# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 17:54:19 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (3S)-3-[4-chloranyl-3-[[methyl(methylsulfonyl)amino]methyl]phenyl]-3-(1-methylbenzotriazol-5-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1cc(ccc1Cl)[C@H](CC(O)=O)c2ccc3n(C)nnc3c2)[S](C)(=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
 XYY  XYY  '(3S)-3-[4-chloranyl-3-[[methyl(methylsulfonyl)amino]methyl]phenyl]-3-(1-methylbenzotriazol-5-yl)propanoic acid'  ligand  50  29  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XYY
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
 XYY  C1    C   CH3   0  -0.531   4.6224   0.4362   0.3212
 XYY  CL1   CL  CL    0  -0.130   3.0147   2.5721  -2.4685
 XYY  N2    N   N     0  -0.559   3.3868   0.6500   1.0615
 XYY  C3    C   CH2   0  -0.409   2.4897   1.6459   0.4844
 XYY  C4    C   CR6   0   0.240   1.6981   1.0331  -0.6419
 XYY  C5    C   CR16  0  -0.339   0.7652   0.0492  -0.3318
 XYY  C6    C   CR6   0   0.207  -0.0167  -0.5722  -1.2956
 XYY  C7    C   CR16  0  -0.354   0.1563  -0.1924  -2.6229
 XYY  C8    C   CR16  0  -0.174   1.0852   0.7754  -2.9677
 XYY  C9    C   CR6   0  -0.146   1.8489   1.3792  -1.9802
 XYY  C11   C   CH1   0  -0.426  -1.0503  -1.5851  -0.8494
 XYY  C12   C   CH2   0  -0.597  -1.4811  -2.5628  -1.9399
 XYY  C13   C   C     0   0.557  -0.3498  -3.4135  -2.4527
 XYY  O14   O   O     0  -0.434   0.6986  -3.5773  -1.8816
 XYY  O15   O   OH1   0  -0.592  -0.6538  -3.9990  -3.6049
 XYY  C16   C   CR6   0   0.175  -2.2637  -0.8771  -0.2806
 XYY  C17   C   CR16  0  -0.295  -2.9966   0.0191  -1.0996
 XYY  C18   C   CR16  0  -0.277  -4.1180   0.6801  -0.6602
 XYY  C19   C   CR56  0   0.377  -4.5056   0.4231   0.6575
 XYY  N20   N   NR5   0  -0.374  -5.5184   0.8601   1.4394
 XYY  C21   C   CH3   0  -0.530  -6.5799   1.7763   1.0996
 XYY  N22   N   N     0  -0.066  -5.4389   0.3024   2.6409
 XYY  N23   N   N     0  -0.333  -4.4265  -0.4784   2.6959
 XYY  C24   C   CR56  0   0.148  -3.7996  -0.4485   1.4849
 XYY  C25   C   CR16  0  -0.378  -2.6598  -1.1139   1.0165
 XYY  S26   S   S     0   1.342   3.4141   0.4712   2.6999
 XYY  O27   O   OS    0  -0.663   2.0338   0.5193   3.1622
 XYY  O28   O   OS    0  -0.665   4.2095  -0.7124   2.9880
 XYY  C29   C   CH3   0  -0.797   4.2667   1.8865   3.3595
 XYY  H11   H   HCH1  0   0.285  -0.6051  -2.1700  -0.0413
 XYY  H1    H   HCH3  0   0.263   4.3655   0.2299  -0.7170
 XYY  H1A   H   HCH3  0   0.240   5.2792   1.3099   0.3454
 XYY  H1B   H   HCH3  0   0.270   5.1571  -0.4274   0.7038
 XYY  H3    H   HCH2  0   0.297   1.7927   2.0041   1.2412
 XYY  H3A   H   HCH2  0   0.272   3.0576   2.5166   0.1504
 XYY  H5    H   HCR6  0   0.251   0.6503  -0.2352   0.7090
 XYY  H7    H   HCR6  0   0.263  -0.4283  -0.6421  -3.4156
 XYY  H8    H   HCR6  0   0.281   1.2149   1.0557  -4.0040
 XYY  H12   H   HCH2  0   0.319  -2.2281  -3.2448  -1.5211
 XYY  H12A  H   HCH2  0   0.283  -1.9844  -2.0615  -2.7691
 XYY  H17   H   HCR6  0   0.262  -2.6605   0.1977  -2.1139
 XYY  H18   H   HCR6  0   0.284  -4.6604   1.3599  -1.3031
 XYY  H21   H   HCH3  0   0.279  -7.2123   1.9067   1.9721
 XYY  H21A  H   HCH3  0   0.267  -6.1679   2.7404   0.8081
 XYY  H21B  H   HCH3  0   0.267  -7.1756   1.3768   0.2812
 XYY  H25   H   HCR6  0   0.268  -2.1107  -1.7935   1.6560
 XYY  H29   H   HCH3  0   0.291   5.2876   1.9032   2.9833
 XYY  H29A  H   HCH3  0   0.292   3.7439   2.7944   3.0659
 XYY  H29B  H   HCH3  0   0.308   4.2764   1.8014   4.4450
 XYY  HO15  H   HOH1  0   0.481   0.0720  -4.5775  -3.8835

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
 XYY  H1B   C1    single    0.970  0.020  1.090
 XYY  C1    H1    single    0.970  0.020  1.090
 XYY  C1    H1A   single    0.970  0.020  1.090
 XYY  C1    N2    single    1.456  0.020  1.456
 XYY  C9    CL1   single    1.738  0.020  1.738
 XYY  C3    N2    single    1.459  0.020  1.459
 XYY  N2    S26   single    1.648  0.020  1.648
 XYY  H3    C3    single    0.970  0.020  1.090
 XYY  C4    C3    single    1.507  0.020  1.507
 XYY  C3    H3A   single    0.970  0.020  1.090
 XYY  C5    C4    aromatic  1.391  0.020  1.391
 XYY  C4    C9    aromatic  1.391  0.020  1.391
 XYY  C6    C5    aromatic  1.388  0.020  1.388
 XYY  H5    C5    single    0.930  0.020  1.080
 XYY  C11   C6    single    1.514  0.020  1.514
 XYY  C6    C7    aromatic  1.391  0.020  1.391
 XYY  H7    C7    single    0.930  0.020  1.080
 XYY  C7    C8    aromatic  1.385  0.020  1.385
 XYY  C8    H8    single    0.930  0.020  1.080
 XYY  C8    C9    aromatic  1.387  0.020  1.387
 XYY  C12   C11   single    1.527  0.020  1.527
 XYY  C16   C11   single    1.516  0.020  1.516
 XYY  H11   C11   single    0.970  0.020  1.090
 XYY  C13   C12   single    1.505  0.020  1.505
 XYY  C12   H12   single    0.970  0.020  1.090
 XYY  C12   H12A  single    0.970  0.020  1.090
 XYY  O14   C13   double    1.205  0.020  1.205
 XYY  O15   C13   single    1.328  0.020  1.328
 XYY  O15   HO15  single    0.850  0.020  0.980
 XYY  C17   C16   aromatic  1.418  0.020  1.418
 XYY  C16   C25   aromatic  1.377  0.020  1.377
 XYY  C18   C17   aromatic  1.374  0.020  1.374
 XYY  H17   C17   single    0.930  0.020  1.080
 XYY  H18   C18   single    0.930  0.020  1.080
 XYY  C18   C19   aromatic  1.397  0.020  1.397
 XYY  N20   C19   aromatic  1.352  0.020  1.352
 XYY  C19   C24   aromatic  1.394  0.020  1.394
 XYY  C21   N20   single    1.443  0.020  1.443
 XYY  N20   N22   aromatic  1.327  0.020  1.327
 XYY  H21   C21   single    0.970  0.020  1.090
 XYY  C21   H21B  single    0.970  0.020  1.090
 XYY  C21   H21A  single    0.970  0.020  1.090
 XYY  N22   N23   aromatic  1.280  0.020  1.280
 XYY  C24   N23   aromatic  1.364  0.020  1.364
 XYY  C24   C25   aromatic  1.400  0.020  1.400
 XYY  C25   H25   single    0.930  0.020  1.080
 XYY  C29   S26   single    1.779  0.020  1.779
 XYY  S26   O27   double    1.456  0.020  1.456
 XYY  S26   O28   double    1.455  0.020  1.455
 XYY  H29   C29   single    0.970  0.020  1.090
 XYY  H29B  C29   single    0.970  0.020  1.090
 XYY  C29   H29A  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
 XYY  H1B   C1   H1A   109.39  3.000
 XYY  H1A   C1   H1    108.31  3.000
 XYY  H1B   C1   H1    107.55  3.000
 XYY  H1A   C1   N2    112.40  3.000
 XYY  H1    C1   N2    108.20  3.000
 XYY  H1B   C1   N2    110.83  3.000
 XYY  S26   N2   C3    118.50  3.000
 XYY  S26   N2   C1    118.38  3.000
 XYY  C3    N2   C1    114.89  3.000
 XYY  H3A   C3   H3    106.44  3.000
 XYY  H3A   C3   C4    111.64  3.000
 XYY  H3    C3   C4    108.47  3.000
 XYY  H3A   C3   N2    110.21  3.000
 XYY  C4    C3   N2    109.93  3.000
 XYY  H3    C3   N2    110.06  3.000
 XYY  C9    C4   C5    117.60  3.000
 XYY  C9    C4   C3    124.14  3.000
 XYY  C5    C4   C3    118.26  3.000
 XYY  H5    C5   C6    119.27  3.000
 XYY  H5    C5   C4    118.05  3.000
 XYY  C6    C5   C4    122.67  3.000
 XYY  C11   C6   C7    123.26  3.000
 XYY  C7    C6   C5    118.04  3.000
 XYY  C11   C6   C5    118.65  3.000
 XYY  H7    C7   C8    118.04  3.000
 XYY  C8    C7   C6    120.77  3.000
 XYY  H7    C7   C6    121.19  3.000
 XYY  H8    C8   C9    120.23  3.000
 XYY  C9    C8   C7    119.76  3.000
 XYY  H8    C8   C7    120.01  3.000
 XYY  C8    C9   C4    121.15  3.000
 XYY  C8    C9   CL1   117.92  3.000
 XYY  C4    C9   CL1   120.93  3.000
 XYY  H11   C11  C16   107.38  3.000
 XYY  H11   C11  C12   107.49  3.000
 XYY  C16   C11  C12   109.96  3.000
 XYY  H11   C11  C6    107.33  3.000
 XYY  C16   C11  C6    110.15  3.000
 XYY  C12   C11  C6    114.24  3.000
 XYY  H12A  C12  H12   105.19  3.000
 XYY  H12A  C12  C13   110.31  3.000
 XYY  H12   C12  C13   106.91  3.000
 XYY  H12A  C12  C11   112.24  3.000
 XYY  H12   C12  C11   108.56  3.000
 XYY  C13   C12  C11   113.15  3.000
 XYY  O15   C13  O14   123.40  3.000
 XYY  O15   C13  C12   111.89  3.000
 XYY  O14   C13  C12   124.69  3.000
 XYY  HO15  O15  C13   109.96  3.000
 XYY  C25   C16  C17   120.28  3.000
 XYY  C25   C16  C11   120.24  3.000
 XYY  C17   C16  C11   119.48  3.000
 XYY  H17   C17  C18   118.25  3.000
 XYY  H17   C17  C16   118.99  3.000
 XYY  C18   C17  C16   122.76  3.000
 XYY  H18   C18  C19   122.48  3.000
 XYY  C19   C18  C17   116.07  3.000
 XYY  H18   C18  C17   121.45  3.000
 XYY  C24   C19  N20   103.78  3.000
 XYY  C24   C19  C18   122.30  3.000
 XYY  N20   C19  C18   133.92  3.000
 XYY  N22   N20  C21   121.61  3.000
 XYY  N22   N20  C19   110.05  3.000
 XYY  C21   N20  C19   128.33  3.000
 XYY  H21B  C21  H21A  109.33  3.000
 XYY  H21A  C21  H21   109.24  3.000
 XYY  H21B  C21  H21   109.25  3.000
 XYY  H21A  C21  N20   110.31  3.000
 XYY  H21B  C21  N20   110.29  3.000
 XYY  H21   C21  N20   108.40  3.000
 XYY  N23   N22  N20   110.04  3.000
 XYY  C24   N23  N22   108.19  3.000
 XYY  C25   C24  N23   131.35  3.000
 XYY  C25   C24  C19   120.72  3.000
 XYY  N23   C24  C19   107.93  3.000
 XYY  H25   C25  C24   120.89  3.000
 XYY  H25   C25  C16   121.23  3.000
 XYY  C24   C25  C16   117.88  3.000
 XYY  C29   S26  O28   108.16  3.000
 XYY  O28   S26  O27   118.83  3.000
 XYY  C29   S26  O27   108.07  3.000
 XYY  O28   S26  N2    107.11  3.000
 XYY  O27   S26  N2    107.24  3.000
 XYY  C29   S26  N2    106.87  3.000
 XYY  H29B  C29  H29A  109.78  3.000
 XYY  H29A  C29  H29   110.16  3.000
 XYY  H29B  C29  H29   109.73  3.000
 XYY  H29A  C29  S26   109.48  3.000
 XYY  H29B  C29  S26   108.17  3.000
 XYY  H29   C29  S26   109.49  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
 XYY  CONST_01  C7    C6   C5   C4      0.00   0.0  0
 XYY  CONST_02  C7    C8   C9   C4      0.00   0.0  0
 XYY  CONST_03  C8    C9   C4   C5      0.00   0.0  0
 XYY  CONST_04  C8    C7   C6   C5      0.00   0.0  0
 XYY  CONST_05  C9    C4   C5   C6      0.00   0.0  0
 XYY  CONST_06  C9    C8   C7   C6      0.00   0.0  0
 XYY  CONST_07  C19   C18  C17  C16     0.00   0.0  0
 XYY  CONST_08  C19   C24  C25  C16     0.00   0.0  0
 XYY  CONST_09  N23   C24  C25  C16   180.00   0.0  0
 XYY  CONST_10  C24   C25  C16  C17     0.00   0.0  0
 XYY  CONST_11  N20   C19  C18  C17   180.00   0.0  0
 XYY  CONST_12  C24   C19  C18  C17     0.00   0.0  0
 XYY  CONST_13  C25   C16  C17  C18     0.00   0.0  0
 XYY  CONST_14  N22   N20  C19  C18   180.00   0.0  0
 XYY  CONST_15  N23   C24  C19  C18   180.00   0.0  0
 XYY  CONST_16  C25   C24  C19  C18     0.00   0.0  0
 XYY  CONST_17  N23   N22  N20  C19     0.00   0.0  0
 XYY  CONST_18  N22   N23  C24  C19     0.00   0.0  0
 XYY  CONST_19  N23   C24  C19  N20     0.00   0.0  0
 XYY  CONST_20  C25   C24  C19  N20   180.00   0.0  0
 XYY  CONST_21  C24   N23  N22  N20     0.00   0.0  0
 XYY  CONST_22  C24   C19  N20  N22     0.00   0.0  0
 XYY  CONST_23  C25   C24  N23  N22   180.00   0.0  0
 XYY  CONST_24  C5    C4   C9   CL1   180.00   0.0  0
 XYY  CONST_25  C7    C8   C9   CL1   180.00   0.0  0
 XYY  CONST_26  C6    C5   C4   C3    180.00   0.0  0
 XYY  CONST_27  C8    C9   C4   C3    180.00   0.0  0
 XYY  CONST_28  C11   C6   C5   C4    180.00   0.0  0
 XYY  CONST_29  C11   C6   C7   C8    180.00   0.0  0
 XYY  CONST_30  C18   C17  C16  C11   180.00   0.0  0
 XYY  CONST_31  C24   C25  C16  C11   180.00   0.0  0
 XYY  CONST_32  C21   N20  C19  C18     0.00   0.0  0
 XYY  CONST_33  C24   C19  N20  C21   180.00   0.0  0
 XYY  CONST_34  N23   N22  N20  C21   180.00   0.0  0
 XYY  CONST_35  H8    C8   C9   C4    180.00   0.0  0
 XYY  CONST_36  H7    C7   C6   C5    180.00   0.0  0
 XYY  CONST_37  H5    C5   C6   C7    180.00   0.0  0
 XYY  CONST_38  H18   C18  C17  C16   180.00   0.0  0
 XYY  CONST_39  H25   C25  C16  C17   180.00   0.0  0
 XYY  CONST_40  H17   C17  C18  C19   180.00   0.0  0
 XYY  CONST_41  HO15  O15  C13  C12   180.00   0.0  0
 XYY  Var_01    C5    C4   C3   N2     67.27  30.0  2
 XYY  Var_02    H21   C21  N20  C19  -179.60  30.0  2
 XYY  Var_03    C4    C3   N2   C1     80.73  30.0  2
 XYY  Var_04    C29   S26  N2   C1     73.49  30.0  3
 XYY  Var_05    O14   C13  C12  C11    17.58  30.0  2
 XYY  Var_06    H29   C29  S26  N2    -61.78  30.0  3
 XYY  Var_07    H1B   C1   N2   C3   -170.24  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
 XYY  chir_01  C11  C6  C12  C16  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
 XYY  plan-1  CL1   0.020
 XYY  plan-1  C3    0.020
 XYY  plan-1  C4    0.020
 XYY  plan-1  C5    0.020
 XYY  plan-1  C6    0.020
 XYY  plan-1  C7    0.020
 XYY  plan-1  C8    0.020
 XYY  plan-1  C9    0.020
 XYY  plan-1  C11   0.020
 XYY  plan-1  H5    0.020
 XYY  plan-1  H7    0.020
 XYY  plan-1  H8    0.020
 XYY  plan-2  C11   0.020
 XYY  plan-2  C16   0.020
 XYY  plan-2  C17   0.020
 XYY  plan-2  C18   0.020
 XYY  plan-2  C19   0.020
 XYY  plan-2  N20   0.020
 XYY  plan-2  C21   0.020
 XYY  plan-2  N22   0.020
 XYY  plan-2  N23   0.020
 XYY  plan-2  C24   0.020
 XYY  plan-2  C25   0.020
 XYY  plan-2  H17   0.020
 XYY  plan-2  H18   0.020
 XYY  plan-2  H25   0.020
 XYY  plan-3  C12   0.020
 XYY  plan-3  C13   0.020
 XYY  plan-3  O14   0.020
 XYY  plan-3  O15   0.020
 XYY  plan-3  HO15  0.020

