# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 02:49:27 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: ~{N}-(5-ethyl-4-oxidanylidene-1,2,3,6-tetrahydro-1,5-benzodiazocin-8-yl)-7-methyl-2-oxidanylidene-1~{H}-pyrazolo[1,5-a]pyrimidine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1Cc2cc(NC(=O)C3=C(C)N4NC(=O)C=C4N=C3)ccc2NCCC1=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
 VDH  VDH  "N-(5-ethyl-4-oxidanylidene-1,2,3,6-tetrahydro-1,5-benzodiazocin-8-yl)-7-methyl-2-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-6-carboxamide"
  ligand  51  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VDH
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
 VDH  N1   N  NT    0  -0.427  -30.6787  14.3851   0.2428
 VDH  N3   N  N     0  -0.434  -24.8363  13.0185   7.0900
 VDH  C4   C  CR6   0   0.151  -28.2804  13.7780   0.4361
 VDH  C5   C  CR16  0  -0.416  -27.8121  13.4948   1.7092
 VDH  C6   C  CR6   0   0.381  -26.8362  12.5277   1.9436
 VDH  C7   C  CR16  0  -0.318  -26.3043  11.8456   0.8511
 VDH  C8   C  CR16  0  -0.318  -26.7758  12.1237  -0.4219
 VDH  C10  C  CR6   0  -0.280  -25.3790  11.5480   5.2568
 VDH  C13  C  CR15  0  -0.660  -24.4994  11.8125   9.2244
 VDH  C17  C  CR6   0   0.254  -27.7638  13.0773  -0.6612
 VDH  C20  C  C     0   0.530  -31.3298  14.0121  -0.8803
 VDH  C1   C  CH3   0  -0.663  -31.3170  12.7356   2.0155
 VDH  C11  C  CR16  0  -0.037  -25.1260  12.8110   5.8346
 VDH  C12  C  CR56  0   0.625  -24.7575  11.9424   7.8855
 VDH  C14  C  CR6   0   0.486  -25.3124  10.4349   6.0787
 VDH  C16  C  CR5   0   0.554  -24.5310  10.4222   9.5471
 VDH  C18  C  CH2   0  -0.312  -29.5258  13.0196  -2.3993
 VDH  C19  C  CH2   0  -0.578  -30.5982  14.1017  -2.2033
 VDH  C2   C  CH2   0  -0.301  -31.3295  14.1789   1.5318
 VDH  C3   C  CH2   0  -0.449  -29.3059  14.8610   0.2439
 VDH  C9   C  C     0   0.503  -25.6081  11.4072   3.7926
 VDH  N2   N  NH1   0  -0.747  -26.4523  12.3313   3.2779
 VDH  N4   N  N     0  -0.395  -24.9739  10.6768   7.3513
 VDH  N5   N  NR15  0  -0.507  -24.9205   9.7700   8.3600
 VDH  N6   N  NH1   0  -0.677  -28.1749  13.3684  -1.9683
 VDH  O1   O  O     0  -0.490  -24.3058   9.8074  10.5776
 VDH  O2   O  O     0  -0.453  -25.0592  10.5336   3.1427
 VDH  O3   O  O     0  -0.499  -32.4755  13.5791  -0.8413
 VDH  H8   H  HCR6  0   0.271  -28.2121  14.0581   2.5470
 VDH  H9   H  HCR6  0   0.279  -25.5399  11.0965   0.9741
 VDH  H10  H  HCR6  0   0.258  -26.3572  11.5777  -1.2596
 VDH  H13  H  HCR5  0   0.280  -24.2823  12.6160   9.9071
 VDH  H15  H  HCH3  0   0.282  -26.2840   8.5826   6.4415
 VDH  H16  H  HCH3  0   0.294  -26.0669   8.9546   4.7306
 VDH  H14  H  HCH3  0   0.293  -24.6923   8.4318   5.6986
 VDH  H1   H  HCH3  0   0.229  -31.7938  12.6716   2.9942
 VDH  H2   H  HCH3  0   0.231  -31.8630  12.0835   1.3359
 VDH  H3   H  HCH3  0   0.231  -30.3011  12.3550   2.1130
 VDH  H12  H  HCR6  0   0.287  -25.1539  13.6944   5.2040
 VDH  H20  H  HCH2  0   0.230  -29.8655  12.0787  -1.9502
 VDH  H19  H  HCH2  0   0.260  -29.4570  12.8362  -3.4708
 VDH  H22  H  HCH2  0   0.267  -30.1617  15.0865  -2.3801
 VDH  H21  H  HCH2  0   0.269  -31.3593  13.9549  -2.9692
 VDH  H5   H  HCH2  0   0.241  -30.8176  14.8138   2.2553
 VDH  H4   H  HCH2  0   0.246  -32.3561  14.5410   1.4713
 VDH  H7   H  HCH2  0   0.277  -29.1005  15.3945  -0.6835
 VDH  H6   H  HCH2  0   0.283  -29.2109  15.5966   1.0440
 VDH  H11  H  HNH1  0   0.424  -26.9355  12.9197   3.9405
 VDH  H17  H  HNR5  0   0.436  -24.5849   8.8413   8.1358
 VDH  H18  H  HNH1  0   0.374  -27.5118  12.9902  -2.6288
 VDH  C15  C  CH3   0  -0.764  -25.6084   9.0267   5.7088

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
 VDH  C18  C19  single    1.536  0.020  1.536
 VDH  C18  N6   single    1.460  0.020  1.460
 VDH  C19  C20  single    1.514  0.020  1.514
 VDH  N6   C17  single    1.401  0.020  1.401
 VDH  O3   C20  double    1.225  0.020  1.225
 VDH  C20  N1   single    1.351  0.020  1.351
 VDH  C17  C8   aromatic  1.394  0.020  1.394
 VDH  C17  C4   aromatic  1.401  0.020  1.401
 VDH  C8   C7   aromatic  1.386  0.020  1.386
 VDH  N1   C3   single    1.453  0.020  1.453
 VDH  N1   C2   single    1.459  0.020  1.459
 VDH  C3   C4   single    1.504  0.020  1.504
 VDH  C4   C5   aromatic  1.386  0.020  1.386
 VDH  C7   C6   aromatic  1.393  0.020  1.393
 VDH  C2   C1   single    1.522  0.020  1.522
 VDH  C5   C6   aromatic  1.394  0.020  1.394
 VDH  C6   N2   single    1.402  0.020  1.402
 VDH  O2   C9   double    1.219  0.020  1.219
 VDH  N2   C9   single    1.353  0.020  1.353
 VDH  C9   C10  single    1.489  0.020  1.489
 VDH  C10  C11  single    1.412  0.020  1.412
 VDH  C10  C14  double    1.385  0.020  1.385
 VDH  C11  N3   double    1.305  0.020  1.305
 VDH  C15  C14  single    1.486  0.020  1.486
 VDH  C14  N4   single    1.339  0.020  1.339
 VDH  N3   C12  single    1.341  0.020  1.341
 VDH  N4   C12  single    1.391  0.020  1.391
 VDH  N4   N5   single    1.357  0.020  1.357
 VDH  C12  C13  double    1.370  0.020  1.370
 VDH  N5   C16  single    1.409  0.020  1.409
 VDH  C13  C16  single    1.428  0.020  1.428
 VDH  C16  O1   double    1.221  0.020  1.221
 VDH  C5   H8   single    0.930  0.020  1.080
 VDH  C7   H9   single    0.930  0.020  1.080
 VDH  C8   H10  single    0.930  0.020  1.080
 VDH  C13  H13  single    0.930  0.020  1.080
 VDH  C15  H15  single    0.970  0.020  1.090
 VDH  C15  H16  single    0.970  0.020  1.090
 VDH  C15  H14  single    0.970  0.020  1.090
 VDH  C1   H1   single    0.970  0.020  1.090
 VDH  C1   H2   single    0.970  0.020  1.090
 VDH  C1   H3   single    0.970  0.020  1.090
 VDH  C11  H12  single    0.930  0.020  1.080
 VDH  C18  H20  single    0.970  0.020  1.090
 VDH  C18  H19  single    0.970  0.020  1.090
 VDH  C19  H22  single    0.970  0.020  1.090
 VDH  C19  H21  single    0.970  0.020  1.090
 VDH  C2   H5   single    0.970  0.020  1.090
 VDH  C2   H4   single    0.970  0.020  1.090
 VDH  C3   H7   single    0.970  0.020  1.090
 VDH  C3   H6   single    0.970  0.020  1.090
 VDH  N2   H11  single    0.860  0.020  1.020
 VDH  N5   H17  single    0.890  0.020  1.040
 VDH  N6   H18  single    0.890  0.020  1.040

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
 VDH  C3   N1   C2   117.85  3.000
 VDH  C2   N1   C20  118.73  3.000
 VDH  C3   N1   C20  123.13  3.000
 VDH  C12  N3   C11  117.15  3.000
 VDH  C3   C4   C17  120.77  3.000
 VDH  C3   C4   C5   119.67  3.000
 VDH  C17  C4   C5   119.53  3.000
 VDH  H8   C5   C6   119.22  3.000
 VDH  H8   C5   C4   118.57  3.000
 VDH  C6   C5   C4   122.20  3.000
 VDH  N2   C6   C7   124.96  3.000
 VDH  N2   C6   C5   116.67  3.000
 VDH  C7   C6   C5   118.36  3.000
 VDH  H9   C7   C8   119.07  3.000
 VDH  H9   C7   C6   121.44  3.000
 VDH  C8   C7   C6   119.48  3.000
 VDH  H10  C8   C17  119.06  3.000
 VDH  H10  C8   C7   118.52  3.000
 VDH  C17  C8   C7   122.42  3.000
 VDH  C9   C10  C14  121.00  3.000
 VDH  C14  C10  C11  117.86  3.000
 VDH  C9   C10  C11  120.98  3.000
 VDH  H13  C13  C16  126.01  3.000
 VDH  H13  C13  C12  125.96  3.000
 VDH  C16  C13  C12  108.01  3.000
 VDH  N6   C17  C8   120.69  3.000
 VDH  C8   C17  C4   117.98  3.000
 VDH  N6   C17  C4   121.25  3.000
 VDH  O3   C20  C19  120.02  3.000
 VDH  O3   C20  N1   121.46  3.000
 VDH  C19  C20  N1   118.50  3.000
 VDH  H3   C1   H2   108.32  3.000
 VDH  H3   C1   H1   107.87  3.000
 VDH  H2   C1   H1   107.80  3.000
 VDH  H3   C1   C2   111.55  3.000
 VDH  H2   C1   C2   111.44  3.000
 VDH  H1   C1   C2   109.71  3.000
 VDH  H12  C11  C10  119.05  3.000
 VDH  H12  C11  N3   115.79  3.000
 VDH  C10  C11  N3   125.15  3.000
 VDH  N4   C12  C13  108.57  3.000
 VDH  C13  C12  N3   131.85  3.000
 VDH  N4   C12  N3   119.57  3.000
 VDH  N4   C14  C15  117.28  3.000
 VDH  N4   C14  C10  115.53  3.000
 VDH  C15  C14  C10  127.17  3.000
 VDH  O1   C16  N5   121.93  3.000
 VDH  O1   C16  C13  132.62  3.000
 VDH  N5   C16  C13  105.45  3.000
 VDH  H19  C18  H20  106.14  3.000
 VDH  H19  C18  N6   105.79  3.000
 VDH  H20  C18  N6   111.76  3.000
 VDH  H19  C18  C19  106.75  3.000
 VDH  H20  C18  C19  109.63  3.000
 VDH  N6   C18  C19  116.10  3.000
 VDH  H21  C19  H22  106.68  3.000
 VDH  H21  C19  C18  107.64  3.000
 VDH  H22  C19  C18  109.61  3.000
 VDH  H21  C19  C20  105.58  3.000
 VDH  H22  C19  C20  112.83  3.000
 VDH  C18  C19  C20  114.02  3.000
 VDH  H4   C2   H5   106.59  3.000
 VDH  H4   C2   C1   109.89  3.000
 VDH  H5   C2   C1   109.72  3.000
 VDH  H4   C2   N1   108.92  3.000
 VDH  H5   C2   N1   107.13  3.000
 VDH  C1   C2   N1   114.28  3.000
 VDH  H6   C3   H7   106.12  3.000
 VDH  H6   C3   C4   109.42  3.000
 VDH  H7   C3   C4   109.44  3.000
 VDH  H6   C3   N1   107.68  3.000
 VDH  H7   C3   N1   109.75  3.000
 VDH  C4   C3   N1   114.11  3.000
 VDH  O2   C9   N2   124.56  3.000
 VDH  N2   C9   C10  113.92  3.000
 VDH  O2   C9   C10  121.51  3.000
 VDH  H11  N2   C9   116.56  3.000
 VDH  H11  N2   C6   114.33  3.000
 VDH  C9   N2   C6   128.92  3.000
 VDH  N5   N4   C14  126.55  3.000
 VDH  N5   N4   C12  108.45  3.000
 VDH  C14  N4   C12  124.67  3.000
 VDH  H17  N5   N4   117.46  3.000
 VDH  H17  N5   C16  121.29  3.000
 VDH  N4   N5   C16  109.12  3.000
 VDH  H18  N6   C18  108.97  3.000
 VDH  H18  N6   C17  109.87  3.000
 VDH  C18  N6   C17  119.82  3.000
 VDH  H14  C15  H16  108.08  3.000
 VDH  H14  C15  H15  107.69  3.000
 VDH  H16  C15  H15  108.51  3.000
 VDH  H14  C15  C14  110.57  3.000
 VDH  H16  C15  C14  111.86  3.000
 VDH  H15  C15  C14  109.99  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
 VDH  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 VDH  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 VDH  CONST_03  C17  C8   C7   C6      0.00   0.0  0
 VDH  CONST_04  C14  N4   C12  N3      0.00   0.0  0
 VDH  CONST_05  N5   N4   C12  N3    180.00   0.0  0
 VDH  CONST_06  C11  N3   C12  C13   180.00   0.0  0
 VDH  CONST_07  C14  N4   C12  C13   180.00   0.0  0
 VDH  CONST_08  N5   N4   C12  C13     0.00   0.0  0
 VDH  CONST_09  N4   N5   C16  C13     0.00   0.0  0
 VDH  CONST_10  N4   C12  N3   C11     0.00   0.0  0
 VDH  CONST_11  N2   C6   C5   C4    180.00   0.0  0
 VDH  CONST_12  N2   C6   C7   C8    180.00   0.0  0
 VDH  CONST_13  O1   C16  N5   N4    180.00   0.0  0
 VDH  CONST_14  H9   C7   C6   C5    180.00   0.0  0
 VDH  CONST_15  H10  C8   C7   C6    180.00   0.0  0
 VDH  CONST_16  H8   C5   C6   C7    180.00   0.0  0
 VDH  CONST_17  H9   C7   C8   C17   180.00   0.0  0
 VDH  CONST_19  C10  C9   N2   C6    180.00   0.0  0
 VDH  CONST_20  C9   N2   C6   C5    180.00   0.0  0
 VDH  CONST_21  C9   N2   C6   C7      0.00   0.0  0
 VDH  CONST_22  H11  N2   C6   C5      0.00   0.0  0
 VDH  CONST_23  H11  N2   C6   C7    180.00   0.0  0
 VDH  CONST_25  O2   C9   N2   C6      0.00   0.0  0
 VDH  CONST_26  H11  N2   C9   C10     0.00   0.0  0
 VDH  CONST_27  H11  N2   C9   O2    180.00   0.0  0
 VDH  Var_01    C16  C13  C12  N3   -179.69   0.0  0
 VDH  Var_02    N4   C12  C13  C16     0.95   0.0  0
 VDH  Var_03    C14  C10  C11  N3     -0.22  30.0  1
 VDH  Var_04    C12  N3   C11  C10     0.88  30.0  1
 VDH  Var_05    C12  N4   C14  C10     3.15  30.0  1
 VDH  Var_06    N5   N4   C14  C10   175.77  30.0  1
 VDH  Var_07    N4   C14  C10  C11    -1.73  30.0  1
 VDH  Var_08    C9   C10  C11  N3   -175.70  30.0  1
 VDH  Var_09    C11  C10  C14  C15   176.53  30.0  1
 VDH  Var_10    C12  N4   C14  C15  -175.28  30.0  1
 VDH  Var_11    N5   N4   C14  C15    -2.67  30.0  1
 VDH  Var_12    N4   C14  C10  C9    173.75  30.0  1
 VDH  Var_13    H13  C13  C12  N3     -1.32   0.0  0
 VDH  Var_14    H13  C13  C12  N4    179.32   0.0  0
 VDH  Var_15    H12  C11  N3   C12  -178.17  30.0  1
 VDH  Var_16    H12  C11  C10  C14   178.81  30.0  1
 VDH  Var_17    C9   C10  C14  C15    -7.99  30.0  1
 VDH  Var_18    O2   C9   C10  C11   134.19  30.0  2
 VDH  Var_19    N2   C9   C10  C11   -45.21  30.0  2
 VDH  Var_20    O2   C9   C10  C14   -41.15  30.0  2
 VDH  Var_21    N2   C9   C10  C14   139.46  30.0  2
 VDH  Var_22    H15  C15  C14  C10  -130.79  30.0  3
 VDH  Var_23    H16  C15  C14  C10   -10.12  30.0  3
 VDH  Var_24    H14  C15  C14  C10   110.40  30.0  3
 VDH  Var_25    H12  C11  C10  C9      3.33  30.0  1
 VDH  Var_26    H15  C15  C14  N4     47.44  30.0  3
 VDH  Var_27    H16  C15  C14  N4    168.11  30.0  3
 VDH  Var_28    H14  C15  C14  N4    -71.37  30.0  3
 VDH  Var_29    H1   C1   C2   N1    178.31  30.0  3
 VDH  Var_30    H2   C1   C2   N1    -62.37  30.0  3
 VDH  Var_31    H3   C1   C2   N1     58.84  30.0  3

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
 VDH  plan-1  C6   0.020
 VDH  plan-1  C10  0.020
 VDH  plan-1  C9   0.020
 VDH  plan-1  N2   0.020
 VDH  plan-1  O2   0.020
 VDH  plan-1  H11  0.020
 VDH  plan-2  C4   0.020
 VDH  plan-2  C5   0.020
 VDH  plan-2  C6   0.020
 VDH  plan-2  C7   0.020
 VDH  plan-2  C8   0.020
 VDH  plan-2  C17  0.020
 VDH  plan-2  C3   0.020
 VDH  plan-2  N2   0.020
 VDH  plan-2  N6   0.020
 VDH  plan-2  H8   0.020
 VDH  plan-2  H9   0.020
 VDH  plan-2  H10  0.020
 VDH  plan-3  N3   0.020
 VDH  plan-3  C13  0.020
 VDH  plan-3  C11  0.020
 VDH  plan-3  C12  0.020
 VDH  plan-3  C14  0.020
 VDH  plan-3  C16  0.020
 VDH  plan-3  N4   0.020
 VDH  plan-3  N5   0.020
 VDH  plan-3  O1   0.020
 VDH  plan-3  H13  0.020
 VDH  plan-3  H17  0.020
 VDH  plan-4  N1   0.020
 VDH  plan-4  C20  0.020
 VDH  plan-4  C19  0.020
 VDH  plan-4  C2   0.020
 VDH  plan-4  C3   0.020
 VDH  plan-4  O3   0.020

