# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:56:47 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 6-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-2-(2-methoxyethyl)-3~{H}-isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN1Cc2ccc(cc2C1=O)c3nc(NC4CCOCC4)ncc3Cl
#
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
 EQZ  EQZ  6-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-2-(2-methoxyethyl)-3~{H}-isoindol-1-one  ligand  51  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EQZ
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
 EQZ  C1   C   CH3   0  -0.393   7.3316  -1.1332   2.3528
 EQZ  C3   C   CH2   0  -0.144   6.9599  -1.3670   0.0590
 EQZ  C6   C   CH2   0  -0.277   4.6546   0.4107  -1.3068
 EQZ  C7   C   CR56  0   0.085   3.2575   0.8133  -0.9606
 EQZ  C8   C   CR16  0  -0.306   2.5894   2.0087  -1.1549
 EQZ  C10  C   CR6   0   0.049   0.6273   1.0216  -0.1116
 EQZ  C11  C   CR16  0  -0.332   1.3028  -0.1840   0.0580
 EQZ  C12  C   CR56  0  -0.055   2.6168  -0.2577  -0.3623
 EQZ  C13  C   CR5   0   0.553   3.5567  -1.3975  -0.2885
 EQZ  C15  C   CR6   0   0.321  -0.7878   1.1107   0.3072
 EQZ  C19  C   CR16  0  -0.062  -5.0328  -1.0272   0.0938
 EQZ  C21  C   C     0  -0.187  -7.3086  -0.4899  -0.7914
 EQZ  C23  C   C     0  -0.184  -6.9645  -2.6050   0.1449
 EQZ  C24  C   C     0  -0.472  -5.4506  -2.4918   0.0412
 EQZ  C26  C   CR16  0   0.032  -2.6609   2.1021   1.3752
 EQZ  C27  C   CR6   0  -0.203  -1.3106   2.1577   1.0695
 EQZ  O2   O   O2    0  -0.477   6.4332  -1.5267   1.3475
 EQZ  C4   C   CH2   0  -0.338   5.9064  -1.7557  -0.9608
 EQZ  N5   N   NR5   0  -0.500   4.7056  -0.9667  -0.8618
 EQZ  C9   C   CR16  0  -0.266   1.2746   2.1029  -0.7194
 EQZ  N16  N   N     0  -0.476  -1.5662   0.1075  -0.0618
 EQZ  C17  C   CR6   0   0.601  -2.8571   0.1326   0.2910
 EQZ  C20  C   C     0  -0.457  -5.8173  -0.2385  -0.9551
 EQZ  O22  O   O     0  -0.483  -7.6217  -1.8643  -0.8591
 EQZ  N25  N   N     0  -0.454  -3.4420   1.1147   0.9871
 EQZ  CL1  CL  CL    0  -0.117  -0.3545   3.4566   1.6849
 EQZ  H31  H   HCH3  0   0.233   6.8350  -1.2564   3.3147
 EQZ  H30  H   HCH3  0   0.204   8.2437  -1.7421   2.3545
 EQZ  H29  H   HCH3  0   0.204   7.6298  -0.0827   2.2499
 EQZ  H32  H   HCH2  0   0.203   7.2871  -0.3296  -0.1051
 EQZ  H33  H   HCH2  0   0.215   7.8434  -2.0019  -0.0994
 EQZ  H36  H   HCH2  0   0.277   4.8533   0.4864  -2.3799
 EQZ  H37  H   HCH2  0   0.275   5.3936   1.0315  -0.7919
 EQZ  H38  H   HCR6  0   0.266   3.0659   2.8532  -1.6352
 EQZ  H40  H   HCR6  0   0.262   0.8126  -1.0344   0.5148
 EQZ  H41  H   HNH1  0   0.392  -3.1448  -1.5929  -0.6785
 EQZ  H42  H   HCR6  0   0.245  -5.2821  -0.6323   1.0830
 EQZ  H45  H   H     0   0.199  -7.6485  -0.0680   0.1664
 EQZ  H46  H   H     0   0.239  -7.8710   0.0056  -1.5841
 EQZ  H48  H   H     0   0.241  -7.2773  -3.6443   0.0336
 EQZ  H47  H   H     0   0.200  -7.2883  -2.2686   1.1412
 EQZ  H49  H   H     0   0.232  -5.1141  -2.9413  -0.8994
 EQZ  H50  H   H     0   0.251  -4.9889  -3.0522   0.8576
 EQZ  H51  H   HCR6  0   0.289  -3.1187   2.8926   1.9605
 EQZ  H34  H   HCH2  0   0.262   6.3304  -1.6454  -1.9615
 EQZ  H35  H   HCH2  0   0.263   5.6362  -2.8048  -0.8392
 EQZ  H39  H   HCR6  0   0.268   0.7385   3.0281  -0.8819
 EQZ  H43  H   H     0   0.244  -5.6175   0.8309  -0.8574
 EQZ  H44  H   H     0   0.227  -5.4945  -0.5449  -1.9548
 EQZ  O14  O   O     0  -0.482   3.3392  -2.5042   0.1751
 EQZ  N18  N   NH1   0  -0.667  -3.6008  -0.9215  -0.0807

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
 EQZ  O22  C23  single    1.410  0.020  1.410
 EQZ  O22  C21  single    1.411  0.020  1.411
 EQZ  C23  C24  single    1.522  0.020  1.522
 EQZ  C24  C19  single    1.524  0.020  1.524
 EQZ  C21  C20  single    1.521  0.020  1.521
 EQZ  C20  C19  single    1.529  0.020  1.529
 EQZ  C19  N18  single    1.446  0.020  1.446
 EQZ  N18  C17  single    1.342  0.020  1.342
 EQZ  C17  N16  aromatic  1.338  0.020  1.338
 EQZ  C17  N25  aromatic  1.338  0.020  1.338
 EQZ  N16  C15  aromatic  1.322  0.020  1.322
 EQZ  C9   C8   aromatic  1.388  0.020  1.388
 EQZ  C9   C10  aromatic  1.399  0.020  1.399
 EQZ  C8   C7   aromatic  1.383  0.020  1.383
 EQZ  N25  C26  aromatic  1.317  0.020  1.317
 EQZ  C7   C6   single    1.495  0.020  1.495
 EQZ  C7   C12  aromatic  1.384  0.020  1.384
 EQZ  C15  C10  single    1.478  0.020  1.478
 EQZ  C15  C27  aromatic  1.397  0.020  1.397
 EQZ  C10  C11  aromatic  1.392  0.020  1.392
 EQZ  C6   N5   single    1.448  0.020  1.448
 EQZ  C12  C11  aromatic  1.381  0.020  1.381
 EQZ  C12  C13  single    1.479  0.020  1.479
 EQZ  N5   C13  single    1.354  0.020  1.354
 EQZ  N5   C4   single    1.440  0.020  1.440
 EQZ  C26  C27  aromatic  1.386  0.020  1.386
 EQZ  C27  CL1  single    1.726  0.020  1.726
 EQZ  C13  O14  double    1.219  0.020  1.219
 EQZ  C4   C3   single    1.517  0.020  1.517
 EQZ  C3   O2   single    1.401  0.020  1.401
 EQZ  O2   C1   single    1.405  0.020  1.405
 EQZ  C1   H31  single    0.970  0.020  1.090
 EQZ  C1   H30  single    0.970  0.020  1.090
 EQZ  C1   H29  single    0.970  0.020  1.090
 EQZ  C3   H32  single    0.970  0.020  1.090
 EQZ  C3   H33  single    0.970  0.020  1.090
 EQZ  C6   H36  single    0.970  0.020  1.090
 EQZ  C6   H37  single    0.970  0.020  1.090
 EQZ  C8   H38  single    0.930  0.020  1.080
 EQZ  C11  H40  single    0.930  0.020  1.080
 EQZ  N18  H41  single    0.860  0.020  1.020
 EQZ  C19  H42  single    0.970  0.020  1.090
 EQZ  C21  H45  single    0.970  0.020  1.090
 EQZ  C21  H46  single    0.970  0.020  1.090
 EQZ  C23  H48  single    0.970  0.020  1.090
 EQZ  C23  H47  single    0.970  0.020  1.090
 EQZ  C24  H49  single    0.970  0.020  1.090
 EQZ  C24  H50  single    0.970  0.020  1.090
 EQZ  C26  H51  single    0.930  0.020  1.080
 EQZ  C4   H34  single    0.970  0.020  1.090
 EQZ  C4   H35  single    0.970  0.020  1.090
 EQZ  C9   H39  single    0.930  0.020  1.080
 EQZ  C20  H43  single    0.970  0.020  1.090
 EQZ  C20  H44  single    0.970  0.020  1.090

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
 EQZ  H29  C1   H30  107.81  3.000
 EQZ  H29  C1   H31  108.36  3.000
 EQZ  H30  C1   H31  108.35  3.000
 EQZ  H29  C1   O2   112.03  3.000
 EQZ  H30  C1   O2   112.18  3.000
 EQZ  H31  C1   O2   107.98  3.000
 EQZ  H33  C3   H32  106.50  3.000
 EQZ  H33  C3   C4   108.26  3.000
 EQZ  H32  C3   C4   110.36  3.000
 EQZ  H33  C3   O2   111.64  3.000
 EQZ  H32  C3   O2   110.89  3.000
 EQZ  C4   C3   O2   109.14  3.000
 EQZ  H37  C6   H36  107.44  3.000
 EQZ  H37  C6   N5   111.80  3.000
 EQZ  H36  C6   N5   111.15  3.000
 EQZ  H37  C6   C7   111.69  3.000
 EQZ  H36  C6   C7   112.23  3.000
 EQZ  N5   C6   C7   102.59  3.000
 EQZ  C12  C7   C8   120.40  3.000
 EQZ  C12  C7   C6   108.93  3.000
 EQZ  C8   C7   C6   130.67  3.000
 EQZ  H38  C8   C9   120.22  3.000
 EQZ  H38  C8   C7   121.62  3.000
 EQZ  C9   C8   C7   118.17  3.000
 EQZ  C9   C10  C15  121.29  3.000
 EQZ  C15  C10  C11  118.82  3.000
 EQZ  C9   C10  C11  119.84  3.000
 EQZ  H40  C11  C12  121.14  3.000
 EQZ  H40  C11  C10  120.78  3.000
 EQZ  C12  C11  C10  118.07  3.000
 EQZ  C13  C12  C11  129.07  3.000
 EQZ  C13  C12  C7   108.89  3.000
 EQZ  C11  C12  C7   122.04  3.000
 EQZ  O14  C13  N5   126.93  3.000
 EQZ  O14  C13  C12  127.23  3.000
 EQZ  N5   C13  C12  105.83  3.000
 EQZ  N16  C15  C27  120.05  3.000
 EQZ  C27  C15  C10  123.92  3.000
 EQZ  N16  C15  C10  116.02  3.000
 EQZ  H42  C19  C20  108.49  3.000
 EQZ  H42  C19  C24  108.40  3.000
 EQZ  C20  C19  C24  109.35  3.000
 EQZ  H42  C19  N18  107.96  3.000
 EQZ  C20  C19  N18  112.80  3.000
 EQZ  C24  C19  N18  109.73  3.000
 EQZ  H46  C21  H45  107.40  3.000
 EQZ  H46  C21  O22  107.04  3.000
 EQZ  H45  C21  O22  110.28  3.000
 EQZ  H46  C21  C20  110.62  3.000
 EQZ  H45  C21  C20  109.46  3.000
 EQZ  O22  C21  C20  111.92  3.000
 EQZ  H47  C23  H48  107.41  3.000
 EQZ  H47  C23  O22  110.30  3.000
 EQZ  H48  C23  O22  107.11  3.000
 EQZ  H47  C23  C24  109.37  3.000
 EQZ  H48  C23  C24  110.43  3.000
 EQZ  O22  C23  C24  112.09  3.000
 EQZ  H50  C24  H49  107.54  3.000
 EQZ  H50  C24  C23  109.35  3.000
 EQZ  H49  C24  C23  109.49  3.000
 EQZ  H50  C24  C19  110.56  3.000
 EQZ  H49  C24  C19  109.86  3.000
 EQZ  C23  C24  C19  109.99  3.000
 EQZ  H51  C26  N25  117.06  3.000
 EQZ  H51  C26  C27  120.06  3.000
 EQZ  N25  C26  C27  122.88  3.000
 EQZ  CL1  C27  C26  119.42  3.000
 EQZ  CL1  C27  C15  123.46  3.000
 EQZ  C26  C27  C15  117.07  3.000
 EQZ  C3   O2   C1   112.69  3.000
 EQZ  H35  C4   H34  107.19  3.000
 EQZ  H35  C4   N5   108.23  3.000
 EQZ  H34  C4   N5   109.34  3.000
 EQZ  H35  C4   C3   110.11  3.000
 EQZ  H34  C4   C3   108.69  3.000
 EQZ  N5   C4   C3   113.11  3.000
 EQZ  C4   N5   C13  124.20  3.000
 EQZ  C4   N5   C6   121.95  3.000
 EQZ  C13  N5   C6   113.75  3.000
 EQZ  H39  C9   C10  119.80  3.000
 EQZ  H39  C9   C8   118.71  3.000
 EQZ  C10  C9   C8   121.47  3.000
 EQZ  C17  N16  C15  118.68  3.000
 EQZ  N25  C17  N16  124.91  3.000
 EQZ  N25  C17  N18  118.56  3.000
 EQZ  N16  C17  N18  116.53  3.000
 EQZ  H44  C20  H43  107.57  3.000
 EQZ  H44  C20  C21  109.95  3.000
 EQZ  H43  C20  C21  109.36  3.000
 EQZ  H44  C20  C19  109.33  3.000
 EQZ  H43  C20  C19  110.48  3.000
 EQZ  C21  C20  C19  110.12  3.000
 EQZ  C23  O22  C21  111.96  3.000
 EQZ  C17  N25  C26  116.36  3.000
 EQZ  H41  N18  C17  115.89  3.000
 EQZ  H41  N18  C19  118.08  3.000
 EQZ  C17  N18  C19  124.92  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
 EQZ  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 EQZ  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 EQZ  CONST_03  C15  C10  C9   C8    180.00   0.0  0
 EQZ  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 EQZ  CONST_05  C11  C12  C7   C8      0.00   0.0  0
 EQZ  CONST_06  C17  N16  C15  C10   180.00   0.0  0
 EQZ  CONST_07  C26  C27  C15  C10   180.00   0.0  0
 EQZ  CONST_10  C9   C8   C7   C12     0.00   0.0  0
 EQZ  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 EQZ  CONST_12  C15  C10  C11  C12   180.00   0.0  0
 EQZ  CONST_13  N25  C17  N16  C15     0.00   0.0  0
 EQZ  CONST_14  N25  C26  C27  C15     0.00   0.0  0
 EQZ  CONST_15  N16  C17  N25  C26     0.00   0.0  0
 EQZ  CONST_16  N16  C15  C27  C26     0.00   0.0  0
 EQZ  CONST_17  C17  N16  C15  C27     0.00   0.0  0
 EQZ  CONST_19  C17  N25  C26  C27     0.00   0.0  0
 EQZ  CONST_21  C12  C13  N5   C6      0.00   0.0  0
 EQZ  CONST_22  CL1  C27  C15  C10     0.00   0.0  0
 EQZ  CONST_23  N18  C17  N16  C15   180.00   0.0  0
 EQZ  CONST_24  C26  N25  C17  N18   180.00   0.0  0
 EQZ  CONST_25  CL1  C27  C15  N16   180.00   0.0  0
 EQZ  CONST_26  CL1  C27  C26  N25   180.00   0.0  0
 EQZ  CONST_27  N16  C17  N18  C19   180.00   0.0  0
 EQZ  CONST_28  N25  C17  N18  C19     0.00   0.0  0
 EQZ  CONST_29  O14  C13  N5   C6    180.00   0.0  0
 EQZ  CONST_30  C4   N5   C13  C12   180.00   0.0  0
 EQZ  CONST_31  H38  C8   C7   C6      0.00   0.0  0
 EQZ  CONST_32  H39  C9   C8   C7    180.00   0.0  0
 EQZ  CONST_33  H40  C11  C12  C7    180.00   0.0  0
 EQZ  CONST_34  H51  C26  C27  C15   180.00   0.0  0
 EQZ  CONST_35  O14  C13  N5   C4      0.00   0.0  0
 EQZ  CONST_36  H41  N18  C17  N16     0.00   0.0  0
 EQZ  Var_01    O22  C23  C24  C19    56.47  30.0  1
 EQZ  Var_02    O22  C21  C20  C19   -56.25  30.0  1
 EQZ  Var_03    C24  C23  O22  C21   -59.93  30.0  1
 EQZ  Var_04    C20  C21  O22  C23    59.78  30.0  1
 EQZ  Var_05    H36  C6   C7   C8    -59.49  30.0  1
 EQZ  Var_06    C6   N5   C4   C3     73.59  30.0  1
 EQZ  Var_07    N5   C4   C3   O2     59.36  30.0  1
 EQZ  Var_08    C4   C3   O2   C1   -177.52  30.0  1
 EQZ  Var_09    H31  C1   O2   C3    178.10  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
 EQZ  chir_01  C19  C24  C20  N18  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
 EQZ  plan-1  C10  0.020
 EQZ  plan-1  C15  0.020
 EQZ  plan-1  C26  0.020
 EQZ  plan-1  C27  0.020
 EQZ  plan-1  N16  0.020
 EQZ  plan-1  C17  0.020
 EQZ  plan-1  N25  0.020
 EQZ  plan-1  CL1  0.020
 EQZ  plan-1  H51  0.020
 EQZ  plan-1  N18  0.020
 EQZ  plan-2  C19  0.020
 EQZ  plan-2  C17  0.020
 EQZ  plan-2  H41  0.020
 EQZ  plan-2  N18  0.020
 EQZ  plan-3  C6   0.020
 EQZ  plan-3  C7   0.020
 EQZ  plan-3  C8   0.020
 EQZ  plan-3  C10  0.020
 EQZ  plan-3  C11  0.020
 EQZ  plan-3  C12  0.020
 EQZ  plan-3  C13  0.020
 EQZ  plan-3  C15  0.020
 EQZ  plan-3  C4   0.020
 EQZ  plan-3  N5   0.020
 EQZ  plan-3  C9   0.020
 EQZ  plan-3  H38  0.020
 EQZ  plan-3  H40  0.020
 EQZ  plan-3  H39  0.020
 EQZ  plan-3  O14  0.020

