# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 00:23:35 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-[(4S)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepin-8-yl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN(c2ccc(Cl)cc2)c3cc(ccc3n4c(C)nnc14)c5ccc(N)nc5
#
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
 559  559  5-[(4S)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepin-8-yl]pyridin-2-amine  ligand  51  30  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_559
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
 559  CAU  C   CR16  0  -0.190  -4.4193  -0.0914  -1.2535
 559  CAT  C   CR16  0  -0.373  -5.5985  -0.7828  -1.1264
 559  CAS  C   CR6   0   0.455  -5.8592  -1.4584   0.0810
 559  NBA  N   NH2   0  -0.831  -7.0244  -2.1287   0.2728
 559  NAR  N   N     0  -0.454  -4.9941  -1.4320   1.0945
 559  CAQ  C   CR16  0  -0.105  -3.8623  -0.7575   0.9479
 559  CAO  C   CR6   0  -0.026  -3.4964  -0.0641  -0.1988
 559  CAM  C   CR6   0   0.113  -2.2185   0.6560  -0.2936
 559  CAN  C   CR16  0  -0.359  -1.0727   0.1615   0.3259
 559  CAC  C   CR6   0   0.283   0.1463   0.8235   0.2415
 559  CAL  C   CR16  0  -0.334  -2.1234   1.8617  -0.9936
 559  CAK  C   CR16  0  -0.266  -0.9248   2.5467  -1.0654
 559  CAB  C   CR6   0   0.281   0.2119   2.0241  -0.4665
 559  NAA  N   NR5   0  -0.573   1.4407   2.7085  -0.5113
 559  CAJ  C   CR5   0   0.386   2.1062   3.2440  -1.5765
 559  CBC  C   CH3   0  -0.757   1.6272   3.2221  -2.9786
 559  NAI  N   N     0  -0.342   3.2336   3.7431  -1.1603
 559  NAH  N   N     0  -0.332   3.3238   3.5391   0.1823
 559  CAG  C   CR5   0   0.448   2.2516   2.9137   0.5628
 559  CAF  C   CH1   0  -0.420   1.9015   2.4694   1.9400
 559  CBB  C   CH3   0  -0.653   0.6475   3.1555   2.4922
 559  CAE  C   CH2   0  -0.281   1.8613   0.9342   2.0199
 559  NAD  N   NT    0  -0.603   1.3104   0.2922   0.8339
 559  CAP  C   CR6   0   0.346   1.6000  -1.0524   0.6074
 559  CAV  C   CR16  0  -0.354   2.1644  -1.8682   1.5911
 559  CAW  C   CR16  0  -0.200   2.4797  -3.1940   1.3239
 559  CAX  C   CR6   0  -0.068   2.2204  -3.7259   0.0749
 559  CLB  CL  CL    0  -0.141   2.6042  -5.3858  -0.2574
 559  CAY  C   CR16  0  -0.202   1.6554  -2.9368  -0.9178
 559  CAZ  C   CR16  0  -0.306   1.3571  -1.6141  -0.6540
 559  H1   H   HCR6  0   0.265  -4.2007   0.4170  -2.1849
 559  H2   H   HCR6  0   0.272  -6.3120  -0.8185  -1.9390
 559  H3   H   HNH2  0   0.395  -7.5623  -2.3965  -0.5338
 559  H4   H   HNH2  0   0.386  -7.0624  -2.7741   1.0441
 559  H5   H   HCR6  0   0.257  -3.2057  -0.7556   1.8130
 559  H6   H   HCR6  0   0.269  -1.1102  -0.7782   0.8633
 559  H7   H   HCR6  0   0.264  -3.0001   2.2921  -1.4594
 559  H8   H   HCR6  0   0.280  -0.8815   3.4999  -1.5751
 559  H9   H   HCH3  0   0.267   0.8245   3.9401  -3.1479
 559  H10  H   HCH3  0   0.278   2.4509   3.4807  -3.6400
 559  H11  H   HCH3  0   0.265   1.2565   2.2360  -3.2580
 559  H12  H   HCH1  0   0.299   2.7366   2.7793   2.5711
 559  H13  H   HCH3  0   0.236  -0.2693   2.8550   1.9879
 559  H14  H   HCH3  0   0.249   0.5381   2.9049   3.5471
 559  H15  H   HCH3  0   0.247   0.7359   4.2388   2.4148
 559  H16  H   HCH2  0   0.269   2.8868   0.5792   2.1251
 559  H17  H   HCH2  0   0.246   1.3230   0.6420   2.9306
 559  H18  H   HCR6  0   0.282   2.3574  -1.4926   2.5861
 559  H19  H   HCR6  0   0.279   2.9147  -3.8041   2.1041
 559  H20  H   HCR6  0   0.279   1.4598  -3.3438  -1.9009
 559  H21  H   HCR6  0   0.275   0.9336  -1.0113  -1.4470

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
 559  CLB  CAX  single    1.736  0.020  1.736
 559  CAX  CAY  aromatic  1.388  0.020  1.388
 559  CAX  CAW  aromatic  1.382  0.020  1.382
 559  CAY  CAZ  aromatic  1.381  0.020  1.381
 559  CAW  CAV  aromatic  1.389  0.020  1.389
 559  NBA  CAS  single    1.358  0.020  1.358
 559  CAT  CAS  aromatic  1.408  0.020  1.408
 559  CAT  CAU  aromatic  1.373  0.020  1.373
 559  CAZ  CAP  aromatic  1.402  0.020  1.402
 559  CAS  NAR  aromatic  1.333  0.020  1.333
 559  CAV  CAP  aromatic  1.397  0.020  1.397
 559  CAU  CAO  aromatic  1.402  0.020  1.402
 559  CAP  NAD  single    1.394  0.020  1.394
 559  NAR  CAQ  aromatic  1.326  0.020  1.326
 559  CAO  CAQ  aromatic  1.389  0.020  1.389
 559  CAO  CAM  single    1.470  0.020  1.470
 559  CAN  CAM  aromatic  1.393  0.020  1.393
 559  CAN  CAC  aromatic  1.390  0.020  1.390
 559  NAD  CAE  single    1.457  0.020  1.457
 559  NAD  CAC  single    1.410  0.020  1.410
 559  CAM  CAL  aromatic  1.397  0.020  1.397
 559  CAE  CAF  single    1.538  0.020  1.538
 559  CAC  CAB  aromatic  1.395  0.020  1.395
 559  CAL  CAK  aromatic  1.382  0.020  1.382
 559  CAB  CAK  aromatic  1.387  0.020  1.387
 559  CAB  NAA  aromatic  1.407  0.020  1.407
 559  CAF  CBB  single    1.532  0.020  1.532
 559  CAF  CAG  single    1.489  0.020  1.489
 559  NAA  CAG  aromatic  1.361  0.020  1.361
 559  NAA  CAJ  aromatic  1.365  0.020  1.365
 559  CAG  NAH  aromatic  1.298  0.020  1.298
 559  NAH  NAI  aromatic  1.361  0.020  1.361
 559  CAJ  CBC  single    1.482  0.020  1.482
 559  CAJ  NAI  aromatic  1.301  0.020  1.301
 559  CAU  H1   single    0.930  0.020  1.080
 559  CAT  H2   single    0.930  0.020  1.080
 559  NBA  H3   single    0.890  0.020  1.040
 559  NBA  H4   single    0.890  0.020  1.040
 559  CAQ  H5   single    0.930  0.020  1.080
 559  CAN  H6   single    0.930  0.020  1.080
 559  CAL  H7   single    0.930  0.020  1.080
 559  CAK  H8   single    0.930  0.020  1.080
 559  CBC  H9   single    0.970  0.020  1.090
 559  CBC  H10  single    0.970  0.020  1.090
 559  CBC  H11  single    0.970  0.020  1.090
 559  CAF  H12  single    0.970  0.020  1.090
 559  CBB  H13  single    0.970  0.020  1.090
 559  CBB  H14  single    0.970  0.020  1.090
 559  CBB  H15  single    0.970  0.020  1.090
 559  CAE  H16  single    0.970  0.020  1.090
 559  CAE  H17  single    0.970  0.020  1.090
 559  CAV  H18  single    0.930  0.020  1.080
 559  CAW  H19  single    0.930  0.020  1.080
 559  CAY  H20  single    0.930  0.020  1.080
 559  CAZ  H21  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
 559  H1   CAU  CAO  120.33  3.000
 559  H1   CAU  CAT  119.29  3.000
 559  CAO  CAU  CAT  120.38  3.000
 559  H2   CAT  CAS  120.41  3.000
 559  H2   CAT  CAU  120.90  3.000
 559  CAS  CAT  CAU  118.69  3.000
 559  NAR  CAS  NBA  117.35  3.000
 559  NAR  CAS  CAT  121.49  3.000
 559  NBA  CAS  CAT  121.13  3.000
 559  H4   NBA  H3   115.07  3.000
 559  H4   NBA  CAS  117.21  3.000
 559  H3   NBA  CAS  118.49  3.000
 559  CAQ  NAR  CAS  118.70  3.000
 559  H5   CAQ  CAO  119.83  3.000
 559  H5   CAQ  NAR  115.40  3.000
 559  CAO  CAQ  NAR  124.76  3.000
 559  CAM  CAO  CAQ  121.79  3.000
 559  CAM  CAO  CAU  122.23  3.000
 559  CAQ  CAO  CAU  115.98  3.000
 559  CAL  CAM  CAN  118.23  3.000
 559  CAL  CAM  CAO  120.94  3.000
 559  CAN  CAM  CAO  120.82  3.000
 559  H6   CAN  CAC  118.28  3.000
 559  H6   CAN  CAM  120.00  3.000
 559  CAC  CAN  CAM  121.69  3.000
 559  NAD  CAC  CAB  119.90  3.000
 559  CAB  CAC  CAN  118.81  3.000
 559  NAD  CAC  CAN  121.28  3.000
 559  H7   CAL  CAK  118.89  3.000
 559  H7   CAL  CAM  120.24  3.000
 559  CAK  CAL  CAM  120.83  3.000
 559  H8   CAK  CAB  120.18  3.000
 559  H8   CAK  CAL  119.72  3.000
 559  CAB  CAK  CAL  120.09  3.000
 559  NAA  CAB  CAK  121.24  3.000
 559  NAA  CAB  CAC  118.40  3.000
 559  CAK  CAB  CAC  120.32  3.000
 559  CAG  NAA  CAJ  105.43  3.000
 559  CAJ  NAA  CAB  129.88  3.000
 559  CAG  NAA  CAB  124.63  3.000
 559  NAI  CAJ  CBC  126.04  3.000
 559  NAI  CAJ  NAA  108.86  3.000
 559  CBC  CAJ  NAA  125.08  3.000
 559  H11  CBC  H10  108.47  3.000
 559  H11  CBC  H9   107.80  3.000
 559  H10  CBC  H9   107.85  3.000
 559  H11  CBC  CAJ  111.46  3.000
 559  H10  CBC  CAJ  109.09  3.000
 559  H9   CBC  CAJ  112.04  3.000
 559  NAH  NAI  CAJ  108.39  3.000
 559  CAG  NAH  NAI  107.85  3.000
 559  CAF  CAG  NAH  127.52  3.000
 559  NAH  CAG  NAA  109.47  3.000
 559  CAF  CAG  NAA  123.01  3.000
 559  H12  CAF  CAE  105.87  3.000
 559  H12  CAF  CBB  106.89  3.000
 559  CAE  CAF  CBB  114.01  3.000
 559  H12  CAF  CAG  105.68  3.000
 559  CBB  CAF  CAG  113.09  3.000
 559  CAE  CAF  CAG  110.62  3.000
 559  H15  CBB  H14  107.79  3.000
 559  H15  CBB  H13  108.04  3.000
 559  H14  CBB  H13  107.48  3.000
 559  H15  CBB  CAF  110.68  3.000
 559  H14  CBB  CAF  109.15  3.000
 559  H13  CBB  CAF  113.49  3.000
 559  H17  CAE  H16  107.13  3.000
 559  H17  CAE  NAD  111.89  3.000
 559  H16  CAE  NAD  106.91  3.000
 559  H17  CAE  CAF  108.76  3.000
 559  H16  CAE  CAF  107.78  3.000
 559  NAD  CAE  CAF  114.05  3.000
 559  CAP  NAD  CAE  118.60  3.000
 559  CAE  NAD  CAC  119.23  3.000
 559  CAP  NAD  CAC  117.82  3.000
 559  CAZ  CAP  CAV  118.01  3.000
 559  CAV  CAP  NAD  122.19  3.000
 559  CAZ  CAP  NAD  119.78  3.000
 559  H18  CAV  CAW  117.92  3.000
 559  H18  CAV  CAP  121.16  3.000
 559  CAW  CAV  CAP  120.91  3.000
 559  H19  CAW  CAX  120.68  3.000
 559  H19  CAW  CAV  119.40  3.000
 559  CAX  CAW  CAV  119.91  3.000
 559  CAY  CAX  CLB  119.77  3.000
 559  CAY  CAX  CAW  120.26  3.000
 559  CLB  CAX  CAW  119.97  3.000
 559  H20  CAY  CAZ  119.65  3.000
 559  H20  CAY  CAX  120.64  3.000
 559  CAZ  CAY  CAX  119.70  3.000
 559  H21  CAZ  CAY  118.54  3.000
 559  H21  CAZ  CAP  120.26  3.000
 559  CAY  CAZ  CAP  121.20  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
 559  CONST_01  NAR  CAS  CAT  CAU    0.00   0.0  0
 559  CONST_02  NAR  CAQ  CAO  CAU    0.00   0.0  0
 559  CONST_05  CAQ  NAR  CAS  CAT    0.00   0.0  0
 559  CONST_06  CAQ  CAO  CAU  CAT    0.00   0.0  0
 559  CONST_07  CAM  CAO  CAU  CAT  180.00   0.0  0
 559  CONST_08  CAO  CAU  CAT  CAS    0.00   0.0  0
 559  CONST_09  CAO  CAQ  NAR  CAS    0.00   0.0  0
 559  CONST_10  CAM  CAO  CAQ  NAR  180.00   0.0  0
 559  CONST_13  CAC  CAN  CAM  CAO  180.00   0.0  0
 559  CONST_14  CAK  CAL  CAM  CAO  180.00   0.0  0
 559  CONST_15  CAB  CAK  CAL  CAM    0.00   0.0  0
 559  CONST_16  CAK  CAL  CAM  CAN    0.00   0.0  0
 559  CONST_17  CAL  CAM  CAN  CAC    0.00   0.0  0
 559  CONST_18  NAH  NAI  CAJ  NAA    0.00   0.0  0
 559  CONST_19  CAG  NAH  NAI  CAJ    0.00   0.0  0
 559  CONST_20  CAX  CAY  CAZ  CAP    0.00   0.0  0
 559  CONST_21  CAX  CAW  CAV  CAP    0.00   0.0  0
 559  CONST_22  CAY  CAX  CAW  CAV    0.00   0.0  0
 559  CONST_23  CAY  CAZ  CAP  CAV    0.00   0.0  0
 559  CONST_24  CAZ  CAY  CAX  CAW    0.00   0.0  0
 559  CONST_25  CAZ  CAP  CAV  CAW    0.00   0.0  0
 559  CONST_26  CAY  CAZ  CAP  NAD  180.00   0.0  0
 559  CONST_27  CAW  CAV  CAP  NAD  180.00   0.0  0
 559  CONST_28  NBA  CAS  CAT  CAU  180.00   0.0  0
 559  CONST_29  CAQ  NAR  CAS  NBA  180.00   0.0  0
 559  CONST_30  NAH  NAI  CAJ  CBC  180.00   0.0  0
 559  CONST_31  CLB  CAX  CAW  CAV  180.00   0.0  0
 559  CONST_32  CAZ  CAY  CAX  CLB  180.00   0.0  0
 559  CONST_33  H5   CAQ  CAO  CAU  180.00   0.0  0
 559  CONST_34  H1   CAU  CAT  CAS  180.00   0.0  0
 559  CONST_35  H2   CAT  CAS  NAR  180.00   0.0  0
 559  CONST_36  H6   CAN  CAM  CAO    0.00   0.0  0
 559  CONST_37  H7   CAL  CAM  CAO    0.00   0.0  0
 559  CONST_38  H8   CAK  CAL  CAM  180.00   0.0  0
 559  CONST_39  H21  CAZ  CAP  NAD    0.00   0.0  0
 559  CONST_40  H18  CAV  CAP  NAD    0.00   0.0  0
 559  CONST_41  H20  CAY  CAZ  CAP  180.00   0.0  0
 559  CONST_42  H19  CAW  CAV  CAP  180.00   0.0  0
 559  CONST_44  H4   NBA  CAS  CAT  180.00   0.0  0
 559  Var_01    H9   CBC  CAJ  NAA   75.10  30.0  2

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
 559  chir_01  CAF  CAE  CBB  CAG  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
 559  plan-1  CAU  0.020
 559  plan-1  CAT  0.020
 559  plan-1  CAS  0.020
 559  plan-1  NBA  0.020
 559  plan-1  NAR  0.020
 559  plan-1  CAQ  0.020
 559  plan-1  CAO  0.020
 559  plan-1  CAM  0.020
 559  plan-1  H1   0.020
 559  plan-1  H2   0.020
 559  plan-1  H5   0.020
 559  plan-2  NAD  0.020
 559  plan-2  CAP  0.020
 559  plan-2  CAV  0.020
 559  plan-2  CAW  0.020
 559  plan-2  CAX  0.020
 559  plan-2  CLB  0.020
 559  plan-2  CAY  0.020
 559  plan-2  CAZ  0.020
 559  plan-2  H18  0.020
 559  plan-2  H19  0.020
 559  plan-2  H20  0.020
 559  plan-2  H21  0.020
 559  plan-3  CAB  0.020
 559  plan-3  NAA  0.020
 559  plan-3  CAJ  0.020
 559  plan-3  CBC  0.020
 559  plan-3  NAI  0.020
 559  plan-3  NAH  0.020
 559  plan-3  CAG  0.020
 559  plan-3  CAF  0.020
 559  plan-4  CAO  0.020
 559  plan-4  CAM  0.020
 559  plan-4  CAN  0.020
 559  plan-4  CAC  0.020
 559  plan-4  CAL  0.020
 559  plan-4  CAK  0.020
 559  plan-4  CAB  0.020
 559  plan-4  NAA  0.020
 559  plan-4  NAD  0.020
 559  plan-4  H6   0.020
 559  plan-4  H7   0.020
 559  plan-4  H8   0.020
 559  plan-5  CAS  0.020
 559  plan-5  NBA  0.020
 559  plan-5  H3   0.020
 559  plan-5  H4   0.020

