# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 17:55:33 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)c1ccc(NC(=O)c2[nH]c3ccc(Cl)cc3c2)cc1
#
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
 A46  A46  5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide  ligand  38  23  .  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_A46
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
 A46  C4    C   CR6   0   0.364   2.0766  -0.2793  -0.1935
 A46  N1    N   NH1   0  -0.764   0.6767  -0.3526  -0.1925
 A46  C6    C   C     0   0.533  -0.2074   0.6743  -0.2386
 A46  C7    C   CR5   0   0.216  -1.6369   0.3123  -0.1536
 A46  O1    O   O     0  -0.457   0.1155   1.8456  -0.3433
 A46  N2    N   NR15  0  -0.754  -2.1506  -0.9596  -0.0732
 A46  C8    C   CR15  0  -0.390  -2.6675   1.2162  -0.1403
 A46  C11   C   CR56  0   0.357  -3.5066  -0.8917  -0.0073
 A46  C12   C   CR56  0   0.066  -3.8722   0.4710  -0.0458
 A46  C13   C   CR16  0  -0.306  -4.4562  -1.9104   0.0822
 A46  C14   C   CR16  0  -0.299  -5.2267   0.8282   0.0104
 A46  C15   C   CR16  0  -0.234  -5.7823  -1.5432   0.1363
 A46  C16   C   CR6   0  -0.049  -6.1494  -0.1861   0.1007
 A46  CL1   CL  CL    0  -0.139  -7.8421   0.2061   0.1739
 A46  C2    C   CR16  0  -0.331   2.7676  -1.3522   0.3691
 A46  C1    C   CR16  0  -0.292   4.1509  -1.3721   0.3736
 A46  C5    C   CR6   0   0.099   4.8874  -0.3255  -0.1703
 A46  C9    C   CR16  0  -0.309   4.1893   0.7359  -0.7353
 A46  C10   C   CR16  0  -0.287   2.8024   0.7703  -0.7555
 A46  C3    C   CH1   0  -0.076   6.3986  -0.3453  -0.1199
 A46  C17   C   CH2   0  -0.165   6.8762   0.4769   1.0688
 A46  O2    O   OH1   0  -0.657   6.9929   0.0603  -1.3306
 A46  O3    O   OH1   0  -0.666   8.2724   0.3528   1.1846
 A46  HN1   H   HNH1  0   0.412   0.3206  -1.2754  -0.0028
 A46  HN2   H   HNR5  0   0.420  -1.6385  -1.8267  -0.0732
 A46  H8    H   HCR5  0   0.265  -2.5676   2.2883  -0.1888
 A46  H13   H   HCR6  0   0.277  -4.1705  -2.9535   0.1087
 A46  H14   H   HCR6  0   0.276  -5.5309   1.8664  -0.0162
 A46  H15   H   HCR6  0   0.280  -6.5481  -2.3032   0.2056
 A46  H2    H   HCR6  0   0.271   2.2189  -2.1806   0.8014
 A46  H1    H   HCR6  0   0.258   4.6626  -2.2203   0.8127
 A46  H9    H   HCR6  0   0.248   4.7197   1.5683  -1.1823
 A46  H10   H   HCR6  0   0.275   2.3049   1.6075  -1.2171
 A46  H3    H   HCH1  0   0.247   6.7181  -1.3812   0.0362
 A46  H17   H   HCH2  0   0.198   6.5684   1.5243   0.9260
 A46  H17A  H   HCH2  0   0.211   6.3559   0.1178   1.9656
 A46  HO2   H   HOH1  0   0.449   6.9640   1.0205  -1.3957
 A46  HO3   H   HOH1  0   0.457   8.5561   0.8721   1.9424

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
 A46  CL1  C16   single    1.739  0.020  1.739
 A46  C15  C16   aromatic  1.406  0.020  1.406
 A46  C15  C13   aromatic  1.377  0.020  1.377
 A46  C16  C14   aromatic  1.374  0.020  1.374
 A46  C13  C11   aromatic  1.396  0.020  1.396
 A46  C14  C12   aromatic  1.402  0.020  1.402
 A46  C11  C12   aromatic  1.411  0.020  1.411
 A46  C11  N2    aromatic  1.359  0.020  1.359
 A46  C12  C8    aromatic  1.420  0.020  1.420
 A46  N2   C7    aromatic  1.374  0.020  1.374
 A46  C8   C7    aromatic  1.371  0.020  1.371
 A46  C7   C6    single    1.477  0.020  1.477
 A46  C6   O1    double    1.220  0.020  1.220
 A46  C6   N1    single    1.356  0.020  1.356
 A46  N1   C4    single    1.402  0.020  1.402
 A46  C4   C2    aromatic  1.395  0.020  1.395
 A46  C4   C10   aromatic  1.394  0.020  1.394
 A46  C2   C1    aromatic  1.384  0.020  1.384
 A46  C10  C9    aromatic  1.387  0.020  1.387
 A46  C1   C5    aromatic  1.391  0.020  1.391
 A46  C9   C5    aromatic  1.390  0.020  1.390
 A46  C5   C3    single    1.512  0.020  1.512
 A46  O3   C17   single    1.407  0.020  1.407
 A46  C3   C17   single    1.522  0.020  1.522
 A46  C3   O2    single    1.408  0.020  1.408
 A46  N1   HN1   single    0.860  0.020  1.020
 A46  N2   HN2   single    0.860  0.020  1.020
 A46  C8   H8    single    0.930  0.020  1.080
 A46  C13  H13   single    0.930  0.020  1.080
 A46  C14  H14   single    0.930  0.020  1.080
 A46  C15  H15   single    0.930  0.020  1.080
 A46  C2   H2    single    0.930  0.020  1.080
 A46  C1   H1    single    0.930  0.020  1.080
 A46  C9   H9    single    0.930  0.020  1.080
 A46  C10  H10   single    0.930  0.020  1.080
 A46  C3   H3    single    0.970  0.020  1.090
 A46  C17  H17   single    0.970  0.020  1.090
 A46  C17  H17A  single    0.970  0.020  1.090
 A46  O2   HO2   single    0.850  0.020  0.980
 A46  O3   HO3   single    0.850  0.020  0.980

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
 A46  C10   C4   C2   118.93  3.000
 A46  C10   C4   N1   124.02  3.000
 A46  C2    C4   N1   117.02  3.000
 A46  HN1   N1   C6   118.02  3.000
 A46  HN1   N1   C4   113.65  3.000
 A46  C6    N1   C4   127.70  3.000
 A46  O1    C6   C7   119.77  3.000
 A46  O1    C6   N1   123.90  3.000
 A46  C7    C6   N1   116.33  3.000
 A46  C8    C7   N2   109.19  3.000
 A46  C8    C7   C6   124.51  3.000
 A46  N2    C7   C6   126.30  3.000
 A46  HN2   N2   C11  123.39  3.000
 A46  HN2   N2   C7   127.37  3.000
 A46  C11   N2   C7   109.24  3.000
 A46  H8    C8   C12  127.14  3.000
 A46  H8    C8   C7   125.86  3.000
 A46  C12   C8   C7   107.00  3.000
 A46  C13   C11  C12  122.02  3.000
 A46  C12   C11  N2   107.78  3.000
 A46  C13   C11  N2   130.20  3.000
 A46  C14   C12  C11  119.68  3.000
 A46  C11   C12  C8   106.79  3.000
 A46  C14   C12  C8   133.53  3.000
 A46  H13   C13  C15  120.70  3.000
 A46  H13   C13  C11  121.71  3.000
 A46  C15   C13  C11  117.59  3.000
 A46  H14   C14  C16  121.40  3.000
 A46  H14   C14  C12  121.00  3.000
 A46  C16   C14  C12  117.60  3.000
 A46  H15   C15  C16  119.68  3.000
 A46  H15   C15  C13  119.81  3.000
 A46  C16   C15  C13  120.51  3.000
 A46  CL1   C16  C15  118.07  3.000
 A46  C15   C16  C14  122.59  3.000
 A46  CL1   C16  C14  119.33  3.000
 A46  H2    C2   C1   119.60  3.000
 A46  H2    C2   C4   119.88  3.000
 A46  C1    C2   C4   120.52  3.000
 A46  H1    C1   C5   119.84  3.000
 A46  H1    C1   C2   119.00  3.000
 A46  C5    C1   C2   121.16  3.000
 A46  C3    C5   C9   121.69  3.000
 A46  C3    C5   C1   120.42  3.000
 A46  C9    C5   C1   117.88  3.000
 A46  H9    C9   C10  117.66  3.000
 A46  H9    C9   C5   120.55  3.000
 A46  C10   C9   C5   121.78  3.000
 A46  H10   C10  C9   119.14  3.000
 A46  H10   C10  C4   121.14  3.000
 A46  C9    C10  C4   119.72  3.000
 A46  H3    C3   O2   105.77  3.000
 A46  H3    C3   C17  107.94  3.000
 A46  O2    C3   C17  112.54  3.000
 A46  H3    C3   C5   107.98  3.000
 A46  O2    C3   C5   112.91  3.000
 A46  C17   C3   C5   109.42  3.000
 A46  H17A  C17  H17  106.55  3.000
 A46  H17A  C17  O3   112.00  3.000
 A46  H17   C17  O3   111.85  3.000
 A46  H17A  C17  C3   108.22  3.000
 A46  H17   C17  C3   108.96  3.000
 A46  O3    C17  C3   109.15  3.000
 A46  HO2   O2   C3   109.43  3.000
 A46  HO3   O3   C17  108.07  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
 A46  CONST_01  C5   C1   C2   C4     0.00   0.0  0
 A46  CONST_02  C5   C9   C10  C4     0.00   0.0  0
 A46  CONST_03  C13  C11  N2   C7   180.00   0.0  0
 A46  CONST_04  C12  C11  N2   C7     0.00   0.0  0
 A46  CONST_05  C14  C12  C8   C7   180.00   0.0  0
 A46  CONST_06  C11  C12  C8   C7     0.00   0.0  0
 A46  CONST_07  C15  C13  C11  N2   180.00   0.0  0
 A46  CONST_08  C14  C12  C11  N2   180.00   0.0  0
 A46  CONST_09  C8   C12  C11  N2     0.00   0.0  0
 A46  CONST_10  C12  C8   C7   N2     0.00   0.0  0
 A46  CONST_11  C16  C14  C12  C8   180.00   0.0  0
 A46  CONST_12  C13  C11  C12  C8   180.00   0.0  0
 A46  CONST_13  C11  N2   C7   C8     0.00   0.0  0
 A46  CONST_14  C16  C15  C13  C11    0.00   0.0  0
 A46  CONST_15  C16  C14  C12  C11    0.00   0.0  0
 A46  CONST_16  C15  C16  C14  C12    0.00   0.0  0
 A46  CONST_17  C15  C13  C11  C12    0.00   0.0  0
 A46  CONST_18  C14  C16  C15  C13    0.00   0.0  0
 A46  CONST_19  C14  C12  C11  C13    0.00   0.0  0
 A46  CONST_20  C9   C10  C4   C2     0.00   0.0  0
 A46  CONST_21  C9   C5   C1   C2     0.00   0.0  0
 A46  CONST_22  C10  C4   C2   C1     0.00   0.0  0
 A46  CONST_23  C10  C9   C5   C1     0.00   0.0  0
 A46  CONST_24  C1   C2   C4   N1   180.00   0.0  0
 A46  CONST_25  C9   C10  C4   N1   180.00   0.0  0
 A46  CONST_26  C11  N2   C7   C6   180.00   0.0  0
 A46  CONST_27  C12  C8   C7   C6   180.00   0.0  0
 A46  CONST_28  CL1  C16  C14  C12  180.00   0.0  0
 A46  CONST_29  CL1  C16  C15  C13  180.00   0.0  0
 A46  CONST_30  C3   C5   C1   C2   180.00   0.0  0
 A46  CONST_31  C3   C5   C9   C10  180.00   0.0  0
 A46  CONST_32  H1   C1   C2   C4   180.00   0.0  0
 A46  CONST_33  H9   C9   C10  C4   180.00   0.0  0
 A46  CONST_34  H13  C13  C11  N2     0.00   0.0  0
 A46  CONST_35  H8   C8   C7   N2   180.00   0.0  0
 A46  CONST_36  H14  C14  C12  C8     0.00   0.0  0
 A46  CONST_37  HN2  N2   C7   C8   180.00   0.0  0
 A46  CONST_38  H15  C15  C13  C11  180.00   0.0  0
 A46  CONST_39  H10  C10  C4   C2   180.00   0.0  0
 A46  CONST_40  H2   C2   C1   C5   180.00   0.0  0
 A46  CONST_41  C7   C6   N1   C4   180.00   0.0  0
 A46  CONST_45  O1   C6   N1   C4     0.00   0.0  0
 A46  Var_01    N2   C7   C6   N1    -2.07  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 A46  chir_01  C3  C5  C17  O2  positiv

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
 A46  plan-1  C4   0.020
 A46  plan-1  N1   0.020
 A46  plan-1  C2   0.020
 A46  plan-1  C1   0.020
 A46  plan-1  C5   0.020
 A46  plan-1  C9   0.020
 A46  plan-1  C10  0.020
 A46  plan-1  C3   0.020
 A46  plan-1  H2   0.020
 A46  plan-1  H1   0.020
 A46  plan-1  H9   0.020
 A46  plan-1  H10  0.020
 A46  plan-2  C6   0.020
 A46  plan-2  C7   0.020
 A46  plan-2  N2   0.020
 A46  plan-2  C8   0.020
 A46  plan-2  C11  0.020
 A46  plan-2  C12  0.020
 A46  plan-2  C13  0.020
 A46  plan-2  C14  0.020
 A46  plan-2  C15  0.020
 A46  plan-2  C16  0.020
 A46  plan-2  CL1  0.020
 A46  plan-2  HN2  0.020
 A46  plan-2  H8   0.020
 A46  plan-2  H13  0.020
 A46  plan-2  H14  0.020
 A46  plan-2  H15  0.020
 A46  plan-3  C4   0.020
 A46  plan-3  N1   0.020
 A46  plan-3  C6   0.020
 A46  plan-3  C7   0.020
 A46  plan-3  O1   0.020
 A46  plan-3  HN1  0.020

