# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:53:05 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 22-methyl-13,18-dioxa-7-thia-3,5-diazatetracyclo[17.3.1.1~2,6~.1~8,12~]pentacosa-1(23),2(25),3,5,8(24),9,11,19,21-nonaen-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2OCCCCOc3cccc(Sc4cc(nc(N)n4)c1c2)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
 VHA  VHA  22-methyl-13,18-dioxa-7-thia-3,5-diazatetracyclo[17.3.1.1~2,6~.1~8,12~]pentacosa-1(23),2(25),3,5,8(24),9,11,19,21-nonaen-4-amine  ligand  48  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VHA
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
 VHA  C1    C  CR16  0  -0.387   1.5984   1.0352  -0.5099
 VHA  C2    C  CR6   0   0.035   2.2923   0.0023   0.1060
 VHA  C3    C  CR6   0   0.059   3.3283   0.2839   1.0036
 VHA  C4    C  CH3   0  -0.738   4.0966  -0.8000   1.7024
 VHA  C5    C  CR16  0  -0.292   3.5941   1.6259   1.2646
 VHA  C6    C  CR16  0  -0.345   2.8827   2.6663   0.6741
 VHA  C7    C  CR6   0   0.378   1.8725   2.3657  -0.2313
 VHA  O8    O  O2    0  -0.490   1.1101   3.2700  -0.8805
 VHA  C9    C  CH2   0  -0.186   0.6935   4.4526  -0.2064
 VHA  C10   C  CH2   0  -0.469  -0.6985   4.8116  -0.6901
 VHA  C11   C  CH2   0  -0.463  -1.8431   3.9669  -0.1302
 VHA  C12   C  CH2   0  -0.173  -1.8487   2.4943  -0.5132
 VHA  O13   O  O2    0  -0.484  -3.0942   1.9636  -0.0553
 VHA  C14   C  CR6   0   0.391  -3.2105   0.6476   0.2039
 VHA  C15   C  CR16  0  -0.354  -2.5029  -0.3470  -0.4669
 VHA  C16   C  CR16  0  -0.338  -4.1270   0.2921   1.1970
 VHA  C17   C  CR16  0  -0.232  -4.2963  -1.0340   1.5439
 VHA  C18   C  CR16  0  -0.265  -3.5435  -2.0296   0.9315
 VHA  C19   C  CR6   0  -0.144  -2.6527  -1.6795  -0.0730
 VHA  S20   S  S2    0   0.104  -1.8122  -3.0118  -0.8950
 VHA  C21   C  CR6   0   0.130  -0.0950  -2.6914  -0.6610
 VHA  N22   N  N     0  -0.484   0.6847  -3.6384  -1.1502
 VHA  C23   C  CR16  0  -0.365   0.4055  -1.5345  -0.0927
 VHA  C24   C  CR6   0   0.243   1.7791  -1.3512  -0.2055
 VHA  N25   N  N     0  -0.469   2.5894  -2.2889  -0.6686
 VHA  C26   C  CR6   0   0.547   2.0050  -3.4230  -1.0791
 VHA  N27   N  NH2   0  -0.824   2.8082  -4.4085  -1.5050
 VHA  H1    H  HCR6  0   0.269   0.8121   0.8076  -1.2191
 VHA  H4    H  HCH3  0   0.249   4.6692  -1.4051   1.0005
 VHA  H4A   H  HCH3  0   0.245   4.7911  -0.3739   2.4250
 VHA  H4B   H  HCH3  0   0.242   3.4328  -1.4795   2.2392
 VHA  H5    H  HCR6  0   0.255   4.3803   1.8728   1.9685
 VHA  H6    H  HCR6  0   0.277   3.1283   3.6913   0.9222
 VHA  H9    H  HCH2  0   0.224   0.6955   4.2991   0.8787
 VHA  H9A   H  HCH2  0   0.235   1.3917   5.2664  -0.4242
 VHA  H10   H  HCH2  0   0.249  -0.8828   5.8479  -0.3971
 VHA  H10A  H  HCH2  0   0.238  -0.7133   4.8022  -1.7839
 VHA  H11   H  HCH2  0   0.234  -1.8498   4.0488   0.9606
 VHA  H11A  H  HCH2  0   0.244  -2.7796   4.4086  -0.4814
 VHA  H12   H  HCH2  0   0.225  -1.7533   2.3681  -1.5970
 VHA  H12A  H  HCH2  0   0.223  -1.0284   1.9524  -0.0353
 VHA  H15   H  HCR6  0   0.302  -1.8390  -0.0978  -1.2854
 VHA  H16   H  HCR6  0   0.271  -4.6926   1.0672   1.6984
 VHA  H17   H  HCR6  0   0.269  -5.0017  -1.2961   2.3214
 VHA  H18   H  HCR6  0   0.273  -3.6502  -3.0621   1.2350
 VHA  H23   H  HCR6  0   0.287  -0.2170  -0.7729   0.3442
 VHA  HN27  H  HNH2  0   0.401   2.4235  -5.3074  -1.7345
 VHA  HN2A  H  HNH2  0   0.401   3.8027  -4.3309  -1.3864

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
 VHA  C1   C2    aromatic  1.388  0.020  1.388
 VHA  C1   C7    aromatic  1.387  0.020  1.387
 VHA  C2   C3    single    1.399  0.020  1.399
 VHA  C2   C24   aromatic  1.481  0.020  1.481
 VHA  C3   C4    single    1.501  0.020  1.501
 VHA  C3   C5    aromatic  1.393  0.020  1.393
 VHA  C5   C6    aromatic  1.392  0.020  1.392
 VHA  C6   C7    single    1.389  0.020  1.389
 VHA  C7   O8    single    1.349  0.020  1.349
 VHA  O8   C9    single    1.424  0.020  1.424
 VHA  C9   C10   single    1.517  0.020  1.517
 VHA  C10  C11   single    1.529  0.020  1.529
 VHA  C11  C12   single    1.522  0.020  1.522
 VHA  C12  O13   single    1.429  0.020  1.429
 VHA  O13  C14   single    1.346  0.020  1.346
 VHA  C14  C15   aromatic  1.393  0.020  1.393
 VHA  C14  C16   single    1.397  0.020  1.397
 VHA  C15  C19   aromatic  1.398  0.020  1.398
 VHA  C16  C17   aromatic  1.381  0.020  1.381
 VHA  C17  C18   aromatic  1.390  0.020  1.390
 VHA  C18  C19   single    1.387  0.020  1.387
 VHA  C19  S20   single    1.777  0.020  1.777
 VHA  S20  C21   single    1.763  0.020  1.763
 VHA  C21  N22   single    1.321  0.020  1.321
 VHA  C21  C23   aromatic  1.383  0.020  1.383
 VHA  N22  C26   aromatic  1.340  0.020  1.340
 VHA  C23  C24   aromatic  1.390  0.020  1.390
 VHA  C24  N25   single    1.323  0.020  1.323
 VHA  N25  C26   aromatic  1.340  0.020  1.340
 VHA  C26  N27   single    1.341  0.020  1.341
 VHA  C1   H1    single    0.930  0.020  1.080
 VHA  C4   H4    single    0.970  0.020  1.090
 VHA  C4   H4A   single    0.970  0.020  1.090
 VHA  C4   H4B   single    0.970  0.020  1.090
 VHA  C5   H5    single    0.930  0.020  1.080
 VHA  C6   H6    single    0.930  0.020  1.080
 VHA  C9   H9    single    0.970  0.020  1.090
 VHA  C9   H9A   single    0.970  0.020  1.090
 VHA  C10  H10   single    0.970  0.020  1.090
 VHA  C10  H10A  single    0.970  0.020  1.090
 VHA  C11  H11   single    0.970  0.020  1.090
 VHA  C11  H11A  single    0.970  0.020  1.090
 VHA  C12  H12   single    0.970  0.020  1.090
 VHA  C12  H12A  single    0.970  0.020  1.090
 VHA  C15  H15   single    0.930  0.020  1.080
 VHA  C16  H16   single    0.930  0.020  1.080
 VHA  C17  H17   single    0.930  0.020  1.080
 VHA  C18  H18   single    0.930  0.020  1.080
 VHA  C23  H23   single    0.930  0.020  1.080
 VHA  N27  HN27  single    0.860  0.020  1.020
 VHA  N27  HN2A  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
 VHA  H1    C1   C7    118.47  3.000
 VHA  H1    C1   C2    119.80  3.000
 VHA  C7    C1   C2    121.73  3.000
 VHA  C24   C2   C3    125.13  3.000
 VHA  C24   C2   C1    114.43  3.000
 VHA  C3    C2   C1    120.32  3.000
 VHA  C5    C3   C4    120.71  3.000
 VHA  C5    C3   C2    117.09  3.000
 VHA  C4    C3   C2    122.16  3.000
 VHA  H4B   C4   H4A   107.77  3.000
 VHA  H4B   C4   H4    106.90  3.000
 VHA  H4A   C4   H4    108.04  3.000
 VHA  H4B   C4   C3    111.55  3.000
 VHA  H4A   C4   C3    110.66  3.000
 VHA  H4    C4   C3    111.73  3.000
 VHA  H5    C5   C6    118.43  3.000
 VHA  H5    C5   C3    118.67  3.000
 VHA  C6    C5   C3    122.90  3.000
 VHA  H6    C6   C7    121.26  3.000
 VHA  H6    C6   C5    119.63  3.000
 VHA  C7    C6   C5    119.11  3.000
 VHA  O8    C7   C6    125.41  3.000
 VHA  O8    C7   C1    115.77  3.000
 VHA  C6    C7   C1    118.82  3.000
 VHA  C9    O8   C7    119.62  3.000
 VHA  H9A   C9   H9    107.47  3.000
 VHA  H9A   C9   C10   110.25  3.000
 VHA  H9    C9   C10   110.52  3.000
 VHA  H9A   C9   O8    109.69  3.000
 VHA  H9    C9   O8    110.61  3.000
 VHA  C10   C9   O8    108.31  3.000
 VHA  H10A  C10  H10   105.91  3.000
 VHA  H10A  C10  C11   110.57  3.000
 VHA  H10   C10  C11   107.43  3.000
 VHA  H10A  C10  C9    109.23  3.000
 VHA  H10   C10  C9    107.09  3.000
 VHA  C11   C10  C9    116.07  3.000
 VHA  H11A  C11  H11   106.54  3.000
 VHA  H11A  C11  C12   107.88  3.000
 VHA  H11   C11  C12   108.87  3.000
 VHA  H11A  C11  C10   107.48  3.000
 VHA  H11   C11  C10   109.18  3.000
 VHA  C12   C11  C10   116.45  3.000
 VHA  H12A  C12  H12   108.07  3.000
 VHA  H12A  C12  O13   109.26  3.000
 VHA  H12   C12  O13   110.50  3.000
 VHA  H12A  C12  C11   111.53  3.000
 VHA  H12   C12  C11   111.11  3.000
 VHA  O13   C12  C11   106.38  3.000
 VHA  C14   O13  C12   119.99  3.000
 VHA  C16   C14  C15   119.60  3.000
 VHA  C16   C14  O13   116.24  3.000
 VHA  C15   C14  O13   124.15  3.000
 VHA  H15   C15  C19   119.88  3.000
 VHA  H15   C15  C14   120.74  3.000
 VHA  C19   C15  C14   119.38  3.000
 VHA  H16   C16  C17   120.47  3.000
 VHA  H16   C16  C14   119.32  3.000
 VHA  C17   C16  C14   120.21  3.000
 VHA  H17   C17  C18   119.74  3.000
 VHA  H17   C17  C16   119.54  3.000
 VHA  C18   C17  C16   120.70  3.000
 VHA  H18   C18  C19   120.49  3.000
 VHA  H18   C18  C17   120.44  3.000
 VHA  C19   C18  C17   119.07  3.000
 VHA  S20   C19  C18   116.71  3.000
 VHA  S20   C19  C15   122.26  3.000
 VHA  C18   C19  C15   120.90  3.000
 VHA  C21   S20  C19   105.26  3.000
 VHA  C23   C21  N22   122.58  3.000
 VHA  C23   C21  S20   124.01  3.000
 VHA  N22   C21  S20   113.31  3.000
 VHA  C26   N22  C21   116.55  3.000
 VHA  H23   C23  C24   120.74  3.000
 VHA  H23   C23  C21   123.33  3.000
 VHA  C24   C23  C21   115.76  3.000
 VHA  N25   C24  C23   122.69  3.000
 VHA  N25   C24  C2    120.61  3.000
 VHA  C23   C24  C2    116.48  3.000
 VHA  C26   N25  C24   116.10  3.000
 VHA  N27   C26  N25   117.26  3.000
 VHA  N27   C26  N22   117.09  3.000
 VHA  N25   C26  N22   125.60  3.000
 VHA  HN2A  N27  HN27  118.38  3.000
 VHA  HN2A  N27  C26   119.92  3.000
 VHA  HN27  N27  C26   120.06  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
 VHA  CONST_01  C5    C3   C2   C1      0.00   0.0  0
 VHA  CONST_04  C5    C6   C7   C1      0.00   0.0  0
 VHA  CONST_05  C6    C7   C1   C2      0.00   0.0  0
 VHA  CONST_06  C6    C5   C3   C2      0.00   0.0  0
 VHA  CONST_07  C21   C23  C24  C2    180.00   0.0  0
 VHA  CONST_08  C26   N25  C24  C2    180.00   0.0  0
 VHA  CONST_09  C7    C1   C2   C3      0.00   0.0  0
 VHA  CONST_12  C7    C6   C5   C3      0.00   0.0  0
 VHA  CONST_13  C24   C2   C3   C5    180.00   0.0  0
 VHA  CONST_14  C24   C2   C1   C7    180.00   0.0  0
 VHA  CONST_15  C18   C19  C15  C14     0.00   0.0  0
 VHA  CONST_16  C18   C17  C16  C14     0.00   0.0  0
 VHA  CONST_17  C17   C16  C14  C15     0.00   0.0  0
 VHA  CONST_18  C17   C18  C19  C15     0.00   0.0  0
 VHA  CONST_19  C19   C15  C14  C16     0.00   0.0  0
 VHA  CONST_20  C19   C18  C17  C16     0.00   0.0  0
 VHA  CONST_21  N25   C26  N22  C21     0.00   0.0  0
 VHA  CONST_22  N25   C24  C23  C21     0.00   0.0  0
 VHA  CONST_23  C24   C23  C21  N22     0.00   0.0  0
 VHA  CONST_24  C24   N25  C26  N22     0.00   0.0  0
 VHA  CONST_25  C26   N22  C21  C23     0.00   0.0  0
 VHA  CONST_26  C26   N25  C24  C23     0.00   0.0  0
 VHA  CONST_27  C4    C3   C2   C1    180.00   0.0  0
 VHA  CONST_28  C24   C2   C3   C4      0.00   0.0  0
 VHA  CONST_29  C6    C5   C3   C4    180.00   0.0  0
 VHA  CONST_30  N27   C26  N22  C21   180.00   0.0  0
 VHA  CONST_31  N27   C26  N25  C24   180.00   0.0  0
 VHA  CONST_32  H6    C6   C7   C1    180.00   0.0  0
 VHA  CONST_33  H5    C5   C3   C2    180.00   0.0  0
 VHA  CONST_34  H23   C23  C24  C2      0.00   0.0  0
 VHA  CONST_35  H1    C1   C2   C3    180.00   0.0  0
 VHA  CONST_36  H15   C15  C14  O13     0.00   0.0  0
 VHA  CONST_37  H16   C16  C14  O13     0.00   0.0  0
 VHA  CONST_38  H17   C17  C16  C14   180.00   0.0  0
 VHA  CONST_39  H18   C18  C19  C15   180.00   0.0  0
 VHA  CONST_40  HN27  N27  C26  N22     0.00   0.0  0
 VHA  CONST_41  HN2A  N27  C26  N22   180.00   0.0  0
 VHA  Var_01    C10   C9   O8   C7   -144.92  30.0  1
 VHA  Var_02    C11   C10  C9   O8     76.12  30.0  1
 VHA  Var_03    C12   C11  C10  C9    -64.90  30.0  1
 VHA  Var_04    O13   C12  C11  C10  -171.42  30.0  1
 VHA  Var_05    C15   C14  O13  C12   -31.27  30.0  1
 VHA  Var_06    N22   C21  S20  C19   176.34  30.0  1
 VHA  Var_07    H4    C4   C3   C2     64.95  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
 VHA  plan-1  C1    0.020
 VHA  plan-1  C2    0.020
 VHA  plan-1  C3    0.020
 VHA  plan-1  C4    0.020
 VHA  plan-1  C5    0.020
 VHA  plan-1  C6    0.020
 VHA  plan-1  C7    0.020
 VHA  plan-1  O8    0.020
 VHA  plan-1  C24   0.020
 VHA  plan-1  H1    0.020
 VHA  plan-1  H5    0.020
 VHA  plan-1  H6    0.020
 VHA  plan-2  O13   0.020
 VHA  plan-2  C14   0.020
 VHA  plan-2  C15   0.020
 VHA  plan-2  C16   0.020
 VHA  plan-2  C17   0.020
 VHA  plan-2  C18   0.020
 VHA  plan-2  C19   0.020
 VHA  plan-2  S20   0.020
 VHA  plan-2  H15   0.020
 VHA  plan-2  H16   0.020
 VHA  plan-2  H17   0.020
 VHA  plan-2  H18   0.020
 VHA  plan-3  C2    0.020
 VHA  plan-3  S20   0.020
 VHA  plan-3  C21   0.020
 VHA  plan-3  N22   0.020
 VHA  plan-3  C23   0.020
 VHA  plan-3  C24   0.020
 VHA  plan-3  N25   0.020
 VHA  plan-3  C26   0.020
 VHA  plan-3  N27   0.020
 VHA  plan-3  H23   0.020
 VHA  plan-4  C26   0.020
 VHA  plan-4  N27   0.020
 VHA  plan-4  HN27  0.020
 VHA  plan-4  HN2A  0.020

