# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 00:47:32 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: (2S)-6-{[{2-[(2S)-butan-2-ylcarbamoyl]benzyl}(methyl)amino]methyl}-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)NC(=O)c1ccccc1CN(C)Cc2ccc3O[C@@H](CCC(O)=O)COc3c2C(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
 B0T  B0T  '(2S)-6-{[{2-[(2S)-butan-2-ylcarbamoyl]benzyl}(methyl)amino]methyl}-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid'  ligand  65  35  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B0T
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
 B0T  C1   C  CR16   0  -0.256  -7.0223   1.2178  -1.4089
 B0T  C2   C  CR16   0  -0.262  -6.7801   2.5437  -1.0885
 B0T  C3   C  CR16   0  -0.274  -6.1474   0.2369  -0.9605
 B0T  C4   C  CR16   0  -0.281  -5.6654   2.8758  -0.3290
 B0T  C5   C  CR16   0  -0.261   0.9091   2.2821   0.1434
 B0T  C6   C  CR16   0  -0.355   2.1493   1.8154  -0.2490
 B0T  C7   C  CR6    0  -0.018  -5.0421   0.5671  -0.1833
 B0T  C8   C  CR6    0  -0.201   0.5269   0.3057   1.4649
 B0T  C9   C  CR6    0   0.056  -4.7905   1.9032   0.1423
 B0T  C10  C  CR6    0   0.133   0.0795   1.5421   0.9849
 B0T  C11  C  CR6    0   0.137   2.5961   0.5885   0.2181
 B0T  C12  C  CR6    0   0.244   1.7852  -0.1577   1.0745
 B0T  C13  C  C      0   0.541  -4.1876  -0.5425   0.3560
 B0T  C15  C  C      0   0.382   7.7434  -1.2484  -1.4728
 B0T  C17  C  CH2    0  -0.490  -1.8129  -2.6837  -1.4335
 B0T  C18  C  CH1    0  -0.069  -2.8237  -2.4870  -0.3062
 B0T  C19  C  CH3    0  -0.659  -3.7017  -3.7183  -0.1121
 B0T  C20  C  CH2    0  -0.210   3.6275  -1.5242   1.5034
 B0T  C21  C  CH1    0  -0.070   4.1455  -1.1862   0.1215
 B0T  C22  C  CH2    0  -0.352  -3.5879   2.3094   0.9521
 B0T  C23  C  CH2    0  -0.325  -1.2644   2.1185   1.3489
 B0T  C24  C  CH3    0  -0.532  -2.0956   2.1835  -0.9198
 B0T  C26  C  CH2    0  -0.423   5.6481  -1.3640   0.0267
 B0T  N1   N  NH1    0  -0.606  -3.6342  -1.3151  -0.5855
 B0T  N2   N  NT     0  -0.336  -2.3480   1.7626   0.4384
 B0T  O1   O  OC    -1  -0.550  -0.4668   0.0381   3.5745
 B0T  O2   O  O      0  -0.608   8.3063  -1.9199  -0.5857
 B0T  O3   O  O      0  -0.562  -4.0970  -0.7431   1.5578
 B0T  O4   O  O      0  -0.597  -0.5629  -1.6836   2.1609
 B0T  O5   O  OC    -1  -0.640   8.2841  -0.7762  -2.4932
 B0T  O6   O  O2     0  -0.323   2.2281  -1.3395   1.5836
 B0T  O7   O  O2     0  -0.356   3.8255   0.1703  -0.1679
 B0T  H1   H  HCR6   0   0.244  -7.8852   0.9439  -2.0019
 B0T  H2   H  HCR6   0   0.245  -7.4489   3.3213  -1.4346
 B0T  H3   H  HCR6   0   0.259  -6.3415  -0.8006  -1.2052
 B0T  H4   H  HCR6   0   0.254  -5.4656   3.9167  -0.1029
 B0T  H5   H  HCR6   0   0.220   0.5736   3.2478  -0.2154
 B0T  H6   H  HCR6   0   0.245   2.7842   2.3978  -0.9051
 B0T  H7   H  HCH3   0   0.244  -0.0754  -1.7569  -2.3407
 B0T  H8   H  HCH3   0   0.207  -1.2654  -0.6006  -1.7504
 B0T  H9   H  HCH3   0   0.214  -0.2447  -1.4474  -0.6072
 B0T  H10  H  HCH2   0   0.214  -2.3452  -2.8127  -2.3836
 B0T  H11  H  HCH2   0   0.231  -1.2955  -3.6296  -1.2535
 B0T  H12  H  HCH1   0   0.313  -2.2734  -2.2811   0.6135
 B0T  H13  H  HCH3   0   0.245  -4.2610  -3.9518  -1.0204
 B0T  H14  H  HCH3   0   0.246  -3.0951  -4.5894   0.1415
 B0T  H15  H  HCH3   0   0.162  -4.4149  -3.5623   0.6970
 B0T  H16  H  HCH2   0   0.249   3.8256  -2.5714   1.7311
 B0T  H17  H  HCH2   0   0.164   4.1387  -0.9071   2.2549
 B0T  H18  H  HCH1   0   0.207   3.6512  -1.8363  -0.6152
 B0T  H19  H  HCH2   0   0.263  -3.5619   3.4123   1.0010
 B0T  H20  H  HCH2   0   0.218  -3.7083   1.9577   1.9802
 B0T  H21  H  HCH2   0   0.246  -1.5471   1.7843   2.3458
 B0T  H22  H  HCH2   0   0.084  -1.1589   3.2175   1.3999
 B0T  H23  H  HCH3   0   0.247  -1.1974   1.6983  -1.2942
 B0T  H24  H  HCH3   0   0.218  -2.9213   1.8895  -1.5674
 B0T  H25  H  HCH3   0   0.147  -1.9594   3.2741  -1.0220
 B0T  H26  H  HCH2   0   0.269   6.0546   0.0802  -1.5277
 B0T  H27  H  HCH2   0   0.247   5.7138  -1.5191  -2.1241
 B0T  H28  H  HCH2   0   0.209   6.1282  -0.7878   0.8234
 B0T  H29  H  HCH2   0   0.264   5.8655  -2.4143   0.2326
 B0T  H30  H  HNH1   0   0.399  -3.7812  -1.0590  -1.5492
 B0T  C25  C  CH2    0  -0.599   6.2336  -0.9784  -1.3239
 B0T  C16  C  CH3    0  -0.647  -0.7924  -1.5598  -1.5421
 B0T  C14  C  C      0   0.393  -0.2551  -0.5250   2.4806

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
 B0T  O2   C15  deloc     1.247  0.020  1.247
 B0T  C15  O5   deloc     1.248  0.020  1.248
 B0T  C15  C25  single    1.541  0.020  1.541
 B0T  C25  C26  single    1.522  0.020  1.522
 B0T  C26  C21  single    1.516  0.020  1.516
 B0T  O7   C21  single    1.423  0.020  1.423
 B0T  O7   C11  single    1.355  0.020  1.355
 B0T  C21  C20  single    1.514  0.020  1.514
 B0T  C6   C11  aromatic  1.387  0.020  1.387
 B0T  C6   C5   aromatic  1.382  0.020  1.382
 B0T  C11  C12  aromatic  1.396  0.020  1.396
 B0T  C5   C10  aromatic  1.394  0.020  1.394
 B0T  C20  O6   single    1.414  0.020  1.414
 B0T  C12  O6   single    1.361  0.020  1.361
 B0T  C12  C8   aromatic  1.397  0.020  1.397
 B0T  C24  N2   single    1.444  0.020  1.444
 B0T  C10  C8   aromatic  1.400  0.020  1.400
 B0T  C10  C23  single    1.507  0.020  1.507
 B0T  C8   C14  single    1.527  0.020  1.527
 B0T  N2   C23  single    1.459  0.020  1.459
 B0T  N2   C22  single    1.449  0.020  1.449
 B0T  C16  C17  single    1.522  0.020  1.522
 B0T  C14  O4   deloc     1.241  0.020  1.241
 B0T  C14  O1   deloc     1.248  0.020  1.248
 B0T  C22  C9   single    1.506  0.020  1.506
 B0T  O3   C13  double    1.222  0.020  1.222
 B0T  C17  C18  single    1.527  0.020  1.527
 B0T  C18  C19  single    1.525  0.020  1.525
 B0T  C18  N1   single    1.452  0.020  1.452
 B0T  C13  N1   single    1.338  0.020  1.338
 B0T  C13  C7   single    1.501  0.020  1.501
 B0T  C9   C7   aromatic  1.398  0.020  1.398
 B0T  C9   C4   aromatic  1.390  0.020  1.390
 B0T  C7   C3   aromatic  1.391  0.020  1.391
 B0T  C4   C2   aromatic  1.389  0.020  1.389
 B0T  C3   C1   aromatic  1.389  0.020  1.389
 B0T  C2   C1   aromatic  1.385  0.020  1.385
 B0T  C1   H1   single    0.930  0.020  1.080
 B0T  C2   H2   single    0.930  0.020  1.080
 B0T  C3   H3   single    0.930  0.020  1.080
 B0T  C4   H4   single    0.930  0.020  1.080
 B0T  C5   H5   single    0.930  0.020  1.080
 B0T  C6   H6   single    0.930  0.020  1.080
 B0T  C16  H7   single    0.970  0.020  1.090
 B0T  C16  H8   single    0.970  0.020  1.090
 B0T  C16  H9   single    0.970  0.020  1.090
 B0T  C17  H10  single    0.970  0.020  1.090
 B0T  C17  H11  single    0.970  0.020  1.090
 B0T  C18  H12  single    0.970  0.020  1.090
 B0T  C19  H13  single    0.970  0.020  1.090
 B0T  C19  H14  single    0.970  0.020  1.090
 B0T  C19  H15  single    0.970  0.020  1.090
 B0T  C20  H16  single    0.970  0.020  1.090
 B0T  C20  H17  single    0.970  0.020  1.090
 B0T  C21  H18  single    0.970  0.020  1.090
 B0T  C22  H19  single    0.970  0.020  1.090
 B0T  C22  H20  single    0.970  0.020  1.090
 B0T  C23  H21  single    0.970  0.020  1.090
 B0T  C23  H22  single    0.970  0.020  1.090
 B0T  C24  H23  single    0.970  0.020  1.090
 B0T  C24  H24  single    0.970  0.020  1.090
 B0T  C24  H25  single    0.970  0.020  1.090
 B0T  C25  H26  single    0.970  0.020  1.090
 B0T  C25  H27  single    0.970  0.020  1.090
 B0T  C26  H28  single    0.970  0.020  1.090
 B0T  C26  H29  single    0.970  0.020  1.090
 B0T  N1   H30  single    0.860  0.020  1.020

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
 B0T  H1   C1   C3   120.03  3.000
 B0T  H1   C1   C2   120.55  3.000
 B0T  C3   C1   C2   119.42  3.000
 B0T  H2   C2   C4   119.92  3.000
 B0T  H2   C2   C1   120.37  3.000
 B0T  C4   C2   C1   119.70  3.000
 B0T  H3   C3   C7   119.72  3.000
 B0T  H3   C3   C1   119.38  3.000
 B0T  C7   C3   C1   120.89  3.000
 B0T  H4   C4   C9   119.02  3.000
 B0T  H4   C4   C2   119.44  3.000
 B0T  C9   C4   C2   121.53  3.000
 B0T  H5   C5   C10  119.25  3.000
 B0T  H5   C5   C6   119.01  3.000
 B0T  C10  C5   C6   121.74  3.000
 B0T  H6   C6   C11  119.40  3.000
 B0T  H6   C6   C5   121.10  3.000
 B0T  C11  C6   C5   119.49  3.000
 B0T  C13  C7   C9   121.37  3.000
 B0T  C9   C7   C3   120.00  3.000
 B0T  C13  C7   C3   118.54  3.000
 B0T  C14  C8   C12  117.82  3.000
 B0T  C14  C8   C10  123.01  3.000
 B0T  C12  C8   C10  119.03  3.000
 B0T  C22  C9   C7   121.79  3.000
 B0T  C7   C9   C4   118.45  3.000
 B0T  C22  C9   C4   119.74  3.000
 B0T  C23  C10  C8   122.69  3.000
 B0T  C23  C10  C5   118.26  3.000
 B0T  C8   C10  C5   119.05  3.000
 B0T  O7   C11  C12  122.49  3.000
 B0T  C12  C11  C6   119.51  3.000
 B0T  O7   C11  C6   118.00  3.000
 B0T  O6   C12  C11  120.31  3.000
 B0T  O6   C12  C8   118.48  3.000
 B0T  C11  C12  C8   121.17  3.000
 B0T  O3   C13  N1   124.53  3.000
 B0T  N1   C13  C7   114.18  3.000
 B0T  O3   C13  C7   121.14  3.000
 B0T  O5   C15  O2   126.16  3.000
 B0T  O5   C15  C25  115.94  3.000
 B0T  O2   C15  C25  117.90  3.000
 B0T  H11  C17  H10  105.70  3.000
 B0T  H11  C17  C18  107.66  3.000
 B0T  H10  C17  C18  109.48  3.000
 B0T  H11  C17  C16  109.47  3.000
 B0T  H10  C17  C16  110.52  3.000
 B0T  C18  C17  C16  113.67  3.000
 B0T  H12  C18  N1   106.94  3.000
 B0T  H12  C18  C19  109.60  3.000
 B0T  N1   C18  C19  110.78  3.000
 B0T  H12  C18  C17  108.22  3.000
 B0T  N1   C18  C17  109.36  3.000
 B0T  C19  C18  C17  111.79  3.000
 B0T  H15  C19  H14  107.79  3.000
 B0T  H15  C19  H13  108.24  3.000
 B0T  H14  C19  H13  107.89  3.000
 B0T  H15  C19  C18  110.85  3.000
 B0T  H14  C19  C18  110.74  3.000
 B0T  H13  C19  C18  111.21  3.000
 B0T  H17  C20  H16  108.19  3.000
 B0T  H17  C20  O6   110.39  3.000
 B0T  H16  C20  O6   107.08  3.000
 B0T  H17  C20  C21  109.86  3.000
 B0T  H16  C20  C21  110.06  3.000
 B0T  O6   C20  C21  111.18  3.000
 B0T  H18  C21  O7   109.03  3.000
 B0T  H18  C21  C26  109.52  3.000
 B0T  O7   C21  C26  108.78  3.000
 B0T  H18  C21  C20  109.00  3.000
 B0T  O7   C21  C20  108.75  3.000
 B0T  C26  C21  C20  111.72  3.000
 B0T  H20  C22  H19  106.40  3.000
 B0T  H20  C22  N2   107.83  3.000
 B0T  H19  C22  N2   111.86  3.000
 B0T  H20  C22  C9   109.33  3.000
 B0T  H19  C22  C9   108.18  3.000
 B0T  N2   C22  C9   113.01  3.000
 B0T  H22  C23  H21  106.72  3.000
 B0T  H22  C23  N2   110.00  3.000
 B0T  H21  C23  N2   107.67  3.000
 B0T  H22  C23  C10  107.84  3.000
 B0T  H21  C23  C10  109.60  3.000
 B0T  N2   C23  C10  114.72  3.000
 B0T  H25  C24  H24  107.76  3.000
 B0T  H25  C24  H23  107.88  3.000
 B0T  H24  C24  H23  107.51  3.000
 B0T  H25  C24  N2   113.37  3.000
 B0T  H24  C24  N2   110.35  3.000
 B0T  H23  C24  N2   109.76  3.000
 B0T  H29  C26  H28  106.37  3.000
 B0T  H29  C26  C25  109.54  3.000
 B0T  H28  C26  C25  110.12  3.000
 B0T  H29  C26  C21  107.35  3.000
 B0T  H28  C26  C21  109.12  3.000
 B0T  C25  C26  C21  114.03  3.000
 B0T  H30  N1   C18  118.07  3.000
 B0T  H30  N1   C13  117.76  3.000
 B0T  C18  N1   C13  124.17  3.000
 B0T  C24  N2   C23  112.70  3.000
 B0T  C23  N2   C22  108.79  3.000
 B0T  C24  N2   C22  111.90  3.000
 B0T  C20  O6   C12  114.48  3.000
 B0T  C21  O7   C11  116.12  3.000
 B0T  H27  C25  H26  105.30  3.000
 B0T  H27  C25  C26  109.89  3.000
 B0T  H26  C25  C26  110.36  3.000
 B0T  H27  C25  C15  107.91  3.000
 B0T  H26  C25  C15  108.19  3.000
 B0T  C26  C25  C15  114.73  3.000
 B0T  H9   C16  H8   106.94  3.000
 B0T  H9   C16  H7   108.45  3.000
 B0T  H8   C16  H7   107.72  3.000
 B0T  H9   C16  C17  110.61  3.000
 B0T  H8   C16  C17  111.88  3.000
 B0T  H7   C16  C17  111.07  3.000
 B0T  O4   C14  O1   127.23  3.000
 B0T  O1   C14  C8   115.10  3.000
 B0T  O4   C14  C8   117.61  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
 B0T  CONST_01  C9   C7   C3   C1      0.00   0.0  0
 B0T  CONST_02  C9   C4   C2   C1      0.00   0.0  0
 B0T  CONST_03  C7   C9   C4   C2      0.00   0.0  0
 B0T  CONST_04  C7   C3   C1   C2      0.00   0.0  0
 B0T  CONST_05  C4   C9   C7   C3      0.00   0.0  0
 B0T  CONST_06  C4   C2   C1   C3      0.00   0.0  0
 B0T  CONST_07  C12  C11  C6   C5      0.00   0.0  0
 B0T  CONST_08  C12  C8   C10  C5      0.00   0.0  0
 B0T  CONST_09  C8   C12  C11  C6      0.00   0.0  0
 B0T  CONST_10  C8   C10  C5   C6      0.00   0.0  0
 B0T  CONST_11  C11  C6   C5   C10     0.00   0.0  0
 B0T  CONST_12  C11  C12  C8   C10     0.00   0.0  0
 B0T  CONST_13  C13  C7   C3   C1    180.00   0.0  0
 B0T  CONST_14  C22  C9   C4   C2    180.00   0.0  0
 B0T  CONST_15  C22  C9   C7   C3    180.00   0.0  0
 B0T  CONST_16  C13  C7   C9   C4    180.00   0.0  0
 B0T  CONST_17  C14  C8   C10  C5    180.00   0.0  0
 B0T  CONST_18  C23  C10  C5   C6    180.00   0.0  0
 B0T  CONST_19  C14  C8   C12  C11   180.00   0.0  0
 B0T  CONST_20  C23  C10  C8   C12   180.00   0.0  0
 B0T  CONST_21  O6   C12  C8   C14     0.00   0.0  0
 B0T  CONST_22  H4   C4   C2   C1    180.00   0.0  0
 B0T  CONST_23  H3   C3   C1   C2    180.00   0.0  0
 B0T  CONST_24  H2   C2   C1   C3    180.00   0.0  0
 B0T  CONST_25  H1   C1   C2   C4    180.00   0.0  0
 B0T  CONST_26  H5   C5   C10  C8    180.00   0.0  0
 B0T  CONST_27  H6   C6   C5   C10   180.00   0.0  0
 B0T  CONST_28  C18  N1   C13  C7    180.00   0.0  0
 B0T  CONST_29  H30  N1   C13  C7      0.00   0.0  0
 B0T  CONST_30  O3   C13  N1   C18     0.00   0.0  0
 B0T  Var_01    C21  C20  O6   C12   -47.47  30.0  1
 B0T  Var_02    O3   C13  C7   C3   -115.40  30.0  2
 B0T  Var_03    N2   C22  C9   C4   -127.64  30.0  2
 B0T  Var_04    N2   C23  C10  C5     89.76  30.0  2
 B0T  Var_05    O4   C14  C8   C10   123.00  30.0  2
 B0T  Var_06    C24  N2   C22  C9     59.50  30.0  1
 B0T  Var_07    C21  C26  C25  C15  -175.78  30.0  3
 B0T  Var_08    O2   C15  C25  C26    10.22  30.0  2
 B0T  Var_09    H7   C16  C17  C18   178.38  30.0  3
 B0T  Var_10    H23  C24  N2   C22  -175.96  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
 B0T  chir_01  C18  C17  C19  N1   positiv
 B0T  chir_02  C21  C26  O7   C20  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
 B0T  plan-1  C1   0.020
 B0T  plan-1  C2   0.020
 B0T  plan-1  C3   0.020
 B0T  plan-1  C4   0.020
 B0T  plan-1  C7   0.020
 B0T  plan-1  C9   0.020
 B0T  plan-1  C13  0.020
 B0T  plan-1  C22  0.020
 B0T  plan-1  H1   0.020
 B0T  plan-1  H2   0.020
 B0T  plan-1  H3   0.020
 B0T  plan-1  H4   0.020
 B0T  plan-2  C5   0.020
 B0T  plan-2  C6   0.020
 B0T  plan-2  C8   0.020
 B0T  plan-2  C10  0.020
 B0T  plan-2  C11  0.020
 B0T  plan-2  C12  0.020
 B0T  plan-2  C23  0.020
 B0T  plan-2  O6   0.020
 B0T  plan-2  O7   0.020
 B0T  plan-2  H5   0.020
 B0T  plan-2  H6   0.020
 B0T  plan-2  C14  0.020
 B0T  plan-3  C7   0.020
 B0T  plan-3  C13  0.020
 B0T  plan-3  C18  0.020
 B0T  plan-3  N1   0.020
 B0T  plan-3  O3   0.020
 B0T  plan-3  H30  0.020
 B0T  plan-4  C15  0.020
 B0T  plan-4  O2   0.020
 B0T  plan-4  O5   0.020
 B0T  plan-4  C25  0.020
 B0T  plan-5  C8   0.020
 B0T  plan-5  O1   0.020
 B0T  plan-5  O4   0.020
 B0T  plan-5  C14  0.020

