# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:14:47 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: 2-[(8S,11S)-11-{(1R)-1-hydroxy-2-[(3-methylbutyl)amino]ethyl}-6,9-dioxo-2-oxa-7,10-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-8-yl]acetamide
#   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](CC(N)=O)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
 PI2  PI2  2-[(8S,11S)-11-{(1R)-1-hydroxy-2-[(3-methylbutyl)amino]ethyl}-6,9-dioxo-2-oxa-7,10-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-8-yl]acetamide  ligand  68  32  .  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_PI2
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
 PI2  C1    C  CH2   0  -0.448   1.3162   0.7620  -5.8746
 PI2  C2    C  C     0   0.574   1.6514  -0.0432  -3.4506
 PI2  O3    O  O     0  -0.479   1.4969  -1.2137  -3.7510
 PI2  C4    C  CH2   0  -0.596   1.8508   1.0538  -4.4791
 PI2  N5    N  NH1   0  -0.632   1.7348   0.3987  -2.1769
 PI2  C6    C  CH1   0  -0.216   1.5059  -0.4051  -1.0025
 PI2  C7    C  C     0   0.593   0.3750   0.2542  -0.2148
 PI2  O8    O  O     0  -0.490   0.4072   1.4555   0.0066
 PI2  C9    C  CH2   0  -0.559   2.7541  -0.4865  -0.1203
 PI2  C10   C  C     0   0.519   3.9005  -1.1261  -0.8759
 PI2  O11   O  O     0  -0.490   3.8135  -2.2600  -1.3237
 PI2  N12   N  NH2   0  -0.796   4.9936  -0.3636  -1.0065
 PI2  N13   N  NH1   0  -0.631  -0.6048  -0.5606   0.1993
 PI2  C14   C  CH1   0  -0.123  -1.8842  -0.0690   0.6717
 PI2  C15   C  CH2   0  -0.507  -2.9956  -0.4910  -0.3082
 PI2  C16   C  C     0   0.104  -2.5512  -0.3383  -1.7376
 PI2  C17   C  C1    0  -0.277  -2.1797   0.8939  -2.2628
 PI2  C18   C  C1    0  -0.360  -1.6361   1.0156  -3.5362
 PI2  C19   C  C1    0  -0.309  -2.3914  -1.4554  -2.5548
 PI2  C20   C  C1    0  -0.322  -1.8643  -1.3532  -3.8292
 PI2  C21   C  C     0   0.382  -1.4638  -0.1161  -4.3292
 PI2  O22   O  O2    0  -0.491  -0.9682  -0.1233  -5.5853
 PI2  C23   C  CH2   0  -0.204  -0.1790   0.9418  -6.0912
 PI2  C24   C  CH1   0   0.030  -2.1567  -0.5232   2.1142
 PI2  O25   O  OH1   0  -0.657  -3.4760  -0.2138   2.4959
 PI2  C26   C  CH2   0  -0.279  -1.1266   0.0683   3.0714
 PI2  N27   N  NH1   0  -0.597  -1.3631  -0.3376   4.4407
 PI2  C28   C  CH2   0  -0.256  -0.4098   0.2491   5.3660
 PI2  C29   C  CH2   0  -0.423  -0.6867  -0.1990   6.7933
 PI2  C30   C  CH1   0  -0.236   0.1690   0.4927   7.8559
 PI2  C31   C  CH3   0  -0.650  -0.2879   0.0743   9.2502
 PI2  C32   C  CH3   0  -0.657   1.6580   0.2059   7.6797
 PI2  H11   H  HCH2  0   0.241   1.6198  -0.2343  -6.2022
 PI2  H12   H  HCH2  0   0.246   1.7968   1.4632  -6.5614
 PI2  H41   H  HCH2  0   0.285   2.9327   1.2086  -4.5501
 PI2  H42   H  HCH2  0   0.254   1.4455   1.9992  -4.1084
 PI2  HN5   H  HNH1  0   0.395   1.8247   1.3918  -2.0242
 PI2  H6    H  HCH1  0   0.282   1.2241  -1.4055  -1.3297
 PI2  H91   H  HCH2  0   0.266   3.0146   0.5092   0.2419
 PI2  H92   H  HCH2  0   0.283   2.5344  -1.1029   0.7554
 PI2  H121  H  HNH2  0   0.401   5.7940  -0.6989  -1.5180
 PI2  H122  H  HNH2  0   0.408   5.0247   0.5816  -0.6671
 PI2  H13   H  HNH1  0   0.399  -0.5626  -1.5256  -0.0916
 PI2  H14   H  HCH1  0   0.255  -1.8132   1.0212   0.6639
 PI2  H151  H  HCH2  0   0.243  -3.2690  -1.5348  -0.1267
 PI2  H152  H  HCH2  0   0.258  -3.8857   0.1047  -0.1004
 PI2  H17   H  H     0   0.247  -2.2842   1.7907  -1.6625
 PI2  H18   H  H     0   0.266  -1.3491   1.9999  -3.8811
 PI2  H19   H  H     0   0.246  -2.6663  -2.4348  -2.1798
 PI2  H20   H  H     0   0.250  -1.7346  -2.2392  -4.4380
 PI2  H231  H  HCH2  0   0.250  -0.3726   0.9507  -7.1646
 PI2  H232  H  HCH2  0   0.225  -0.5067   1.9118  -5.7079
 PI2  H24   H  HCH1  0   0.225  -2.0885  -1.6181   2.1480
 PI2  H25   H  HOH1  0   0.444  -3.5363   0.7364   2.6440
 PI2  H261  H  HCH2  0   0.217  -1.1871   1.1629   3.0194
 PI2  H262  H  HCH2  0   0.205  -0.1195  -0.1975   2.7185
 PI2  H27   H  HNH1  0   0.335  -1.2896  -1.3478   4.4995
 PI2  H281  H  HCH2  0   0.211  -0.5068   1.3389   5.3053
 PI2  H282  H  HCH2  0   0.190   0.6310   0.0195   5.0898
 PI2  H291  H  HCH2  0   0.207  -0.5423  -1.2841   6.8710
 PI2  H292  H  HCH2  0   0.218  -1.7437  -0.0122   7.0078
 PI2  H30   H  HCH1  0   0.211   0.0146   1.5744   7.7590
 PI2  H311  H  HCH3  0   0.224   0.2728   0.5963  10.0272
 PI2  H312  H  HCH3  0   0.223  -1.3473   0.2874   9.4038
 PI2  H313  H  HCH3  0   0.212  -0.1408  -0.9982   9.4000
 PI2  H321  H  HCH3  0   0.211   1.8520  -0.8685   7.7354
 PI2  H322  H  HCH3  0   0.228   2.0395   0.5615   6.7219
 PI2  H323  H  HCH3  0   0.225   2.2451   0.6875   8.4638

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
 PI2  C1   C4    single    1.523  0.020  1.523
 PI2  C1   C23   single    1.521  0.020  1.521
 PI2  C1   H11   single    0.970  0.020  1.090
 PI2  C1   H12   single    0.970  0.020  1.090
 PI2  C2   O3    double    1.218  0.020  1.218
 PI2  C2   C4    single    1.517  0.020  1.517
 PI2  C2   N5    single    1.351  0.020  1.351
 PI2  C4   H41   single    0.970  0.020  1.090
 PI2  C4   H42   single    0.970  0.020  1.090
 PI2  N5   C6    single    1.441  0.020  1.441
 PI2  N5   HN5   single    0.860  0.020  1.020
 PI2  C6   C7    single    1.528  0.020  1.528
 PI2  C6   C9    single    1.531  0.020  1.531
 PI2  C6   H6    single    0.970  0.020  1.090
 PI2  C7   O8    double    1.222  0.020  1.222
 PI2  C7   N13   single    1.340  0.020  1.340
 PI2  C9   C10   single    1.515  0.020  1.515
 PI2  C9   H91   single    0.970  0.020  1.090
 PI2  C9   H92   single    0.970  0.020  1.090
 PI2  C10  O11   double    1.222  0.020  1.222
 PI2  C10  N12   single    1.339  0.020  1.339
 PI2  N12  H121  single    0.860  0.020  1.020
 PI2  N12  H122  single    0.860  0.020  1.020
 PI2  N13  C14   single    1.450  0.020  1.450
 PI2  N13  H13   single    0.860  0.020  1.020
 PI2  C14  C15   single    1.541  0.020  1.541
 PI2  C14  C24   single    1.537  0.020  1.537
 PI2  C14  H14   single    0.970  0.020  1.090
 PI2  C15  C16   single    1.505  0.020  1.505
 PI2  C15  H151  single    0.970  0.020  1.090
 PI2  C15  H152  single    0.970  0.020  1.090
 PI2  C16  C17   aromatic  1.390  0.020  1.390
 PI2  C16  C19   aromatic  1.393  0.020  1.393
 PI2  C17  C18   aromatic  1.390  0.020  1.390
 PI2  C17  H17   single    0.930  0.020  1.080
 PI2  C18  C21   aromatic  1.393  0.020  1.393
 PI2  C18  H18   single    0.930  0.020  1.080
 PI2  C19  C20   aromatic  1.383  0.020  1.383
 PI2  C19  H19   single    0.930  0.020  1.080
 PI2  C20  C21   aromatic  1.393  0.020  1.393
 PI2  C20  H20   single    0.930  0.020  1.080
 PI2  C21  O22   single    1.350  0.020  1.350
 PI2  O22  C23   single    1.419  0.020  1.419
 PI2  C23  H231  single    0.970  0.020  1.090
 PI2  C23  H232  single    0.970  0.020  1.090
 PI2  C24  O25   single    1.408  0.020  1.408
 PI2  C24  C26   single    1.526  0.020  1.526
 PI2  C24  H24   single    0.970  0.020  1.090
 PI2  O25  H25   single    0.850  0.020  0.980
 PI2  C26  N27   single    1.448  0.020  1.448
 PI2  C26  H261  single    0.970  0.020  1.090
 PI2  C26  H262  single    0.970  0.020  1.090
 PI2  N27  C28   single    1.452  0.020  1.452
 PI2  N27  H27   single    0.890  0.020  1.040
 PI2  C28  C29   single    1.521  0.020  1.521
 PI2  C28  H281  single    0.970  0.020  1.090
 PI2  C28  H282  single    0.970  0.020  1.090
 PI2  C29  C30   single    1.530  0.020  1.530
 PI2  C29  H291  single    0.970  0.020  1.090
 PI2  C29  H292  single    0.970  0.020  1.090
 PI2  C30  C31   single    1.526  0.020  1.526
 PI2  C30  C32   single    1.527  0.020  1.527
 PI2  C30  H30   single    0.970  0.020  1.090
 PI2  C31  H311  single    0.970  0.020  1.090
 PI2  C31  H312  single    0.970  0.020  1.090
 PI2  C31  H313  single    0.970  0.020  1.090
 PI2  C32  H321  single    0.970  0.020  1.090
 PI2  C32  H322  single    0.970  0.020  1.090
 PI2  C32  H323  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
 PI2  H12   C1   H11   105.94  3.000
 PI2  H12   C1   C23   105.48  3.000
 PI2  H11   C1   C23   109.78  3.000
 PI2  H12   C1   C4    107.37  3.000
 PI2  H11   C1   C4    110.62  3.000
 PI2  C23   C1   C4    116.93  3.000
 PI2  N5    C2   C4    113.24  3.000
 PI2  N5    C2   O3    123.69  3.000
 PI2  C4    C2   O3    122.98  3.000
 PI2  H42   C4   H41   105.43  3.000
 PI2  H42   C4   C2    110.29  3.000
 PI2  H41   C4   C2    106.02  3.000
 PI2  H42   C4   C1    110.26  3.000
 PI2  H41   C4   C1    108.33  3.000
 PI2  C2    C4   C1    115.89  3.000
 PI2  HN5   N5   C6    116.09  3.000
 PI2  HN5   N5   C2    118.06  3.000
 PI2  C6    N5   C2    125.17  3.000
 PI2  H6    C6   C9    109.58  3.000
 PI2  H6    C6   C7    111.07  3.000
 PI2  C9    C6   C7    109.23  3.000
 PI2  H6    C6   N5    107.96  3.000
 PI2  C9    C6   N5    111.70  3.000
 PI2  C7    C6   N5    107.28  3.000
 PI2  N13   C7   O8    124.13  3.000
 PI2  N13   C7   C6    115.99  3.000
 PI2  O8    C7   C6    119.88  3.000
 PI2  H92   C9   H91   107.25  3.000
 PI2  H92   C9   C10   108.27  3.000
 PI2  H91   C9   C10   111.73  3.000
 PI2  H92   C9   C6    109.14  3.000
 PI2  H91   C9   C6    109.73  3.000
 PI2  C10   C9   C6    110.62  3.000
 PI2  N12   C10  O11   123.41  3.000
 PI2  N12   C10  C9    115.22  3.000
 PI2  O11   C10  C9    121.38  3.000
 PI2  H122  N12  H121  117.38  3.000
 PI2  H122  N12  C10   121.87  3.000
 PI2  H121  N12  C10   120.57  3.000
 PI2  H13   N13  C14   117.09  3.000
 PI2  H13   N13  C7    117.51  3.000
 PI2  C14   N13  C7    122.67  3.000
 PI2  H14   C14  C24   108.25  3.000
 PI2  H14   C14  C15   108.40  3.000
 PI2  C24   C14  C15   112.84  3.000
 PI2  H14   C14  N13   106.18  3.000
 PI2  C24   C14  N13   111.24  3.000
 PI2  C15   C14  N13   109.66  3.000
 PI2  H152  C15  H151  106.59  3.000
 PI2  H152  C15  C16   111.49  3.000
 PI2  H151  C15  C16   109.16  3.000
 PI2  H152  C15  C14   108.53  3.000
 PI2  H151  C15  C14   109.63  3.000
 PI2  C16   C15  C14   111.31  3.000
 PI2  C19   C16  C17   117.30  3.000
 PI2  C19   C16  C15   120.64  3.000
 PI2  C17   C16  C15   121.86  3.000
 PI2  H17   C17  C18   118.20  3.000
 PI2  H17   C17  C16   119.89  3.000
 PI2  C18   C17  C16   121.89  3.000
 PI2  H18   C18  C21   121.67  3.000
 PI2  H18   C18  C17   118.39  3.000
 PI2  C21   C18  C17   119.93  3.000
 PI2  H19   C19  C20   118.82  3.000
 PI2  H19   C19  C16   119.50  3.000
 PI2  C20   C19  C16   121.66  3.000
 PI2  H20   C20  C21   119.36  3.000
 PI2  H20   C20  C19   120.22  3.000
 PI2  C21   C20  C19   120.40  3.000
 PI2  O22   C21  C20   115.77  3.000
 PI2  O22   C21  C18   125.41  3.000
 PI2  C20   C21  C18   118.79  3.000
 PI2  C23   O22  C21   122.13  3.000
 PI2  H232  C23  H231  106.53  3.000
 PI2  H232  C23  O22   111.98  3.000
 PI2  H231  C23  O22   104.96  3.000
 PI2  H232  C23  C1    110.46  3.000
 PI2  H231  C23  C1    108.39  3.000
 PI2  O22   C23  C1    114.03  3.000
 PI2  H24   C24  C26   108.99  3.000
 PI2  H24   C24  O25   105.61  3.000
 PI2  C26   C24  O25   112.17  3.000
 PI2  H24   C24  C14   108.23  3.000
 PI2  C26   C24  C14   110.77  3.000
 PI2  O25   C24  C14   110.84  3.000
 PI2  H25   O25  C24   108.48  3.000
 PI2  H262  C26  H261  106.04  3.000
 PI2  H262  C26  N27   112.67  3.000
 PI2  H261  C26  N27   108.39  3.000
 PI2  H262  C26  C24   108.86  3.000
 PI2  H261  C26  C24   108.64  3.000
 PI2  N27   C26  C24   111.99  3.000
 PI2  H27   N27  C28   108.53  3.000
 PI2  H27   N27  C26   108.79  3.000
 PI2  C28   N27  C26   112.47  3.000
 PI2  H282  C28  H281  106.09  3.000
 PI2  H282  C28  C29   110.24  3.000
 PI2  H281  C28  C29   109.20  3.000
 PI2  H282  C28  N27   112.11  3.000
 PI2  H281  C28  N27   107.96  3.000
 PI2  C29   C28  N27   111.06  3.000
 PI2  H292  C29  H291  106.38  3.000
 PI2  H292  C29  C30   109.08  3.000
 PI2  H291  C29  C30   108.93  3.000
 PI2  H292  C29  C28   108.02  3.000
 PI2  H291  C29  C28   109.50  3.000
 PI2  C30   C29  C28   114.63  3.000
 PI2  H30   C30  C32   108.20  3.000
 PI2  H30   C30  C31   108.00  3.000
 PI2  C32   C30  C31   110.25  3.000
 PI2  H30   C30  C29   107.81  3.000
 PI2  C32   C30  C29   112.36  3.000
 PI2  C31   C30  C29   110.08  3.000
 PI2  H313  C31  H312  107.63  3.000
 PI2  H313  C31  H311  107.62  3.000
 PI2  H312  C31  H311  107.77  3.000
 PI2  H313  C31  C30   110.74  3.000
 PI2  H312  C31  C30   111.45  3.000
 PI2  H311  C31  C30   111.45  3.000
 PI2  H323  C32  H322  107.39  3.000
 PI2  H323  C32  H321  107.55  3.000
 PI2  H322  C32  H321  107.65  3.000
 PI2  H323  C32  C30   111.02  3.000
 PI2  H322  C32  C30   112.42  3.000
 PI2  H321  C32  C30   110.60  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
 PI2  CONST_01  C21   C18  C17  C16     0.00   0.0  0
 PI2  CONST_02  C21   C20  C19  C16     0.00   0.0  0
 PI2  CONST_03  C20   C19  C16  C17     0.00   0.0  0
 PI2  CONST_04  C20   C21  C18  C17     0.00   0.0  0
 PI2  CONST_05  C19   C16  C17  C18     0.00   0.0  0
 PI2  CONST_06  C19   C20  C21  C18     0.00   0.0  0
 PI2  CONST_07  C6    N5   C2   C4    180.00   0.0  0
 PI2  CONST_08  C14   N13  C7   C6    180.00   0.0  0
 PI2  CONST_09  C6    N5   C2   O3      0.00   0.0  0
 PI2  CONST_11  H17   C17  C16  C15     0.00   0.0  0
 PI2  CONST_12  H19   C19  C16  C15     0.00   0.0  0
 PI2  CONST_13  H18   C18  C17  C16   180.00   0.0  0
 PI2  CONST_14  H20   C20  C19  C16   180.00   0.0  0
 PI2  CONST_15  HN5   N5   C2   C4      0.00   0.0  0
 PI2  CONST_16  H13   N13  C7   C6      0.00   0.0  0
 PI2  CONST_17  H121  N12  C10  C9    180.00   0.0  0
 PI2  CONST_18  H122  N12  C10  C9      0.00   0.0  0
 PI2  Var_01    N5    C2   C4   C1   -159.90  30.0  1
 PI2  Var_02    C23   C1   C4   C2     79.59  30.0  1
 PI2  Var_03    O22   C23  C1   C4    -77.81  30.0  1
 PI2  Var_04    C17   C16  C15  C14   -60.71  30.0  1
 PI2  Var_05    O11   C10  C9   C6    -59.69  30.0  3
 PI2  Var_06    C28   N27  C26  C24  -178.43  30.0  3
 PI2  Var_07    C29   C28  N27  C26  -179.95  30.0  3
 PI2  Var_08    C30   C29  C28  N27  -173.42  30.0  3
 PI2  Var_09    C31   C30  C29  C28   174.28  30.0  3
 PI2  Var_10    H311  C31  C30  C29  -176.94  30.0  3
 PI2  Var_11    H321  C32  C30  C29   -59.17  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
 PI2  chir_01  C6   N5   C7   C9   positiv
 PI2  chir_02  C14  N13  C15  C24  negativ
 PI2  chir_03  C24  O25  C14  C26  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
 PI2  plan-1  C15   0.020
 PI2  plan-1  C16   0.020
 PI2  plan-1  C17   0.020
 PI2  plan-1  C18   0.020
 PI2  plan-1  C19   0.020
 PI2  plan-1  C20   0.020
 PI2  plan-1  C21   0.020
 PI2  plan-1  O22   0.020
 PI2  plan-1  H17   0.020
 PI2  plan-1  H18   0.020
 PI2  plan-1  H19   0.020
 PI2  plan-1  H20   0.020
 PI2  plan-2  C2    0.020
 PI2  plan-2  O3    0.020
 PI2  plan-2  C4    0.020
 PI2  plan-2  N5    0.020
 PI2  plan-2  C6    0.020
 PI2  plan-2  HN5   0.020
 PI2  plan-3  C6    0.020
 PI2  plan-3  C7    0.020
 PI2  plan-3  O8    0.020
 PI2  plan-3  N13   0.020
 PI2  plan-3  C14   0.020
 PI2  plan-3  H13   0.020
 PI2  plan-4  C9    0.020
 PI2  plan-4  C10   0.020
 PI2  plan-4  O11   0.020
 PI2  plan-4  N12   0.020
 PI2  plan-4  H121  0.020
 PI2  plan-4  H122  0.020

