# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:59:46 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 2-{1-[(4-chlorophenyl)carbonyl]-5-methoxy-2-methyl-1H-indol-3-yl}-N-[(1R)-1-(hydroxymethyl)propyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](CO)NC(=O)Cc1c(C)n(C(=O)c2ccc(Cl)cc2)c3ccc(OC)cc13
#
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
 IM8  IM8  2-{1-[(4-chlorophenyl)carbonyl]-5-methoxy-2-methyl-1H-indol-3-yl}-N-[(1R)-1-(hydroxymethyl)propyl]acetamide  ligand  55  30  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_IM8
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
 IM8  C2    C   CR16  0  -0.483   1.7566  -1.6307  -0.3841
 IM8  C3    C   CR6   0   0.393   1.6400  -2.9791  -0.0693
 IM8  C4    C   CR16  0  -0.396   0.4560  -3.4712   0.4948
 IM8  C5    C   CR16  0  -0.275  -0.6125  -2.6271   0.7720
 IM8  C6    C   CH3   0  -0.435   2.6825  -5.1168  -0.0053
 IM8  C7    C   CR5   0   0.007   0.5250   0.6354  -0.2737
 IM8  C8    C   CR5   0   0.277  -0.7125   0.9656   0.1763
 IM8  C     C   CR56  0   0.330  -0.4797  -1.2794   0.4795
 IM8  C1    C   CR56  0   0.102   0.6930  -0.7829  -0.1039
 IM8  C10   C   CR6   0  -0.064  -3.6912   0.5853   0.6298
 IM8  C11   C   CR16  0  -0.260  -4.6483   1.0874   1.5068
 IM8  C12   C   CR16  0  -0.202  -5.6894   1.8675   1.0349
 IM8  C13   C   CR6   0  -0.035  -5.7862   2.1093  -0.3283
 IM8  C14   C   CR16  0  -0.196  -4.8608   1.5909  -1.2216
 IM8  C15   C   CR16  0  -0.265  -3.8076   0.8348  -0.7344
 IM8  C16   C   CH3   0  -0.735  -1.2707   2.3346   0.3555
 IM8  C17   C   CH2   0  -0.703   1.5812   1.5420  -0.8077
 IM8  C18   C   C     0   0.546   2.8186   1.5033   0.0770
 IM8  N     N   NR5   0  -0.671  -1.3643  -0.2027   0.6122
 IM8  O     O   O2    0  -0.482   2.7225  -3.7441  -0.3368
 IM8  O1    O   O     0  -0.407  -2.8950  -1.1744   1.9677
 IM8  O2    O   O     0  -0.486   2.7446   1.7154   1.2784
 IM8  O3    O   OH1   0  -0.670   5.2421  -1.3502  -0.4836
 IM8  CL    CL  CL    0  -0.110  -7.0908   3.0726  -0.9255
 IM8  N2    N   NH1   0  -0.623   3.9653   1.2172  -0.5581
 IM8  C19   C   CH1   0  -0.105   5.2262   0.9709   0.1167
 IM8  C20   C   CH2   0  -0.159   5.2994  -0.4678   0.6156
 IM8  C21   C   CH2   0  -0.442   6.3882   1.3402  -0.8010
 IM8  C22   C   CH3   0  -0.659   6.4157   2.8166  -1.1695
 IM8  H2    H   HCR6  0   0.248   2.6739  -1.2627  -0.8257
 IM8  H4    H   HCR6  0   0.280   0.3479  -4.5195   0.7364
 IM8  H5    H   HCR6  0   0.275  -1.5046  -3.0395   1.2169
 IM8  H61   H   HCH3  0   0.259   3.6499  -5.5296  -0.2806
 IM8  H62   H   HCH3  0   0.227   2.5253  -5.2747   1.0649
 IM8  H63   H   HCH3  0   0.227   1.9046  -5.6498  -0.5582
 IM8  H11   H   HCR6  0   0.279  -4.5745   0.8877   2.5676
 IM8  H12   H   HCR6  0   0.289  -6.4195   2.2762   1.7196
 IM8  H14   H   HCR6  0   0.291  -4.9555   1.7745  -2.2828
 IM8  H15   H   HCR6  0   0.289  -3.0845   0.4312  -1.4320
 IM8  H161  H   HCH3  0   0.266  -1.9830   2.6163  -0.4188
 IM8  H162  H   HCH3  0   0.263  -1.7710   2.4439   1.3176
 IM8  H163  H   HCH3  0   0.271  -0.4577   3.0567   0.3307
 IM8  H171  H   HCH2  0   0.290   1.2276   2.5743  -0.8452
 IM8  H172  H   HCH2  0   0.275   1.8244   1.2640  -1.8370
 IM8  HO3   H   HOH1  0   0.452   4.9217  -2.2034  -0.1785
 IM8  HN2   H   HNH1  0   0.398   3.9184   0.9912  -1.5391
 IM8  H19   H   HCH1  0   0.250   5.2632   1.6158   0.9983
 IM8  H201  H   HCH2  0   0.206   6.2309  -0.5919   1.1846
 IM8  H202  H   HCH2  0   0.218   4.4728  -0.6411   1.3134
 IM8  H211  H   HCH2  0   0.230   6.3557   0.7275  -1.7063
 IM8  H212  H   HCH2  0   0.234   7.3159   1.0746  -0.2882
 IM8  H221  H   HCH3  0   0.232   7.2926   3.0495  -1.7737
 IM8  H222  H   HCH3  0   0.222   5.5358   3.1092  -1.7431
 IM8  H223  H   HCH3  0   0.220   6.4515   3.4426  -0.2762
 IM8  C9    C   C     0   0.518  -2.6369  -0.3184   1.1512

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
 IM8  C2   C3    aromatic  1.390  0.020  1.390
 IM8  C2   C1    aromatic  1.389  0.020  1.389
 IM8  C2   H2    single    0.930  0.020  1.080
 IM8  C3   C4    aromatic  1.401  0.020  1.401
 IM8  C3   O     single    1.352  0.020  1.352
 IM8  C4   C5    aromatic  1.390  0.020  1.390
 IM8  C4   H4    single    0.930  0.020  1.080
 IM8  C5   C     aromatic  1.385  0.020  1.385
 IM8  C5   H5    single    0.930  0.020  1.080
 IM8  C6   O     single    1.413  0.020  1.413
 IM8  C6   H61   single    0.970  0.020  1.090
 IM8  C6   H62   single    0.970  0.020  1.090
 IM8  C6   H63   single    0.970  0.020  1.090
 IM8  C7   C8    aromatic  1.358  0.020  1.358
 IM8  C7   C1    aromatic  1.438  0.020  1.438
 IM8  C7   C17   single    1.491  0.020  1.491
 IM8  C8   C16   single    1.489  0.020  1.489
 IM8  C8   N     aromatic  1.407  0.020  1.407
 IM8  C9   C10   single    1.483  0.020  1.483
 IM8  C9   N     single    1.387  0.020  1.387
 IM8  C9   O1    double    1.211  0.020  1.211
 IM8  C    C1    aromatic  1.401  0.020  1.401
 IM8  C    N     aromatic  1.400  0.020  1.400
 IM8  C10  C11   aromatic  1.392  0.020  1.392
 IM8  C10  C15   aromatic  1.392  0.020  1.392
 IM8  C11  C12   aromatic  1.384  0.020  1.384
 IM8  C11  H11   single    0.930  0.020  1.080
 IM8  C12  C13   aromatic  1.388  0.020  1.388
 IM8  C12  H12   single    0.930  0.020  1.080
 IM8  C13  C14   aromatic  1.387  0.020  1.387
 IM8  C13  CL    single    1.728  0.020  1.728
 IM8  C14  C15   aromatic  1.385  0.020  1.385
 IM8  C14  H14   single    0.930  0.020  1.080
 IM8  C15  H15   single    0.930  0.020  1.080
 IM8  C16  H161  single    0.970  0.020  1.090
 IM8  C16  H162  single    0.970  0.020  1.090
 IM8  C16  H163  single    0.970  0.020  1.090
 IM8  C17  C18   single    1.522  0.020  1.522
 IM8  C17  H171  single    0.970  0.020  1.090
 IM8  C17  H172  single    0.970  0.020  1.090
 IM8  C18  O2    double    1.222  0.020  1.222
 IM8  C18  N2    single    1.342  0.020  1.342
 IM8  O3   C20   single    1.411  0.020  1.411
 IM8  O3   HO3   single    0.850  0.020  0.980
 IM8  N2   C19   single    1.451  0.020  1.451
 IM8  N2   HN2   single    0.860  0.020  1.020
 IM8  C19  C20   single    1.525  0.020  1.525
 IM8  C19  C21   single    1.526  0.020  1.526
 IM8  C19  H19   single    0.970  0.020  1.090
 IM8  C20  H201  single    0.970  0.020  1.090
 IM8  C20  H202  single    0.970  0.020  1.090
 IM8  C21  C22   single    1.522  0.020  1.522
 IM8  C21  H211  single    0.970  0.020  1.090
 IM8  C21  H212  single    0.970  0.020  1.090
 IM8  C22  H221  single    0.970  0.020  1.090
 IM8  C22  H222  single    0.970  0.020  1.090
 IM8  C22  H223  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
 IM8  H2    C2   C1    121.58  3.000
 IM8  H2    C2   C3    119.57  3.000
 IM8  C1    C2   C3    118.84  3.000
 IM8  O     C3   C4    123.89  3.000
 IM8  O     C3   C2    115.91  3.000
 IM8  C4    C3   C2    120.20  3.000
 IM8  H4    C4   C5    117.87  3.000
 IM8  H4    C4   C3    121.00  3.000
 IM8  C5    C4   C3    121.12  3.000
 IM8  H5    C5   C     122.56  3.000
 IM8  H5    C5   C4    119.07  3.000
 IM8  C     C5   C4    118.36  3.000
 IM8  H63   C6   H62   108.81  3.000
 IM8  H63   C6   H61   108.66  3.000
 IM8  H62   C6   H61   108.73  3.000
 IM8  H63   C6   O     112.04  3.000
 IM8  H62   C6   O     111.97  3.000
 IM8  H61   C6   O     106.52  3.000
 IM8  C17   C7   C1    124.00  3.000
 IM8  C17   C7   C8    128.07  3.000
 IM8  C1    C7   C8    107.89  3.000
 IM8  N     C8   C16   123.53  3.000
 IM8  N     C8   C7    108.84  3.000
 IM8  C16   C8   C7    127.24  3.000
 IM8  N     C    C1    107.22  3.000
 IM8  N     C    C5    131.88  3.000
 IM8  C1    C    C5    120.86  3.000
 IM8  C     C1   C7    107.51  3.000
 IM8  C     C1   C2    120.59  3.000
 IM8  C7    C1   C2    131.89  3.000
 IM8  C15   C10  C11   119.70  3.000
 IM8  C15   C10  C9    120.88  3.000
 IM8  C11   C10  C9    119.15  3.000
 IM8  H11   C11  C12   119.32  3.000
 IM8  H11   C11  C10   120.28  3.000
 IM8  C12   C11  C10   120.39  3.000
 IM8  H12   C12  C13   120.60  3.000
 IM8  H12   C12  C11   120.34  3.000
 IM8  C13   C12  C11   119.05  3.000
 IM8  CL    C13  C14   119.31  3.000
 IM8  CL    C13  C12   119.29  3.000
 IM8  C14   C13  C12   121.40  3.000
 IM8  H14   C14  C15   120.30  3.000
 IM8  H14   C14  C13   120.69  3.000
 IM8  C15   C14  C13   119.01  3.000
 IM8  H15   C15  C14   118.99  3.000
 IM8  H15   C15  C10   120.59  3.000
 IM8  C14   C15  C10   120.41  3.000
 IM8  H163  C16  H162  107.25  3.000
 IM8  H163  C16  H161  107.51  3.000
 IM8  H162  C16  H161  107.54  3.000
 IM8  H163  C16  C8    109.11  3.000
 IM8  H162  C16  C8    111.75  3.000
 IM8  H161  C16  C8    113.41  3.000
 IM8  H172  C17  H171  106.26  3.000
 IM8  H172  C17  C18   111.10  3.000
 IM8  H171  C17  C18   107.90  3.000
 IM8  H172  C17  C7    109.88  3.000
 IM8  H171  C17  C7    110.96  3.000
 IM8  C18   C17  C7    110.63  3.000
 IM8  N2    C18  O2    123.64  3.000
 IM8  N2    C18  C17   115.16  3.000
 IM8  O2    C18  C17   121.20  3.000
 IM8  C     N    C9    123.55  3.000
 IM8  C     N    C8    108.45  3.000
 IM8  C9    N    C8    127.93  3.000
 IM8  C6    O    C3    118.73  3.000
 IM8  HO3   O3   C20   108.75  3.000
 IM8  HN2   N2   C19   117.06  3.000
 IM8  HN2   N2   C18   117.96  3.000
 IM8  C19   N2   C18   123.97  3.000
 IM8  H19   C19  C21   108.45  3.000
 IM8  H19   C19  C20   106.94  3.000
 IM8  C21   C19  C20   112.87  3.000
 IM8  H19   C19  N2    107.72  3.000
 IM8  C21   C19  N2    109.93  3.000
 IM8  C20   C19  N2    110.74  3.000
 IM8  H202  C20  H201  106.98  3.000
 IM8  H202  C20  C19   108.75  3.000
 IM8  H201  C20  C19   108.46  3.000
 IM8  H202  C20  O3    111.52  3.000
 IM8  H201  C20  O3    111.55  3.000
 IM8  C19   C20  O3    109.47  3.000
 IM8  H212  C21  H211  106.11  3.000
 IM8  H212  C21  C22   109.52  3.000
 IM8  H211  C21  C22   110.10  3.000
 IM8  H212  C21  C19   107.78  3.000
 IM8  H211  C21  C19   109.85  3.000
 IM8  C22   C21  C19   113.21  3.000
 IM8  H223  C22  H222  107.65  3.000
 IM8  H223  C22  H221  107.75  3.000
 IM8  H222  C22  H221  107.47  3.000
 IM8  H223  C22  C21   111.03  3.000
 IM8  H222  C22  C21   111.90  3.000
 IM8  H221  C22  C21   110.85  3.000
 IM8  O1    C9   N     121.11  3.000
 IM8  O1    C9   C10   121.08  3.000
 IM8  N     C9   C10   117.70  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
 IM8  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 IM8  CONST_02  C8    C7   C1   C2    180.00   0.0  0
 IM8  CONST_03  C5    C    C1   C2      0.00   0.0  0
 IM8  CONST_04  N     C    C1   C2    180.00   0.0  0
 IM8  CONST_05  C7    C1   C2   C3    180.00   0.0  0
 IM8  CONST_06  C     C1   C2   C3      0.00   0.0  0
 IM8  CONST_07  C     C5   C4   C3      0.00   0.0  0
 IM8  CONST_08  C1    C2   C3   C4      0.00   0.0  0
 IM8  CONST_09  C1    C    C5   C4      0.00   0.0  0
 IM8  CONST_10  N     C    C5   C4    180.00   0.0  0
 IM8  CONST_11  C7    C1   C    C5    180.00   0.0  0
 IM8  CONST_12  C8    N    C    C5    180.00   0.0  0
 IM8  CONST_13  C     N    C8   C7      0.00   0.0  0
 IM8  CONST_14  N     C    C1   C7      0.00   0.0  0
 IM8  CONST_15  C     C1   C7   C8      0.00   0.0  0
 IM8  CONST_16  C1    C    N    C8      0.00   0.0  0
 IM8  CONST_17  N     C8   C7   C1      0.00   0.0  0
 IM8  CONST_18  C13   C12  C11  C10     0.00   0.0  0
 IM8  CONST_19  C13   C14  C15  C10     0.00   0.0  0
 IM8  CONST_20  C14   C15  C10  C11     0.00   0.0  0
 IM8  CONST_21  C14   C13  C12  C11     0.00   0.0  0
 IM8  CONST_22  C15   C10  C11  C12     0.00   0.0  0
 IM8  CONST_23  C15   C14  C13  C12     0.00   0.0  0
 IM8  CONST_24  C17   C7   C1   C2      0.00   0.0  0
 IM8  CONST_25  O     C3   C4   C5    180.00   0.0  0
 IM8  CONST_26  C9    N    C    C5      0.00   0.0  0
 IM8  CONST_27  C9    N    C8   C7    180.00   0.0  0
 IM8  CONST_28  C12   C11  C10  C9    180.00   0.0  0
 IM8  CONST_29  C14   C15  C10  C9    180.00   0.0  0
 IM8  CONST_30  C1    C    N    C9    180.00   0.0  0
 IM8  CONST_31  C17   C7   C1   C     180.00   0.0  0
 IM8  CONST_32  C16   C8   N    C     180.00   0.0  0
 IM8  CONST_33  O     C3   C2   C1    180.00   0.0  0
 IM8  CONST_34  C16   C8   C7   C1    180.00   0.0  0
 IM8  CONST_35  CL    C13  C12  C11   180.00   0.0  0
 IM8  CONST_36  CL    C13  C14  C15   180.00   0.0  0
 IM8  CONST_37  N     C8   C7   C17   180.00   0.0  0
 IM8  CONST_40  H4    C4   C3   C2    180.00   0.0  0
 IM8  CONST_41  H5    C5   C4   C3    180.00   0.0  0
 IM8  CONST_42  H2    C2   C3   C4    180.00   0.0  0
 IM8  CONST_43  H12   C12  C11  C10   180.00   0.0  0
 IM8  CONST_44  H14   C14  C15  C10   180.00   0.0  0
 IM8  CONST_45  H15   C15  C10  C11   180.00   0.0  0
 IM8  CONST_46  H11   C11  C12  C13   180.00   0.0  0
 IM8  CONST_49  C19   N2   C18  C17   180.00   0.0  0
 IM8  CONST_50  C19   N2   C18  O2      0.00   0.0  0
 IM8  CONST_51  HN2   N2   C18  C17     0.00   0.0  0
 IM8  Var_01    N     C9   C10  C11  -143.22  30.0  3
 IM8  Var_02    C18   C17  C7   C8    117.26  30.0  2
 IM8  Var_03    H161  C16  C8   C7    104.51  30.0  2
 IM8  Var_04    O2    C18  C17  C7    -53.88  30.0  3
 IM8  Var_05    H61   C6   O    C3   -178.71  30.0  3
 IM8  Var_06    H221  C22  C21  C19   176.52  30.0  3

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
 IM8  chir_01  C19  N2  C20  C21  negativ

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
 IM8  plan-1  C10  0.020
 IM8  plan-1  C11  0.020
 IM8  plan-1  C12  0.020
 IM8  plan-1  C13  0.020
 IM8  plan-1  C14  0.020
 IM8  plan-1  C15  0.020
 IM8  plan-1  CL   0.020
 IM8  plan-1  H11  0.020
 IM8  plan-1  H12  0.020
 IM8  plan-1  H14  0.020
 IM8  plan-1  H15  0.020
 IM8  plan-1  C9   0.020
 IM8  plan-2  C2   0.020
 IM8  plan-2  C3   0.020
 IM8  plan-2  C4   0.020
 IM8  plan-2  C5   0.020
 IM8  plan-2  C7   0.020
 IM8  plan-2  C8   0.020
 IM8  plan-2  C    0.020
 IM8  plan-2  C1   0.020
 IM8  plan-2  C10  0.020
 IM8  plan-2  C16  0.020
 IM8  plan-2  C17  0.020
 IM8  plan-2  N    0.020
 IM8  plan-2  O    0.020
 IM8  plan-2  O1   0.020
 IM8  plan-2  H2   0.020
 IM8  plan-2  H4   0.020
 IM8  plan-2  H5   0.020
 IM8  plan-2  C9   0.020
 IM8  plan-3  C17  0.020
 IM8  plan-3  C18  0.020
 IM8  plan-3  O2   0.020
 IM8  plan-3  N2   0.020
 IM8  plan-3  C19  0.020
 IM8  plan-3  HN2  0.020

