# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:01:42 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-(5,11-dioxo-5,11-dihydro-6H-indeno[1,2-c]isoquinolin-6-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCN1C(=O)c2ccccc2C3=C1c4ccccc4C3=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
 M38  M38  '4-(5,11-dioxo-5,11-dihydro-6H-indeno[1,2-c]isoquinolin-6-yl)butanoic acid'  ligand  39  25  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M38
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
 M38  C1    C  CR16   0  -0.352   3.4377   4.7849   5.6689
 M38  C2    C  CR16   0  -0.226   4.2640   5.7795   6.1435
 M38  C3    C  CR16   0  -0.260   5.0880   6.5040   5.2763
 M38  C4    C  CR16   0  -0.274   5.0743   6.2223   3.9288
 M38  C5    C  CR66   0  -0.183   4.2421   5.2142   3.4285
 M38  C6    C  CR66   0   0.356   3.4134   4.4843   4.2969
 M38  C7    C  CR56   0  -0.245   2.5880   3.4823   3.7064
 M38  C8    C  CR56   0   0.324   2.6221   3.2342   2.3568
 M38  C9    C  CR6    0   0.540   4.2622   4.9440   1.9907
 M38  N10   N  NR6    0  -0.615   3.4500   3.9029   1.5239
 M38  C11   C  CR5    0   0.331   1.6230   2.5770   4.3292
 M38  C12   C  CR56   0  -0.074   1.0559   1.7640   3.2176
 M38  C13   C  CR56   0   0.170   1.6451   2.1624   2.0116
 M38  C14   C  CR16   0  -0.284   0.0940   0.7875   3.2866
 M38  C15   C  CR16   0  -0.254  -0.3085   0.1743   2.0973
 M38  C16   C  CR16   0  -0.233   0.2527   0.5667   0.8961
 M38  C17   C  CR16   0  -0.321   1.2306   1.5664   0.8352
 M38  O18   O  O      0  -0.383   1.3200   2.4799   5.4987
 M38  O19   O  OC    -1  -0.629   1.6730   4.4792  -4.3273
 M38  O20   O  O      0  -0.605   0.6838   5.4144  -2.5636
 M38  O21   O  OC     0  -0.449   4.9524   5.5707   1.2076
 M38  C22   C  CH2    0  -0.346   3.5215   3.6006   0.0924
 M38  C23   C  CH2    0  -0.442   2.4822   4.3590  -0.7204
 M38  C24   C  C      0   0.419   1.5463   4.6960  -3.1045
 M38  C25   C  CH2    0  -0.595   2.5612   3.9840  -2.1902
 M38  H1    H  HCR6   0   0.263   2.8056   4.2389   6.3530
 M38  H2    H  HCR6   0   0.269   4.2734   6.0028   7.2025
 M38  H3    H  HCR6   0   0.265   5.7316   7.2827   5.6630
 M38  H4    H  HCR6   0   0.265   5.7091   6.7760   3.2509
 M38  H14   H  HCR6   0   0.271  -0.3434   0.5045   4.2354
 M38  H15   H  HCR6   0   0.274  -1.0625  -0.6005   2.1146
 M38  H16   H  HCR6   0   0.276  -0.0669   0.0974  -0.0246
 M38  H17   H  HCR6   0   0.270   1.6152   1.8355  -0.1360
 M38  H221  H  HCH2   0   0.267   3.4332   2.5228  -0.0249
 M38  H222  H  HCH2   0   0.284   4.5228   3.8552  -0.2453
 M38  H231  H  HCH2   0   0.228   1.4807   4.1541  -0.3354
 M38  H232  H  HCH2   0   0.241   2.6461   5.4310  -0.5939
 M38  H251  H  HCH2   0   0.230   2.4171   2.9024  -2.3062
 M38  H252  H  HCH2   0   0.229   3.5699   4.1776  -2.5707

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
 M38  C1   C2    aromatic  1.377  0.020  1.377
 M38  C1   C6    aromatic  1.405  0.020  1.405
 M38  C1   H1    single    0.930  0.020  1.080
 M38  C2   C3    aromatic  1.399  0.020  1.399
 M38  C2   H2    single    0.930  0.020  1.080
 M38  C3   C4    aromatic  1.377  0.020  1.377
 M38  C3   H3    single    0.930  0.020  1.080
 M38  C4   C5    aromatic  1.400  0.020  1.400
 M38  C4   H4    single    0.930  0.020  1.080
 M38  C5   C6    aromatic  1.405  0.020  1.405
 M38  C5   C9    aromatic  1.463  0.020  1.463
 M38  C6   C7    aromatic  1.426  0.020  1.426
 M38  C7   C8    aromatic  1.373  0.020  1.373
 M38  C7   C11   single    1.462  0.020  1.462
 M38  C8   N10   aromatic  1.351  0.020  1.351
 M38  C8   C13   aromatic  1.491  0.020  1.491
 M38  C9   N10   aromatic  1.401  0.020  1.401
 M38  C9   O21   double    1.218  0.020  1.218
 M38  N10  C22   single    1.465  0.020  1.465
 M38  C11  C12   single    1.489  0.020  1.489
 M38  C11  O18   double    1.212  0.020  1.212
 M38  C12  C13   aromatic  1.400  0.020  1.400
 M38  C12  C14   aromatic  1.372  0.020  1.372
 M38  C13  C17   aromatic  1.382  0.020  1.382
 M38  C14  C15   aromatic  1.397  0.020  1.397
 M38  C14  H14   single    0.930  0.020  1.080
 M38  C15  C16   aromatic  1.383  0.020  1.383
 M38  C15  H15   single    0.930  0.020  1.080
 M38  C16  C17   aromatic  1.400  0.020  1.400
 M38  C16  H16   single    0.930  0.020  1.080
 M38  C17  H17   single    0.930  0.020  1.080
 M38  O19  C24   deloc     1.248  0.020  1.248
 M38  O20  C24   deloc     1.246  0.020  1.246
 M38  C22  C23   single    1.522  0.020  1.522
 M38  C22  H221  single    0.970  0.020  1.090
 M38  C22  H222  single    0.970  0.020  1.090
 M38  C23  C25   single    1.519  0.020  1.519
 M38  C23  H231  single    0.970  0.020  1.090
 M38  C23  H232  single    0.970  0.020  1.090
 M38  C24  C25   single    1.540  0.020  1.540
 M38  C25  H251  single    0.970  0.020  1.090
 M38  C25  H252  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
 M38  H1    C1   C6    120.03  3.000
 M38  H1    C1   C2    119.88  3.000
 M38  C6    C1   C2    120.09  3.000
 M38  H2    C2   C3    119.65  3.000
 M38  H2    C2   C1    119.42  3.000
 M38  C3    C2   C1    120.92  3.000
 M38  H3    C3   C4    120.21  3.000
 M38  H3    C3   C2    120.12  3.000
 M38  C4    C3   C2    119.67  3.000
 M38  H4    C4   C5    119.59  3.000
 M38  H4    C4   C3    120.20  3.000
 M38  C5    C4   C3    120.21  3.000
 M38  C9    C5   C6    121.30  3.000
 M38  C9    C5   C4    118.43  3.000
 M38  C6    C5   C4    120.26  3.000
 M38  C7    C6   C5    116.77  3.000
 M38  C7    C6   C1    124.39  3.000
 M38  C5    C6   C1    118.84  3.000
 M38  C11   C7   C8    108.86  3.000
 M38  C11   C7   C6    129.83  3.000
 M38  C8    C7   C6    121.31  3.000
 M38  C13   C8   N10   127.92  3.000
 M38  C13   C8   C7    109.96  3.000
 M38  N10   C8   C7    122.12  3.000
 M38  O21   C9   N10   119.80  3.000
 M38  O21   C9   C5    123.01  3.000
 M38  N10   C9   C5    117.19  3.000
 M38  C22   N10  C9    116.80  3.000
 M38  C22   N10  C8    122.01  3.000
 M38  C9    N10  C8    121.18  3.000
 M38  O18   C11  C12   125.54  3.000
 M38  O18   C11  C7    128.72  3.000
 M38  C12   C11  C7    105.74  3.000
 M38  C14   C12  C13   122.73  3.000
 M38  C14   C12  C11   128.15  3.000
 M38  C13   C12  C11   109.11  3.000
 M38  C17   C13  C12   118.96  3.000
 M38  C17   C13  C8    134.71  3.000
 M38  C12   C13  C8    106.32  3.000
 M38  H14   C14  C15   121.00  3.000
 M38  H14   C14  C12   120.88  3.000
 M38  C15   C14  C12   118.12  3.000
 M38  H15   C15  C16   120.02  3.000
 M38  H15   C15  C14   120.11  3.000
 M38  C16   C15  C14   119.87  3.000
 M38  H16   C16  C17   118.63  3.000
 M38  H16   C16  C15   119.77  3.000
 M38  C17   C16  C15   121.60  3.000
 M38  H17   C17  C16   117.80  3.000
 M38  H17   C17  C13   123.49  3.000
 M38  C16   C17  C13   118.71  3.000
 M38  H222  C22  H221  105.86  3.000
 M38  H222  C22  C23   110.27  3.000
 M38  H221  C22  C23   112.38  3.000
 M38  H222  C22  N10   107.48  3.000
 M38  H221  C22  N10   107.81  3.000
 M38  C23   C22  N10   112.69  3.000
 M38  H232  C23  H231  106.31  3.000
 M38  H232  C23  C25   110.28  3.000
 M38  H231  C23  C25   110.03  3.000
 M38  H232  C23  C22   108.96  3.000
 M38  H231  C23  C22   110.15  3.000
 M38  C25   C23  C22   110.99  3.000
 M38  C25   C24  O20   117.70  3.000
 M38  C25   C24  O19   115.74  3.000
 M38  O20   C24  O19   126.56  3.000
 M38  H252  C25  H251  104.98  3.000
 M38  H252  C25  C24   108.59  3.000
 M38  H251  C25  C24   107.84  3.000
 M38  H252  C25  C23   109.90  3.000
 M38  H251  C25  C23   109.80  3.000
 M38  C24   C25  C23   115.21  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
 M38  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 M38  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 M38  CONST_03  C9   C5   C6   C1    180.00   0.0  0
 M38  CONST_04  C8   C7   C6   C1    180.00   0.0  0
 M38  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 M38  CONST_06  C7   C6   C1   C2    180.00   0.0  0
 M38  CONST_07  C5   C4   C3   C2      0.00   0.0  0
 M38  CONST_08  C6   C1   C2   C3      0.00   0.0  0
 M38  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 M38  CONST_10  C9   C5   C4   C3    180.00   0.0  0
 M38  CONST_11  C7   C6   C5   C4    180.00   0.0  0
 M38  CONST_12  N10  C9   C5   C4    180.00   0.0  0
 M38  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 M38  CONST_14  C8   N10  C9   C5      0.00   0.0  0
 M38  CONST_15  N10  C9   C5   C6      0.00   0.0  0
 M38  CONST_16  N10  C8   C7   C6      0.00   0.0  0
 M38  CONST_17  C13  C8   C7   C6    180.00   0.0  0
 M38  CONST_18  C9   C5   C6   C7      0.00   0.0  0
 M38  CONST_19  C9   N10  C8   C7      0.00   0.0  0
 M38  CONST_20  C12  C13  C8   C7      0.00   0.0  0
 M38  CONST_21  C17  C13  C8   C7    180.00   0.0  0
 M38  CONST_22  C14  C12  C13  C8    180.00   0.0  0
 M38  CONST_23  C16  C17  C13  C8    180.00   0.0  0
 M38  CONST_24  C13  C8   N10  C9    180.00   0.0  0
 M38  CONST_25  C12  C13  C8   N10   180.00   0.0  0
 M38  CONST_26  C17  C13  C8   N10     0.00   0.0  0
 M38  CONST_27  C16  C17  C13  C12     0.00   0.0  0
 M38  CONST_28  C16  C15  C14  C12     0.00   0.0  0
 M38  CONST_29  C15  C14  C12  C13     0.00   0.0  0
 M38  CONST_30  C15  C16  C17  C13     0.00   0.0  0
 M38  CONST_31  C17  C13  C12  C14     0.00   0.0  0
 M38  CONST_32  C17  C16  C15  C14     0.00   0.0  0
 M38  CONST_33  O21  C9   C5   C4      0.00   0.0  0
 M38  CONST_34  C22  N10  C9   C5    180.00   0.0  0
 M38  CONST_35  O21  C9   C5   C6    180.00   0.0  0
 M38  CONST_36  C22  N10  C8   C7    180.00   0.0  0
 M38  CONST_37  O21  C9   N10  C8    180.00   0.0  0
 M38  CONST_38  C22  N10  C8   C13     0.00   0.0  0
 M38  CONST_39  H3   C3   C2   C1    180.00   0.0  0
 M38  CONST_40  H4   C4   C3   C2    180.00   0.0  0
 M38  CONST_41  H1   C1   C2   C3    180.00   0.0  0
 M38  CONST_42  H2   C2   C3   C4    180.00   0.0  0
 M38  CONST_43  H17  C17  C13  C8      0.00   0.0  0
 M38  CONST_44  H14  C14  C12  C11     0.00   0.0  0
 M38  CONST_45  H15  C15  C14  C12   180.00   0.0  0
 M38  CONST_46  H16  C16  C17  C13   180.00   0.0  0
 M38  CONST_47  C22  N10  C9   O21     0.00   0.0  0
 M38  Var_01    C23  C22  N10  C8     86.55  30.0  2
 M38  Var_02    C25  C23  C22  N10  -178.18  30.0  3
 M38  Var_03    C23  C25  C24  O19   174.37  30.0  3
 M38  Var_04    C24  C25  C23  C22   179.89  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
 M38  plan-1  C1   0.020
 M38  plan-1  C2   0.020
 M38  plan-1  C3   0.020
 M38  plan-1  C4   0.020
 M38  plan-1  C5   0.020
 M38  plan-1  C6   0.020
 M38  plan-1  C7   0.020
 M38  plan-1  C8   0.020
 M38  plan-1  C9   0.020
 M38  plan-1  N10  0.020
 M38  plan-1  C11  0.020
 M38  plan-1  C12  0.020
 M38  plan-1  C13  0.020
 M38  plan-1  C14  0.020
 M38  plan-1  C15  0.020
 M38  plan-1  C16  0.020
 M38  plan-1  C17  0.020
 M38  plan-1  O18  0.020
 M38  plan-1  O21  0.020
 M38  plan-1  C22  0.020
 M38  plan-1  H1   0.020
 M38  plan-1  H2   0.020
 M38  plan-1  H3   0.020
 M38  plan-1  H4   0.020
 M38  plan-1  H14  0.020
 M38  plan-1  H15  0.020
 M38  plan-1  H16  0.020
 M38  plan-1  H17  0.020
 M38  plan-2  O19  0.020
 M38  plan-2  O20  0.020
 M38  plan-2  C24  0.020
 M38  plan-2  C25  0.020

