# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 01:27:33 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 5-[(2S)-4-methyl-2-{[(pyridin-4-ylcarbonyl)amino]methyl}pentyl]-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](CNC(=O)c1ccncc1)Cc2ccc3OCOc3c2C(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
 S3G  S3G  '5-[(2S)-4-methyl-2-{[(pyridin-4-ylcarbonyl)amino]methyl}pentyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  52  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S3G
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
 S3G  C1    C  CR16  0  -0.343   2.7714   0.7272  -1.9885
 S3G  C2    C  CR16  0  -0.324   3.6813   1.7416  -1.6646
 S3G  C3    C  CR16  0  -0.341  -5.2002   1.7281  -0.3887
 S3G  C4    C  CR16  0  -0.368  -4.1107   0.4120   1.2711
 S3G  C5    C  CR16  0  -0.056  -6.2041   1.9637   0.5368
 S3G  C6    C  CR16  0  -0.053  -5.1750   0.6960   2.1151
 S3G  C7    C  CR6   0   0.066  -4.1165   0.9445  -0.0122
 S3G  C8    C  CR6   0  -0.198   2.9539  -0.2694   0.2074
 S3G  C9    C  CR6   0   0.125   2.4036  -0.2720  -1.1011
 S3G  C10   C  CR56  0   0.298   4.1959   1.7239  -0.3980
 S3G  C11   C  CR56  0   0.338   3.8315   0.7501   0.5210
 S3G  C12   C  C     0   0.512  -3.0420   0.6540  -1.0170
 S3G  C13   C  C     0   0.484   2.6657  -1.3376   1.1984
 S3G  C14   C  CH2   0   0.070   5.2350   2.1648   1.5174
 S3G  C15   C  CH3   0  -0.648  -2.6593  -4.0429  -0.7399
 S3G  C16   C  CH3   0  -0.668  -1.7323  -2.7610   1.1997
 S3G  C17   C  CH2   0  -0.520   1.3876  -1.2946  -1.5360
 S3G  C18   C  CH2   0  -0.396  -0.8003  -2.4358  -1.1379
 S3G  C19   C  CH2   0  -0.256  -0.6480   0.1254  -1.2864
 S3G  C20   C  CH1   0  -0.244  -2.0462  -2.7188  -0.2919
 S3G  C21   C  CH1   0  -0.270   0.0189  -1.1765  -0.8381
 S3G  N22   N  N     0  -0.398  -6.2014   1.4599   1.7663
 S3G  N23   N  NH1   0  -0.636  -1.8153   0.4781  -0.5086
 S3G  O24   O  OH1   0  -0.583   2.5649  -0.8611   2.4313
 S3G  O25   O  O     0  -0.476  -3.3160   0.5791  -2.2060
 S3G  O26   O  O     0  -0.425   2.5453  -2.5076   0.9311
 S3G  O27   O  O     0  -0.483   5.1061   2.5561   0.1594
 S3G  O28   O  O     0  -0.471   4.5112   0.9481   1.6679
 S3G  H1    H  HCR6  0   0.262   2.3357   0.7273  -2.9792
 S3G  H2    H  HCR6  0   0.280   3.9611   2.4956  -2.3875
 S3G  H5    H  HCR6  0   0.271  -7.0510   2.5854   0.2695
 S3G  H4    H  HCR6  0   0.276  -3.3154  -0.2318   1.6238
 S3G  H6    H  HCR6  0   0.273  -5.1937   0.2813   3.1165
 S3G  H171  H  HCH2  0   0.250   1.2357  -1.1945  -2.6145
 S3G  H172  H  HCH2  0   0.263   1.7749  -2.2997  -1.3765
 S3G  H23   H  HNH1  0   0.407  -1.6653   0.6861   0.4660
 S3G  H24   H  HOH1  0   0.486   2.4261  -1.5897   3.0558
 S3G  H141  H  HCH2  0   0.248   6.2852   1.9983   1.7597
 S3G  H142  H  HCH2  0   0.241   4.8064   2.9300   2.1711
 S3G  H151  H  HCH3  0   0.226  -3.5636  -4.2757  -0.1750
 S3G  H152  H  HCH3  0   0.224  -2.9259  -4.0202  -1.7982
 S3G  H153  H  HCH3  0   0.212  -1.9568  -4.8674  -0.5931
 S3G  H20   H  HCH1  0   0.223  -2.7941  -1.9406  -0.4627
 S3G  H161  H  HCH3  0   0.221  -0.9407  -3.4849   1.4109
 S3G  H162  H  HCH3  0   0.219  -1.4019  -1.7961   1.5873
 S3G  H163  H  HCH3  0   0.229  -2.6123  -3.0556   1.7743
 S3G  H21   H  HCH1  0   0.234   0.1858  -1.1138   0.2423
 S3G  H181  H  HCH2  0   0.217  -0.1334  -3.2974  -1.0141
 S3G  H182  H  HCH2  0   0.221  -1.0818  -2.4279  -2.1974
 S3G  H191  H  HCH2  0   0.256   0.0701   0.9465  -1.2159
 S3G  H192  H  HCH2  0   0.248  -0.9422   0.0505  -2.3331
 S3G  H3    H  HCR6  0   0.276  -5.2637   2.1578  -1.3789

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
 S3G  C1   C2    aromatic  1.401  0.020  1.401
 S3G  C1   C9    aromatic  1.386  0.020  1.386
 S3G  C2   C10   aromatic  1.367  0.020  1.367
 S3G  C3   C5    aromatic  1.386  0.020  1.386
 S3G  C3   C7    aromatic  1.389  0.020  1.389
 S3G  C4   C6    aromatic  1.388  0.020  1.388
 S3G  C4   C7    aromatic  1.389  0.020  1.389
 S3G  C5   N22   aromatic  1.329  0.020  1.329
 S3G  C6   N22   aromatic  1.326  0.020  1.326
 S3G  C7   C12   single    1.499  0.020  1.499
 S3G  C8   C9    aromatic  1.419  0.020  1.419
 S3G  C8   C11   aromatic  1.381  0.020  1.381
 S3G  C8   C13   single    1.485  0.020  1.485
 S3G  C9   C17   single    1.506  0.020  1.506
 S3G  C10  C11   aromatic  1.388  0.020  1.388
 S3G  C10  O27   single    1.353  0.020  1.353
 S3G  C11  O28   single    1.348  0.020  1.348
 S3G  C12  N23   single    1.339  0.020  1.339
 S3G  C12  O25   double    1.223  0.020  1.223
 S3G  C13  O24   single    1.326  0.020  1.326
 S3G  C13  O26   double    1.206  0.020  1.206
 S3G  C14  O27   single    1.419  0.020  1.419
 S3G  C14  O28   single    1.424  0.020  1.424
 S3G  C15  C20   single    1.526  0.020  1.526
 S3G  C16  C20   single    1.525  0.020  1.525
 S3G  C17  C21   single    1.541  0.020  1.541
 S3G  C18  C20   single    1.532  0.020  1.532
 S3G  C18  C21   single    1.532  0.020  1.532
 S3G  C19  C21   single    1.530  0.020  1.530
 S3G  C19  N23   single    1.446  0.020  1.446
 S3G  C1   H1    single    0.930  0.020  1.080
 S3G  C2   H2    single    0.930  0.020  1.080
 S3G  C3   H3    single    0.930  0.020  1.080
 S3G  C5   H5    single    0.930  0.020  1.080
 S3G  C4   H4    single    0.930  0.020  1.080
 S3G  C6   H6    single    0.930  0.020  1.080
 S3G  C17  H171  single    0.970  0.020  1.090
 S3G  C17  H172  single    0.970  0.020  1.090
 S3G  N23  H23   single    0.860  0.020  1.020
 S3G  O24  H24   single    0.850  0.020  0.980
 S3G  C14  H141  single    0.970  0.020  1.090
 S3G  C14  H142  single    0.970  0.020  1.090
 S3G  C15  H151  single    0.970  0.020  1.090
 S3G  C15  H152  single    0.970  0.020  1.090
 S3G  C15  H153  single    0.970  0.020  1.090
 S3G  C20  H20   single    0.970  0.020  1.090
 S3G  C16  H161  single    0.970  0.020  1.090
 S3G  C16  H162  single    0.970  0.020  1.090
 S3G  C16  H163  single    0.970  0.020  1.090
 S3G  C21  H21   single    0.970  0.020  1.090
 S3G  C18  H181  single    0.970  0.020  1.090
 S3G  C18  H182  single    0.970  0.020  1.090
 S3G  C19  H191  single    0.970  0.020  1.090
 S3G  C19  H192  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
 S3G  H1    C1   C9    118.65  3.000
 S3G  H1    C1   C2    118.24  3.000
 S3G  C9    C1   C2    123.12  3.000
 S3G  H2    C2   C10   122.07  3.000
 S3G  H2    C2   C1    121.23  3.000
 S3G  C10   C2   C1    116.70  3.000
 S3G  H3    C3   C7    121.20  3.000
 S3G  H3    C3   C5    120.11  3.000
 S3G  C7    C3   C5    118.69  3.000
 S3G  H4    C4   C7    122.15  3.000
 S3G  H4    C4   C6    119.14  3.000
 S3G  C7    C4   C6    118.70  3.000
 S3G  H5    C5   N22   116.56  3.000
 S3G  H5    C5   C3    119.92  3.000
 S3G  N22   C5   C3    123.52  3.000
 S3G  H6    C6   N22   116.75  3.000
 S3G  H6    C6   C4    119.79  3.000
 S3G  N22   C6   C4    123.47  3.000
 S3G  C12   C7   C4    122.79  3.000
 S3G  C12   C7   C3    119.13  3.000
 S3G  C4    C7   C3    118.01  3.000
 S3G  C13   C8   C11   120.17  3.000
 S3G  C13   C8   C9    122.58  3.000
 S3G  C11   C8   C9    117.19  3.000
 S3G  C17   C9   C8    121.94  3.000
 S3G  C17   C9   C1    118.93  3.000
 S3G  C8    C9   C1    119.08  3.000
 S3G  O27   C10  C11   109.59  3.000
 S3G  O27   C10  C2    128.81  3.000
 S3G  C11   C10  C2    121.58  3.000
 S3G  O28   C11  C10   109.15  3.000
 S3G  O28   C11  C8    128.47  3.000
 S3G  C10   C11  C8    122.30  3.000
 S3G  O25   C12  N23   124.50  3.000
 S3G  O25   C12  C7    120.20  3.000
 S3G  N23   C12  C7    115.30  3.000
 S3G  O26   C13  O24   123.17  3.000
 S3G  O26   C13  C8    124.69  3.000
 S3G  O24   C13  C8    112.14  3.000
 S3G  H142  C14  H141  110.57  3.000
 S3G  H142  C14  O28   109.60  3.000
 S3G  H141  C14  O28   109.61  3.000
 S3G  H142  C14  O27   110.08  3.000
 S3G  H141  C14  O27   110.01  3.000
 S3G  O28   C14  O27   106.89  3.000
 S3G  H153  C15  H152  107.63  3.000
 S3G  H153  C15  H151  107.59  3.000
 S3G  H152  C15  H151  107.69  3.000
 S3G  H153  C15  C20   110.90  3.000
 S3G  H152  C15  C20   111.38  3.000
 S3G  H151  C15  C20   111.46  3.000
 S3G  H163  C16  H162  107.21  3.000
 S3G  H163  C16  H161  107.66  3.000
 S3G  H162  C16  H161  107.32  3.000
 S3G  H163  C16  C20   110.88  3.000
 S3G  H162  C16  C20   112.67  3.000
 S3G  H161  C16  C20   110.88  3.000
 S3G  H172  C17  H171  106.16  3.000
 S3G  H172  C17  C21   108.68  3.000
 S3G  H171  C17  C21   108.44  3.000
 S3G  H172  C17  C9    110.16  3.000
 S3G  H171  C17  C9    108.44  3.000
 S3G  C21   C17  C9    114.61  3.000
 S3G  H182  C18  H181  105.72  3.000
 S3G  H182  C18  C21   108.70  3.000
 S3G  H181  C18  C21   107.37  3.000
 S3G  H182  C18  C20   109.04  3.000
 S3G  H181  C18  C20   106.68  3.000
 S3G  C21   C18  C20   118.59  3.000
 S3G  H192  C19  H191  106.91  3.000
 S3G  H192  C19  N23   108.39  3.000
 S3G  H191  C19  N23   108.21  3.000
 S3G  H192  C19  C21   109.91  3.000
 S3G  H191  C19  C21   109.50  3.000
 S3G  N23   C19  C21   113.69  3.000
 S3G  H20   C20  C18   109.79  3.000
 S3G  H20   C20  C16   108.27  3.000
 S3G  C18   C20  C16   112.20  3.000
 S3G  H20   C20  C15   107.27  3.000
 S3G  C18   C20  C15   108.95  3.000
 S3G  C16   C20  C15   110.23  3.000
 S3G  H21   C21  C19   107.87  3.000
 S3G  H21   C21  C18   108.76  3.000
 S3G  C19   C21  C18   114.15  3.000
 S3G  H21   C21  C17   108.41  3.000
 S3G  C19   C21  C17   108.64  3.000
 S3G  C18   C21  C17   108.86  3.000
 S3G  C6    N22  C5    117.60  3.000
 S3G  H23   N23  C19   116.76  3.000
 S3G  H23   N23  C12   118.44  3.000
 S3G  C19   N23  C12   124.54  3.000
 S3G  H24   O24  C13   109.87  3.000
 S3G  C14   O27  C10   106.60  3.000
 S3G  C14   O28  C11   106.97  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
 S3G  CONST_01  C11   C10  C2   C1      0.00   0.0  0
 S3G  CONST_02  C11   C8   C9   C1      0.00   0.0  0
 S3G  CONST_03  C8    C9   C1   C2      0.00   0.0  0
 S3G  CONST_04  C8    C11  C10  C2      0.00   0.0  0
 S3G  CONST_05  C6    N22  C5   C3      0.00   0.0  0
 S3G  CONST_06  C6    C4   C7   C3      0.00   0.0  0
 S3G  CONST_07  C5    N22  C6   C4      0.00   0.0  0
 S3G  CONST_08  C5    C3   C7   C4      0.00   0.0  0
 S3G  CONST_09  N22   C5   C3   C7      0.00   0.0  0
 S3G  CONST_10  N22   C6   C4   C7      0.00   0.0  0
 S3G  CONST_11  C10   C2   C1   C9      0.00   0.0  0
 S3G  CONST_12  C10   C11  C8   C9      0.00   0.0  0
 S3G  CONST_13  C13   C8   C9   C1    180.00   0.0  0
 S3G  CONST_14  C17   C9   C1   C2    180.00   0.0  0
 S3G  CONST_15  C12   C7   C3   C5    180.00   0.0  0
 S3G  CONST_16  C12   C7   C4   C6    180.00   0.0  0
 S3G  CONST_17  C13   C8   C11  C10   180.00   0.0  0
 S3G  CONST_18  C17   C9   C8   C11   180.00   0.0  0
 S3G  CONST_19  O28   C11  C8   C13     0.00   0.0  0
 S3G  CONST_20  H4    C4   C7   C3    180.00   0.0  0
 S3G  CONST_21  H3    C3   C7   C4    180.00   0.0  0
 S3G  CONST_22  H6    C6   N22  C5    180.00   0.0  0
 S3G  CONST_23  H5    C5   N22  C6    180.00   0.0  0
 S3G  CONST_24  H1    C1   C9   C8    180.00   0.0  0
 S3G  CONST_25  H2    C2   C1   C9    180.00   0.0  0
 S3G  CONST_26  C19   N23  C12  C7    180.00   0.0  0
 S3G  CONST_27  H23   N23  C12  C7      0.00   0.0  0
 S3G  CONST_28  H24   O24  C13  C8    180.00   0.0  0
 S3G  CONST_29  O25   C12  N23  C19     0.00   0.0  0
 S3G  Var_01    O28   C14  O27  C10     8.50  30.0  1
 S3G  Var_02    O27   C14  O28  C11    -8.77  30.0  1
 S3G  Var_03    C21   C17  C9   C1   -109.75  30.0  2
 S3G  Var_04    N23   C12  C7   C3    149.90  30.0  2
 S3G  Var_05    O24   C13  C8   C9   -143.28  30.0  2
 S3G  Var_06    C21   C19  N23  C12  -121.52  30.0  2
 S3G  Var_07    C21   C18  C20  C15  -177.92  30.0  2
 S3G  Var_08    H161  C16  C20  C15    66.47  30.0  3
 S3G  Var_09    H151  C15  C20  C16    57.58  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
 S3G  chir_01  C21  C17  C18  C19  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
 S3G  plan-1  C3   0.020
 S3G  plan-1  C4   0.020
 S3G  plan-1  C5   0.020
 S3G  plan-1  C6   0.020
 S3G  plan-1  C7   0.020
 S3G  plan-1  C12  0.020
 S3G  plan-1  N22  0.020
 S3G  plan-1  H5   0.020
 S3G  plan-1  H4   0.020
 S3G  plan-1  H6   0.020
 S3G  plan-1  H3   0.020
 S3G  plan-2  C1   0.020
 S3G  plan-2  C2   0.020
 S3G  plan-2  C8   0.020
 S3G  plan-2  C9   0.020
 S3G  plan-2  C10  0.020
 S3G  plan-2  C11  0.020
 S3G  plan-2  C13  0.020
 S3G  plan-2  C17  0.020
 S3G  plan-2  O27  0.020
 S3G  plan-2  O28  0.020
 S3G  plan-2  H1   0.020
 S3G  plan-2  H2   0.020
 S3G  plan-3  C7   0.020
 S3G  plan-3  C12  0.020
 S3G  plan-3  C19  0.020
 S3G  plan-3  N23  0.020
 S3G  plan-3  O25  0.020
 S3G  plan-3  H23  0.020
 S3G  plan-4  C8   0.020
 S3G  plan-4  C13  0.020
 S3G  plan-4  O24  0.020
 S3G  plan-4  O26  0.020
 S3G  plan-4  H24  0.020

