# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:56:01 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 5-[(2S)-4-methyl-2-{[(pyridin-3-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)c1cccnc1)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
 4D2  4D2  '5-[(2S)-4-methyl-2-{[(pyridin-3-ylcarbonyl)amino]methyl}pentyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  52  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4D2
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
 4D2  C1    C  CR16  0  -0.328   6.2005  -2.0426   0.4949
 4D2  C2    C  CR16  0  -0.167   5.2046  -1.7714  -0.4307
 4D2  C3    C  CR16  0  -0.253  -2.7674  -0.7638  -1.9835
 4D2  C4    C  CR16  0  -0.353  -3.6803  -1.7670  -1.6397
 4D2  C5    C  CR16  0  -0.011   6.0752  -1.5163   1.7739
 4D2  C6    C  CR16  0  -0.083   4.1078  -0.5123   1.2649
 4D2  C7    C  CR6   0  -0.125   4.1138  -1.0054  -0.0374
 4D2  C8    C  CR6   0  -0.132  -2.9721   0.2987   0.1784
 4D2  C9    C  CR6   0   0.119  -2.4076   0.2605  -1.1229
 4D2  C10   C  CR56  0   0.325  -4.2110  -1.7094  -0.3823
 4D2  C11   C  CR56  0   0.268  -3.8576  -0.7076   0.5101
 4D2  C12   C  C     0   0.555   3.0504  -0.6978  -1.0443
 4D2  C14   C  CH2   0   0.023  -5.2525  -2.0971   1.5304
 4D2  C15   C  CH3   0  -0.641   2.6442   4.0282  -0.6885
 4D2  C16   C  CH3   0  -0.701   1.6814   2.7240   1.2162
 4D2  C17   C  CH2   0  -0.581  -1.3878   1.2716  -1.5760
 4D2  C18   C  CH2   0  -0.381   0.7928   2.4264  -1.1417
 4D2  C19   C  CH2   0  -0.248   0.6634  -0.1303  -1.3248
 4D2  C20   C  CH1   0  -0.302   2.0235   2.6987  -0.2698
 4D2  C21   C  CH1   0  -0.320  -0.0216   1.1596  -0.8702
 4D2  N22   N  N     0  -0.420   5.0589  -0.7573   2.1529
 4D2  N23   N  NH1   0  -0.609   1.8155  -0.4859  -0.5313
 4D2  O24   O  OH1   0  -0.634  -2.6635   0.9709   2.3970
 4D2  O25   O  O     0  -0.549   3.3093  -0.6537  -2.2278
 4D2  O26   O  O     0  -0.223  -2.5174   2.5505   0.8389
 4D2  O27   O  O     0  -0.354  -5.1325  -2.5214   0.1889
 4D2  O28   O  O     0  -0.512  -4.5590  -0.8696   1.6514
 4D2  H1    H  HCR6  0   0.274   7.0585  -2.6461   0.2342
 4D2  H2    H  HCR6  0   0.292   5.2622  -2.1464  -1.4439
 4D2  H5    H  HCR6  0   0.260   6.8354  -1.7109   2.5219
 4D2  H3    H  HCR6  0   0.277  -2.3219  -0.7912  -2.9691
 4D2  H4    H  HCR6  0   0.265  -3.9553  -2.5424  -2.3405
 4D2  H6    H  HCR6  0   0.264   3.3088   0.1399   1.6084
 4D2  H171  H  HCH2  0   0.275  -1.2320   1.1502  -2.6525
 4D2  H172  H  HCH2  0   0.234  -1.7773   2.2785  -1.4390
 4D2  H23   H  HNH1  0   0.395   1.6572  -0.7006   0.4366
 4D2  H24   H  HOH1  0   0.419  -2.5318   1.7361   2.9709
 4D2  H141  H  HCH2  0   0.219  -6.3050  -1.9505   1.7821
 4D2  H142  H  HCH2  0   0.202  -4.8052  -2.8407   2.2019
 4D2  H151  H  HCH3  0   0.194   3.5390   4.2523  -0.1062
 4D2  H152  H  HCH3  0   0.235   2.9308   4.0185  -1.7408
 4D2  H153  H  HCH3  0   0.259   1.9417   4.8525  -0.5438
 4D2  H20   H  HCH1  0   0.250   2.7732   1.9220  -0.4381
 4D2  H161  H  HCH3  0   0.238   0.8856   3.4438   1.4235
 4D2  H162  H  HCH3  0   0.241   1.3431   1.7544   1.5859
 4D2  H163  H  HCH3  0   0.235   2.5493   3.0092   1.8128
 4D2  H21   H  HCH1  0   0.271  -0.2017   1.0879   0.2070
 4D2  H181  H  HCH2  0   0.216   0.1191   3.2823  -1.0187
 4D2  H182  H  HCH2  0   0.201   1.0952   2.4331  -2.1951
 4D2  H191  H  HCH2  0   0.253  -0.0559  -0.9546  -1.2964
 4D2  H192  H  HCH2  0   0.272   0.9932  -0.0372  -2.3596
 4D2  C13   C  C     0   0.395  -2.6886   1.3985   1.1349

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
 4D2  C1   C2    aromatic  1.386  0.020  1.386
 4D2  C1   C5    aromatic  1.389  0.020  1.389
 4D2  C2   C7    aromatic  1.390  0.020  1.390
 4D2  C3   C4    aromatic  1.399  0.020  1.399
 4D2  C3   C9    aromatic  1.385  0.020  1.385
 4D2  C4   C10   aromatic  1.366  0.020  1.366
 4D2  C5   N22   aromatic  1.324  0.020  1.324
 4D2  C6   C7    aromatic  1.393  0.020  1.393
 4D2  C6   N22   aromatic  1.324  0.020  1.324
 4D2  C7   C12   single    1.496  0.020  1.496
 4D2  C8   C9    aromatic  1.419  0.020  1.419
 4D2  C8   C11   aromatic  1.381  0.020  1.381
 4D2  C8   C13   single    1.485  0.020  1.485
 4D2  C9   C17   single    1.506  0.020  1.506
 4D2  C10  C11   aromatic  1.387  0.020  1.387
 4D2  C10  O27   single    1.355  0.020  1.355
 4D2  C11  O28   single    1.349  0.020  1.349
 4D2  C12  N23   single    1.354  0.020  1.354
 4D2  C12  O25   double    1.212  0.020  1.212
 4D2  C13  O24   single    1.333  0.020  1.333
 4D2  C13  O26   double    1.202  0.020  1.202
 4D2  C14  O27   single    1.412  0.020  1.412
 4D2  C14  O28   single    1.415  0.020  1.415
 4D2  C15  C20   single    1.526  0.020  1.526
 4D2  C16  C20   single    1.525  0.020  1.525
 4D2  C17  C21   single    1.542  0.020  1.542
 4D2  C18  C20   single    1.533  0.020  1.533
 4D2  C18  C21   single    1.530  0.020  1.530
 4D2  C19  C21   single    1.530  0.020  1.530
 4D2  C19  N23   single    1.443  0.020  1.443
 4D2  C1   H1    single    0.930  0.020  1.080
 4D2  C2   H2    single    0.930  0.020  1.080
 4D2  C5   H5    single    0.930  0.020  1.080
 4D2  C3   H3    single    0.930  0.020  1.080
 4D2  C4   H4    single    0.930  0.020  1.080
 4D2  C6   H6    single    0.930  0.020  1.080
 4D2  C17  H171  single    0.970  0.020  1.090
 4D2  C17  H172  single    0.970  0.020  1.090
 4D2  N23  H23   single    0.860  0.020  1.020
 4D2  O24  H24   single    0.850  0.020  0.980
 4D2  C14  H141  single    0.970  0.020  1.090
 4D2  C14  H142  single    0.970  0.020  1.090
 4D2  C15  H151  single    0.970  0.020  1.090
 4D2  C15  H152  single    0.970  0.020  1.090
 4D2  C15  H153  single    0.970  0.020  1.090
 4D2  C20  H20   single    0.970  0.020  1.090
 4D2  C16  H161  single    0.970  0.020  1.090
 4D2  C16  H162  single    0.970  0.020  1.090
 4D2  C16  H163  single    0.970  0.020  1.090
 4D2  C21  H21   single    0.970  0.020  1.090
 4D2  C18  H181  single    0.970  0.020  1.090
 4D2  C18  H182  single    0.970  0.020  1.090
 4D2  C19  H191  single    0.970  0.020  1.090
 4D2  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
 4D2  H1    C1   C5    120.36  3.000
 4D2  H1    C1   C2    121.22  3.000
 4D2  C5    C1   C2    118.42  3.000
 4D2  H2    C2   C7    119.86  3.000
 4D2  H2    C2   C1    121.28  3.000
 4D2  C7    C2   C1    118.86  3.000
 4D2  H3    C3   C9    118.53  3.000
 4D2  H3    C3   C4    118.31  3.000
 4D2  C9    C3   C4    123.15  3.000
 4D2  H4    C4   C10   121.89  3.000
 4D2  H4    C4   C3    121.41  3.000
 4D2  C10   C4   C3    116.70  3.000
 4D2  H5    C5   N22   116.34  3.000
 4D2  H5    C5   C1    120.27  3.000
 4D2  N22   C5   C1    123.39  3.000
 4D2  H6    C6   N22   115.28  3.000
 4D2  H6    C6   C7    120.73  3.000
 4D2  N22   C6   C7    123.96  3.000
 4D2  C12   C7   C6    123.60  3.000
 4D2  C12   C7   C2    118.73  3.000
 4D2  C6    C7   C2    117.59  3.000
 4D2  C13   C8   C11   120.50  3.000
 4D2  C13   C8   C9    122.32  3.000
 4D2  C11   C8   C9    117.12  3.000
 4D2  C17   C9   C8    121.82  3.000
 4D2  C17   C9   C3    119.04  3.000
 4D2  C8    C9   C3    119.09  3.000
 4D2  O27   C10  C11   109.57  3.000
 4D2  O27   C10  C4    128.84  3.000
 4D2  C11   C10  C4    121.57  3.000
 4D2  O28   C11  C10   108.96  3.000
 4D2  O28   C11  C8    128.61  3.000
 4D2  C10   C11  C8    122.35  3.000
 4D2  O25   C12  N23   123.99  3.000
 4D2  O25   C12  C7    120.84  3.000
 4D2  N23   C12  C7    115.17  3.000
 4D2  H142  C14  H141  110.05  3.000
 4D2  H142  C14  O28   109.62  3.000
 4D2  H141  C14  O28   109.64  3.000
 4D2  H142  C14  O27   110.07  3.000
 4D2  H141  C14  O27   109.95  3.000
 4D2  O28   C14  O27   107.47  3.000
 4D2  H153  C15  H152  107.66  3.000
 4D2  H153  C15  H151  107.56  3.000
 4D2  H152  C15  H151  107.54  3.000
 4D2  H153  C15  C20   111.07  3.000
 4D2  H152  C15  C20   111.34  3.000
 4D2  H151  C15  C20   111.48  3.000
 4D2  H163  C16  H162  107.07  3.000
 4D2  H163  C16  H161  107.66  3.000
 4D2  H162  C16  H161  107.17  3.000
 4D2  H163  C16  C20   111.02  3.000
 4D2  H162  C16  C20   112.63  3.000
 4D2  H161  C16  C20   111.04  3.000
 4D2  H172  C17  H171  106.10  3.000
 4D2  H172  C17  C21   109.07  3.000
 4D2  H171  C17  C21   108.43  3.000
 4D2  H172  C17  C9    109.93  3.000
 4D2  H171  C17  C9    108.53  3.000
 4D2  C21   C17  C9    114.43  3.000
 4D2  H182  C18  H181  105.82  3.000
 4D2  H182  C18  C21   108.81  3.000
 4D2  H181  C18  C21   107.42  3.000
 4D2  H182  C18  C20   108.92  3.000
 4D2  H181  C18  C20   106.91  3.000
 4D2  C21   C18  C20   118.26  3.000
 4D2  H192  C19  H191  106.73  3.000
 4D2  H192  C19  N23   107.54  3.000
 4D2  H191  C19  N23   108.95  3.000
 4D2  H192  C19  C21   110.22  3.000
 4D2  H191  C19  C21   109.46  3.000
 4D2  N23   C19  C21   113.69  3.000
 4D2  H20   C20  C18   109.70  3.000
 4D2  H20   C20  C16   108.41  3.000
 4D2  C18   C20  C16   112.16  3.000
 4D2  H20   C20  C15   107.34  3.000
 4D2  C18   C20  C15   108.99  3.000
 4D2  C16   C20  C15   110.13  3.000
 4D2  H21   C21  C19   108.11  3.000
 4D2  H21   C21  C18   108.45  3.000
 4D2  C19   C21  C18   114.02  3.000
 4D2  H21   C21  C17   108.03  3.000
 4D2  C19   C21  C17   108.78  3.000
 4D2  C18   C21  C17   109.28  3.000
 4D2  C6    N22  C5    117.74  3.000
 4D2  H23   N23  C19   117.18  3.000
 4D2  H23   N23  C12   118.40  3.000
 4D2  C19   N23  C12   123.94  3.000
 4D2  H24   O24  C13   108.13  3.000
 4D2  C14   O27  C10   106.16  3.000
 4D2  C14   O28  C11   106.66  3.000
 4D2  O26   C13  O24   122.56  3.000
 4D2  O26   C13  C8    125.35  3.000
 4D2  O24   C13  C8    112.08  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
 4D2  CONST_01  C6    C7   C2   C1      0.00   0.0  0
 4D2  CONST_02  C6    N22  C5   C1      0.00   0.0  0
 4D2  CONST_03  N22   C5   C1   C2      0.00   0.0  0
 4D2  CONST_04  N22   C6   C7   C2      0.00   0.0  0
 4D2  CONST_05  C11   C10  C4   C3      0.00   0.0  0
 4D2  CONST_06  C11   C8   C9   C3      0.00   0.0  0
 4D2  CONST_07  C8    C9   C3   C4      0.00   0.0  0
 4D2  CONST_08  C8    C11  C10  C4      0.00   0.0  0
 4D2  CONST_09  C7    C2   C1   C5      0.00   0.0  0
 4D2  CONST_10  C7    C6   N22  C5      0.00   0.0  0
 4D2  CONST_11  C10   C4   C3   C9      0.00   0.0  0
 4D2  CONST_12  C10   C11  C8   C9      0.00   0.0  0
 4D2  CONST_13  C12   C7   C2   C1    180.00   0.0  0
 4D2  CONST_14  C13   C8   C9   C3    180.00   0.0  0
 4D2  CONST_15  C17   C9   C3   C4    180.00   0.0  0
 4D2  CONST_16  C13   C8   C11  C10   180.00   0.0  0
 4D2  CONST_17  C17   C9   C8   C11   180.00   0.0  0
 4D2  CONST_18  N22   C6   C7   C12   180.00   0.0  0
 4D2  CONST_19  O28   C11  C8   C13     0.00   0.0  0
 4D2  CONST_20  H5    C5   C1   C2    180.00   0.0  0
 4D2  CONST_21  H6    C6   C7   C2    180.00   0.0  0
 4D2  CONST_22  H2    C2   C1   C5    180.00   0.0  0
 4D2  CONST_23  H1    C1   C2   C7    180.00   0.0  0
 4D2  CONST_24  H3    C3   C9   C8    180.00   0.0  0
 4D2  CONST_25  H4    C4   C3   C9    180.00   0.0  0
 4D2  CONST_26  C19   N23  C12  C7    180.00   0.0  0
 4D2  CONST_27  H23   N23  C12  C7      0.00   0.0  0
 4D2  CONST_28  H24   O24  C13  C8    180.00   0.0  0
 4D2  CONST_29  O25   C12  N23  C19     0.00   0.0  0
 4D2  Var_01    O28   C14  O27  C10    10.47  30.0  1
 4D2  Var_02    O27   C14  O28  C11   -10.81  30.0  1
 4D2  Var_03    N23   C12  C7   C2    152.66  30.0  2
 4D2  Var_04    C21   C17  C9   C3   -109.06  30.0  2
 4D2  Var_05    O24   C13  C8   C9   -146.28  30.0  2
 4D2  Var_06    C21   C19  N23  C12  -124.35  30.0  2
 4D2  Var_07    C21   C18  C20  C15  -178.14  30.0  2
 4D2  Var_08    H161  C16  C20  C15    66.52  30.0  3
 4D2  Var_09    H151  C15  C20  C16    57.79  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
 4D2  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
 4D2  plan-1  C1   0.020
 4D2  plan-1  C2   0.020
 4D2  plan-1  C5   0.020
 4D2  plan-1  C6   0.020
 4D2  plan-1  C7   0.020
 4D2  plan-1  C12  0.020
 4D2  plan-1  N22  0.020
 4D2  plan-1  H1   0.020
 4D2  plan-1  H2   0.020
 4D2  plan-1  H5   0.020
 4D2  plan-1  H6   0.020
 4D2  plan-2  C3   0.020
 4D2  plan-2  C4   0.020
 4D2  plan-2  C8   0.020
 4D2  plan-2  C9   0.020
 4D2  plan-2  C10  0.020
 4D2  plan-2  C11  0.020
 4D2  plan-2  C17  0.020
 4D2  plan-2  O27  0.020
 4D2  plan-2  O28  0.020
 4D2  plan-2  H3   0.020
 4D2  plan-2  H4   0.020
 4D2  plan-2  C13  0.020
 4D2  plan-3  C7   0.020
 4D2  plan-3  C12  0.020
 4D2  plan-3  C19  0.020
 4D2  plan-3  N23  0.020
 4D2  plan-3  O25  0.020
 4D2  plan-3  H23  0.020
 4D2  plan-4  C8   0.020
 4D2  plan-4  O24  0.020
 4D2  plan-4  O26  0.020
 4D2  plan-4  H24  0.020
 4D2  plan-4  C13  0.020

