# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 10:28:07 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1c2CCCC(=O)c2c3C(=O)c4cccc(OCC=C(C)C)c4c13
#
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
 9YE  9YE  4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione  ligand  52  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9YE
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
 9YE  C1   C  CR16  0  -0.309  -0.0218  -3.9881   0.1954
 9YE  C10  C  CR5   0   0.356  -1.9014   1.3906   0.0467
 9YE  C11  C  CR5   0  -0.145  -2.7502   0.3049  -0.0795
 9YE  C12  C  CH2   0  -0.527  -2.3524   2.8075  -0.0608
 9YE  C13  C  CH2   0  -0.459  -3.6754   2.8518  -0.8232
 9YE  C14  C  CH2   0  -0.573  -4.6941   1.8649  -0.2636
 9YE  C15  C  C     0   0.301  -4.1852   0.4415  -0.2611
 9YE  C16  C  CH2   0  -0.261   3.8470  -0.7280   0.5361
 9YE  C18  C  CH3   0  -0.650   1.1233   2.2868  -0.8389
 9YE  C19  C  CH3   0  -0.671   0.3513   2.8716   1.5101
 9YE  C2   C  CR16  0  -0.248   1.3613  -4.1390   0.3177
 9YE  C20  C  C1    0  -0.301   4.3796   0.6568   0.6940
 9YE  C21  C  C     0   0.120   4.7738   1.4662  -0.2923
 9YE  C22  C  CH3   0  -0.719   4.7647   1.1129  -1.7478
 9YE  C23  C  CH3   0  -0.707   5.2603   2.8519   0.0084
 9YE  C3   C  CR16  0  -0.379   2.1842  -3.0339   0.4217
 9YE  C4   C  CR6   0   0.371   1.6612  -1.7276   0.4190
 9YE  C5   C  CR56  0   0.074   0.2850  -1.5696   0.3117
 9YE  C6   C  CR56  0  -0.115  -0.5244  -2.7117   0.1913
 9YE  C7   C  CR55  0   0.297  -0.6442  -0.4229   0.2319
 9YE  C8   C  CR55  0  -0.060  -1.9381  -0.8497   0.0364
 9YE  C9   C  CR5   0   0.286  -1.9660  -2.3050   0.0197
 9YE  N1   N  NR5   0  -0.586  -0.6229   0.9387   0.2642
 9YE  O1   O  O     0  -0.374  -2.8918  -3.0739  -0.1062
 9YE  O2   O  O     0  -0.412  -4.9260  -0.5184  -0.3681
 9YE  O3   O  O2    0  -0.468   2.4201  -0.6292   0.5065
 9YE  H1   H  HCR6  0   0.263  -0.6739  -4.8461   0.0969
 9YE  H2   H  HCH2  0   0.267  -2.4884   3.2389   0.9365
 9YE  H3   H  HCH2  0   0.270  -1.6184   3.4299  -0.5735
 9YE  H4   H  HCH2  0   0.255  -4.0811   3.8628  -0.7805
 9YE  H5   H  HCH2  0   0.243  -3.4913   2.6276  -1.8770
 9YE  H6   H  HCH2  0   0.268  -4.9274   2.1275   0.7756
 9YE  H7   H  HCH2  0   0.267  -5.6325   1.9089  -0.8184
 9YE  H8   H  HCH2  0   0.239   4.2017  -1.2135  -0.3770
 9YE  H9   H  HCH2  0   0.244   4.1600  -1.3452   1.3837
 9YE  H10  H  HCH1  0   0.296   1.3033   1.0972   0.9051
 9YE  H11  H  HCH3  0   0.240   2.0702   2.7961  -0.6593
 9YE  H12  H  HCH3  0   0.242   1.3164   1.4654  -1.5284
 9YE  H13  H  HCH3  0   0.232   0.4470   2.9922  -1.3219
 9YE  H14  H  HCH3  0   0.247  -0.1431   2.4906   2.4037
 9YE  H15  H  HCH3  0   0.251   1.3281   3.2509   1.8108
 9YE  H16  H  HCH3  0   0.239  -0.2181   3.7178   1.1314
 9YE  H17  H  HCR6  0   0.270   1.8028  -5.1266   0.3235
 9YE  H18  H  H     0   0.239   4.4126   1.0320   1.7123
 9YE  H19  H  HCH3  0   0.243   4.0961   1.7864  -2.2894
 9YE  H20  H  HCH3  0   0.243   5.7586   1.2508  -2.1793
 9YE  H21  H  HCH3  0   0.244   4.4443   0.0945  -1.9539
 9YE  H22  H  HCH3  0   0.237   4.6478   3.5963  -0.5064
 9YE  H23  H  HCH3  0   0.241   5.2399   3.0732   1.0747
 9YE  H24  H  HCH3  0   0.240   6.2830   2.9917  -0.3495
 9YE  H25  H  HCR6  0   0.294   3.2513  -3.1886   0.5012
 9YE  C17  C  CH1   0  -0.155   0.5709   1.7718   0.4807

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
 9YE  C23  C21  single    1.499  0.020  1.499
 9YE  C21  C22  single    1.498  0.020  1.498
 9YE  C21  C20  double    1.335  0.020  1.335
 9YE  C20  C16  single    1.492  0.020  1.492
 9YE  C16  O3   single    1.431  0.020  1.431
 9YE  C18  C17  single    1.520  0.020  1.520
 9YE  C19  C17  single    1.522  0.020  1.522
 9YE  C17  N1   single    1.472  0.020  1.472
 9YE  O3   C4   single    1.338  0.020  1.338
 9YE  N1   C10  aromatic  1.373  0.020  1.373
 9YE  N1   C7   aromatic  1.362  0.020  1.362
 9YE  C4   C3   aromatic  1.407  0.020  1.407
 9YE  C4   C5   aromatic  1.389  0.020  1.389
 9YE  C12  C10  single    1.491  0.020  1.491
 9YE  C12  C13  single    1.528  0.020  1.528
 9YE  C3   C2   aromatic  1.382  0.020  1.382
 9YE  C10  C11  aromatic  1.384  0.020  1.384
 9YE  C7   C5   aromatic  1.478  0.020  1.478
 9YE  C7   C8   aromatic  1.376  0.020  1.376
 9YE  C13  C14  single    1.525  0.020  1.525
 9YE  C5   C6   aromatic  1.405  0.020  1.405
 9YE  C2   C1   aromatic  1.397  0.020  1.397
 9YE  C11  C8   aromatic  1.416  0.020  1.416
 9YE  C11  C15  single    1.453  0.020  1.453
 9YE  C8   C9   single    1.456  0.020  1.456
 9YE  C6   C1   aromatic  1.372  0.020  1.372
 9YE  C6   C9   single    1.508  0.020  1.508
 9YE  C14  C15  single    1.512  0.020  1.512
 9YE  C15  O2   double    1.217  0.020  1.217
 9YE  C9   O1   double    1.210  0.020  1.210
 9YE  C1   H1   single    0.930  0.020  1.080
 9YE  C12  H2   single    0.970  0.020  1.090
 9YE  C12  H3   single    0.970  0.020  1.090
 9YE  C13  H4   single    0.970  0.020  1.090
 9YE  C13  H5   single    0.970  0.020  1.090
 9YE  C14  H6   single    0.970  0.020  1.090
 9YE  C14  H7   single    0.970  0.020  1.090
 9YE  C16  H8   single    0.970  0.020  1.090
 9YE  C16  H9   single    0.970  0.020  1.090
 9YE  C17  H10  single    0.970  0.020  1.090
 9YE  C18  H11  single    0.970  0.020  1.090
 9YE  C18  H12  single    0.970  0.020  1.090
 9YE  C18  H13  single    0.970  0.020  1.090
 9YE  C19  H14  single    0.970  0.020  1.090
 9YE  C19  H15  single    0.970  0.020  1.090
 9YE  C19  H16  single    0.970  0.020  1.090
 9YE  C2   H17  single    0.930  0.020  1.080
 9YE  C20  H18  single    0.930  0.020  1.080
 9YE  C22  H19  single    0.970  0.020  1.090
 9YE  C22  H20  single    0.970  0.020  1.090
 9YE  C22  H21  single    0.970  0.020  1.090
 9YE  C23  H22  single    0.970  0.020  1.090
 9YE  C23  H23  single    0.970  0.020  1.090
 9YE  C23  H24  single    0.970  0.020  1.090
 9YE  C3   H25  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
 9YE  H1   C1   C6   121.11  3.000
 9YE  H1   C1   C2   121.27  3.000
 9YE  C6   C1   C2   117.62  3.000
 9YE  N1   C10  C12  127.28  3.000
 9YE  C12  C10  C11  123.61  3.000
 9YE  N1   C10  C11  109.11  3.000
 9YE  C8   C11  C15  130.79  3.000
 9YE  C15  C11  C10  122.92  3.000
 9YE  C8   C11  C10  106.28  3.000
 9YE  H3   C12  H2   106.67  3.000
 9YE  H3   C12  C13  109.38  3.000
 9YE  H2   C12  C13  109.61  3.000
 9YE  H3   C12  C10  111.88  3.000
 9YE  H2   C12  C10  110.26  3.000
 9YE  C13  C12  C10  109.00  3.000
 9YE  H5   C13  H4   106.90  3.000
 9YE  H5   C13  C14  109.49  3.000
 9YE  H4   C13  C14  109.70  3.000
 9YE  H5   C13  C12  109.23  3.000
 9YE  H4   C13  C12  109.24  3.000
 9YE  C14  C13  C12  112.13  3.000
 9YE  H7   C14  H6   106.81  3.000
 9YE  H7   C14  C15  109.17  3.000
 9YE  H6   C14  C15  107.18  3.000
 9YE  H7   C14  C13  111.22  3.000
 9YE  H6   C14  C13  109.57  3.000
 9YE  C15  C14  C13  112.65  3.000
 9YE  O2   C15  C14  122.51  3.000
 9YE  O2   C15  C11  122.54  3.000
 9YE  C14  C15  C11  114.92  3.000
 9YE  H9   C16  H8   107.68  3.000
 9YE  H9   C16  O3   109.90  3.000
 9YE  H8   C16  O3   109.69  3.000
 9YE  H9   C16  C20  109.84  3.000
 9YE  H8   C16  C20  112.63  3.000
 9YE  O3   C16  C20  107.11  3.000
 9YE  H13  C18  H12  108.51  3.000
 9YE  H13  C18  H11  108.04  3.000
 9YE  H12  C18  H11  107.60  3.000
 9YE  H13  C18  C17  112.23  3.000
 9YE  H12  C18  C17  110.99  3.000
 9YE  H11  C18  C17  109.32  3.000
 9YE  H16  C19  H15  107.12  3.000
 9YE  H16  C19  H14  108.65  3.000
 9YE  H15  C19  H14  107.57  3.000
 9YE  H16  C19  C17  113.71  3.000
 9YE  H15  C19  C17  107.97  3.000
 9YE  H14  C19  C17  111.55  3.000
 9YE  H17  C2   C3   119.12  3.000
 9YE  H17  C2   C1   120.22  3.000
 9YE  C3   C2   C1   120.66  3.000
 9YE  H18  C20  C21  118.31  3.000
 9YE  H18  C20  C16  115.52  3.000
 9YE  C21  C20  C16  126.14  3.000
 9YE  C23  C21  C22  114.52  3.000
 9YE  C22  C21  C20  124.95  3.000
 9YE  C23  C21  C20  120.53  3.000
 9YE  H21  C22  H20  108.15  3.000
 9YE  H21  C22  H19  107.64  3.000
 9YE  H20  C22  H19  106.45  3.000
 9YE  H21  C22  C21  114.01  3.000
 9YE  H20  C22  C21  110.40  3.000
 9YE  H19  C22  C21  109.87  3.000
 9YE  H24  C23  H23  108.20  3.000
 9YE  H24  C23  H22  106.45  3.000
 9YE  H23  C23  H22  108.19  3.000
 9YE  H24  C23  C21  110.88  3.000
 9YE  H23  C23  C21  112.21  3.000
 9YE  H22  C23  C21  110.69  3.000
 9YE  H25  C3   C4   119.99  3.000
 9YE  H25  C3   C2   118.61  3.000
 9YE  C4   C3   C2   121.40  3.000
 9YE  O3   C4   C5   118.26  3.000
 9YE  C5   C4   C3   118.29  3.000
 9YE  O3   C4   C3   123.45  3.000
 9YE  C7   C5   C6   105.30  3.000
 9YE  C6   C5   C4   119.00  3.000
 9YE  C7   C5   C4   135.65  3.000
 9YE  C9   C6   C5   109.96  3.000
 9YE  C9   C6   C1   126.99  3.000
 9YE  C5   C6   C1   123.03  3.000
 9YE  N1   C7   C8   109.15  3.000
 9YE  C8   C7   C5   110.98  3.000
 9YE  N1   C7   C5   139.86  3.000
 9YE  C9   C8   C7   109.25  3.000
 9YE  C9   C8   C11  143.42  3.000
 9YE  C7   C8   C11  107.33  3.000
 9YE  O1   C9   C8   130.63  3.000
 9YE  O1   C9   C6   124.89  3.000
 9YE  C8   C9   C6   104.48  3.000
 9YE  C7   N1   C17  125.59  3.000
 9YE  C7   N1   C10  108.09  3.000
 9YE  C17  N1   C10  126.31  3.000
 9YE  C4   O3   C16  120.69  3.000
 9YE  H10  C17  N1   104.70  3.000
 9YE  H10  C17  C19  106.43  3.000
 9YE  N1   C17  C19  113.04  3.000
 9YE  H10  C17  C18  107.79  3.000
 9YE  N1   C17  C18  111.02  3.000
 9YE  C19  C17  C18  113.24  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
 9YE  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 9YE  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 9YE  CONST_03  C7   C5   C6   C1    180.00   0.0  0
 9YE  CONST_04  C5   C7   N1   C10   180.00   0.0  0
 9YE  CONST_05  C8   C7   N1   C10     0.00   0.0  0
 9YE  CONST_06  C7   C8   C11  C10     0.00   0.0  0
 9YE  CONST_07  C7   N1   C10  C11     0.00   0.0  0
 9YE  CONST_08  N1   C7   C8   C11     0.00   0.0  0
 9YE  CONST_09  C5   C7   C8   C11   180.00   0.0  0
 9YE  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 9YE  CONST_11  C5   C6   C1   C2      0.00   0.0  0
 9YE  CONST_12  C7   C5   C4   C3    180.00   0.0  0
 9YE  CONST_13  C6   C5   C4   C3      0.00   0.0  0
 9YE  CONST_14  C6   C1   C2   C3      0.00   0.0  0
 9YE  CONST_15  N1   C7   C5   C4      0.00   0.0  0
 9YE  CONST_16  C8   C7   C5   C4    180.00   0.0  0
 9YE  CONST_17  N1   C7   C5   C6    180.00   0.0  0
 9YE  CONST_18  C8   C7   C5   C6      0.00   0.0  0
 9YE  CONST_19  N1   C10  C11  C8      0.00   0.0  0
 9YE  CONST_20  C17  N1   C10  C11   180.00   0.0  0
 9YE  CONST_21  C17  N1   C10  C12     0.00   0.0  0
 9YE  CONST_22  C5   C7   N1   C17     0.00   0.0  0
 9YE  CONST_23  C8   C7   N1   C17   180.00   0.0  0
 9YE  CONST_24  O3   C4   C3   C2    180.00   0.0  0
 9YE  CONST_25  O3   C4   C5   C6    180.00   0.0  0
 9YE  CONST_26  O3   C4   C5   C7      0.00   0.0  0
 9YE  CONST_27  H25  C3   C2   C1    180.00   0.0  0
 9YE  CONST_28  H1   C1   C2   C3    180.00   0.0  0
 9YE  CONST_29  H17  C2   C3   C4    180.00   0.0  0
 9YE  Var_01    C14  C13  C12  C10    50.08  30.0  1
 9YE  Var_02    C14  C15  C11  C10    -1.65  30.0  1
 9YE  Var_03    C13  C12  C10  C11   -21.21  30.0  1
 9YE  Var_04    C13  C14  C15  C11    31.27  30.0  1
 9YE  Var_05    C15  C14  C13  C12   -57.07  30.0  1
 9YE  Var_06    O1   C9   C6   C1      2.00  30.0  1
 9YE  Var_07    C18  C17  N1   C10   -80.58  30.0  2
 9YE  Var_08    C3   C4   O3   C16     3.46  30.0  2
 9YE  Var_09    H8   C16  O3   C4     59.81  30.0  3
 9YE  Var_10    H11  C18  C17  N1   -173.17  30.0  3
 9YE  Var_11    H14  C19  C17  N1     46.53  30.0  3
 9YE  Var_12    C23  C21  C20  C16   178.54   0.0  2
 9YE  Var_13    O3   C16  C20  C21   -94.74  30.0  3
 9YE  Var_14    H22  C23  C21  C20  -121.07  30.0  3
 9YE  Var_15    H19  C22  C21  C20   118.20  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
 9YE  plan-1  C11  0.020
 9YE  plan-1  C14  0.020
 9YE  plan-1  C15  0.020
 9YE  plan-1  O2   0.020
 9YE  plan-2  C1   0.020
 9YE  plan-2  C10  0.020
 9YE  plan-2  C11  0.020
 9YE  plan-2  C12  0.020
 9YE  plan-2  C15  0.020
 9YE  plan-2  C2   0.020
 9YE  plan-2  C3   0.020
 9YE  plan-2  C4   0.020
 9YE  plan-2  C5   0.020
 9YE  plan-2  C6   0.020
 9YE  plan-2  C7   0.020
 9YE  plan-2  C8   0.020
 9YE  plan-2  C9   0.020
 9YE  plan-2  N1   0.020
 9YE  plan-2  O3   0.020
 9YE  plan-2  H1   0.020
 9YE  plan-2  H17  0.020
 9YE  plan-2  H25  0.020
 9YE  plan-2  C17  0.020
 9YE  plan-3  C6   0.020
 9YE  plan-3  C8   0.020
 9YE  plan-3  C9   0.020
 9YE  plan-3  O1   0.020
 9YE  plan-4  C16  0.020
 9YE  plan-4  C20  0.020
 9YE  plan-4  C21  0.020
 9YE  plan-4  C22  0.020
 9YE  plan-4  C23  0.020
 9YE  plan-4  H18  0.020

