# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:04:30 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (8R)-5-(4-aminophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)N1N=C(c2ccc(N)cc2)c3cc4OCOc4cc3C[C@H]1C
#
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
 GYK  GYK  (8R)-5-(4-aminophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide  ligand  46  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GYK
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
 GYK  C01  C  CH3   0  -0.671  -1.3126   3.1745   2.2659
 GYK  C02  C  CH1   0  -0.051  -1.6706   1.9463   1.4376
 GYK  C03  C  CH2   0  -0.581  -1.3165   0.6627   2.1874
 GYK  C04  C  CR6   0   0.139  -1.3575  -0.5453   1.3009
 GYK  C05  C  CR16  0  -0.419  -2.3422  -1.5272   1.4644
 GYK  C06  C  CR56  0   0.320  -2.3140  -2.6003   0.6083
 GYK  C07  C  CR56  0   0.298  -1.3490  -2.7285  -0.3785
 GYK  C08  C  CR16  0  -0.360  -0.3660  -1.7914  -0.5507
 GYK  C09  C  CR6   0  -0.013  -0.3861  -0.6798   0.3092
 GYK  C10  C  C     0   0.207   0.6222   0.3864   0.1279
 GYK  N11  N  N     0  -0.293   0.3289   1.6351   0.0581
 GYK  N12  N  NT    0  -0.412  -1.0310   1.9464   0.1179
 GYK  C13  C  C     0   0.737  -1.4706   2.8715  -0.8084
 GYK  O14  O  O     0  -0.548  -2.5845   3.3814  -0.7259
 GYK  N15  N  NH1   0  -0.672  -0.6307   3.1237  -1.8315
 GYK  C16  C  CH3   0  -0.506  -0.9674   4.0770  -2.8585
 GYK  C17  C  CR6   0   0.002   2.0362   0.0131   0.0007
 GYK  C18  C  CR16  0  -0.277   2.9480   0.8373  -0.6690
 GYK  C19  C  CR16  0  -0.313   4.2767   0.4937  -0.7867
 GYK  C20  C  CR6   0   0.322   4.7663  -0.6943  -0.2165
 GYK  C21  C  CR16  0  -0.316   3.8590  -1.5165   0.4668
 GYK  C22  C  CR16  0  -0.287   2.5265  -1.1676   0.5646
 GYK  N23  N  NH2   0  -0.854   6.0912  -1.0136  -0.2892
 GYK  O24  O  O     0  -0.487  -1.5506  -3.8851  -1.0565
 GYK  C25  C  CH2   0   0.067  -2.7992  -4.3927  -0.6076
 GYK  O26  O  O     0  -0.482  -3.1403  -3.6682   0.5697
 GYK  H1   H  HCH3  0   0.227  -0.2340   3.2453   2.4157
 GYK  H2   H  HCH3  0   0.240  -1.6550   4.0907   1.7864
 GYK  H3   H  HCH3  0   0.233  -1.7840   3.1183   3.2481
 GYK  H4   H  HCH1  0   0.260  -2.7441   1.9386   1.2479
 GYK  H5   H  HCH2  0   0.254  -0.3220   0.7585   2.6345
 GYK  H6   H  HCH2  0   0.278  -2.0157   0.5558   3.0176
 GYK  H7   H  HCR6  0   0.272  -3.0934  -1.4388   2.2383
 GYK  H8   H  HCR6  0   0.278   0.3843  -1.8942  -1.3233
 GYK  H11  H  HNH1  0   0.405   0.3104   2.7722  -1.7821
 GYK  H12  H  HCH3  0   0.233  -1.8957   3.8097  -3.3629
 GYK  H13  H  HCH3  0   0.228  -1.0715   5.0929  -2.4716
 GYK  H14  H  HCH3  0   0.245  -0.1707   4.0759  -3.5973
 GYK  H15  H  HCR6  0   0.256   2.6050   1.7586  -1.1216
 GYK  H16  H  HCR6  0   0.261   4.9527   1.1433  -1.3299
 GYK  H17  H  HCR6  0   0.261   4.2062  -2.4357   0.9225
 GYK  H18  H  HCR6  0   0.258   1.8596  -1.8266   1.1059
 GYK  H19  H  HNH2  0   0.388   6.3454  -1.9741  -0.1284
 GYK  H20  H  HNH2  0   0.388   6.6357  -0.5719  -1.0113
 GYK  H21  H  HCH2  0   0.237  -3.5654  -4.2338  -1.3732
 GYK  H9   H  HCH2  0   0.248  -2.7055  -5.4526  -0.3732

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
 GYK  N23  C20  single    1.365  0.020  1.365
 GYK  C20  C21  aromatic  1.402  0.020  1.402
 GYK  C20  C19  aromatic  1.406  0.020  1.406
 GYK  C21  C22  aromatic  1.381  0.020  1.381
 GYK  C19  C18  aromatic  1.378  0.020  1.378
 GYK  O24  C25  single    1.421  0.020  1.421
 GYK  O24  C07  single    1.356  0.020  1.356
 GYK  C25  O26  single    1.424  0.020  1.424
 GYK  C22  C17  aromatic  1.397  0.020  1.397
 GYK  C18  C17  aromatic  1.400  0.020  1.400
 GYK  C07  C08  aromatic  1.369  0.020  1.369
 GYK  C07  C06  aromatic  1.386  0.020  1.386
 GYK  C08  C09  aromatic  1.406  0.020  1.406
 GYK  C17  C10  single    1.468  0.020  1.468
 GYK  O26  C06  single    1.351  0.020  1.351
 GYK  C06  C05  aromatic  1.373  0.020  1.373
 GYK  C09  C10  single    1.479  0.020  1.479
 GYK  C09  C04  aromatic  1.395  0.020  1.395
 GYK  C10  N11  double    1.285  0.020  1.285
 GYK  C05  C04  aromatic  1.400  0.020  1.400
 GYK  C04  C03  single    1.499  0.020  1.499
 GYK  N11  N12  single    1.396  0.020  1.396
 GYK  C03  C02  single    1.528  0.020  1.528
 GYK  N12  C02  single    1.466  0.020  1.466
 GYK  N12  C13  single    1.381  0.020  1.381
 GYK  N15  C13  single    1.348  0.020  1.348
 GYK  N15  C16  single    1.441  0.020  1.441
 GYK  C01  C02  single    1.524  0.020  1.524
 GYK  C13  O14  double    1.228  0.020  1.228
 GYK  C01  H1   single    0.970  0.020  1.090
 GYK  C01  H2   single    0.970  0.020  1.090
 GYK  C01  H3   single    0.970  0.020  1.090
 GYK  C02  H4   single    0.970  0.020  1.090
 GYK  C03  H5   single    0.970  0.020  1.090
 GYK  C03  H6   single    0.970  0.020  1.090
 GYK  C05  H7   single    0.930  0.020  1.080
 GYK  C08  H8   single    0.930  0.020  1.080
 GYK  N15  H11  single    0.860  0.020  1.020
 GYK  C16  H12  single    0.970  0.020  1.090
 GYK  C16  H13  single    0.970  0.020  1.090
 GYK  C16  H14  single    0.970  0.020  1.090
 GYK  C18  H15  single    0.930  0.020  1.080
 GYK  C19  H16  single    0.930  0.020  1.080
 GYK  C21  H17  single    0.930  0.020  1.080
 GYK  C22  H18  single    0.930  0.020  1.080
 GYK  N23  H19  single    0.890  0.020  1.040
 GYK  N23  H20  single    0.890  0.020  1.040
 GYK  C25  H21  single    0.970  0.020  1.090
 GYK  C25  H9   single    0.970  0.020  1.090

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
 GYK  H3   C01  H2   107.69  3.000
 GYK  H3   C01  H1   107.87  3.000
 GYK  H2   C01  H1   108.46  3.000
 GYK  H3   C01  C02  110.26  3.000
 GYK  H2   C01  C02  111.38  3.000
 GYK  H1   C01  C02  111.04  3.000
 GYK  H4   C02  N12  105.84  3.000
 GYK  H4   C02  C03  107.91  3.000
 GYK  N12  C02  C03  109.91  3.000
 GYK  H4   C02  C01  109.37  3.000
 GYK  N12  C02  C01  112.74  3.000
 GYK  C03  C02  C01  110.84  3.000
 GYK  H6   C03  H5   106.27  3.000
 GYK  H6   C03  C04  110.71  3.000
 GYK  H5   C03  C04  109.69  3.000
 GYK  H6   C03  C02  107.89  3.000
 GYK  H5   C03  C02  109.72  3.000
 GYK  C04  C03  C02  112.36  3.000
 GYK  C09  C04  C05  120.35  3.000
 GYK  C05  C04  C03  121.02  3.000
 GYK  C09  C04  C03  118.63  3.000
 GYK  H7   C05  C06  121.60  3.000
 GYK  H7   C05  C04  120.97  3.000
 GYK  C06  C05  C04  117.44  3.000
 GYK  O26  C06  C07  109.41  3.000
 GYK  O26  C06  C05  128.55  3.000
 GYK  C07  C06  C05  122.04  3.000
 GYK  O24  C07  C08  128.89  3.000
 GYK  C08  C07  C06  121.74  3.000
 GYK  O24  C07  C06  109.36  3.000
 GYK  H8   C08  C09  121.46  3.000
 GYK  H8   C08  C07  121.52  3.000
 GYK  C09  C08  C07  117.01  3.000
 GYK  C10  C09  C08  119.05  3.000
 GYK  C10  C09  C04  119.51  3.000
 GYK  C08  C09  C04  121.41  3.000
 GYK  C17  C10  N11  117.54  3.000
 GYK  N11  C10  C09  123.50  3.000
 GYK  C17  C10  C09  118.96  3.000
 GYK  N12  N11  C10  115.90  3.000
 GYK  C13  N12  N11  115.50  3.000
 GYK  C13  N12  C02  117.70  3.000
 GYK  N11  N12  C02  117.60  3.000
 GYK  N15  C13  O14  122.60  3.000
 GYK  O14  C13  N12  121.46  3.000
 GYK  N15  C13  N12  115.87  3.000
 GYK  H11  N15  C16  118.99  3.000
 GYK  H11  N15  C13  118.72  3.000
 GYK  C16  N15  C13  121.28  3.000
 GYK  H14  C16  H13  108.17  3.000
 GYK  H14  C16  H12  108.04  3.000
 GYK  H13  C16  H12  108.11  3.000
 GYK  H14  C16  N15  108.21  3.000
 GYK  H13  C16  N15  112.65  3.000
 GYK  H12  C16  N15  111.51  3.000
 GYK  C22  C17  C18  117.52  3.000
 GYK  C18  C17  C10  121.28  3.000
 GYK  C22  C17  C10  121.19  3.000
 GYK  H15  C18  C19  118.84  3.000
 GYK  H15  C18  C17  119.66  3.000
 GYK  C19  C18  C17  121.49  3.000
 GYK  H16  C19  C20  119.52  3.000
 GYK  H16  C19  C18  119.68  3.000
 GYK  C20  C19  C18  120.80  3.000
 GYK  N23  C20  C21  121.13  3.000
 GYK  C21  C20  C19  117.90  3.000
 GYK  N23  C20  C19  120.94  3.000
 GYK  H17  C21  C22  119.60  3.000
 GYK  H17  C21  C20  119.69  3.000
 GYK  C22  C21  C20  120.71  3.000
 GYK  H18  C22  C21  118.43  3.000
 GYK  H18  C22  C17  120.00  3.000
 GYK  C21  C22  C17  121.57  3.000
 GYK  H20  N23  H19  113.38  3.000
 GYK  H20  N23  C20  117.44  3.000
 GYK  H19  N23  C20  117.38  3.000
 GYK  C25  O24  C07  106.11  3.000
 GYK  H9   C25  H21  110.59  3.000
 GYK  H9   C25  O26  109.74  3.000
 GYK  H21  C25  O26  109.68  3.000
 GYK  H9   C25  O24  109.88  3.000
 GYK  H21  C25  O24  110.02  3.000
 GYK  O26  C25  O24  106.86  3.000
 GYK  C25  O26  C06  106.22  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
 GYK  CONST_01  C07  C08  C09  C04     0.00   0.0  0
 GYK  CONST_02  C07  C06  C05  C04     0.00   0.0  0
 GYK  CONST_03  C08  C07  C06  C05     0.00   0.0  0
 GYK  CONST_04  C08  C09  C04  C05     0.00   0.0  0
 GYK  CONST_05  C09  C08  C07  C06     0.00   0.0  0
 GYK  CONST_06  C09  C04  C05  C06     0.00   0.0  0
 GYK  CONST_07  C20  C21  C22  C17     0.00   0.0  0
 GYK  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 GYK  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 GYK  CONST_10  C21  C22  C17  C18     0.00   0.0  0
 GYK  CONST_11  C22  C21  C20  C19     0.00   0.0  0
 GYK  CONST_12  C22  C17  C18  C19     0.00   0.0  0
 GYK  CONST_13  C21  C22  C17  C10   180.00   0.0  0
 GYK  CONST_14  C19  C18  C17  C10   180.00   0.0  0
 GYK  CONST_15  N23  C20  C19  C18   180.00   0.0  0
 GYK  CONST_16  N23  C20  C21  C22   180.00   0.0  0
 GYK  CONST_17  H7   C05  C04  C03     0.00   0.0  0
 GYK  CONST_18  H8   C08  C09  C04   180.00   0.0  0
 GYK  CONST_19  H18  C22  C17  C10     0.00   0.0  0
 GYK  CONST_20  H15  C18  C17  C10     0.00   0.0  0
 GYK  CONST_21  H17  C21  C22  C17   180.00   0.0  0
 GYK  CONST_22  H16  C19  C18  C17   180.00   0.0  0
 GYK  CONST_24  O14  C13  N12  N11   180.00   0.0  0
 GYK  CONST_26  N15  C13  N12  N11     0.00   0.0  0
 GYK  CONST_29  C16  N15  C13  N12   180.00   0.0  0
 GYK  CONST_30  H11  N15  C13  N12     0.00   0.0  0
 GYK  CONST_31  C16  N15  C13  O14     0.00   0.0  0
 GYK  Var_01    C09  C04  C03  C02    69.16  30.0  1
 GYK  Var_02    C17  C10  C09  C04   132.92  30.0  1
 GYK  Var_03    O24  C25  O26  C06    13.87  30.0  1
 GYK  Var_04    O26  C25  O24  C07   -13.91  30.0  1
 GYK  Var_05    C22  C17  C10  C09   -26.44  30.0  2
 GYK  Var_06    C13  N12  N11  C10  -134.81  30.0  1
 GYK  Var_07    H12  C16  N15  C13   -58.47  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
 GYK  chir_01  C02  C03  N12  C01  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
 GYK  plan-1  C10  0.020
 GYK  plan-1  C17  0.020
 GYK  plan-1  C18  0.020
 GYK  plan-1  C19  0.020
 GYK  plan-1  C20  0.020
 GYK  plan-1  C21  0.020
 GYK  plan-1  C22  0.020
 GYK  plan-1  N23  0.020
 GYK  plan-1  H15  0.020
 GYK  plan-1  H16  0.020
 GYK  plan-1  H17  0.020
 GYK  plan-1  H18  0.020
 GYK  plan-2  C03  0.020
 GYK  plan-2  C04  0.020
 GYK  plan-2  C05  0.020
 GYK  plan-2  C06  0.020
 GYK  plan-2  C07  0.020
 GYK  plan-2  C08  0.020
 GYK  plan-2  C09  0.020
 GYK  plan-2  C10  0.020
 GYK  plan-2  O24  0.020
 GYK  plan-2  O26  0.020
 GYK  plan-2  H7   0.020
 GYK  plan-2  H8   0.020
 GYK  plan-3  C02  0.020
 GYK  plan-3  N11  0.020
 GYK  plan-3  N12  0.020
 GYK  plan-3  C13  0.020
 GYK  plan-3  O14  0.020
 GYK  plan-3  N15  0.020
 GYK  plan-3  C16  0.020
 GYK  plan-3  H11  0.020
 GYK  plan-4  C20  0.020
 GYK  plan-4  N23  0.020
 GYK  plan-4  H19  0.020
 GYK  plan-4  H20  0.020

