# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:13:59 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: 2-[[4-[(3S,5R)-3,5-dimethylpiperidin-1-yl]-3-phenoxy-phenyl]carbonylamino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](C)CN(C1)c2ccc(cc2Oc3ccccc3)C(=O)Nc4ccccc4C(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
 B83  B83  '2-[[4-[(3S,5R)-3,5-dimethylpiperidin-1-yl]-3-phenoxy-phenyl]carbonylamino]benzoic acid'  ligand  60  33  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B83
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
 B83  C1    C  CR6    0  -0.231  -5.3943   1.1247  -0.3705
 B83  C2    C  CR6    0   0.351  -4.6001   0.1170   0.2246
 B83  C3    C  CR16   0  -0.324  -5.2241  -0.9631   0.8596
 B83  C4    C  CR16   0  -0.251  -6.6062  -1.0455   0.9072
 B83  C5    C  CR16   0  -0.263  -7.3961  -0.0632   0.3288
 B83  C6    C  CR16   0  -0.283  -6.7793   1.0056  -0.3001
 B83  C7    C  C      0   0.467  -4.8194   2.3411  -1.0889
 B83  O8    O  O      0  -0.602  -3.5634   2.4338  -1.1653
 B83  O9    O  OC    -1  -0.558  -5.6221   3.1594  -1.5538
 B83  N10   N  NH1    0  -0.793  -3.2184   0.2710   0.1517
 B83  C11   C  C      0   0.520  -2.2361  -0.5467   0.5867
 B83  O12   O  O      0  -0.480  -2.4127  -1.6488   1.0903
 B83  C13   C  CR6    0  -0.049  -0.8532  -0.0154   0.3974
 B83  C14   C  CR16   0  -0.310  -0.5579   1.3364   0.2862
 B83  C15   C  CR16   0  -0.329   0.7586   1.7545   0.1548
 B83  C16   C  CR6    0   0.271   1.8178   0.8515   0.0999
 B83  C17   C  CR6    0   0.351   1.4984  -0.5210   0.1859
 B83  C18   C  CR16   0  -0.374   0.1943  -0.9387   0.3614
 B83  O19   O  O2     0  -0.511   2.5453  -1.3828   0.0643
 B83  C20   C  CR6    0   0.304   2.3145  -2.7348   0.1077
 B83  C21   C  CR16   0  -0.300   1.9891  -3.4112  -1.0591
 B83  C22   C  CR16   0  -0.254   1.8076  -4.7869  -1.0164
 B83  C23   C  CR16   0  -0.256   1.9474  -5.4761   0.1816
 B83  C24   C  CR16   0  -0.254   2.2739  -4.7857   1.3414
 B83  C25   C  CR16   0  -0.304   2.4561  -3.4094   1.3109
 B83  N26   N  NT     0  -0.498   3.1439   1.2433  -0.0797
 B83  C27   C  CH2    0  -0.284   3.3700   2.5498  -0.6710
 B83  C28   C  CH1    0  -0.244   4.7933   2.6560  -1.2087
 B83  C29   C  CH2    0  -0.399   5.7953   2.3477  -0.1009
 B83  C30   C  CH1    0  -0.250   5.5023   1.0136   0.5780
 B83  C31   C  CH2    0  -0.271   4.0508   0.9829   1.0355
 B83  C32   C  CH3    0  -0.660   6.4424   0.7599   1.7482
 B83  C33   C  CH3    0  -0.659   5.0358   4.0295  -1.8184
 B83  H3    H  HCR6   0   0.276  -4.6344  -1.7408   1.3148
 B83  H4    H  HCR6   0   0.254  -7.0641  -1.8918   1.4033
 B83  H5    H  HCR6   0   0.248  -8.4756  -0.1287   0.3668
 B83  H6    H  HCR6   0   0.250  -7.3813   1.7804  -0.7547
 B83  HN10  H  HNH1   0   0.448  -2.9951   1.1363  -0.3773
 B83  H14   H  HCR6   0   0.250  -1.3322   2.0902   0.3365
 B83  H15   H  HCR6   0   0.272   0.9594   2.8161   0.1028
 B83  H18   H  HCR6   0   0.274  -0.0320  -1.9938   0.4413
 B83  H21   H  HCR6   0   0.274   1.8824  -2.8682  -1.9899
 B83  H22   H  HCR6   0   0.264   1.5560  -5.3198  -1.9239
 B83  H23   H  HCR6   0   0.261   1.8074  -6.5485   0.2103
 B83  H24   H  HCR6   0   0.264   2.3880  -5.3180   2.2766
 B83  H25   H  HCR6   0   0.272   2.7144  -2.8662   2.2112
 B83  H27   H  HCH2   0   0.248   2.6599   2.6936  -1.4879
 B83  H27A  H  HCH2   0   0.199   3.1983   3.3628   0.0555
 B83  H28   H  HCH1   0   0.220   4.9022   1.8981  -1.9933
 B83  H29   H  HCH2   0   0.229   6.8132   2.3531  -0.5026
 B83  H29A  H  HCH2   0   0.203   5.7535   3.1467   0.6515
 B83  H30   H  HCH1   0   0.220   5.6296   0.2122  -0.1593
 B83  H31   H  HCH2   0   0.203   3.9031   1.7392   1.8248
 B83  H31A  H  HCH2   0   0.252   3.8241   0.0150   1.4778
 B83  H32   H  HCH3   0   0.216   6.3365   1.5341   2.5112
 B83  H32A  H  HCH3   0   0.227   6.2450  -0.2039   2.2208
 B83  H32B  H  HCH3   0   0.230   7.4828   0.7608   1.4196
 B83  H33   H  HCH3   0   0.216   4.9314   4.8162  -1.0678
 B83  H33A  H  HCH3   0   0.230   6.0434   4.0991  -2.2311
 B83  H33B  H  HCH3   0   0.228   4.3311   4.2426  -2.6241

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
 B83  C2   C1    aromatic  1.414  0.020  1.414
 B83  C1   C6    aromatic  1.392  0.020  1.392
 B83  C1   C7    single    1.525  0.020  1.525
 B83  C3   C2    aromatic  1.400  0.020  1.400
 B83  N10  C2    single    1.392  0.020  1.392
 B83  C3   C4    aromatic  1.385  0.020  1.385
 B83  C3   H3    single    0.930  0.020  1.080
 B83  C4   C5    aromatic  1.387  0.020  1.387
 B83  C4   H4    single    0.930  0.020  1.080
 B83  C5   C6    aromatic  1.385  0.020  1.385
 B83  C5   H5    single    0.930  0.020  1.080
 B83  C6   H6    single    0.930  0.020  1.080
 B83  O8   C7    deloc     1.262  0.020  1.262
 B83  C7   O9    deloc     1.237  0.020  1.237
 B83  C11  N10   single    1.350  0.020  1.350
 B83  N10  HN10  single    0.860  0.020  1.020
 B83  O12  C11   double    1.224  0.020  1.224
 B83  C11  C13   single    1.493  0.020  1.493
 B83  C18  C13   aromatic  1.397  0.020  1.397
 B83  C13  C14   aromatic  1.388  0.020  1.388
 B83  C14  C15   aromatic  1.388  0.020  1.388
 B83  C14  H14   single    0.930  0.020  1.080
 B83  C16  C15   aromatic  1.393  0.020  1.393
 B83  C15  H15   single    0.930  0.020  1.080
 B83  C17  C16   aromatic  1.412  0.020  1.412
 B83  C16  N26   single    1.394  0.020  1.394
 B83  O19  C17   single    1.361  0.020  1.361
 B83  C18  C17   aromatic  1.381  0.020  1.381
 B83  C18  H18   single    0.930  0.020  1.080
 B83  C20  O19   single    1.372  0.020  1.372
 B83  C25  C20   aromatic  1.387  0.020  1.387
 B83  C20  C21   aromatic  1.387  0.020  1.387
 B83  C22  C21   aromatic  1.388  0.020  1.388
 B83  C21  H21   single    0.930  0.020  1.080
 B83  C23  C22   aromatic  1.389  0.020  1.389
 B83  C22  H22   single    0.930  0.020  1.080
 B83  C24  C23   aromatic  1.389  0.020  1.389
 B83  C23  H23   single    0.930  0.020  1.080
 B83  C24  C25   aromatic  1.389  0.020  1.389
 B83  C24  H24   single    0.930  0.020  1.080
 B83  C25  H25   single    0.930  0.020  1.080
 B83  C27  N26   single    1.452  0.020  1.452
 B83  N26  C31   single    1.461  0.020  1.461
 B83  C28  C27   single    1.525  0.020  1.525
 B83  C27  H27   single    0.970  0.020  1.090
 B83  C27  H27A  single    0.970  0.020  1.090
 B83  C33  C28   single    1.522  0.020  1.522
 B83  C28  C29   single    1.525  0.020  1.525
 B83  C28  H28   single    0.970  0.020  1.090
 B83  C29  C30   single    1.525  0.020  1.525
 B83  C29  H29   single    0.970  0.020  1.090
 B83  C29  H29A  single    0.970  0.020  1.090
 B83  C30  C31   single    1.522  0.020  1.522
 B83  C30  C32   single    1.522  0.020  1.522
 B83  C30  H30   single    0.970  0.020  1.090
 B83  C31  H31   single    0.970  0.020  1.090
 B83  C31  H31A  single    0.970  0.020  1.090
 B83  C32  H32   single    0.970  0.020  1.090
 B83  C32  H32A  single    0.970  0.020  1.090
 B83  C32  H32B  single    0.970  0.020  1.090
 B83  C33  H33   single    0.970  0.020  1.090
 B83  C33  H33A  single    0.970  0.020  1.090
 B83  C33  H33B  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
 B83  C7    C1   C6    117.85  3.000
 B83  C7    C1   C2    123.69  3.000
 B83  C6    C1   C2    118.46  3.000
 B83  N10   C2   C3    123.47  3.000
 B83  N10   C2   C1    117.16  3.000
 B83  C3    C2   C1    119.36  3.000
 B83  H3    C3   C4    119.26  3.000
 B83  H3    C3   C2    120.32  3.000
 B83  C4    C3   C2    120.41  3.000
 B83  H4    C4   C5    120.26  3.000
 B83  H4    C4   C3    118.96  3.000
 B83  C5    C4   C3    120.78  3.000
 B83  H5    C5   C6    120.46  3.000
 B83  H5    C5   C4    120.71  3.000
 B83  C6    C5   C4    118.83  3.000
 B83  H6    C6   C5    119.73  3.000
 B83  H6    C6   C1    118.12  3.000
 B83  C5    C6   C1    122.15  3.000
 B83  O9    C7   O8    125.08  3.000
 B83  O9    C7   C1    117.39  3.000
 B83  O8    C7   C1    117.54  3.000
 B83  HN10  N10  C11   120.82  3.000
 B83  HN10  N10  C2    109.40  3.000
 B83  C11   N10  C2    129.66  3.000
 B83  C13   C11  O12   120.39  3.000
 B83  C13   C11  N10   114.67  3.000
 B83  O12   C11  N10   124.94  3.000
 B83  C18   C13  C14   118.83  3.000
 B83  C14   C13  C11   123.61  3.000
 B83  C18   C13  C11   117.55  3.000
 B83  H14   C14  C15   118.26  3.000
 B83  H14   C14  C13   121.51  3.000
 B83  C15   C14  C13   120.19  3.000
 B83  H15   C15  C16   119.55  3.000
 B83  H15   C15  C14   118.45  3.000
 B83  C16   C15  C14   122.00  3.000
 B83  N26   C16  C17   119.74  3.000
 B83  N26   C16  C15   123.10  3.000
 B83  C17   C16  C15   117.12  3.000
 B83  O19   C17  C18   123.11  3.000
 B83  C18   C17  C16   121.03  3.000
 B83  O19   C17  C16   115.85  3.000
 B83  H18   C18  C17   120.13  3.000
 B83  H18   C18  C13   119.07  3.000
 B83  C17   C18  C13   120.78  3.000
 B83  C20   O19  C17   119.44  3.000
 B83  C25   C20  C21   121.10  3.000
 B83  C21   C20  O19   119.55  3.000
 B83  C25   C20  O19   119.31  3.000
 B83  H21   C21  C22   120.69  3.000
 B83  H21   C21  C20   120.10  3.000
 B83  C22   C21  C20   119.21  3.000
 B83  H22   C22  C23   120.15  3.000
 B83  H22   C22  C21   119.52  3.000
 B83  C23   C22  C21   120.33  3.000
 B83  H23   C23  C24   120.07  3.000
 B83  H23   C23  C22   120.12  3.000
 B83  C24   C23  C22   119.81  3.000
 B83  H24   C24  C25   119.52  3.000
 B83  H24   C24  C23   120.13  3.000
 B83  C25   C24  C23   120.35  3.000
 B83  H25   C25  C24   120.68  3.000
 B83  H25   C25  C20   120.12  3.000
 B83  C24   C25  C20   119.20  3.000
 B83  C31   N26  C27   112.00  3.000
 B83  C31   N26  C16   116.23  3.000
 B83  C27   N26  C16   116.96  3.000
 B83  H27A  C27  H27   107.12  3.000
 B83  H27A  C27  C28   109.02  3.000
 B83  H27   C27  C28   109.51  3.000
 B83  H27A  C27  N26   111.76  3.000
 B83  H27   C27  N26   108.78  3.000
 B83  C28   C27  N26   110.58  3.000
 B83  H28   C28  C33   108.74  3.000
 B83  H28   C28  C29   108.35  3.000
 B83  C33   C28  C29   111.63  3.000
 B83  H28   C28  C27   107.27  3.000
 B83  C29   C28  C27   110.06  3.000
 B83  C33   C28  C27   110.65  3.000
 B83  H29A  C29  H29   106.46  3.000
 B83  H29A  C29  C30   108.91  3.000
 B83  H29   C29  C30   110.26  3.000
 B83  H29A  C29  C28   109.00  3.000
 B83  H29   C29  C28   110.09  3.000
 B83  C30   C29  C28   111.96  3.000
 B83  H30   C30  C32   108.87  3.000
 B83  H30   C30  C31   107.34  3.000
 B83  C32   C30  C31   110.76  3.000
 B83  H30   C30  C29   108.52  3.000
 B83  C32   C30  C29   111.67  3.000
 B83  C31   C30  C29   109.55  3.000
 B83  H31A  C31  H31   106.93  3.000
 B83  H31A  C31  C30   109.80  3.000
 B83  H31   C31  C30   109.20  3.000
 B83  H31A  C31  N26   109.85  3.000
 B83  H31   C31  N26   109.93  3.000
 B83  C30   C31  N26   111.04  3.000
 B83  H32B  C32  H32A  107.68  3.000
 B83  H32B  C32  H32   107.59  3.000
 B83  H32A  C32  H32   107.81  3.000
 B83  H32B  C32  C30   110.93  3.000
 B83  H32A  C32  C30   111.61  3.000
 B83  H32   C32  C30   111.04  3.000
 B83  H33B  C33  H33A  107.73  3.000
 B83  H33B  C33  H33   107.75  3.000
 B83  H33A  C33  H33   107.59  3.000
 B83  H33B  C33  C28   111.65  3.000
 B83  H33A  C33  C28   110.87  3.000
 B83  H33   C33  C28   111.06  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
 B83  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 B83  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 B83  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 B83  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 B83  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 B83  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 B83  CONST_07  C16   C17  C18  C13     0.00   0.0  0
 B83  CONST_08  C16   C15  C14  C13     0.00   0.0  0
 B83  CONST_09  C17   C18  C13  C14     0.00   0.0  0
 B83  CONST_10  C17   C16  C15  C14     0.00   0.0  0
 B83  CONST_11  C18   C13  C14  C15     0.00   0.0  0
 B83  CONST_12  C18   C17  C16  C15     0.00   0.0  0
 B83  CONST_13  C23   C24  C25  C20     0.00   0.0  0
 B83  CONST_14  C23   C22  C21  C20     0.00   0.0  0
 B83  CONST_15  C24   C25  C20  C21     0.00   0.0  0
 B83  CONST_16  C24   C23  C22  C21     0.00   0.0  0
 B83  CONST_17  C25   C20  C21  C22     0.00   0.0  0
 B83  CONST_18  C25   C24  C23  C22     0.00   0.0  0
 B83  CONST_19  N26   C16  C15  C14   180.00   0.0  0
 B83  CONST_20  N26   C16  C17  C18   180.00   0.0  0
 B83  CONST_21  C7    C1   C2   C3    180.00   0.0  0
 B83  CONST_22  N10   C2   C3   C4    180.00   0.0  0
 B83  CONST_23  C7    C1   C6   C5    180.00   0.0  0
 B83  CONST_24  N10   C2   C1   C6    180.00   0.0  0
 B83  CONST_25  C17   C18  C13  C11   180.00   0.0  0
 B83  CONST_26  C15   C14  C13  C11   180.00   0.0  0
 B83  CONST_27  O19   C17  C18  C13   180.00   0.0  0
 B83  CONST_28  O19   C17  C16  C15   180.00   0.0  0
 B83  CONST_29  N26   C16  C17  O19     0.00   0.0  0
 B83  CONST_30  C24   C25  C20  O19   180.00   0.0  0
 B83  CONST_31  C22   C21  C20  O19   180.00   0.0  0
 B83  CONST_32  H3    C3   C2   C1    180.00   0.0  0
 B83  CONST_33  H5    C5   C6   C1    180.00   0.0  0
 B83  CONST_34  H6    C6   C1   C2    180.00   0.0  0
 B83  CONST_35  H4    C4   C3   C2    180.00   0.0  0
 B83  CONST_36  H15   C15  C14  C13   180.00   0.0  0
 B83  CONST_37  H18   C18  C13  C14   180.00   0.0  0
 B83  CONST_38  H14   C14  C15  C16   180.00   0.0  0
 B83  CONST_39  H24   C24  C25  C20   180.00   0.0  0
 B83  CONST_40  H22   C22  C21  C20   180.00   0.0  0
 B83  CONST_41  H25   C25  C20  C21   180.00   0.0  0
 B83  CONST_42  H23   C23  C22  C21   180.00   0.0  0
 B83  CONST_43  H21   C21  C22  C23   180.00   0.0  0
 B83  CONST_44  C13   C11  N10  C2    180.00   0.0  0
 B83  CONST_45  C11   N10  C2   C1    180.00   0.0  0
 B83  CONST_46  C11   N10  C2   C3      0.00   0.0  0
 B83  CONST_47  HN10  N10  C2   C1      0.00   0.0  0
 B83  CONST_48  O12   C11  N10  C2      0.00   0.0  0
 B83  Var_01    C27   N26  C16  C15   -21.11  30.0  2
 B83  Var_02    C28   C27  N26  C16  -161.89  30.0  1
 B83  Var_03    C30   C31  N26  C16   161.21  30.0  1
 B83  Var_04    C25   C20  O19  C17   -95.16  30.0  2
 B83  Var_05    O8    C7   C1   C2      0.96  30.0  2
 B83  Var_06    C18   C13  C11  N10  -157.55  30.0  2

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
 B83  chir_01  C28  C27  C33  C29  negativ
 B83  chir_02  C30  C29  C31  C32  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
 B83  plan-1  C1    0.020
 B83  plan-1  C2    0.020
 B83  plan-1  C3    0.020
 B83  plan-1  C4    0.020
 B83  plan-1  C5    0.020
 B83  plan-1  C6    0.020
 B83  plan-1  C7    0.020
 B83  plan-1  N10   0.020
 B83  plan-1  H3    0.020
 B83  plan-1  H4    0.020
 B83  plan-1  H5    0.020
 B83  plan-1  H6    0.020
 B83  plan-2  C11   0.020
 B83  plan-2  C13   0.020
 B83  plan-2  C14   0.020
 B83  plan-2  C15   0.020
 B83  plan-2  C16   0.020
 B83  plan-2  C17   0.020
 B83  plan-2  C18   0.020
 B83  plan-2  O19   0.020
 B83  plan-2  N26   0.020
 B83  plan-2  H14   0.020
 B83  plan-2  H15   0.020
 B83  plan-2  H18   0.020
 B83  plan-3  O19   0.020
 B83  plan-3  C20   0.020
 B83  plan-3  C21   0.020
 B83  plan-3  C22   0.020
 B83  plan-3  C23   0.020
 B83  plan-3  C24   0.020
 B83  plan-3  C25   0.020
 B83  plan-3  H21   0.020
 B83  plan-3  H22   0.020
 B83  plan-3  H23   0.020
 B83  plan-3  H24   0.020
 B83  plan-3  H25   0.020
 B83  plan-4  C2    0.020
 B83  plan-4  N10   0.020
 B83  plan-4  C11   0.020
 B83  plan-4  O12   0.020
 B83  plan-4  C13   0.020
 B83  plan-4  HN10  0.020
 B83  plan-5  C1    0.020
 B83  plan-5  C7    0.020
 B83  plan-5  O8    0.020
 B83  plan-5  O9    0.020

