# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:48:52 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: (3~{R})-4-ethyl-3-methyl-3-propyl-1~{H}-1,4-benzodiazepine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@]1(C)N(CC)C(=O)c2ccccc2NC1=O
#
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
 OCK  OCK  (3~{R})-4-ethyl-3-methyl-3-propyl-1~{H}-1,4-benzodiazepine-2,5-dione  ligand  39  19  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OCK
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
 OCK  C1   C  CR6   0  -0.082  36.2145   6.6974  140.7726
 OCK  C2   C  CR16  0  -0.272  36.1442   6.4253  142.1407
 OCK  C3   C  CR16  0  -0.256  35.4051   5.3658  142.6288
 OCK  C4   C  CR16  0  -0.247  34.7458   4.5290  141.7349
 OCK  C5   C  CR16  0  -0.315  34.7981   4.7846  140.3790
 OCK  C6   C  CR6   0   0.344  35.5099   5.8806  139.8870
 OCK  C11  C  CH2   0  -0.426  34.5272   9.8921  140.5712
 OCK  C7   C  C     0   0.585  35.4297   7.2537  137.8084
 OCK  C8   C  CT    0  -0.085  35.5710   8.5697  138.5948
 OCK  C9   C  CH3   0  -0.694  35.4927   9.7162  137.5829
 OCK  C10  C  CH2   0  -0.431  34.3761   8.7546  139.5683
 OCK  C12  C  CH3   0  -0.657  33.2766  10.0380  141.4275
 OCK  N1   N  NT    0  -0.477  36.8878   8.5388  139.2706
 OCK  C13  C  CH2   0  -0.317  37.9739   9.4285  138.8480
 OCK  C14  C  CH3   0  -0.663  38.0495  10.7394  139.6166
 OCK  C    C  C     0   0.548  37.1604   7.7668  140.3507
 OCK  O    O  O     0  -0.479  38.1960   7.9026  140.9915
 OCK  N    N  NH1   0  -0.730  35.4964   6.0873  138.5095
 OCK  H1   H  HCR6  0   0.263  36.6879   7.0602  142.8272
 OCK  H2   H  HCR6  0   0.261  35.3546   5.1818  143.6932
 OCK  H3   H  HCR6  0   0.267  34.1790   3.6808  142.0956
 OCK  H4   H  HCR6  0   0.276  34.2691   4.1422  139.6856
 OCK  H5   H  HCH2  0   0.226  35.3847   9.7117  141.2244
 OCK  H6   H  HCH2  0   0.228  34.7292  10.8357  140.0591
 OCK  H7   H  HCH3  0   0.255  35.6700  10.6772  138.0595
 OCK  H8   H  HCH3  0   0.257  36.1850   9.6119  136.7521
 OCK  H9   H  HCH3  0   0.261  34.4903   9.7432  137.1612
 OCK  H10  H  HCH2  0   0.249  33.4996   8.9416  138.9422
 OCK  H11  H  HCH2  0   0.261  34.1391   7.8482  140.1218
 OCK  H12  H  HCH3  0   0.231  33.3863  10.8481  142.1487
 OCK  H13  H  HCH3  0   0.220  32.3989  10.2535  140.8163
 OCK  H14  H  HCH3  0   0.220  33.0736   9.1228  141.9867
 OCK  H15  H  HCH2  0   0.257  37.8734   9.6225  137.7850
 OCK  H16  H  HCH2  0   0.257  38.9111   8.8866  138.9617
 OCK  H17  H  HCH3  0   0.233  38.8921  11.3261  139.2485
 OCK  H18  H  HCH3  0   0.229  37.1502  11.3428  139.4957
 OCK  H19  H  HCH3  0   0.234  38.2000  10.5703  140.6813
 OCK  H20  H  HNH1  0   0.408  35.3040   5.2675  137.9483
 OCK  O1   O  O     0  -0.439  35.2753   7.2237  136.6043

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
 OCK  O1   C7   double    1.214  0.020  1.214
 OCK  C9   C8   single    1.531  0.020  1.531
 OCK  C7   N    single    1.363  0.020  1.363
 OCK  C7   C8   single    1.540  0.020  1.540
 OCK  N    C6   single    1.393  0.020  1.393
 OCK  C8   N1   single    1.480  0.020  1.480
 OCK  C8   C10  single    1.552  0.020  1.552
 OCK  C13  C14  single    1.521  0.020  1.521
 OCK  C13  N1   single    1.466  0.020  1.466
 OCK  N1   C    single    1.355  0.020  1.355
 OCK  C10  C11  single    1.524  0.020  1.524
 OCK  C6   C5   aromatic  1.396  0.020  1.396
 OCK  C6   C1   aromatic  1.396  0.020  1.396
 OCK  C5   C4   aromatic  1.381  0.020  1.381
 OCK  C    C1   single    1.489  0.020  1.489
 OCK  C    O    double    1.225  0.020  1.225
 OCK  C11  C12  single    1.523  0.020  1.523
 OCK  C1   C2   aromatic  1.397  0.020  1.397
 OCK  C4   C3   aromatic  1.391  0.020  1.391
 OCK  C2   C3   aromatic  1.381  0.020  1.381
 OCK  C2   H1   single    0.930  0.020  1.080
 OCK  C3   H2   single    0.930  0.020  1.080
 OCK  C4   H3   single    0.930  0.020  1.080
 OCK  C5   H4   single    0.930  0.020  1.080
 OCK  C11  H5   single    0.970  0.020  1.090
 OCK  C11  H6   single    0.970  0.020  1.090
 OCK  C9   H7   single    0.970  0.020  1.090
 OCK  C9   H8   single    0.970  0.020  1.090
 OCK  C9   H9   single    0.970  0.020  1.090
 OCK  C10  H10  single    0.970  0.020  1.090
 OCK  C10  H11  single    0.970  0.020  1.090
 OCK  C12  H12  single    0.970  0.020  1.090
 OCK  C12  H13  single    0.970  0.020  1.090
 OCK  C12  H14  single    0.970  0.020  1.090
 OCK  C13  H15  single    0.970  0.020  1.090
 OCK  C13  H16  single    0.970  0.020  1.090
 OCK  C14  H17  single    0.970  0.020  1.090
 OCK  C14  H18  single    0.970  0.020  1.090
 OCK  C14  H19  single    0.970  0.020  1.090
 OCK  N    H20  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
 OCK  C    C1   C6   124.15  3.000
 OCK  C    C1   C2   116.71  3.000
 OCK  C6   C1   C2   118.83  3.000
 OCK  H1   C2   C3   119.67  3.000
 OCK  H1   C2   C1   118.82  3.000
 OCK  C3   C2   C1   121.50  3.000
 OCK  H2   C3   C4   120.54  3.000
 OCK  H2   C3   C2   120.22  3.000
 OCK  C4   C3   C2   119.23  3.000
 OCK  H3   C4   C5   119.49  3.000
 OCK  H3   C4   C3   120.38  3.000
 OCK  C5   C4   C3   120.12  3.000
 OCK  H4   C5   C6   119.26  3.000
 OCK  H4   C5   C4   120.03  3.000
 OCK  C6   C5   C4   120.70  3.000
 OCK  N    C6   C5   117.39  3.000
 OCK  C5   C6   C1   119.54  3.000
 OCK  N    C6   C1   123.06  3.000
 OCK  H6   C11  H5   106.12  3.000
 OCK  H6   C11  C12  109.43  3.000
 OCK  H5   C11  C12  108.91  3.000
 OCK  H6   C11  C10  110.76  3.000
 OCK  H5   C11  C10  110.36  3.000
 OCK  C12  C11  C10  111.12  3.000
 OCK  N    C7   C8   117.67  3.000
 OCK  C8   C7   O1   122.63  3.000
 OCK  N    C7   O1   119.69  3.000
 OCK  N1   C8   C10  113.63  3.000
 OCK  C10  C8   C9   106.61  3.000
 OCK  N1   C8   C9   111.27  3.000
 OCK  C10  C8   C7   110.58  3.000
 OCK  N1   C8   C7   107.28  3.000
 OCK  C9   C8   C7   107.33  3.000
 OCK  H9   C9   H8   107.04  3.000
 OCK  H9   C9   H7   107.35  3.000
 OCK  H8   C9   H7   108.43  3.000
 OCK  H9   C9   C8   108.78  3.000
 OCK  H8   C9   C8   113.63  3.000
 OCK  H7   C9   C8   111.34  3.000
 OCK  H11  C10  H10  105.01  3.000
 OCK  H11  C10  C8   112.79  3.000
 OCK  H10  C10  C8   106.17  3.000
 OCK  H11  C10  C11  107.97  3.000
 OCK  H10  C10  C11  109.19  3.000
 OCK  C8   C10  C11  115.17  3.000
 OCK  H14  C12  H13  107.63  3.000
 OCK  H14  C12  H12  107.63  3.000
 OCK  H13  C12  H12  107.75  3.000
 OCK  H14  C12  C11  111.13  3.000
 OCK  H13  C12  C11  111.38  3.000
 OCK  H12  C12  C11  111.14  3.000
 OCK  C    N1   C13  115.23  3.000
 OCK  C    N1   C8   123.68  3.000
 OCK  C13  N1   C8   120.97  3.000
 OCK  H16  C13  H15  105.73  3.000
 OCK  H16  C13  C14  109.47  3.000
 OCK  H15  C13  C14  110.21  3.000
 OCK  H16  C13  N1   107.79  3.000
 OCK  H15  C13  N1   108.80  3.000
 OCK  C14  C13  N1   114.46  3.000
 OCK  H19  C14  H18  107.98  3.000
 OCK  H19  C14  H17  107.87  3.000
 OCK  H18  C14  H17  107.60  3.000
 OCK  H19  C14  C13  111.54  3.000
 OCK  H18  C14  C13  112.33  3.000
 OCK  H17  C14  C13  109.35  3.000
 OCK  O    C    N1   121.58  3.000
 OCK  O    C    C1   117.93  3.000
 OCK  N1   C    C1   120.48  3.000
 OCK  H20  N    C7   113.50  3.000
 OCK  H20  N    C6   115.47  3.000
 OCK  C7   N    C6   129.52  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
 OCK  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 OCK  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 OCK  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 OCK  CONST_04  H2   C3   C2   C1   180.00   0.0  0
 OCK  CONST_05  H3   C4   C3   C2   180.00   0.0  0
 OCK  CONST_06  H4   C5   C4   C3   180.00   0.0  0
 OCK  CONST_07  H1   C2   C3   C4   180.00   0.0  0
 OCK  Var_01    C12  C11  C10  C8   176.96  30.0  3
 OCK  Var_02    H17  C14  C13  N1   179.03  30.0  3
 OCK  Var_03    H12  C12  C11  C10  179.70  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
 OCK  chir_01  C8  C7  N1  C10  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
 OCK  plan-1  C6   0.020
 OCK  plan-1  C7   0.020
 OCK  plan-1  C8   0.020
 OCK  plan-1  N    0.020
 OCK  plan-1  H20  0.020
 OCK  plan-1  O1   0.020
 OCK  plan-2  C1   0.020
 OCK  plan-2  C2   0.020
 OCK  plan-2  C3   0.020
 OCK  plan-2  C4   0.020
 OCK  plan-2  C5   0.020
 OCK  plan-2  C6   0.020
 OCK  plan-2  C8   0.020
 OCK  plan-2  N1   0.020
 OCK  plan-2  C13  0.020
 OCK  plan-2  C    0.020
 OCK  plan-2  O    0.020
 OCK  plan-2  N    0.020
 OCK  plan-2  H1   0.020
 OCK  plan-2  H2   0.020
 OCK  plan-2  H3   0.020
 OCK  plan-2  H4   0.020

