# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 18:46:53 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 4-amino-20,22-dimethyl-13-oxa-7-thia-3,5,17-triazatetracyclo[17.3.1.1~2,6~.1~8,12~]pentacosa-1(23),2(25),3,5,8(24),9,11,19,21-nonaen-18-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c2cc1C(=O)NCCCOc3cccc(Sc4cc2nc(N)n4)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
 VHC  VHC  4-amino-20,22-dimethyl-13-oxa-7-thia-3,5,17-triazatetracyclo[17.3.1.1~2,6~.1~8,12~]pentacosa-1(23),2(25),3,5,8(24),9,11,19,21-nonaen-18-one  ligand  51  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VHC
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
 VHC  C1    C  CH3   0  -0.725   5.2046  -0.2126  -0.8734
 VHC  C2    C  CR6   0   0.112   3.8547   0.3917  -0.6152
 VHC  C3    C  CR16  0  -0.349   3.7127   1.7737  -0.6925
 VHC  C4    C  CR6   0   0.105   2.5126   2.4449  -0.4753
 VHC  C5    C  CH3   0  -0.731   2.4775   3.9370  -0.6324
 VHC  C6    C  CR6   0   0.030   1.3867   1.6770  -0.1491
 VHC  C7    C  CR16  0  -0.318   1.5175   0.2922  -0.0570
 VHC  C8    C  CR6   0  -0.076   2.7207  -0.3618  -0.2848
 VHC  C9    C  C     0   0.494   2.7690  -1.8579  -0.2392
 VHC  O10   O  O     0  -0.487   3.3806  -2.4967  -1.0856
 VHC  N11   N  NH1   0  -0.625   2.0875  -2.4338   0.7673
 VHC  C13   C  CH2   0  -0.286   2.0621  -3.8646   0.9877
 VHC  C14   C  CH2   0  -0.488   0.7285  -4.3839   1.5076
 VHC  C15   C  CH2   0  -0.189  -0.4543  -4.1523   0.5864
 VHC  O16   O  O2    0  -0.472  -0.9762  -2.8546   0.8347
 VHC  C17   C  CR6   0   0.411  -1.9341  -2.3610   0.0332
 VHC  C18   C  CR16  0  -0.320  -2.3960  -1.0884   0.3623
 VHC  C19   C  CR16  0  -0.381  -2.4722  -3.0216  -1.0720
 VHC  C20   C  CR16  0  -0.231  -3.4157  -2.3756  -1.8604
 VHC  C21   C  CR16  0  -0.276  -3.8183  -1.0766  -1.5887
 VHC  C22   C  CR6   0  -0.153  -3.2958  -0.4384  -0.4688
 VHC  S23   S  S2    0   0.119  -3.8253   1.2117  -0.0909
 VHC  C24   C  CR6   0   0.110  -2.2930   2.0564   0.1504
 VHC  N25   N  N     0  -0.478  -2.4026   3.1785   0.8343
 VHC  C26   C  CR16  0  -0.366  -1.0815   1.5736  -0.3198
 VHC  C27   C  CR6   0   0.250   0.0509   2.2528   0.1161
 VHC  N28   N  N     0  -0.473  -0.0322   3.3742   0.8187
 VHC  C29   C  CR6   0   0.545  -1.2588   3.8251   1.0968
 VHC  N30   N  NH2   0  -0.825  -1.3516   4.9955   1.7466
 VHC  H1    H  HCH3  0   0.245   5.4688  -0.9647  -0.1310
 VHC  H1A   H  HCH3  0   0.254   5.2406  -0.6986  -1.8480
 VHC  H1B   H  HCH3  0   0.243   5.9728   0.5586  -0.8556
 VHC  H3    H  HCR6  0   0.249   4.5879   2.3622  -0.9440
 VHC  H5    H  HCH3  0   0.244   1.6523   4.2566  -1.2691
 VHC  H5A   H  HCH3  0   0.256   2.3456   4.4374   0.3254
 VHC  H5B   H  HCH3  0   0.244   3.4048   4.2937  -1.0785
 VHC  H7    H  HCR6  0   0.261   0.6441  -0.2949   0.2022
 VHC  HN11  H  HNH1  0   0.402   1.7176  -1.8448   1.4967
 VHC  H13   H  HCH2  0   0.250   2.2976  -4.3549   0.0443
 VHC  H13A  H  HCH2  0   0.250   2.8490  -4.1469   1.6939
 VHC  H14   H  HCH2  0   0.259   0.8445  -5.4616   1.6396
 VHC  H14A  H  HCH2  0   0.249   0.5079  -3.9843   2.5010
 VHC  H15   H  HCH2  0   0.228  -0.1430  -4.2520  -0.4595
 VHC  H15A  H  HCH2  0   0.240  -1.2308  -4.9017   0.7714
 VHC  H18   H  HCR6  0   0.283  -2.0037  -0.5999   1.2457
 VHC  H19   H  HCR6  0   0.286  -2.1676  -4.0253  -1.3332
 VHC  H20   H  HCR6  0   0.268  -3.8250  -2.8927  -2.7184
 VHC  H21   H  HCR6  0   0.271  -4.5166  -0.5675  -2.2392
 VHC  H26   H  HCR6  0   0.288  -1.0097   0.6983  -0.9441
 VHC  HN30  H  HNH2  0   0.401  -2.2490   5.4268   1.8804
 VHC  HN3A  H  HNH2  0   0.400  -0.5293   5.5590   1.8715

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
 VHC  C1   C2    single    1.501  0.020  1.501
 VHC  C2   C3    aromatic  1.391  0.020  1.391
 VHC  C2   C8    single    1.401  0.020  1.401
 VHC  C3   C4    aromatic  1.392  0.020  1.392
 VHC  C4   C5    single    1.501  0.020  1.501
 VHC  C4   C6    single    1.401  0.020  1.401
 VHC  C6   C7    aromatic  1.394  0.020  1.394
 VHC  C6   C27   aromatic  1.479  0.020  1.479
 VHC  C7   C8    aromatic  1.388  0.020  1.388
 VHC  C8   C9    single    1.498  0.020  1.498
 VHC  C9   O10   double    1.224  0.020  1.224
 VHC  C9   N11   single    1.345  0.020  1.345
 VHC  N11  C13   single    1.448  0.020  1.448
 VHC  C13  C14   single    1.523  0.020  1.523
 VHC  C14  C15   single    1.517  0.020  1.517
 VHC  C15  O16   single    1.421  0.020  1.421
 VHC  O16  C17   single    1.343  0.020  1.343
 VHC  C17  C18   aromatic  1.393  0.020  1.393
 VHC  C17  C19   single    1.395  0.020  1.395
 VHC  C18  C22   aromatic  1.387  0.020  1.387
 VHC  C19  C20   aromatic  1.389  0.020  1.389
 VHC  C20  C21   aromatic  1.387  0.020  1.387
 VHC  C21  C22   single    1.391  0.020  1.391
 VHC  C22  S23   single    1.774  0.020  1.774
 VHC  S23  C24   single    1.766  0.020  1.766
 VHC  C24  N25   single    1.319  0.020  1.319
 VHC  C24  C26   aromatic  1.386  0.020  1.386
 VHC  N25  C29   aromatic  1.340  0.020  1.340
 VHC  C26  C27   aromatic  1.391  0.020  1.391
 VHC  C27  N28   single    1.326  0.020  1.326
 VHC  N28  C29   aromatic  1.336  0.020  1.336
 VHC  C29  N30   single    1.342  0.020  1.342
 VHC  C1   H1    single    0.970  0.020  1.090
 VHC  C1   H1A   single    0.970  0.020  1.090
 VHC  C1   H1B   single    0.970  0.020  1.090
 VHC  C3   H3    single    0.930  0.020  1.080
 VHC  C5   H5    single    0.970  0.020  1.090
 VHC  C5   H5A   single    0.970  0.020  1.090
 VHC  C5   H5B   single    0.970  0.020  1.090
 VHC  C7   H7    single    0.930  0.020  1.080
 VHC  N11  HN11  single    0.860  0.020  1.020
 VHC  C13  H13   single    0.970  0.020  1.090
 VHC  C13  H13A  single    0.970  0.020  1.090
 VHC  C14  H14   single    0.970  0.020  1.090
 VHC  C14  H14A  single    0.970  0.020  1.090
 VHC  C15  H15   single    0.970  0.020  1.090
 VHC  C15  H15A  single    0.970  0.020  1.090
 VHC  C18  H18   single    0.930  0.020  1.080
 VHC  C19  H19   single    0.930  0.020  1.080
 VHC  C20  H20   single    0.930  0.020  1.080
 VHC  C21  H21   single    0.930  0.020  1.080
 VHC  C26  H26   single    0.930  0.020  1.080
 VHC  N30  HN30  single    0.860  0.020  1.020
 VHC  N30  HN3A  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
 VHC  H1B   C1   H1A   107.90  3.000
 VHC  H1B   C1   H1    107.87  3.000
 VHC  H1A   C1   H1    107.07  3.000
 VHC  H1B   C1   C2    110.27  3.000
 VHC  H1A   C1   C2    111.29  3.000
 VHC  H1    C1   C2    112.26  3.000
 VHC  C8    C2   C3    117.69  3.000
 VHC  C8    C2   C1    123.49  3.000
 VHC  C3    C2   C1    118.82  3.000
 VHC  H3    C3   C4    118.06  3.000
 VHC  H3    C3   C2    118.01  3.000
 VHC  C4    C3   C2    123.93  3.000
 VHC  C6    C4   C5    123.39  3.000
 VHC  C6    C4   C3    117.69  3.000
 VHC  C5    C4   C3    118.90  3.000
 VHC  H5B   C5   H5A   108.24  3.000
 VHC  H5B   C5   H5    108.01  3.000
 VHC  H5A   C5   H5    106.70  3.000
 VHC  H5B   C5   C4    110.40  3.000
 VHC  H5A   C5   C4    111.57  3.000
 VHC  H5    C5   C4    111.74  3.000
 VHC  C27   C6   C7    117.37  3.000
 VHC  C27   C6   C4    123.66  3.000
 VHC  C7    C6   C4    118.97  3.000
 VHC  H7    C7   C8    118.85  3.000
 VHC  H7    C7   C6    118.57  3.000
 VHC  C8    C7   C6    122.58  3.000
 VHC  C9    C8   C7    119.58  3.000
 VHC  C9    C8   C2    121.22  3.000
 VHC  C7    C8   C2    119.13  3.000
 VHC  N11   C9   O10   123.17  3.000
 VHC  N11   C9   C8    115.73  3.000
 VHC  O10   C9   C8    121.09  3.000
 VHC  HN11  N11  C13   117.44  3.000
 VHC  HN11  N11  C9    118.51  3.000
 VHC  C13   N11  C9    123.09  3.000
 VHC  H13A  C13  H13   106.70  3.000
 VHC  H13A  C13  C14   108.75  3.000
 VHC  H13   C13  C14   109.37  3.000
 VHC  H13A  C13  N11   109.91  3.000
 VHC  H13   C13  N11   108.01  3.000
 VHC  C14   C13  N11   113.86  3.000
 VHC  H14A  C14  H14   105.81  3.000
 VHC  H14A  C14  C15   109.79  3.000
 VHC  H14   C14  C15   107.87  3.000
 VHC  H14A  C14  C13   111.24  3.000
 VHC  H14   C14  C13   106.55  3.000
 VHC  C15   C14  C13   115.05  3.000
 VHC  H15A  C15  H15   107.49  3.000
 VHC  H15A  C15  O16   109.58  3.000
 VHC  H15   C15  O16   110.75  3.000
 VHC  H15A  C15  C14   110.23  3.000
 VHC  H15   C15  C14   110.13  3.000
 VHC  O16   C15  C14   108.65  3.000
 VHC  C17   O16  C15   119.56  3.000
 VHC  C19   C17  C18   119.45  3.000
 VHC  C19   C17  O16   125.01  3.000
 VHC  C18   C17  O16   115.54  3.000
 VHC  H18   C18  C22   120.83  3.000
 VHC  H18   C18  C17   118.98  3.000
 VHC  C22   C18  C17   120.11  3.000
 VHC  H19   C19  C20   119.08  3.000
 VHC  H19   C19  C17   121.48  3.000
 VHC  C20   C19  C17   119.43  3.000
 VHC  H20   C20  C21   119.54  3.000
 VHC  H20   C20  C19   119.00  3.000
 VHC  C21   C20  C19   121.44  3.000
 VHC  H21   C21  C22   120.72  3.000
 VHC  H21   C21  C20   120.69  3.000
 VHC  C22   C21  C20   118.58  3.000
 VHC  S23   C22  C21   119.10  3.000
 VHC  S23   C22  C18   120.14  3.000
 VHC  C21   C22  C18   120.75  3.000
 VHC  C24   S23  C22   102.42  3.000
 VHC  C26   C24  N25   123.02  3.000
 VHC  C26   C24  S23   123.04  3.000
 VHC  N25   C24  S23   113.93  3.000
 VHC  C29   N25  C24   116.19  3.000
 VHC  H26   C26  C27   121.61  3.000
 VHC  H26   C26  C24   122.52  3.000
 VHC  C27   C26  C24   115.80  3.000
 VHC  N28   C27  C26   121.88  3.000
 VHC  N28   C27  C6    118.75  3.000
 VHC  C26   C27  C6    119.30  3.000
 VHC  C29   N28  C27   116.95  3.000
 VHC  N30   C29  N28   117.30  3.000
 VHC  N30   C29  N25   117.18  3.000
 VHC  N28   C29  N25   125.45  3.000
 VHC  HN3A  N30  HN30  118.28  3.000
 VHC  HN3A  N30  C29   119.52  3.000
 VHC  HN30  N30  C29   120.05  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
 VHC  CONST_01  C6    C4   C3   C2      0.00   0.0  0
 VHC  CONST_02  C6    C7   C8   C2      0.00   0.0  0
 VHC  CONST_03  C7    C8   C2   C3      0.00   0.0  0
 VHC  CONST_04  C7    C6   C4   C3      0.00   0.0  0
 VHC  CONST_05  C27   C6   C4   C3    180.00   0.0  0
 VHC  CONST_06  C8    C2   C3   C4      0.00   0.0  0
 VHC  CONST_07  C8    C7   C6   C4      0.00   0.0  0
 VHC  CONST_10  C24   C26  C27  C6    180.00   0.0  0
 VHC  CONST_11  C29   N28  C27  C6    180.00   0.0  0
 VHC  CONST_14  C27   C6   C7   C8    180.00   0.0  0
 VHC  CONST_15  C21   C22  C18  C17     0.00   0.0  0
 VHC  CONST_16  C21   C20  C19  C17     0.00   0.0  0
 VHC  CONST_17  C20   C19  C17  C18     0.00   0.0  0
 VHC  CONST_18  C20   C21  C22  C18     0.00   0.0  0
 VHC  CONST_19  C22   C18  C17  C19     0.00   0.0  0
 VHC  CONST_20  C22   C21  C20  C19     0.00   0.0  0
 VHC  CONST_21  N28   C29  N25  C24     0.00   0.0  0
 VHC  CONST_22  N28   C27  C26  C24     0.00   0.0  0
 VHC  CONST_23  C27   C26  C24  N25     0.00   0.0  0
 VHC  CONST_24  C27   N28  C29  N25     0.00   0.0  0
 VHC  CONST_25  C29   N25  C24  C26     0.00   0.0  0
 VHC  CONST_26  C29   N28  C27  C26     0.00   0.0  0
 VHC  CONST_27  C13   N11  C9   C8    180.00   0.0  0
 VHC  CONST_28  C4    C3   C2   C1    180.00   0.0  0
 VHC  CONST_29  C7    C8   C2   C1    180.00   0.0  0
 VHC  CONST_30  C9    C8   C2   C1      0.00   0.0  0
 VHC  CONST_31  C5    C4   C3   C2    180.00   0.0  0
 VHC  CONST_32  C7    C6   C4   C5    180.00   0.0  0
 VHC  CONST_33  C27   C6   C4   C5      0.00   0.0  0
 VHC  CONST_34  N30   C29  N25  C24   180.00   0.0  0
 VHC  CONST_35  N30   C29  N28  C27   180.00   0.0  0
 VHC  CONST_36  C13   N11  C9   O10     0.00   0.0  0
 VHC  CONST_37  H7    C7   C8   C2    180.00   0.0  0
 VHC  CONST_38  H3    C3   C4   C6    180.00   0.0  0
 VHC  CONST_39  H26   C26  C27  C6      0.00   0.0  0
 VHC  CONST_40  H18   C18  C17  O16     0.00   0.0  0
 VHC  CONST_41  H19   C19  C17  O16     0.00   0.0  0
 VHC  CONST_42  H20   C20  C19  C17   180.00   0.0  0
 VHC  CONST_43  H21   C21  C22  C18   180.00   0.0  0
 VHC  CONST_44  HN11  N11  C9   C8      0.00   0.0  0
 VHC  CONST_45  HN30  N30  C29  N25     0.00   0.0  0
 VHC  CONST_46  HN3A  N30  C29  N25   180.00   0.0  0
 VHC  Var_01    N11   C9   C8   C2    140.19  30.0  1
 VHC  Var_02    C14   C13  N11  C9   -144.59  30.0  1
 VHC  Var_03    C15   C14  C13  N11    61.06  30.0  1
 VHC  Var_04    O16   C15  C14  C13   -85.62  30.0  1
 VHC  Var_05    C18   C17  O16  C15   179.28  30.0  1
 VHC  Var_06    N25   C24  S23  C22  -160.17  30.0  1
 VHC  Var_07    H1    C1   C2   C3    134.25  30.0  2
 VHC  Var_08    H5    C5   C4   C3    130.09  30.0  2

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
 VHC  plan-1  C1    0.020
 VHC  plan-1  C2    0.020
 VHC  plan-1  C3    0.020
 VHC  plan-1  C4    0.020
 VHC  plan-1  C5    0.020
 VHC  plan-1  C6    0.020
 VHC  plan-1  C7    0.020
 VHC  plan-1  C8    0.020
 VHC  plan-1  C9    0.020
 VHC  plan-1  C27   0.020
 VHC  plan-1  H3    0.020
 VHC  plan-1  H7    0.020
 VHC  plan-2  O16   0.020
 VHC  plan-2  C17   0.020
 VHC  plan-2  C18   0.020
 VHC  plan-2  C19   0.020
 VHC  plan-2  C20   0.020
 VHC  plan-2  C21   0.020
 VHC  plan-2  C22   0.020
 VHC  plan-2  S23   0.020
 VHC  plan-2  H18   0.020
 VHC  plan-2  H19   0.020
 VHC  plan-2  H20   0.020
 VHC  plan-2  H21   0.020
 VHC  plan-3  C6    0.020
 VHC  plan-3  S23   0.020
 VHC  plan-3  C24   0.020
 VHC  plan-3  N25   0.020
 VHC  plan-3  C26   0.020
 VHC  plan-3  C27   0.020
 VHC  plan-3  N28   0.020
 VHC  plan-3  C29   0.020
 VHC  plan-3  N30   0.020
 VHC  plan-3  H26   0.020
 VHC  plan-4  C8    0.020
 VHC  plan-4  C9    0.020
 VHC  plan-4  O10   0.020
 VHC  plan-4  N11   0.020
 VHC  plan-4  C13   0.020
 VHC  plan-4  HN11  0.020
 VHC  plan-5  C29   0.020
 VHC  plan-5  N30   0.020
 VHC  plan-5  HN30  0.020
 VHC  plan-5  HN3A  0.020

