# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:24:48 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: (8S,11S)-11-{(1R)-1-hydroxy-2-[(3-methylbutyl)amino]ethyl}-8-(1-methylethyl)-2-oxa-7,10-diazabicyclo[11.2.2]heptadeca-1(15),13,16-triene-6,9-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCNC[C@@H](O)[C@@H]1Cc2ccc(OCCCC(=O)N[C@@H](C(C)C)C(=O)N1)cc2
#
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
 PI3  PI3  (8S,11S)-11-{(1R)-1-hydroxy-2-[(3-methylbutyl)amino]ethyl}-8-(1-methylethyl)-2-oxa-7,10-diazabicyclo[11.2.2]heptadeca-1(15),13,16-triene-6,9-dione  ligand  70  31  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PI3
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
 PI3  C1    C  CH2   0  -0.444   1.6269   0.7649  -5.9386
 PI3  C2    C  C     0   0.572   1.9479   0.0693  -3.4787
 PI3  O3    O  O     0  -0.486   1.9775  -1.1199  -3.7501
 PI3  C4    C  CH2   0  -0.596   2.0564   1.1586  -4.5310
 PI3  N5    N  NH1   0  -0.635   1.8850   0.5466  -2.2208
 PI3  C6    C  CH1   0  -0.169   1.7284  -0.2521  -1.0276
 PI3  C7    C  C     0   0.575   0.5807   0.3857  -0.2468
 PI3  O8    O  O     0  -0.493   0.5957   1.5860  -0.0126
 PI3  C9    C  CH1   0  -0.223   3.0089  -0.3069  -0.1777
 PI3  C10   C  CH3   0  -0.683   2.7745  -1.0805   1.1165
 PI3  C11   C  CH3   0  -0.655   4.1555  -0.9261  -0.9670
 PI3  N12   N  NH1   0  -0.627  -0.4062  -0.4372   0.1384
 PI3  C13   C  CH1   0  -0.118  -1.7048   0.0396   0.5707
 PI3  C14   C  CH2   0  -0.512  -2.7889  -0.4162  -0.4289
 PI3  C15   C  C     0   0.105  -2.2931  -0.3447  -1.8466
 PI3  C16   C  C1    0  -0.276  -1.9836   0.8651  -2.4563
 PI3  C17   C  C1    0  -0.356  -1.3939   0.9235  -3.7136
 PI3  C18   C  C1    0  -0.306  -2.0148  -1.5095  -2.5588
 PI3  C19   C  C1    0  -0.319  -1.4380  -1.4721  -3.8148
 PI3  C20   C  C     0   0.381  -1.1058  -0.2528  -4.4021
 PI3  O21   O  O2    0  -0.489  -0.5568  -0.3270  -5.6328
 PI3  C22   C  CH2   0  -0.205   0.1329   0.7653  -6.2192
 PI3  C23   C  CH1   0   0.031  -2.0140  -0.4035   2.0093
 PI3  O24   O  OH1   0  -0.658  -3.3426  -0.0883   2.3529
 PI3  C25   C  CH2   0  -0.296  -1.0100   0.1877   2.9926
 PI3  N26   N  NH1   0  -0.611  -1.2694  -0.2320   4.3531
 PI3  C27   C  CH2   0  -0.292  -0.3043   0.3143   5.2911
 PI3  C28   C  CH2   0  -0.453  -0.5902  -0.1559   6.7094
 PI3  C29   C  CH1   0  -0.235   0.2823   0.4963   7.7831
 PI3  C30   C  CH3   0  -0.702  -0.1775   0.0576   9.1703
 PI3  C31   C  CH3   0  -0.722   1.7648   0.1837   7.5941
 PI3  H11   H  HCH2  0   0.240   2.0544  -0.2024  -6.2091
 PI3  H12A  H  HCH2  0   0.243   2.0579   1.4916  -6.6318
 PI3  H41   H  HCH2  0   0.282   3.1127   1.4456  -4.5601
 PI3  H42   H  HCH2  0   0.252   1.5204   2.0546  -4.2067
 PI3  HN5   H  HNH1  0   0.392   1.8524   1.5465  -2.0938
 PI3  H6    H  HCH1  0   0.261   1.4658  -1.2657  -1.3401
 PI3  H9    H  HCH1  0   0.226   3.2783   0.7231   0.0804
 PI3  H101  H  HCH3  0   0.235   3.7017  -1.1527   1.6857
 PI3  H102  H  HCH3  0   0.245   2.0371  -0.6038   1.7644
 PI3  H103  H  HCH3  0   0.222   2.4322  -2.0982   0.9146
 PI3  H111  H  HCH3  0   0.219   3.9214  -1.9519  -1.2592
 PI3  H112  H  HCH3  0   0.232   4.3850  -0.3633  -1.8714
 PI3  H113  H  HCH3  0   0.229   5.0614  -0.9536  -0.3596
 PI3  H12   H  HNH1  0   0.395  -0.3484  -1.3997  -0.1571
 PI3  H13   H  HCH1  0   0.255  -1.6527   1.1309   0.5501
 PI3  H141  H  HCH2  0   0.240  -3.0877  -1.4443  -0.2030
 PI3  H142  H  HCH2  0   0.256  -3.6738   0.2060  -0.2889
 PI3  H16   H  H     0   0.244  -2.1851   1.7974  -1.9412
 PI3  H17   H  H     0   0.263  -1.1601   1.8954  -4.1268
 PI3  H18   H  H     0   0.244  -2.2387  -2.4729  -2.1150
 PI3  H19   H  H     0   0.247  -1.2210  -2.3928  -4.3419
 PI3  H221  H  HCH2  0   0.250  -0.0195   0.6541  -7.2936
 PI3  H222  H  HCH2  0   0.222  -0.3094   1.7253  -5.9390
 PI3  H23   H  HCH1  0   0.216  -1.9503  -1.4985   2.0505
 PI3  H24   H  HOH1  0   0.441  -3.4070   0.8650   2.4776
 PI3  H251  H  HCH2  0   0.222  -1.0737   1.2824   2.9469
 PI3  H252  H  HCH2  0   0.217   0.0054  -0.0712   2.6589
 PI3  H26   H  HNH1  0   0.353  -1.2230  -1.2446   4.3967
 PI3  H271  H  HCH2  0   0.229  -0.3750   1.4070   5.2511
 PI3  H272  H  HCH2  0   0.213   0.7307   0.0651   5.0095
 PI3  H281  H  HCH2  0   0.236  -0.4681  -1.2450   6.7653
 PI3  H282  H  HCH2  0   0.227  -1.6427   0.0488   6.9299
 PI3  H29   H  HCH1  0   0.223   0.1491   1.5825   7.7094
 PI3  H301  H  HCH3  0   0.229   0.3936   0.5559   9.9554
 PI3  H302  H  HCH3  0   0.237  -1.2330   0.2841   9.3309
 PI3  H303  H  HCH3  0   0.234  -0.0469  -1.0199   9.2991
 PI3  H311  H  HCH3  0   0.237   1.9358  -0.8958   7.6149
 PI3  H312  H  HCH3  0   0.253   2.1518   0.5619   6.6472
 PI3  H313  H  HCH3  0   0.234   2.3634   0.6276   8.3919

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
 PI3  C1   C4    single    1.523  0.020  1.523
 PI3  C1   C22   single    1.520  0.020  1.520
 PI3  C1   H11   single    0.970  0.020  1.090
 PI3  C1   H12A  single    0.970  0.020  1.090
 PI3  C2   O3    double    1.220  0.020  1.220
 PI3  C2   C4    single    1.518  0.020  1.518
 PI3  C2   N5    single    1.347  0.020  1.347
 PI3  C4   H41   single    0.970  0.020  1.090
 PI3  C4   H42   single    0.970  0.020  1.090
 PI3  N5   C6    single    1.444  0.020  1.444
 PI3  N5   HN5   single    0.860  0.020  1.020
 PI3  C6   C7    single    1.528  0.020  1.528
 PI3  C6   C9    single    1.538  0.020  1.538
 PI3  C6   H6    single    0.970  0.020  1.090
 PI3  C7   O8    double    1.223  0.020  1.223
 PI3  C7   N12   single    1.341  0.020  1.341
 PI3  C9   C10   single    1.526  0.020  1.526
 PI3  C9   C11   single    1.524  0.020  1.524
 PI3  C9   H9    single    0.970  0.020  1.090
 PI3  C10  H101  single    0.970  0.020  1.090
 PI3  C10  H102  single    0.970  0.020  1.090
 PI3  C10  H103  single    0.970  0.020  1.090
 PI3  C11  H111  single    0.970  0.020  1.090
 PI3  C11  H112  single    0.970  0.020  1.090
 PI3  C11  H113  single    0.970  0.020  1.090
 PI3  N12  C13   single    1.449  0.020  1.449
 PI3  N12  H12   single    0.890  0.020  1.040
 PI3  C13  C14   single    1.543  0.020  1.543
 PI3  C13  C23   single    1.537  0.020  1.537
 PI3  C13  H13   single    0.970  0.020  1.090
 PI3  C14  C15   single    1.504  0.020  1.504
 PI3  C14  H141  single    0.970  0.020  1.090
 PI3  C14  H142  single    0.970  0.020  1.090
 PI3  C15  C16   aromatic  1.390  0.020  1.390
 PI3  C15  C18   aromatic  1.393  0.020  1.393
 PI3  C16  C17   aromatic  1.390  0.020  1.390
 PI3  C16  H16   single    0.930  0.020  1.080
 PI3  C17  C20   aromatic  1.393  0.020  1.393
 PI3  C17  H17   single    0.930  0.020  1.080
 PI3  C18  C19   aromatic  1.383  0.020  1.383
 PI3  C18  H18   single    0.930  0.020  1.080
 PI3  C19  C20   aromatic  1.394  0.020  1.394
 PI3  C19  H19   single    0.930  0.020  1.080
 PI3  C20  O21   single    1.350  0.020  1.350
 PI3  O21  C22   single    1.419  0.020  1.419
 PI3  C22  H221  single    0.970  0.020  1.090
 PI3  C22  H222  single    0.970  0.020  1.090
 PI3  C23  O24   single    1.408  0.020  1.408
 PI3  C23  C25   single    1.525  0.020  1.525
 PI3  C23  H23   single    0.970  0.020  1.090
 PI3  O24  H24   single    0.850  0.020  0.980
 PI3  C25  N26   single    1.447  0.020  1.447
 PI3  C25  H251  single    0.970  0.020  1.090
 PI3  C25  H252  single    0.970  0.020  1.090
 PI3  N26  C27   single    1.453  0.020  1.453
 PI3  N26  H26   single    0.890  0.020  1.040
 PI3  C27  C28   single    1.521  0.020  1.521
 PI3  C27  H271  single    0.970  0.020  1.090
 PI3  C27  H272  single    0.970  0.020  1.090
 PI3  C28  C29   single    1.530  0.020  1.530
 PI3  C28  H281  single    0.970  0.020  1.090
 PI3  C28  H282  single    0.970  0.020  1.090
 PI3  C29  C30   single    1.526  0.020  1.526
 PI3  C29  C31   single    1.527  0.020  1.527
 PI3  C29  H29   single    0.970  0.020  1.090
 PI3  C30  H301  single    0.970  0.020  1.090
 PI3  C30  H302  single    0.970  0.020  1.090
 PI3  C30  H303  single    0.970  0.020  1.090
 PI3  C31  H311  single    0.970  0.020  1.090
 PI3  C31  H312  single    0.970  0.020  1.090
 PI3  C31  H313  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
 PI3  H12A  C1   H11   106.11  3.000
 PI3  H12A  C1   C22   105.68  3.000
 PI3  H11   C1   C22   109.84  3.000
 PI3  H12A  C1   C4    107.64  3.000
 PI3  H11   C1   C4    110.34  3.000
 PI3  C22   C1   C4    116.59  3.000
 PI3  N5    C2   C4    113.35  3.000
 PI3  N5    C2   O3    123.65  3.000
 PI3  C4    C2   O3    122.91  3.000
 PI3  H42   C4   H41   105.43  3.000
 PI3  H42   C4   C2    110.33  3.000
 PI3  H41   C4   C2    105.98  3.000
 PI3  H42   C4   C1    110.34  3.000
 PI3  H41   C4   C1    108.37  3.000
 PI3  C2    C4   C1    115.77  3.000
 PI3  HN5   N5   C6    116.15  3.000
 PI3  HN5   N5   C2    118.06  3.000
 PI3  C6    N5   C2    125.50  3.000
 PI3  H6    C6   C9    108.97  3.000
 PI3  H6    C6   C7    110.67  3.000
 PI3  C9    C6   C7    110.98  3.000
 PI3  H6    C6   N5    107.62  3.000
 PI3  C9    C6   N5    112.71  3.000
 PI3  C7    C6   N5    105.83  3.000
 PI3  N12   C7   O8    123.79  3.000
 PI3  N12   C7   C6    116.32  3.000
 PI3  O8    C7   C6    119.90  3.000
 PI3  H9    C9   C11   108.61  3.000
 PI3  H9    C9   C10   108.34  3.000
 PI3  C11   C9   C10   110.42  3.000
 PI3  H9    C9   C6    107.55  3.000
 PI3  C11   C9   C6    110.78  3.000
 PI3  C10   C9   C6    111.04  3.000
 PI3  H103  C10  H102  107.75  3.000
 PI3  H103  C10  H101  107.53  3.000
 PI3  H102  C10  H101  107.08  3.000
 PI3  H103  C10  C9    111.32  3.000
 PI3  H102  C10  C9    112.70  3.000
 PI3  H101  C10  C9    110.23  3.000
 PI3  H113  C11  H112  107.46  3.000
 PI3  H113  C11  H111  107.66  3.000
 PI3  H112  C11  H111  107.95  3.000
 PI3  H113  C11  C9    110.29  3.000
 PI3  H112  C11  C9    112.25  3.000
 PI3  H111  C11  C9    111.05  3.000
 PI3  H12   N12  C13   116.92  3.000
 PI3  H12   N12  C7    117.34  3.000
 PI3  C13   N12  C7    122.89  3.000
 PI3  H13   C13  C23   108.37  3.000
 PI3  H13   C13  C14   108.43  3.000
 PI3  C23   C13  C14   112.32  3.000
 PI3  H13   C13  N12   106.27  3.000
 PI3  C23   C13  N12   111.39  3.000
 PI3  C14   C13  N12   109.82  3.000
 PI3  H142  C14  H141  106.74  3.000
 PI3  H142  C14  C15   111.19  3.000
 PI3  H141  C14  C15   109.23  3.000
 PI3  H142  C14  C13   108.56  3.000
 PI3  H141  C14  C13   109.61  3.000
 PI3  C15   C14  C13   111.41  3.000
 PI3  C18   C15  C16   117.33  3.000
 PI3  C18   C15  C14   120.54  3.000
 PI3  C16   C15  C14   121.90  3.000
 PI3  H16   C16  C17   118.20  3.000
 PI3  H16   C16  C15   119.92  3.000
 PI3  C17   C16  C15   121.86  3.000
 PI3  H17   C17  C20   121.68  3.000
 PI3  H17   C17  C16   118.36  3.000
 PI3  C20   C17  C16   119.96  3.000
 PI3  H18   C18  C19   118.82  3.000
 PI3  H18   C18  C15   119.50  3.000
 PI3  C19   C18  C15   121.67  3.000
 PI3  H19   C19  C20   119.41  3.000
 PI3  H19   C19  C18   120.18  3.000
 PI3  C20   C19  C18   120.39  3.000
 PI3  O21   C20  C19   115.67  3.000
 PI3  O21   C20  C17   125.54  3.000
 PI3  C19   C20  C17   118.76  3.000
 PI3  C22   O21  C20   122.16  3.000
 PI3  H222  C22  H221  106.58  3.000
 PI3  H222  C22  O21   111.92  3.000
 PI3  H221  C22  O21   105.11  3.000
 PI3  H222  C22  C1    110.51  3.000
 PI3  H221  C22  C1    108.61  3.000
 PI3  O21   C22  C1    113.66  3.000
 PI3  H23   C23  C25   108.93  3.000
 PI3  H23   C23  O24   105.60  3.000
 PI3  C25   C23  O24   112.16  3.000
 PI3  H23   C23  C13   108.13  3.000
 PI3  C25   C23  C13   111.07  3.000
 PI3  O24   C23  C13   110.72  3.000
 PI3  H24   O24  C23   108.43  3.000
 PI3  H252  C25  H251  106.01  3.000
 PI3  H252  C25  N26   112.49  3.000
 PI3  H251  C25  N26   108.54  3.000
 PI3  H252  C25  C23   108.72  3.000
 PI3  H251  C25  C23   108.77  3.000
 PI3  N26   C25  C23   112.07  3.000
 PI3  H26   N26  C27   108.49  3.000
 PI3  H26   N26  C25   108.76  3.000
 PI3  C27   N26  C25   112.26  3.000
 PI3  H272  C27  H271  106.08  3.000
 PI3  H272  C27  C28   110.19  3.000
 PI3  H271  C27  C28   109.27  3.000
 PI3  H272  C27  N26   111.98  3.000
 PI3  H271  C27  N26   107.97  3.000
 PI3  C28   C27  N26   111.16  3.000
 PI3  H282  C28  H281  106.40  3.000
 PI3  H282  C28  C29   109.11  3.000
 PI3  H281  C28  C29   108.90  3.000
 PI3  H282  C28  C27   108.10  3.000
 PI3  H281  C28  C27   109.47  3.000
 PI3  C29   C28  C27   114.55  3.000
 PI3  H29   C29  C31   108.20  3.000
 PI3  H29   C29  C30   108.02  3.000
 PI3  C31   C29  C30   110.26  3.000
 PI3  H29   C29  C28   107.80  3.000
 PI3  C31   C29  C28   112.32  3.000
 PI3  C30   C29  C28   110.10  3.000
 PI3  H303  C30  H302  107.63  3.000
 PI3  H303  C30  H301  107.63  3.000
 PI3  H302  C30  H301  107.78  3.000
 PI3  H303  C30  C29   110.77  3.000
 PI3  H302  C30  C29   111.44  3.000
 PI3  H301  C30  C29   111.41  3.000
 PI3  H313  C31  H312  107.39  3.000
 PI3  H313  C31  H311  107.57  3.000
 PI3  H312  C31  H311  107.67  3.000
 PI3  H313  C31  C29   111.02  3.000
 PI3  H312  C31  C29   112.40  3.000
 PI3  H311  C31  C29   110.59  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
 PI3  CONST_01  C20   C17  C16  C15     0.00   0.0  0
 PI3  CONST_02  C20   C19  C18  C15     0.00   0.0  0
 PI3  CONST_03  C19   C18  C15  C16     0.00   0.0  0
 PI3  CONST_04  C19   C20  C17  C16     0.00   0.0  0
 PI3  CONST_05  C18   C15  C16  C17     0.00   0.0  0
 PI3  CONST_06  C18   C19  C20  C17     0.00   0.0  0
 PI3  CONST_07  C6    N5   C2   C4    180.00   0.0  0
 PI3  CONST_09  C6    N5   C2   O3      0.00   0.0  0
 PI3  CONST_11  H16   C16  C15  C14     0.00   0.0  0
 PI3  CONST_12  H18   C18  C15  C14     0.00   0.0  0
 PI3  CONST_13  H17   C17  C16  C15   180.00   0.0  0
 PI3  CONST_14  H19   C19  C18  C15   180.00   0.0  0
 PI3  CONST_15  HN5   N5   C2   C4      0.00   0.0  0
 PI3  CONST_16  H12   N12  C7   C6      0.00   0.0  0
 PI3  Var_01    N5    C2   C4   C1   -158.45  30.0  1
 PI3  Var_02    C22   C1   C4   C2     80.23  30.0  1
 PI3  Var_03    O21   C22  C1   C4    -74.02  30.0  1
 PI3  Var_04    C16   C15  C14  C13   -65.94  30.0  1
 PI3  Var_05    H101  C10  C9   C6    177.27  30.0  3
 PI3  Var_06    H111  C11  C9   C6    -61.20  30.0  3
 PI3  Var_07    C27   N26  C25  C23   179.21  30.0  3
 PI3  Var_08    C28   C27  N26  C25  -179.31  30.0  3
 PI3  Var_09    C29   C28  C27  N26  -173.46  30.0  3
 PI3  Var_10    C30   C29  C28  C27   174.51  30.0  3
 PI3  Var_11    H301  C30  C29  C28  -176.69  30.0  3
 PI3  Var_12    H311  C31  C29  C28   -58.54  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
 PI3  chir_01  C6   N5   C7   C9   positiv
 PI3  chir_02  C13  N12  C14  C23  negativ
 PI3  chir_03  C23  O24  C13  C25  negativ

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
 PI3  plan-1  C14  0.020
 PI3  plan-1  C15  0.020
 PI3  plan-1  C16  0.020
 PI3  plan-1  C17  0.020
 PI3  plan-1  C18  0.020
 PI3  plan-1  C19  0.020
 PI3  plan-1  C20  0.020
 PI3  plan-1  O21  0.020
 PI3  plan-1  H16  0.020
 PI3  plan-1  H17  0.020
 PI3  plan-1  H18  0.020
 PI3  plan-1  H19  0.020
 PI3  plan-2  C2   0.020
 PI3  plan-2  O3   0.020
 PI3  plan-2  C4   0.020
 PI3  plan-2  N5   0.020
 PI3  plan-2  C6   0.020
 PI3  plan-2  HN5  0.020
 PI3  plan-3  C6   0.020
 PI3  plan-3  C7   0.020
 PI3  plan-3  O8   0.020
 PI3  plan-3  N12  0.020
 PI3  plan-3  C13  0.020
 PI3  plan-3  H12  0.020

