# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 15:24:56 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 2-fluoro-6-[(3S)-tetrahydrofuran-3-ylamino]-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)c3cc(F)c(C(N)=O)c(N[C@H]4CCOC4)c3
#
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
 2LC  2LC  2-fluoro-6-[(3S)-tetrahydrofuran-3-ylamino]-4-(3,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indol-1-yl)benzamide  ligand  55  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2LC
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
 2LC  C1   C  CH3   0  -0.736   4.4387   1.2881  -3.4127
 2LC  C2   C  CR5   0   0.031   3.3583   0.9058  -2.4594
 2LC  C3   C  CR15  0  -0.117   2.1186   0.4504  -2.7869
 2LC  N4   N  NR5   0  -0.615   1.3959   0.2232  -1.6252
 2LC  C5   C  CR5   0   0.405   2.1704   0.5219  -0.5523
 2LC  C6   C  CR5   0  -0.182   3.3941   0.9501  -1.0271
 2LC  C7   C  C     0   0.318   4.4672   1.3000  -0.1217
 2LC  O8   O  O     0  -0.430   5.5759   1.6446  -0.4986
 2LC  C9   C  CH2   0  -0.541   4.1088   1.2474   1.3502
 2LC  C10  C  CT    0  -0.135   3.0782   0.1729   1.7302
 2LC  C11  C  CH3   0  -0.635   3.6580  -1.2252   1.5079
 2LC  C12  C  CH3   0  -0.644   2.7086   0.3319   3.2027
 2LC  C13  C  CH2   0  -0.493   1.8110   0.3714   0.8814
 2LC  C14  C  CR6   0   0.385   0.0893  -0.3016  -1.5918
 2LC  C15  C  CR16  0  -0.435  -0.8508   0.2732  -0.7561
 2LC  C16  C  CR6   0   0.467  -2.1485  -0.2563  -0.6620
 2LC  N17  N  NH1   0  -0.709  -3.0605   0.3007   0.1723
 2LC  C18  C  CH1   0  -0.170  -2.7849   1.3973   1.0724
 2LC  C20  C  CH2   0  -0.538  -4.0687   1.8075   1.7843
 2LC  C21  C  CH2   0  -0.153  -4.1610   0.7763   2.9034
 2LC  O22  O  O2    0  -0.496  -2.8223   0.4196   3.2185
 2LC  C23  C  CH2   0  -0.143  -1.9314   0.9826   2.2728
 2LC  C24  C  CR6   0  -0.370  -2.4853  -1.3564  -1.4860
 2LC  C25  C  C     0   0.462  -3.8638  -1.9420  -1.5364
 2LC  N26  N  NH2   0  -0.792  -4.3365  -2.3712  -0.3531
 2LC  O27  O  O     0  -0.455  -4.5015  -1.9933  -2.5737
 2LC  C28  C  CR6   0   0.575  -1.5129  -1.8624  -2.3298
 2LC  F29  F  F     0  -0.302  -1.8289  -2.9196  -3.0871
 2LC  C30  C  CR16  0  -0.509  -0.2207  -1.3882  -2.3996
 2LC  H1   H  HCH3  0   0.238   5.3253   0.6661  -3.2840
 2LC  H2   H  HCH3  0   0.235   4.1004   1.1796  -4.4427
 2LC  H3   H  HCH3  0   0.238   4.7537   2.3220  -3.2697
 2LC  H4   H  HCR5  0   0.290   1.6675   0.2931  -3.7537
 2LC  H5   H  HCH2  0   0.258   5.0238   1.1237   1.9348
 2LC  H6   H  HCH2  0   0.269   3.7068   2.2358   1.6106
 2LC  H7   H  HCH3  0   0.232   4.5464  -1.3753   2.1241
 2LC  H8   H  HCH3  0   0.231   2.9313  -1.9909   1.7863
 2LC  H9   H  HCH3  0   0.233   3.9412  -1.4028   0.4694
 2LC  H10  H  HCH3  0   0.228   2.2996   1.3243   3.4035
 2LC  H11  H  HCH3  0   0.232   1.9597  -0.4049   3.5006
 2LC  H12  H  HCH3  0   0.235   3.5823   0.1946   3.8420
 2LC  H13  H  HCH2  0   0.264   1.2930   1.2731   1.2302
 2LC  H14  H  HCH2  0   0.269   1.1202  -0.4626   1.0319
 2LC  H15  H  HCR6  0   0.292  -0.5818   1.1588  -0.1991
 2LC  H16  H  HNH1  0   0.397  -4.0004  -0.0599   0.1621
 2LC  H17  H  HCH1  0   0.277  -2.3360   2.2356   0.5329
 2LC  H18  H  HCH2  0   0.271  -3.9480   2.8130   2.1889
 2LC  H19  H  HCH2  0   0.271  -4.9420   1.8143   1.1319
 2LC  H20  H  HCH2  0   0.231  -4.6600   1.1725   3.7904
 2LC  H21  H  HCH2  0   0.209  -4.7154  -0.1131   2.5814
 2LC  H22  H  HCH2  0   0.228  -1.1641   0.2458   2.0203
 2LC  H23  H  HCH2  0   0.216  -1.4268   1.8652   2.6849
 2LC  H24  H  HNH2  0   0.414  -3.7275  -2.4984   0.4385
 2LC  H25  H  HNH2  0   0.411  -5.2398  -2.8177  -0.3074
 2LC  H26  H  HCR6  0   0.291   0.5131  -1.8682  -3.0319

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
 2LC  O22  C23  single    1.416  0.020  1.416
 2LC  O22  C21  single    1.421  0.020  1.421
 2LC  C23  C18  single    1.530  0.020  1.530
 2LC  C21  C20  single    1.525  0.020  1.525
 2LC  C18  C20  single    1.524  0.020  1.524
 2LC  C18  N17  single    1.445  0.020  1.445
 2LC  N17  C16  single    1.356  0.020  1.356
 2LC  C1   C2   single    1.491  0.020  1.491
 2LC  C3   C2   aromatic  1.361  0.020  1.361
 2LC  C3   N4   aromatic  1.387  0.020  1.387
 2LC  C16  C15  aromatic  1.405  0.020  1.405
 2LC  C16  C24  aromatic  1.415  0.020  1.415
 2LC  C15  C14  aromatic  1.383  0.020  1.383
 2LC  C2   C6   aromatic  1.433  0.020  1.433
 2LC  O27  C25  double    1.219  0.020  1.219
 2LC  C14  N4   single    1.408  0.020  1.408
 2LC  C14  C30  aromatic  1.389  0.020  1.389
 2LC  N4   C5   aromatic  1.357  0.020  1.357
 2LC  C24  C25  single    1.499  0.020  1.499
 2LC  C24  C28  aromatic  1.383  0.020  1.383
 2LC  C25  N26  single    1.345  0.020  1.345
 2LC  C6   C5   aromatic  1.381  0.020  1.381
 2LC  C6   C7   single    1.447  0.020  1.447
 2LC  C5   C13  single    1.486  0.020  1.486
 2LC  C30  C28  aromatic  1.378  0.020  1.378
 2LC  C28  F29  single    1.338  0.020  1.338
 2LC  O8   C7   double    1.221  0.020  1.221
 2LC  C7   C9   single    1.516  0.020  1.516
 2LC  C13  C10  single    1.538  0.020  1.538
 2LC  C11  C10  single    1.530  0.020  1.530
 2LC  C9   C10  single    1.537  0.020  1.537
 2LC  C10  C12  single    1.526  0.020  1.526
 2LC  C1   H1   single    0.970  0.020  1.090
 2LC  C1   H2   single    0.970  0.020  1.090
 2LC  C1   H3   single    0.970  0.020  1.090
 2LC  C3   H4   single    0.930  0.020  1.080
 2LC  C9   H5   single    0.970  0.020  1.090
 2LC  C9   H6   single    0.970  0.020  1.090
 2LC  C11  H7   single    0.970  0.020  1.090
 2LC  C11  H8   single    0.970  0.020  1.090
 2LC  C11  H9   single    0.970  0.020  1.090
 2LC  C12  H10  single    0.970  0.020  1.090
 2LC  C12  H11  single    0.970  0.020  1.090
 2LC  C12  H12  single    0.970  0.020  1.090
 2LC  C13  H13  single    0.970  0.020  1.090
 2LC  C13  H14  single    0.970  0.020  1.090
 2LC  C15  H15  single    0.930  0.020  1.080
 2LC  N17  H16  single    0.860  0.020  1.020
 2LC  C18  H17  single    0.970  0.020  1.090
 2LC  C20  H18  single    0.970  0.020  1.090
 2LC  C20  H19  single    0.970  0.020  1.090
 2LC  C21  H20  single    0.970  0.020  1.090
 2LC  C21  H21  single    0.970  0.020  1.090
 2LC  C23  H22  single    0.970  0.020  1.090
 2LC  C23  H23  single    0.970  0.020  1.090
 2LC  N26  H24  single    0.860  0.020  1.020
 2LC  N26  H25  single    0.860  0.020  1.020
 2LC  C30  H26  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
 2LC  H3   C1   H2   107.94  3.000
 2LC  H3   C1   H1   106.88  3.000
 2LC  H2   C1   H1   107.89  3.000
 2LC  H3   C1   C2   111.64  3.000
 2LC  H2   C1   C2   110.73  3.000
 2LC  H1   C1   C2   111.56  3.000
 2LC  C6   C2   C3   105.88  3.000
 2LC  C6   C2   C1   127.80  3.000
 2LC  C3   C2   C1   126.32  3.000
 2LC  H4   C3   N4   120.61  3.000
 2LC  H4   C3   C2   130.21  3.000
 2LC  N4   C3   C2   109.15  3.000
 2LC  C14  N4   C5   126.37  3.000
 2LC  C5   N4   C3   109.20  3.000
 2LC  C14  N4   C3   124.35  3.000
 2LC  C13  C5   C6   125.29  3.000
 2LC  C13  C5   N4   127.07  3.000
 2LC  C6   C5   N4   107.60  3.000
 2LC  C7   C6   C5   121.14  3.000
 2LC  C7   C6   C2   130.63  3.000
 2LC  C5   C6   C2   108.18  3.000
 2LC  C9   C7   O8   121.63  3.000
 2LC  C9   C7   C6   115.08  3.000
 2LC  O8   C7   C6   123.27  3.000
 2LC  H6   C9   H5   106.34  3.000
 2LC  H6   C9   C10  108.98  3.000
 2LC  H5   C9   C10  110.50  3.000
 2LC  H6   C9   C7   106.59  3.000
 2LC  H5   C9   C7   108.99  3.000
 2LC  C10  C9   C7   115.03  3.000
 2LC  C13  C10  C12  108.63  3.000
 2LC  C12  C10  C11  109.09  3.000
 2LC  C13  C10  C11  110.49  3.000
 2LC  C12  C10  C9   109.16  3.000
 2LC  C11  C10  C9   110.42  3.000
 2LC  C13  C10  C9   109.02  3.000
 2LC  H9   C11  H8   107.54  3.000
 2LC  H9   C11  H7   107.68  3.000
 2LC  H8   C11  H7   107.54  3.000
 2LC  H9   C11  C10  112.68  3.000
 2LC  H8   C11  C10  110.59  3.000
 2LC  H7   C11  C10  110.62  3.000
 2LC  H12  C12  H11  107.72  3.000
 2LC  H12  C12  H10  107.85  3.000
 2LC  H11  C12  H10  107.83  3.000
 2LC  H12  C12  C10  110.99  3.000
 2LC  H11  C12  C10  111.03  3.000
 2LC  H10  C12  C10  111.27  3.000
 2LC  H14  C13  H13  106.55  3.000
 2LC  H14  C13  C10  110.25  3.000
 2LC  H13  C13  C10  108.64  3.000
 2LC  H14  C13  C5   111.28  3.000
 2LC  H13  C13  C5   109.75  3.000
 2LC  C10  C13  C5   110.26  3.000
 2LC  C30  C14  C15  121.66  3.000
 2LC  C30  C14  N4   119.00  3.000
 2LC  C15  C14  N4   119.34  3.000
 2LC  H15  C15  C16  120.30  3.000
 2LC  H15  C15  C14  118.89  3.000
 2LC  C16  C15  C14  120.78  3.000
 2LC  C24  C16  N17  121.17  3.000
 2LC  C24  C16  C15  118.29  3.000
 2LC  N17  C16  C15  120.51  3.000
 2LC  H16  N17  C18  117.14  3.000
 2LC  H16  N17  C16  118.34  3.000
 2LC  C18  N17  C16  124.52  3.000
 2LC  H17  C18  C23  111.46  3.000
 2LC  H17  C18  C20  111.71  3.000
 2LC  C23  C18  C20  100.16  3.000
 2LC  H17  C18  N17  110.65  3.000
 2LC  C20  C18  N17  109.54  3.000
 2LC  C23  C18  N17  112.91  3.000
 2LC  H19  C20  H18  107.75  3.000
 2LC  H19  C20  C21  113.27  3.000
 2LC  H18  C20  C21  110.98  3.000
 2LC  H19  C20  C18  113.38  3.000
 2LC  H18  C20  C18  109.16  3.000
 2LC  C21  C20  C18  102.23  3.000
 2LC  H21  C21  H20  107.56  3.000
 2LC  H21  C21  O22  109.75  3.000
 2LC  H20  C21  O22  109.96  3.000
 2LC  H21  C21  C20  111.33  3.000
 2LC  H20  C21  C20  112.24  3.000
 2LC  O22  C21  C20  105.99  3.000
 2LC  C23  O22  C21  110.17  3.000
 2LC  H23  C23  H22  107.83  3.000
 2LC  H23  C23  O22  111.00  3.000
 2LC  H22  C23  O22  109.14  3.000
 2LC  H23  C23  C18  109.46  3.000
 2LC  H22  C23  C18  113.13  3.000
 2LC  O22  C23  C18  106.30  3.000
 2LC  C28  C24  C25  118.89  3.000
 2LC  C28  C24  C16  118.18  3.000
 2LC  C25  C24  C16  122.84  3.000
 2LC  O27  C25  N26  123.48  3.000
 2LC  N26  C25  C24  114.74  3.000
 2LC  O27  C25  C24  121.76  3.000
 2LC  H25  N26  H24  116.75  3.000
 2LC  H25  N26  C25  119.74  3.000
 2LC  H24  N26  C25  121.31  3.000
 2LC  C30  C28  F29  117.68  3.000
 2LC  F29  C28  C24  117.92  3.000
 2LC  C30  C28  C24  124.34  3.000
 2LC  H26  C30  C28  120.89  3.000
 2LC  H26  C30  C14  122.41  3.000
 2LC  C28  C30  C14  116.68  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
 2LC  CONST_01  C14  N4   C3   C2    180.00   0.0  0
 2LC  CONST_02  C5   N4   C3   C2      0.00   0.0  0
 2LC  CONST_03  N4   C5   C6   C2      0.00   0.0  0
 2LC  CONST_04  C5   C6   C2   C3      0.00   0.0  0
 2LC  CONST_07  C6   C5   N4   C3      0.00   0.0  0
 2LC  CONST_08  C6   C2   C3   N4      0.00   0.0  0
 2LC  CONST_09  C16  C15  C14  N4    180.00   0.0  0
 2LC  CONST_10  C28  C30  C14  N4    180.00   0.0  0
 2LC  CONST_13  C14  N4   C5   C6    180.00   0.0  0
 2LC  CONST_14  C24  C16  C15  C14     0.00   0.0  0
 2LC  CONST_15  C24  C28  C30  C14     0.00   0.0  0
 2LC  CONST_16  C28  C24  C16  C15     0.00   0.0  0
 2LC  CONST_17  C28  C30  C14  C15     0.00   0.0  0
 2LC  CONST_18  C30  C14  C15  C16     0.00   0.0  0
 2LC  CONST_19  C30  C28  C24  C16     0.00   0.0  0
 2LC  CONST_20  C14  N4   C5   C13     0.00   0.0  0
 2LC  CONST_21  N4   C3   C2   C1    180.00   0.0  0
 2LC  CONST_22  C5   C6   C2   C1    180.00   0.0  0
 2LC  CONST_23  C7   C6   C2   C1      0.00   0.0  0
 2LC  CONST_24  N17  C16  C15  C14   180.00   0.0  0
 2LC  CONST_25  F29  C28  C30  C14   180.00   0.0  0
 2LC  CONST_26  C25  C24  C16  C15   180.00   0.0  0
 2LC  CONST_27  F29  C28  C24  C16   180.00   0.0  0
 2LC  CONST_28  C28  C24  C16  N17   180.00   0.0  0
 2LC  CONST_29  C30  C28  C24  C25   180.00   0.0  0
 2LC  CONST_30  C18  N17  C16  C15     0.00   0.0  0
 2LC  CONST_31  C24  C16  N17  C18   180.00   0.0  0
 2LC  CONST_32  H15  C15  C14  N4      0.00   0.0  0
 2LC  CONST_33  H26  C30  C14  N4      0.00   0.0  0
 2LC  CONST_34  H4   C3   N4   C5    180.00   0.0  0
 2LC  CONST_35  H16  N17  C16  C15   180.00   0.0  0
 2LC  CONST_36  H24  N26  C25  C24     0.00   0.0  0
 2LC  CONST_37  H25  N26  C25  C24   180.00   0.0  0
 2LC  Var_01    C9   C7   C6   C2    179.08  30.0  1
 2LC  Var_02    C10  C13  C5   N4    153.47  30.0  1
 2LC  Var_03    C9   C10  C13  C5     48.76  30.0  1
 2LC  Var_04    C10  C9   C7   C6     32.65  30.0  1
 2LC  Var_05    C13  C10  C9   C7    -55.65  30.0  1
 2LC  Var_06    O22  C21  C20  C18    29.72  30.0  1
 2LC  Var_07    H22  C23  O22  C21  -138.69  30.0  1
 2LC  Var_08    O27  C25  C24  C16   120.95  30.0  2
 2LC  Var_09    H1   C1   C2   C3   -118.76  30.0  2
 2LC  Var_10    H7   C11  C10  C9     60.42  30.0  3
 2LC  Var_11    H10  C12  C10  C9     58.67  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
 2LC  chir_01  C18  C23  C20  N17  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
 2LC  plan-1  N4   0.020
 2LC  plan-1  C14  0.020
 2LC  plan-1  C15  0.020
 2LC  plan-1  C16  0.020
 2LC  plan-1  N17  0.020
 2LC  plan-1  C24  0.020
 2LC  plan-1  C25  0.020
 2LC  plan-1  C28  0.020
 2LC  plan-1  F29  0.020
 2LC  plan-1  C30  0.020
 2LC  plan-1  H15  0.020
 2LC  plan-1  H26  0.020
 2LC  plan-2  C1   0.020
 2LC  plan-2  C2   0.020
 2LC  plan-2  C3   0.020
 2LC  plan-2  N4   0.020
 2LC  plan-2  C5   0.020
 2LC  plan-2  C6   0.020
 2LC  plan-2  C7   0.020
 2LC  plan-2  C13  0.020
 2LC  plan-2  C14  0.020
 2LC  plan-2  H4   0.020
 2LC  plan-3  C24  0.020
 2LC  plan-3  C25  0.020
 2LC  plan-3  N26  0.020
 2LC  plan-3  O27  0.020
 2LC  plan-3  H24  0.020
 2LC  plan-3  H25  0.020
 2LC  plan-4  C16  0.020
 2LC  plan-4  N17  0.020
 2LC  plan-4  C18  0.020
 2LC  plan-4  H16  0.020
 2LC  plan-5  C6   0.020
 2LC  plan-5  C7   0.020
 2LC  plan-5  O8   0.020
 2LC  plan-5  C9   0.020

