# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 23:06:51 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-(3,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indol-1-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cn(c2CC(C)(C)CC(=O)c12)c3ccc(cc3)C(N)=O
#
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
 40W  40W  4-(3,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indol-1-yl)benzamide  ligand  42  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_40W
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
 40W  N1   N  NH2   0  -0.811  -5.6128   1.4768   0.5136
 40W  C4   C  CR5   0  -0.179   2.5211  -0.8163  -0.0500
 40W  C5   C  C     0   0.317   3.8060  -0.1831  -0.2461
 40W  C6   C  CH2   0  -0.539   3.7530   1.2742  -0.6603
 40W  C7   C  CT    0  -0.136   2.5589   2.0733  -0.1158
 40W  C8   C  CH2   0  -0.477   1.2498   1.3498  -0.4738
 40W  C10  C  CH3   0  -0.635   2.6782   2.2304   1.4008
 40W  C13  C  CR16  0  -0.269  -3.2647  -0.9878  -0.7570
 40W  C15  C  CR16  0  -0.285  -2.8974   0.6191   0.9882
 40W  C17  C  C     0   0.490  -5.2359   0.2692   0.0708
 40W  O1   O  O     0  -0.479  -6.0278  -0.5657  -0.3445
 40W  C14  C  CR6   0  -0.033  -3.7671  -0.0175   0.1060
 40W  C12  C  CR16  0  -0.264  -1.9132  -1.2855  -0.7737
 40W  C16  C  CR16  0  -0.272  -1.5483   0.3058   0.9968
 40W  C11  C  CR6   0   0.316  -1.0536  -0.6334   0.1014
 40W  N    N  NR5   0  -0.608   0.3231  -0.9495   0.0923
 40W  C2   C  CR15  0  -0.124   0.8275  -2.2239   0.2984
 40W  C3   C  CR5   0   0.395   1.3471  -0.0913  -0.1247
 40W  O    O  O     0  -0.433   4.8685  -0.7746  -0.1334
 40W  C1   C  CR5   0   0.036   2.1866  -2.1817   0.2281
 40W  C    C  CH3   0  -0.737   3.1192  -3.3307   0.4080
 40W  H1   H  HNH2  0   0.415  -4.9549   2.2040   0.7338
 40W  H2   H  HNH2  0   0.408  -6.5874   1.7305   0.5048
 40W  H3   H  HCH2  0   0.257   4.6917   1.7557  -0.3757
 40W  H4   H  HCH2  0   0.269   3.7190   1.2835  -1.7577
 40W  H5   H  HCH2  0   0.263   0.4089   1.8401   0.0213
 40W  H6   H  HCH2  0   0.269   1.0641   1.4425  -1.5510
 40W  H7   H  HCH3  0   0.232   2.6755   1.2730   1.9250
 40W  H8   H  HCH3  0   0.232   3.6052   2.7442   1.6619
 40W  H9   H  HCH3  0   0.230   1.8493   2.8219   1.7945
 40W  H10  H  HCR6  0   0.271  -3.9297  -1.5002  -1.4386
 40W  H11  H  HCR6  0   0.270  -3.2612   1.3419   1.7069
 40W  H12  H  HCR6  0   0.280  -1.5238  -2.0172  -1.4697
 40W  H13  H  HCR6  0   0.284  -0.8884   0.7767   1.7136
 40W  H14  H  HCR5  0   0.287   0.1617  -3.0476   0.5033
 40W  H15  H  HCH3  0   0.232   1.7085   4.0517  -0.3958
 40W  H16  H  HCH3  0   0.233   3.4644   4.0044  -0.5365
 40W  H17  H  HCH3  0   0.228   2.4576   3.3854  -1.8479
 40W  H18  H  HCH3  0   0.238   3.7877  -3.1778   1.2558
 40W  H19  H  HCH3  0   0.235   2.5678  -4.2545   0.5788
 40W  H20  H  HCH3  0   0.237   3.7503  -3.4745  -0.4695
 40W  C9   C  CH3   0  -0.642   2.5477   3.4566  -0.7622

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
 40W  C10  C7   single    1.529  0.020  1.529
 40W  N1   C17  single    1.340  0.020  1.340
 40W  C9   C7   single    1.527  0.020  1.527
 40W  C7   C8   single    1.538  0.020  1.538
 40W  C7   C6   single    1.536  0.020  1.536
 40W  C13  C12  aromatic  1.384  0.020  1.384
 40W  C13  C14  aromatic  1.392  0.020  1.392
 40W  C17  C14  single    1.497  0.020  1.497
 40W  C17  O1   double    1.223  0.020  1.223
 40W  C12  C11  aromatic  1.389  0.020  1.389
 40W  C8   C3   single    1.486  0.020  1.486
 40W  C14  C15  aromatic  1.393  0.020  1.393
 40W  C6   C5   single    1.516  0.020  1.516
 40W  C5   O    double    1.221  0.020  1.221
 40W  C5   C4   single    1.446  0.020  1.446
 40W  C3   C4   aromatic  1.382  0.020  1.382
 40W  C3   N    aromatic  1.354  0.020  1.354
 40W  C11  N    single    1.413  0.020  1.413
 40W  C11  C16  aromatic  1.389  0.020  1.389
 40W  C4   C1   aromatic  1.433  0.020  1.433
 40W  C15  C16  aromatic  1.385  0.020  1.385
 40W  N    C2   aromatic  1.386  0.020  1.386
 40W  C1   C2   aromatic  1.362  0.020  1.362
 40W  C1   C    single    1.491  0.020  1.491
 40W  N1   H1   single    0.860  0.020  1.020
 40W  N1   H2   single    0.860  0.020  1.020
 40W  C6   H3   single    0.970  0.020  1.090
 40W  C6   H4   single    0.970  0.020  1.090
 40W  C8   H5   single    0.970  0.020  1.090
 40W  C8   H6   single    0.970  0.020  1.090
 40W  C10  H7   single    0.970  0.020  1.090
 40W  C10  H8   single    0.970  0.020  1.090
 40W  C10  H9   single    0.970  0.020  1.090
 40W  C13  H10  single    0.930  0.020  1.080
 40W  C15  H11  single    0.930  0.020  1.080
 40W  C12  H12  single    0.930  0.020  1.080
 40W  C16  H13  single    0.930  0.020  1.080
 40W  C2   H14  single    0.930  0.020  1.080
 40W  C9   H15  single    0.970  0.020  1.090
 40W  C9   H16  single    0.970  0.020  1.090
 40W  C9   H17  single    0.970  0.020  1.090
 40W  C    H18  single    0.970  0.020  1.090
 40W  C    H19  single    0.970  0.020  1.090
 40W  C    H20  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
 40W  H2   N1   H1   116.94  3.000
 40W  H2   N1   C17  119.74  3.000
 40W  H1   N1   C17  122.70  3.000
 40W  C1   C4   C3   108.19  3.000
 40W  C1   C4   C5   130.62  3.000
 40W  C3   C4   C5   121.20  3.000
 40W  O    C5   C6   121.41  3.000
 40W  O    C5   C4   123.27  3.000
 40W  C6   C5   C4   115.27  3.000
 40W  H4   C6   H3   106.45  3.000
 40W  H4   C6   C7   109.01  3.000
 40W  H3   C6   C7   110.25  3.000
 40W  H4   C6   C5   106.40  3.000
 40W  H3   C6   C5   108.81  3.000
 40W  C7   C6   C5   115.49  3.000
 40W  C9   C7   C10  109.10  3.000
 40W  C9   C7   C8   108.75  3.000
 40W  C10  C7   C8   110.22  3.000
 40W  C8   C7   C6   109.53  3.000
 40W  C9   C7   C6   109.08  3.000
 40W  C10  C7   C6   110.14  3.000
 40W  H6   C8   H5   106.07  3.000
 40W  H6   C8   C3   108.89  3.000
 40W  H5   C8   C3   112.29  3.000
 40W  H6   C8   C7   109.45  3.000
 40W  H5   C8   C7   109.80  3.000
 40W  C3   C8   C7   110.23  3.000
 40W  H9   C10  H8   107.67  3.000
 40W  H9   C10  H7   107.47  3.000
 40W  H8   C10  H7   107.46  3.000
 40W  H9   C10  C7   110.74  3.000
 40W  H8   C10  C7   110.60  3.000
 40W  H7   C10  C7   112.70  3.000
 40W  H10  C13  C12  119.41  3.000
 40W  H10  C13  C14  119.93  3.000
 40W  C12  C13  C14  120.65  3.000
 40W  H11  C15  C16  118.32  3.000
 40W  H11  C15  C14  121.06  3.000
 40W  C16  C15  C14  120.58  3.000
 40W  C14  C17  O1   120.83  3.000
 40W  O1   C17  N1   123.03  3.000
 40W  C14  C17  N1   116.14  3.000
 40W  C17  C14  C15  122.69  3.000
 40W  C15  C14  C13  119.06  3.000
 40W  C17  C14  C13  118.22  3.000
 40W  H12  C12  C11  119.99  3.000
 40W  H12  C12  C13  120.30  3.000
 40W  C11  C12  C13  119.71  3.000
 40W  H13  C16  C11  120.28  3.000
 40W  H13  C16  C15  119.98  3.000
 40W  C11  C16  C15  119.73  3.000
 40W  N    C11  C16  120.18  3.000
 40W  C16  C11  C12  120.21  3.000
 40W  N    C11  C12  119.60  3.000
 40W  C3   N    C2   109.36  3.000
 40W  C2   N    C11  124.02  3.000
 40W  C3   N    C11  126.62  3.000
 40W  H14  C2   C1   130.51  3.000
 40W  H14  C2   N    120.38  3.000
 40W  C1   C2   N    109.09  3.000
 40W  N    C3   C8   127.09  3.000
 40W  N    C3   C4   107.54  3.000
 40W  C8   C3   C4   125.25  3.000
 40W  C    C1   C2   126.46  3.000
 40W  C    C1   C4   127.72  3.000
 40W  C2   C1   C4   105.81  3.000
 40W  H20  C    H19  107.90  3.000
 40W  H20  C    H18  106.81  3.000
 40W  H19  C    H18  107.90  3.000
 40W  H20  C    C1   111.50  3.000
 40W  H19  C    C1   110.85  3.000
 40W  H18  C    C1   111.67  3.000
 40W  H17  C9   H16  107.92  3.000
 40W  H17  C9   H15  107.81  3.000
 40W  H16  C9   H15  107.61  3.000
 40W  H17  C9   C7   111.25  3.000
 40W  H16  C9   C7   111.16  3.000
 40W  H15  C9   C7   110.93  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
 40W  CONST_01  C11  N    C3   C4    180.00   0.0  0
 40W  CONST_02  C2   N    C3   C4      0.00   0.0  0
 40W  CONST_03  N    C2   C1   C4      0.00   0.0  0
 40W  CONST_04  N    C11  C12  C13   180.00   0.0  0
 40W  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 40W  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 40W  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 40W  CONST_08  C12  C11  C16  C15     0.00   0.0  0
 40W  CONST_09  N    C11  C16  C15   180.00   0.0  0
 40W  CONST_10  C11  C12  C13  C14     0.00   0.0  0
 40W  CONST_11  C11  C16  C15  C14     0.00   0.0  0
 40W  CONST_16  C1   C2   N    C11   180.00   0.0  0
 40W  CONST_17  C1   C4   C3   N       0.00   0.0  0
 40W  CONST_18  C3   C4   C1   C2      0.00   0.0  0
 40W  CONST_19  C1   C2   N    C3      0.00   0.0  0
 40W  CONST_20  C11  N    C3   C8      0.00   0.0  0
 40W  CONST_21  C    C1   C4   C5      0.00   0.0  0
 40W  CONST_22  C12  C13  C14  C17   180.00   0.0  0
 40W  CONST_23  C16  C15  C14  C17   180.00   0.0  0
 40W  CONST_24  C    C1   C2   N     180.00   0.0  0
 40W  CONST_25  C    C1   C4   C3    180.00   0.0  0
 40W  CONST_26  H14  C2   C1   C4    180.00   0.0  0
 40W  CONST_27  H11  C15  C14  C13   180.00   0.0  0
 40W  CONST_28  H10  C13  C14  C15   180.00   0.0  0
 40W  CONST_29  H12  C12  C13  C14   180.00   0.0  0
 40W  CONST_30  H13  C16  C15  C14   180.00   0.0  0
 40W  CONST_31  H1   N1   C17  C14     0.00   0.0  0
 40W  CONST_32  H2   N1   C17  C14   180.00   0.0  0
 40W  Var_01    C7   C6   C5   C4     31.67  30.0  1
 40W  Var_02    C7   C8   C3   C4    -26.04  30.0  1
 40W  Var_03    C8   C7   C6   C5    -53.78  30.0  1
 40W  Var_04    C3   C8   C7   C6     48.36  30.0  1
 40W  Var_05    C3   C4   C5   C6     -5.47  30.0  1
 40W  Var_06    C13  C14  C17  N1   -156.57  30.0  2
 40W  Var_07    H18  C    C1   C4     61.40  30.0  2
 40W  Var_08    H7   C10  C7   C6    -61.23  30.0  3
 40W  Var_09    H15  C9   C7   C6    179.98  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
 40W  plan-1  C13  0.020
 40W  plan-1  C15  0.020
 40W  plan-1  C17  0.020
 40W  plan-1  C14  0.020
 40W  plan-1  C12  0.020
 40W  plan-1  C16  0.020
 40W  plan-1  C11  0.020
 40W  plan-1  N    0.020
 40W  plan-1  H10  0.020
 40W  plan-1  H11  0.020
 40W  plan-1  H12  0.020
 40W  plan-1  H13  0.020
 40W  plan-2  C4   0.020
 40W  plan-2  C5   0.020
 40W  plan-2  C8   0.020
 40W  plan-2  C11  0.020
 40W  plan-2  N    0.020
 40W  plan-2  C2   0.020
 40W  plan-2  C3   0.020
 40W  plan-2  C1   0.020
 40W  plan-2  C    0.020
 40W  plan-2  H14  0.020
 40W  plan-3  N1   0.020
 40W  plan-3  C17  0.020
 40W  plan-3  O1   0.020
 40W  plan-3  C14  0.020
 40W  plan-3  H1   0.020
 40W  plan-3  H2   0.020
 40W  plan-4  C4   0.020
 40W  plan-4  C5   0.020
 40W  plan-4  C6   0.020
 40W  plan-4  O    0.020

