.000
 SL7  C3   N2   C2   103.21  3.000
 SL7  C    N    C2   117.86  3.000
 SL7  C    N    C1   117.58  3.000
 SL7  C2   N    C1   119.69  3.000
 SL7  H18  C    H17  108.42  3.000
 SL7  H18  C    H16  108.03  3.000
 SL7  H17  C    H16  108.44  3.000
 SL7  H18  C    N    110.49  3.000
 SL7  H17  C    N    112.49  3.000
 SL7  H16  C    N    108.85  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
 SL7  CONST_01  C4   C3   N2   C2    180.00   0.0  0
 SL7  CONST_02  O    C3   N2   C2      0.00   0.0  0
 SL7  CONST_03  C3   O    N1   C2      0.00   0.0  0
 SL7  CONST_04  C6   C5   C4   C3    180.00   0.0  0
 SL7  CONST_05  C8   C18  C4   C3    180.00   0.0  0
 SL7  CONST_06  N1   C2   N2   C3      0.00   0.0  0
 SL7  CONST_07  C4   C5   C6   C7      0.00   0.0  0
 SL7  CONST_08  C4   C18  C8   C7      0.00   0.0  0
 SL7  CONST_09  C5   C6   C7   C8      0.00   0.0  0
 SL7  CONST_10  C5   C4   C18  C8      0.00   0.0  0
 SL7  CONST_11  C13  C16  C17  C10     0.00   0.0  0
 SL7  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 SL7  CONST_13  C14  C12  C11  C10   180.00   0.0  0
 SL7  CONST_14  N4   C13  C12  C11   180.00   0.0  0
 SL7  CONST_15  C16  C13  C12  C11     0.00   0.0  0
 SL7  CONST_16  N5   C14  C12  C11   180.00   0.0  0
 SL7  CONST_17  C16  C17  C10  C11     0.00   0.0  0
 SL7  CONST_18  N5   N4   C13  C12     0.00   0.0  0
 SL7  CONST_19  C17  C16  C13  C12     0.00   0.0  0
 SL7  CONST_20  N4   N5   C14  C12     0.00   0.0  0
 SL7  CONST_21  C17  C10  C11  C12     0.00   0.0  0
 SL7  CONST_22  C14  N5   N4   C13     0.00   0.0  0
 SL7  CONST_23  N5   C14  C12  C13     0.00   0.0  0
 SL7  CONST_24  N4   C13  C12  C14     0.00   0.0  0
 SL7  CONST_25  C16  C13  C12  C14   180.00   0.0  0
 SL7  CONST_26  N5   N4   C13  C16   180.00   0.0  0
 SL7  CONST_27  C17  C16  C13  N4    180.00   0.0  0
 SL7  CONST_28  C18  C8   C7   C6      0.00   0.0  0
 SL7  CONST_29  C18  C4   C5   C6      0.00   0.0  0
 SL7  CONST_30  O    C3   C4   C5      0.00   0.0  0
 SL7  CONST_31  N2   C3   C4   C5    180.00   0.0  0
 SL7  CONST_32  O    C3   C4   C18   180.00   0.0  0
 SL7  CONST_33  N2   C3   C4   C18     0.00   0.0  0
 SL7  CONST_34  N1   O    C3   C4    180.00   0.0  0
 SL7  CONST_35  N2   C2   N1   O       0.00   0.0  0
 SL7  CONST_36  N2   C3   O    N1      0.00   0.0  0
 SL7  CONST_37  O3   C18  C4   C3      0.00   0.0  0
 SL7  CONST_38  N    C2   N2   C3    180.00   0.0  0
 SL7  CONST_39  O3   C18  C8   C7    180.00   0.0  0
 SL7  CONST_40  C6   C7   C8   C9    180.00   0.0  0
 SL7  CONST_41  C4   C18  C8   C9    180.00   0.0  0
 SL7  CONST_42  C15  C14  C12  C11     0.00   0.0  0
 SL7  CONST_43  N3   C10  C11  C12   180.00   0.0  0
 SL7  CONST_44  C15  C14  C12  C13   180.00   0.0  0
 SL7  CONST_45  N4   N5   C14  C15   180.00   0.0  0
 SL7  CONST_46  N3   C10  C17  C16   180.00   0.0  0
 SL7  CONST_47  O3   C18  C4   C5    180.00   0.0  0
 SL7  CONST_48  N    C2   N1   O     180.00   0.0  0
 SL7  CONST_49  H14  C5   C4   C3      0.00   0.0  0
 SL7  CONST_50  H13  C6   C7   C8    180.00   0.0  0
 SL7  CONST_51  H8   C16  C17  C10   180.00   0.0  0
 SL7  CONST_52  H11  C17  C10  C11   180.00   0.0  0
 SL7  CONST_53  H10  N5   C14  C12   180.00   0.0  0
 SL7  CONST_54  H7   C11  C12  C13   180.00   0.0  0
 SL7  CONST_55  H4   C7   C6   C5    180.00   0.0  0
 SL7  CONST_58  C17  C10  N3   C9    180.00   0.0  0
 SL7  CONST_60  C    N    C2   N1      0.00   0.0  0
 SL7  CONST_61  C    N    C2   N2    180.00   0.0  0
 SL7  Var_01    N3   C9   C8   C7    -10.98  30.0  2
 SL7  Var_02    C10  N3   C9   C8    -82.91  30.0  1
 SL7  Var_03    O2   C15  C14  C12  -178.43  30.0  2
 SL7  Var_04    H1   C1   N    C2   -159.23  30.0  3
 SL7  Var_05    H16  C    N    C2    165.96  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
 SL7  plan-1  C2   0.020
 SL7  plan-1  C3   0.020
 SL7  plan-1  C4   0.020
 SL7  plan-1  O    0.020
 SL7  plan-1  N1   0.020
 SL7  plan-1  N2   0.020
 SL7  plan-1  N    0.020
 SL7  plan-2  C3   0.020
 SL7  plan-2  C7   0.020
 SL7  plan-2  C8   0.020
 SL7  plan-2  C9   0.020
 SL7  plan-2  C6   0.020
 SL7  plan-2  C5   0.020
 SL7  plan-2  C18  0.020
 SL7  plan-2  O3   0.020
 SL7  plan-2  C4   0.020
 SL7  plan-2  H4   0.020
 SL7  plan-2  H13  0.020
 SL7  plan-2  H14  0.020
 SL7  plan-3  C10  0.020
 SL7  plan-3  C11  0.020
 SL7  plan-3  C12  0.020
 SL7  plan-3  C13  0.020
 SL7  plan-3  C14  0.020
 SL7  plan-3  C15  0.020
 SL7  plan-3  C16  0.020
 SL7  plan-3  N5   0.020
 SL7  plan-3  N4   0.020
 SL7  plan-3  C17  0.020
 SL7  plan-3  N3   0.020
 SL7  plan-3  H7   0.020
 SL7  plan-3  H8   0.020
 SL7  plan-3  H10  0.020
 SL7  plan-3  H11  0.020
 SL7  plan-4  C9   0.020
 SL7  plan-4  C10  0.020
 SL7  plan-4  N3   0.020
 SL7  plan-4  H12  0.020
 SL7  plan-5  C1   0.020
 SL7  plan-5  C2   0.020
 SL7  plan-5  N    0.020
 SL7  plan-5  C    0.020
 SL7  plan-6  C14  0.020
 SL7  plan-6  C15  0.020
 SL7  plan-6  O2   0.020
 SL7  plan-6  O1   0.020

