# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 09:11:23 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-(6-chloro-5-phenyl-1H-indazol-3-yl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)Nc1n[nH]c2cc(Cl)c(cc12)c3ccccc3
#
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
 A07  A07  N-(6-chloro-5-phenyl-1H-indazol-3-yl)butanamide  ligand  38  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A07
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
 A07  C1    C   CR6   0   0.056  -2.7433   1.0200   0.0268
 A07  C2    C   CR16  0  -0.281  -3.6872   1.1446  -0.9924
 A07  C3    C   CR16  0  -0.243  -4.5411   2.2364  -1.0318
 A07  C4    C   CR16  0  -0.264  -4.4659   3.2193  -0.0520
 A07  C5    C   CR16  0  -0.242  -3.5285   3.1046   0.9648
 A07  C6    C   CR16  0  -0.292  -2.6722   2.0117   1.0029
 A07  C12   C   CR6   0  -0.122  -2.2209  -1.4620   0.1606
 A07  C13   C   CR16  0  -0.238  -1.3616  -2.5347   0.1733
 A07  C14   C   CR56  0   0.427   0.0012  -2.2435   0.0736
 A07  C15   C   CR56  0  -0.110   0.4683  -0.9249  -0.0212
 A07  C16   C   CR16  0  -0.370  -0.4359   0.1382  -0.0303
 A07  C17   C   CR6   0   0.131  -1.7919  -0.1144   0.0510
 A07  N20   N   NR15  0  -0.562   1.0927  -3.0313   0.0564
 A07  N21   N   N     0  -0.250   2.2334  -2.3280  -0.0486
 A07  C22   C   CR5   0   0.452   1.8871  -1.0689  -0.0932
 A07  N23   N   NH1   0  -0.736   2.7699  -0.0102  -0.2042
 A07  C24   C   C     0   0.544   4.1230  -0.0358  -0.0193
 A07  C25   C   CH2   0  -0.596   4.7780   1.3155  -0.2033
 A07  C26   C   CH2   0  -0.419   6.2758   1.3131   0.0556
 A07  C29   C   CH3   0  -0.665   6.8825   2.6924  -0.1613
 A07  O35   O   O     0  -0.450   4.7315  -1.0472   0.2617
 A07  H2    H   HCR6  0   0.254  -3.7457   0.3922  -1.7687
 A07  H3    H   HCR6  0   0.258  -5.2636   2.3231  -1.8328
 A07  H4    H   HCR6  0   0.258  -5.1329   4.0709  -0.0836
 A07  H5    H   HCR6  0   0.258  -3.4622   3.8646   1.7323
 A07  H6    H   HCR6  0   0.254  -1.9470   1.9240   1.8025
 A07  H13   H   HCR6  0   0.296  -1.7233  -3.5494   0.2671
 A07  H16   H   HCR6  0   0.262  -0.0949   1.1628  -0.1153
 A07  HN23  H   HNH1  0   0.422   2.3541   0.8844  -0.4136
 A07  H25   H   HCH2  0   0.272   4.5726   1.6600  -1.2226
 A07  H25A  H   HCH2  0   0.269   4.2821   2.0382   0.4533
 A07  H26   H   HCH2  0   0.226   6.4727   0.9814   1.0773
 A07  H26A  H   HCH2  0   0.227   6.7629   0.5911  -0.6028
 A07  H29   H   HCH3  0   0.233   7.9545   2.6859   0.0361
 A07  H29A  H   HCH3  0   0.220   6.7378   3.0330  -1.1883
 A07  H29B  H   HCH3  0   0.220   6.4297   3.4349   0.4982
 A07  HN20  H   HNR5  0   0.421   1.1362  -4.0352   0.1113
 A07  CL1   CL  CL    0  -0.116  -3.9135  -1.7946   0.3352

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
 A07  C17  C1    single    1.481  0.020  1.481
 A07  C1   C2    aromatic  1.395  0.020  1.395
 A07  C1   C6    aromatic  1.393  0.020  1.393
 A07  CL1  C12   single    1.734  0.020  1.734
 A07  C2   C3    aromatic  1.387  0.020  1.387
 A07  C2   H2    single    0.930  0.020  1.080
 A07  C3   C4    aromatic  1.390  0.020  1.390
 A07  C3   H3    single    0.930  0.020  1.080
 A07  C5   C4    aromatic  1.388  0.020  1.388
 A07  C4   H4    single    0.930  0.020  1.080
 A07  C6   C5    aromatic  1.389  0.020  1.389
 A07  C5   H5    single    0.930  0.020  1.080
 A07  C6   H6    single    0.930  0.020  1.080
 A07  C13  C12   aromatic  1.375  0.020  1.375
 A07  C12  C17   aromatic  1.418  0.020  1.418
 A07  C13  C14   aromatic  1.397  0.020  1.397
 A07  C13  H13   single    0.930  0.020  1.080
 A07  N20  C14   aromatic  1.346  0.020  1.346
 A07  C14  C15   aromatic  1.402  0.020  1.402
 A07  C22  C15   aromatic  1.428  0.020  1.428
 A07  C15  C16   aromatic  1.396  0.020  1.396
 A07  C17  C16   aromatic  1.382  0.020  1.382
 A07  C16  H16   single    0.930  0.020  1.080
 A07  N20  N21   aromatic  1.344  0.020  1.344
 A07  N21  C22   aromatic  1.307  0.020  1.307
 A07  C22  N23   single    1.383  0.020  1.383
 A07  N23  C24   single    1.366  0.020  1.366
 A07  N23  HN23  single    0.860  0.020  1.020
 A07  C24  O35   double    1.213  0.020  1.213
 A07  C24  C25   single    1.513  0.020  1.513
 A07  C26  C25   single    1.520  0.020  1.520
 A07  C25  H25   single    0.970  0.020  1.090
 A07  C25  H25A  single    0.970  0.020  1.090
 A07  C26  C29   single    1.522  0.020  1.522
 A07  C26  H26   single    0.970  0.020  1.090
 A07  C26  H26A  single    0.970  0.020  1.090
 A07  C29  H29   single    0.970  0.020  1.090
 A07  C29  H29A  single    0.970  0.020  1.090
 A07  C29  H29B  single    0.970  0.020  1.090
 A07  N20  HN20  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
 A07  C17   C1   C6    120.07  3.000
 A07  C6    C1   C2    118.88  3.000
 A07  C17   C1   C2    121.01  3.000
 A07  H2    C2   C3    119.58  3.000
 A07  H2    C2   C1    119.90  3.000
 A07  C3    C2   C1    120.52  3.000
 A07  H3    C3   C4    120.08  3.000
 A07  H3    C3   C2    119.68  3.000
 A07  C4    C3   C2    120.23  3.000
 A07  H4    C4   C5    120.18  3.000
 A07  H4    C4   C3    120.17  3.000
 A07  C5    C4   C3    119.65  3.000
 A07  H5    C5   C6    119.69  3.000
 A07  H5    C5   C4    120.20  3.000
 A07  C6    C5   C4    120.11  3.000
 A07  H6    C6   C5    119.79  3.000
 A07  H6    C6   C1    119.59  3.000
 A07  C5    C6   C1    120.62  3.000
 A07  C17   C12  C13   123.58  3.000
 A07  C17   C12  CL1   119.03  3.000
 A07  C13   C12  CL1   117.36  3.000
 A07  H13   C13  C14   121.87  3.000
 A07  H13   C13  C12   121.60  3.000
 A07  C14   C13  C12   116.52  3.000
 A07  N20   C14  C15   106.22  3.000
 A07  C15   C14  C13   121.72  3.000
 A07  N20   C14  C13   132.05  3.000
 A07  C22   C15  C16   136.07  3.000
 A07  C16   C15  C14   120.07  3.000
 A07  C22   C15  C14   103.86  3.000
 A07  H16   C16  C17   119.11  3.000
 A07  H16   C16  C15   121.14  3.000
 A07  C17   C16  C15   119.74  3.000
 A07  C16   C17  C12   118.37  3.000
 A07  C16   C17  C1    119.31  3.000
 A07  C12   C17  C1    122.33  3.000
 A07  HN20  N20  N21   119.32  3.000
 A07  HN20  N20  C14   128.18  3.000
 A07  N21   N20  C14   112.51  3.000
 A07  C22   N21  N20   106.38  3.000
 A07  N23   C22  N21   124.84  3.000
 A07  N23   C22  C15   124.13  3.000
 A07  N21   C22  C15   111.03  3.000
 A07  HN23  N23  C24   116.94  3.000
 A07  HN23  N23  C22   115.63  3.000
 A07  C24   N23  C22   127.39  3.000
 A07  O35   C24  C25   123.75  3.000
 A07  C25   C24  N23   113.31  3.000
 A07  O35   C24  N23   122.94  3.000
 A07  H25A  C25  H25   105.40  3.000
 A07  H25A  C25  C26   110.19  3.000
 A07  H25   C25  C26   110.11  3.000
 A07  H25A  C25  C24   108.69  3.000
 A07  H25   C25  C24   108.23  3.000
 A07  C26   C25  C24   113.86  3.000
 A07  H26A  C26  H26   106.43  3.000
 A07  H26A  C26  C29   109.60  3.000
 A07  H26   C26  C29   109.67  3.000
 A07  H26A  C26  C25   109.75  3.000
 A07  H26   C26  C25   109.72  3.000
 A07  C29   C26  C25   111.53  3.000
 A07  H29B  C29  H29A  107.53  3.000
 A07  H29B  C29  H29   107.61  3.000
 A07  H29A  C29  H29   107.62  3.000
 A07  H29B  C29  C26   111.40  3.000
 A07  H29A  C29  C26   111.34  3.000
 A07  H29   C29  C26   111.15  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
 A07  CONST_01  C13   C12  C17  C1   180.00   0.0  0
 A07  CONST_02  C15   C16  C17  C1   180.00   0.0  0
 A07  CONST_03  C4    C3   C2   C1     0.00   0.0  0
 A07  CONST_04  C4    C5   C6   C1     0.00   0.0  0
 A07  CONST_07  C5    C6   C1   C2     0.00   0.0  0
 A07  CONST_08  C5    C4   C3   C2     0.00   0.0  0
 A07  CONST_09  C17   C1   C2   C3   180.00   0.0  0
 A07  CONST_10  C6    C1   C2   C3     0.00   0.0  0
 A07  CONST_11  C6    C5   C4   C3     0.00   0.0  0
 A07  CONST_12  C17   C1   C6   C5   180.00   0.0  0
 A07  CONST_15  N20   C14  C13  C12  180.00   0.0  0
 A07  CONST_16  C15   C14  C13  C12    0.00   0.0  0
 A07  CONST_17  C15   C16  C17  C12    0.00   0.0  0
 A07  CONST_18  C16   C17  C12  C13    0.00   0.0  0
 A07  CONST_19  N21   N20  C14  C13  180.00   0.0  0
 A07  CONST_20  C22   C15  C14  C13  180.00   0.0  0
 A07  CONST_21  C16   C15  C14  C13    0.00   0.0  0
 A07  CONST_22  C17   C12  C13  C14    0.00   0.0  0
 A07  CONST_23  C22   N21  N20  C14    0.00   0.0  0
 A07  CONST_24  N21   C22  C15  C14    0.00   0.0  0
 A07  CONST_25  C17   C16  C15  C14    0.00   0.0  0
 A07  CONST_26  N21   N20  C14  C15    0.00   0.0  0
 A07  CONST_27  N20   N21  C22  C15    0.00   0.0  0
 A07  CONST_28  N20   C14  C15  C16  180.00   0.0  0
 A07  CONST_29  N21   C22  C15  C16  180.00   0.0  0
 A07  CONST_30  C22   C15  C16  C17  180.00   0.0  0
 A07  CONST_31  C22   C15  C14  N20    0.00   0.0  0
 A07  CONST_32  CL1   C12  C17  C1     0.00   0.0  0
 A07  CONST_33  C14   C13  C12  CL1  180.00   0.0  0
 A07  CONST_34  C16   C17  C12  CL1  180.00   0.0  0
 A07  CONST_35  N23   C22  C15  C14  180.00   0.0  0
 A07  CONST_36  N23   C22  C15  C16    0.00   0.0  0
 A07  CONST_37  N23   C22  N21  N20  180.00   0.0  0
 A07  CONST_38  H16   C16  C17  C1     0.00   0.0  0
 A07  CONST_39  H3    C3   C2   C1   180.00   0.0  0
 A07  CONST_40  H5    C5   C6   C1   180.00   0.0  0
 A07  CONST_41  H6    C6   C1   C2   180.00   0.0  0
 A07  CONST_42  H4    C4   C3   C2   180.00   0.0  0
 A07  CONST_43  H2    C2   C3   C4   180.00   0.0  0
 A07  CONST_44  HN20  N20  C14  C13    0.00   0.0  0
 A07  CONST_45  H13   C13  C14  C15  180.00   0.0  0
 A07  CONST_46  C24   N23  C22  C15  180.00   0.0  0
 A07  CONST_47  C24   N23  C22  N21    0.00   0.0  0
 A07  CONST_48  HN23  N23  C22  C15    0.00   0.0  0
 A07  CONST_49  O35   C24  N23  C22    0.00   0.0  0
 A07  CONST_50  C25   C24  N23  C22  180.00   0.0  0
 A07  Var_01    C26   C25  C24  N23  177.61  30.0  3
 A07  Var_02    C29   C26  C25  C24  179.28  30.0  1
 A07  Var_03    H29   C29  C26  C25  179.40  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
 A07  plan-1  C1    0.020
 A07  plan-1  C2    0.020
 A07  plan-1  C3    0.020
 A07  plan-1  C4    0.020
 A07  plan-1  C5    0.020
 A07  plan-1  C6    0.020
 A07  plan-1  C17   0.020
 A07  plan-1  H2    0.020
 A07  plan-1  H3    0.020
 A07  plan-1  H4    0.020
 A07  plan-1  H5    0.020
 A07  plan-1  H6    0.020
 A07  plan-2  C1    0.020
 A07  plan-2  C12   0.020
 A07  plan-2  C13   0.020
 A07  plan-2  C14   0.020
 A07  plan-2  C15   0.020
 A07  plan-2  C16   0.020
 A07  plan-2  C17   0.020
 A07  plan-2  N20   0.020
 A07  plan-2  N21   0.020
 A07  plan-2  C22   0.020
 A07  plan-2  N23   0.020
 A07  plan-2  H13   0.020
 A07  plan-2  H16   0.020
 A07  plan-2  HN20  0.020
 A07  plan-2  CL1   0.020
 A07  plan-3  C22   0.020
 A07  plan-3  N23   0.020
 A07  plan-3  C24   0.020
 A07  plan-3  C25   0.020
 A07  plan-3  O35   0.020
 A07  plan-3  HN23  0.020

