# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 11:38:28 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 7-[(5R)-5-C-(4-chloro-3-fluorophenyl)-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(ccc12)[C@@H]3O[C@@H]([C@@H](O)[C@H]3O)[C@H](O)c4ccc(Cl)c(F)c4
#
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
 ZR4  ZR4  "7-[(5R)-5-C-(4-chloro-3-fluorophenyl)-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine"
  ligand  43  27  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZR4
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
 ZR4  C17  C   CR16  0  -0.311  -26.1422  -29.4974  -38.0914
 ZR4  C16  C   CR16  0  -0.191  -24.9941  -28.7310  -37.9783
 ZR4  C5   C   CR15  0  -0.437  -33.7345  -31.5413  -39.5932
 ZR4  C13  C   CR16  0  -0.468  -27.3994  -27.5606  -38.7375
 ZR4  C6   C   CR15  0  -0.012  -32.4615  -31.0621  -39.6256
 ZR4  C3   C   CR16  0   0.042  -33.2883  -34.0284  -42.7579
 ZR4  C1   C   CR56  0  -0.083  -33.8371  -32.4828  -40.6613
 ZR4  C12  C   CR6   0   0.072  -27.3522  -28.9239  -38.4720
 ZR4  C14  C   CR6   0   0.635  -26.2510  -26.8046  -38.6214
 ZR4  C15  C   CR6   0  -0.244  -25.0463  -27.3708  -38.2423
 ZR4  C2   C   CR56  0   0.511  -32.5938  -32.5267  -41.2960
 ZR4  C4   C   CR6   0   0.436  -34.8249  -33.3241  -41.2088
 ZR4  C9   C   CR15  0  -0.042  -28.6608  -29.8042  -41.2011
 ZR4  C10  C   CR15  0  -0.007  -30.1510  -29.9664  -41.5014
 ZR4  C8   C   CR15  0  -0.003  -28.5227  -30.6054  -39.8946
 ZR4  C7   C   CR15  0   0.203  -30.4004  -31.3940  -41.0211
 ZR4  C11  C   CH1   0  -0.026  -28.5887  -29.7883  -38.6020
 ZR4  N1   N   N     0  -0.463  -32.2796  -33.2864  -42.3473
 ZR4  N2   N   N     0  -0.476  -34.5213  -34.0904  -42.2603
 ZR4  N3   N   NR5   0  -0.552  -31.7638  -31.6577  -40.6566
 ZR4  O1   O   O     0  -0.493  -29.5694  -31.5710  -39.9054
 ZR4  O3   O   OH1   0  -0.666  -27.9420  -30.4010  -42.2506
 ZR4  O4   O   OH1   0  -0.653  -30.5376  -29.8543  -42.8358
 ZR4  O2   O   OH1   0  -0.651  -29.7743  -29.0423  -38.5962
 ZR4  F1   F   F     0  -0.295  -26.3007  -25.4952  -38.8768
 ZR4  CL1  CL  CL    0  -0.092  -23.6464  -26.3787  -38.0945
 ZR4  H13  H   HCR6  0   0.269  -26.0915  -30.5565  -37.8687
 ZR4  H12  H   HCR6  0   0.289  -24.0600  -29.1846  -37.6758
 ZR4  H2   H   HCR5  0   0.254  -34.4977  -31.2547  -38.8873
 ZR4  H11  H   HCR6  0   0.286  -28.3212  -27.0749  -39.0309
 ZR4  H3   H   HCR5  0   0.292  -31.9821  -30.3400  -38.9851
 ZR4  H1   H   HCR6  0   0.243  -33.0952  -34.6725  -43.6099
 ZR4  H8   H   HCR5  0   0.254  -28.3786  -28.7527  -41.0729
 ZR4  H9   H   HCR5  0   0.248  -30.7025  -29.2707  -40.8591
 ZR4  H7   H   HCR5  0   0.262  -27.5619  -31.1328  -39.8890
 ZR4  H6   H   HCR5  0   0.252  -30.1548  -32.1040  -41.8186
 ZR4  H10  H   HCH1  0   0.258  -28.5775  -30.5096  -37.7726
 ZR4  H5   H   HNH2  0   0.396  -36.7037  -34.0809  -41.0705
 ZR4  H4   H   HNH2  0   0.407  -36.3134  -32.9322  -39.8578
 ZR4  H15  H   HOH1  0   0.454  -27.0021  -30.3176  -42.0599
 ZR4  H16  H   HOH1  0   0.459  -30.5470  -28.9233  -43.0782
 ZR4  H14  H   HOH1  0   0.465  -29.9344  -28.7109  -37.7059
 ZR4  N4   N   NH2   0  -0.822  -36.0767  -33.3720  -40.7300

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
 ZR4  O4   C10  single    1.394  0.020  1.394
 ZR4  C3   N1   aromatic  1.318  0.020  1.318
 ZR4  C3   N2   aromatic  1.331  0.020  1.331
 ZR4  O3   C9   single    1.405  0.020  1.405
 ZR4  N1   C2   aromatic  1.335  0.020  1.335
 ZR4  N2   C4   aromatic  1.336  0.020  1.336
 ZR4  C10  C7   single    1.527  0.020  1.527
 ZR4  C10  C9   single    1.529  0.020  1.529
 ZR4  C2   N3   aromatic  1.361  0.020  1.361
 ZR4  C2   C1   aromatic  1.397  0.020  1.397
 ZR4  C4   C1   aromatic  1.408  0.020  1.408
 ZR4  C4   N4   single    1.341  0.020  1.341
 ZR4  C7   N3   single    1.436  0.020  1.436
 ZR4  C7   O1   single    1.402  0.020  1.402
 ZR4  C9   C8   single    1.539  0.020  1.539
 ZR4  N3   C6   aromatic  1.380  0.020  1.380
 ZR4  C1   C5   aromatic  1.428  0.020  1.428
 ZR4  C6   C5   aromatic  1.361  0.020  1.361
 ZR4  C8   O1   single    1.424  0.020  1.424
 ZR4  C8   C11  single    1.531  0.020  1.531
 ZR4  F1   C14  single    1.335  0.020  1.335
 ZR4  C11  C12  single    1.514  0.020  1.514
 ZR4  C11  O2   single    1.401  0.020  1.401
 ZR4  C14  C13  aromatic  1.380  0.020  1.380
 ZR4  C14  C15  aromatic  1.384  0.020  1.384
 ZR4  C13  C12  aromatic  1.390  0.020  1.390
 ZR4  C12  C17  aromatic  1.392  0.020  1.392
 ZR4  C16  C15  aromatic  1.387  0.020  1.387
 ZR4  C16  C17  aromatic  1.385  0.020  1.385
 ZR4  C15  CL1  single    1.722  0.020  1.722
 ZR4  C17  H13  single    0.930  0.020  1.080
 ZR4  C16  H12  single    0.930  0.020  1.080
 ZR4  C5   H2   single    0.930  0.020  1.080
 ZR4  C13  H11  single    0.930  0.020  1.080
 ZR4  C6   H3   single    0.930  0.020  1.080
 ZR4  C3   H1   single    0.930  0.020  1.080
 ZR4  C9   H8   single    0.970  0.020  1.090
 ZR4  C10  H9   single    0.970  0.020  1.090
 ZR4  C8   H7   single    0.970  0.020  1.090
 ZR4  C7   H6   single    0.970  0.020  1.090
 ZR4  C11  H10  single    0.970  0.020  1.090
 ZR4  N4   H5   single    0.860  0.020  1.020
 ZR4  N4   H4   single    0.860  0.020  1.020
 ZR4  O3   H15  single    0.850  0.020  0.980
 ZR4  O4   H16  single    0.850  0.020  0.980
 ZR4  O2   H14  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
 ZR4  H13  C17  C12  119.97  3.000
 ZR4  H13  C17  C16  119.04  3.000
 ZR4  C12  C17  C16  120.99  3.000
 ZR4  H12  C16  C15  119.82  3.000
 ZR4  H12  C16  C17  120.44  3.000
 ZR4  C15  C16  C17  119.74  3.000
 ZR4  H2   C5   C1   127.90  3.000
 ZR4  H2   C5   C6   125.74  3.000
 ZR4  C1   C5   C6   106.36  3.000
 ZR4  H11  C13  C14  119.06  3.000
 ZR4  H11  C13  C12  121.39  3.000
 ZR4  C14  C13  C12  119.55  3.000
 ZR4  H3   C6   N3   120.54  3.000
 ZR4  H3   C6   C5   129.64  3.000
 ZR4  N3   C6   C5   109.81  3.000
 ZR4  H1   C3   N2   115.51  3.000
 ZR4  H1   C3   N1   116.27  3.000
 ZR4  N2   C3   N1   128.22  3.000
 ZR4  C4   C1   C2   115.40  3.000
 ZR4  C4   C1   C5   137.33  3.000
 ZR4  C2   C1   C5   107.27  3.000
 ZR4  C11  C12  C13  121.05  3.000
 ZR4  C13  C12  C17  119.07  3.000
 ZR4  C11  C12  C17  119.88  3.000
 ZR4  F1   C14  C15  119.08  3.000
 ZR4  C15  C14  C13  121.56  3.000
 ZR4  F1   C14  C13  119.36  3.000
 ZR4  CL1  C15  C14  119.69  3.000
 ZR4  CL1  C15  C16  121.21  3.000
 ZR4  C14  C15  C16  119.10  3.000
 ZR4  N3   C2   N1   126.15  3.000
 ZR4  N3   C2   C1   108.01  3.000
 ZR4  N1   C2   C1   125.83  3.000
 ZR4  N4   C4   N2   118.20  3.000
 ZR4  N4   C4   C1   122.50  3.000
 ZR4  N2   C4   C1   119.29  3.000
 ZR4  H8   C9   O3   111.29  3.000
 ZR4  H8   C9   C8   112.15  3.000
 ZR4  O3   C9   C8   111.53  3.000
 ZR4  H8   C9   C10  112.07  3.000
 ZR4  C8   C9   C10  101.48  3.000
 ZR4  O3   C9   C10  107.87  3.000
 ZR4  H9   C10  O4   111.75  3.000
 ZR4  H9   C10  C7   109.09  3.000
 ZR4  O4   C10  C7   109.33  3.000
 ZR4  H9   C10  C9   107.94  3.000
 ZR4  C7   C10  C9   101.34  3.000
 ZR4  O4   C10  C9   116.74  3.000
 ZR4  H7   C8   O1   108.55  3.000
 ZR4  H7   C8   C11  106.88  3.000
 ZR4  O1   C8   C11  109.67  3.000
 ZR4  H7   C8   C9   109.49  3.000
 ZR4  C11  C8   C9   115.80  3.000
 ZR4  O1   C8   C9   106.29  3.000
 ZR4  H6   C7   O1   111.37  3.000
 ZR4  H6   C7   N3   106.18  3.000
 ZR4  O1   C7   N3   109.73  3.000
 ZR4  H6   C7   C10  109.90  3.000
 ZR4  O1   C7   C10  105.75  3.000
 ZR4  N3   C7   C10  114.00  3.000
 ZR4  H10  C11  O2   110.79  3.000
 ZR4  H10  C11  C8   106.64  3.000
 ZR4  O2   C11  C8   108.92  3.000
 ZR4  H10  C11  C12  107.55  3.000
 ZR4  O2   C11  C12  112.76  3.000
 ZR4  C8   C11  C12  110.00  3.000
 ZR4  C2   N1   C3   112.69  3.000
 ZR4  C4   N2   C3   118.56  3.000
 ZR4  C7   N3   C2   125.24  3.000
 ZR4  C7   N3   C6   126.20  3.000
 ZR4  C2   N3   C6   108.55  3.000
 ZR4  C7   O1   C8   110.86  3.000
 ZR4  H15  O3   C9   108.35  3.000
 ZR4  H16  O4   C10  108.77  3.000
 ZR4  H14  O2   C11  109.13  3.000
 ZR4  H4   N4   H5   117.09  3.000
 ZR4  H4   N4   C4   120.93  3.000
 ZR4  H5   N4   C4   119.09  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
 ZR4  CONST_01  C14  C13  C12  C17    0.00  0.0  0
 ZR4  CONST_02  C14  C15  C16  C17    0.00  0.0  0
 ZR4  CONST_03  C13  C14  C15  C16    0.00  0.0  0
 ZR4  CONST_04  C13  C12  C17  C16    0.00  0.0  0
 ZR4  CONST_05  N1   C2   C1   C5   180.00  0.0  0
 ZR4  CONST_06  N3   C2   C1   C5     0.00  0.0  0
 ZR4  CONST_07  N2   C4   C1   C5   180.00  0.0  0
 ZR4  CONST_08  C2   N3   C6   C5     0.00  0.0  0
 ZR4  CONST_09  N1   C2   N3   C6   180.00  0.0  0
 ZR4  CONST_10  C1   C2   N3   C6     0.00  0.0  0
 ZR4  CONST_11  C2   C1   C5   C6     0.00  0.0  0
 ZR4  CONST_12  C4   C1   C5   C6   180.00  0.0  0
 ZR4  CONST_13  N3   C2   N1   C3   180.00  0.0  0
 ZR4  CONST_14  C1   C2   N1   C3     0.00  0.0  0
 ZR4  CONST_15  C1   C4   N2   C3     0.00  0.0  0
 ZR4  CONST_16  N3   C6   C5   C1     0.00  0.0  0
 ZR4  CONST_17  C15  C14  C13  C12    0.00  0.0  0
 ZR4  CONST_18  C15  C16  C17  C12    0.00  0.0  0
 ZR4  CONST_19  N2   C3   N1   C2     0.00  0.0  0
 ZR4  CONST_20  N2   C4   C1   C2     0.00  0.0  0
 ZR4  CONST_21  N1   C3   N2   C4     0.00  0.0  0
 ZR4  CONST_22  N1   C2   C1   C4     0.00  0.0  0
 ZR4  CONST_23  N3   C2   C1   C4   180.00  0.0  0
 ZR4  CONST_24  C7   N3   C6   C5   180.00  0.0  0
 ZR4  CONST_25  C7   N3   C2   C1   180.00  0.0  0
 ZR4  CONST_26  N1   C2   N3   C7     0.00  0.0  0
 ZR4  CONST_27  CL1  C15  C16  C17  180.00  0.0  0
 ZR4  CONST_28  F1   C14  C15  C16  180.00  0.0  0
 ZR4  CONST_29  C11  C12  C17  C16  180.00  0.0  0
 ZR4  CONST_30  N4   C4   C1   C5     0.00  0.0  0
 ZR4  CONST_31  CL1  C15  C14  C13  180.00  0.0  0
 ZR4  CONST_32  N4   C4   N2   C3   180.00  0.0  0
 ZR4  CONST_33  F1   C14  C13  C12  180.00  0.0  0
 ZR4  CONST_34  C11  C12  C13  C14  180.00  0.0  0
 ZR4  CONST_35  N4   C4   C1   C2   180.00  0.0  0
 ZR4  CONST_36  H11  C13  C12  C17  180.00  0.0  0
 ZR4  CONST_37  H13  C17  C12  C13  180.00  0.0  0
 ZR4  CONST_38  H3   C6   C5   C1   180.00  0.0  0
 ZR4  CONST_39  H12  C16  C17  C12  180.00  0.0  0
 ZR4  CONST_40  H12  C16  C15  C14  180.00  0.0  0
 ZR4  CONST_41  H11  C13  C14  C15  180.00  0.0  0
 ZR4  CONST_42  H13  C17  C16  C15  180.00  0.0  0
 ZR4  CONST_43  H1   C3   N1   C2   180.00  0.0  0
 ZR4  CONST_44  H3   C6   N3   C2   180.00  0.0  0
 ZR4  CONST_45  H2   C5   C1   C2   180.00  0.0  0
 ZR4  CONST_46  H1   C3   N2   C4   180.00  0.0  0
 ZR4  CONST_47  H2   C5   C1   C4     0.00  0.0  0
 ZR4  CONST_48  H3   C6   N3   C7     0.00  0.0  0
 ZR4  CONST_49  H2   C5   C6   N3   180.00  0.0  0
 ZR4  CONST_50  H5   N4   C4   C1   180.00  0.0  0
 ZR4  CONST_51  H4   N4   C4   C1     0.00  0.0  0
 ZR4  CONST_52  H5   N4   C4   N2     0.00  0.0  0
 ZR4  CONST_53  H4   N4   C4   N2   180.00  0.0  0

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
 ZR4  chir_01  C9   O3  C10  C8   negativ
 ZR4  chir_02  C10  O4  C7   C9   negativ
 ZR4  chir_03  C8   O1  C9   C11  negativ
 ZR4  chir_04  C7   O1  N3   C10  negativ
 ZR4  chir_05  C11  O2  C8   C12  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
 ZR4  plan-1  C17  0.020
 ZR4  plan-1  C16  0.020
 ZR4  plan-1  C13  0.020
 ZR4  plan-1  C12  0.020
 ZR4  plan-1  C14  0.020
 ZR4  plan-1  C15  0.020
 ZR4  plan-1  C11  0.020
 ZR4  plan-1  F1   0.020
 ZR4  plan-1  CL1  0.020
 ZR4  plan-1  H13  0.020
 ZR4  plan-1  H12  0.020
 ZR4  plan-1  H11  0.020
 ZR4  plan-2  C5   0.020
 ZR4  plan-2  C6   0.020
 ZR4  plan-2  C3   0.020
 ZR4  plan-2  C1   0.020
 ZR4  plan-2  C2   0.020
 ZR4  plan-2  C4   0.020
 ZR4  plan-2  C7   0.020
 ZR4  plan-2  N1   0.020
 ZR4  plan-2  N2   0.020
 ZR4  plan-2  N3   0.020
 ZR4  plan-2  H2   0.020
 ZR4  plan-2  H3   0.020
 ZR4  plan-2  H1   0.020
 ZR4  plan-2  N4   0.020
 ZR4  plan-3  C4   0.020
 ZR4  plan-3  H5   0.020
 ZR4  plan-3  H4   0.020
 ZR4  plan-3  N4   0.020

