# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 09:36:35 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  57  31  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.256  -3.3337  -3.6053  -0.4945
 Y7N  C2    C  CR16  0  -0.257  -2.6150  -4.7976  -0.5088
 Y7N  C3    C  CR16  0  -0.321  -2.6827  -2.3866  -0.3629
 Y7N  C4    C  CR16  0  -0.294  -2.3658   0.0726   1.8922
 Y7N  C5    C  CR16  0  -0.314  -1.2296  -4.7850  -0.3975
 Y7N  C6    C  CR16  0  -0.321  -3.5997   0.4719   2.4154
 Y7N  C7    C  CR56  0   0.105  -1.2954  -2.3705  -0.2436
 Y7N  C8    C  CR6   0   0.020  -1.8742   0.5453   0.6840
 Y7N  C9    C  CR6   0  -0.206  -2.6371   1.4782  -0.0676
 Y7N  C10   C  CR56  0   0.053  -0.5768  -3.5701  -0.2689
 Y7N  C11   C  CR56  0   0.300  -4.3259   1.3613   1.6714
 Y7N  C12   C  CR56  0   0.332  -3.8650   1.8455   0.4553
 Y7N  C13   C  CR5   0   0.123  -0.3564  -1.2494  -0.1236
 Y7N  C14   C  C1    0  -0.351  -0.5690   0.0171   0.2330
 Y7N  C15   C  C     0   0.508  -2.2383   2.0356  -1.3795
 Y7N  C17   C  CH2   0  -0.497   0.8942  -3.3139  -0.1275
 Y7N  C18   C  CH2   0   0.068  -5.7871   2.8608   0.9328
 Y7N  C19   C  CR15  0  -0.123   1.0121  -1.8179  -0.4736
 Y7N  C20   C  CH2   0  -0.590   4.0555   0.2565   0.3996
 Y7N  C21   C  CH2   0  -0.412   5.4247   0.4402  -0.2391
 Y7N  C22   C  CH2   0  -0.421   6.3838   1.1915   0.6747
 Y7N  C23   C  CH2   0  -0.425   7.7577   1.3978   0.0510
 Y7N  C24   C  CH2   0  -0.271   8.7080   2.1578   0.9626
 Y7N  N26   N  NH1   0  -0.647   2.1156  -1.1527   0.1564
 Y7N  N25   N  NH2   0  -0.801  10.0115   2.3298   0.3361
 Y7N  O31   O  O     0  -0.432  -3.0258   2.4763  -2.1824
 Y7N  O27   O  OH1   0  -0.586  -0.9311   2.0211  -1.5810
 Y7N  O28   O  O     0  -0.494   3.0947  -0.3485  -1.7162
 Y7N  O29   O  O     0  -0.481  -5.5399   1.8929   1.9402
 Y7N  O30   O  O     0  -0.464  -4.7770   2.6920  -0.0566
 Y7N  H1    H  HCR6  0   0.256  -4.4112  -3.6269  -0.5931
 Y7N  H2    H  HCR6  0   0.257  -3.1387  -5.7389  -0.6161
 Y7N  H3    H  HCR6  0   0.250  -3.2582  -1.4709  -0.3677
 Y7N  H5    H  HCR6  0   0.251  -0.6704  -5.7125  -0.4169
 Y7N  H4    H  HCR6  0   0.263  -1.7717  -0.6384   2.4498
 Y7N  H6    H  HCR6  0   0.283  -3.9566   0.0918   3.3627
 Y7N  H14   H  H     0   0.253   0.2774   0.6948   0.2521
 Y7N  H171  H  HCH2  0   0.261   1.2153  -3.4908   0.9045
 Y7N  H172  H  HCH2  0   0.264   1.5109  -3.9405  -0.7719
 Y7N  H19   H  HCR5  0   0.286   1.1485  -1.7258  -1.5535
 Y7N  H27   H  HOH1  0   0.488  -0.7301   2.3687  -2.4633
 Y7N  H201  H  HCH2  0   0.269   3.6325   1.2364   0.6497
 Y7N  H202  H  HCH2  0   0.251   4.1507  -0.2761   1.3498
 Y7N  H26   H  HNH1  0   0.397   2.1533  -1.1790   1.1638
 Y7N  H181  H  HCH2  0   0.250  -6.7673   2.6933   0.4860
 Y7N  H182  H  HCH2  0   0.241  -5.7234   3.8680   1.3555
 Y7N  H211  H  HCH2  0   0.223   5.8495  -0.5365  -0.4901
 Y7N  H212  H  HCH2  0   0.223   5.3214   0.9824  -1.1818
 Y7N  H221  H  HCH2  0   0.213   5.9498   2.1634   0.9344
 Y7N  H222  H  HCH2  0   0.212   6.4915   0.6476   1.6196
 Y7N  H231  H  HCH2  0   0.213   8.2016   0.4300  -0.2028
 Y7N  H232  H  HCH2  0   0.210   7.6478   1.9432  -0.8936
 Y7N  H241  H  HCH2  0   0.186   8.2342   3.1060   1.2572
 Y7N  H242  H  HCH2  0   0.210   8.8466   1.5887   1.8864
 Y7N  H251  H  HNH2  0   0.336   9.9173   2.9470  -0.4616
 Y7N  H252  H  HNH2  0   0.345  10.6321   2.8089   0.9760
 Y7N  C16   C  C     0   0.567   3.0580  -0.4429  -0.4982

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  1.399  0.020  1.399
 Y7N  C4   C8    aromatic  1.387  0.020  1.387
 Y7N  C5   C10   aromatic  1.385  0.020  1.385
 Y7N  C6   C11   aromatic  1.368  0.020  1.368
 Y7N  C7   C10   aromatic  1.399  0.020  1.399
 Y7N  C7   C13   single    1.467  0.020  1.467
 Y7N  C8   C9    aromatic  1.420  0.020  1.420
 Y7N  C8   C14   single    1.479  0.020  1.479
 Y7N  C9   C12   aromatic  1.384  0.020  1.384
 Y7N  C9   C15   single    1.480  0.020  1.480
 Y7N  C10  C17   single    1.500  0.020  1.500
 Y7N  C11  C12   aromatic  1.388  0.020  1.388
 Y7N  C11  O29   single    1.352  0.020  1.352
 Y7N  C12  O30   single    1.345  0.020  1.345
 Y7N  C13  C14   double    1.333  0.020  1.333
 Y7N  C13  C19   single    1.523  0.020  1.523
 Y7N  C15  O31   double    1.208  0.020  1.208
 Y7N  C15  O27   single    1.323  0.020  1.323
 Y7N  C16  C20   single    1.513  0.020  1.513
 Y7N  C16  N26   single    1.349  0.020  1.349
 Y7N  C16  O28   double    1.222  0.020  1.222
 Y7N  C17  C19   single    1.540  0.020  1.540
 Y7N  C18  O29   single    1.419  0.020  1.419
 Y7N  C18  O30   single    1.424  0.020  1.424
 Y7N  C19  N26   single    1.434  0.020  1.434
 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  O27  H27   single    0.850  0.020  0.980
 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    119.55  3.000
 Y7N  H1    C1   C2    119.73  3.000
 Y7N  C3    C1   C2    120.72  3.000
 Y7N  H2    C2   C5    119.87  3.000
 Y7N  H2    C2   C1    119.74  3.000
 Y7N  C5    C2   C1    120.40  3.000
 Y7N  H3    C3   C7    121.38  3.000
 Y7N  H3    C3   C1    119.57  3.000
 Y7N  C7    C3   C1    119.05  3.000
 Y7N  H4    C4   C8    118.58  3.000
 Y7N  H4    C4   C6    118.66  3.000
 Y7N  C8    C4   C6    122.76  3.000
 Y7N  H5    C5   C10   120.63  3.000
 Y7N  H5    C5   C2    120.35  3.000
 Y7N  C10   C5   C2    119.02  3.000
 Y7N  H6    C6   C11   121.99  3.000
 Y7N  H6    C6   C4    121.23  3.000
 Y7N  C11   C6   C4    116.77  3.000
 Y7N  C13   C7   C10   109.15  3.000
 Y7N  C13   C7   C3    130.80  3.000
 Y7N  C10   C7   C3    120.03  3.000
 Y7N  C14   C8   C9    123.19  3.000
 Y7N  C14   C8   C4    117.18  3.000
 Y7N  C9    C8   C4    119.63  3.000
 Y7N  C15   C9   C12   118.29  3.000
 Y7N  C15   C9   C8    124.87  3.000
 Y7N  C12   C9   C8    116.80  3.000
 Y7N  C17   C10  C7    110.84  3.000
 Y7N  C17   C10  C5    128.37  3.000
 Y7N  C7    C10  C5    120.79  3.000
 Y7N  O29   C11  C12   109.58  3.000
 Y7N  O29   C11  C6    128.60  3.000
 Y7N  C12   C11  C6    121.81  3.000
 Y7N  O30   C12  C11   109.13  3.000
 Y7N  O30   C12  C9    128.65  3.000
 Y7N  C11   C12  C9    122.21  3.000
 Y7N  C19   C13  C14   124.03  3.000
 Y7N  C19   C13  C7    105.73  3.000
 Y7N  C14   C13  C7    130.23  3.000
 Y7N  H14   C14  C13   118.30  3.000
 Y7N  H14   C14  C8    117.41  3.000
 Y7N  C13   C14  C8    124.19  3.000
 Y7N  O27   C15  O31   123.16  3.000
 Y7N  O27   C15  C9    113.40  3.000
 Y7N  O31   C15  C9    123.43  3.000
 Y7N  H172  C17  H171  107.35  3.000
 Y7N  H172  C17  C19   112.47  3.000
 Y7N  H171  C17  C19   110.25  3.000
 Y7N  H172  C17  C10   113.64  3.000
 Y7N  H171  C17  C10   110.42  3.000
 Y7N  C19   C17  C10   102.70  3.000
 Y7N  H182  C18  H181  110.62  3.000
 Y7N  H182  C18  O30   109.64  3.000
 Y7N  H181  C18  O30   109.57  3.000
 Y7N  H182  C18  O29   110.09  3.000
 Y7N  H181  C18  O29   110.05  3.000
 Y7N  O30   C18  O29   106.79  3.000
 Y7N  H19   C19  N26   107.40  3.000
 Y7N  H19   C19  C17   108.27  3.000
 Y7N  N26   C19  C17   114.25  3.000
 Y7N  H19   C19  C13   107.94  3.000
 Y7N  N26   C19  C13   114.67  3.000
 Y7N  C17   C19  C13   104.02  3.000
 Y7N  H202  C20  H201  105.71  3.000
 Y7N  H202  C20  C21   110.19  3.000
 Y7N  H201  C20  C21   109.57  3.000
 Y7N  H202  C20  C16   110.35  3.000
 Y7N  H201  C20  C16   107.11  3.000
 Y7N  C21   C20  C16   113.56  3.000
 Y7N  H212  C21  H211  106.37  3.000
 Y7N  H212  C21  C22   109.42  3.000
 Y7N  H211  C21  C22   109.47  3.000
 Y7N  H212  C21  C20   109.70  3.000
 Y7N  H211  C21  C20   109.74  3.000
 Y7N  C22   C21  C20   111.98  3.000
 Y7N  H222  C22  H221  105.96  3.000
 Y7N  H222  C22  C23   109.38  3.000
 Y7N  H221  C22  C23   109.53  3.000
 Y7N  H222  C22  C21   109.55  3.000
 Y7N  H221  C22  C21   109.29  3.000
 Y7N  C23   C22  C21   112.91  3.000
 Y7N  H232  C23  H231  106.31  3.000
 Y7N  H232  C23  C24   109.31  3.000
 Y7N  H231  C23  C24   109.11  3.000
 Y7N  H232  C23  C22   109.26  3.000
 Y7N  H231  C23  C22   109.94  3.000
 Y7N  C24   C23  C22   112.71  3.000
 Y7N  H242  C24  H241  106.07  3.000
 Y7N  H242  C24  N25   108.15  3.000
 Y7N  H241  C24  N25   113.50  3.000
 Y7N  H242  C24  C23   109.00  3.000
 Y7N  H241  C24  C23   108.79  3.000
 Y7N  N25   C24  C23   111.13  3.000
 Y7N  H26   N26  C19   117.09  3.000
 Y7N  H26   N26  C16   118.18  3.000
 Y7N  C19   N26  C16   124.63  3.000
 Y7N  H252  N25  H251  105.46  3.000
 Y7N  H252  N25  C24   109.43  3.000
 Y7N  H251  N25  C24   109.12  3.000
 Y7N  H27   O27  C15   109.85  3.000
 Y7N  C18   O29  C11   106.47  3.000
 Y7N  C18   O30  C12   106.93  3.000
 Y7N  O28   C16  N26   123.03  3.000
 Y7N  O28   C16  C20   122.40  3.000
 Y7N  N26   C16  C20   114.56  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  H27   O27  C15  C9    180.00   0.0  0
 Y7N  CONST_27  H26   N26  C16  C20     0.00   0.0  0
 Y7N  Var_01    C19   C13  C7   C3   -162.32  30.0  1
 Y7N  Var_02    C19   C17  C10  C5    162.84  30.0  1
 Y7N  Var_03    O30   C18  O29  C11    10.25  30.0  1
 Y7N  Var_04    O29   C18  O30  C12   -10.15  30.0  1
 Y7N  Var_05    C13   C14  C8   C4     66.72  30.0  2
 Y7N  Var_06    C8    C14  C13  C7      4.09  30.0  2
 Y7N  Var_07    O31   C15  C9   C8    156.23  30.0  2
 Y7N  Var_08    C22   C21  C20  C16   177.93  30.0  3
 Y7N  Var_09    C23   C22  C21  C20  -179.50  30.0  3
 Y7N  Var_10    N26   C16  C20  C21   151.02  30.0  1
 Y7N  Var_11    C24   C23  C22  C21   179.55  30.0  3
 Y7N  Var_12    N25   C24  C23  C22   179.72  30.0  3
 Y7N  Var_13    H251  N25  C24  C23    67.03  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  H4   0.020
 Y7N  plan-2  H6   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
 Y7N  plan-4  H27  0.020

