# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:36:05 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-(4-fluorophenyl)-3,3-dimethyl-1H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)C(=O)Nc2ccc(cc12)c3ccc(F)cc3
#
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
 5ZM  5ZM  5-(4-fluorophenyl)-3,3-dimethyl-1H-indol-2-one  ligand  33  19  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5ZM
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
 5ZM  C1    C  CH3   0  -0.629  -3.0573  -1.6639  -1.4667
 5ZM  C2    C  CR5   0  -0.333  -2.9542  -0.9806  -0.1015
 5ZM  C3    C  CR56  0   0.146  -1.7283  -0.1182   0.0198
 5ZM  C4    C  CR16  0  -0.404  -0.3925  -0.4431  -0.0285
 5ZM  C5    C  CR6   0   0.088   0.5745   0.5625   0.1153
 5ZM  C6    C  CR16  0  -0.325   0.1506   1.8786   0.3042
 5ZM  C7    C  CR16  0  -0.292  -1.1971   2.2206   0.3521
 5ZM  C8    C  CR56  0   0.363  -2.1215   1.2042   0.2085
 5ZM  N9    N  NR15  0  -0.738  -3.5078   1.2712   0.2206
 5ZM  C10   C  CR5   0   0.576  -4.0806   0.0486   0.0479
 5ZM  O11   O  O     0  -0.453  -5.2714  -0.1799   0.0193
 5ZM  C12   C  CR6   0   0.080   2.0120   0.2306   0.0721
 5ZM  C13   C  CR16  0  -0.297   2.9320   1.0861  -0.5372
 5ZM  C14   C  CR16  0  -0.396   4.2842   0.7822  -0.5784
 5ZM  C15   C  CR6   0   0.513   4.7153  -0.3982  -0.0055
 5ZM  C16   C  CR16  0  -0.397   3.8398  -1.2746   0.6054
 5ZM  C17   C  CR16  0  -0.294   2.4921  -0.9510   0.6407
 5ZM  F18   F  F     0  -0.316   6.0225  -0.7037  -0.0449
 5ZM  C19   C  CH3   0  -0.629  -3.0443  -2.0124   1.0251
 5ZM  H11C  H  HCH3  0   0.244  -2.2471  -2.3847  -1.5855
 5ZM  H12C  H  HCH3  0   0.243  -4.0011  -2.2035  -1.5529
 5ZM  H13C  H  HCH3  0   0.242  -2.9937  -0.9461  -2.2848
 5ZM  H191  H  HCH3  0   0.244  -2.2137  -2.7144   0.9486
 5ZM  H192  H  HCH3  0   0.242  -3.0011  -1.5431   2.0083
 5ZM  H193  H  HCH3  0   0.243  -3.9732  -2.5789   0.9549
 5ZM  H4    H  HCR6  0   0.252  -0.0895  -1.4703  -0.1978
 5ZM  H6    H  HCR6  0   0.258   0.8857   2.6619   0.4392
 5ZM  H7    H  HCR6  0   0.269  -1.5000   3.2476   0.5081
 5ZM  H9    H  HNR5  0   0.411  -4.0382   2.1201   0.3488
 5ZM  H13   H  HCR6  0   0.264   2.5926   1.9995  -1.0087
 5ZM  H17   H  HCR6  0   0.264   1.8101  -1.6276   1.1399
 5ZM  H14   H  HCR6  0   0.280   4.9871   1.4502  -1.0587
 5ZM  H16   H  HCR6  0   0.281   4.2012  -2.1900   1.0552

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
 5ZM  C1   C2    single    1.530  0.020  1.530
 5ZM  C2   C3    single    1.504  0.020  1.504
 5ZM  C2   C10   single    1.533  0.020  1.533
 5ZM  C2   C19   single    1.530  0.020  1.530
 5ZM  C3   C4    aromatic  1.376  0.020  1.376
 5ZM  C3   C8    aromatic  1.392  0.020  1.392
 5ZM  C4   C5    aromatic  1.403  0.020  1.403
 5ZM  C5   C6    aromatic  1.395  0.020  1.395
 5ZM  C5   C12   single    1.476  0.020  1.476
 5ZM  C6   C7    aromatic  1.391  0.020  1.391
 5ZM  C7   C8    aromatic  1.381  0.020  1.381
 5ZM  C8   N9    single    1.388  0.020  1.388
 5ZM  N9   C10   single    1.361  0.020  1.361
 5ZM  C10  O11   double    1.213  0.020  1.213
 5ZM  C12  C13   aromatic  1.396  0.020  1.396
 5ZM  C12  C17   aromatic  1.396  0.020  1.396
 5ZM  C13  C14   aromatic  1.387  0.020  1.387
 5ZM  C14  C15   aromatic  1.381  0.020  1.381
 5ZM  C15  C16   aromatic  1.381  0.020  1.381
 5ZM  C15  F18   single    1.343  0.020  1.343
 5ZM  C16  C17   aromatic  1.386  0.020  1.386
 5ZM  C1   H11C  single    0.970  0.020  1.090
 5ZM  C1   H12C  single    0.970  0.020  1.090
 5ZM  C1   H13C  single    0.970  0.020  1.090
 5ZM  C19  H191  single    0.970  0.020  1.090
 5ZM  C19  H192  single    0.970  0.020  1.090
 5ZM  C19  H193  single    0.970  0.020  1.090
 5ZM  C4   H4    single    0.930  0.020  1.080
 5ZM  C6   H6    single    0.930  0.020  1.080
 5ZM  C7   H7    single    0.930  0.020  1.080
 5ZM  N9   H9    single    0.860  0.020  1.020
 5ZM  C13  H13   single    0.930  0.020  1.080
 5ZM  C17  H17   single    0.930  0.020  1.080
 5ZM  C14  H14   single    0.930  0.020  1.080
 5ZM  C16  H16   single    0.930  0.020  1.080

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
 5ZM  H13C  C1   H12C  108.47  3.000
 5ZM  H13C  C1   H11C  108.06  3.000
 5ZM  H12C  C1   H11C  107.89  3.000
 5ZM  H13C  C1   C2    111.81  3.000
 5ZM  H12C  C1   C2    110.47  3.000
 5ZM  H11C  C1   C2    110.01  3.000
 5ZM  C19   C2   C10   109.73  3.000
 5ZM  C19   C2   C3    112.04  3.000
 5ZM  C10   C2   C3    101.89  3.000
 5ZM  C19   C2   C1    110.59  3.000
 5ZM  C10   C2   C1    109.71  3.000
 5ZM  C3    C2   C1    112.52  3.000
 5ZM  C8    C3   C4    120.22  3.000
 5ZM  C8    C3   C2    108.99  3.000
 5ZM  C4    C3   C2    130.79  3.000
 5ZM  H4    C4   C5    120.17  3.000
 5ZM  H4    C4   C3    120.04  3.000
 5ZM  C5    C4   C3    119.78  3.000
 5ZM  C12   C5   C6    120.79  3.000
 5ZM  C12   C5   C4    120.48  3.000
 5ZM  C6    C5   C4    118.73  3.000
 5ZM  H6    C6   C7    118.40  3.000
 5ZM  H6    C6   C5    119.54  3.000
 5ZM  C7    C6   C5    122.05  3.000
 5ZM  H7    C7   C8    121.74  3.000
 5ZM  H7    C7   C6    120.63  3.000
 5ZM  C8    C7   C6    117.63  3.000
 5ZM  N9    C8   C7    129.19  3.000
 5ZM  N9    C8   C3    109.22  3.000
 5ZM  C7    C8   C3    121.60  3.000
 5ZM  H9    N9   C10   123.40  3.000
 5ZM  H9    N9   C8    124.52  3.000
 5ZM  C10   N9   C8    112.07  3.000
 5ZM  O11   C10  N9    125.83  3.000
 5ZM  O11   C10  C2    126.34  3.000
 5ZM  N9    C10  C2    107.83  3.000
 5ZM  C17   C12  C13   118.01  3.000
 5ZM  C17   C12  C5    120.88  3.000
 5ZM  C13   C12  C5    121.11  3.000
 5ZM  H13   C13  C14   118.54  3.000
 5ZM  H13   C13  C12   120.03  3.000
 5ZM  C14   C13  C12   121.41  3.000
 5ZM  H14   C14  C15   120.59  3.000
 5ZM  H14   C14  C13   120.76  3.000
 5ZM  C15   C14  C13   118.65  3.000
 5ZM  F18   C15  C16   119.05  3.000
 5ZM  F18   C15  C14   119.08  3.000
 5ZM  C16   C15  C14   121.87  3.000
 5ZM  H16   C16  C17   120.77  3.000
 5ZM  H16   C16  C15   120.59  3.000
 5ZM  C17   C16  C15   118.64  3.000
 5ZM  H17   C17  C16   118.57  3.000
 5ZM  H17   C17  C12   120.00  3.000
 5ZM  C16   C17  C12   121.42  3.000
 5ZM  H193  C19  H192  108.39  3.000
 5ZM  H193  C19  H191  108.06  3.000
 5ZM  H192  C19  H191  108.07  3.000
 5ZM  H193  C19  C2    110.68  3.000
 5ZM  H192  C19  C2    111.79  3.000
 5ZM  H191  C19  C2    109.73  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
 5ZM  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 5ZM  CONST_02  C12   C5   C4   C3    180.00   0.0  0
 5ZM  CONST_03  C6    C7   C8   C3      0.00   0.0  0
 5ZM  CONST_04  C7    C8   C3   C4      0.00   0.0  0
 5ZM  CONST_05  C7    C6   C5   C4      0.00   0.0  0
 5ZM  CONST_08  C8    C3   C4   C5      0.00   0.0  0
 5ZM  CONST_09  C8    C7   C6   C5      0.00   0.0  0
 5ZM  CONST_10  C14   C13  C12  C5    180.00   0.0  0
 5ZM  CONST_11  C16   C17  C12  C5    180.00   0.0  0
 5ZM  CONST_14  C12   C5   C6   C7    180.00   0.0  0
 5ZM  CONST_15  C15   C14  C13  C12     0.00   0.0  0
 5ZM  CONST_16  C15   C16  C17  C12     0.00   0.0  0
 5ZM  CONST_17  C16   C17  C12  C13     0.00   0.0  0
 5ZM  CONST_18  C16   C15  C14  C13     0.00   0.0  0
 5ZM  CONST_19  C17   C12  C13  C14     0.00   0.0  0
 5ZM  CONST_20  C17   C16  C15  C14     0.00   0.0  0
 5ZM  CONST_21  C8    N9   C10  C2      0.00   0.0  0
 5ZM  CONST_22  F18   C15  C14  C13   180.00   0.0  0
 5ZM  CONST_23  F18   C15  C16  C17   180.00   0.0  0
 5ZM  CONST_24  O11   C10  N9   C8    180.00   0.0  0
 5ZM  CONST_25  H4    C4   C3   C2      0.00   0.0  0
 5ZM  CONST_26  H7    C7   C8   C3    180.00   0.0  0
 5ZM  CONST_27  H6    C6   C5   C4    180.00   0.0  0
 5ZM  CONST_28  H13   C13  C12  C5      0.00   0.0  0
 5ZM  CONST_29  H17   C17  C12  C5      0.00   0.0  0
 5ZM  CONST_30  H14   C14  C13  C12   180.00   0.0  0
 5ZM  CONST_31  H16   C16  C17  C12   180.00   0.0  0
 5ZM  CONST_32  H9    N9   C10  C2    180.00   0.0  0
 5ZM  Var_01    C4    C3   C2   C1    -62.62  30.0  1
 5ZM  Var_02    N9    C10  C2   C1   -119.36  30.0  1
 5ZM  Var_03    H11C  C1   C2   C3     66.31  30.0  3
 5ZM  Var_04    H191  C19  C2   C3    -64.70  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
 5ZM  plan-1  C5   0.020
 5ZM  plan-1  C12  0.020
 5ZM  plan-1  C13  0.020
 5ZM  plan-1  C14  0.020
 5ZM  plan-1  C15  0.020
 5ZM  plan-1  C16  0.020
 5ZM  plan-1  C17  0.020
 5ZM  plan-1  F18  0.020
 5ZM  plan-1  H13  0.020
 5ZM  plan-1  H17  0.020
 5ZM  plan-1  H14  0.020
 5ZM  plan-1  H16  0.020
 5ZM  plan-2  C2   0.020
 5ZM  plan-2  C3   0.020
 5ZM  plan-2  C4   0.020
 5ZM  plan-2  C5   0.020
 5ZM  plan-2  C6   0.020
 5ZM  plan-2  C7   0.020
 5ZM  plan-2  C8   0.020
 5ZM  plan-2  N9   0.020
 5ZM  plan-2  C10  0.020
 5ZM  plan-2  O11  0.020
 5ZM  plan-2  C12  0.020
 5ZM  plan-2  H4   0.020
 5ZM  plan-2  H6   0.020
 5ZM  plan-2  H7   0.020
 5ZM  plan-2  H9   0.020

