# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 20:44:10 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-[(4R)-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
 558  558  5-[(4R)-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_558
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
 558  CAU  C   CR16  0  -0.193  -4.7014   0.4487   0.3082
 558  CAT  C   CR16  0  -0.373  -5.8507  -0.2994   0.2469
 558  CAS  C   CR6   0   0.456  -5.7408  -1.7014   0.1754
 558  NBA  N   NH2   0  -0.831  -6.8397  -2.4873   0.0566
 558  NAR  N   N     0  -0.454  -4.5539  -2.3078   0.1822
 558  CAQ  C   CR16  0  -0.101  -3.4590  -1.5635   0.2414
 558  CAO  C   CR6   0  -0.025  -3.4466  -0.1753   0.3000
 558  CAM  C   CR6   0   0.117  -2.1895   0.5826   0.3685
 558  CAN  C   CR16  0  -0.359  -1.0518   0.1371  -0.3007
 558  CAC  C   CR6   0   0.285   0.1580   0.8174  -0.2207
 558  CAL  C   CR16  0  -0.335  -2.1044   1.7736   1.0945
 558  CAK  C   CR16  0  -0.265  -0.9216   2.4866   1.1477
 558  CAB  C   CR6   0   0.274   0.2141   2.0013   0.5158
 558  NAA  N   NR5   0  -0.572   1.4282   2.7118   0.5566
 558  CAJ  C   CR5   0   0.386   2.1041   3.2310   1.6234
 558  CBC  C   CH3   0  -0.757   1.6531   3.1609   3.0332
 558  NAI  N   N     0  -0.342   3.2102   3.7694   1.1991
 558  NAH  N   N     0  -0.332   3.2761   3.6083  -0.1504
 558  CAG  C   CR5   0   0.448   2.2106   2.9692  -0.5270
 558  CAF  C   CH1   0  -0.421   1.8418   2.5521  -1.9074
 558  CBB  C   CH3   0  -0.654   0.5588   3.2175  -2.4164
 558  CAE  C   CH2   0  -0.281   1.8438   1.0200  -2.0274
 558  NAD  N   NT    0  -0.603   1.3131   0.3261  -0.8609
 558  CAP  C   CR6   0   0.345   1.6202  -1.0247  -0.6984
 558  CAV  C   CR16  0  -0.305   1.4033  -1.6462   0.5394
 558  CAW  C   CR16  0  -0.201   1.7176  -2.9766   0.7370
 558  CAX  C   CR6   0  -0.068   2.2725  -3.7143  -0.3000
 558  CLB  CL  CL    0  -0.141   2.6747  -5.3839  -0.0509
 558  CAY  C   CR16  0  -0.200   2.5068  -3.1226  -1.5267
 558  CAZ  C   CR16  0  -0.353   2.1759  -1.7891  -1.7270
 558  H1   H   HCR6  0   0.264  -4.7763   1.5285   0.3445
 558  H2   H   HCR6  0   0.271  -6.8227   0.1763   0.2421
 558  H3   H   HNH2  0   0.396  -7.7382  -2.1069   0.2992
 558  H4   H   HNH2  0   0.387  -6.7264  -3.4713   0.2331
 558  H5   H   HCR6  0   0.251  -2.5236  -2.1153   0.2650
 558  H6   H   HCR6  0   0.270  -1.0988  -0.7579  -0.9090
 558  H7   H   HCR6  0   0.263  -2.9659   2.1511   1.6294
 558  H8   H   HCR6  0   0.280  -0.8832   3.4223   1.6893
 558  H9   H   HCH3  0   0.265   1.3022   2.1618   3.2914
 558  H10  H   HCH3  0   0.278   2.4856   3.4133   3.6859
 558  H11  H   HCH3  0   0.267   0.8435   3.8616   3.2383
 558  H12  H   HCH1  0   0.299   2.6551   2.9000  -2.5474
 558  H13  H   HCH3  0   0.247   0.6209   4.3005  -2.3132
 558  H14  H   HCH3  0   0.250   0.4334   2.9908  -3.4750
 558  H15  H   HCH3  0   0.237  -0.3391   2.8811  -1.9013
 558  H16  H   HCH2  0   0.246   1.3121   0.7388  -2.9455
 558  H17  H   HCH2  0   0.269   2.8787   0.6963  -2.1439
 558  H18  H   HCR6  0   0.275   0.9881  -1.0847   1.3662
 558  H19  H   HCR6  0   0.279   1.5417  -3.4303   1.7031
 558  H20  H   HCR6  0   0.279   2.9341  -3.6918  -2.3412
 558  H21  H   HCR6  0   0.282   2.3492  -1.3669  -2.7068

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
 558  NAI  NAH  aromatic  1.361  0.020  1.361
 558  NAI  CAJ  aromatic  1.301  0.020  1.301
 558  CBC  CAJ  single    1.482  0.020  1.482
 558  NAH  CAG  aromatic  1.298  0.020  1.298
 558  CAJ  NAA  aromatic  1.365  0.020  1.365
 558  CAG  NAA  aromatic  1.361  0.020  1.361
 558  CAG  CAF  single    1.488  0.020  1.488
 558  NAA  CAB  aromatic  1.407  0.020  1.407
 558  CBB  CAF  single    1.532  0.020  1.532
 558  CAK  CAB  aromatic  1.387  0.020  1.387
 558  CAK  CAL  aromatic  1.382  0.020  1.382
 558  CAF  CAE  single    1.537  0.020  1.537
 558  CAB  CAC  aromatic  1.395  0.020  1.395
 558  CAL  CAM  aromatic  1.397  0.020  1.397
 558  CAE  NAD  single    1.457  0.020  1.457
 558  CAC  NAD  single    1.409  0.020  1.409
 558  CAC  CAN  aromatic  1.390  0.020  1.390
 558  CAM  CAN  aromatic  1.393  0.020  1.393
 558  CAM  CAO  single    1.470  0.020  1.470
 558  NAD  CAP  single    1.395  0.020  1.395
 558  CAQ  CAO  aromatic  1.389  0.020  1.389
 558  CAQ  NAR  aromatic  1.325  0.020  1.325
 558  CAO  CAU  aromatic  1.401  0.020  1.401
 558  CAP  CAV  aromatic  1.402  0.020  1.402
 558  CAP  CAZ  aromatic  1.397  0.020  1.397
 558  NAR  CAS  aromatic  1.333  0.020  1.333
 558  CAU  CAT  aromatic  1.373  0.020  1.373
 558  CAV  CAW  aromatic  1.381  0.020  1.381
 558  CAZ  CAY  aromatic  1.389  0.020  1.389
 558  CAS  CAT  aromatic  1.408  0.020  1.408
 558  CAS  NBA  single    1.356  0.020  1.356
 558  CAW  CAX  aromatic  1.388  0.020  1.388
 558  CAY  CAX  aromatic  1.382  0.020  1.382
 558  CAX  CLB  single    1.735  0.020  1.735
 558  CAU  H1   single    0.930  0.020  1.080
 558  CAT  H2   single    0.930  0.020  1.080
 558  NBA  H3   single    0.890  0.020  1.040
 558  NBA  H4   single    0.890  0.020  1.040
 558  CAQ  H5   single    0.930  0.020  1.080
 558  CAN  H6   single    0.930  0.020  1.080
 558  CAL  H7   single    0.930  0.020  1.080
 558  CAK  H8   single    0.930  0.020  1.080
 558  CBC  H9   single    0.970  0.020  1.090
 558  CBC  H10  single    0.970  0.020  1.090
 558  CBC  H11  single    0.970  0.020  1.090
 558  CAF  H12  single    0.970  0.020  1.090
 558  CBB  H13  single    0.970  0.020  1.090
 558  CBB  H14  single    0.970  0.020  1.090
 558  CBB  H15  single    0.970  0.020  1.090
 558  CAE  H16  single    0.970  0.020  1.090
 558  CAE  H17  single    0.970  0.020  1.090
 558  CAV  H18  single    0.930  0.020  1.080
 558  CAW  H19  single    0.930  0.020  1.080
 558  CAY  H20  single    0.930  0.020  1.080
 558  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
 558  H1   CAU  CAO  120.40  3.000
 558  H1   CAU  CAT  119.14  3.000
 558  CAO  CAU  CAT  120.45  3.000
 558  H2   CAT  CAS  120.50  3.000
 558  H2   CAT  CAU  120.84  3.000
 558  CAS  CAT  CAU  118.65  3.000
 558  NAR  CAS  NBA  117.28  3.000
 558  NBA  CAS  CAT  121.21  3.000
 558  NAR  CAS  CAT  121.49  3.000
 558  H4   NBA  H3   115.36  3.000
 558  H4   NBA  CAS  117.39  3.000
 558  H3   NBA  CAS  118.93  3.000
 558  CAQ  NAR  CAS  118.71  3.000
 558  H5   CAQ  CAO  119.93  3.000
 558  H5   CAQ  NAR  115.28  3.000
 558  CAO  CAQ  NAR  124.78  3.000
 558  CAM  CAO  CAQ  121.66  3.000
 558  CAQ  CAO  CAU  115.92  3.000
 558  CAM  CAO  CAU  122.41  3.000
 558  CAL  CAM  CAN  118.19  3.000
 558  CAN  CAM  CAO  120.75  3.000
 558  CAL  CAM  CAO  121.06  3.000
 558  H6   CAN  CAC  118.32  3.000
 558  H6   CAN  CAM  119.91  3.000
 558  CAC  CAN  CAM  121.77  3.000
 558  NAD  CAC  CAB  120.18  3.000
 558  NAD  CAC  CAN  121.10  3.000
 558  CAB  CAC  CAN  118.72  3.000
 558  H7   CAL  CAK  118.84  3.000
 558  H7   CAL  CAM  120.38  3.000
 558  CAK  CAL  CAM  120.78  3.000
 558  H8   CAK  CAB  120.10  3.000
 558  H8   CAK  CAL  119.72  3.000
 558  CAB  CAK  CAL  120.17  3.000
 558  NAA  CAB  CAK  121.09  3.000
 558  CAK  CAB  CAC  120.28  3.000
 558  NAA  CAB  CAC  118.58  3.000
 558  CAG  NAA  CAJ  105.40  3.000
 558  CAG  NAA  CAB  124.63  3.000
 558  CAJ  NAA  CAB  129.92  3.000
 558  NAI  CAJ  CBC  126.05  3.000
 558  CBC  CAJ  NAA  125.08  3.000
 558  NAI  CAJ  NAA  108.86  3.000
 558  H11  CBC  H10  107.85  3.000
 558  H11  CBC  H9   107.79  3.000
 558  H10  CBC  H9   108.49  3.000
 558  H11  CBC  CAJ  111.99  3.000
 558  H10  CBC  CAJ  109.09  3.000
 558  H9   CBC  CAJ  111.51  3.000
 558  NAH  NAI  CAJ  108.40  3.000
 558  CAG  NAH  NAI  107.83  3.000
 558  CAF  CAG  NAH  127.61  3.000
 558  CAF  CAG  NAA  122.88  3.000
 558  NAH  CAG  NAA  109.51  3.000
 558  H12  CAF  CAE  105.72  3.000
 558  H12  CAF  CBB  106.89  3.000
 558  CAE  CAF  CBB  114.09  3.000
 558  H12  CAF  CAG  105.65  3.000
 558  CAE  CAF  CAG  110.58  3.000
 558  CBB  CAF  CAG  113.19  3.000
 558  H15  CBB  H14  107.48  3.000
 558  H15  CBB  H13  108.02  3.000
 558  H14  CBB  H13  107.78  3.000
 558  H15  CBB  CAF  113.54  3.000
 558  H14  CBB  CAF  109.19  3.000
 558  H13  CBB  CAF  110.64  3.000
 558  H17  CAE  H16  107.12  3.000
 558  H17  CAE  NAD  106.84  3.000
 558  H16  CAE  NAD  111.78  3.000
 558  H17  CAE  CAF  107.79  3.000
 558  H16  CAE  CAF  108.67  3.000
 558  NAD  CAE  CAF  114.31  3.000
 558  CAP  NAD  CAE  118.31  3.000
 558  CAP  NAD  CAC  117.73  3.000
 558  CAE  NAD  CAC  119.75  3.000
 558  CAZ  CAP  CAV  117.98  3.000
 558  CAZ  CAP  NAD  122.13  3.000
 558  CAV  CAP  NAD  119.88  3.000
 558  H18  CAV  CAW  118.54  3.000
 558  H18  CAV  CAP  120.25  3.000
 558  CAW  CAV  CAP  121.20  3.000
 558  H19  CAW  CAX  120.62  3.000
 558  H19  CAW  CAV  119.65  3.000
 558  CAX  CAW  CAV  119.73  3.000
 558  CAY  CAX  CLB  120.00  3.000
 558  CLB  CAX  CAW  119.78  3.000
 558  CAY  CAX  CAW  120.22  3.000
 558  H20  CAY  CAZ  119.40  3.000
 558  H20  CAY  CAX  120.67  3.000
 558  CAZ  CAY  CAX  119.93  3.000
 558  H21  CAZ  CAY  117.89  3.000
 558  H21  CAZ  CAP  121.17  3.000
 558  CAY  CAZ  CAP  120.94  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
 558  CONST_03  NAR  CAQ  CAO  CAU    0.00   0.0  0
 558  CONST_04  NAR  CAS  CAT  CAU    0.00   0.0  0
 558  CONST_05  CAM  CAO  CAU  CAT  180.00   0.0  0
 558  CONST_06  CAQ  CAO  CAU  CAT    0.00   0.0  0
 558  CONST_07  CAQ  NAR  CAS  CAT    0.00   0.0  0
 558  CONST_08  CAO  CAQ  NAR  CAS    0.00   0.0  0
 558  CONST_09  CAO  CAU  CAT  CAS    0.00   0.0  0
 558  CONST_10  CAM  CAO  CAQ  NAR  180.00   0.0  0
 558  CONST_13  CAK  CAL  CAM  CAO  180.00   0.0  0
 558  CONST_14  CAC  CAN  CAM  CAO  180.00   0.0  0
 558  CONST_15  CAB  CAK  CAL  CAM    0.00   0.0  0
 558  CONST_16  CAB  CAC  CAN  CAM    0.00   0.0  0
 558  CONST_17  NAA  CAB  CAC  CAN  180.00   0.0  0
 558  CONST_18  CAK  CAB  CAC  CAN    0.00   0.0  0
 558  CONST_19  CAK  CAL  CAM  CAN    0.00   0.0  0
 558  CONST_22  CAL  CAK  CAB  CAC    0.00   0.0  0
 558  CONST_23  CAL  CAM  CAN  CAC    0.00   0.0  0
 558  CONST_24  NAA  CAB  CAK  CAL  180.00   0.0  0
 558  CONST_27  NAI  CAJ  NAA  CAB  180.00   0.0  0
 558  CONST_28  NAH  CAG  NAA  CAB  180.00   0.0  0
 558  CONST_29  NAH  NAI  CAJ  NAA    0.00   0.0  0
 558  CONST_30  NAI  NAH  CAG  NAA    0.00   0.0  0
 558  CONST_31  CAG  NAH  NAI  CAJ    0.00   0.0  0
 558  CONST_32  NAH  CAG  NAA  CAJ    0.00   0.0  0
 558  CONST_33  CAG  NAA  CAJ  NAI    0.00   0.0  0
 558  CONST_34  CAX  CAW  CAV  CAP    0.00   0.0  0
 558  CONST_35  CAX  CAY  CAZ  CAP    0.00   0.0  0
 558  CONST_36  CAY  CAZ  CAP  CAV    0.00   0.0  0
 558  CONST_37  CAY  CAX  CAW  CAV    0.00   0.0  0
 558  CONST_38  CAZ  CAP  CAV  CAW    0.00   0.0  0
 558  CONST_39  CAZ  CAY  CAX  CAW    0.00   0.0  0
 558  CONST_40  CAW  CAV  CAP  NAD  180.00   0.0  0
 558  CONST_41  CAY  CAZ  CAP  NAD  180.00   0.0  0
 558  CONST_42  NBA  CAS  CAT  CAU  180.00   0.0  0
 558  CONST_43  CAQ  NAR  CAS  NBA  180.00   0.0  0
 558  CONST_44  CBC  CAJ  NAA  CAB    0.00   0.0  0
 558  CONST_45  NAH  NAI  CAJ  CBC  180.00   0.0  0
 558  CONST_46  CAG  NAA  CAJ  CBC  180.00   0.0  0
 558  CONST_47  CLB  CAX  CAW  CAV  180.00   0.0  0
 558  CONST_48  CAZ  CAY  CAX  CLB  180.00   0.0  0
 558  CONST_49  H5   CAQ  CAO  CAU  180.00   0.0  0
 558  CONST_50  H1   CAU  CAT  CAS  180.00   0.0  0
 558  CONST_51  H2   CAT  CAS  NAR  180.00   0.0  0
 558  CONST_52  H7   CAL  CAM  CAO    0.00   0.0  0
 558  CONST_53  H6   CAN  CAM  CAO    0.00   0.0  0
 558  CONST_54  H8   CAK  CAL  CAM  180.00   0.0  0
 558  CONST_55  H18  CAV  CAP  NAD    0.00   0.0  0
 558  CONST_56  H21  CAZ  CAP  NAD    0.00   0.0  0
 558  CONST_57  H19  CAW  CAV  CAP  180.00   0.0  0
 558  CONST_58  H20  CAY  CAZ  CAP  180.00   0.0  0
 558  CONST_60  H4   NBA  CAS  CAT  180.00   0.0  0
 558  Var_01    CAE  NAD  CAC  CAN  109.45  30.0  1
 558  Var_02    CAF  CAE  NAD  CAC   41.95  30.0  1
 558  Var_03    CAV  CAP  NAD  CAC  -37.97  30.0  2
 558  Var_04    H9   CBC  CAJ  NAA   45.50  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
 558  chir_01  CAF  CAG  CBB  CAE  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
 558  plan-1  CAU  0.020
 558  plan-1  CAT  0.020
 558  plan-1  CAS  0.020
 558  plan-1  NBA  0.020
 558  plan-1  NAR  0.020
 558  plan-1  CAQ  0.020
 558  plan-1  CAO  0.020
 558  plan-1  CAM  0.020
 558  plan-1  H1   0.020
 558  plan-1  H2   0.020
 558  plan-1  H5   0.020
 558  plan-2  NAD  0.020
 558  plan-2  CAP  0.020
 558  plan-2  CAV  0.020
 558  plan-2  CAW  0.020
 558  plan-2  CAX  0.020
 558  plan-2  CLB  0.020
 558  plan-2  CAY  0.020
 558  plan-2  CAZ  0.020
 558  plan-2  H18  0.020
 558  plan-2  H19  0.020
 558  plan-2  H20  0.020
 558  plan-2  H21  0.020
 558  plan-3  CAB  0.020
 558  plan-3  NAA  0.020
 558  plan-3  CAJ  0.020
 558  plan-3  CBC  0.020
 558  plan-3  NAI  0.020
 558  plan-3  NAH  0.020
 558  plan-3  CAG  0.020
 558  plan-3  CAF  0.020
 558  plan-4  CAO  0.020
 558  plan-4  CAM  0.020
 558  plan-4  CAN  0.020
 558  plan-4  CAC  0.020
 558  plan-4  CAL  0.020
 558  plan-4  CAK  0.020
 558  plan-4  CAB  0.020
 558  plan-4  NAA  0.020
 558  plan-4  NAD  0.020
 558  plan-4  H6   0.020
 558  plan-4  H7   0.020
 558  plan-4  H8   0.020
 558  plan-5  CAS  0.020
 558  plan-5  NBA  0.020
 558  plan-5  H3   0.020
 558  plan-5  H4   0.020

