# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 22:05:28 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 2-(diphenylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)CCCCCCNC(=O)c1cnc(nc1)N(c2ccccc2)c3ccccc3
#
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
 AH4  AH4  2-(diphenylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]pyrimidine-5-carboxamide  ligand  59  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AH4
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
 AH4  N11  N  NH1   0  -0.377  -11.0188   1.0364  -0.6760
 AH4  C21  C  CR6   0   0.302    5.0017   1.6368   0.0197
 AH4  C31  C  CR16  0  -0.261    7.0735  -2.3482  -1.2205
 AH4  C22  C  CR16  0  -0.276    5.7789   2.2047  -0.9825
 AH4  C32  C  CR16  0  -0.264    5.9742  -1.5049  -1.1681
 AH4  C02  C  C     0   0.543   -0.4660  -1.6923  -0.0882
 AH4  C04  C  CH2   0  -0.238   -2.8590  -1.3188   0.1991
 AH4  C05  C  CH2   0  -0.465   -3.8420  -0.1611   0.1769
 AH4  C06  C  CH2   0  -0.418   -5.2785  -0.6685   0.1965
 AH4  C07  C  CH2   0  -0.416   -6.3184   0.4427   0.1805
 AH4  C08  C  CH2   0  -0.417   -7.7418  -0.0999   0.1923
 AH4  C09  C  CH2   0  -0.585   -8.7841   1.0116   0.1753
 AH4  C10  C  C     0   0.529  -10.1971   0.4808   0.2365
 AH4  C14  C  CR6   0  -0.211    0.8996  -1.1126  -0.0573
 AH4  C15  C  CR16  0   0.007    1.9985  -1.9557   0.0901
 AH4  C17  C  CR16  0  -0.017    1.2138   0.2333  -0.2150
 AH4  C19  C  CR6   0   0.596    3.4232  -0.2096  -0.0428
 AH4  C23  C  CR16  0  -0.255    6.1114   3.5510  -0.9218
 AH4  C24  C  CR16  0  -0.257    5.6632   4.3349   0.1322
 AH4  C25  C  CR16  0  -0.261    4.8856   3.7635   1.1324
 AH4  C26  C  CR16  0  -0.266    4.5608   2.4165   1.0835
 AH4  C27  C  CR6   0   0.298    5.8100  -0.6496  -0.0841
 AH4  C28  C  CR16  0  -0.275    6.7534  -0.6307   0.9356
 AH4  C29  C  CR16  0  -0.255    7.8581  -1.4691   0.8725
 AH4  C30  C  CR16  0  -0.256    8.0192  -2.3327  -0.2022
 AH4  N03  N  NH1   0  -0.663   -1.4852  -0.8583   0.1716
 AH4  N16  N  N     0  -0.441    3.2411  -1.5232   0.1126
 AH4  N18  N  N     0  -0.441    2.4517   0.6874  -0.2161
 AH4  N20  N  NT    0  -0.675    4.7083   0.2474  -0.0301
 AH4  O01  O  O     0  -0.496   -0.6311  -2.8793  -0.3454
 AH4  O12  O  OH1   0  -0.546  -12.3622   0.8170  -0.6043
 AH4  O13  O  O     0  -0.481  -10.5553  -0.3804   1.0212
 AH4  H1   H  HNH1  0   0.414  -10.7550   1.8574  -1.2019
 AH4  H3   H  HCR6  0   0.266    6.1259   1.5976  -1.8093
 AH4  H4   H  HCR6  0   0.265    5.2481  -1.5100  -1.9704
 AH4  H5   H  HCH2  0   0.230   -3.0342  -1.9367   1.0866
 AH4  H6   H  HCH2  0   0.237   -3.0276  -1.9612  -0.6667
 AH4  H7   H  HCH2  0   0.227   -3.6723   0.4919   1.0395
 AH4  H8   H  HCH2  0   0.230   -3.6752   0.4479  -0.7166
 AH4  H9   H  HCH2  0   0.217   -5.4380  -1.3262  -0.6646
 AH4  H10  H  HCH2  0   0.217   -5.4283  -1.2925   1.0841
 AH4  H11  H  HCH2  0   0.216   -6.1715   1.0984   1.0454
 AH4  H12  H  HCH2  0   0.216   -6.1729   1.0704  -0.7050
 AH4  H13  H  HCH2  0   0.227   -7.8878  -0.7524  -0.6742
 AH4  H14  H  HCH2  0   0.227   -7.8855  -0.7245   1.0772
 AH4  H15  H  HCH2  0   0.268   -8.6461   1.6612   1.0458
 AH4  H16  H  HCH2  0   0.251   -8.6423   1.6462  -0.7034
 AH4  H17  H  HCR6  0   0.277    1.8569  -3.0243   0.2073
 AH4  H18  H  HCR6  0   0.273    0.4422   0.9799  -0.3756
 AH4  H19  H  HCR6  0   0.261    6.7164   3.9874  -1.7056
 AH4  H20  H  HCR6  0   0.260    5.9214   5.3846   0.1776
 AH4  H21  H  HCR6  0   0.261    4.5381   4.3663   1.9613
 AH4  H22  H  HCR6  0   0.265    3.9701   1.9700   1.8728
 AH4  H23  H  HCR6  0   0.265    6.6253   0.0389   1.7769
 AH4  H24  H  HCR6  0   0.262    8.5894  -1.4495   1.6696
 AH4  H25  H  HCR6  0   0.260    8.8791  -2.9876  -0.2489
 AH4  H26  H  HNH1  0   0.405   -1.2925   0.0505   0.5612
 AH4  H27  H  HOH1  0   0.477  -12.5564   0.1314  -1.2559
 AH4  H2   H  HCR6  0   0.261    7.1967  -3.0125  -2.0657

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
 AH4  C24  C25  aromatic  1.390  0.020  1.390
 AH4  C24  C23  aromatic  1.388  0.020  1.388
 AH4  C25  C26  aromatic  1.386  0.020  1.386
 AH4  C05  C04  single    1.519  0.020  1.519
 AH4  C05  C06  single    1.524  0.020  1.524
 AH4  C23  C22  aromatic  1.388  0.020  1.388
 AH4  C07  C06  single    1.522  0.020  1.522
 AH4  C07  C08  single    1.523  0.020  1.523
 AH4  C04  N03  single    1.449  0.020  1.449
 AH4  C09  C08  single    1.524  0.020  1.524
 AH4  C09  C10  single    1.511  0.020  1.511
 AH4  N03  C02  single    1.342  0.020  1.342
 AH4  C26  C21  aromatic  1.391  0.020  1.391
 AH4  C17  N18  aromatic  1.319  0.020  1.319
 AH4  C17  C14  aromatic  1.391  0.020  1.391
 AH4  C22  C21  aromatic  1.390  0.020  1.390
 AH4  N18  C19  aromatic  1.334  0.020  1.334
 AH4  C21  N20  single    1.421  0.020  1.421
 AH4  C10  N11  single    1.348  0.020  1.348
 AH4  C10  O13  double    1.219  0.020  1.219
 AH4  N11  O12  single    1.363  0.020  1.363
 AH4  C02  C14  single    1.484  0.020  1.484
 AH4  C02  O01  double    1.226  0.020  1.226
 AH4  C14  C15  aromatic  1.393  0.020  1.393
 AH4  C19  N20  single    1.364  0.020  1.364
 AH4  C19  N16  aromatic  1.335  0.020  1.335
 AH4  N20  C27  single    1.422  0.020  1.422
 AH4  C15  N16  aromatic  1.316  0.020  1.316
 AH4  C27  C28  aromatic  1.389  0.020  1.389
 AH4  C27  C32  aromatic  1.390  0.020  1.390
 AH4  C28  C29  aromatic  1.388  0.020  1.388
 AH4  C32  C31  aromatic  1.386  0.020  1.386
 AH4  C29  C30  aromatic  1.388  0.020  1.388
 AH4  C31  C30  aromatic  1.390  0.020  1.390
 AH4  N11  H1   single    0.890  0.020  1.040
 AH4  C31  H2   single    0.930  0.020  1.080
 AH4  C22  H3   single    0.930  0.020  1.080
 AH4  C32  H4   single    0.930  0.020  1.080
 AH4  C04  H5   single    0.970  0.020  1.090
 AH4  C04  H6   single    0.970  0.020  1.090
 AH4  C05  H7   single    0.970  0.020  1.090
 AH4  C05  H8   single    0.970  0.020  1.090
 AH4  C06  H9   single    0.970  0.020  1.090
 AH4  C06  H10  single    0.970  0.020  1.090
 AH4  C07  H11  single    0.970  0.020  1.090
 AH4  C07  H12  single    0.970  0.020  1.090
 AH4  C08  H13  single    0.970  0.020  1.090
 AH4  C08  H14  single    0.970  0.020  1.090
 AH4  C09  H15  single    0.970  0.020  1.090
 AH4  C09  H16  single    0.970  0.020  1.090
 AH4  C15  H17  single    0.930  0.020  1.080
 AH4  C17  H18  single    0.930  0.020  1.080
 AH4  C23  H19  single    0.930  0.020  1.080
 AH4  C24  H20  single    0.930  0.020  1.080
 AH4  C25  H21  single    0.930  0.020  1.080
 AH4  C26  H22  single    0.930  0.020  1.080
 AH4  C28  H23  single    0.930  0.020  1.080
 AH4  C29  H24  single    0.930  0.020  1.080
 AH4  C30  H25  single    0.930  0.020  1.080
 AH4  N03  H26  single    0.860  0.020  1.020
 AH4  O12  H27  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
 AH4  H1   N11  O12  114.56  3.000
 AH4  H1   N11  C10  121.89  3.000
 AH4  O12  N11  C10  119.93  3.000
 AH4  N20  C21  C26  120.63  3.000
 AH4  N20  C21  C22  119.33  3.000
 AH4  C26  C21  C22  119.99  3.000
 AH4  H2   C31  C30  120.11  3.000
 AH4  H2   C31  C32  119.55  3.000
 AH4  C30  C31  C32  120.34  3.000
 AH4  H3   C22  C23  120.02  3.000
 AH4  H3   C22  C21  120.05  3.000
 AH4  C23  C22  C21  119.92  3.000
 AH4  H4   C32  C27  120.11  3.000
 AH4  H4   C32  C31  120.07  3.000
 AH4  C27  C32  C31  119.82  3.000
 AH4  O01  C02  N03  122.69  3.000
 AH4  O01  C02  C14  120.44  3.000
 AH4  N03  C02  C14  116.87  3.000
 AH4  H6   C04  H5   106.62  3.000
 AH4  H6   C04  N03  108.57  3.000
 AH4  H5   C04  N03  110.25  3.000
 AH4  H6   C04  C05  109.71  3.000
 AH4  H5   C04  C05  109.77  3.000
 AH4  N03  C04  C05  111.78  3.000
 AH4  H8   C05  H7   106.72  3.000
 AH4  H8   C05  C06  109.85  3.000
 AH4  H7   C05  C06  109.55  3.000
 AH4  H8   C05  C04  109.72  3.000
 AH4  H7   C05  C04  110.04  3.000
 AH4  C06  C05  C04  110.86  3.000
 AH4  H10  C06  H9   105.97  3.000
 AH4  H10  C06  C07  109.33  3.000
 AH4  H9   C06  C07  109.31  3.000
 AH4  H10  C06  C05  109.21  3.000
 AH4  H9   C06  C05  109.09  3.000
 AH4  C07  C06  C05  113.63  3.000
 AH4  H12  C07  H11  106.11  3.000
 AH4  H12  C07  C08  109.54  3.000
 AH4  H11  C07  C08  109.42  3.000
 AH4  H12  C07  C06  109.65  3.000
 AH4  H11  C07  C06  109.71  3.000
 AH4  C08  C07  C06  112.23  3.000
 AH4  H14  C08  H13  106.43  3.000
 AH4  H14  C08  C09  109.64  3.000
 AH4  H13  C08  C09  109.56  3.000
 AH4  H14  C08  C07  109.43  3.000
 AH4  H13  C08  C07  109.32  3.000
 AH4  C09  C08  C07  112.29  3.000
 AH4  H16  C09  H15  106.16  3.000
 AH4  H16  C09  C10  110.97  3.000
 AH4  H15  C09  C10  107.11  3.000
 AH4  H16  C09  C08  110.10  3.000
 AH4  H15  C09  C08  109.74  3.000
 AH4  C10  C09  C08  112.52  3.000
 AH4  O13  C10  C09  123.32  3.000
 AH4  O13  C10  N11  123.22  3.000
 AH4  C09  C10  N11  113.46  3.000
 AH4  C17  C14  C15  114.80  3.000
 AH4  C15  C14  C02  119.46  3.000
 AH4  C17  C14  C02  125.69  3.000
 AH4  H17  C15  N16  116.45  3.000
 AH4  H17  C15  C14  120.33  3.000
 AH4  N16  C15  C14  123.22  3.000
 AH4  H18  C17  N18  115.48  3.000
 AH4  H18  C17  C14  121.45  3.000
 AH4  N18  C17  C14  123.05  3.000
 AH4  N20  C19  N18  117.53  3.000
 AH4  N20  C19  N16  117.20  3.000
 AH4  N18  C19  N16  125.28  3.000
 AH4  H19  C23  C24  120.19  3.000
 AH4  H19  C23  C22  119.57  3.000
 AH4  C24  C23  C22  120.24  3.000
 AH4  H20  C24  C25  120.14  3.000
 AH4  H20  C24  C23  120.19  3.000
 AH4  C25  C24  C23  119.67  3.000
 AH4  H21  C25  C26  119.53  3.000
 AH4  H21  C25  C24  120.13  3.000
 AH4  C26  C25  C24  120.34  3.000
 AH4  H22  C26  C25  120.20  3.000
 AH4  H22  C26  C21  119.98  3.000
 AH4  C25  C26  C21  119.83  3.000
 AH4  N20  C27  C28  119.32  3.000
 AH4  C28  C27  C32  120.02  3.000
 AH4  N20  C27  C32  120.61  3.000
 AH4  H23  C28  C29  120.20  3.000
 AH4  H23  C28  C27  119.89  3.000
 AH4  C29  C28  C27  119.92  3.000
 AH4  H24  C29  C30  120.21  3.000
 AH4  H24  C29  C28  119.57  3.000
 AH4  C30  C29  C28  120.22  3.000
 AH4  H25  C30  C29  120.15  3.000
 AH4  H25  C30  C31  120.16  3.000
 AH4  C29  C30  C31  119.68  3.000
 AH4  H26  N03  C04  117.43  3.000
 AH4  H26  N03  C02  119.35  3.000
 AH4  C04  N03  C02  121.74  3.000
 AH4  C19  N16  C15  116.75  3.000
 AH4  C19  N18  C17  116.88  3.000
 AH4  C27  N20  C19  121.22  3.000
 AH4  C27  N20  C21  117.28  3.000
 AH4  C19  N20  C21  121.50  3.000
 AH4  H27  O12  N11  106.08  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
 AH4  CONST_01  C24  C25  C26  C21     0.00   0.0  0
 AH4  CONST_02  C24  C23  C22  C21     0.00   0.0  0
 AH4  CONST_03  C28  C27  C32  C31     0.00   0.0  0
 AH4  CONST_04  C28  C29  C30  C31     0.00   0.0  0
 AH4  CONST_05  C25  C24  C23  C22     0.00   0.0  0
 AH4  CONST_06  C25  C26  C21  C22     0.00   0.0  0
 AH4  CONST_07  C29  C28  C27  C32     0.00   0.0  0
 AH4  CONST_08  C29  C30  C31  C32     0.00   0.0  0
 AH4  CONST_09  C19  N18  C17  C14     0.00   0.0  0
 AH4  CONST_10  C19  N16  C15  C14     0.00   0.0  0
 AH4  CONST_11  N18  C17  C14  C15     0.00   0.0  0
 AH4  CONST_12  N18  C19  N16  C15     0.00   0.0  0
 AH4  CONST_13  N16  C19  N18  C17     0.00   0.0  0
 AH4  CONST_14  N16  C15  C14  C17     0.00   0.0  0
 AH4  CONST_15  C26  C25  C24  C23     0.00   0.0  0
 AH4  CONST_16  C26  C21  C22  C23     0.00   0.0  0
 AH4  CONST_17  C30  C29  C28  C27     0.00   0.0  0
 AH4  CONST_18  C30  C31  C32  C27     0.00   0.0  0
 AH4  CONST_19  N20  C27  C32  C31   180.00   0.0  0
 AH4  CONST_20  N18  C17  C14  C02   180.00   0.0  0
 AH4  CONST_21  N16  C15  C14  C02   180.00   0.0  0
 AH4  CONST_22  N20  C19  N16  C15   180.00   0.0  0
 AH4  CONST_23  N20  C19  N18  C17   180.00   0.0  0
 AH4  CONST_24  N20  C21  C22  C23   180.00   0.0  0
 AH4  CONST_25  N20  C21  C26  C25   180.00   0.0  0
 AH4  CONST_26  N20  C27  C28  C29   180.00   0.0  0
 AH4  CONST_27  H21  C25  C26  C21   180.00   0.0  0
 AH4  CONST_28  H19  C23  C22  C21   180.00   0.0  0
 AH4  CONST_29  H24  C29  C30  C31   180.00   0.0  0
 AH4  CONST_30  H20  C24  C23  C22   180.00   0.0  0
 AH4  CONST_31  H22  C26  C21  C22   180.00   0.0  0
 AH4  CONST_32  H23  C28  C27  C32   180.00   0.0  0
 AH4  CONST_33  H25  C30  C31  C32   180.00   0.0  0
 AH4  CONST_34  H18  C17  C14  C15   180.00   0.0  0
 AH4  CONST_35  H17  C15  C14  C17   180.00   0.0  0
 AH4  CONST_36  H3   C22  C23  C24   180.00   0.0  0
 AH4  CONST_37  H2   C31  C32  C27   180.00   0.0  0
 AH4  CONST_38  H4   C32  C27  C28   180.00   0.0  0
 AH4  CONST_39  C14  C02  N03  C04   180.00   0.0  0
 AH4  CONST_40  H26  N03  C02  C14     0.00   0.0  0
 AH4  CONST_41  O01  C02  N03  C04     0.00   0.0  0
 AH4  CONST_42  O12  N11  C10  C09   180.00   0.0  0
 AH4  CONST_43  O13  C10  N11  O12     0.00   0.0  0
 AH4  CONST_44  H1   N11  C10  C09     0.00   0.0  0
 AH4  Var_01    N18  C19  N20  C21    10.18  30.0  2
 AH4  Var_02    C28  C27  N20  C21    58.61  30.0  2
 AH4  Var_03    C19  N20  C21  C22  -122.67  30.0  2
 AH4  Var_04    N03  C02  C14  C15   160.54  30.0  2
 AH4  Var_05    C08  C09  C10  N11  -132.53  30.0  1
 AH4  Var_06    C05  C04  N03  C02  -166.20  30.0  1
 AH4  Var_07    C07  C06  C05  C04   179.81  30.0  3
 AH4  Var_08    C08  C07  C06  C05   179.66  30.0  1
 AH4  Var_09    N03  C04  C05  C06   179.60  30.0  3
 AH4  Var_10    C09  C08  C07  C06  -179.96  30.0  3
 AH4  Var_11    C10  C09  C08  C07  -177.96  30.0  1

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
 AH4  plan-1  C02  0.020
 AH4  plan-1  C14  0.020
 AH4  plan-1  C15  0.020
 AH4  plan-1  C17  0.020
 AH4  plan-1  C19  0.020
 AH4  plan-1  N16  0.020
 AH4  plan-1  N18  0.020
 AH4  plan-1  N20  0.020
 AH4  plan-1  H17  0.020
 AH4  plan-1  H18  0.020
 AH4  plan-2  C21  0.020
 AH4  plan-2  C22  0.020
 AH4  plan-2  C23  0.020
 AH4  plan-2  C24  0.020
 AH4  plan-2  C25  0.020
 AH4  plan-2  C26  0.020
 AH4  plan-2  N20  0.020
 AH4  plan-2  H3   0.020
 AH4  plan-2  H19  0.020
 AH4  plan-2  H20  0.020
 AH4  plan-2  H21  0.020
 AH4  plan-2  H22  0.020
 AH4  plan-3  C31  0.020
 AH4  plan-3  C32  0.020
 AH4  plan-3  C27  0.020
 AH4  plan-3  C28  0.020
 AH4  plan-3  C29  0.020
 AH4  plan-3  C30  0.020
 AH4  plan-3  N20  0.020
 AH4  plan-3  H4   0.020
 AH4  plan-3  H23  0.020
 AH4  plan-3  H24  0.020
 AH4  plan-3  H25  0.020
 AH4  plan-3  H2   0.020
 AH4  plan-4  C02  0.020
 AH4  plan-4  C04  0.020
 AH4  plan-4  C14  0.020
 AH4  plan-4  N03  0.020
 AH4  plan-4  O01  0.020
 AH4  plan-4  H26  0.020
 AH4  plan-5  N11  0.020
 AH4  plan-5  C09  0.020
 AH4  plan-5  C10  0.020
 AH4  plan-5  O12  0.020
 AH4  plan-5  O13  0.020
 AH4  plan-5  H1   0.020

