# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 21:13:37 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 4-{[(2-chloro-3-fluorobenzyl)carbamoyl](methyl)amino}-3,4-dideoxy-5-O-(isoquinolin-3-ylcarbamoyl)-D-erythro-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN([C@H](COC(=O)Nc1cc2ccccc2cn1)C[C@@H](O)CO)C(=O)NCc3cccc(F)c3Cl
#
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
 52E  52E  4-{[(2-chloro-3-fluorobenzyl)carbamoyl](methyl)amino}-3,4-dideoxy-5-O-(isoquinolin-3-ylcarbamoyl)-D-erythro-pentitol  ligand  61  35  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_52E
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
 52E  N1   N   NH1   0  -0.687  -3.0447   0.6985   1.4169
 52E  C6   C   CR6   0  -0.292  -5.6072   1.2375  -0.1773
 52E  N3   N   NH1   0  -0.752   3.7111  -0.1396   0.1579
 52E  C5   C   CR6   0   0.625  -6.4078   2.0038  -1.0082
 52E  C15  C   CH2   0  -0.469  -0.3362  -2.6485  -0.2843
 52E  C16  C   CH1   0   0.006  -1.6488  -3.2463  -0.7866
 52E  C17  C   CH2   0  -0.155  -1.3623  -4.2248  -1.9163
 52E  O30  O   OH1   0  -0.671  -2.5662  -4.8274  -2.3268
 52E  O31  O   OH1   0  -0.644  -2.6016  -2.2789  -1.1646
 52E  N2   N   NT    0  -0.485  -1.2254  -0.6079   0.8669
 52E  N4   N   N     0  -0.414   5.6020   0.5897   1.3346
 52E  C7   C   CR16  0  -0.430  -6.8371   3.2640  -0.6437
 52E  C8   C   CR16  0  -0.218  -6.4497   3.7640   0.5890
 52E  C9   C   CR16  0  -0.336  -5.6453   3.0067   1.4286
 52E  C10  C   CR6   0   0.165  -5.2131   1.7362   1.0637
 52E  C11  C   CH2   0  -0.330  -4.3428   0.9360   1.9946
 52E  C12  C   C     0   0.777  -2.3943  -0.4861   1.5617
 52E  C13  C   CH3   0  -0.581  -0.8559   0.3703  -0.1353
 52E  C14  C   CH1   0  -0.153  -0.4613  -1.8359   1.0066
 52E  C18  C   CH2   0  -0.158   0.8842  -1.6085   1.6801
 52E  C20  C   CR6   0   0.506   5.0615   0.2064   0.1642
 52E  C21  C   CR16  0  -0.465   5.7586   0.1908  -1.0203
 52E  C22  C   CR66  0   0.236   7.1074   0.5907  -1.0247
 52E  C23  C   CR66  0  -0.007   7.6884   0.9721   0.2078
 52E  C24  C   CR16  0  -0.095   6.8590   0.9413   1.3486
 52E  C25  C   CR16  0  -0.314   7.9075   0.6143  -2.1918
 52E  C26  C   CR16  0  -0.242   9.2170   1.0017  -2.1155
 52E  C27  C   CR16  0  -0.262   9.7944   1.3823  -0.8825
 52E  C28  C   CR16  0  -0.302   9.0433   1.3687   0.2596
 52E  O29  O   O     0  -0.558  -2.8358  -1.3718   2.2909
 52E  O32  O   O2    0  -0.484   1.7638  -0.9380   0.7780
 52E  O33  O   O     0  -0.476   3.4570  -1.0523   2.2516
 52E  F35  F   F     0  -0.297  -6.7731   1.5033  -2.1916
 52E  H1   H   HNH1  0   0.405  -2.6065   1.4732   0.9494
 52E  H2   H   HNH1  0   0.419   3.2497  -0.1065  -0.7389
 52E  H3   H   HCH2  0   0.244   0.3533  -3.4731  -0.0798
 52E  H4   H   HCH2  0   0.238   0.1341  -2.0667  -1.0839
 52E  H5   H   HCH1  0   0.222  -2.1137  -3.8007   0.0361
 52E  H6   H   HCH2  0   0.188  -0.8759  -3.6841  -2.7425
 52E  H7   H   HCH2  0   0.196  -0.6389  -4.9690  -1.5587
 52E  H8   H   HOH1  0   0.454  -2.3607  -5.4643  -3.0167
 52E  H9   H   HOH1  0   0.437  -2.2271  -1.7326  -1.8630
 52E  H10  H   HCR6  0   0.291  -7.4627   3.8362  -1.3156
 52E  H11  H   HCR6  0   0.274  -6.7747   4.7497   0.8918
 52E  H12  H   HCR6  0   0.268  -5.3431   3.4062   2.3884
 52E  H13  H   HCH2  0   0.268  -4.8070  -0.0264   2.2090
 52E  H14  H   HCH2  0   0.257  -4.2671   1.4690   2.9468
 52E  H15  H   HCH3  0   0.240  -1.6638   0.5372  -0.8518
 52E  H16  H   HCH3  0   0.247  -0.5760   1.3304   0.3056
 52E  H17  H   HCH3  0   0.269   0.0060   0.0241  -0.6940
 52E  H18  H   HCH1  0   0.279  -1.0123  -2.4505   1.7190
 52E  H19  H   HCH2  0   0.248   0.7489  -1.0138   2.5865
 52E  H20  H   HCH2  0   0.241   1.3084  -2.5738   1.9668
 52E  H21  H   HCR6  0   0.276   5.2844  -0.1297  -1.9400
 52E  H22  H   HCR6  0   0.270   7.2712   1.2394   2.3085
 52E  H23  H   HCR6  0   0.261   7.4728   0.3236  -3.1399
 52E  H24  H   HCR6  0   0.267   9.8251   1.0206  -3.0106
 52E  H25  H   HCR6  0   0.264  10.8328   1.6838  -0.8506
 52E  H26  H   HCR6  0   0.262   9.4740   1.6592   1.2102
 52E  CL1  CL  CL    0  -0.072  -5.1257  -0.3293  -0.7054
 52E  C19  C   C     0   0.747   3.0225  -0.7390   1.1716

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
 52E  F35  C5   single    1.336  0.020  1.336
 52E  C5   C7   aromatic  1.380  0.020  1.380
 52E  C5   C6   aromatic  1.385  0.020  1.385
 52E  CL1  C6   single    1.722  0.020  1.722
 52E  C7   C8   aromatic  1.386  0.020  1.386
 52E  C6   C10  aromatic  1.394  0.020  1.394
 52E  C8   C9   aromatic  1.388  0.020  1.388
 52E  C10  C9   aromatic  1.391  0.020  1.391
 52E  C10  C11  single    1.505  0.020  1.505
 52E  C11  N1   single    1.441  0.020  1.441
 52E  C27  C26  aromatic  1.414  0.020  1.414
 52E  C27  C28  aromatic  1.367  0.020  1.367
 52E  C26  C25  aromatic  1.368  0.020  1.368
 52E  N1   C12  single    1.359  0.020  1.359
 52E  C28  C23  aromatic  1.413  0.020  1.413
 52E  C25  C22  aromatic  1.415  0.020  1.415
 52E  C23  C22  aromatic  1.415  0.020  1.415
 52E  C23  C24  aromatic  1.411  0.020  1.411
 52E  C22  C21  aromatic  1.407  0.020  1.407
 52E  C13  N2   single    1.448  0.020  1.448
 52E  C24  N4   aromatic  1.305  0.020  1.305
 52E  C21  C20  aromatic  1.375  0.020  1.375
 52E  C12  N2   single    1.365  0.020  1.365
 52E  C12  O29  double    1.229  0.020  1.229
 52E  N4   C20  aromatic  1.345  0.020  1.345
 52E  C20  N3   single    1.394  0.020  1.394
 52E  N2   C14  single    1.453  0.020  1.453
 52E  N3   C19  single    1.364  0.020  1.364
 52E  O32  C19  single    1.334  0.020  1.334
 52E  O32  C18  single    1.427  0.020  1.427
 52E  C19  O33  double    1.206  0.020  1.206
 52E  C14  C18  single    1.522  0.020  1.522
 52E  C14  C15  single    1.531  0.020  1.531
 52E  C15  C16  single    1.527  0.020  1.527
 52E  O31  C16  single    1.409  0.020  1.409
 52E  C16  C17  single    1.522  0.020  1.522
 52E  C17  O30  single    1.407  0.020  1.407
 52E  N1   H1   single    0.860  0.020  1.020
 52E  N3   H2   single    0.860  0.020  1.020
 52E  C15  H3   single    0.970  0.020  1.090
 52E  C15  H4   single    0.970  0.020  1.090
 52E  C16  H5   single    0.970  0.020  1.090
 52E  C17  H6   single    0.970  0.020  1.090
 52E  C17  H7   single    0.970  0.020  1.090
 52E  O30  H8   single    0.850  0.020  0.980
 52E  O31  H9   single    0.850  0.020  0.980
 52E  C7   H10  single    0.930  0.020  1.080
 52E  C8   H11  single    0.930  0.020  1.080
 52E  C9   H12  single    0.930  0.020  1.080
 52E  C11  H13  single    0.970  0.020  1.090
 52E  C11  H14  single    0.970  0.020  1.090
 52E  C13  H15  single    0.970  0.020  1.090
 52E  C13  H16  single    0.970  0.020  1.090
 52E  C13  H17  single    0.970  0.020  1.090
 52E  C14  H18  single    0.970  0.020  1.090
 52E  C18  H19  single    0.970  0.020  1.090
 52E  C18  H20  single    0.970  0.020  1.090
 52E  C21  H21  single    0.930  0.020  1.080
 52E  C24  H22  single    0.930  0.020  1.080
 52E  C25  H23  single    0.930  0.020  1.080
 52E  C26  H24  single    0.930  0.020  1.080
 52E  C27  H25  single    0.930  0.020  1.080
 52E  C28  H26  single    0.930  0.020  1.080

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
 52E  H1   N1   C12  120.83  3.000
 52E  H1   N1   C11  116.89  3.000
 52E  C12  N1   C11  122.15  3.000
 52E  CL1  C6   C10  121.29  3.000
 52E  C10  C6   C5   119.97  3.000
 52E  CL1  C6   C5   118.75  3.000
 52E  H2   N3   C20  116.02  3.000
 52E  H2   N3   C19  116.36  3.000
 52E  C20  N3   C19  126.49  3.000
 52E  F35  C5   C7   119.41  3.000
 52E  C7   C5   C6   121.76  3.000
 52E  F35  C5   C6   118.83  3.000
 52E  H4   C15  H3   105.44  3.000
 52E  H4   C15  C14  111.65  3.000
 52E  H3   C15  C14  107.09  3.000
 52E  H4   C15  C16  109.69  3.000
 52E  H3   C15  C16  107.95  3.000
 52E  C14  C15  C16  114.51  3.000
 52E  H5   C16  O31  105.18  3.000
 52E  H5   C16  C17  108.18  3.000
 52E  O31  C16  C17  111.69  3.000
 52E  H5   C16  C15  108.41  3.000
 52E  C17  C16  C15  109.51  3.000
 52E  O31  C16  C15  113.61  3.000
 52E  H7   C17  H6   106.64  3.000
 52E  H7   C17  O30  111.62  3.000
 52E  H6   C17  O30  111.68  3.000
 52E  H7   C17  C16  108.55  3.000
 52E  H6   C17  C16  108.94  3.000
 52E  O30  C17  C16  109.32  3.000
 52E  H8   O30  C17  108.07  3.000
 52E  H9   O31  C16  108.74  3.000
 52E  C14  N2   C13  120.21  3.000
 52E  C14  N2   C12  118.47  3.000
 52E  C13  N2   C12  120.69  3.000
 52E  C24  N4   C20  118.24  3.000
 52E  H10  C7   C8   121.57  3.000
 52E  H10  C7   C5   119.91  3.000
 52E  C8   C7   C5   118.52  3.000
 52E  H11  C8   C9   120.16  3.000
 52E  H11  C8   C7   119.61  3.000
 52E  C9   C8   C7   120.23  3.000
 52E  H12  C9   C10  118.88  3.000
 52E  H12  C9   C8   119.79  3.000
 52E  C10  C9   C8   121.33  3.000
 52E  C11  C10  C9   120.21  3.000
 52E  C11  C10  C6   121.60  3.000
 52E  C9   C10  C6   118.19  3.000
 52E  H14  C11  H13  106.77  3.000
 52E  H14  C11  C10  108.63  3.000
 52E  H13  C11  C10  110.18  3.000
 52E  H14  C11  N1   111.54  3.000
 52E  H13  C11  N1   108.49  3.000
 52E  C10  C11  N1   111.14  3.000
 52E  O29  C12  N2   123.03  3.000
 52E  O29  C12  N1   121.29  3.000
 52E  N2   C12  N1   115.67  3.000
 52E  H17  C13  H16  106.56  3.000
 52E  H17  C13  H15  107.38  3.000
 52E  H16  C13  H15  108.64  3.000
 52E  H17  C13  N2   110.11  3.000
 52E  H16  C13  N2   112.30  3.000
 52E  H15  C13  N2   111.61  3.000
 52E  H18  C14  C18  104.00  3.000
 52E  H18  C14  N2   105.87  3.000
 52E  C18  C14  N2   112.41  3.000
 52E  H18  C14  C15  107.04  3.000
 52E  C18  C14  C15  112.35  3.000
 52E  N2   C14  C15  114.24  3.000
 52E  H20  C18  H19  108.14  3.000
 52E  H20  C18  O32  109.97  3.000
 52E  H19  C18  O32  110.18  3.000
 52E  H20  C18  C14  109.11  3.000
 52E  H19  C18  C14  109.82  3.000
 52E  O32  C18  C14  109.60  3.000
 52E  C21  C20  N4   123.32  3.000
 52E  N4   C20  N3   117.64  3.000
 52E  C21  C20  N3   118.99  3.000
 52E  H21  C21  C22  120.07  3.000
 52E  H21  C21  C20  120.87  3.000
 52E  C22  C21  C20  119.06  3.000
 52E  C25  C22  C23  118.79  3.000
 52E  C23  C22  C21  117.88  3.000
 52E  C25  C22  C21  123.32  3.000
 52E  C28  C23  C24  122.71  3.000
 52E  C24  C23  C22  117.20  3.000
 52E  C28  C23  C22  120.10  3.000
 52E  H22  C24  C23  119.04  3.000
 52E  H22  C24  N4   116.67  3.000
 52E  C23  C24  N4   124.28  3.000
 52E  H23  C25  C26  120.61  3.000
 52E  H23  C25  C22  119.38  3.000
 52E  C26  C25  C22  120.00  3.000
 52E  H24  C26  C27  119.15  3.000
 52E  H24  C26  C25  119.79  3.000
 52E  C27  C26  C25  121.06  3.000
 52E  H25  C27  C28  120.37  3.000
 52E  H25  C27  C26  119.53  3.000
 52E  C28  C27  C26  120.10  3.000
 52E  H26  C28  C27  120.80  3.000
 52E  H26  C28  C23  119.26  3.000
 52E  C27  C28  C23  119.94  3.000
 52E  C19  O32  C18  117.73  3.000
 52E  O33  C19  O32  124.45  3.000
 52E  O33  C19  N3   126.73  3.000
 52E  O32  C19  N3   108.82  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
 52E  CONST_01  C8   C7   C5   C6      0.00   0.0  0
 52E  CONST_02  C8   C9   C10  C6      0.00   0.0  0
 52E  CONST_03  C9   C8   C7   C5      0.00   0.0  0
 52E  CONST_04  C9   C10  C6   C5      0.00   0.0  0
 52E  CONST_05  C28  C23  C24  N4    180.00   0.0  0
 52E  CONST_06  C22  C23  C24  N4      0.00   0.0  0
 52E  CONST_07  C22  C21  C20  N4      0.00   0.0  0
 52E  CONST_08  C10  C6   C5   C7      0.00   0.0  0
 52E  CONST_09  C10  C9   C8   C7      0.00   0.0  0
 52E  CONST_10  C25  C22  C21  C20   180.00   0.0  0
 52E  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 52E  CONST_12  C23  C24  N4   C20     0.00   0.0  0
 52E  CONST_13  C26  C25  C22  C21   180.00   0.0  0
 52E  CONST_14  C28  C23  C22  C21   180.00   0.0  0
 52E  CONST_15  C24  C23  C22  C21     0.00   0.0  0
 52E  CONST_16  C24  N4   C20  C21     0.00   0.0  0
 52E  CONST_17  C27  C26  C25  C22     0.00   0.0  0
 52E  CONST_18  C27  C28  C23  C22     0.00   0.0  0
 52E  CONST_19  C26  C27  C28  C23     0.00   0.0  0
 52E  CONST_20  C26  C25  C22  C23     0.00   0.0  0
 52E  CONST_21  C27  C28  C23  C24   180.00   0.0  0
 52E  CONST_22  C25  C22  C23  C24   180.00   0.0  0
 52E  CONST_23  C28  C27  C26  C25     0.00   0.0  0
 52E  CONST_24  C28  C23  C22  C25     0.00   0.0  0
 52E  CONST_25  C22  C21  C20  N3    180.00   0.0  0
 52E  CONST_26  C24  N4   C20  N3    180.00   0.0  0
 52E  CONST_27  C11  C10  C6   C5    180.00   0.0  0
 52E  CONST_28  CL1  C6   C5   C7    180.00   0.0  0
 52E  CONST_29  F35  C5   C7   C8    180.00   0.0  0
 52E  CONST_30  C11  C10  C9   C8    180.00   0.0  0
 52E  CONST_31  CL1  C6   C10  C9    180.00   0.0  0
 52E  CONST_32  F35  C5   C6   C10   180.00   0.0  0
 52E  CONST_33  H10  C7   C5   C6    180.00   0.0  0
 52E  CONST_34  H12  C9   C10  C6    180.00   0.0  0
 52E  CONST_35  H11  C8   C7   C5    180.00   0.0  0
 52E  CONST_36  H21  C21  C20  N4    180.00   0.0  0
 52E  CONST_37  H22  C24  N4   C20   180.00   0.0  0
 52E  CONST_38  H23  C25  C22  C21     0.00   0.0  0
 52E  CONST_39  H24  C26  C25  C22   180.00   0.0  0
 52E  CONST_40  H26  C28  C23  C22   180.00   0.0  0
 52E  CONST_41  H25  C27  C28  C23   180.00   0.0  0
 52E  CONST_45  O32  C19  N3   C20   180.00   0.0  0
 52E  CONST_46  O33  C19  N3   C20     0.00   0.0  0
 52E  CONST_47  O29  C12  N1   C11     0.00   0.0  0
 52E  CONST_48  O29  C12  N2   C13   180.00   0.0  0
 52E  CONST_49  O29  C12  N2   C14     0.00   0.0  0
 52E  CONST_50  C13  N2   C12  N1      0.00   0.0  0
 52E  CONST_51  C14  N2   C12  N1    180.00   0.0  0
 52E  CONST_52  C11  N1   C12  N2    180.00   0.0  0
 52E  CONST_53  H1   N1   C12  O29   180.00   0.0  0
 52E  Var_01    C6   C10  C11  N1     63.84  30.0  2
 52E  Var_02    C12  N1   C11  C10  -141.07  30.0  3
 52E  Var_03    H15  C13  N2   C12   -51.21  30.0  3
 52E  Var_04    H19  C18  O32  C19    63.58  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
 52E  chir_01  C16  C15  O31  C17  negativ
 52E  chir_02  C14  N2   C15  C18  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
 52E  plan-1  C6   0.020
 52E  plan-1  C5   0.020
 52E  plan-1  C7   0.020
 52E  plan-1  C8   0.020
 52E  plan-1  C9   0.020
 52E  plan-1  C10  0.020
 52E  plan-1  C11  0.020
 52E  plan-1  F35  0.020
 52E  plan-1  H10  0.020
 52E  plan-1  H11  0.020
 52E  plan-1  H12  0.020
 52E  plan-1  CL1  0.020
 52E  plan-2  N3   0.020
 52E  plan-2  O32  0.020
 52E  plan-2  O33  0.020
 52E  plan-2  C19  0.020
 52E  plan-3  N3   0.020
 52E  plan-3  N4   0.020
 52E  plan-3  C20  0.020
 52E  plan-3  C21  0.020
 52E  plan-3  C22  0.020
 52E  plan-3  C23  0.020
 52E  plan-3  C24  0.020
 52E  plan-3  C25  0.020
 52E  plan-3  C26  0.020
 52E  plan-3  C27  0.020
 52E  plan-3  C28  0.020
 52E  plan-3  H21  0.020
 52E  plan-3  H22  0.020
 52E  plan-3  H23  0.020
 52E  plan-3  H24  0.020
 52E  plan-3  H25  0.020
 52E  plan-3  H26  0.020
 52E  plan-4  N1   0.020
 52E  plan-4  N2   0.020
 52E  plan-4  C11  0.020
 52E  plan-4  C12  0.020
 52E  plan-4  C13  0.020
 52E  plan-4  C14  0.020
 52E  plan-4  O29  0.020
 52E  plan-4  H1   0.020
 52E  plan-5  N3   0.020
 52E  plan-5  C20  0.020
 52E  plan-5  H2   0.020
 52E  plan-5  C19  0.020

