# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 06:20:52 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: (3~{Z},6~{Z})-3-[(4-~{tert}-butyl-1~{H}-imidazol-5-yl)methylidene]-6-[[3-(4-fluorophenyl)carbonylphenyl]methylidene]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1nc[nH]c1\C=C2/NC(=O)C(/NC2=O)=C/c3cccc(c3)C(=O)c4ccc(F)cc4
#
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
 87U  87U  (3~{Z},6~{Z})-3-[(4-~{tert}-butyl-1~{H}-imidazol-5-yl)methylidene]-6-[[3-(4-fluorophenyl)carbonylphenyl]methylidene]piperazine-2,5-dione  ligand  57  34  .  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_87U
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
 87U  CAA  C  CH3   0  -0.632    9.1605   0.7030   0.9740
 87U  CAB  C  CH3   0  -0.636    6.9244   0.8398   2.0523
 87U  CAC  C  CH3   0  -0.640    7.5986   2.5227   0.3154
 87U  CAJ  C  CR16  0  -0.219   -3.1074   1.8269  -0.9281
 87U  CAK  C  CR15  0   0.099    7.0719  -1.3420  -1.8601
 87U  CAL  C  CR16  0  -0.323   -1.9298   1.1043  -1.0333
 87U  CAM  C  CR16  0  -0.287   -4.1994   1.2940  -0.2605
 87U  CAN  C  CR16  0  -0.398   -8.2824   0.0781  -1.0594
 87U  CAO  C  CR16  0  -0.401   -8.9653  -0.1068   1.2586
 87U  CAP  C  CR16  0  -0.260   -6.9631  -0.0992  -0.6748
 87U  CAQ  C  CR16  0  -0.248   -7.6464  -0.3043   1.6234
 87U  CAR  C  CR16  0  -0.320   -2.9217  -0.6893   0.2163
 87U  CAW  C  C     0   0.365   -5.2353  -0.5556   1.0962
 87U  CAX  C  CR6   0   0.539   -9.2583   0.0785  -0.0814
 87U  CAY  C  CR6   0   0.125   -1.8171  -0.1628  -0.4513
 87U  CAZ  C  CR5   0   0.290    5.7999   0.0828  -0.7785
 87U  NAS  N  NR15  0  -0.633    5.8109  -0.9025  -1.7413
 87U  NAT  N  N     0  -0.447    7.8744  -0.7315  -1.0237
 87U  NAU  N  NR16  0  -0.750    1.0110   0.7540  -0.0565
 87U  NAV  N  NR16  0  -0.755    3.0210  -0.9938  -0.5191
 87U  OAD  O  O     0  -0.386   -5.0075  -1.2366   2.0759
 87U  CBA  C  CR6   0  -0.049   -6.6302  -0.2899   0.6660
 87U  CBB  C  CR6   0  -0.016   -4.1108   0.0261   0.3119
 87U  CBC  C  CR5   0   0.194    7.1123   0.1658  -0.3416
 87U  CBD  C  CR6   0   0.544    1.7735  -1.5196  -0.5648
 87U  CBE  C  CR6   0   0.549    2.2619   1.2740   0.0195
 87U  CBF  C  CR6   0   0.222    0.6639  -0.5441  -0.4040
 87U  CBG  C  CR6   0   0.223    3.3589   0.3409  -0.3187
 87U  CBH  C  CT    0  -0.206    7.6901   1.0501   0.7385
 87U  H1   H  HCH3  0   0.226    9.2845  -0.3312   1.2971
 87U  H2   H  HCH3  0   0.227    9.7615   0.8435   0.0757
 87U  H3   H  HCH3  0   0.225    9.5654   1.3490   1.7552
 87U  H4   H  HCH3  0   0.228    7.3632   1.4462   2.8473
 87U  H5   H  HCH3  0   0.229    5.8730   1.1168   1.9679
 87U  H6   H  HCH3  0   0.229    6.9687  -0.2040   2.3684
 87U  H7   H  HCH3  0   0.231    8.1423   2.7011  -0.6137
 87U  H8   H  HCH3  0   0.230    6.5688   2.8507   0.1657
 87U  H9   H  HCH3  0   0.230    8.0325   3.1651   1.0846
 87U  H10  H  H     0   0.286   -0.7318  -2.0307  -0.7132
 87U  H12  H  H     0   0.283    4.7537   1.8409  -0.0975
 87U  H14  H  HCR6  0   0.273   -3.1779   2.8073  -1.3792
 87U  H15  H  HCR5  0   0.285    7.3545  -2.0999  -2.5743
 87U  H16  H  HCR6  0   0.283   -1.1075   1.5209  -1.6017
 87U  H17  H  HCR6  0   0.278   -5.1088   1.8749  -0.1778
 87U  H18  H  HCR6  0   0.290   -8.5453   0.2122  -2.1000
 87U  H19  H  HCR6  0   0.289   -9.7534  -0.0996   1.9993
 87U  H20  H  HCR6  0   0.284   -6.1975  -0.1128  -1.4387
 87U  H21  H  HCR6  0   0.277   -7.4047  -0.4560   2.6668
 87U  H22  H  HCR6  0   0.267   -2.8513  -1.6746   0.6609
 87U  H23  H  HNR5  0   0.422    5.0558  -1.1454  -2.3649
 87U  H11  H  HNR6  0   0.423    0.2656   1.3882   0.2025
 87U  H13  H  HNR6  0   0.417    3.7712  -1.6725  -0.5430
 87U  CAI  C  C1    0  -0.399    4.6189   0.8063  -0.3822
 87U  CAH  C  C1    0  -0.351   -0.6000  -0.9694  -0.5465
 87U  OAE  O  O     0  -0.448    1.5836  -2.7100  -0.7283
 87U  OAF  O  O     0  -0.452    2.4534   2.4338   0.3360
 87U  FAG  F  F     0  -0.304  -10.5329   0.2628  -0.4415

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
 87U  CAB  CBH  single    1.535  0.020  1.535
 87U  NAT  CAK  aromatic  1.310  0.020  1.310
 87U  NAT  CBC  aromatic  1.360  0.020  1.360
 87U  CAK  NAS  aromatic  1.341  0.020  1.341
 87U  CAA  CBH  single    1.529  0.020  1.529
 87U  CBH  CBC  single    1.511  0.020  1.511
 87U  CBH  CAC  single    1.535  0.020  1.535
 87U  CBC  CAZ  aromatic  1.386  0.020  1.386
 87U  NAS  CAZ  aromatic  1.378  0.020  1.378
 87U  CAZ  CAI  single    1.441  0.020  1.441
 87U  CAI  CBG  double    1.345  0.020  1.345
 87U  NAV  CBG  single    1.391  0.020  1.391
 87U  NAV  CBD  single    1.355  0.020  1.355
 87U  CBG  CBE  single    1.479  0.020  1.479
 87U  OAE  CBD  double    1.217  0.020  1.217
 87U  CBD  CBF  single    1.486  0.020  1.486
 87U  CBE  OAF  double    1.217  0.020  1.217
 87U  CBE  NAU  single    1.357  0.020  1.357
 87U  CBF  NAU  single    1.388  0.020  1.388
 87U  CBF  CAH  double    1.341  0.020  1.341
 87U  CAH  CAY  single    1.463  0.020  1.463
 87U  CAY  CAL  aromatic  1.399  0.020  1.399
 87U  CAY  CAR  aromatic  1.394  0.020  1.394
 87U  CAL  CAJ  aromatic  1.386  0.020  1.386
 87U  CAR  CBB  aromatic  1.391  0.020  1.391
 87U  CAJ  CAM  aromatic  1.386  0.020  1.386
 87U  CBB  CAM  aromatic  1.394  0.020  1.394
 87U  CBB  CAW  single    1.489  0.020  1.489
 87U  OAD  CAW  double    1.215  0.020  1.215
 87U  CAW  CBA  single    1.484  0.020  1.484
 87U  CBA  CAQ  aromatic  1.396  0.020  1.396
 87U  CBA  CAP  aromatic  1.395  0.020  1.395
 87U  CAQ  CAO  aromatic  1.383  0.020  1.383
 87U  CAP  CAN  aromatic  1.386  0.020  1.386
 87U  CAO  CAX  aromatic  1.384  0.020  1.384
 87U  CAN  CAX  aromatic  1.382  0.020  1.382
 87U  CAX  FAG  single    1.337  0.020  1.337
 87U  CAA  H1   single    0.970  0.020  1.090
 87U  CAA  H2   single    0.970  0.020  1.090
 87U  CAA  H3   single    0.970  0.020  1.090
 87U  CAB  H4   single    0.970  0.020  1.090
 87U  CAB  H5   single    0.970  0.020  1.090
 87U  CAB  H6   single    0.970  0.020  1.090
 87U  CAC  H7   single    0.970  0.020  1.090
 87U  CAC  H8   single    0.970  0.020  1.090
 87U  CAC  H9   single    0.970  0.020  1.090
 87U  CAH  H10  single    0.930  0.020  1.080
 87U  CAI  H12  single    0.930  0.020  1.080
 87U  CAJ  H14  single    0.930  0.020  1.080
 87U  CAK  H15  single    0.930  0.020  1.080
 87U  CAL  H16  single    0.930  0.020  1.080
 87U  CAM  H17  single    0.930  0.020  1.080
 87U  CAN  H18  single    0.930  0.020  1.080
 87U  CAO  H19  single    0.930  0.020  1.080
 87U  CAP  H20  single    0.930  0.020  1.080
 87U  CAQ  H21  single    0.930  0.020  1.080
 87U  CAR  H22  single    0.930  0.020  1.080
 87U  NAS  H23  single    0.860  0.020  1.020
 87U  NAU  H11  single    0.860  0.020  1.020
 87U  NAV  H13  single    0.860  0.020  1.020

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
 87U  H3   CAA  H2   108.00  3.000
 87U  H3   CAA  H1   107.88  3.000
 87U  H2   CAA  H1   107.68  3.000
 87U  H3   CAA  CBH  109.43  3.000
 87U  H2   CAA  CBH  111.96  3.000
 87U  H1   CAA  CBH  111.73  3.000
 87U  H6   CAB  H5   107.73  3.000
 87U  H6   CAB  H4   107.70  3.000
 87U  H5   CAB  H4   107.62  3.000
 87U  H6   CAB  CBH  111.01  3.000
 87U  H5   CAB  CBH  112.32  3.000
 87U  H4   CAB  CBH  110.27  3.000
 87U  H9   CAC  H8   107.15  3.000
 87U  H9   CAC  H7   107.79  3.000
 87U  H8   CAC  H7   107.72  3.000
 87U  H9   CAC  CBH  110.27  3.000
 87U  H8   CAC  CBH  112.49  3.000
 87U  H7   CAC  CBH  111.21  3.000
 87U  H14  CAJ  CAM  119.86  3.000
 87U  H14  CAJ  CAL  119.77  3.000
 87U  CAM  CAJ  CAL  120.36  3.000
 87U  H15  CAK  NAT  126.12  3.000
 87U  H15  CAK  NAS  122.36  3.000
 87U  NAT  CAK  NAS  111.51  3.000
 87U  H16  CAL  CAY  120.37  3.000
 87U  H16  CAL  CAJ  118.98  3.000
 87U  CAY  CAL  CAJ  120.61  3.000
 87U  H17  CAM  CBB  120.68  3.000
 87U  H17  CAM  CAJ  119.50  3.000
 87U  CBB  CAM  CAJ  119.82  3.000
 87U  H18  CAN  CAX  120.62  3.000
 87U  H18  CAN  CAP  120.95  3.000
 87U  CAX  CAN  CAP  118.43  3.000
 87U  H19  CAO  CAX  120.52  3.000
 87U  H19  CAO  CAQ  121.02  3.000
 87U  CAX  CAO  CAQ  118.46  3.000
 87U  H20  CAP  CBA  120.55  3.000
 87U  H20  CAP  CAN  118.66  3.000
 87U  CBA  CAP  CAN  120.77  3.000
 87U  H21  CAQ  CBA  120.01  3.000
 87U  H21  CAQ  CAO  119.19  3.000
 87U  CBA  CAQ  CAO  120.79  3.000
 87U  H22  CAR  CBB  119.68  3.000
 87U  H22  CAR  CAY  119.25  3.000
 87U  CBB  CAR  CAY  121.07  3.000
 87U  CBB  CAW  CBA  119.16  3.000
 87U  CBA  CAW  OAD  120.70  3.000
 87U  CBB  CAW  OAD  120.14  3.000
 87U  FAG  CAX  CAO  118.75  3.000
 87U  FAG  CAX  CAN  118.86  3.000
 87U  CAO  CAX  CAN  122.39  3.000
 87U  CAR  CAY  CAL  118.52  3.000
 87U  CAR  CAY  CAH  118.82  3.000
 87U  CAL  CAY  CAH  122.63  3.000
 87U  CBC  CAZ  NAS  104.81  3.000
 87U  NAS  CAZ  CAI  123.92  3.000
 87U  CBC  CAZ  CAI  131.27  3.000
 87U  H23  NAS  CAZ  126.74  3.000
 87U  H23  NAS  CAK  124.76  3.000
 87U  CAZ  NAS  CAK  107.69  3.000
 87U  CBC  NAT  CAK  106.52  3.000
 87U  H11  NAU  CBF  117.76  3.000
 87U  H11  NAU  CBE  115.11  3.000
 87U  CBF  NAU  CBE  127.09  3.000
 87U  H13  NAV  CBG  117.83  3.000
 87U  H13  NAV  CBD  114.94  3.000
 87U  CBG  NAV  CBD  126.93  3.000
 87U  CAW  CBA  CAQ  118.92  3.000
 87U  CAQ  CBA  CAP  119.14  3.000
 87U  CAW  CBA  CAP  121.84  3.000
 87U  CAW  CBB  CAR  118.74  3.000
 87U  CAW  CBB  CAM  121.57  3.000
 87U  CAR  CBB  CAM  119.60  3.000
 87U  CBH  CBC  NAT  122.02  3.000
 87U  CBH  CBC  CAZ  128.51  3.000
 87U  NAT  CBC  CAZ  109.45  3.000
 87U  CBF  CBD  OAE  122.71  3.000
 87U  CBF  CBD  NAV  115.42  3.000
 87U  OAE  CBD  NAV  121.88  3.000
 87U  CBG  CBE  OAF  122.93  3.000
 87U  OAF  CBE  NAU  121.65  3.000
 87U  CBG  CBE  NAU  115.41  3.000
 87U  CBD  CBF  NAU  117.02  3.000
 87U  NAU  CBF  CAH  123.98  3.000
 87U  CBD  CBF  CAH  118.94  3.000
 87U  CBE  CBG  NAV  117.26  3.000
 87U  CBE  CBG  CAI  119.16  3.000
 87U  NAV  CBG  CAI  123.56  3.000
 87U  CBC  CBH  CAC  109.98  3.000
 87U  CAC  CBH  CAB  109.73  3.000
 87U  CBC  CBH  CAB  109.93  3.000
 87U  CAC  CBH  CAA  108.52  3.000
 87U  CBC  CBH  CAA  110.18  3.000
 87U  CAB  CBH  CAA  108.47  3.000
 87U  H12  CAI  CBG  115.82  3.000
 87U  H12  CAI  CAZ  116.79  3.000
 87U  CBG  CAI  CAZ  127.40  3.000
 87U  H10  CAH  CBF  116.23  3.000
 87U  H10  CAH  CAY  116.70  3.000
 87U  CBF  CAH  CAY  127.03  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
 87U  CONST_01  CAR  CAY  CAL  CAJ     0.00   0.0  0
 87U  CONST_02  CAR  CBB  CAM  CAJ     0.00   0.0  0
 87U  CONST_03  CAZ  CBC  NAT  CAK     0.00   0.0  0
 87U  CONST_04  CBC  CAZ  NAS  CAK     0.00   0.0  0
 87U  CONST_05  CBB  CAR  CAY  CAL     0.00   0.0  0
 87U  CONST_06  CBB  CAM  CAJ  CAL     0.00   0.0  0
 87U  CONST_07  CAY  CAL  CAJ  CAM     0.00   0.0  0
 87U  CONST_08  CAY  CAR  CBB  CAM     0.00   0.0  0
 87U  CONST_09  CAQ  CBA  CAP  CAN     0.00   0.0  0
 87U  CONST_10  CAQ  CAO  CAX  CAN     0.00   0.0  0
 87U  CONST_11  CAP  CBA  CAQ  CAO     0.00   0.0  0
 87U  CONST_12  CAP  CAN  CAX  CAO     0.00   0.0  0
 87U  CONST_13  CBA  CAQ  CAO  CAX     0.00   0.0  0
 87U  CONST_14  CBA  CAP  CAN  CAX     0.00   0.0  0
 87U  CONST_15  NAT  CAK  NAS  CAZ     0.00   0.0  0
 87U  CONST_16  CBC  NAT  CAK  NAS     0.00   0.0  0
 87U  CONST_17  NAT  CBC  CAZ  NAS     0.00   0.0  0
 87U  CONST_18  CBG  NAV  CBD  CBF     0.00   0.0  0
 87U  CONST_19  CBG  CBE  NAU  CBF     0.00   0.0  0
 87U  CONST_20  CAJ  CAL  CAY  CAH   180.00   0.0  0
 87U  CONST_21  CBB  CAR  CAY  CAH   180.00   0.0  0
 87U  CONST_22  NAT  CBC  CAZ  CAI   180.00   0.0  0
 87U  CONST_23  CAK  NAS  CAZ  CAI   180.00   0.0  0
 87U  CONST_24  CAW  CBB  CAM  CAJ   180.00   0.0  0
 87U  CONST_25  CBH  CBC  NAT  CAK   180.00   0.0  0
 87U  CONST_26  CAW  CBA  CAP  CAN   180.00   0.0  0
 87U  CONST_27  CAW  CBA  CAQ  CAO   180.00   0.0  0
 87U  CONST_28  FAG  CAX  CAN  CAP   180.00   0.0  0
 87U  CONST_29  FAG  CAX  CAO  CAQ   180.00   0.0  0
 87U  CONST_30  CAY  CAR  CBB  CAW   180.00   0.0  0
 87U  CONST_31  CBH  CBC  CAZ  NAS   180.00   0.0  0
 87U  CONST_32  CBG  NAV  CBD  OAE   180.00   0.0  0
 87U  CONST_33  CBF  NAU  CBE  OAF   180.00   0.0  0
 87U  CONST_34  H22  CAR  CAY  CAL   180.00   0.0  0
 87U  CONST_35  H17  CAM  CAJ  CAL   180.00   0.0  0
 87U  CONST_36  H16  CAL  CAJ  CAM   180.00   0.0  0
 87U  CONST_37  H19  CAO  CAX  CAN   180.00   0.0  0
 87U  CONST_38  H18  CAN  CAX  CAO   180.00   0.0  0
 87U  CONST_39  H21  CAQ  CBA  CAP   180.00   0.0  0
 87U  CONST_40  H20  CAP  CBA  CAQ   180.00   0.0  0
 87U  CONST_41  H14  CAJ  CAL  CAY   180.00   0.0  0
 87U  CONST_42  H15  CAK  NAS  CAZ   180.00   0.0  0
 87U  CONST_43  H23  NAS  CAK  NAT   180.00   0.0  0
 87U  CONST_44  H13  NAV  CBD  CBF   180.00   0.0  0
 87U  CONST_45  H11  NAU  CBE  CBG   180.00   0.0  0
 87U  Var_01    CBF  CAH  CAY  CAL    42.99  30.0  1
 87U  Var_02    CBA  CAW  CBB  CAM    36.67  30.0  2
 87U  Var_03    CBB  CAW  CBA  CAP    30.90  30.0  2
 87U  Var_04    CBD  CBF  CAH  CAY  -178.79  30.0  2
 87U  Var_05    NAV  CBG  CAI  CAZ     6.29  30.0  2
 87U  Var_06    CBG  CAI  CAZ  NAS    34.10  30.0  2
 87U  Var_07    NAT  CBC  CBH  CAA    -3.79  30.0  2
 87U  Var_08    H4   CAB  CBH  CBC   177.71  30.0  3
 87U  Var_09    H1   CAA  CBH  CBC   -60.64  30.0  3
 87U  Var_10    H7   CAC  CBH  CBC   -59.39  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
 87U  plan-1  CAK  0.020
 87U  plan-1  CAZ  0.020
 87U  plan-1  NAS  0.020
 87U  plan-1  NAT  0.020
 87U  plan-1  CBC  0.020
 87U  plan-1  CBH  0.020
 87U  plan-1  H15  0.020
 87U  plan-1  H23  0.020
 87U  plan-1  CAI  0.020
 87U  plan-2  CAJ  0.020
 87U  plan-2  CAL  0.020
 87U  plan-2  CAM  0.020
 87U  plan-2  CAR  0.020
 87U  plan-2  CAW  0.020
 87U  plan-2  CAY  0.020
 87U  plan-2  CBB  0.020
 87U  plan-2  H14  0.020
 87U  plan-2  H16  0.020
 87U  plan-2  H17  0.020
 87U  plan-2  H22  0.020
 87U  plan-2  CAH  0.020
 87U  plan-3  NAU  0.020
 87U  plan-3  NAV  0.020
 87U  plan-3  CBD  0.020
 87U  plan-3  CBE  0.020
 87U  plan-3  CBF  0.020
 87U  plan-3  CBG  0.020
 87U  plan-3  H11  0.020
 87U  plan-3  H13  0.020
 87U  plan-3  CAI  0.020
 87U  plan-3  CAH  0.020
 87U  plan-3  OAE  0.020
 87U  plan-3  OAF  0.020
 87U  plan-4  CAN  0.020
 87U  plan-4  CAO  0.020
 87U  plan-4  CAP  0.020
 87U  plan-4  CAQ  0.020
 87U  plan-4  CAW  0.020
 87U  plan-4  CAX  0.020
 87U  plan-4  CBA  0.020
 87U  plan-4  H18  0.020
 87U  plan-4  H19  0.020
 87U  plan-4  H20  0.020
 87U  plan-4  H21  0.020
 87U  plan-4  FAG  0.020
 87U  plan-5  CAW  0.020
 87U  plan-5  OAD  0.020
 87U  plan-5  CBA  0.020
 87U  plan-5  CBB  0.020

