# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 11:57:38 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (4R)-6-(3-cyclopropyl-1-methyl-1H-indazol-5-yl)-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC(=O)Nc2cccc(c3ccc4n(C)nc(C5CC5)c4c3)c2N1
#
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
 69B  69B  (4R)-6-(3-cyclopropyl-1-methyl-1H-indazol-5-yl)-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one  ligand  48  26  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_69B
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
 69B  CAY  C  CH2   0  -0.471  -5.2345   2.4166   0.7000
 69B  CAZ  C  CH2   0  -0.472  -5.4063   1.5875   1.9292
 69B  CAW  C  CH1   0  -0.369  -4.1067   1.5385   1.1833
 69B  CAV  C  CR5   0   0.262  -3.7230   0.3441   0.4135
 69B  CAR  C  CR56  0  -0.088  -2.4477   0.0660  -0.1579
 69B  CAS  C  CR16  0  -0.387  -1.2070   0.7121  -0.1913
 69B  NAU  N  N     0  -0.284  -4.5597  -0.6256   0.1329
 69B  NAT  N  NR5   0  -0.392  -3.8974  -1.5398  -0.5926
 69B  CAX  C  CH3   0  -0.524  -4.5821  -2.6853  -1.1304
 69B  CAQ  C  CR56  0   0.441  -2.6152  -1.1674  -0.8057
 69B  CAP  C  CR16  0  -0.304  -1.5662  -1.7767  -1.5068
 69B  CAO  C  CR16  0  -0.273  -0.3569  -1.1246  -1.5159
 69B  CAN  C  CR6   0   0.079  -0.1583   0.1179  -0.8642
 69B  CAJ  C  CR6   0   0.034   1.1508   0.8057  -0.9246
 69B  CAF  C  CR6   0   0.151   2.3375   0.1594  -0.5596
 69B  NAE  N  NH1   0  -0.646   2.3302  -1.1999  -0.1626
 69B  CAD  C  CH1   0  -0.109   2.5368  -1.4273   1.2661
 69B  CAI  C  CH3   0  -0.639   1.2513  -1.2153   2.0491
 69B  CAC  C  CH2   0  -0.612   3.6651  -0.5582   1.8626
 69B  CAB  C  C     0   0.493   4.8849  -0.4697   0.9795
 69B  OAH  O  O     0  -0.470   5.9568  -0.9778   1.2635
 69B  NAA  N  NH1   0  -0.716   4.7283   0.2407  -0.1718
 69B  CAG  C  CR6   0   0.359   3.5445   0.8708  -0.5905
 69B  CAM  C  CR16  0  -0.330   3.5878   2.1808  -1.0521
 69B  CAL  C  CR16  0  -0.244   2.4144   2.8054  -1.4408
 69B  CAK  C  CR16  0  -0.330   1.2063   2.1310  -1.3593
 69B  H1   H  HCH2  0   0.250  -5.7499   2.1059  -0.2002
 69B  H2   H  HCH2  0   0.254  -5.1208   3.4875   0.8091
 69B  H3   H  HCH2  0   0.257  -5.4123   2.0876   2.8889
 69B  H4   H  HCH2  0   0.252  -6.0465   0.7171   1.8709
 69B  H5   H  HCH1  0   0.264  -3.2698   2.0569   1.6366
 69B  H6   H  HCR6  0   0.249  -1.0637   1.6600   0.3142
 69B  H7   H  HCH3  0   0.251  -4.9968  -2.4797  -2.1183
 69B  H8   H  HCH3  0   0.255  -3.8918  -3.5226  -1.2073
 69B  H9   H  HCH3  0   0.265  -5.3896  -2.9660  -0.4594
 69B  H10  H  HCR6  0   0.268  -1.6943  -2.7165  -2.0277
 69B  H11  H  HCR6  0   0.247   0.4700  -1.5683  -2.0518
 69B  H12  H  HNH1  0   0.362   3.0368  -1.7039  -0.6858
 69B  H13  H  HCH1  0   0.249   2.8315  -2.4753   1.3586
 69B  H14  H  HCH3  0   0.237   0.4582  -1.8574   1.6678
 69B  H15  H  HCH3  0   0.230   1.4039  -1.4421   3.1052
 69B  H16  H  HCH3  0   0.224   0.9094  -0.1812   1.9763
 69B  H17  H  HCH2  0   0.265   3.2831   0.4518   2.0445
 69B  H18  H  HCH2  0   0.278   3.9643  -0.9678   2.8271
 69B  H19  H  HNH1  0   0.402   5.5672   0.4148  -0.7088
 69B  H20  H  HCR6  0   0.268   4.5322   2.7093  -1.0932
 69B  H21  H  HCR6  0   0.260   2.4418   3.8252  -1.8015
 69B  H22  H  HCR6  0   0.253   0.2934   2.6278  -1.6624

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
 69B  CAX  NAT  single    1.439  0.020  1.439
 69B  CAY  CAZ  single    1.493  0.020  1.493
 69B  CAY  CAW  single    1.509  0.020  1.509
 69B  NAU  NAT  aromatic  1.342  0.020  1.342
 69B  NAU  CAV  aromatic  1.311  0.020  1.311
 69B  NAT  CAQ  aromatic  1.352  0.020  1.352
 69B  CAZ  CAW  single    1.499  0.020  1.499
 69B  CAV  CAW  single    1.472  0.020  1.472
 69B  CAV  CAR  aromatic  1.425  0.020  1.425
 69B  CAQ  CAP  aromatic  1.401  0.020  1.401
 69B  CAQ  CAR  aromatic  1.403  0.020  1.403
 69B  CAP  CAO  aromatic  1.374  0.020  1.374
 69B  CAR  CAS  aromatic  1.399  0.020  1.399
 69B  CAI  CAD  single    1.520  0.020  1.520
 69B  CAO  CAN  aromatic  1.417  0.020  1.417
 69B  CAS  CAN  aromatic  1.380  0.020  1.380
 69B  CAD  NAE  single    1.461  0.020  1.461
 69B  CAD  CAC  single    1.544  0.020  1.544
 69B  CAN  CAJ  single    1.480  0.020  1.480
 69B  NAE  CAF  single    1.416  0.020  1.416
 69B  CAJ  CAF  aromatic  1.400  0.020  1.400
 69B  CAJ  CAK  aromatic  1.396  0.020  1.396
 69B  CAF  CAG  aromatic  1.401  0.020  1.401
 69B  CAC  CAB  single    1.509  0.020  1.509
 69B  OAH  CAB  double    1.220  0.020  1.220
 69B  CAB  NAA  single    1.362  0.020  1.362
 69B  CAK  CAL  aromatic  1.386  0.020  1.386
 69B  CAG  NAA  single    1.405  0.020  1.405
 69B  CAG  CAM  aromatic  1.390  0.020  1.390
 69B  CAL  CAM  aromatic  1.385  0.020  1.385
 69B  CAY  H1   single    0.970  0.020  1.090
 69B  CAY  H2   single    0.970  0.020  1.090
 69B  CAZ  H3   single    0.970  0.020  1.090
 69B  CAZ  H4   single    0.970  0.020  1.090
 69B  CAW  H5   single    0.970  0.020  1.090
 69B  CAS  H6   single    0.930  0.020  1.080
 69B  CAX  H7   single    0.970  0.020  1.090
 69B  CAX  H8   single    0.970  0.020  1.090
 69B  CAX  H9   single    0.970  0.020  1.090
 69B  CAP  H10  single    0.930  0.020  1.080
 69B  CAO  H11  single    0.930  0.020  1.080
 69B  NAE  H12  single    0.890  0.020  1.040
 69B  CAD  H13  single    0.970  0.020  1.090
 69B  CAI  H14  single    0.970  0.020  1.090
 69B  CAI  H15  single    0.970  0.020  1.090
 69B  CAI  H16  single    0.970  0.020  1.090
 69B  CAC  H17  single    0.970  0.020  1.090
 69B  CAC  H18  single    0.970  0.020  1.090
 69B  NAA  H19  single    0.860  0.020  1.020
 69B  CAM  H20  single    0.930  0.020  1.080
 69B  CAL  H21  single    0.930  0.020  1.080
 69B  CAK  H22  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
 69B  H2   CAY  H1   114.69  3.000
 69B  H2   CAY  CAW  117.71  3.000
 69B  H1   CAY  CAW  117.07  3.000
 69B  H2   CAY  CAZ  118.60  3.000
 69B  H1   CAY  CAZ  118.07  3.000
 69B  CAW  CAY  CAZ   59.93  3.000
 69B  H4   CAZ  H3   114.60  3.000
 69B  H4   CAZ  CAW  117.37  3.000
 69B  H3   CAZ  CAW  117.46  3.000
 69B  H4   CAZ  CAY  118.07  3.000
 69B  H3   CAZ  CAY  118.31  3.000
 69B  CAW  CAZ  CAY   60.57  3.000
 69B  H5   CAW  CAV  113.92  3.000
 69B  H5   CAW  CAZ  116.47  3.000
 69B  CAV  CAW  CAZ  120.85  3.000
 69B  H5   CAW  CAY  115.65  3.000
 69B  CAV  CAW  CAY  119.97  3.000
 69B  CAZ  CAW  CAY   59.50  3.000
 69B  NAU  CAV  CAR  109.94  3.000
 69B  CAR  CAV  CAW  126.97  3.000
 69B  NAU  CAV  CAW  123.07  3.000
 69B  CAQ  CAR  CAS  120.04  3.000
 69B  CAS  CAR  CAV  135.49  3.000
 69B  CAQ  CAR  CAV  104.47  3.000
 69B  H6   CAS  CAN  120.22  3.000
 69B  H6   CAS  CAR  120.66  3.000
 69B  CAN  CAS  CAR  119.11  3.000
 69B  NAT  NAU  CAV  107.74  3.000
 69B  CAQ  NAT  CAX  127.71  3.000
 69B  CAQ  NAT  NAU  111.44  3.000
 69B  CAX  NAT  NAU  120.64  3.000
 69B  H9   CAX  H8   108.44  3.000
 69B  H9   CAX  H7   108.99  3.000
 69B  H8   CAX  H7   108.80  3.000
 69B  H9   CAX  NAT  109.17  3.000
 69B  H8   CAX  NAT  109.71  3.000
 69B  H7   CAX  NAT  111.67  3.000
 69B  CAP  CAQ  NAT  132.00  3.000
 69B  CAP  CAQ  CAR  121.60  3.000
 69B  NAT  CAQ  CAR  106.41  3.000
 69B  H10  CAP  CAO  120.88  3.000
 69B  H10  CAP  CAQ  122.00  3.000
 69B  CAO  CAP  CAQ  117.12  3.000
 69B  H11  CAO  CAN  118.74  3.000
 69B  H11  CAO  CAP  118.81  3.000
 69B  CAN  CAO  CAP  122.44  3.000
 69B  CAJ  CAN  CAO  120.84  3.000
 69B  CAJ  CAN  CAS  119.46  3.000
 69B  CAO  CAN  CAS  119.68  3.000
 69B  CAK  CAJ  CAF  119.07  3.000
 69B  CAK  CAJ  CAN  119.28  3.000
 69B  CAF  CAJ  CAN  121.65  3.000
 69B  CAG  CAF  NAE  119.86  3.000
 69B  CAG  CAF  CAJ  119.34  3.000
 69B  NAE  CAF  CAJ  120.79  3.000
 69B  H12  NAE  CAD  109.19  3.000
 69B  H12  NAE  CAF  109.21  3.000
 69B  CAD  NAE  CAF  115.01  3.000
 69B  H13  CAD  CAC  108.06  3.000
 69B  H13  CAD  CAI  108.56  3.000
 69B  CAC  CAD  CAI  109.90  3.000
 69B  H13  CAD  NAE  105.67  3.000
 69B  CAC  CAD  NAE  113.17  3.000
 69B  CAI  CAD  NAE  111.25  3.000
 69B  H16  CAI  H15  107.78  3.000
 69B  H16  CAI  H14  107.88  3.000
 69B  H15  CAI  H14  108.55  3.000
 69B  H16  CAI  CAD  111.26  3.000
 69B  H15  CAI  CAD  110.58  3.000
 69B  H14  CAI  CAD  110.68  3.000
 69B  H18  CAC  H17  107.19  3.000
 69B  H18  CAC  CAB  108.56  3.000
 69B  H17  CAC  CAB  108.97  3.000
 69B  H18  CAC  CAD  109.33  3.000
 69B  H17  CAC  CAD  109.17  3.000
 69B  CAB  CAC  CAD  113.43  3.000
 69B  NAA  CAB  OAH  121.01  3.000
 69B  NAA  CAB  CAC  115.63  3.000
 69B  OAH  CAB  CAC  123.35  3.000
 69B  H19  NAA  CAG  117.62  3.000
 69B  H19  NAA  CAB  116.32  3.000
 69B  CAG  NAA  CAB  125.65  3.000
 69B  CAM  CAG  NAA  119.71  3.000
 69B  CAM  CAG  CAF  120.84  3.000
 69B  NAA  CAG  CAF  119.44  3.000
 69B  H20  CAM  CAL  120.53  3.000
 69B  H20  CAM  CAG  119.99  3.000
 69B  CAL  CAM  CAG  119.48  3.000
 69B  H21  CAL  CAK  120.02  3.000
 69B  H21  CAL  CAM  119.81  3.000
 69B  CAK  CAL  CAM  120.17  3.000
 69B  H22  CAK  CAL  119.68  3.000
 69B  H22  CAK  CAJ  119.30  3.000
 69B  CAL  CAK  CAJ  121.00  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
 69B  CONST_01  CAQ  NAT  NAU  CAV     0.00   0.0  0
 69B  CONST_02  NAT  CAQ  CAR  CAV     0.00   0.0  0
 69B  CONST_03  CAP  CAQ  CAR  CAV   180.00   0.0  0
 69B  CONST_04  CAN  CAS  CAR  CAV   180.00   0.0  0
 69B  CONST_05  NAT  NAU  CAV  CAR     0.00   0.0  0
 69B  CONST_06  NAU  NAT  CAQ  CAR     0.00   0.0  0
 69B  CONST_07  CAO  CAP  CAQ  CAR     0.00   0.0  0
 69B  CONST_08  CAO  CAN  CAS  CAR     0.00   0.0  0
 69B  CONST_09  CAJ  CAN  CAS  CAR   180.00   0.0  0
 69B  CONST_10  NAU  CAV  CAR  CAS   180.00   0.0  0
 69B  CONST_11  NAT  CAQ  CAR  CAS   180.00   0.0  0
 69B  CONST_12  CAP  CAQ  CAR  CAS     0.00   0.0  0
 69B  CONST_13  CAP  CAO  CAN  CAS     0.00   0.0  0
 69B  CONST_16  CAP  CAQ  NAT  NAU   180.00   0.0  0
 69B  CONST_17  CAQ  CAR  CAV  NAU     0.00   0.0  0
 69B  CONST_18  CAO  CAP  CAQ  NAT   180.00   0.0  0
 69B  CONST_19  CAN  CAO  CAP  CAQ     0.00   0.0  0
 69B  CONST_20  CAN  CAS  CAR  CAQ     0.00   0.0  0
 69B  CONST_21  CAJ  CAN  CAO  CAP   180.00   0.0  0
 69B  CONST_24  CAL  CAK  CAJ  CAN   180.00   0.0  0
 69B  CONST_25  CAM  CAL  CAK  CAJ     0.00   0.0  0
 69B  CONST_26  CAL  CAK  CAJ  CAF     0.00   0.0  0
 69B  CONST_27  CAK  CAL  CAM  CAG     0.00   0.0  0
 69B  CONST_28  NAT  NAU  CAV  CAW   180.00   0.0  0
 69B  CONST_29  CAQ  CAR  CAV  CAW   180.00   0.0  0
 69B  CONST_30  CAS  CAR  CAV  CAW     0.00   0.0  0
 69B  CONST_31  CAX  NAT  NAU  CAV   180.00   0.0  0
 69B  CONST_32  CAX  NAT  CAQ  CAR   180.00   0.0  0
 69B  CONST_33  CAP  CAQ  NAT  CAX     0.00   0.0  0
 69B  CONST_34  H6   CAS  CAR  CAV     0.00   0.0  0
 69B  CONST_35  H10  CAP  CAQ  CAR   180.00   0.0  0
 69B  CONST_36  H11  CAO  CAN  CAS   180.00   0.0  0
 69B  CONST_37  H22  CAK  CAJ  CAN     0.00   0.0  0
 69B  CONST_38  H21  CAL  CAK  CAJ   180.00   0.0  0
 69B  CONST_39  H20  CAM  CAL  CAK   180.00   0.0  0
 69B  Var_01    CAV  CAW  CAZ  CAY  -108.88  30.0  1
 69B  Var_02    NAU  CAV  CAW  CAY   -57.71  30.0  1
 69B  Var_03    H7   CAX  NAT  NAU    88.95  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
 69B  chir_02  CAD  CAI  NAE  CAC  negativ
 69B  chir_03  CAW  CAY  CAZ  CAV  both

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
 69B  plan-1  CAW  0.020
 69B  plan-1  CAV  0.020
 69B  plan-1  CAR  0.020
 69B  plan-1  CAS  0.020
 69B  plan-1  NAU  0.020
 69B  plan-1  NAT  0.020
 69B  plan-1  CAX  0.020
 69B  plan-1  CAQ  0.020
 69B  plan-1  CAP  0.020
 69B  plan-1  CAO  0.020
 69B  plan-1  CAN  0.020
 69B  plan-1  CAJ  0.020
 69B  plan-1  H6   0.020
 69B  plan-1  H10  0.020
 69B  plan-1  H11  0.020
 69B  plan-2  CAN  0.020
 69B  plan-2  CAJ  0.020
 69B  plan-2  CAF  0.020
 69B  plan-2  NAE  0.020
 69B  plan-2  NAA  0.020
 69B  plan-2  CAG  0.020
 69B  plan-2  CAM  0.020
 69B  plan-2  CAL  0.020
 69B  plan-2  CAK  0.020
 69B  plan-2  H20  0.020
 69B  plan-2  H21  0.020
 69B  plan-2  H22  0.020
 69B  plan-3  CAC  0.020
 69B  plan-3  CAB  0.020
 69B  plan-3  OAH  0.020
 69B  plan-3  NAA  0.020
 69B  plan-3  CAG  0.020
 69B  plan-3  H19  0.020

