# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 09:58:28 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: N-({2,6-dimethoxy-4-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]phenyl}methyl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OCc2cccc(c2C)c3ccccc3)cc(OC)c1CN[C@H](C)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
 KSD  KSD  N-({2,6-dimethoxy-4-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]phenyl}methyl)-D-alanine  ligand  61  32  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KSD
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
 KSD  C4   C  CR16  0  -0.242   -4.3797  -2.7134  -0.4635
 KSD  C14  C  CH2   0  -0.218   -1.7240  -0.0869   0.2171
 KSD  C5   C  CR16  0  -0.318   -3.1438  -2.1199  -0.2526
 KSD  C6   C  CR6   0   0.033   -3.0522  -0.7515  -0.0317
 KSD  C11  C  CR16  0  -0.242   -8.0900   1.9521  -1.2726
 KSD  C7   C  CR6   0   0.031   -6.7145   0.2156  -0.3016
 KSD  C8   C  CR16  0  -0.298   -7.7739  -0.1196   0.5410
 KSD  C9   C  CR16  0  -0.241   -8.9749   0.5745   0.4822
 KSD  C10  C  CR16  0  -0.266   -9.1369   1.6129  -0.4249
 KSD  C12  C  CR16  0  -0.286   -6.8897   1.2591  -1.2109
 KSD  C13  C  CH3   0  -0.774   -4.0911   1.5165   0.2633
 KSD  N1   N  NH1   0  -0.602    5.4515   0.4386  -0.1982
 KSD  C3   C  CR16  0  -0.300   -5.5236  -1.9378  -0.4676
 KSD  C1   C  CR6   0   0.036   -4.2091   0.0440  -0.0210
 KSD  C15  C  CR6   0   0.456    0.5817  -0.6600   0.3151
 KSD  C16  C  CR16  0  -0.525    1.5286  -1.6750   0.2075
 KSD  C17  C  CR6   0   0.391    2.8643  -1.3765   0.4435
 KSD  C18  C  CR6   0  -0.152    3.2820  -0.0861   0.7989
 KSD  C19  C  CR6   0   0.425    2.3065   0.9091   0.8738
 KSD  C2   C  CR6   0   0.055   -5.4516  -0.5599  -0.2581
 KSD  C20  C  CR16  0  -0.569    0.9549   0.6366   0.6422
 KSD  C21  C  CH3   0  -0.439    1.8125   3.1985   1.3102
 KSD  C22  C  CH3   0  -0.437    3.5098  -3.6205  -0.0159
 KSD  C23  C  CH2   0  -0.325    4.7348   0.2055   1.0502
 KSD  C24  C  CH1   0  -0.184    6.8608   0.7024   0.0101
 KSD  C25  C  C     0   0.538    7.6454   0.2946  -1.2202
 KSD  C26  C  CH3   0  -0.653    7.0969   2.1790   0.3348
 KSD  O1   O  O2    0  -0.485   -0.6909  -1.0327   0.0763
 KSD  O2   O  O2    0  -0.469    2.7424   2.1413   1.1911
 KSD  O3   O  O2    0  -0.471    3.8432  -2.2959   0.3482
 KSD  O4   O  O     0  -0.440    7.1687  -0.2087  -2.2070
 KSD  O5   O  OH1   0  -0.591    8.9410   0.5398  -1.0828
 KSD  H1   H  HCR6  0   0.254   -4.4455  -3.7804  -0.6315
 KSD  H2   H  HCH2  0   0.246   -1.5822   0.7427  -0.4867
 KSD  H3   H  HCH2  0   0.244   -1.7071   0.3452   1.2263
 KSD  H4   H  HCR6  0   0.252   -2.2562  -2.7360  -0.2606
 KSD  H5   H  HCR6  0   0.257   -8.2072   2.7563  -1.9875
 KSD  H6   H  HCR6  0   0.253   -7.6550  -0.9250   1.2555
 KSD  H7   H  HCR6  0   0.256   -9.7840   0.3037   1.1484
 KSD  H8   H  HCR6  0   0.256  -10.0731   2.1541  -0.4726
 KSD  H9   H  HCR6  0   0.253   -6.0843   1.5233  -1.8854
 KSD  H10  H  HCH3  0   0.255   -3.7359   2.0694  -0.6096
 KSD  H11  H  HCH3  0   0.263   -5.0425   1.9532   0.5560
 KSD  H12  H  HCH3  0   0.251   -3.3875   1.7143   1.0726
 KSD  H13  H  HNH1  0   0.349    5.3465  -0.3777  -0.7870
 KSD  H15  H  HCR6  0   0.250   -6.4864  -2.3975  -0.6537
 KSD  H16  H  HCR6  0   0.281    1.1986  -2.6695  -0.0586
 KSD  H17  H  HCR6  0   0.301    0.2196   1.4239   0.7080
 KSD  H18  H  HCH3  0   0.262    2.3846   4.0791   1.5914
 KSD  H19  H  HCH3  0   0.230    1.2998   3.4014   0.3664
 KSD  H20  H  HCH3  0   0.229    1.0653   3.0037   2.0838
 KSD  H21  H  HCH3  0   0.230    2.8350  -4.0853   0.7072
 KSD  H22  H  HCH3  0   0.230    3.0522  -3.6669  -1.0071
 KSD  H23  H  HCH3  0   0.262    4.4426  -4.1783  -0.0339
 KSD  H24  H  HCH2  0   0.212    5.1824  -0.6142   1.6306
 KSD  H25  H  HCH2  0   0.241    4.8232   1.0927   1.6758
 KSD  H26  H  HCH1  0   0.248    7.2729   0.1015   0.8399
 KSD  H27  H  HCH3  0   0.243    6.4913   2.4750   1.1904
 KSD  H28  H  HCH3  0   0.237    8.1364   2.3774   0.5883
 KSD  H29  H  HCH3  0   0.232    6.8131   2.8101  -0.5075
 KSD  H30  H  HOH1  0   0.484    9.4187   0.2550  -1.8762

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
 KSD  C21  O2   single    1.413  0.020  1.413
 KSD  O2   C19  single    1.345  0.020  1.345
 KSD  C19  C20  aromatic  1.398  0.020  1.398
 KSD  C19  C18  aromatic  1.396  0.020  1.396
 KSD  N1   C23  single    1.458  0.020  1.458
 KSD  N1   C24  single    1.449  0.020  1.449
 KSD  C20  C15  aromatic  1.388  0.020  1.388
 KSD  C13  C1   single    1.504  0.020  1.504
 KSD  C26  C24  single    1.530  0.020  1.530
 KSD  C23  C18  single    1.503  0.020  1.503
 KSD  C18  C17  aromatic  1.402  0.020  1.402
 KSD  C24  C25  single    1.515  0.020  1.515
 KSD  C14  O1   single    1.408  0.020  1.408
 KSD  C14  C6   single    1.506  0.020  1.506
 KSD  C10  C9   aromatic  1.388  0.020  1.388
 KSD  C10  C11  aromatic  1.389  0.020  1.389
 KSD  C9   C8   aromatic  1.388  0.020  1.388
 KSD  C11  C12  aromatic  1.387  0.020  1.387
 KSD  C15  O1   single    1.347  0.020  1.347
 KSD  C15  C16  aromatic  1.392  0.020  1.392
 KSD  C1   C6   aromatic  1.404  0.020  1.404
 KSD  C1   C2   aromatic  1.402  0.020  1.402
 KSD  C8   C7   aromatic  1.394  0.020  1.394
 KSD  C12  C7   aromatic  1.395  0.020  1.395
 KSD  C7   C2   single    1.483  0.020  1.483
 KSD  C6   C5   aromatic  1.389  0.020  1.389
 KSD  C17  C16  aromatic  1.389  0.020  1.389
 KSD  C17  O3   single    1.346  0.020  1.346
 KSD  C25  O4   double    1.206  0.020  1.206
 KSD  C25  O5   single    1.326  0.020  1.326
 KSD  C2   C3   aromatic  1.396  0.020  1.396
 KSD  O3   C22  single    1.414  0.020  1.414
 KSD  C5   C4   aromatic  1.387  0.020  1.387
 KSD  C3   C4   aromatic  1.382  0.020  1.382
 KSD  C4   H1   single    0.930  0.020  1.080
 KSD  C14  H2   single    0.970  0.020  1.090
 KSD  C14  H3   single    0.970  0.020  1.090
 KSD  C5   H4   single    0.930  0.020  1.080
 KSD  C11  H5   single    0.930  0.020  1.080
 KSD  C8   H6   single    0.930  0.020  1.080
 KSD  C9   H7   single    0.930  0.020  1.080
 KSD  C10  H8   single    0.930  0.020  1.080
 KSD  C12  H9   single    0.930  0.020  1.080
 KSD  C13  H10  single    0.970  0.020  1.090
 KSD  C13  H11  single    0.970  0.020  1.090
 KSD  C13  H12  single    0.970  0.020  1.090
 KSD  N1   H13  single    0.890  0.020  1.040
 KSD  C3   H15  single    0.930  0.020  1.080
 KSD  C16  H16  single    0.930  0.020  1.080
 KSD  C20  H17  single    0.930  0.020  1.080
 KSD  C21  H18  single    0.970  0.020  1.090
 KSD  C21  H19  single    0.970  0.020  1.090
 KSD  C21  H20  single    0.970  0.020  1.090
 KSD  C22  H21  single    0.970  0.020  1.090
 KSD  C22  H22  single    0.970  0.020  1.090
 KSD  C22  H23  single    0.970  0.020  1.090
 KSD  C23  H24  single    0.970  0.020  1.090
 KSD  C23  H25  single    0.970  0.020  1.090
 KSD  C24  H26  single    0.970  0.020  1.090
 KSD  C26  H27  single    0.970  0.020  1.090
 KSD  C26  H28  single    0.970  0.020  1.090
 KSD  C26  H29  single    0.970  0.020  1.090
 KSD  O5   H30  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
 KSD  H1   C4   C3   120.18  3.000
 KSD  H1   C4   C5   119.97  3.000
 KSD  C3   C4   C5   119.85  3.000
 KSD  H3   C14  H2   106.86  3.000
 KSD  H3   C14  O1   110.19  3.000
 KSD  H2   C14  O1   110.43  3.000
 KSD  H3   C14  C6   109.82  3.000
 KSD  H2   C14  C6   109.98  3.000
 KSD  O1   C14  C6   109.53  3.000
 KSD  H4   C5   C6   120.58  3.000
 KSD  H4   C5   C4   119.13  3.000
 KSD  C6   C5   C4   120.29  3.000
 KSD  C1   C6   C5   120.33  3.000
 KSD  C5   C6   C14  121.27  3.000
 KSD  C1   C6   C14  118.39  3.000
 KSD  H5   C11  C12  119.62  3.000
 KSD  H5   C11  C10  120.18  3.000
 KSD  C12  C11  C10  120.19  3.000
 KSD  C2   C7   C12  121.15  3.000
 KSD  C2   C7   C8   120.24  3.000
 KSD  C12  C7   C8   118.57  3.000
 KSD  H6   C8   C9   119.64  3.000
 KSD  H6   C8   C7   119.60  3.000
 KSD  C9   C8   C7   120.76  3.000
 KSD  H7   C9   C10  120.13  3.000
 KSD  H7   C9   C8   119.70  3.000
 KSD  C10  C9   C8   120.17  3.000
 KSD  H8   C10  C9   120.24  3.000
 KSD  H8   C10  C11  120.19  3.000
 KSD  C9   C10  C11  119.57  3.000
 KSD  H9   C12  C7   119.67  3.000
 KSD  H9   C12  C11  119.58  3.000
 KSD  C7   C12  C11  120.75  3.000
 KSD  H12  C13  H11  106.98  3.000
 KSD  H12  C13  H10  106.94  3.000
 KSD  H11  C13  H10  107.24  3.000
 KSD  H12  C13  C1   111.62  3.000
 KSD  H11  C13  C1   112.05  3.000
 KSD  H10  C13  C1   111.70  3.000
 KSD  H13  N1   C24  109.35  3.000
 KSD  H13  N1   C23  108.55  3.000
 KSD  C24  N1   C23  112.58  3.000
 KSD  H15  C3   C2   119.39  3.000
 KSD  H15  C3   C4   119.87  3.000
 KSD  C2   C3   C4   120.73  3.000
 KSD  C2   C1   C13  121.55  3.000
 KSD  C2   C1   C6   119.01  3.000
 KSD  C13  C1   C6   119.43  3.000
 KSD  O1   C15  C20  123.64  3.000
 KSD  O1   C15  C16  115.28  3.000
 KSD  C20  C15  C16  121.08  3.000
 KSD  H16  C16  C17  122.21  3.000
 KSD  H16  C16  C15  118.82  3.000
 KSD  C17  C16  C15  118.97  3.000
 KSD  O3   C17  C18  115.46  3.000
 KSD  O3   C17  C16  122.72  3.000
 KSD  C18  C17  C16  121.83  3.000
 KSD  C23  C18  C19  121.90  3.000
 KSD  C23  C18  C17  120.59  3.000
 KSD  C19  C18  C17  117.49  3.000
 KSD  O2   C19  C20  122.07  3.000
 KSD  C20  C19  C18  121.86  3.000
 KSD  O2   C19  C18  116.07  3.000
 KSD  C1   C2   C3   119.77  3.000
 KSD  C3   C2   C7   117.91  3.000
 KSD  C1   C2   C7   122.32  3.000
 KSD  H17  C20  C19  120.42  3.000
 KSD  H17  C20  C15  120.83  3.000
 KSD  C19  C20  C15  118.75  3.000
 KSD  H20  C21  H19  108.88  3.000
 KSD  H20  C21  H18  108.72  3.000
 KSD  H19  C21  H18  108.65  3.000
 KSD  H20  C21  O2   112.10  3.000
 KSD  H19  C21  O2   112.01  3.000
 KSD  H18  C21  O2   106.35  3.000
 KSD  H23  C22  H22  108.81  3.000
 KSD  H23  C22  H21  108.82  3.000
 KSD  H22  C22  H21  108.88  3.000
 KSD  H23  C22  O3   106.42  3.000
 KSD  H22  C22  O3   111.85  3.000
 KSD  H21  C22  O3   111.95  3.000
 KSD  H25  C23  H24  105.72  3.000
 KSD  H25  C23  C18  109.42  3.000
 KSD  H24  C23  C18  109.70  3.000
 KSD  H25  C23  N1   108.76  3.000
 KSD  H24  C23  N1   111.78  3.000
 KSD  C18  C23  N1   111.28  3.000
 KSD  H26  C24  C26  107.94  3.000
 KSD  H26  C24  C25  105.69  3.000
 KSD  C26  C24  C25  110.62  3.000
 KSD  H26  C24  N1   111.84  3.000
 KSD  C25  C24  N1   109.76  3.000
 KSD  C26  C24  N1   110.87  3.000
 KSD  O5   C25  O4   123.25  3.000
 KSD  O5   C25  C24  111.85  3.000
 KSD  O4   C25  C24  124.89  3.000
 KSD  H29  C26  H28  108.85  3.000
 KSD  H29  C26  H27  107.74  3.000
 KSD  H28  C26  H27  107.37  3.000
 KSD  H29  C26  C24  110.76  3.000
 KSD  H28  C26  C24  111.89  3.000
 KSD  H27  C26  C24  110.07  3.000
 KSD  C15  O1   C14  119.31  3.000
 KSD  C21  O2   C19  119.47  3.000
 KSD  C22  O3   C17  119.12  3.000
 KSD  H30  O5   C25  110.04  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
 KSD  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 KSD  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 KSD  CONST_03  C7   C2   C3   C4    180.00   0.0  0
 KSD  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 KSD  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 KSD  CONST_06  C7   C2   C1   C6    180.00   0.0  0
 KSD  CONST_07  C3   C2   C1   C6      0.00   0.0  0
 KSD  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 KSD  CONST_09  C8   C9   C10  C11     0.00   0.0  0
 KSD  CONST_10  C8   C7   C12  C11     0.00   0.0  0
 KSD  CONST_11  C2   C7   C12  C11   180.00   0.0  0
 KSD  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 KSD  CONST_13  C10  C11  C12  C7      0.00   0.0  0
 KSD  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 KSD  CONST_17  C12  C7   C8   C9      0.00   0.0  0
 KSD  CONST_18  C2   C7   C8   C9    180.00   0.0  0
 KSD  CONST_21  C18  C19  C20  C15     0.00   0.0  0
 KSD  CONST_22  C18  C17  C16  C15     0.00   0.0  0
 KSD  CONST_23  C19  C20  C15  C16     0.00   0.0  0
 KSD  CONST_24  C19  C18  C17  C16     0.00   0.0  0
 KSD  CONST_25  C20  C19  C18  C17     0.00   0.0  0
 KSD  CONST_26  C20  C15  C16  C17     0.00   0.0  0
 KSD  CONST_27  C14  C6   C5   C4    180.00   0.0  0
 KSD  CONST_28  C2   C1   C6   C14   180.00   0.0  0
 KSD  CONST_29  C13  C1   C6   C5    180.00   0.0  0
 KSD  CONST_30  C13  C1   C2   C7      0.00   0.0  0
 KSD  CONST_31  C3   C2   C1   C13   180.00   0.0  0
 KSD  CONST_32  O2   C19  C20  C15   180.00   0.0  0
 KSD  CONST_33  O3   C17  C16  C15   180.00   0.0  0
 KSD  CONST_34  C23  C18  C17  C16   180.00   0.0  0
 KSD  CONST_35  O2   C19  C18  C17   180.00   0.0  0
 KSD  CONST_36  O1   C15  C16  C17   180.00   0.0  0
 KSD  CONST_37  O1   C15  C20  C19   180.00   0.0  0
 KSD  CONST_38  O3   C17  C18  C19   180.00   0.0  0
 KSD  CONST_39  C23  C18  C19  C20   180.00   0.0  0
 KSD  CONST_40  H15  C3   C4   C5    180.00   0.0  0
 KSD  CONST_41  H1   C4   C5   C6    180.00   0.0  0
 KSD  CONST_42  H7   C9   C10  C11   180.00   0.0  0
 KSD  CONST_43  H5   C11  C12  C7    180.00   0.0  0
 KSD  CONST_44  H8   C10  C9   C8    180.00   0.0  0
 KSD  CONST_45  H9   C12  C7   C8    180.00   0.0  0
 KSD  CONST_46  H6   C8   C9   C10   180.00   0.0  0
 KSD  CONST_47  H4   C5   C4   C3    180.00   0.0  0
 KSD  CONST_48  H17  C20  C15  C16   180.00   0.0  0
 KSD  CONST_49  H16  C16  C17  C18   180.00   0.0  0
 KSD  CONST_50  H30  O5   C25  C24   180.00   0.0  0
 KSD  Var_01    C20  C15  O1   C14    -2.92  30.0  2
 KSD  Var_02    O1   C14  C6   C5      4.63  30.0  1
 KSD  Var_03    C19  C18  C23  N1    -96.07  30.0  2
 KSD  Var_04    H10  C13  C1   C6     77.94  30.0  2
 KSD  Var_05    C24  N1   C23  C18  -179.11  30.0  1
 KSD  Var_06    H21  C22  O3   C17   -61.45  30.0  3
 KSD  Var_07    H18  C21  O2   C19   178.73  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
 KSD  chir_01  C24  N1  C26  C25  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
 KSD  plan-1  C11  0.020
 KSD  plan-1  C7   0.020
 KSD  plan-1  C8   0.020
 KSD  plan-1  C9   0.020
 KSD  plan-1  C10  0.020
 KSD  plan-1  C12  0.020
 KSD  plan-1  C2   0.020
 KSD  plan-1  H5   0.020
 KSD  plan-1  H6   0.020
 KSD  plan-1  H7   0.020
 KSD  plan-1  H8   0.020
 KSD  plan-1  H9   0.020
 KSD  plan-2  C4   0.020
 KSD  plan-2  C14  0.020
 KSD  plan-2  C5   0.020
 KSD  plan-2  C6   0.020
 KSD  plan-2  C7   0.020
 KSD  plan-2  C13  0.020
 KSD  plan-2  C3   0.020
 KSD  plan-2  C1   0.020
 KSD  plan-2  C2   0.020
 KSD  plan-2  H1   0.020
 KSD  plan-2  H4   0.020
 KSD  plan-2  H15  0.020
 KSD  plan-3  C15  0.020
 KSD  plan-3  C16  0.020
 KSD  plan-3  C17  0.020
 KSD  plan-3  C18  0.020
 KSD  plan-3  C19  0.020
 KSD  plan-3  C20  0.020
 KSD  plan-3  C23  0.020
 KSD  plan-3  O1   0.020
 KSD  plan-3  O2   0.020
 KSD  plan-3  O3   0.020
 KSD  plan-3  H16  0.020
 KSD  plan-3  H17  0.020
 KSD  plan-4  C24  0.020
 KSD  plan-4  C25  0.020
 KSD  plan-4  O4   0.020
 KSD  plan-4  O5   0.020
 KSD  plan-4  H30  0.020

