# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 10:55:36 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (4R)-6-[3-(benzyloxy)phenyl]-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(c2N1)c3cccc(OCc4ccccc4)c3
#
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
 69F  69F  (4R)-6-[3-(benzyloxy)phenyl]-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one  ligand  49  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_69F
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
 69F  C4   C  CH2   0  -0.617   3.8900   1.6968   1.3448
 69F  C5   C  C     0   0.488   5.2108   1.0219   1.0713
 69F  C11  C  CR16  0  -0.321   1.5729  -2.4482   0.4340
 69F  C8   C  CR6   0   0.349   3.9421  -1.0320   0.6115
 69F  C9   C  CR16  0  -0.326   3.8350  -2.2749   1.2227
 69F  C10  C  CR16  0  -0.245   2.6478  -2.9819   1.1272
 69F  C12  C  CR6   0   0.021   1.6773  -1.2157  -0.2109
 69F  C13  C  CR6   0   0.174   2.8802  -0.5071  -0.1381
 69F  C1   C  CH3   0  -0.678   3.5170   3.1009  -0.7372
 69F  C2   C  CH1   0  -0.099   3.0430   1.9026   0.0675
 69F  O6   O  O     0  -0.469   6.2880   1.5876   1.1572
 69F  N7   N  NH1   0  -0.714   5.1318  -0.2938   0.7291
 69F  N14  N  NH1   0  -0.644   3.0283   0.7323  -0.8045
 69F  C15  C  CR6   0   0.109   0.5199  -0.7040  -0.9801
 69F  C16  C  CR16  0  -0.293   0.6361  -0.3739  -2.3329
 69F  C17  C  CR16  0  -0.234  -0.4821   0.0349  -3.0347
 69F  C18  C  CR16  0  -0.395  -1.7273   0.1376  -2.4202
 69F  C19  C  CR6   0   0.404  -1.8449  -0.1846  -1.0728
 69F  C20  C  CR16  0  -0.404  -0.7190  -0.6075  -0.3622
 69F  O21  O  O2    0  -0.472  -2.9943  -0.1192  -0.3682
 69F  C22  C  CH2   0  -0.268  -4.1841   0.2633  -1.0456
 69F  C23  C  CR6   0   0.101  -5.2960   0.2394  -0.0413
 69F  C24  C  CR16  0  -0.292  -6.0111  -0.9324   0.1895
 69F  C25  C  CR16  0  -0.242  -7.0218  -0.9660   1.1403
 69F  C26  C  CR16  0  -0.262  -7.3247   0.1754   1.8721
 69F  C27  C  CR16  0  -0.242  -6.6151   1.3484   1.6489
 69F  C28  C  CR16  0  -0.293  -5.6049   1.3778   0.6970
 69F  H1   H  HCH2  0   0.280   3.3256   1.0932   2.0610
 69F  H2   H  HCH2  0   0.277   4.0791   2.6596   1.8194
 69F  H3   H  HCR6  0   0.255   0.6479  -3.0073   0.3693
 69F  H4   H  HCR6  0   0.270   4.6700  -2.6738   1.7846
 69F  H5   H  HCR6  0   0.262   2.5563  -3.9482   1.6052
 69F  H6   H  HCH3  0   0.226   4.5425   2.9651  -1.0900
 69F  H7   H  HCH3  0   0.244   2.8799   3.2554  -1.6078
 69F  H8   H  HCH3  0   0.240   3.4926   4.0067  -0.1325
 69F  H9   H  HCH1  0   0.253   2.0171   2.0906   0.3977
 69F  H10  H  HNH1  0   0.402   6.0065  -0.7956   0.6576
 69F  H11  H  HNH1  0   0.355   3.8768   0.7185  -1.3616
 69F  H12  H  HCR6  0   0.241   1.5913  -0.4515  -2.8316
 69F  H13  H  HCR6  0   0.257  -0.3951   0.2781  -4.0859
 69F  H14  H  HCR6  0   0.280  -2.5774   0.4642  -3.0035
 69F  H15  H  HCR6  0   0.256  -0.8248  -0.8528   0.6883
 69F  H16  H  HCH2  0   0.241  -4.0762   1.2657  -1.4737
 69F  H17  H  HCH2  0   0.241  -4.3945  -0.4301  -1.8667
 69F  H18  H  HCR6  0   0.254  -5.7809  -1.8228  -0.3840
 69F  H19  H  HCR6  0   0.258  -7.5750  -1.8812   1.3076
 69F  H20  H  HCR6  0   0.259  -8.1145   0.1520   2.6115
 69F  H21  H  HCR6  0   0.258  -6.8494   2.2407   2.2148
 69F  H22  H  HCR6  0   0.254  -5.0565   2.2961   0.5221

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
 69F  C25  C26  aromatic  1.389  0.020  1.389
 69F  C25  C24  aromatic  1.388  0.020  1.388
 69F  N7   C8   single    1.405  0.020  1.405
 69F  N7   C5   single    1.362  0.020  1.362
 69F  C9   C10  aromatic  1.385  0.020  1.385
 69F  C9   C8   aromatic  1.389  0.020  1.389
 69F  C26  C27  aromatic  1.389  0.020  1.389
 69F  O6   C5   double    1.220  0.020  1.220
 69F  C24  C23  aromatic  1.392  0.020  1.392
 69F  C10  C11  aromatic  1.386  0.020  1.386
 69F  C8   C13  aromatic  1.402  0.020  1.402
 69F  C27  C28  aromatic  1.388  0.020  1.388
 69F  C23  C28  aromatic  1.392  0.020  1.392
 69F  C23  C22  single    1.499  0.020  1.499
 69F  C5   C4   single    1.508  0.020  1.508
 69F  C22  O21  single    1.422  0.020  1.422
 69F  C11  C12  aromatic  1.395  0.020  1.395
 69F  C13  C12  aromatic  1.398  0.020  1.398
 69F  C13  N14  single    1.415  0.020  1.415
 69F  C12  C15  single    1.481  0.020  1.481
 69F  N14  C2   single    1.459  0.020  1.459
 69F  C20  C15  aromatic  1.388  0.020  1.388
 69F  C20  C19  aromatic  1.397  0.020  1.397
 69F  C1   C2   single    1.519  0.020  1.519
 69F  C4   C2   single    1.546  0.020  1.546
 69F  O21  C19  single    1.350  0.020  1.350
 69F  C15  C16  aromatic  1.397  0.020  1.397
 69F  C19  C18  aromatic  1.390  0.020  1.390
 69F  C16  C17  aromatic  1.382  0.020  1.382
 69F  C18  C17  aromatic  1.392  0.020  1.392
 69F  C4   H1   single    0.970  0.020  1.090
 69F  C4   H2   single    0.970  0.020  1.090
 69F  C11  H3   single    0.930  0.020  1.080
 69F  C9   H4   single    0.930  0.020  1.080
 69F  C10  H5   single    0.930  0.020  1.080
 69F  C1   H6   single    0.970  0.020  1.090
 69F  C1   H7   single    0.970  0.020  1.090
 69F  C1   H8   single    0.970  0.020  1.090
 69F  C2   H9   single    0.970  0.020  1.090
 69F  N7   H10  single    0.860  0.020  1.020
 69F  N14  H11  single    0.890  0.020  1.040
 69F  C16  H12  single    0.930  0.020  1.080
 69F  C17  H13  single    0.930  0.020  1.080
 69F  C18  H14  single    0.930  0.020  1.080
 69F  C20  H15  single    0.930  0.020  1.080
 69F  C22  H16  single    0.970  0.020  1.090
 69F  C22  H17  single    0.970  0.020  1.090
 69F  C24  H18  single    0.930  0.020  1.080
 69F  C25  H19  single    0.930  0.020  1.080
 69F  C26  H20  single    0.930  0.020  1.080
 69F  C27  H21  single    0.930  0.020  1.080
 69F  C28  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
 69F  H2   C4   H1   106.97  3.000
 69F  H2   C4   C2   109.71  3.000
 69F  H1   C4   C2   109.37  3.000
 69F  H2   C4   C5   108.80  3.000
 69F  H1   C4   C5   108.89  3.000
 69F  C2   C4   C5   112.92  3.000
 69F  N7   C5   O6   121.13  3.000
 69F  O6   C5   C4   123.58  3.000
 69F  N7   C5   C4   115.29  3.000
 69F  H3   C11  C12  119.51  3.000
 69F  H3   C11  C10  119.58  3.000
 69F  C12  C11  C10  120.90  3.000
 69F  N7   C8   C13  119.31  3.000
 69F  C13  C8   C9   120.78  3.000
 69F  N7   C8   C9   119.90  3.000
 69F  H4   C9   C10  120.58  3.000
 69F  H4   C9   C8   119.90  3.000
 69F  C10  C9   C8   119.51  3.000
 69F  H5   C10  C9   119.87  3.000
 69F  H5   C10  C11  119.95  3.000
 69F  C9   C10  C11  120.17  3.000
 69F  C15  C12  C13  121.63  3.000
 69F  C15  C12  C11  119.14  3.000
 69F  C13  C12  C11  119.22  3.000
 69F  N14  C13  C12  120.63  3.000
 69F  N14  C13  C8   120.03  3.000
 69F  C12  C13  C8   119.34  3.000
 69F  H8   C1   H7   108.21  3.000
 69F  H8   C1   H6   107.67  3.000
 69F  H7   C1   H6   107.95  3.000
 69F  H8   C1   C2   110.78  3.000
 69F  H7   C1   C2   110.64  3.000
 69F  H6   C1   C2   111.45  3.000
 69F  H9   C2   N14  107.98  3.000
 69F  H9   C2   C1   108.47  3.000
 69F  N14  C2   C1   108.61  3.000
 69F  H9   C2   C4   106.69  3.000
 69F  C1   C2   C4   111.81  3.000
 69F  N14  C2   C4   113.10  3.000
 69F  H10  N7   C8   117.77  3.000
 69F  H10  N7   C5   116.56  3.000
 69F  C8   N7   C5   125.29  3.000
 69F  H11  N14  C2   109.29  3.000
 69F  H11  N14  C13  109.51  3.000
 69F  C2   N14  C13  114.96  3.000
 69F  C20  C15  C16  119.26  3.000
 69F  C16  C15  C12  121.30  3.000
 69F  C20  C15  C12  119.37  3.000
 69F  H12  C16  C17  120.14  3.000
 69F  H12  C16  C15  120.23  3.000
 69F  C17  C16  C15  119.62  3.000
 69F  H13  C17  C18  118.94  3.000
 69F  H13  C17  C16  119.64  3.000
 69F  C18  C17  C16  121.42  3.000
 69F  H14  C18  C19  121.75  3.000
 69F  H14  C18  C17  119.15  3.000
 69F  C19  C18  C17  119.09  3.000
 69F  O21  C19  C20  115.82  3.000
 69F  O21  C19  C18  124.52  3.000
 69F  C20  C19  C18  119.67  3.000
 69F  H15  C20  C19  118.87  3.000
 69F  H15  C20  C15  120.19  3.000
 69F  C19  C20  C15  120.93  3.000
 69F  C22  O21  C19  118.49  3.000
 69F  H17  C22  H16  107.78  3.000
 69F  H17  C22  C23  110.48  3.000
 69F  H16  C22  C23  110.46  3.000
 69F  H17  C22  O21  110.35  3.000
 69F  H16  C22  O21  110.49  3.000
 69F  C23  C22  O21  107.30  3.000
 69F  C28  C23  C24  119.12  3.000
 69F  C28  C23  C22  120.47  3.000
 69F  C24  C23  C22  120.38  3.000
 69F  H18  C24  C25  119.82  3.000
 69F  H18  C24  C23  119.65  3.000
 69F  C25  C24  C23  120.53  3.000
 69F  H19  C25  C26  120.13  3.000
 69F  H19  C25  C24  119.89  3.000
 69F  C26  C25  C24  119.98  3.000
 69F  H20  C26  C27  120.06  3.000
 69F  H20  C26  C25  120.08  3.000
 69F  C27  C26  C25  119.86  3.000
 69F  H21  C27  C28  119.90  3.000
 69F  H21  C27  C26  120.11  3.000
 69F  C28  C27  C26  119.99  3.000
 69F  H22  C28  C27  119.79  3.000
 69F  H22  C28  C23  119.69  3.000
 69F  C27  C28  C23  120.52  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
 69F  CONST_01  C8   C9   C10  C11    0.00   0.0  0
 69F  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 69F  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 69F  CONST_06  C15  C12  C11  C10  180.00   0.0  0
 69F  CONST_07  C19  C20  C15  C12  180.00   0.0  0
 69F  CONST_08  C17  C16  C15  C12  180.00   0.0  0
 69F  CONST_11  C18  C19  C20  C15    0.00   0.0  0
 69F  CONST_12  C18  C17  C16  C15    0.00   0.0  0
 69F  CONST_13  C19  C20  C15  C16    0.00   0.0  0
 69F  CONST_14  C19  C18  C17  C16    0.00   0.0  0
 69F  CONST_15  C20  C15  C16  C17    0.00   0.0  0
 69F  CONST_16  C20  C19  C18  C17    0.00   0.0  0
 69F  CONST_17  C26  C25  C24  C23    0.00   0.0  0
 69F  CONST_18  C26  C27  C28  C23    0.00   0.0  0
 69F  CONST_19  C27  C26  C25  C24    0.00   0.0  0
 69F  CONST_20  C27  C28  C23  C24    0.00   0.0  0
 69F  CONST_21  C28  C27  C26  C25    0.00   0.0  0
 69F  CONST_22  C28  C23  C24  C25    0.00   0.0  0
 69F  CONST_23  O21  C19  C20  C15  180.00   0.0  0
 69F  CONST_24  O21  C19  C18  C17  180.00   0.0  0
 69F  CONST_25  C25  C24  C23  C22  180.00   0.0  0
 69F  CONST_26  C27  C28  C23  C22  180.00   0.0  0
 69F  CONST_27  H4   C9   C10  C11  180.00   0.0  0
 69F  CONST_28  H5   C10  C9   C8   180.00   0.0  0
 69F  CONST_29  H3   C11  C10  C9   180.00   0.0  0
 69F  CONST_30  H15  C20  C15  C12    0.00   0.0  0
 69F  CONST_31  H12  C16  C15  C12    0.00   0.0  0
 69F  CONST_32  H13  C17  C16  C15  180.00   0.0  0
 69F  CONST_33  H14  C18  C17  C16  180.00   0.0  0
 69F  CONST_34  H19  C25  C24  C23  180.00   0.0  0
 69F  CONST_35  H21  C27  C28  C23  180.00   0.0  0
 69F  CONST_36  H20  C26  C25  C24  180.00   0.0  0
 69F  CONST_37  H22  C28  C23  C24  180.00   0.0  0
 69F  CONST_38  H18  C24  C25  C26  180.00   0.0  0
 69F  Var_01    C23  C22  O21  C19  179.42  30.0  1
 69F  Var_02    C24  C23  C22  O21  -88.19  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
 69F  chir_01  C2  N14  C1  C4  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
 69F  plan-1  C12  0.020
 69F  plan-1  C15  0.020
 69F  plan-1  C16  0.020
 69F  plan-1  C17  0.020
 69F  plan-1  C18  0.020
 69F  plan-1  C19  0.020
 69F  plan-1  C20  0.020
 69F  plan-1  O21  0.020
 69F  plan-1  H12  0.020
 69F  plan-1  H13  0.020
 69F  plan-1  H14  0.020
 69F  plan-1  H15  0.020
 69F  plan-2  C22  0.020
 69F  plan-2  C23  0.020
 69F  plan-2  C24  0.020
 69F  plan-2  C25  0.020
 69F  plan-2  C26  0.020
 69F  plan-2  C27  0.020
 69F  plan-2  C28  0.020
 69F  plan-2  H18  0.020
 69F  plan-2  H19  0.020
 69F  plan-2  H20  0.020
 69F  plan-2  H21  0.020
 69F  plan-2  H22  0.020
 69F  plan-3  C11  0.020
 69F  plan-3  C8   0.020
 69F  plan-3  C9   0.020
 69F  plan-3  C10  0.020
 69F  plan-3  C12  0.020
 69F  plan-3  C13  0.020
 69F  plan-3  N7   0.020
 69F  plan-3  N14  0.020
 69F  plan-3  C15  0.020
 69F  plan-3  H3   0.020
 69F  plan-3  H4   0.020
 69F  plan-3  H5   0.020
 69F  plan-4  C4   0.020
 69F  plan-4  C5   0.020
 69F  plan-4  C8   0.020
 69F  plan-4  O6   0.020
 69F  plan-4  N7   0.020
 69F  plan-4  H10  0.020

