# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 09:36:17 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: (2S)-6-({(1R,2S)-2-[(4-aminobutanoyl)amino]-2,3-dihydro-1H-inden-1-yl}methyl)-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC(=O)N[C@H]1Cc2ccccc2[C@H]1Cc3ccc4O[C@@H](CCC(O)=O)COc4c3C(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
 3GM  3GM  '(2S)-6-({(1R,2S)-2-[(4-aminobutanoyl)amino]-2,3-dihydro-1H-inden-1-yl}methyl)-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid'  ligand  63  35  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3GM
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
 3GM  C1    C  CR16   0  -0.262   0.3006  -4.5415  -0.5129
 3GM  C2    C  CR16   0  -0.262  -0.3649  -3.5251  -1.1917
 3GM  C3    C  CR16   0  -0.332   1.5180  -4.2936   0.1134
 3GM  C4    C  CR16   0  -0.297   0.1722  -2.2439  -1.2465
 3GM  C5    C  CR16   0  -0.309  -0.6174  -0.4223   1.6370
 3GM  C6    C  CR16   0  -0.370  -2.0008  -0.4311   1.6730
 3GM  C7    C  CR6    0  -0.190  -0.6404   0.9949  -0.2999
 3GM  C8    C  CR6    0   0.087   2.0533  -3.0160   0.0544
 3GM  C9    C  CR6    0   0.138   1.3812  -1.9974  -0.6151
 3GM  C10   C  CR6    0   0.100   0.0796   0.2783   0.6560
 3GM  C11   C  CR6    0   0.294  -2.7190   0.2741   0.7183
 3GM  C12   C  CR6    0   0.307  -2.0308   0.9885  -0.2625
 3GM  C15   C  C      0   0.416  -8.4105  -0.1880   0.6834
 3GM  C16   C  CH2    0  -0.521   3.3448  -2.5010   0.6218
 3GM  C17   C  CH2    0  -0.182  -4.0599   1.9450  -0.9130
 3GM  C18   C  CH1    0  -0.327   2.1340  -0.7014  -0.5077
 3GM  C19   C  CH1    0  -0.056   3.5618  -1.2186  -0.1954
 3GM  C20   C  CH1    0  -0.012  -4.7360   0.6836  -0.4127
 3GM  C21   C  CH2    0  -0.508   1.5815   0.2017   0.6179
 3GM  C22   C  CH2    0  -0.571   5.9944   1.5588   0.6647
 3GM  C24   C  CH2    0  -0.445  -6.1996   0.9049  -0.0889
 3GM  C25   C  CH2    0  -0.429   7.4677   1.4683   0.2753
 3GM  C26   C  CH2    0  -0.272   8.3310   2.4237   1.0846
 3GM  N27   N  NH1    0  -0.651   4.4421  -0.2865   0.4612
 3GM  N28   N  NH2    0  -0.800   9.7286   2.3096   0.6952
 3GM  O29   O  O      0  -0.588   0.0893   1.2116  -2.5219
 3GM  O30   O  OC    -1  -0.631  -9.0278  -1.2381   0.9597
 3GM  O31   O  OC    -1  -0.595   0.5158   2.8814  -1.1019
 3GM  O32   O  O      0  -0.503   5.0946   0.7808  -1.4135
 3GM  O33   O  O      0  -0.608  -8.8920   0.9608   0.6351
 3GM  O34   O  O2     0  -0.481  -2.6961   1.7046  -1.2090
 3GM  O35   O  O2     0  -0.491  -4.0738   0.2455   0.7700
 3GM  H1    H  HCR6   0   0.246  -0.1264  -5.5362  -0.4817
 3GM  H2    H  HCR6   0   0.244  -1.3067  -3.7361  -1.6825
 3GM  H3    H  HCR6   0   0.242   2.0385  -5.0912   0.6303
 3GM  H4    H  HCR6   0   0.247  -0.3354  -1.4478  -1.7773
 3GM  H5    H  HCR6   0   0.230  -0.0677  -0.9857   2.3817
 3GM  H6    H  HCR6   0   0.250  -2.5341  -0.9815   2.4386
 3GM  H161  H  HCH2   0   0.248   3.2382  -2.2791   1.6906
 3GM  H162  H  HCH2   0   0.263   4.1753  -3.2017   0.5253
 3GM  H18   H  HCH1   0   0.260   2.1179  -0.1460  -1.4460
 3GM  H211  H  HCH2   0   0.246   2.0063   1.2004   0.5016
 3GM  H212  H  HCH2   0   0.234   1.9278  -0.1732   1.5850
 3GM  H221  H  HCH2   0   0.259   5.6413   2.5850   0.5255
 3GM  H222  H  HCH2   0   0.246   5.8724   1.3261   1.7251
 3GM  H27   H  HNH1   0   0.396   4.4901  -0.3044   1.4670
 3GM  H231  H  HCH2   0   0.233  -6.4285  -0.7348   1.2956
 3GM  H232  H  HCH2   0   0.220  -6.7900  -1.1481  -0.3561
 3GM  H19   H  HCH1   0   0.272   4.0218  -1.4980  -1.1462
 3GM  H171  H  HCH2   0   0.250  -4.5305   2.2849  -1.8352
 3GM  H172  H  HCH2   0   0.226  -4.1542   2.7421  -0.1648
 3GM  H20   H  HCH1   0   0.232  -4.6382  -0.0948  -1.1833
 3GM  H241  H  HCH2   0   0.221  -6.2895   1.7007   0.6554
 3GM  H242  H  HCH2   0   0.227  -6.6847   1.2749  -0.9959
 3GM  H251  H  HCH2   0   0.226   7.8195   0.4427   0.4280
 3GM  H252  H  HCH2   0   0.229   7.5866   1.6903  -0.7870
 3GM  H261  H  HCH2   0   0.215   8.0046   3.4486   0.8875
 3GM  H262  H  HCH2   0   0.190   8.1564   2.2459   2.1558
 3GM  H281  H  HNH2   0   0.347  10.2772   2.9939   1.2000
 3GM  H282  H  HNH2   0   0.338  10.0850   1.4075   0.9870
 3GM  C23   C  CH2    0  -0.587  -6.9088  -0.3536   0.3889
 3GM  C14   C  C      0   0.548   5.1352   0.6596  -0.1960
 3GM  C13   C  C      0   0.355   0.0509   1.7696  -1.4103

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
 3GM  C1   C2    aromatic  1.392  0.020  1.392
 3GM  C1   C3    aromatic  1.391  0.020  1.391
 3GM  C2   C4    aromatic  1.390  0.020  1.390
 3GM  C3   C8    aromatic  1.386  0.020  1.386
 3GM  C4   C9    aromatic  1.386  0.020  1.386
 3GM  C5   C6    aromatic  1.384  0.020  1.384
 3GM  C5   C10   aromatic  1.393  0.020  1.393
 3GM  C6   C11   aromatic  1.387  0.020  1.387
 3GM  C7   C10   aromatic  1.395  0.020  1.395
 3GM  C7   C12   aromatic  1.391  0.020  1.391
 3GM  C7   C13   single    1.520  0.020  1.520
 3GM  C8   C9    aromatic  1.392  0.020  1.392
 3GM  C8   C16   single    1.502  0.020  1.502
 3GM  C9   C18   single    1.503  0.020  1.503
 3GM  C10  C21   single    1.504  0.020  1.504
 3GM  C11  C12   aromatic  1.395  0.020  1.395
 3GM  C11  O35   single    1.356  0.020  1.356
 3GM  C12  O34   single    1.361  0.020  1.361
 3GM  C13  O29   deloc     1.244  0.020  1.244
 3GM  C13  O31   deloc     1.244  0.020  1.244
 3GM  C14  C22   single    1.512  0.020  1.512
 3GM  C14  N27   single    1.344  0.020  1.344
 3GM  C14  O32   double    1.224  0.020  1.224
 3GM  C15  C23   single    1.539  0.020  1.539
 3GM  C15  O30   deloc     1.249  0.020  1.249
 3GM  C15  O33   deloc     1.246  0.020  1.246
 3GM  C16  C19   single    1.536  0.020  1.536
 3GM  C17  C20   single    1.516  0.020  1.516
 3GM  C17  O34   single    1.416  0.020  1.416
 3GM  C18  C19   single    1.550  0.020  1.550
 3GM  C18  C21   single    1.545  0.020  1.545
 3GM  C19  N27   single    1.440  0.020  1.440
 3GM  C20  C24   single    1.515  0.020  1.515
 3GM  C20  O35   single    1.425  0.020  1.425
 3GM  C22  C25   single    1.527  0.020  1.527
 3GM  C23  C24   single    1.521  0.020  1.521
 3GM  C25  C26   single    1.521  0.020  1.521
 3GM  C26  N28   single    1.455  0.020  1.455
 3GM  C1   H1    single    0.930  0.020  1.080
 3GM  C2   H2    single    0.930  0.020  1.080
 3GM  C3   H3    single    0.930  0.020  1.080
 3GM  C4   H4    single    0.930  0.020  1.080
 3GM  C5   H5    single    0.930  0.020  1.080
 3GM  C6   H6    single    0.930  0.020  1.080
 3GM  C16  H161  single    0.970  0.020  1.090
 3GM  C16  H162  single    0.970  0.020  1.090
 3GM  C18  H18   single    0.970  0.020  1.090
 3GM  C21  H211  single    0.970  0.020  1.090
 3GM  C21  H212  single    0.970  0.020  1.090
 3GM  C22  H221  single    0.970  0.020  1.090
 3GM  C22  H222  single    0.970  0.020  1.090
 3GM  N27  H27   single    0.860  0.020  1.020
 3GM  C23  H231  single    0.970  0.020  1.090
 3GM  C23  H232  single    0.970  0.020  1.090
 3GM  C19  H19   single    0.970  0.020  1.090
 3GM  C17  H171  single    0.970  0.020  1.090
 3GM  C17  H172  single    0.970  0.020  1.090
 3GM  C20  H20   single    0.970  0.020  1.090
 3GM  C24  H241  single    0.970  0.020  1.090
 3GM  C24  H242  single    0.970  0.020  1.090
 3GM  C25  H251  single    0.970  0.020  1.090
 3GM  C25  H252  single    0.970  0.020  1.090
 3GM  C26  H261  single    0.970  0.020  1.090
 3GM  C26  H262  single    0.970  0.020  1.090
 3GM  N28  H281  single    0.890  0.020  1.040
 3GM  N28  H282  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
 3GM  H1    C1   C3    119.72  3.000
 3GM  H1    C1   C2    119.76  3.000
 3GM  C3    C1   C2    120.52  3.000
 3GM  H2    C2   C4    119.85  3.000
 3GM  H2    C2   C1    119.65  3.000
 3GM  C4    C2   C1    120.50  3.000
 3GM  H3    C3   C8    120.87  3.000
 3GM  H3    C3   C1    120.25  3.000
 3GM  C8    C3   C1    118.87  3.000
 3GM  H4    C4   C9    120.09  3.000
 3GM  H4    C4   C2    121.03  3.000
 3GM  C9    C4   C2    118.88  3.000
 3GM  H5    C5   C10   119.47  3.000
 3GM  H5    C5   C6    119.07  3.000
 3GM  C10   C5   C6    121.45  3.000
 3GM  H6    C6   C11   119.33  3.000
 3GM  H6    C6   C5    120.91  3.000
 3GM  C11   C6   C5    119.76  3.000
 3GM  C13   C7   C12   118.46  3.000
 3GM  C13   C7   C10   121.85  3.000
 3GM  C12   C7   C10   119.68  3.000
 3GM  C16   C8   C9    110.24  3.000
 3GM  C16   C8   C3    129.20  3.000
 3GM  C9    C8   C3    120.56  3.000
 3GM  C18   C9   C8    110.79  3.000
 3GM  C18   C9   C4    128.53  3.000
 3GM  C8    C9   C4    120.67  3.000
 3GM  C21   C10  C7    121.61  3.000
 3GM  C21   C10  C5    119.46  3.000
 3GM  C7    C10  C5    118.88  3.000
 3GM  O35   C11  C12   122.04  3.000
 3GM  O35   C11  C6    118.70  3.000
 3GM  C12   C11  C6    119.26  3.000
 3GM  O34   C12  C11   121.16  3.000
 3GM  O34   C12  C7    117.88  3.000
 3GM  C11   C12  C7    120.96  3.000
 3GM  O33   C15  O30   126.33  3.000
 3GM  O33   C15  C23   117.94  3.000
 3GM  O30   C15  C23   115.72  3.000
 3GM  H162  C16  H161  106.87  3.000
 3GM  H162  C16  C19   112.44  3.000
 3GM  H161  C16  C19   111.30  3.000
 3GM  H162  C16  C8    113.64  3.000
 3GM  H161  C16  C8    110.73  3.000
 3GM  C19   C16  C8    101.93  3.000
 3GM  H172  C17  H171  108.26  3.000
 3GM  H172  C17  O34   110.40  3.000
 3GM  H171  C17  O34   106.97  3.000
 3GM  H172  C17  C20   109.94  3.000
 3GM  H171  C17  C20   110.26  3.000
 3GM  O34   C17  C20   110.93  3.000
 3GM  H18   C18  C21   108.90  3.000
 3GM  H18   C18  C19   110.90  3.000
 3GM  C21   C18  C19   112.18  3.000
 3GM  H18   C18  C9    111.74  3.000
 3GM  C21   C18  C9    112.15  3.000
 3GM  C19   C18  C9    100.84  3.000
 3GM  H19   C19  N27   107.75  3.000
 3GM  H19   C19  C18   107.33  3.000
 3GM  N27   C19  C18   116.02  3.000
 3GM  H19   C19  C16   108.00  3.000
 3GM  N27   C19  C16   112.58  3.000
 3GM  C18   C19  C16   104.81  3.000
 3GM  H20   C20  O35   108.83  3.000
 3GM  H20   C20  C24   109.82  3.000
 3GM  O35   C20  C24   108.45  3.000
 3GM  H20   C20  C17   108.54  3.000
 3GM  O35   C20  C17   108.82  3.000
 3GM  C24   C20  C17   112.32  3.000
 3GM  H212  C21  H211  106.54  3.000
 3GM  H212  C21  C18   109.31  3.000
 3GM  H211  C21  C18   108.54  3.000
 3GM  H212  C21  C10   108.14  3.000
 3GM  H211  C21  C10   110.16  3.000
 3GM  C18   C21  C10   113.90  3.000
 3GM  H222  C22  H221  106.69  3.000
 3GM  H222  C22  C25   110.04  3.000
 3GM  H221  C22  C25   109.55  3.000
 3GM  H222  C22  C14   111.24  3.000
 3GM  H221  C22  C14   107.57  3.000
 3GM  C25   C22  C14   111.59  3.000
 3GM  H242  C24  H241  106.38  3.000
 3GM  H242  C24  C23   109.50  3.000
 3GM  H241  C24  C23   110.48  3.000
 3GM  H242  C24  C20   107.50  3.000
 3GM  H241  C24  C20   109.34  3.000
 3GM  C23   C24  C20   113.36  3.000
 3GM  H252  C25  H251  106.92  3.000
 3GM  H252  C25  C26   109.16  3.000
 3GM  H251  C25  C26   109.38  3.000
 3GM  H252  C25  C22   109.95  3.000
 3GM  H251  C25  C22   109.27  3.000
 3GM  C26   C25  C22   112.02  3.000
 3GM  H262  C26  H261  106.25  3.000
 3GM  H262  C26  N28   113.60  3.000
 3GM  H261  C26  N28   108.17  3.000
 3GM  H262  C26  C25   109.07  3.000
 3GM  H261  C26  C25   108.87  3.000
 3GM  N28   C26  C25   110.70  3.000
 3GM  H27   N27  C19   118.22  3.000
 3GM  H27   N27  C14   118.43  3.000
 3GM  C19   N27  C14   123.21  3.000
 3GM  H282  N28  H281  105.53  3.000
 3GM  H282  N28  C26   109.31  3.000
 3GM  H281  N28  C26   109.52  3.000
 3GM  C17   O34  C12   114.51  3.000
 3GM  C20   O35  C11   115.23  3.000
 3GM  H232  C23  H231  105.25  3.000
 3GM  H232  C23  C24   109.62  3.000
 3GM  H231  C23  C24   110.11  3.000
 3GM  H232  C23  C15   108.29  3.000
 3GM  H231  C23  C15   107.88  3.000
 3GM  C24   C23  C15   115.20  3.000
 3GM  O32   C14  N27   122.59  3.000
 3GM  O32   C14  C22   121.73  3.000
 3GM  N27   C14  C22   115.66  3.000
 3GM  O31   C13  O29   127.64  3.000
 3GM  O31   C13  C7    116.38  3.000
 3GM  O29   C13  C7    115.98  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
 3GM  CONST_01  C9    C4   C2   C1      0.00   0.0  0
 3GM  CONST_02  C9    C8   C3   C1      0.00   0.0  0
 3GM  CONST_03  C8    C3   C1   C2      0.00   0.0  0
 3GM  CONST_04  C8    C9   C4   C2      0.00   0.0  0
 3GM  CONST_05  C4    C2   C1   C3      0.00   0.0  0
 3GM  CONST_06  C4    C9   C8   C3      0.00   0.0  0
 3GM  CONST_07  C12   C11  C6   C5      0.00   0.0  0
 3GM  CONST_08  C12   C7   C10  C5      0.00   0.0  0
 3GM  CONST_09  C7    C10  C5   C6      0.00   0.0  0
 3GM  CONST_10  C7    C12  C11  C6      0.00   0.0  0
 3GM  CONST_11  C11   C6   C5   C10     0.00   0.0  0
 3GM  CONST_12  C11   C12  C7   C10     0.00   0.0  0
 3GM  CONST_13  C13   C7   C10  C5    180.00   0.0  0
 3GM  CONST_14  C21   C10  C5   C6    180.00   0.0  0
 3GM  CONST_15  C13   C7   C12  C11   180.00   0.0  0
 3GM  CONST_16  C21   C10  C7   C12   180.00   0.0  0
 3GM  CONST_17  O34   C12  C7   C13     0.00   0.0  0
 3GM  CONST_18  H4    C4   C2   C1    180.00   0.0  0
 3GM  CONST_19  H3    C3   C1   C2    180.00   0.0  0
 3GM  CONST_20  H2    C2   C1   C3    180.00   0.0  0
 3GM  CONST_21  H1    C1   C2   C4    180.00   0.0  0
 3GM  CONST_22  H5    C5   C10  C7    180.00   0.0  0
 3GM  CONST_23  H6    C6   C5   C10   180.00   0.0  0
 3GM  CONST_24  C22   C14  N27  C19   180.00   0.0  0
 3GM  CONST_25  O32   C14  N27  C19     0.00   0.0  0
 3GM  CONST_26  H27   N27  C14  C22     0.00   0.0  0
 3GM  Var_01    C19   C16  C8   C3    160.75  30.0  1
 3GM  Var_02    C20   C17  O34  C12   -45.32  30.0  1
 3GM  Var_03    C18   C21  C10  C5    104.47  30.0  2
 3GM  Var_04    O29   C13  C7   C10   100.16  30.0  2
 3GM  Var_05    C20   C24  C23  C15  -177.97  30.0  3
 3GM  Var_06    C26   C25  C22  C14   176.95  30.0  3
 3GM  Var_07    N28   C26  C25  C22   179.74  30.0  3
 3GM  Var_08    O30   C15  C23  C24   173.81  30.0  3
 3GM  Var_09    N27   C14  C22  C25   120.17  30.0  1
 3GM  Var_10    H281  N28  C26  C25   176.31  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
 3GM  chir_01  C18  C9   C19  C21  positiv
 3GM  chir_02  C19  N27  C16  C18  negativ
 3GM  chir_03  C20  C17  C24  O35  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
 3GM  plan-1  C1   0.020
 3GM  plan-1  C2   0.020
 3GM  plan-1  C3   0.020
 3GM  plan-1  C4   0.020
 3GM  plan-1  C8   0.020
 3GM  plan-1  C9   0.020
 3GM  plan-1  C16  0.020
 3GM  plan-1  C18  0.020
 3GM  plan-1  H1   0.020
 3GM  plan-1  H2   0.020
 3GM  plan-1  H3   0.020
 3GM  plan-1  H4   0.020
 3GM  plan-2  C5   0.020
 3GM  plan-2  C6   0.020
 3GM  plan-2  C7   0.020
 3GM  plan-2  C10  0.020
 3GM  plan-2  C11  0.020
 3GM  plan-2  C12  0.020
 3GM  plan-2  C21  0.020
 3GM  plan-2  O34  0.020
 3GM  plan-2  O35  0.020
 3GM  plan-2  H5   0.020
 3GM  plan-2  H6   0.020
 3GM  plan-2  C13  0.020
 3GM  plan-3  C19  0.020
 3GM  plan-3  C22  0.020
 3GM  plan-3  N27  0.020
 3GM  plan-3  O32  0.020
 3GM  plan-3  H27  0.020
 3GM  plan-3  C14  0.020
 3GM  plan-4  C15  0.020
 3GM  plan-4  O30  0.020
 3GM  plan-4  O33  0.020
 3GM  plan-4  C23  0.020
 3GM  plan-5  C7   0.020
 3GM  plan-5  O29  0.020
 3GM  plan-5  O31  0.020
 3GM  plan-5  C13  0.020

