# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:02:53 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 5-[(E)-{(2S)-2-[(6-aminohexanoyl)amino]-2,3-dihydro-1H-inden-1-ylidene}methyl]-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCC(=O)N[C@H]1Cc2ccccc2\C1=C/c3ccc4OCOc4c3C(O)=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
 Y7N  Y7N  '5-[(E)-{(2S)-2-[(6-aminohexanoyl)amino]-2,3-dihydro-1H-inden-1-ylidene}methyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  56  31  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y7N
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
 Y7N  C1    C  CR16   0  -0.257  -3.2799  -3.7672  -0.4956
 Y7N  C2    C  CR16   0  -0.260  -2.5449  -4.9492  -0.4584
 Y7N  C3    C  CR16   0  -0.322  -2.6502  -2.5359  -0.3781
 Y7N  C4    C  CR16   0  -0.304  -2.4732  -0.0717   1.7632
 Y7N  C5    C  CR16   0  -0.316  -1.1631  -4.9118  -0.3115
 Y7N  C6    C  CR16   0  -0.341  -3.7001   0.3788   2.2550
 Y7N  C7    C  CR56   0   0.099  -1.2671  -2.4943  -0.2205
 Y7N  C8    C  CR6    0  -0.005  -1.8767   0.4724   0.6291
 Y7N  C9    C  CR6    0  -0.201  -2.5051   1.5246  -0.0786
 Y7N  C10   C  CR56   0   0.051  -0.5319  -3.6839  -0.1988
 Y7N  C11   C  CR56   0   0.285  -4.3022   1.3912   1.5525
 Y7N  C12   C  CR56   0   0.292  -3.7275   1.9327   0.4133
 Y7N  C13   C  CR5    0   0.106  -0.3472  -1.3547  -0.1164
 Y7N  C14   C  C1     0  -0.343  -0.5771  -0.0775   0.1971
 Y7N  C15   C  C      0   0.375  -1.9126   2.1730  -1.3200
 Y7N  C17   C  CH2    0  -0.496   0.9320  -3.4004  -0.0364
 Y7N  C18   C  CH2    0   0.066  -5.5389   3.1128   0.9198
 Y7N  C19   C  CR15   0  -0.123   1.0330  -1.9163  -0.4355
 Y7N  C20   C  CH2    0  -0.591   4.0422   0.2250   0.3950
 Y7N  C21   C  CH2    0  -0.411   5.4100   0.4304  -0.2396
 Y7N  C22   C  CH2    0  -0.421   6.3469   1.2214   0.6636
 Y7N  C23   C  CH2    0  -0.425   7.7158   1.4522   0.0373
 Y7N  C24   C  CH2    0  -0.272   8.6498   2.2434   0.9390
 Y7N  N26   N  NH1    0  -0.645   2.1219  -1.2145   0.1812
 Y7N  N25   N  NH2    0  -0.801   9.9474   2.4399   0.3074
 Y7N  O31   O  O      0  -0.587  -2.7165   2.4569  -2.2256
 Y7N  O27   O  OC    -1  -0.582  -0.6845   2.3706  -1.3125
 Y7N  O28   O  O      0  -0.497   3.1393  -0.5019  -1.7083
 Y7N  O29   O  O      0  -0.489  -5.4906   1.9987   1.7988
 Y7N  O30   O  O      0  -0.476  -4.5539   2.8958  -0.0753
 Y7N  H1    H  HCR6   0   0.254  -4.3540  -3.8076  -0.6229
 Y7N  H2    H  HCR6   0   0.254  -3.0520  -5.9008  -0.5538
 Y7N  H3    H  HCR6   0   0.251  -3.2362  -1.6281  -0.4202
 Y7N  H5    H  HCR6   0   0.249  -0.5895  -5.8306  -0.2916
 Y7N  H6    H  HCR6   0   0.267  -4.1444  -0.0474   3.1442
 Y7N  H14   H  H      0   0.245   0.2581   0.6110   0.1659
 Y7N  H171  H  HCH2   0   0.258   1.2351  -3.5339   1.0078
 Y7N  H172  H  HCH2   0   0.261   1.5713  -4.0408  -0.6445
 Y7N  H19   H  HCR5   0   0.281   1.1820  -1.8640  -1.5165
 Y7N  H201  H  HCH2   0   0.269   3.5888   1.1985   0.6152
 Y7N  H202  H  HCH2   0   0.251   4.1456  -0.2776   1.3607
 Y7N  H26   H  HNH1   0   0.395   2.1294  -1.1774   1.1891
 Y7N  H181  H  HCH2   0   0.242  -6.5239   3.1770   0.4579
 Y7N  H182  H  HCH2   0   0.225  -5.3164   4.0327   1.4741
 Y7N  H211  H  HCH2   0   0.222   5.8601  -0.5399  -0.4701
 Y7N  H212  H  HCH2   0   0.223   5.2991   0.9520  -1.1930
 Y7N  H221  H  HCH2   0   0.213   5.8879   2.1861   0.9070
 Y7N  H222  H  HCH2   0   0.212   6.4673   0.6960   1.6174
 Y7N  H231  H  HCH2   0   0.213   8.1812   0.4918  -0.2059
 Y7N  H232  H  HCH2   0   0.210   7.5929   1.9838  -0.9135
 Y7N  H241  H  HCH2   0   0.187   8.1546   3.1831   1.2256
 Y7N  H242  H  HCH2   0   0.210   8.8042   1.6870   1.8680
 Y7N  H251  H  HNH2   0   0.336   9.8392   3.0563  -0.4889
 Y7N  H252  H  HNH2   0   0.345  10.5622   2.9287   0.9455
 Y7N  C16   C  C      0   0.566   3.0724  -0.5309  -0.4879
 Y7N  H4    H  HCR6   0   0.249  -1.9668  -0.8720   2.2870

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
 Y7N  C1   C2    aromatic  1.392  0.020  1.392
 Y7N  C1   C3    aromatic  1.388  0.020  1.388
 Y7N  C2   C5    aromatic  1.390  0.020  1.390
 Y7N  C3   C7    aromatic  1.393  0.020  1.393
 Y7N  C4   C6    aromatic  1.396  0.020  1.396
 Y7N  C4   C8    aromatic  1.392  0.020  1.392
 Y7N  C5   C10   aromatic  1.385  0.020  1.385
 Y7N  C6   C11   aromatic  1.371  0.020  1.371
 Y7N  C7   C10   aromatic  1.399  0.020  1.399
 Y7N  C7   C13   single    1.468  0.020  1.468
 Y7N  C8   C9    aromatic  1.415  0.020  1.415
 Y7N  C8   C14   single    1.476  0.020  1.476
 Y7N  C9   C12   aromatic  1.379  0.020  1.379
 Y7N  C9   C15   single    1.521  0.020  1.521
 Y7N  C10  C17   single    1.500  0.020  1.500
 Y7N  C11  C12   aromatic  1.386  0.020  1.386
 Y7N  C11  O29   single    1.357  0.020  1.357
 Y7N  C12  O30   single    1.360  0.020  1.360
 Y7N  C13  C14   double    1.335  0.020  1.335
 Y7N  C13  C19   single    1.524  0.020  1.524
 Y7N  C15  O31   deloc     1.244  0.020  1.244
 Y7N  C15  O27   deloc     1.244  0.020  1.244
 Y7N  C16  C20   single    1.514  0.020  1.514
 Y7N  C16  N26   single    1.349  0.020  1.349
 Y7N  C16  O28   double    1.223  0.020  1.223
 Y7N  C17  C19   single    1.540  0.020  1.540
 Y7N  C18  O29   single    1.420  0.020  1.420
 Y7N  C18  O30   single    1.417  0.020  1.417
 Y7N  C19  N26   single    1.435  0.020  1.435
 Y7N  C20  C21   single    1.522  0.020  1.522
 Y7N  C21  C22   single    1.523  0.020  1.523
 Y7N  C22  C23   single    1.523  0.020  1.523
 Y7N  C23  C24   single    1.520  0.020  1.520
 Y7N  C24  N25   single    1.456  0.020  1.456
 Y7N  C1   H1    single    0.930  0.020  1.080
 Y7N  C2   H2    single    0.930  0.020  1.080
 Y7N  C3   H3    single    0.930  0.020  1.080
 Y7N  C5   H5    single    0.930  0.020  1.080
 Y7N  C4   H4    single    0.930  0.020  1.080
 Y7N  C6   H6    single    0.930  0.020  1.080
 Y7N  C14  H14   single    0.930  0.020  1.080
 Y7N  C17  H171  single    0.970  0.020  1.090
 Y7N  C17  H172  single    0.970  0.020  1.090
 Y7N  C19  H19   single    0.970  0.020  1.090
 Y7N  C20  H201  single    0.970  0.020  1.090
 Y7N  C20  H202  single    0.970  0.020  1.090
 Y7N  N26  H26   single    0.860  0.020  1.020
 Y7N  C18  H181  single    0.970  0.020  1.090
 Y7N  C18  H182  single    0.970  0.020  1.090
 Y7N  C21  H211  single    0.970  0.020  1.090
 Y7N  C21  H212  single    0.970  0.020  1.090
 Y7N  C22  H221  single    0.970  0.020  1.090
 Y7N  C22  H222  single    0.970  0.020  1.090
 Y7N  C23  H231  single    0.970  0.020  1.090
 Y7N  C23  H232  single    0.970  0.020  1.090
 Y7N  C24  H241  single    0.970  0.020  1.090
 Y7N  C24  H242  single    0.970  0.020  1.090
 Y7N  N25  H251  single    0.890  0.020  1.040
 Y7N  N25  H252  single    0.890  0.020  1.040

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
 Y7N  H1    C1   C3    119.56  3.000
 Y7N  H1    C1   C2    119.68  3.000
 Y7N  C3    C1   C2    120.75  3.000
 Y7N  H2    C2   C5    119.91  3.000
 Y7N  H2    C2   C1    119.78  3.000
 Y7N  C5    C2   C1    120.31  3.000
 Y7N  H3    C3   C7    121.17  3.000
 Y7N  H3    C3   C1    119.71  3.000
 Y7N  C7    C3   C1    119.12  3.000
 Y7N  H4    C4   C8    118.87  3.000
 Y7N  H4    C4   C6    118.63  3.000
 Y7N  C8    C4   C6    122.50  3.000
 Y7N  H5    C5   C10   120.60  3.000
 Y7N  H5    C5   C2    120.36  3.000
 Y7N  C10   C5   C2    119.04  3.000
 Y7N  H6    C6   C11   122.12  3.000
 Y7N  H6    C6   C4    121.55  3.000
 Y7N  C11   C6   C4    116.32  3.000
 Y7N  C13   C7   C10   109.25  3.000
 Y7N  C13   C7   C3    130.80  3.000
 Y7N  C10   C7   C3    119.89  3.000
 Y7N  C14   C8   C9    121.45  3.000
 Y7N  C14   C8   C4    118.04  3.000
 Y7N  C9    C8   C4    120.51  3.000
 Y7N  C15   C9   C12   120.68  3.000
 Y7N  C15   C9   C8    123.52  3.000
 Y7N  C12   C9   C8    115.79  3.000
 Y7N  C17   C10  C7    110.73  3.000
 Y7N  C17   C10  C5    128.40  3.000
 Y7N  C7    C10  C5    120.87  3.000
 Y7N  O29   C11  C12   109.72  3.000
 Y7N  O29   C11  C6    128.45  3.000
 Y7N  C12   C11  C6    121.83  3.000
 Y7N  O30   C12  C11   108.66  3.000
 Y7N  O30   C12  C9    128.31  3.000
 Y7N  C11   C12  C9    123.02  3.000
 Y7N  C19   C13  C14   123.90  3.000
 Y7N  C19   C13  C7    105.46  3.000
 Y7N  C14   C13  C7    130.64  3.000
 Y7N  H14   C14  C13   117.95  3.000
 Y7N  H14   C14  C8    116.79  3.000
 Y7N  C13   C14  C8    125.23  3.000
 Y7N  O27   C15  O31   127.32  3.000
 Y7N  O27   C15  C9    116.58  3.000
 Y7N  O31   C15  C9    116.09  3.000
 Y7N  H172  C17  H171  107.33  3.000
 Y7N  H172  C17  C19   112.52  3.000
 Y7N  H171  C17  C19   110.26  3.000
 Y7N  H172  C17  C10   113.64  3.000
 Y7N  H171  C17  C10   110.50  3.000
 Y7N  C19   C17  C10   102.60  3.000
 Y7N  H182  C18  H181  110.38  3.000
 Y7N  H182  C18  O30   110.01  3.000
 Y7N  H181  C18  O30   109.85  3.000
 Y7N  H182  C18  O29   109.77  3.000
 Y7N  H181  C18  O29   109.84  3.000
 Y7N  O30   C18  O29   106.92  3.000
 Y7N  H19   C19  N26   107.36  3.000
 Y7N  H19   C19  C17   108.15  3.000
 Y7N  N26   C19  C17   114.19  3.000
 Y7N  H19   C19  C13   108.25  3.000
 Y7N  N26   C19  C13   114.65  3.000
 Y7N  C17   C19  C13   103.97  3.000
 Y7N  H202  C20  H201  105.66  3.000
 Y7N  H202  C20  C21   110.20  3.000
 Y7N  H201  C20  C21   109.61  3.000
 Y7N  H202  C20  C16   110.25  3.000
 Y7N  H201  C20  C16   107.19  3.000
 Y7N  C21   C20  C16   113.58  3.000
 Y7N  H212  C21  H211  106.34  3.000
 Y7N  H212  C21  C22   109.39  3.000
 Y7N  H211  C21  C22   109.42  3.000
 Y7N  H212  C21  C20   109.71  3.000
 Y7N  H211  C21  C20   109.75  3.000
 Y7N  C22   C21  C20   112.07  3.000
 Y7N  H222  C22  H221  105.95  3.000
 Y7N  H222  C22  C23   109.38  3.000
 Y7N  H221  C22  C23   109.53  3.000
 Y7N  H222  C22  C21   109.57  3.000
 Y7N  H221  C22  C21   109.36  3.000
 Y7N  C23   C22  C21   112.82  3.000
 Y7N  H232  C23  H231  106.29  3.000
 Y7N  H232  C23  C24   109.33  3.000
 Y7N  H231  C23  C24   109.10  3.000
 Y7N  H232  C23  C22   109.23  3.000
 Y7N  H231  C23  C22   109.91  3.000
 Y7N  C24   C23  C22   112.78  3.000
 Y7N  H242  C24  H241  106.07  3.000
 Y7N  H242  C24  N25   108.13  3.000
 Y7N  H241  C24  N25   113.50  3.000
 Y7N  H242  C24  C23   109.01  3.000
 Y7N  H241  C24  C23   108.81  3.000
 Y7N  N25   C24  C23   111.12  3.000
 Y7N  H26   N26  C19   116.95  3.000
 Y7N  H26   N26  C16   118.16  3.000
 Y7N  C19   N26  C16   124.72  3.000
 Y7N  H252  N25  H251  105.47  3.000
 Y7N  H252  N25  C24   109.45  3.000
 Y7N  H251  N25  C24   109.14  3.000
 Y7N  C18   O29  C11   105.59  3.000
 Y7N  C18   O30  C12   106.18  3.000
 Y7N  O28   C16  N26   123.09  3.000
 Y7N  O28   C16  C20   122.37  3.000
 Y7N  N26   C16  C20   114.54  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
 Y7N  CONST_01  C10   C5   C2   C1      0.00   0.0  0
 Y7N  CONST_02  C10   C7   C3   C1      0.00   0.0  0
 Y7N  CONST_03  C7    C3   C1   C2      0.00   0.0  0
 Y7N  CONST_04  C7    C10  C5   C2      0.00   0.0  0
 Y7N  CONST_05  C5    C2   C1   C3      0.00   0.0  0
 Y7N  CONST_06  C5    C10  C7   C3      0.00   0.0  0
 Y7N  CONST_07  C12   C11  C6   C4      0.00   0.0  0
 Y7N  CONST_08  C12   C9   C8   C4      0.00   0.0  0
 Y7N  CONST_09  C9    C8   C4   C6      0.00   0.0  0
 Y7N  CONST_10  C9    C12  C11  C6      0.00   0.0  0
 Y7N  CONST_11  C11   C6   C4   C8      0.00   0.0  0
 Y7N  CONST_12  C11   C12  C9   C8      0.00   0.0  0
 Y7N  CONST_13  C15   C9   C8   C4    180.00   0.0  0
 Y7N  CONST_14  C14   C8   C4   C6    180.00   0.0  0
 Y7N  CONST_15  C15   C9   C12  C11   180.00   0.0  0
 Y7N  CONST_16  C14   C8   C9   C12   180.00   0.0  0
 Y7N  CONST_17  O30   C12  C9   C15     0.00   0.0  0
 Y7N  CONST_18  H5    C5   C2   C1    180.00   0.0  0
 Y7N  CONST_19  H3    C3   C1   C2    180.00   0.0  0
 Y7N  CONST_20  H2    C2   C1   C3    180.00   0.0  0
 Y7N  CONST_21  H1    C1   C2   C5    180.00   0.0  0
 Y7N  CONST_22  H6    C6   C4   C8    180.00   0.0  0
 Y7N  CONST_23  H4    C4   C8   C9    180.00   0.0  0
 Y7N  CONST_24  C20   C16  N26  C19   180.00   0.0  0
 Y7N  CONST_25  O28   C16  N26  C19     0.00   0.0  0
 Y7N  CONST_26  H26   N26  C16  C20     0.00   0.0  0
 Y7N  Var_01    C19   C13  C7   C3   -161.18  30.0  1
 Y7N  Var_02    C19   C17  C10  C5    162.02  30.0  1
 Y7N  Var_03    O30   C18  O29  C11    16.65  30.0  1
 Y7N  Var_04    O29   C18  O30  C12   -16.75  30.0  1
 Y7N  Var_05    C13   C14  C8   C4     58.19  30.0  2
 Y7N  Var_06    C8    C14  C13  C7      5.04  30.0  2
 Y7N  Var_07    O31   C15  C9   C8    140.52  30.0  2
 Y7N  Var_08    C22   C21  C20  C16   178.67  30.0  3
 Y7N  Var_09    C23   C22  C21  C20  -179.27  30.0  3
 Y7N  Var_10    N26   C16  C20  C21   152.98  30.0  1
 Y7N  Var_11    C24   C23  C22  C21   179.93  30.0  3
 Y7N  Var_12    N25   C24  C23  C22   179.85  30.0  3
 Y7N  Var_13    H251  N25  C24  C23    67.77  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
 Y7N  chir_01  C19  C13  C17  N26  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
 Y7N  plan-1  C1   0.020
 Y7N  plan-1  C2   0.020
 Y7N  plan-1  C3   0.020
 Y7N  plan-1  C5   0.020
 Y7N  plan-1  C7   0.020
 Y7N  plan-1  C10  0.020
 Y7N  plan-1  C13  0.020
 Y7N  plan-1  C17  0.020
 Y7N  plan-1  H1   0.020
 Y7N  plan-1  H2   0.020
 Y7N  plan-1  H3   0.020
 Y7N  plan-1  H5   0.020
 Y7N  plan-2  C4   0.020
 Y7N  plan-2  C6   0.020
 Y7N  plan-2  C8   0.020
 Y7N  plan-2  C9   0.020
 Y7N  plan-2  C11  0.020
 Y7N  plan-2  C12  0.020
 Y7N  plan-2  C14  0.020
 Y7N  plan-2  C15  0.020
 Y7N  plan-2  O29  0.020
 Y7N  plan-2  O30  0.020
 Y7N  plan-2  H6   0.020
 Y7N  plan-2  H4   0.020
 Y7N  plan-3  C19  0.020
 Y7N  plan-3  C20  0.020
 Y7N  plan-3  N26  0.020
 Y7N  plan-3  O28  0.020
 Y7N  plan-3  H26  0.020
 Y7N  plan-3  C16  0.020
 Y7N  plan-4  C9   0.020
 Y7N  plan-4  C15  0.020
 Y7N  plan-4  O31  0.020
 Y7N  plan-4  O27  0.020

