# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:51:06 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO)c1cccc(c1)c2cccc(COc3ccccc3CC(O)=O)c2
#
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
 J6T  J6T  '2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid'  ligand  51  28  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J6T
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
 J6T  C1   C  CR16  0  -0.320  -1.4558  -1.1390  -1.5924
 J6T  C2   C  CR6   0   0.111  -1.4009  -0.0514  -0.7187
 J6T  C3   C  CR16  0  -0.362  -0.2217   0.6919  -0.6631
 J6T  C11  C  CR16  0  -0.382   4.7167   2.1322  -0.6437
 J6T  C12  C  CR16  0  -0.252   5.9999   2.5312  -0.2809
 J6T  C13  C  CR16  0  -0.273   6.7088   1.8369   0.6836
 J6T  C14  C  CR16  0  -0.299   6.1233   0.7300   1.2916
 J6T  C15  C  CR6   0   0.035   4.8488   0.3112   0.9499
 J6T  C16  C  CH2   0  -0.662   4.1962  -0.8657   1.6076
 J6T  C17  C  C     0   0.559   3.9415  -2.0009   0.6464
 J6T  C20  C  CR16  0  -0.378  -3.8624   0.1258  -0.3346
 J6T  C21  C  CR6   0   0.143  -4.9692   0.4453   0.4447
 J6T  C22  C  CR16  0  -0.334  -4.7612   0.9642   1.7185
 J6T  C23  C  CR16  0  -0.221  -3.4708   1.1460   2.1971
 J6T  C24  C  CR16  0  -0.332  -2.3766   0.8162   1.4134
 J6T  C25  C  CH1   0  -0.202  -6.3663   0.1890  -0.0970
 J6T  C27  C  CH2   0  -0.127  -6.7622  -1.2352   0.2773
 J6T  C4   C  CR6   0   0.134   0.8767   0.3667  -1.4482
 J6T  C5   C  CR16  0  -0.301   0.8016  -0.7218  -2.3099
 J6T  C6   C  CR16  0  -0.228  -0.3651  -1.4689  -2.3820
 J6T  C7   C  CR6   0   0.115  -2.5588   0.3010   0.1290
 J6T  C8   C  CH2   0  -0.272   2.1447   1.1563  -1.3308
 J6T  O9   O  O2    0  -0.461   2.9128   0.5495  -0.3018
 J6T  C10  C  CR6   0   0.384   4.1432   1.0245  -0.0301
 J6T  O18  O  O     0  -0.440   4.5592  -2.1938  -0.3693
 J6T  O19  O  OH1   0  -0.594   2.9778  -2.8065   1.0784
 J6T  N26  N  NH2   0  -0.780  -7.3927   1.1209   0.3244
 J6T  O28  O  OH1   0  -0.665  -7.9820  -1.5675  -0.3390
 J6T  H1   H  HCR6  0   0.255  -2.3520  -1.7447  -1.6449
 J6T  H2   H  HCR6  0   0.253  -0.1606   1.5536  -0.0082
 J6T  H3   H  HCR6  0   0.281   4.1852   2.6949  -1.3995
 J6T  H4   H  HCR6  0   0.258   6.4382   3.3949  -0.7641
 J6T  H5   H  HCR6  0   0.252   7.7066   2.1465   0.9636
 J6T  H6   H  HCR6  0   0.253   6.6718   0.1801   2.0470
 J6T  H7   H  HCH2  0   0.306   4.8440  -1.2556   2.3993
 J6T  H8   H  HCH2  0   0.287   3.2607  -0.5830   2.0949
 J6T  H9   H  HCR6  0   0.248  -4.0254  -0.2500  -1.3396
 J6T  H10  H  HCR6  0   0.240  -5.6019   1.2353   2.3457
 J6T  H11  H  HCR6  0   0.256  -3.3158   1.5432   3.1921
 J6T  H12  H  HCR6  0   0.254  -1.3784   0.9476   1.8115
 J6T  H13  H  HCH1  0   0.243  -6.3049   0.2382  -1.1903
 J6T  H14  H  HCH2  0   0.206  -5.9551  -1.9104  -0.0326
 J6T  H15  H  HCH2  0   0.190  -6.8277  -1.3035   1.3742
 J6T  H16  H  HCR6  0   0.253   1.6515  -0.9836  -2.9286
 J6T  H17  H  HCR6  0   0.260  -0.4232  -2.3180  -3.0504
 J6T  H18  H  HCH2  0   0.243   2.6961   1.1439  -2.2765
 J6T  H19  H  HCH2  0   0.241   1.9309   2.2008  -1.0804
 J6T  H20  H  HOH1  0   0.478   2.8703  -3.5487   0.4653
 J6T  H21  H  HNH2  0   0.344  -7.5495   1.0574   1.3231
 J6T  H22  H  HNH2  0   0.349  -7.0985   2.0711   0.1379
 J6T  H24  H  HOH1  0   0.453  -8.1635  -2.4930  -0.1529

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
 J6T  O28  C27  single    1.406  0.020  1.406
 J6T  C27  C25  single    1.525  0.020  1.525
 J6T  N26  C25  single    1.449  0.020  1.449
 J6T  C25  C21  single    1.520  0.020  1.520
 J6T  C21  C20  aromatic  1.391  0.020  1.391
 J6T  C21  C22  aromatic  1.391  0.020  1.391
 J6T  C20  C7   aromatic  1.395  0.020  1.395
 J6T  C22  C23  aromatic  1.388  0.020  1.388
 J6T  C7   C2   single    1.478  0.020  1.478
 J6T  C7   C24  aromatic  1.396  0.020  1.396
 J6T  C23  C24  aromatic  1.386  0.020  1.386
 J6T  C1   C2   aromatic  1.396  0.020  1.396
 J6T  C1   C6   aromatic  1.386  0.020  1.386
 J6T  C2   C3   aromatic  1.395  0.020  1.395
 J6T  C6   C5   aromatic  1.387  0.020  1.387
 J6T  C3   C4   aromatic  1.389  0.020  1.389
 J6T  C5   C4   aromatic  1.390  0.020  1.390
 J6T  C4   C8   single    1.498  0.020  1.498
 J6T  O18  C17  double    1.204  0.020  1.204
 J6T  C8   O9   single    1.420  0.020  1.420
 J6T  O19  C17  single    1.328  0.020  1.328
 J6T  O9   C10  single    1.347  0.020  1.347
 J6T  C17  C16  single    1.509  0.020  1.509
 J6T  C10  C11  aromatic  1.390  0.020  1.390
 J6T  C10  C15  aromatic  1.402  0.020  1.402
 J6T  C11  C12  aromatic  1.392  0.020  1.392
 J6T  C15  C16  single    1.498  0.020  1.498
 J6T  C15  C14  aromatic  1.384  0.020  1.384
 J6T  C12  C13  aromatic  1.384  0.020  1.384
 J6T  C14  C13  aromatic  1.392  0.020  1.392
 J6T  C1   H1   single    0.930  0.020  1.080
 J6T  C3   H2   single    0.930  0.020  1.080
 J6T  C11  H3   single    0.930  0.020  1.080
 J6T  C12  H4   single    0.930  0.020  1.080
 J6T  C13  H5   single    0.930  0.020  1.080
 J6T  C14  H6   single    0.930  0.020  1.080
 J6T  C16  H7   single    0.970  0.020  1.090
 J6T  C16  H8   single    0.970  0.020  1.090
 J6T  C20  H9   single    0.930  0.020  1.080
 J6T  C22  H10  single    0.930  0.020  1.080
 J6T  C23  H11  single    0.930  0.020  1.080
 J6T  C24  H12  single    0.930  0.020  1.080
 J6T  C25  H13  single    0.970  0.020  1.090
 J6T  C27  H14  single    0.970  0.020  1.090
 J6T  C27  H15  single    0.970  0.020  1.090
 J6T  C5   H16  single    0.930  0.020  1.080
 J6T  C6   H17  single    0.930  0.020  1.080
 J6T  C8   H18  single    0.970  0.020  1.090
 J6T  C8   H19  single    0.970  0.020  1.090
 J6T  O19  H20  single    0.850  0.020  0.980
 J6T  N26  H21  single    0.890  0.020  1.040
 J6T  N26  H22  single    0.890  0.020  1.040
 J6T  O28  H24  single    0.850  0.020  0.980

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
 J6T  H1   C1   C6   119.37  3.000
 J6T  H1   C1   C2   119.91  3.000
 J6T  C6   C1   C2   120.72  3.000
 J6T  C7   C2   C3   120.83  3.000
 J6T  C3   C2   C1   118.25  3.000
 J6T  C7   C2   C1   120.93  3.000
 J6T  H2   C3   C4   118.88  3.000
 J6T  H2   C3   C2   119.69  3.000
 J6T  C4   C3   C2   121.42  3.000
 J6T  H3   C11  C10  121.34  3.000
 J6T  H3   C11  C12  119.07  3.000
 J6T  C10  C11  C12  119.59  3.000
 J6T  H4   C12  C13  120.27  3.000
 J6T  H4   C12  C11  119.07  3.000
 J6T  C13  C12  C11  120.67  3.000
 J6T  H5   C13  C14  120.17  3.000
 J6T  H5   C13  C12  120.62  3.000
 J6T  C14  C13  C12  119.21  3.000
 J6T  H6   C14  C15  118.99  3.000
 J6T  H6   C14  C13  119.68  3.000
 J6T  C15  C14  C13  121.33  3.000
 J6T  C10  C15  C16  119.16  3.000
 J6T  C16  C15  C14  122.03  3.000
 J6T  C10  C15  C14  118.80  3.000
 J6T  H8   C16  H7   106.04  3.000
 J6T  H8   C16  C17  109.54  3.000
 J6T  H7   C16  C17  107.01  3.000
 J6T  H8   C16  C15  111.46  3.000
 J6T  H7   C16  C15  109.85  3.000
 J6T  C17  C16  C15  112.64  3.000
 J6T  O19  C17  O18  123.32  3.000
 J6T  O19  C17  C16  111.81  3.000
 J6T  O18  C17  C16  124.83  3.000
 J6T  H9   C20  C7   119.46  3.000
 J6T  H9   C20  C21  118.61  3.000
 J6T  C7   C20  C21  121.92  3.000
 J6T  C25  C21  C22  121.78  3.000
 J6T  C22  C21  C20  118.67  3.000
 J6T  C25  C21  C20  119.54  3.000
 J6T  H10  C22  C23  119.27  3.000
 J6T  H10  C22  C21  120.50  3.000
 J6T  C23  C22  C21  120.24  3.000
 J6T  H11  C23  C24  119.61  3.000
 J6T  H11  C23  C22  119.88  3.000
 J6T  C24  C23  C22  120.51  3.000
 J6T  H12  C24  C7   120.23  3.000
 J6T  H12  C24  C23  119.42  3.000
 J6T  C7   C24  C23  120.35  3.000
 J6T  H13  C25  N26  107.52  3.000
 J6T  H13  C25  C27  107.54  3.000
 J6T  N26  C25  C27  110.20  3.000
 J6T  H13  C25  C21  107.24  3.000
 J6T  N26  C25  C21  116.04  3.000
 J6T  C27  C25  C21  107.97  3.000
 J6T  H15  C27  H14  106.68  3.000
 J6T  H15  C27  O28  111.74  3.000
 J6T  H14  C27  O28  111.65  3.000
 J6T  H15  C27  C25  108.54  3.000
 J6T  H14  C27  C25  108.33  3.000
 J6T  O28  C27  C25  109.77  3.000
 J6T  C8   C4   C5   120.46  3.000
 J6T  C8   C4   C3   120.11  3.000
 J6T  C5   C4   C3   119.40  3.000
 J6T  H16  C5   C6   119.99  3.000
 J6T  H16  C5   C4   120.05  3.000
 J6T  C6   C5   C4   119.96  3.000
 J6T  H17  C6   C5   119.99  3.000
 J6T  H17  C6   C1   119.75  3.000
 J6T  C5   C6   C1   120.26  3.000
 J6T  C24  C7   C20  118.31  3.000
 J6T  C24  C7   C2   120.91  3.000
 J6T  C20  C7   C2   120.78  3.000
 J6T  H19  C8   H18  107.85  3.000
 J6T  H19  C8   O9   110.33  3.000
 J6T  H18  C8   O9   110.40  3.000
 J6T  H19  C8   C4   110.82  3.000
 J6T  H18  C8   C4   110.64  3.000
 J6T  O9   C8   C4   106.82  3.000
 J6T  C10  O9   C8   119.32  3.000
 J6T  O9   C10  C15  114.91  3.000
 J6T  C15  C10  C11  120.41  3.000
 J6T  O9   C10  C11  124.68  3.000
 J6T  H20  O19  C17  109.84  3.000
 J6T  H22  N26  H21  106.59  3.000
 J6T  H22  N26  C25  110.14  3.000
 J6T  H21  N26  C25  110.86  3.000
 J6T  H24  O28  C27  107.85  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
 J6T  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 J6T  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 J6T  CONST_05  C21  C20  C7   C2    180.00   0.0  0
 J6T  CONST_06  C23  C24  C7   C2    180.00   0.0  0
 J6T  CONST_07  C5   C6   C1   C2      0.00   0.0  0
 J6T  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 J6T  CONST_11  C6   C1   C2   C3      0.00   0.0  0
 J6T  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 J6T  CONST_13  C14  C15  C10  C11     0.00   0.0  0
 J6T  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 J6T  CONST_15  C15  C10  C11  C12     0.00   0.0  0
 J6T  CONST_16  C15  C14  C13  C12     0.00   0.0  0
 J6T  CONST_17  C10  C11  C12  C13     0.00   0.0  0
 J6T  CONST_18  C10  C15  C14  C13     0.00   0.0  0
 J6T  CONST_19  C23  C22  C21  C20     0.00   0.0  0
 J6T  CONST_20  C23  C24  C7   C20     0.00   0.0  0
 J6T  CONST_21  C24  C7   C20  C21     0.00   0.0  0
 J6T  CONST_22  C24  C23  C22  C21     0.00   0.0  0
 J6T  CONST_23  C7   C20  C21  C22     0.00   0.0  0
 J6T  CONST_24  C7   C24  C23  C22     0.00   0.0  0
 J6T  CONST_25  C7   C2   C3   C4    180.00   0.0  0
 J6T  CONST_26  C7   C2   C1   C6    180.00   0.0  0
 J6T  CONST_27  C8   C4   C3   C2    180.00   0.0  0
 J6T  CONST_28  C16  C15  C10  C11   180.00   0.0  0
 J6T  CONST_29  O9   C10  C11  C12   180.00   0.0  0
 J6T  CONST_30  C16  C15  C14  C13   180.00   0.0  0
 J6T  CONST_31  O9   C10  C15  C14   180.00   0.0  0
 J6T  CONST_32  C25  C21  C22  C23   180.00   0.0  0
 J6T  CONST_33  C7   C20  C21  C25   180.00   0.0  0
 J6T  CONST_34  C8   C4   C5   C6    180.00   0.0  0
 J6T  CONST_35  H2   C3   C2   C1    180.00   0.0  0
 J6T  CONST_36  H16  C5   C6   C1    180.00   0.0  0
 J6T  CONST_37  H9   C20  C7   C2      0.00   0.0  0
 J6T  CONST_38  H12  C24  C7   C2      0.00   0.0  0
 J6T  CONST_39  H17  C6   C1   C2    180.00   0.0  0
 J6T  CONST_40  H1   C1   C2   C3    180.00   0.0  0
 J6T  CONST_41  H5   C13  C12  C11   180.00   0.0  0
 J6T  CONST_42  H6   C14  C13  C12   180.00   0.0  0
 J6T  CONST_43  H3   C11  C12  C13   180.00   0.0  0
 J6T  CONST_44  H4   C12  C13  C14   180.00   0.0  0
 J6T  CONST_45  H10  C22  C21  C20   180.00   0.0  0
 J6T  CONST_46  H11  C23  C22  C21   180.00   0.0  0
 J6T  CONST_47  H20  O19  C17  C16   180.00   0.0  0
 J6T  Var_01    O9   C8   C4   C3     88.14  30.0  2
 J6T  Var_02    C17  C16  C15  C14  -115.43  30.0  2
 J6T  Var_03    O18  C17  C16  C15    24.80  30.0  1

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
 J6T  chir_01  C25  C27  N26  C21  negativ

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
 J6T  plan-1  C1   0.020
 J6T  plan-1  C2   0.020
 J6T  plan-1  C3   0.020
 J6T  plan-1  C4   0.020
 J6T  plan-1  C5   0.020
 J6T  plan-1  C6   0.020
 J6T  plan-1  C7   0.020
 J6T  plan-1  C8   0.020
 J6T  plan-1  H1   0.020
 J6T  plan-1  H2   0.020
 J6T  plan-1  H16  0.020
 J6T  plan-1  H17  0.020
 J6T  plan-2  C2   0.020
 J6T  plan-2  C20  0.020
 J6T  plan-2  C21  0.020
 J6T  plan-2  C22  0.020
 J6T  plan-2  C23  0.020
 J6T  plan-2  C24  0.020
 J6T  plan-2  C25  0.020
 J6T  plan-2  C7   0.020
 J6T  plan-2  H9   0.020
 J6T  plan-2  H10  0.020
 J6T  plan-2  H11  0.020
 J6T  plan-2  H12  0.020
 J6T  plan-3  C11  0.020
 J6T  plan-3  C12  0.020
 J6T  plan-3  C13  0.020
 J6T  plan-3  C14  0.020
 J6T  plan-3  C15  0.020
 J6T  plan-3  C16  0.020
 J6T  plan-3  O9   0.020
 J6T  plan-3  C10  0.020
 J6T  plan-3  H3   0.020
 J6T  plan-3  H4   0.020
 J6T  plan-3  H5   0.020
 J6T  plan-3  H6   0.020
 J6T  plan-4  C16  0.020
 J6T  plan-4  C17  0.020
 J6T  plan-4  O18  0.020
 J6T  plan-4  O19  0.020
 J6T  plan-4  H20  0.020

