# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:04:43 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: ~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-4-phenyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)c2ccc(cc2)c3ccccc3)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 JNB  JNB  ~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-4-phenyl-benzamide  ligand  47  26  .  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_JNB
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
 JNB  C2   C  C     0   0.562  -0.2240  -0.5839   0.9299
 JNB  C3   C  CR6   0  -0.056   1.2168  -0.4107   0.5749
 JNB  C4   C  CR16  0  -0.277   1.6566   0.2500  -0.5702
 JNB  C5   C  CR16  0  -0.294   3.0087   0.3723  -0.8406
 JNB  C6   C  CR6   0   0.092   3.9665  -0.1621   0.0218
 JNB  C7   C  CR16  0  -0.298   3.5200  -0.8341   1.1615
 JNB  N1   N  NH1   0  -0.718  -1.0982   0.2554   0.3239
 JNB  C8   C  CR16  0  -0.250   2.1694  -0.9613   1.4300
 JNB  C1'  C  CH1   0   0.215  -2.5122   0.1509   0.4742
 JNB  C2'  C  CH1   0  -0.037  -3.1634   1.5340   0.3847
 JNB  C3'  C  CH1   0  -0.004  -4.6760   1.3741   0.4556
 JNB  C4'  C  CH1   0   0.036  -5.1662   0.3736  -0.5848
 JNB  C5'  C  CH1   0  -0.015  -4.3941  -0.9381  -0.4358
 JNB  C6'  C  CH2   0  -0.156  -4.7692  -1.9393  -1.5074
 JNB  O6'  O  OH1   0  -0.669  -4.0764  -3.1413  -1.2698
 JNB  O2   O  O     0  -0.471  -0.5757  -1.4203   1.7447
 JNB  O5'  O  O2    0  -0.487  -3.0089  -0.6834  -0.5460
 JNB  O4'  O  OH1   0  -0.672  -6.5349   0.0990  -0.4213
 JNB  O3'  O  OH1   0  -0.671  -5.3468   2.5885   0.2234
 JNB  O2'  O  OH1   0  -0.663  -2.7748   2.3575   1.4540
 JNB  C9   C  CR6   0   0.093   5.4075  -0.0216  -0.2647
 JNB  C14  C  CR16  0  -0.309   6.3292   0.1410   0.7716
 JNB  C13  C  CR16  0  -0.239   7.6827   0.2788   0.5012
 JNB  C12  C  CR16  0  -0.263   8.1404   0.2546  -0.8098
 JNB  C11  C  CR16  0  -0.239   7.2334   0.0914  -1.8487
 JNB  C10  C  CR16  0  -0.310   5.8800  -0.0452  -1.5783
 JNB  H1   H  HCR6  0   0.256   0.9620   0.6734  -1.2844
 JNB  H2   H  HCR6  0   0.265   3.3152   0.9075  -1.7299
 JNB  H3   H  HCR6  0   0.261   4.2339  -1.2825   1.8406
 JNB  H4   H  HNH1  0   0.412  -0.7566   0.9068  -0.3653
 JNB  H5   H  HCR6  0   0.263   1.8528  -1.4937   2.3166
 JNB  H6   H  HCH1  0   0.233  -2.7279  -0.2814   1.4591
 JNB  H7   H  HCH1  0   0.229  -2.9006   1.9802  -0.5872
 JNB  H8   H  HCH1  0   0.218  -4.9258   0.9728   1.4509
 JNB  H9   H  HCH1  0   0.213  -4.9600   0.7813  -1.5874
 JNB  H10  H  HCH1  0   0.224  -4.6212  -1.3667   0.5546
 JNB  H11  H  HCH2  0   0.214  -5.8538  -2.0843  -1.4795
 JNB  H12  H  HCH2  0   0.195  -4.5245  -1.5153  -2.4916
 JNB  H13  H  HOH1  0   0.457  -4.3913  -3.7932  -1.9019
 JNB  H14  H  HOH1  0   0.455  -7.0222   0.9216  -0.5346
 JNB  H15  H  HOH1  0   0.457  -5.2088   3.1676   0.9793
 JNB  H16  H  HOH1  0   0.458  -1.8722   2.6574   1.3101
 JNB  H17  H  HCR6  0   0.257   5.9874   0.1807   1.7985
 JNB  H18  H  HCR6  0   0.260   8.3807   0.4116   1.3174
 JNB  H19  H  HCR6  0   0.260   9.1967   0.3609  -1.0193
 JNB  H20  H  HCR6  0   0.260   7.5796   0.0641  -2.8738
 JNB  H21  H  HCR6  0   0.257   5.1894  -0.1916  -2.3992

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
 JNB  O3'  C3'  single    1.407  0.020  1.407
 JNB  O4'  C4'  single    1.406  0.020  1.406
 JNB  C3'  C4'  single    1.524  0.020  1.524
 JNB  C3'  C2'  single    1.523  0.020  1.523
 JNB  C4'  C5'  single    1.529  0.020  1.529
 JNB  O2'  C2'  single    1.404  0.020  1.404
 JNB  C2'  C1'  single    1.531  0.020  1.531
 JNB  O6'  C6'  single    1.408  0.020  1.408
 JNB  C5'  C6'  single    1.514  0.020  1.514
 JNB  C5'  O5'  single    1.413  0.020  1.413
 JNB  C1'  O5'  single    1.408  0.020  1.408
 JNB  C1'  N1   single    1.426  0.020  1.426
 JNB  N1   C2   single    1.355  0.020  1.355
 JNB  C2   O2   double    1.220  0.020  1.220
 JNB  C2   C3   single    1.494  0.020  1.494
 JNB  C4   C3   aromatic  1.393  0.020  1.393
 JNB  C4   C5   aromatic  1.384  0.020  1.384
 JNB  C3   C8   aromatic  1.394  0.020  1.394
 JNB  C5   C6   aromatic  1.395  0.020  1.395
 JNB  C8   C7   aromatic  1.383  0.020  1.383
 JNB  C6   C7   aromatic  1.396  0.020  1.396
 JNB  C6   C9   single    1.476  0.020  1.476
 JNB  C10  C9   aromatic  1.396  0.020  1.396
 JNB  C10  C11  aromatic  1.387  0.020  1.387
 JNB  C9   C14  aromatic  1.396  0.020  1.396
 JNB  C11  C12  aromatic  1.389  0.020  1.389
 JNB  C14  C13  aromatic  1.387  0.020  1.387
 JNB  C12  C13  aromatic  1.389  0.020  1.389
 JNB  C4   H1   single    0.930  0.020  1.080
 JNB  C5   H2   single    0.930  0.020  1.080
 JNB  C7   H3   single    0.930  0.020  1.080
 JNB  N1   H4   single    0.860  0.020  1.020
 JNB  C8   H5   single    0.930  0.020  1.080
 JNB  C1'  H6   single    0.970  0.020  1.090
 JNB  C2'  H7   single    0.970  0.020  1.090
 JNB  C3'  H8   single    0.970  0.020  1.090
 JNB  C4'  H9   single    0.970  0.020  1.090
 JNB  C5'  H10  single    0.970  0.020  1.090
 JNB  C6'  H11  single    0.970  0.020  1.090
 JNB  C6'  H12  single    0.970  0.020  1.090
 JNB  O6'  H13  single    0.850  0.020  0.980
 JNB  O4'  H14  single    0.850  0.020  0.980
 JNB  O3'  H15  single    0.850  0.020  0.980
 JNB  O2'  H16  single    0.850  0.020  0.980
 JNB  C14  H17  single    0.930  0.020  1.080
 JNB  C13  H18  single    0.930  0.020  1.080
 JNB  C12  H19  single    0.930  0.020  1.080
 JNB  C11  H20  single    0.930  0.020  1.080
 JNB  C10  H21  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
 JNB  O2   C2   N1   122.52  3.000
 JNB  O2   C2   C3   121.09  3.000
 JNB  N1   C2   C3   116.37  3.000
 JNB  C8   C3   C4   118.42  3.000
 JNB  C8   C3   C2   117.88  3.000
 JNB  C4   C3   C2   123.69  3.000
 JNB  H1   C4   C5   117.60  3.000
 JNB  H1   C4   C3   121.68  3.000
 JNB  C5   C4   C3   120.72  3.000
 JNB  H2   C5   C6   120.19  3.000
 JNB  H2   C5   C4   118.75  3.000
 JNB  C6   C5   C4   121.06  3.000
 JNB  C9   C6   C7   121.09  3.000
 JNB  C9   C6   C5   120.92  3.000
 JNB  C7   C6   C5   117.99  3.000
 JNB  H3   C7   C8   118.96  3.000
 JNB  H3   C7   C6   120.03  3.000
 JNB  C8   C7   C6   121.00  3.000
 JNB  H4   N1   C1'  117.10  3.000
 JNB  H4   N1   C2   119.17  3.000
 JNB  C1'  N1   C2   123.18  3.000
 JNB  H5   C8   C7   119.36  3.000
 JNB  H5   C8   C3   119.83  3.000
 JNB  C7   C8   C3   120.81  3.000
 JNB  H6   C1'  O5'  110.34  3.000
 JNB  H6   C1'  C2'  108.95  3.000
 JNB  O5'  C1'  C2'  110.04  3.000
 JNB  H6   C1'  N1   108.57  3.000
 JNB  O5'  C1'  N1   108.47  3.000
 JNB  C2'  C1'  N1   110.45  3.000
 JNB  H7   C2'  O2'  111.61  3.000
 JNB  H7   C2'  C3'  108.71  3.000
 JNB  O2'  C2'  C3'  107.52  3.000
 JNB  H7   C2'  C1'  108.42  3.000
 JNB  O2'  C2'  C1'  111.55  3.000
 JNB  C3'  C2'  C1'  108.96  3.000
 JNB  H8   C3'  O3'  110.82  3.000
 JNB  H8   C3'  C4'  107.73  3.000
 JNB  O3'  C3'  C4'  107.50  3.000
 JNB  H8   C3'  C2'  107.79  3.000
 JNB  C4'  C3'  C2'  110.89  3.000
 JNB  O3'  C3'  C2'  112.05  3.000
 JNB  H9   C4'  O4'  111.12  3.000
 JNB  H9   C4'  C5'  108.15  3.000
 JNB  O4'  C4'  C5'  108.23  3.000
 JNB  H9   C4'  C3'  108.53  3.000
 JNB  C5'  C4'  C3'  109.52  3.000
 JNB  O4'  C4'  C3'  111.22  3.000
 JNB  H10  C5'  O5'  110.01  3.000
 JNB  H10  C5'  C6'  109.12  3.000
 JNB  O5'  C5'  C6'  107.88  3.000
 JNB  H10  C5'  C4'  108.47  3.000
 JNB  O5'  C5'  C4'  109.44  3.000
 JNB  C6'  C5'  C4'  111.91  3.000
 JNB  H12  C6'  H11  107.13  3.000
 JNB  H12  C6'  O6'  111.78  3.000
 JNB  H11  C6'  O6'  111.73  3.000
 JNB  H12  C6'  C5'  108.88  3.000
 JNB  H11  C6'  C5'  108.37  3.000
 JNB  O6'  C6'  C5'  108.86  3.000
 JNB  H13  O6'  C6'  107.87  3.000
 JNB  C5'  O5'  C1'  113.33  3.000
 JNB  H14  O4'  C4'  108.20  3.000
 JNB  H15  O3'  C3'  108.75  3.000
 JNB  H16  O2'  C2'  109.18  3.000
 JNB  C10  C9   C14  118.48  3.000
 JNB  C14  C9   C6   120.77  3.000
 JNB  C10  C9   C6   120.76  3.000
 JNB  H17  C14  C13  119.29  3.000
 JNB  H17  C14  C9   119.97  3.000
 JNB  C13  C14  C9   120.73  3.000
 JNB  H18  C13  C12  120.10  3.000
 JNB  H18  C13  C14  119.64  3.000
 JNB  C12  C13  C14  120.26  3.000
 JNB  H19  C12  C11  120.28  3.000
 JNB  H19  C12  C13  120.19  3.000
 JNB  C11  C12  C13  119.54  3.000
 JNB  H20  C11  C10  119.62  3.000
 JNB  H20  C11  C12  120.18  3.000
 JNB  C10  C11  C12  120.20  3.000
 JNB  H21  C10  C11  119.20  3.000
 JNB  H21  C10  C9   119.99  3.000
 JNB  C11  C10  C9   120.80  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
 JNB  CONST_01  C6   C5   C4   C3     0.00   0.0  0
 JNB  CONST_02  C6   C7   C8   C3     0.00   0.0  0
 JNB  CONST_03  C7   C8   C3   C4     0.00   0.0  0
 JNB  CONST_04  C7   C6   C5   C4     0.00   0.0  0
 JNB  CONST_05  C9   C6   C5   C4   180.00   0.0  0
 JNB  CONST_06  C8   C3   C4   C5     0.00   0.0  0
 JNB  CONST_07  C8   C7   C6   C5     0.00   0.0  0
 JNB  CONST_10  C11  C10  C9   C6   180.00   0.0  0
 JNB  CONST_11  C13  C14  C9   C6   180.00   0.0  0
 JNB  CONST_14  C9   C6   C7   C8   180.00   0.0  0
 JNB  CONST_15  C12  C11  C10  C9     0.00   0.0  0
 JNB  CONST_16  C12  C13  C14  C9     0.00   0.0  0
 JNB  CONST_17  C11  C10  C9   C14    0.00   0.0  0
 JNB  CONST_18  C11  C12  C13  C14    0.00   0.0  0
 JNB  CONST_19  C10  C9   C14  C13    0.00   0.0  0
 JNB  CONST_20  C10  C11  C12  C13    0.00   0.0  0
 JNB  CONST_21  C5   C4   C3   C2   180.00   0.0  0
 JNB  CONST_22  C7   C8   C3   C2   180.00   0.0  0
 JNB  CONST_23  H2   C5   C4   C3   180.00   0.0  0
 JNB  CONST_24  H3   C7   C8   C3   180.00   0.0  0
 JNB  CONST_25  H5   C8   C3   C4   180.00   0.0  0
 JNB  CONST_26  H1   C4   C5   C6   180.00   0.0  0
 JNB  CONST_27  H21  C10  C9   C6     0.00   0.0  0
 JNB  CONST_28  H17  C14  C9   C6     0.00   0.0  0
 JNB  CONST_29  H20  C11  C10  C9   180.00   0.0  0
 JNB  CONST_30  H18  C13  C14  C9   180.00   0.0  0
 JNB  CONST_31  H19  C12  C13  C14  180.00   0.0  0
 JNB  CONST_32  C1'  N1   C2   C3   180.00   0.0  0
 JNB  CONST_33  O2   C2   N1   C1'    0.00   0.0  0
 JNB  CONST_34  H4   N1   C2   C3     0.00   0.0  0
 JNB  Var_01    N1   C2   C3   C4   -19.20  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
 JNB  chir_01  C1'  C2'  O5'  N1   negativ
 JNB  chir_02  C2'  O2'  C1'  C3'  negativ
 JNB  chir_03  C3'  O3'  C2'  C4'  positiv
 JNB  chir_04  C4'  O4'  C5'  C3'  positiv
 JNB  chir_05  C5'  O5'  C4'  C6'  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
 JNB  plan-1  C2   0.020
 JNB  plan-1  C3   0.020
 JNB  plan-1  C4   0.020
 JNB  plan-1  C5   0.020
 JNB  plan-1  C6   0.020
 JNB  plan-1  C7   0.020
 JNB  plan-1  C8   0.020
 JNB  plan-1  C9   0.020
 JNB  plan-1  H1   0.020
 JNB  plan-1  H2   0.020
 JNB  plan-1  H3   0.020
 JNB  plan-1  H5   0.020
 JNB  plan-2  C6   0.020
 JNB  plan-2  C9   0.020
 JNB  plan-2  C14  0.020
 JNB  plan-2  C13  0.020
 JNB  plan-2  C12  0.020
 JNB  plan-2  C11  0.020
 JNB  plan-2  C10  0.020
 JNB  plan-2  H17  0.020
 JNB  plan-2  H18  0.020
 JNB  plan-2  H19  0.020
 JNB  plan-2  H20  0.020
 JNB  plan-2  H21  0.020
 JNB  plan-3  C2   0.020
 JNB  plan-3  C3   0.020
 JNB  plan-3  N1   0.020
 JNB  plan-3  C1'  0.020
 JNB  plan-3  O2   0.020
 JNB  plan-3  H4   0.020

