# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 04:23:18 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 4-[[(3~{R},7~{S})-2-cyclopentyl-9-methyl-8-oxidanylidene-2,9,12,14-tetrazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),10,12-trien-13-yl]amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)[C@H]2CCC[C@H]2N(C3CCCC3)c4nc(Nc5ccc(cc5)C(N)=O)ncc14
#
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
 B7B  B7B  4-[[(3~{R},7~{S})-2-cyclopentyl-9-methyl-8-oxidanylidene-2,9,12,14-tetrazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),10,12-trien-13-yl]amino]benzamide  ligand  59  31  .  2021-08-06  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_B7B
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
 B7B  C4   C  CR6   0   0.425  -1.5961  -0.2486   0.0003
 B7B  C5   C  CR6   0   0.165  -1.6156   0.8528   0.8650
 B7B  C6   C  CR16  0  -0.010  -0.3918   1.4488   1.1179
 B7B  N1   N  N     0  -0.453   0.7451   1.0070   0.6039
 B7B  N3   N  N     0  -0.447  -0.4651  -0.6938  -0.5075
 B7B  CAM  C  CH2   0  -0.450  -4.3278  -2.7903   0.0181
 B7B  CAJ  C  CH2   0  -0.443  -4.4677  -3.8443   1.1344
 B7B  CAK  C  CH2   0  -0.452  -3.4335  -3.4571   2.2116
 B7B  CAN  C  CH2   0  -0.466  -2.5071  -2.4570   1.5250
 B7B  CBA  C  CH1   0  -0.076  -3.4625  -1.6785   0.6231
 B7B  NBE  N  NT    0  -0.495  -2.7810  -0.8873  -0.4016
 B7B  CBC  C  CR15  0  -0.120  -3.6334  -0.0477  -1.2368
 B7B  CAP  C  CH2   0  -0.442  -3.0278   0.2383  -2.6158
 B7B  CAL  C  CH2   0  -0.466  -2.2277   1.5328  -2.4762
 B7B  CAO  C  CH2   0  -0.451  -2.9893   2.3630  -1.4315
 B7B  CBB  C  CR15  0  -0.407  -3.9434   1.3818  -0.6976
 B7B  CAU  C  C     0   0.541  -3.9562   1.5205   0.8068
 B7B  OAD  O  O     0  -0.477  -4.9677   1.8372   1.4130
 B7B  NBD  N  NT    0  -0.544  -2.7945   1.2996   1.4849
 B7B  CAA  C  CH3   0  -0.544  -2.8169   1.4384   2.9358
 B7B  C2   C  CR6   0   0.593   0.6625  -0.0576  -0.1826
 B7B  NAS  N  NH1   0  -0.771   1.7850  -0.5945  -0.7429
 B7B  CAV  C  CR6   0   0.373   3.1087  -0.1961  -0.7186
 B7B  CAE  C  CR16  0  -0.346   4.0172  -1.0102  -1.4104
 B7B  CAG  C  CR16  0  -0.257   5.3566  -0.6936  -1.4627
 B7B  CAW  C  CR6   0  -0.059   5.8546   0.4404  -0.8200
 B7B  CAT  C  C     0   0.491   7.3136   0.7287  -0.9237
 B7B  OAC  O  O     0  -0.487   8.0199   0.1254  -1.7231
 B7B  NAB  N  NH2   0  -0.822   7.8066   1.6762  -0.1094
 B7B  CAH  C  CR16  0  -0.270   4.9478   1.2473  -0.1385
 B7B  CAF  C  CR16  0  -0.299   3.5967   0.9470  -0.0788
 B7B  H1   H  HCR6  0   0.292  -0.3256   2.3179   1.7646
 B7B  H3   H  HCH2  0   0.239  -5.2961  -2.4346  -0.3357
 B7B  H4   H  HCH2  0   0.231  -5.4762  -3.8629   1.5481
 B7B  H5   H  HCH2  0   0.232  -4.2739  -4.8425   0.7408
 B7B  H6   H  HCH2  0   0.227  -3.9293  -2.9747   3.0566
 B7B  H7   H  HCH2  0   0.236  -2.8948  -4.3172   2.6090
 B7B  H8   H  HCH2  0   0.242  -1.9649  -1.8282   2.2340
 B7B  H9   H  HCH2  0   0.230  -1.7685  -2.9756   0.9061
 B7B  H10  H  HCH1  0   0.218  -4.1012  -1.0577   1.2701
 B7B  H11  H  HCR5  0   0.274  -4.5692  -0.5945  -1.3505
 B7B  H12  H  HCH2  0   0.245  -2.4414  -0.6058  -2.9797
 B7B  H13  H  HCH2  0   0.244  -3.8473   0.3918  -3.3223
 B7B  H14  H  HCH2  0   0.232  -1.2086   1.3319  -2.1434
 B7B  H15  H  HCH2  0   0.247  -2.1421   2.0604  -3.4266
 B7B  H16  H  HCH2  0   0.246  -2.3087   2.8793  -0.7542
 B7B  H17  H  HCH2  0   0.255  -3.5857   3.1392  -1.9107
 B7B  H18  H  HCR5  0   0.285  -4.9633   1.6104  -1.0079
 B7B  H19  H  HCH3  0   0.252  -2.9963   2.4694   3.2385
 B7B  H20  H  HCH3  0   0.253  -3.5927   0.8092   3.3718
 B7B  H21  H  HCH3  0   0.254  -1.8595   1.1220   3.3392
 B7B  H22  H  HNH1  0   0.414   1.5920  -1.4154  -1.2976
 B7B  H23  H  HCR6  0   0.273   3.6617  -1.9024  -1.9123
 B7B  H24  H  HCR6  0   0.262   6.0277  -1.3419  -2.0094
 B7B  H25  H  HNH2  0   0.411   7.2774   2.0862   0.6389
 B7B  H26  H  HNH2  0   0.403   8.7925   1.8789  -0.1290
 B7B  H27  H  HCR6  0   0.251   5.2673   2.1571   0.3540
 B7B  H28  H  HCR6  0   0.291   2.9321   1.6020   0.4590
 B7B  H2   H  HCH2  0   0.228  -3.7966  -3.2033  -0.8428

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
 B7B  N1   C6   aromatic  1.324  0.020  1.324
 B7B  N1   C2   aromatic  1.326  0.020  1.326
 B7B  NAS  C2   single    1.365  0.020  1.365
 B7B  NAS  CAV  single    1.383  0.020  1.383
 B7B  C6   C5   aromatic  1.385  0.020  1.385
 B7B  C2   N3   aromatic  1.335  0.020  1.335
 B7B  CAE  CAV  aromatic  1.402  0.020  1.402
 B7B  CAE  CAG  aromatic  1.377  0.020  1.377
 B7B  CAV  CAF  aromatic  1.398  0.020  1.398
 B7B  CAF  CAH  aromatic  1.385  0.020  1.385
 B7B  CAG  CAW  aromatic  1.395  0.020  1.395
 B7B  N3   C4   aromatic  1.317  0.020  1.317
 B7B  C5   NBD  single    1.405  0.020  1.405
 B7B  C5   C4   aromatic  1.400  0.020  1.400
 B7B  CAA  NBD  single    1.458  0.020  1.458
 B7B  NAB  CAT  single    1.343  0.020  1.343
 B7B  CAH  CAW  aromatic  1.392  0.020  1.392
 B7B  NBD  CAU  single    1.363  0.020  1.363
 B7B  CAW  CAT  single    1.491  0.020  1.491
 B7B  C4   NBE  single    1.405  0.020  1.405
 B7B  CAU  OAD  double    1.221  0.020  1.221
 B7B  CAU  CBB  single    1.511  0.020  1.511
 B7B  CAT  OAC  double    1.226  0.020  1.226
 B7B  CBB  CBC  single    1.559  0.020  1.559
 B7B  CBB  CAO  single    1.553  0.020  1.553
 B7B  NBE  CBA  single    1.463  0.020  1.463
 B7B  NBE  CBC  single    1.459  0.020  1.459
 B7B  CBA  CAM  single    1.533  0.020  1.533
 B7B  CBA  CAN  single    1.527  0.020  1.527
 B7B  CBC  CAP  single    1.533  0.020  1.533
 B7B  CAO  CAL  single    1.536  0.020  1.536
 B7B  CAM  CAJ  single    1.542  0.020  1.542
 B7B  CAJ  CAK  single    1.543  0.020  1.543
 B7B  CAN  CAK  single    1.526  0.020  1.526
 B7B  CAP  CAL  single    1.528  0.020  1.528
 B7B  C6   H1   single    0.930  0.020  1.080
 B7B  CAM  H2   single    0.970  0.020  1.090
 B7B  CAM  H3   single    0.970  0.020  1.090
 B7B  CAJ  H4   single    0.970  0.020  1.090
 B7B  CAJ  H5   single    0.970  0.020  1.090
 B7B  CAK  H6   single    0.970  0.020  1.090
 B7B  CAK  H7   single    0.970  0.020  1.090
 B7B  CAN  H8   single    0.970  0.020  1.090
 B7B  CAN  H9   single    0.970  0.020  1.090
 B7B  CBA  H10  single    0.970  0.020  1.090
 B7B  CBC  H11  single    0.970  0.020  1.090
 B7B  CAP  H12  single    0.970  0.020  1.090
 B7B  CAP  H13  single    0.970  0.020  1.090
 B7B  CAL  H14  single    0.970  0.020  1.090
 B7B  CAL  H15  single    0.970  0.020  1.090
 B7B  CAO  H16  single    0.970  0.020  1.090
 B7B  CAO  H17  single    0.970  0.020  1.090
 B7B  CBB  H18  single    0.970  0.020  1.090
 B7B  CAA  H19  single    0.970  0.020  1.090
 B7B  CAA  H20  single    0.970  0.020  1.090
 B7B  CAA  H21  single    0.970  0.020  1.090
 B7B  NAS  H22  single    0.860  0.020  1.020
 B7B  CAE  H23  single    0.930  0.020  1.080
 B7B  CAG  H24  single    0.930  0.020  1.080
 B7B  NAB  H25  single    0.860  0.020  1.020
 B7B  NAB  H26  single    0.860  0.020  1.020
 B7B  CAH  H27  single    0.930  0.020  1.080
 B7B  CAF  H28  single    0.930  0.020  1.080

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
 B7B  NBE  C4   N3   117.39  3.000
 B7B  NBE  C4   C5   121.50  3.000
 B7B  N3   C4   C5   121.05  3.000
 B7B  NBD  C5   C6   121.62  3.000
 B7B  NBD  C5   C4   122.29  3.000
 B7B  C6   C5   C4   116.04  3.000
 B7B  H1   C6   N1   116.51  3.000
 B7B  H1   C6   C5   120.49  3.000
 B7B  N1   C6   C5   123.00  3.000
 B7B  C2   N1   C6   116.41  3.000
 B7B  C2   N3   C4   118.05  3.000
 B7B  H3   CAM  H2   107.41  3.000
 B7B  H3   CAM  CBA  113.12  3.000
 B7B  H2   CAM  CBA  108.09  3.000
 B7B  H3   CAM  CAJ  112.17  3.000
 B7B  H2   CAM  CAJ  110.87  3.000
 B7B  CBA  CAM  CAJ  105.15  3.000
 B7B  H5   CAJ  H4   106.61  3.000
 B7B  H5   CAJ  CAK  111.27  3.000
 B7B  H4   CAJ  CAK  111.06  3.000
 B7B  H5   CAJ  CAM  110.39  3.000
 B7B  H4   CAJ  CAM  111.74  3.000
 B7B  CAK  CAJ  CAM  105.85  3.000
 B7B  H7   CAK  H6   106.91  3.000
 B7B  H7   CAK  CAN  112.40  3.000
 B7B  H6   CAK  CAN  109.53  3.000
 B7B  H7   CAK  CAJ  112.82  3.000
 B7B  H6   CAK  CAJ  110.29  3.000
 B7B  CAN  CAK  CAJ  104.91  3.000
 B7B  H9   CAN  H8   107.76  3.000
 B7B  H9   CAN  CBA  109.26  3.000
 B7B  H8   CAN  CBA  113.61  3.000
 B7B  H9   CAN  CAK  110.70  3.000
 B7B  H8   CAN  CAK  112.75  3.000
 B7B  CBA  CAN  CAK  102.71  3.000
 B7B  H10  CBA  NBE  112.15  3.000
 B7B  H10  CBA  CAN  107.66  3.000
 B7B  NBE  CBA  CAN  113.45  3.000
 B7B  H10  CBA  CAM  108.26  3.000
 B7B  CAN  CBA  CAM  102.50  3.000
 B7B  NBE  CBA  CAM  112.25  3.000
 B7B  CBC  NBE  CBA  116.10  3.000
 B7B  CBC  NBE  C4   113.26  3.000
 B7B  CBA  NBE  C4   116.00  3.000
 B7B  H11  CBC  CBB  108.99  3.000
 B7B  H11  CBC  CAP  109.82  3.000
 B7B  CBB  CBC  CAP  102.63  3.000
 B7B  H11  CBC  NBE  105.82  3.000
 B7B  CAP  CBC  NBE  113.04  3.000
 B7B  CBB  CBC  NBE  116.48  3.000
 B7B  H13  CAP  H12  107.24  3.000
 B7B  H13  CAP  CAL  109.43  3.000
 B7B  H12  CAP  CAL  113.88  3.000
 B7B  H13  CAP  CBC  108.15  3.000
 B7B  H12  CAP  CBC  111.61  3.000
 B7B  CAL  CAP  CBC  106.42  3.000
 B7B  H15  CAL  H14  106.36  3.000
 B7B  H15  CAL  CAO  111.72  3.000
 B7B  H14  CAL  CAO  110.81  3.000
 B7B  H15  CAL  CAP  111.80  3.000
 B7B  H14  CAL  CAP  111.16  3.000
 B7B  CAO  CAL  CAP  105.09  3.000
 B7B  H17  CAO  H16  106.11  3.000
 B7B  H17  CAO  CBB  108.76  3.000
 B7B  H16  CAO  CBB  112.91  3.000
 B7B  H17  CAO  CAL  110.92  3.000
 B7B  H16  CAO  CAL  111.65  3.000
 B7B  CBB  CAO  CAL  106.53  3.000
 B7B  H18  CBB  CAU  104.85  3.000
 B7B  H18  CBB  CAO  107.92  3.000
 B7B  CAU  CBB  CAO  114.69  3.000
 B7B  H18  CBB  CBC  106.25  3.000
 B7B  CAO  CBB  CBC  107.08  3.000
 B7B  CAU  CBB  CBC  115.48  3.000
 B7B  NBD  CAU  OAD  120.07  3.000
 B7B  OAD  CAU  CBB  121.68  3.000
 B7B  NBD  CAU  CBB  118.24  3.000
 B7B  CAA  NBD  CAU  117.81  3.000
 B7B  CAU  NBD  C5   123.18  3.000
 B7B  CAA  NBD  C5   118.84  3.000
 B7B  H21  CAA  H20  108.10  3.000
 B7B  H21  CAA  H19  108.52  3.000
 B7B  H20  CAA  H19  108.54  3.000
 B7B  H21  CAA  NBD  109.17  3.000
 B7B  H20  CAA  NBD  110.75  3.000
 B7B  H19  CAA  NBD  111.67  3.000
 B7B  NAS  C2   N3   114.04  3.000
 B7B  N3   C2   N1   125.42  3.000
 B7B  NAS  C2   N1   120.54  3.000
 B7B  H22  NAS  CAV  115.28  3.000
 B7B  H22  NAS  C2   112.85  3.000
 B7B  CAV  NAS  C2   131.83  3.000
 B7B  CAF  CAV  CAE  118.31  3.000
 B7B  CAF  CAV  NAS  125.30  3.000
 B7B  CAE  CAV  NAS  116.38  3.000
 B7B  H23  CAE  CAG  119.39  3.000
 B7B  H23  CAE  CAV  119.59  3.000
 B7B  CAG  CAE  CAV  121.02  3.000
 B7B  H24  CAG  CAW  119.91  3.000
 B7B  H24  CAG  CAE  119.00  3.000
 B7B  CAW  CAG  CAE  121.09  3.000
 B7B  CAH  CAW  CAT  124.02  3.000
 B7B  CAT  CAW  CAG  118.32  3.000
 B7B  CAH  CAW  CAG  117.65  3.000
 B7B  NAB  CAT  OAC  122.08  3.000
 B7B  OAC  CAT  CAW  120.95  3.000
 B7B  NAB  CAT  CAW  116.97  3.000
 B7B  H26  NAB  H25  116.65  3.000
 B7B  H26  NAB  CAT  119.33  3.000
 B7B  H25  NAB  CAT  123.12  3.000
 B7B  H27  CAH  CAF  116.77  3.000
 B7B  H27  CAH  CAW  121.16  3.000
 B7B  CAF  CAH  CAW  122.06  3.000
 B7B  H28  CAF  CAH  119.44  3.000
 B7B  H28  CAF  CAV  120.69  3.000
 B7B  CAH  CAF  CAV  119.87  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
 B7B  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 B7B  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 B7B  CONST_03  C2   N1   C6   C5      0.00   0.0  0
 B7B  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 B7B  CONST_05  N3   C2   N1   C6      0.00   0.0  0
 B7B  CONST_06  N3   C4   C5   C6      0.00   0.0  0
 B7B  CONST_07  CAW  CAG  CAE  CAV     0.00   0.0  0
 B7B  CONST_08  CAW  CAH  CAF  CAV     0.00   0.0  0
 B7B  CONST_09  CAH  CAF  CAV  CAE     0.00   0.0  0
 B7B  CONST_10  CAH  CAW  CAG  CAE     0.00   0.0  0
 B7B  CONST_11  CAF  CAV  CAE  CAG     0.00   0.0  0
 B7B  CONST_12  CAF  CAH  CAW  CAG     0.00   0.0  0
 B7B  CONST_13  CBB  CAU  NBD  C5      0.00   0.0  0
 B7B  CONST_14  NAS  C2   N3   C4    180.00   0.0  0
 B7B  CONST_15  NAS  C2   N1   C6    180.00   0.0  0
 B7B  CONST_16  CAG  CAE  CAV  NAS   180.00   0.0  0
 B7B  CONST_17  CAH  CAF  CAV  NAS   180.00   0.0  0
 B7B  CONST_18  CAT  CAW  CAG  CAE   180.00   0.0  0
 B7B  CONST_19  CAF  CAH  CAW  CAT   180.00   0.0  0
 B7B  CONST_20  OAD  CAU  NBD  C5    180.00   0.0  0
 B7B  CONST_21  CAA  NBD  CAU  CBB   180.00   0.0  0
 B7B  CONST_22  H1   C6   C5   C4    180.00   0.0  0
 B7B  CONST_23  H24  CAG  CAE  CAV   180.00   0.0  0
 B7B  CONST_24  H27  CAH  CAF  CAV   180.00   0.0  0
 B7B  CONST_25  H28  CAF  CAV  CAE   180.00   0.0  0
 B7B  CONST_26  H23  CAE  CAG  CAW   180.00   0.0  0
 B7B  CONST_27  CAA  NBD  CAU  OAD     0.00   0.0  0
 B7B  CONST_28  H25  NAB  CAT  CAW     0.00   0.0  0
 B7B  CONST_29  H26  NAB  CAT  CAW   180.00   0.0  0
 B7B  Var_01    CAU  NBD  C5   C4    -49.43  30.0  1
 B7B  Var_02    CBA  NBE  C4   C5    -71.53  30.0  1
 B7B  Var_03    CAN  CAK  CAJ  CAM   -14.73  30.0  1
 B7B  Var_04    CBA  CAN  CAK  CAJ    36.23  30.0  1
 B7B  Var_05    CBA  CAM  CAJ  CAK   -12.30  30.0  1
 B7B  Var_06    CAO  CAL  CAP  CBC   -32.60  30.0  1
 B7B  Var_07    CBB  CAO  CAL  CAP    16.45  30.0  1
 B7B  Var_08    CAV  NAS  C2   N1     -3.91  30.0  1
 B7B  Var_09    CAE  CAV  NAS  C2    179.48  30.0  2
 B7B  Var_10    NAB  CAT  CAW  CAG  -168.36  30.0  2
 B7B  Var_11    H19  CAA  NBD  C5    118.11  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
 B7B  chir_01  CBA  NBE  CAM  CAN  negativ
 B7B  chir_02  CBC  NBE  CBB  CAP  negativ
 B7B  chir_03  CBB  CAO  CBC  CAU  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
 B7B  plan-1  NAS  0.020
 B7B  plan-1  CAV  0.020
 B7B  plan-1  CAE  0.020
 B7B  plan-1  CAG  0.020
 B7B  plan-1  CAW  0.020
 B7B  plan-1  CAT  0.020
 B7B  plan-1  CAH  0.020
 B7B  plan-1  CAF  0.020
 B7B  plan-1  H23  0.020
 B7B  plan-1  H24  0.020
 B7B  plan-1  H27  0.020
 B7B  plan-1  H28  0.020
 B7B  plan-2  C4   0.020
 B7B  plan-2  C5   0.020
 B7B  plan-2  C6   0.020
 B7B  plan-2  N1   0.020
 B7B  plan-2  N3   0.020
 B7B  plan-2  NBE  0.020
 B7B  plan-2  NBD  0.020
 B7B  plan-2  C2   0.020
 B7B  plan-2  NAS  0.020
 B7B  plan-2  H1   0.020
 B7B  plan-3  C5   0.020
 B7B  plan-3  CBB  0.020
 B7B  plan-3  CAU  0.020
 B7B  plan-3  OAD  0.020
 B7B  plan-3  NBD  0.020
 B7B  plan-3  CAA  0.020
 B7B  plan-4  CAW  0.020
 B7B  plan-4  CAT  0.020
 B7B  plan-4  OAC  0.020
 B7B  plan-4  NAB  0.020
 B7B  plan-4  H25  0.020
 B7B  plan-4  H26  0.020

