# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 02:13:48 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 6-{[{2-[(cyclohexylmethyl)carbamoyl]benzyl}(methyl)amino]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](CNC(=O)Cc1c[nH]c2ccccc12)Cc3ccc4OCOc4c3C(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
 VXO  VXO  '6-{[{2-[(cyclohexylmethyl)carbamoyl]benzyl}(methyl)amino]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid'  ligand  59  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VXO
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
 VXO  C1    C  CR16   0  -0.272  -6.7354   0.9555   1.3411
 VXO  C2    C  CR16   0  -0.284  -7.7901   0.0662   1.0740
 VXO  C3    C  CR16   0  -0.372  -5.5445   0.8767   0.6459
 VXO  C4    C  CR16   0  -0.340   2.7584  -1.3014   2.1257
 VXO  C5    C  CR16   0  -0.306  -7.6751  -0.9141   0.1068
 VXO  C6    C  CR16   0  -0.349   3.2769  -2.5872   1.9304
 VXO  C7    C  CR15   0  -0.088  -4.8019  -1.5135  -1.9709
 VXO  C8    C  CR56   0   0.044  -5.4004  -0.1025  -0.3429
 VXO  C9    C  CR6    0  -0.182   3.8620  -0.4363   0.1419
 VXO  C10   C  CR6    0   0.094   3.0356  -0.2405   1.2710
 VXO  C11   C  CR5    0   0.048  -4.3400  -0.4600  -1.2356
 VXO  C12   C  CR56   0   0.351  -6.4727  -0.9867  -0.5958
 VXO  C13   C  CR56   0   0.281   4.0710  -2.7574   0.8255
 VXO  C14   C  CR56   0   0.287   4.3353  -1.7135  -0.0452
 VXO  C16   C  C      0   0.560  -2.1190  -0.0039  -0.1410
 VXO  C17   C  CH2    0   0.067   5.2253  -3.5650  -0.8835
 VXO  C20   C  CH2    0  -0.725  -3.0121   0.1969  -1.3579
 VXO  C21   C  CH2    0  -0.522   2.4007   1.1022   1.5164
 VXO  C22   C  CH2    0  -0.402   0.8961   2.9175   0.6146
 VXO  C23   C  CH2    0  -0.208   0.0608   0.5426   0.8343
 VXO  C24   C  CH1    0  -0.238   1.8867   3.8717  -0.0587
 VXO  C25   C  CH1    0  -0.305   1.2625   1.4330   0.5356
 VXO  N26   N  NR15   0  -0.688  -6.0750  -1.8326  -1.5895
 VXO  N27   N  NH1    0  -0.647  -0.9481   0.6504  -0.1983
 VXO  O28   O  O      0  -0.582   4.8814   1.6280  -0.3458
 VXO  O29   O  OC    -1  -0.593   3.9168   0.4955  -2.0137
 VXO  O30   O  O      0  -0.489  -2.4370  -0.6973   0.8124
 VXO  O31   O  O      0  -0.491   4.7292  -3.8725   0.4117
 VXO  O32   O  O      0  -0.484   5.1755  -2.1554  -1.0225
 VXO  H1    H  HCR6   0   0.245  -6.8602   1.7092   2.1079
 VXO  H2    H  HCR6   0   0.248  -8.7104   0.1499   1.6376
 VXO  H3    H  HCR6   0   0.237  -4.7379   1.5672   0.8620
 VXO  H5    H  HCR6   0   0.257  -8.4893  -1.5986  -0.0959
 VXO  H4    H  HCR6   0   0.245   2.1072  -1.1284   2.9744
 VXO  H6    H  HCR6   0   0.264   3.0618  -3.3951   2.6168
 VXO  H7    H  HCR5   0   0.281  -4.3087  -2.0680  -2.7543
 VXO  H26   H  HNR5   0   0.407  -6.6304  -2.5654  -1.9970
 VXO  H211  H  HCH2   0   0.236   2.0037   1.1364   2.5359
 VXO  H212  H  HCH2   0   0.260   3.1612   1.8798   1.4503
 VXO  H201  H  HCH2   0   0.291  -2.4857  -0.1866  -2.2369
 VXO  H202  H  HCH2   0   0.278  -3.1248   1.2731  -1.5286
 VXO  H27   H  HNH1   0   0.393  -0.7178   1.1563  -1.0388
 VXO  H171  H  HCH2   0   0.241   6.2545  -3.9113  -0.9765
 VXO  H172  H  HCH2   0   0.225   4.5938  -4.0386  -1.6449
 VXO  H181  H  HCH3   0   0.248   2.2159   2.7087  -1.8792
 VXO  H182  H  HCH3   0   0.206   0.9027   3.8930  -1.9931
 VXO  H183  H  HCH3   0   0.223   2.5853   4.4164  -2.0370
 VXO  H24   H  HCH1   0   0.227   2.8953   3.6469   0.3039
 VXO  H191  H  HCH3   0   0.215   0.5512   5.5817  -0.0249
 VXO  H192  H  HCH3   0   0.227   1.5854   5.4614   1.3984
 VXO  H193  H  HCH3   0   0.215   2.2563   6.0154  -0.1348
 VXO  H25   H  HCH1   0   0.236   1.6080   1.2007  -0.4788
 VXO  H221  H  HCH2   0   0.217   0.7946   3.1864   1.6731
 VXO  H222  H  HCH2   0   0.212  -0.0933   3.0904   0.1742
 VXO  H231  H  HCH2   0   0.237   0.3848  -0.4978   0.9288
 VXO  H232  H  HCH2   0   0.220  -0.3677   0.8264   1.8009
 VXO  C15   C  C      0   0.377   4.2503   0.6724  -0.8292
 VXO  C18   C  CH3    0  -0.677   1.8966   3.7057  -1.5755
 VXO  C19   C  CH3    0  -0.658   1.5537   5.3126   0.3174

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
 VXO  C1   C2    aromatic  1.405  0.020  1.405
 VXO  C1   C3    aromatic  1.381  0.020  1.381
 VXO  C2   C5    aromatic  1.382  0.020  1.382
 VXO  C3   C8    aromatic  1.399  0.020  1.399
 VXO  C4   C6    aromatic  1.400  0.020  1.400
 VXO  C4   C10   aromatic  1.390  0.020  1.390
 VXO  C5   C12   aromatic  1.395  0.020  1.395
 VXO  C6   C13   aromatic  1.371  0.020  1.371
 VXO  C7   C11   aromatic  1.365  0.020  1.365
 VXO  C7   N26   aromatic  1.367  0.020  1.367
 VXO  C8   C11   aromatic  1.432  0.020  1.432
 VXO  C8   C12   aromatic  1.413  0.020  1.413
 VXO  C9   C10   aromatic  1.413  0.020  1.413
 VXO  C9   C14   aromatic  1.375  0.020  1.375
 VXO  C9   C15   single    1.524  0.020  1.524
 VXO  C10  C21   single    1.505  0.020  1.505
 VXO  C11  C20   single    1.487  0.020  1.487
 VXO  C12  N26   aromatic  1.364  0.020  1.364
 VXO  C13  C14   aromatic  1.385  0.020  1.385
 VXO  C13  O31   single    1.359  0.020  1.359
 VXO  C14  O32   single    1.362  0.020  1.362
 VXO  C15  O28   deloc     1.243  0.020  1.243
 VXO  C15  O29   deloc     1.243  0.020  1.243
 VXO  C16  C20   single    1.523  0.020  1.523
 VXO  C16  N27   single    1.343  0.020  1.343
 VXO  C16  O30   double    1.221  0.020  1.221
 VXO  C17  O31   single    1.421  0.020  1.421
 VXO  C17  O32   single    1.417  0.020  1.417
 VXO  C18  C24   single    1.526  0.020  1.526
 VXO  C19  C24   single    1.526  0.020  1.526
 VXO  C21  C25   single    1.539  0.020  1.539
 VXO  C22  C24   single    1.531  0.020  1.531
 VXO  C22  C25   single    1.531  0.020  1.531
 VXO  C23  C25   single    1.525  0.020  1.525
 VXO  C23  N27   single    1.448  0.020  1.448
 VXO  C1   H1    single    0.930  0.020  1.080
 VXO  C2   H2    single    0.930  0.020  1.080
 VXO  C3   H3    single    0.930  0.020  1.080
 VXO  C5   H5    single    0.930  0.020  1.080
 VXO  C4   H4    single    0.930  0.020  1.080
 VXO  C6   H6    single    0.930  0.020  1.080
 VXO  C7   H7    single    0.930  0.020  1.080
 VXO  N26  H26   single    0.860  0.020  1.020
 VXO  C21  H211  single    0.970  0.020  1.090
 VXO  C21  H212  single    0.970  0.020  1.090
 VXO  C20  H201  single    0.970  0.020  1.090
 VXO  C20  H202  single    0.970  0.020  1.090
 VXO  N27  H27   single    0.860  0.020  1.020
 VXO  C17  H171  single    0.970  0.020  1.090
 VXO  C17  H172  single    0.970  0.020  1.090
 VXO  C18  H181  single    0.970  0.020  1.090
 VXO  C18  H182  single    0.970  0.020  1.090
 VXO  C18  H183  single    0.970  0.020  1.090
 VXO  C24  H24   single    0.970  0.020  1.090
 VXO  C19  H191  single    0.970  0.020  1.090
 VXO  C19  H192  single    0.970  0.020  1.090
 VXO  C19  H193  single    0.970  0.020  1.090
 VXO  C25  H25   single    0.970  0.020  1.090
 VXO  C22  H221  single    0.970  0.020  1.090
 VXO  C22  H222  single    0.970  0.020  1.090
 VXO  C23  H231  single    0.970  0.020  1.090
 VXO  C23  H232  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
 VXO  H1    C1   C3    119.72  3.000
 VXO  H1    C1   C2    119.27  3.000
 VXO  C3    C1   C2    121.02  3.000
 VXO  H2    C2   C5    119.34  3.000
 VXO  H2    C2   C1    119.35  3.000
 VXO  C5    C2   C1    121.30  3.000
 VXO  H3    C3   C8    120.69  3.000
 VXO  H3    C3   C1    120.33  3.000
 VXO  C8    C3   C1    118.97  3.000
 VXO  H4    C4   C10   118.65  3.000
 VXO  H4    C4   C6    118.58  3.000
 VXO  C10   C4   C6    122.76  3.000
 VXO  H5    C5   C12   121.41  3.000
 VXO  H5    C5   C2    121.12  3.000
 VXO  C12   C5   C2    117.47  3.000
 VXO  H6    C6   C13   122.26  3.000
 VXO  H6    C6   C4    121.58  3.000
 VXO  C13   C6   C4    116.16  3.000
 VXO  H7    C7   N26   120.55  3.000
 VXO  H7    C7   C11   129.26  3.000
 VXO  N26   C7   C11   110.18  3.000
 VXO  C12   C8   C11   107.12  3.000
 VXO  C12   C8   C3    119.11  3.000
 VXO  C11   C8   C3    133.77  3.000
 VXO  C15   C9   C14   120.08  3.000
 VXO  C15   C9   C10   123.87  3.000
 VXO  C14   C9   C10   116.04  3.000
 VXO  C21   C10  C9    120.04  3.000
 VXO  C21   C10  C4    119.75  3.000
 VXO  C9    C10  C4    120.14  3.000
 VXO  C20   C11  C8    127.06  3.000
 VXO  C20   C11  C7    126.79  3.000
 VXO  C8    C11  C7    106.14  3.000
 VXO  N26   C12  C8    107.29  3.000
 VXO  N26   C12  C5    130.59  3.000
 VXO  C8    C12  C5    122.12  3.000
 VXO  O31   C13  C14   109.55  3.000
 VXO  O31   C13  C6    128.87  3.000
 VXO  C14   C13  C6    121.57  3.000
 VXO  O32   C14  C13   108.91  3.000
 VXO  O32   C14  C9    127.68  3.000
 VXO  C13   C14  C9    123.30  3.000
 VXO  O30   C16  N27   122.49  3.000
 VXO  O30   C16  C20   123.10  3.000
 VXO  N27   C16  C20   114.40  3.000
 VXO  H172  C17  H171  110.32  3.000
 VXO  H172  C17  O32   109.95  3.000
 VXO  H171  C17  O32   109.93  3.000
 VXO  H172  C17  O31   109.78  3.000
 VXO  H171  C17  O31   109.80  3.000
 VXO  O32   C17  O31   107.00  3.000
 VXO  H202  C20  H201  105.59  3.000
 VXO  H202  C20  C16   108.32  3.000
 VXO  H201  C20  C16   108.28  3.000
 VXO  H202  C20  C11   110.80  3.000
 VXO  H201  C20  C11   109.94  3.000
 VXO  C16   C20  C11   113.57  3.000
 VXO  H212  C21  H211  106.70  3.000
 VXO  H212  C21  C25   108.92  3.000
 VXO  H211  C21  C25   108.58  3.000
 VXO  H212  C21  C10   109.41  3.000
 VXO  H211  C21  C10   109.44  3.000
 VXO  C25   C21  C10   113.57  3.000
 VXO  H222  C22  H221  105.39  3.000
 VXO  H222  C22  C25   110.36  3.000
 VXO  H221  C22  C25   108.03  3.000
 VXO  H222  C22  C24   107.99  3.000
 VXO  H221  C22  C24   109.36  3.000
 VXO  C25   C22  C24   115.25  3.000
 VXO  H232  C23  H231  106.64  3.000
 VXO  H232  C23  N27   109.74  3.000
 VXO  H231  C23  N27   109.81  3.000
 VXO  H232  C23  C25   109.27  3.000
 VXO  H231  C23  C25   109.80  3.000
 VXO  N27   C23  C25   111.47  3.000
 VXO  H24   C24  C22   108.80  3.000
 VXO  H24   C24  C19   108.25  3.000
 VXO  C22   C24  C19   109.80  3.000
 VXO  H24   C24  C18   107.51  3.000
 VXO  C22   C24  C18   111.93  3.000
 VXO  C19   C24  C18   110.44  3.000
 VXO  H25   C25  C23   107.80  3.000
 VXO  H25   C25  C22   109.18  3.000
 VXO  C23   C25  C22   111.55  3.000
 VXO  H25   C25  C21   108.12  3.000
 VXO  C23   C25  C21   109.42  3.000
 VXO  C22   C25  C21   110.65  3.000
 VXO  H26   N26  C12   125.87  3.000
 VXO  H26   N26  C7    124.85  3.000
 VXO  C12   N26  C7    109.27  3.000
 VXO  H27   N27  C23   118.23  3.000
 VXO  H27   N27  C16   118.66  3.000
 VXO  C23   N27  C16   122.76  3.000
 VXO  C17   O31  C13   105.61  3.000
 VXO  C17   O32  C14   105.90  3.000
 VXO  O29   C15  O28   128.03  3.000
 VXO  O29   C15  C9    115.80  3.000
 VXO  O28   C15  C9    116.16  3.000
 VXO  H183  C18  H182  107.47  3.000
 VXO  H183  C18  H181  107.03  3.000
 VXO  H182  C18  H181  108.44  3.000
 VXO  H183  C18  C24   110.70  3.000
 VXO  H182  C18  C24   110.79  3.000
 VXO  H181  C18  C24   112.23  3.000
 VXO  H193  C19  H192  107.68  3.000
 VXO  H193  C19  H191  107.58  3.000
 VXO  H192  C19  H191  107.65  3.000
 VXO  H193  C19  C24   111.42  3.000
 VXO  H192  C19  C24   111.50  3.000
 VXO  H191  C19  C24   110.82  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
 VXO  CONST_01  C12   C5   C2   C1      0.00   0.0  0
 VXO  CONST_02  C11   C8   C3   C1    180.00   0.0  0
 VXO  CONST_03  C12   C8   C3   C1      0.00   0.0  0
 VXO  CONST_04  C8    C3   C1   C2      0.00   0.0  0
 VXO  CONST_05  C8    C12  C5   C2      0.00   0.0  0
 VXO  CONST_06  N26   C12  C5   C2    180.00   0.0  0
 VXO  CONST_07  C5    C2   C1   C3      0.00   0.0  0
 VXO  CONST_08  C7    C11  C8   C3    180.00   0.0  0
 VXO  CONST_09  C5    C12  C8   C3      0.00   0.0  0
 VXO  CONST_10  N26   C12  C8   C3    180.00   0.0  0
 VXO  CONST_11  C14   C13  C6   C4      0.00   0.0  0
 VXO  CONST_12  C14   C9   C10  C4      0.00   0.0  0
 VXO  CONST_13  C11   C8   C12  C5    180.00   0.0  0
 VXO  CONST_14  C7    N26  C12  C5    180.00   0.0  0
 VXO  CONST_15  C9    C10  C4   C6      0.00   0.0  0
 VXO  CONST_16  C9    C14  C13  C6      0.00   0.0  0
 VXO  CONST_17  C12   C8   C11  C7      0.00   0.0  0
 VXO  CONST_18  C8    C12  N26  C7      0.00   0.0  0
 VXO  CONST_19  N26   C7   C11  C8      0.00   0.0  0
 VXO  CONST_20  C13   C6   C4   C10     0.00   0.0  0
 VXO  CONST_21  C13   C14  C9   C10     0.00   0.0  0
 VXO  CONST_22  C12   N26  C7   C11     0.00   0.0  0
 VXO  CONST_23  N26   C12  C8   C11     0.00   0.0  0
 VXO  CONST_24  C20   C11  C8   C3      0.00   0.0  0
 VXO  CONST_25  C15   C9   C10  C4    180.00   0.0  0
 VXO  CONST_26  C21   C10  C4   C6    180.00   0.0  0
 VXO  CONST_27  C20   C11  C8   C12   180.00   0.0  0
 VXO  CONST_28  C15   C9   C14  C13   180.00   0.0  0
 VXO  CONST_29  C21   C10  C9   C14   180.00   0.0  0
 VXO  CONST_30  O32   C14  C9   C15     0.00   0.0  0
 VXO  CONST_31  N26   C7   C11  C20   180.00   0.0  0
 VXO  CONST_32  H5    C5   C2   C1    180.00   0.0  0
 VXO  CONST_33  H3    C3   C1   C2    180.00   0.0  0
 VXO  CONST_34  H2    C2   C1   C3    180.00   0.0  0
 VXO  CONST_35  H1    C1   C2   C5    180.00   0.0  0
 VXO  CONST_36  H26   N26  C12  C5      0.00   0.0  0
 VXO  CONST_37  H7    C7   C11  C8    180.00   0.0  0
 VXO  CONST_38  H4    C4   C10  C9    180.00   0.0  0
 VXO  CONST_39  H6    C6   C4   C10   180.00   0.0  0
 VXO  CONST_40  C23   N27  C16  C20   180.00   0.0  0
 VXO  CONST_41  O30   C16  N27  C23     0.00   0.0  0
 VXO  CONST_42  H27   N27  C16  C20     0.00   0.0  0
 VXO  Var_01    O32   C17  O31  C13    16.81  30.0  1
 VXO  Var_02    O31   C17  O32  C14   -17.08  30.0  1
 VXO  Var_03    C25   C21  C10  C4   -105.31  30.0  2
 VXO  Var_04    C16   C20  C11  C7   -113.07  30.0  2
 VXO  Var_05    O28   C15  C9   C10    60.58  30.0  2
 VXO  Var_06    N27   C16  C20  C11  -176.10  30.0  1
 VXO  Var_07    C25   C23  N27  C16  -177.81  30.0  2
 VXO  Var_08    C25   C22  C24  C18    67.75  30.0  1
 VXO  Var_09    H191  C19  C24  C18    62.63  30.0  3
 VXO  Var_10    H181  C18  C24  C19   175.04  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
 VXO  chir_01  C25  C21  C22  C23  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
 VXO  plan-1  C1   0.020
 VXO  plan-1  C2   0.020
 VXO  plan-1  C3   0.020
 VXO  plan-1  C5   0.020
 VXO  plan-1  C7   0.020
 VXO  plan-1  C8   0.020
 VXO  plan-1  C11  0.020
 VXO  plan-1  C12  0.020
 VXO  plan-1  C20  0.020
 VXO  plan-1  N26  0.020
 VXO  plan-1  H1   0.020
 VXO  plan-1  H2   0.020
 VXO  plan-1  H3   0.020
 VXO  plan-1  H5   0.020
 VXO  plan-1  H7   0.020
 VXO  plan-1  H26  0.020
 VXO  plan-2  C4   0.020
 VXO  plan-2  C6   0.020
 VXO  plan-2  C9   0.020
 VXO  plan-2  C10  0.020
 VXO  plan-2  C13  0.020
 VXO  plan-2  C14  0.020
 VXO  plan-2  C21  0.020
 VXO  plan-2  O31  0.020
 VXO  plan-2  O32  0.020
 VXO  plan-2  H4   0.020
 VXO  plan-2  H6   0.020
 VXO  plan-2  C15  0.020
 VXO  plan-3  C16  0.020
 VXO  plan-3  C20  0.020
 VXO  plan-3  C23  0.020
 VXO  plan-3  N27  0.020
 VXO  plan-3  O30  0.020
 VXO  plan-3  H27  0.020
 VXO  plan-4  C9   0.020
 VXO  plan-4  O28  0.020
 VXO  plan-4  O29  0.020
 VXO  plan-4  C15  0.020

