# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:18:26 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: [2,4-dihydroxy-5-(propan-2-yl)phenyl]{5-[(4-methylpiperazin-1-yl)methyl]-1,3-dihydro-2H-isoindol-2-yl}methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1cc(c(O)cc1O)C(=O)N2Cc3ccc(CN4CCN(C)CC4)cc3C2
#
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
 XJX  XJX  '[2,4-dihydroxy-5-(propan-2-yl)phenyl]{5-[(4-methylpiperazin-1-yl)methyl]-1,3-dihydro-2H-isoindol-2-yl}methanone'  ligand  61  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XJX
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
 XJX  C1    C  CH3   0  -0.653  -4.7976   3.0875  -0.5993
 XJX  C2    C  CH1   0  -0.341  -5.7895   1.9452  -0.3946
 XJX  C3    C  CH3   0  -0.630  -6.4747   1.5670  -1.7099
 XJX  C4    C  CR6   0   0.025  -5.1627   0.7211   0.2407
 XJX  C5    C  CR16  0  -0.315  -3.8950   0.3054  -0.1227
 XJX  C6    C  CR6   0  -0.184  -3.2837  -0.8496   0.3652
 XJX  C7    C  C     0   0.591  -1.9360  -1.3062  -0.0369
 XJX  O8    O  O     0  -0.546  -1.6881  -2.5239  -0.0418
 XJX  N9    N  NR5   0  -0.509  -0.9768  -0.4283  -0.3690
 XJX  C10   C  CH2   0  -0.311  -0.9822   1.0166  -0.1290
 XJX  C11   C  CR56  0   0.047   0.4745   1.3563  -0.1412
 XJX  C12   C  CR16  0  -0.301   1.0877   2.5631   0.1466
 XJX  C13   C  CR16  0  -0.313   2.4698   2.6487   0.0355
 XJX  C14   C  CR6   0   0.077   3.2357   1.5579  -0.3747
 XJX  C15   C  CH2   0  -0.309   4.7249   1.7119  -0.5548
 XJX  N16   N  NT    0  -0.420   5.4653   0.5108  -0.2450
 XJX  C18   C  CH2   0  -0.283   6.8318   0.5789  -0.7251
 XJX  C19   C  CH2   0  -0.283   7.5538  -0.7283  -0.4626
 XJX  N20   N  NT    0  -0.412   7.5335  -1.0480   0.9499
 XJX  C22   C  CH3   0  -0.517   8.2647  -2.2592   1.2377
 XJX  C23   C  CH2   0  -0.281   6.1681  -1.1137   1.4299
 XJX  C24   C  CH2   0  -0.284   5.4447   0.1931   1.1700
 XJX  C25   C  CR16  0  -0.353   2.6025   0.3494  -0.6573
 XJX  C26   C  CR56  0   0.071   1.2272   0.2621  -0.5298
 XJX  C27   C  CH2   0  -0.285   0.3484  -0.9278  -0.7461
 XJX  C28   C  CR6   0   0.348  -4.0370  -1.6748   1.2265
 XJX  O29   O  OH1   0  -0.636  -3.5811  -2.8444   1.6831
 XJX  C30   C  CR16  0  -0.437  -5.2988  -1.2660   1.6361
 XJX  C31   C  CR6   0   0.326  -5.8594  -0.0910   1.1523
 XJX  O32   O  OH1   0  -0.618  -7.0987   0.1922   1.5874
 XJX  H11C  H  HCH3  0   0.241  -5.3202   3.9724  -0.9634
 XJX  H12C  H  HCH3  0   0.238  -4.2980   3.3538   0.3325
 XJX  H13C  H  HCH3  0   0.222  -4.0323   2.8453  -1.3389
 XJX  H2    H  HCH1  0   0.228  -6.5583   2.3494   0.2748
 XJX  H31C  H  HCH3  0   0.225  -5.7437   1.1799  -2.4225
 XJX  H32C  H  HCH3  0   0.232  -7.2317   0.7961  -1.5606
 XJX  H33C  H  HCH3  0   0.232  -6.9617   2.4322  -2.1621
 XJX  H5    H  HCR6  0   0.252  -3.3709   0.9017  -0.8546
 XJX  H10A  H  HCH2  0   0.266  -1.4964   1.5645  -0.9235
 XJX  H27A  H  HCH2  0   0.268   0.6420  -1.7726  -0.1206
 XJX  H10B  H  HCH2  0   0.279  -1.4744   1.2590   0.8152
 XJX  H27B  H  HCH2  0   0.265   0.3579  -1.2729  -1.7843
 XJX  H12   H  HCR6  0   0.251   0.5117   3.4245   0.4611
 XJX  H13   H  HCR6  0   0.250   2.9648   3.5825   0.2749
 XJX  H151  H  HCH2  0   0.255   4.9183   1.9621  -1.6034
 XJX  H152  H  HCH2  0   0.211   5.0735   2.5810   0.0290
 XJX  H25   H  HCR6  0   0.245   3.1904  -0.5095  -0.9584
 XJX  H181  H  HCH2  0   0.237   6.8245   0.7750  -1.8002
 XJX  H182  H  HCH2  0   0.190   7.3922   1.4024  -0.2496
 XJX  H241  H  HCH2  0   0.195   5.9084   0.9960   1.7695
 XJX  H242  H  HCH2  0   0.240   4.4104   0.0969   1.5058
 XJX  H191  H  HCH2  0   0.188   7.0907  -1.5270  -1.0690
 XJX  H192  H  HCH2  0   0.234   8.5912  -0.6347  -0.7934
 XJX  H221  H  HCH3  0   0.232   9.3018  -2.1570   0.9139
 XJX  H222  H  HCH3  0   0.232   8.2672  -2.4477   2.3126
 XJX  H223  H  HCH3  0   0.190   7.8455  -3.1500   0.7438
 XJX  H231  H  HCH2  0   0.188   5.6061  -1.9360   0.9522
 XJX  H232  H  HCH2  0   0.234   6.1757  -1.3133   2.5044
 XJX  H29   H  HOH1  0   0.473  -2.7828  -3.0651   1.1525
 XJX  H30   H  HCR6  0   0.271  -5.8659  -1.8892   2.3172
 XJX  H32   H  HOH1  0   0.476  -7.4133   1.0313   1.2336

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
 XJX  C1   C2    single    1.527  0.020  1.527
 XJX  C2   C3    single    1.531  0.020  1.531
 XJX  C2   C4    single    1.515  0.020  1.515
 XJX  C4   C5    aromatic  1.383  0.020  1.383
 XJX  C4   C31   aromatic  1.406  0.020  1.406
 XJX  C5   C6    aromatic  1.395  0.020  1.395
 XJX  C6   C7    single    1.479  0.020  1.479
 XJX  C6   C28   aromatic  1.411  0.020  1.411
 XJX  C7   O8    double    1.243  0.020  1.243
 XJX  C7   N9    single    1.342  0.020  1.342
 XJX  N9   C10   single    1.465  0.020  1.465
 XJX  N9   C27   single    1.466  0.020  1.466
 XJX  C10  C11   single    1.496  0.020  1.496
 XJX  C11  C12   aromatic  1.384  0.020  1.384
 XJX  C11  C26   aromatic  1.384  0.020  1.384
 XJX  C12  C13   aromatic  1.389  0.020  1.389
 XJX  C13  C14   aromatic  1.395  0.020  1.395
 XJX  C14  C15   single    1.508  0.020  1.508
 XJX  C14  C25   aromatic  1.393  0.020  1.393
 XJX  C15  N16   single    1.445  0.020  1.445
 XJX  N16  C18   single    1.450  0.020  1.450
 XJX  N16  C24   single    1.450  0.020  1.450
 XJX  C18  C19   single    1.516  0.020  1.516
 XJX  C19  N20   single    1.448  0.020  1.448
 XJX  N20  C22   single    1.444  0.020  1.444
 XJX  N20  C23   single    1.449  0.020  1.449
 XJX  C23  C24   single    1.516  0.020  1.516
 XJX  C25  C26   aromatic  1.384  0.020  1.384
 XJX  C26  C27   single    1.495  0.020  1.495
 XJX  C28  O29   single    1.336  0.020  1.336
 XJX  C28  C30   aromatic  1.388  0.020  1.388
 XJX  C30  C31   aromatic  1.389  0.020  1.389
 XJX  C31  O32   single    1.344  0.020  1.344
 XJX  C1   H11C  single    0.970  0.020  1.090
 XJX  C1   H12C  single    0.970  0.020  1.090
 XJX  C1   H13C  single    0.970  0.020  1.090
 XJX  C2   H2    single    0.970  0.020  1.090
 XJX  C3   H31C  single    0.970  0.020  1.090
 XJX  C3   H32C  single    0.970  0.020  1.090
 XJX  C3   H33C  single    0.970  0.020  1.090
 XJX  C5   H5    single    0.930  0.020  1.080
 XJX  C10  H10A  single    0.970  0.020  1.090
 XJX  C10  H10B  single    0.970  0.020  1.090
 XJX  C27  H27A  single    0.970  0.020  1.090
 XJX  C27  H27B  single    0.970  0.020  1.090
 XJX  C12  H12   single    0.930  0.020  1.080
 XJX  C13  H13   single    0.930  0.020  1.080
 XJX  C15  H151  single    0.970  0.020  1.090
 XJX  C15  H152  single    0.970  0.020  1.090
 XJX  C25  H25   single    0.930  0.020  1.080
 XJX  C18  H181  single    0.970  0.020  1.090
 XJX  C18  H182  single    0.970  0.020  1.090
 XJX  C24  H241  single    0.970  0.020  1.090
 XJX  C24  H242  single    0.970  0.020  1.090
 XJX  C19  H191  single    0.970  0.020  1.090
 XJX  C19  H192  single    0.970  0.020  1.090
 XJX  C22  H221  single    0.970  0.020  1.090
 XJX  C22  H222  single    0.970  0.020  1.090
 XJX  C22  H223  single    0.970  0.020  1.090
 XJX  C23  H231  single    0.970  0.020  1.090
 XJX  C23  H232  single    0.970  0.020  1.090
 XJX  O29  H29   single    0.850  0.020  0.980
 XJX  C30  H30   single    0.930  0.020  1.080
 XJX  O32  H32   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
 XJX  H13C  C1   H12C  108.18  3.000
 XJX  H13C  C1   H11C  106.85  3.000
 XJX  H12C  C1   H11C  107.86  3.000
 XJX  H13C  C1   C2    112.36  3.000
 XJX  H12C  C1   C2    111.46  3.000
 XJX  H11C  C1   C2    109.92  3.000
 XJX  H2    C2   C4    109.38  3.000
 XJX  H2    C2   C3    107.57  3.000
 XJX  C4    C2   C3    110.24  3.000
 XJX  H2    C2   C1    105.16  3.000
 XJX  C4    C2   C1    113.08  3.000
 XJX  C3    C2   C1    111.13  3.000
 XJX  H33C  C3   H32C  107.90  3.000
 XJX  H33C  C3   H31C  108.03  3.000
 XJX  H32C  C3   H31C  107.67  3.000
 XJX  H33C  C3   C2    111.10  3.000
 XJX  H32C  C3   C2    111.58  3.000
 XJX  H31C  C3   C2    110.42  3.000
 XJX  C31   C4   C5    116.82  3.000
 XJX  C31   C4   C2    122.26  3.000
 XJX  C5    C4   C2    120.80  3.000
 XJX  H5    C5   C6    118.79  3.000
 XJX  H5    C5   C4    117.20  3.000
 XJX  C6    C5   C4    123.97  3.000
 XJX  C28   C6   C7    118.17  3.000
 XJX  C28   C6   C5    117.64  3.000
 XJX  C7    C6   C5    124.06  3.000
 XJX  N9    C7   O8    119.83  3.000
 XJX  N9    C7   C6    121.11  3.000
 XJX  O8    C7   C6    119.05  3.000
 XJX  C27   N9   C10   112.44  3.000
 XJX  C27   N9   C7    119.15  3.000
 XJX  C10   N9   C7    127.02  3.000
 XJX  H10B  C10  H10A  107.76  3.000
 XJX  H10B  C10  C11   113.31  3.000
 XJX  H10A  C10  C11   109.77  3.000
 XJX  H10B  C10  N9    111.24  3.000
 XJX  H10A  C10  N9    112.14  3.000
 XJX  C11   C10  N9    102.66  3.000
 XJX  C26   C11  C12   120.46  3.000
 XJX  C26   C11  C10   110.64  3.000
 XJX  C12   C11  C10   128.89  3.000
 XJX  H12   C12  C13   120.23  3.000
 XJX  H12   C12  C11   121.22  3.000
 XJX  C13   C12  C11   118.55  3.000
 XJX  H13   C13  C14   119.22  3.000
 XJX  H13   C13  C12   119.33  3.000
 XJX  C14   C13  C12   121.45  3.000
 XJX  C25   C14  C15   120.87  3.000
 XJX  C25   C14  C13   119.24  3.000
 XJX  C15   C14  C13   119.85  3.000
 XJX  H152  C15  H151  105.71  3.000
 XJX  H152  C15  N16   112.30  3.000
 XJX  H151  C15  N16   107.74  3.000
 XJX  H152  C15  C14   109.22  3.000
 XJX  H151  C15  C14   108.19  3.000
 XJX  N16   C15  C14   113.31  3.000
 XJX  C24   N16  C18   110.29  3.000
 XJX  C24   N16  C15   112.58  3.000
 XJX  C18   N16  C15   111.90  3.000
 XJX  H182  C18  H181  107.06  3.000
 XJX  H182  C18  C19   109.08  3.000
 XJX  H181  C18  C19   109.16  3.000
 XJX  H182  C18  N16   111.77  3.000
 XJX  H181  C18  N16   109.14  3.000
 XJX  C19   C18  N16   110.54  3.000
 XJX  H192  C19  H191  107.08  3.000
 XJX  H192  C19  N20   109.11  3.000
 XJX  H191  C19  N20   111.71  3.000
 XJX  H192  C19  C18   109.01  3.000
 XJX  H191  C19  C18   109.19  3.000
 XJX  N20   C19  C18   110.64  3.000
 XJX  C23   N20  C22   111.92  3.000
 XJX  C23   N20  C19   110.26  3.000
 XJX  C22   N20  C19   111.87  3.000
 XJX  H223  C22  H222  107.62  3.000
 XJX  H223  C22  H221  107.72  3.000
 XJX  H222  C22  H221  107.84  3.000
 XJX  H223  C22  N20   113.35  3.000
 XJX  H222  C22  N20   110.02  3.000
 XJX  H221  C22  N20   110.10  3.000
 XJX  H232  C23  H231  107.02  3.000
 XJX  H232  C23  C24   109.22  3.000
 XJX  H231  C23  C24   108.95  3.000
 XJX  H232  C23  N20   109.11  3.000
 XJX  H231  C23  N20   111.71  3.000
 XJX  C24   C23  N20   110.72  3.000
 XJX  H242  C24  H241  107.16  3.000
 XJX  H242  C24  C23   108.87  3.000
 XJX  H241  C24  C23   109.47  3.000
 XJX  H242  C24  N16   109.44  3.000
 XJX  H241  C24  N16   111.38  3.000
 XJX  C23   C24  N16   110.44  3.000
 XJX  H25   C25  C26   120.98  3.000
 XJX  H25   C25  C14   119.82  3.000
 XJX  C26   C25  C14   119.19  3.000
 XJX  C27   C26  C25   128.39  3.000
 XJX  C27   C26  C11   110.51  3.000
 XJX  C25   C26  C11   121.10  3.000
 XJX  H27B  C27  H27A  107.30  3.000
 XJX  H27B  C27  C26   112.53  3.000
 XJX  H27A  C27  C26   112.03  3.000
 XJX  H27B  C27  N9    111.07  3.000
 XJX  H27A  C27  N9    111.07  3.000
 XJX  C26   C27  N9    102.89  3.000
 XJX  C30   C28  O29   117.85  3.000
 XJX  C30   C28  C6    119.55  3.000
 XJX  O29   C28  C6    122.59  3.000
 XJX  H29   O29  C28   106.80  3.000
 XJX  H30   C30  C31   119.62  3.000
 XJX  H30   C30  C28   119.47  3.000
 XJX  C31   C30  C28   120.88  3.000
 XJX  O32   C31  C30   115.96  3.000
 XJX  O32   C31  C4    123.05  3.000
 XJX  C30   C31  C4    120.97  3.000
 XJX  H32   O32  C31   111.46  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
 XJX  CONST_01  C28   C6   C5   C4      0.00   0.0  0
 XJX  CONST_02  C28   C30  C31  C4      0.00   0.0  0
 XJX  CONST_03  C30   C31  C4   C5      0.00   0.0  0
 XJX  CONST_04  C30   C28  C6   C5      0.00   0.0  0
 XJX  CONST_05  C31   C4   C5   C6      0.00   0.0  0
 XJX  CONST_06  C31   C30  C28  C6      0.00   0.0  0
 XJX  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 XJX  CONST_08  C14   C25  C26  C11     0.00   0.0  0
 XJX  CONST_09  C25   C26  C11  C12     0.00   0.0  0
 XJX  CONST_10  C25   C14  C13  C12     0.00   0.0  0
 XJX  CONST_11  C26   C11  C12  C13     0.00   0.0  0
 XJX  CONST_12  C26   C25  C14  C13     0.00   0.0  0
 XJX  CONST_13  C6    C5   C4   C2    180.00   0.0  0
 XJX  CONST_14  C30   C31  C4   C2    180.00   0.0  0
 XJX  CONST_15  C7    C6   C5   C4    180.00   0.0  0
 XJX  CONST_16  O32   C31  C4   C5    180.00   0.0  0
 XJX  CONST_17  O29   C28  C6   C5    180.00   0.0  0
 XJX  CONST_18  C30   C28  C6   C7    180.00   0.0  0
 XJX  CONST_19  C15   C14  C13  C12   180.00   0.0  0
 XJX  CONST_20  C26   C25  C14  C15   180.00   0.0  0
 XJX  CONST_21  O32   C31  C30  C28   180.00   0.0  0
 XJX  CONST_22  C31   C30  C28  O29   180.00   0.0  0
 XJX  CONST_23  C10   N9   C7   C6      0.00   0.0  0
 XJX  CONST_24  C27   N9   C7   C6    180.00   0.0  0
 XJX  CONST_25  H30   C30  C31  C4    180.00   0.0  0
 XJX  CONST_26  H12   C12  C11  C10     0.00   0.0  0
 XJX  CONST_27  H13   C13  C12  C11   180.00   0.0  0
 XJX  CONST_28  H25   C25  C26  C11   180.00   0.0  0
 XJX  CONST_29  H5    C5   C6   C28   180.00   0.0  0
 XJX  CONST_31  C27   N9   C7   O8      0.00   0.0  0
 XJX  Var_01    C12   C11  C10  N9   -173.88  30.0  1
 XJX  Var_02    C11   C26  C27  N9     -3.09  30.0  1
 XJX  Var_03    C26   C27  N9   C10     8.17  30.0  1
 XJX  Var_04    C27   N9   C10  C11    -9.71  30.0  1
 XJX  Var_05    N20   C19  C18  N16   -57.55  30.0  1
 XJX  Var_06    N20   C23  C24  N16    57.56  30.0  1
 XJX  Var_07    C23   C24  N16  C18   -57.40  30.0  1
 XJX  Var_08    C23   N20  C19  C18    57.29  30.0  1
 XJX  Var_09    C24   N16  C18  C19    57.44  30.0  1
 XJX  Var_10    C24   C23  N20  C19   -57.36  30.0  1
 XJX  Var_11    N9    C7   C6   C5     31.58  30.0  2
 XJX  Var_12    N16   C15  C14  C13   147.50  30.0  2
 XJX  Var_13    C18   N16  C15  C14   166.19  30.0  3
 XJX  Var_14    C5    C4   C2   C1    -39.84  30.0  2
 XJX  Var_15    H221  C22  N20  C19    58.80  30.0  3
 XJX  Var_16    H11C  C1   C2   C4   -174.30  30.0  3
 XJX  Var_17    H31C  C3   C2   C4    -62.18  30.0  3

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
 XJX  plan-1  C2   0.020
 XJX  plan-1  C4   0.020
 XJX  plan-1  C5   0.020
 XJX  plan-1  C6   0.020
 XJX  plan-1  C7   0.020
 XJX  plan-1  C28  0.020
 XJX  plan-1  O29  0.020
 XJX  plan-1  C30  0.020
 XJX  plan-1  C31  0.020
 XJX  plan-1  O32  0.020
 XJX  plan-1  H5   0.020
 XJX  plan-1  H30  0.020
 XJX  plan-2  C10  0.020
 XJX  plan-2  C11  0.020
 XJX  plan-2  C12  0.020
 XJX  plan-2  C13  0.020
 XJX  plan-2  C14  0.020
 XJX  plan-2  C15  0.020
 XJX  plan-2  C25  0.020
 XJX  plan-2  C26  0.020
 XJX  plan-2  C27  0.020
 XJX  plan-2  H12  0.020
 XJX  plan-2  H13  0.020
 XJX  plan-2  H25  0.020
 XJX  plan-3  C6   0.020
 XJX  plan-3  C7   0.020
 XJX  plan-3  O8   0.020
 XJX  plan-3  N9   0.020
 XJX  plan-3  C10  0.020
 XJX  plan-3  C27  0.020

