# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:16:10 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: N-acetyl-D-phenylalanyl-N-[(1R,6Z)-6-amino-1-(dihydroxyboranyl)-6-iminohexyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCCC(N)=N)B(O)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
 DI3  DI3  N-acetyl-D-phenylalanyl-N-[(1R,6Z)-6-amino-1-(dihydroxyboranyl)-6-iminohexyl]-L-prolinamide  ligand  67  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DI3
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
 DI3  B1    B  B     0   0.507  -1.1201   1.5862   -3.0696
 DI3  C     C  CH1   0  -0.234  -0.2578   0.2443   -2.9496
 DI3  C2    C  CH2   0  -0.483  -0.2422  -0.5320   -4.2681
 DI3  C3    C  CH2   0  -0.442   0.4786   0.2164   -5.3820
 DI3  C4    C  CH2   0  -0.405   0.5978  -0.6081   -6.6581
 DI3  C5    C  CH2   0  -0.514   1.3593   0.1379   -7.7401
 DI3  C6    C  C     0   0.396   1.4795  -0.5845   -9.0580
 DI3  C7    C  CH1   0  -0.163  -1.7923  -1.0118    0.2759
 DI3  C9    C  CH2   0  -0.484  -3.3305  -1.0231    0.2659
 DI3  C10   C  CH2   0  -0.466  -3.7059  -1.1165    1.7408
 DI3  C11   C  CH2   0  -0.290  -2.6377  -0.2729    2.4166
 DI3  C13   C  CH2   0  -0.553   0.0732  -1.0223    4.3652
 DI3  C14   C  CH1   0  -0.187   0.1171   0.1438    3.3582
 DI3  C16   C  CH3   0  -0.783   3.6397   1.5519    3.3411
 DI3  C17   C  CR16  0  -0.241   1.5816  -0.1405    7.7424
 DI3  C18   C  CR16  0  -0.271   0.4911   0.4104    8.4015
 DI3  C19   C  CR16  0  -0.240  -0.7357   0.4828    7.7532
 DI3  C20   C  CR16  0  -0.309  -0.8642   0.0098    6.4550
 DI3  C21   C  CR6   0   0.151   0.2249  -0.5405    5.7810
 DI3  C22   C  CR16  0  -0.315   1.4478  -0.6119    6.4425
 DI3  N     N  NH1   0  -0.648  -0.8000  -0.5929   -1.8942
 DI3  N1    N  N     0  -0.672   0.7888  -1.6341   -9.2852
 DI3  N2    N  NH2   0  -0.817   2.3868  -0.0268   -9.9135
 DI3  N3    N  NT    0  -0.480  -1.4531  -0.5675    1.6179
 DI3  N4    N  NH1   0  -0.627   1.3323   0.9152    3.4094
 DI3  O     O  OH1   0  -0.629  -2.4483   1.4536   -3.3442
 DI3  O1    O  OH1   0  -0.621  -0.5514   2.8283   -3.1288
 DI3  O4    O  O     0  -0.492   2.8988  -0.7273    3.2840
 DI3  H     H  HCH1  0   0.233   0.7862   0.4862   -2.6999
 DI3  H21   H  HCH2  0   0.228   0.2621  -1.4930   -4.1108
 DI3  H22A  H  HCH2  0   0.232  -1.2641  -0.7695   -4.5777
 DI3  H31   H  HCH2  0   0.229  -0.0419   1.1528   -5.6113
 DI3  H32   H  HCH2  0   0.216   1.4780   0.5021   -5.0359
 DI3  H41   H  HCH2  0   0.217   1.1033  -1.5522   -6.4363
 DI3  H42   H  HCH2  0   0.220  -0.3973  -0.8733   -7.0213
 DI3  H51   H  HCH2  0   0.254   0.8762   1.1027   -7.9353
 DI3  H52   H  HCH2  0   0.248   2.3638   0.3865   -7.3826
 DI3  H7    H  HCH1  0   0.280  -1.3985  -2.0180    0.1017
 DI3  H91   H  HCH2  0   0.268  -3.7199  -1.8463   -0.3303
 DI3  H92   H  HCH2  0   0.253  -3.7150  -0.0924   -0.1556
 DI3  H101  H  HCH2  0   0.247  -3.6395  -2.1486    2.0898
 DI3  H102  H  HCH2  0   0.259  -4.7116  -0.7536    1.9468
 DI3  H111  H  HCH2  0   0.257  -2.5051  -0.5425    3.4629
 DI3  H112  H  HCH2  0   0.252  -2.8827   0.7922    2.3690
 DI3  H131  H  HCH2  0   0.266  -0.8849  -1.5361    4.2585
 DI3  H132  H  HCH2  0   0.282   0.8446  -1.7495    4.1230
 DI3  H14   H  HCH1  0   0.293  -0.6715   0.8483    3.6344
 DI3  H161  H  HCH3  0   0.260   4.6376   1.1240    3.3863
 DI3  H162  H  HCH3  0   0.266   3.5614   2.1567    2.4364
 DI3  H163  H  HCH3  0   0.261   3.5045   2.2203    4.1922
 DI3  H17   H  HCR6  0   0.253   2.5407  -0.2046    8.2406
 DI3  H18   H  HCR6  0   0.254   0.5956   0.7773    9.4144
 DI3  H19   H  HCR6  0   0.254  -1.5947   0.9036    8.2600
 DI3  H20   H  HCR6  0   0.248  -1.8286   0.0647    5.9611
 DI3  H22   H  HCR6  0   0.246   2.3029  -1.0426    5.9372
 DI3  HN    H  HNH1  0   0.393  -0.6404  -1.5880   -1.9293
 DI3  HN1   H  H     0   0.311   0.9653  -1.9897  -10.2220
 DI3  HN21  H  HNH2  0   0.383   2.3460  -0.2815  -10.8873
 DI3  HN22  H  HNH2  0   0.389   2.6825   0.9211   -9.7488
 DI3  HN4   H  HNH1  0   0.406   1.2125   1.9146    3.4245
 DI3  HO    H  HOH1  0   0.481  -2.9016   2.2934   -3.4697
 DI3  HO1   H  HOH1  0   0.474   0.3912   2.8161   -2.9417
 DI3  C8    C  C     0   0.593  -1.2577  -0.0471   -0.7695
 DI3  C12   C  C     0   0.571  -0.1662  -0.3461    1.9353
 DI3  O2    O  O     0  -0.504  -1.3232   1.1685   -0.6123
 DI3  C15   C  C     0   0.519   2.5990   0.4549    3.3357
 DI3  O3    O  O     0  -0.478   0.7297  -0.5386    1.1283

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
 DI3  B1   C     single    1.600  0.020  1.600
 DI3  B1   O     single    1.363  0.020  1.363
 DI3  B1   O1    single    1.367  0.020  1.367
 DI3  C    C2    single    1.530  0.020  1.530
 DI3  C    N     single    1.452  0.020  1.452
 DI3  C    H     single    0.970  0.020  1.090
 DI3  C2   C3    single    1.523  0.020  1.523
 DI3  C2   H21   single    0.970  0.020  1.090
 DI3  C2   H22A  single    0.970  0.020  1.090
 DI3  C3   C4    single    1.524  0.020  1.524
 DI3  C3   H31   single    0.970  0.020  1.090
 DI3  C3   H32   single    0.970  0.020  1.090
 DI3  C4   C5    single    1.519  0.020  1.519
 DI3  C4   H41   single    0.970  0.020  1.090
 DI3  C4   H42   single    0.970  0.020  1.090
 DI3  C5   C6    single    1.508  0.020  1.508
 DI3  C5   H51   single    0.970  0.020  1.090
 DI3  C5   H52   single    0.970  0.020  1.090
 DI3  C6   N1    double    1.277  0.020  1.277
 DI3  C6   N2    single    1.366  0.020  1.366
 DI3  C7   C8    single    1.520  0.020  1.520
 DI3  C7   C9    single    1.538  0.020  1.538
 DI3  C7   N3    single    1.454  0.020  1.454
 DI3  C7   H7    single    0.970  0.020  1.090
 DI3  C8   N     single    1.331  0.020  1.331
 DI3  C8   O2    double    1.227  0.020  1.227
 DI3  C9   C10   single    1.525  0.020  1.525
 DI3  C9   H91   single    0.970  0.020  1.090
 DI3  C9   H92   single    0.970  0.020  1.090
 DI3  C10  C11   single    1.520  0.020  1.520
 DI3  C10  H101  single    0.970  0.020  1.090
 DI3  C10  H102  single    0.970  0.020  1.090
 DI3  C11  N3    single    1.459  0.020  1.459
 DI3  C11  H111  single    0.970  0.020  1.090
 DI3  C11  H112  single    0.970  0.020  1.090
 DI3  C12  C14   single    1.531  0.020  1.531
 DI3  C12  N3    single    1.344  0.020  1.344
 DI3  C12  O3    double    1.221  0.020  1.221
 DI3  C13  C14   single    1.541  0.020  1.541
 DI3  C13  C21   single    1.503  0.020  1.503
 DI3  C13  H131  single    0.970  0.020  1.090
 DI3  C13  H132  single    0.970  0.020  1.090
 DI3  C14  N4    single    1.440  0.020  1.440
 DI3  C14  H14   single    0.970  0.020  1.090
 DI3  C15  C16   single    1.512  0.020  1.512
 DI3  C15  N4    single    1.350  0.020  1.350
 DI3  C15  O4    double    1.221  0.020  1.221
 DI3  C16  H161  single    0.970  0.020  1.090
 DI3  C16  H162  single    0.970  0.020  1.090
 DI3  C16  H163  single    0.970  0.020  1.090
 DI3  C17  C18   aromatic  1.388  0.020  1.388
 DI3  C17  C22   aromatic  1.389  0.020  1.389
 DI3  C17  H17   single    0.930  0.020  1.080
 DI3  C18  C19   aromatic  1.389  0.020  1.389
 DI3  C18  H18   single    0.930  0.020  1.080
 DI3  C19  C20   aromatic  1.388  0.020  1.388
 DI3  C19  H19   single    0.930  0.020  1.080
 DI3  C20  C21   aromatic  1.394  0.020  1.394
 DI3  C20  H20   single    0.930  0.020  1.080
 DI3  C21  C22   aromatic  1.392  0.020  1.392
 DI3  C22  H22   single    0.930  0.020  1.080
 DI3  N    HN    single    0.860  0.020  1.020
 DI3  N1   HN1   single    0.890  0.020  1.040
 DI3  N2   HN21  single    0.890  0.020  1.040
 DI3  N2   HN22  single    0.890  0.020  1.040
 DI3  N4   HN4   single    0.860  0.020  1.020
 DI3  O    HO    single    0.850  0.020  0.980
 DI3  O1   HO1   single    0.850  0.020  0.980

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
 DI3  O1    B1   O     119.02  3.000
 DI3  O1    B1   C     122.76  3.000
 DI3  O     B1   C     117.31  3.000
 DI3  H     C    N     108.43  3.000
 DI3  H     C    C2    107.30  3.000
 DI3  N     C    C2    109.73  3.000
 DI3  H     C    B1    110.12  3.000
 DI3  N     C    B1    109.69  3.000
 DI3  C2    C    B1    111.50  3.000
 DI3  H22A  C2   H21   106.26  3.000
 DI3  H22A  C2   C3    109.98  3.000
 DI3  H21   C2   C3    108.53  3.000
 DI3  H22A  C2   C     110.16  3.000
 DI3  H21   C2   C     109.00  3.000
 DI3  C3    C2   C     112.69  3.000
 DI3  H32   C3   H31   106.06  3.000
 DI3  H32   C3   C4    109.53  3.000
 DI3  H31   C3   C4    108.92  3.000
 DI3  H32   C3   C2    109.19  3.000
 DI3  H31   C3   C2    110.37  3.000
 DI3  C4    C3   C2    112.55  3.000
 DI3  H42   C4   H41   106.20  3.000
 DI3  H42   C4   C5    109.83  3.000
 DI3  H41   C4   C5    109.68  3.000
 DI3  H42   C4   C3    109.79  3.000
 DI3  H41   C4   C3    109.47  3.000
 DI3  C5    C4   C3    111.72  3.000
 DI3  H52   C5   H51   105.23  3.000
 DI3  H52   C5   C6    108.73  3.000
 DI3  H51   C5   C6    107.53  3.000
 DI3  H52   C5   C4    109.81  3.000
 DI3  H51   C5   C4    109.76  3.000
 DI3  C6    C5   C4    115.29  3.000
 DI3  N2    C6   N1    125.69  3.000
 DI3  N2    C6   C5    113.87  3.000
 DI3  N1    C6   C5    120.42  3.000
 DI3  H7    C7   N3    110.12  3.000
 DI3  H7    C7   C9    110.61  3.000
 DI3  N3    C7   C9    103.97  3.000
 DI3  H7    C7   C8    110.34  3.000
 DI3  N3    C7   C8    111.04  3.000
 DI3  C9    C7   C8    110.61  3.000
 DI3  H92   C9   H91   107.90  3.000
 DI3  H92   C9   C10   109.82  3.000
 DI3  H91   C9   C10   113.29  3.000
 DI3  H92   C9   C7    110.39  3.000
 DI3  H91   C9   C7    111.52  3.000
 DI3  C10   C9   C7    103.91  3.000
 DI3  H102  C10  H101  108.10  3.000
 DI3  H102  C10  C11   112.34  3.000
 DI3  H101  C10  C11   109.88  3.000
 DI3  H102  C10  C9    112.95  3.000
 DI3  H101  C10  C9    110.63  3.000
 DI3  C11   C10  C9    102.89  3.000
 DI3  H112  C11  H111  108.07  3.000
 DI3  H112  C11  N3    110.77  3.000
 DI3  H111  C11  N3    112.17  3.000
 DI3  H112  C11  C10   111.33  3.000
 DI3  H111  C11  C10   112.06  3.000
 DI3  N3    C11  C10   102.43  3.000
 DI3  H132  C13  H131  106.61  3.000
 DI3  H132  C13  C21   110.64  3.000
 DI3  H131  C13  C21   109.34  3.000
 DI3  H132  C13  C14   109.89  3.000
 DI3  H131  C13  C14   108.48  3.000
 DI3  C21   C13  C14   111.71  3.000
 DI3  H14   C14  N4    104.75  3.000
 DI3  H14   C14  C13   107.58  3.000
 DI3  N4    C14  C13   113.95  3.000
 DI3  H14   C14  C12   107.91  3.000
 DI3  N4    C14  C12   111.13  3.000
 DI3  C13   C14  C12   111.09  3.000
 DI3  H163  C16  H162  107.36  3.000
 DI3  H163  C16  H161  108.83  3.000
 DI3  H162  C16  H161  108.58  3.000
 DI3  H163  C16  C15   111.23  3.000
 DI3  H162  C16  C15   110.48  3.000
 DI3  H161  C16  C15   110.27  3.000
 DI3  H17   C17  C22   119.72  3.000
 DI3  H17   C17  C18   120.06  3.000
 DI3  C22   C17  C18   120.21  3.000
 DI3  H18   C18  C19   120.28  3.000
 DI3  H18   C18  C17   120.20  3.000
 DI3  C19   C18  C17   119.52  3.000
 DI3  H19   C19  C20   119.81  3.000
 DI3  H19   C19  C18   120.16  3.000
 DI3  C20   C19  C18   120.03  3.000
 DI3  H20   C20  C21   119.63  3.000
 DI3  H20   C20  C19   119.40  3.000
 DI3  C21   C20  C19   120.97  3.000
 DI3  C22   C21  C20   118.48  3.000
 DI3  C22   C21  C13   121.31  3.000
 DI3  C20   C21  C13   120.20  3.000
 DI3  H22   C22  C21   119.50  3.000
 DI3  H22   C22  C17   119.71  3.000
 DI3  C21   C22  C17   120.79  3.000
 DI3  HN    N    C8    119.23  3.000
 DI3  HN    N    C     118.98  3.000
 DI3  C8    N    C     120.40  3.000
 DI3  HN1   N1   C6    110.94  3.000
 DI3  HN22  N2   HN21  114.10  3.000
 DI3  HN22  N2   C6    118.49  3.000
 DI3  HN21  N2   C6    118.37  3.000
 DI3  C12   N3   C11   127.96  3.000
 DI3  C12   N3   C7    119.46  3.000
 DI3  C11   N3   C7    112.19  3.000
 DI3  HN4   N4   C15   116.81  3.000
 DI3  HN4   N4   C14   115.59  3.000
 DI3  C15   N4   C14   127.39  3.000
 DI3  HO    O    B1    113.60  3.000
 DI3  HO1   O1   B1    112.83  3.000
 DI3  O2    C8   N     122.18  3.000
 DI3  O2    C8   C7    121.46  3.000
 DI3  N     C8   C7    116.22  3.000
 DI3  O3    C12  N3    121.37  3.000
 DI3  O3    C12  C14   121.92  3.000
 DI3  N3    C12  C14   116.70  3.000
 DI3  O4    C15  N4    124.27  3.000
 DI3  O4    C15  C16   122.25  3.000
 DI3  N4    C15  C16   113.47  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
 DI3  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 DI3  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 DI3  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 DI3  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 DI3  CONST_05  C22   C17  C18  C19     0.00   0.0  0
 DI3  CONST_06  C22   C21  C20  C19     0.00   0.0  0
 DI3  CONST_07  C19   C20  C21  C13   180.00   0.0  0
 DI3  CONST_08  C17   C22  C21  C13   180.00   0.0  0
 DI3  CONST_09  H19   C19  C18  C17   180.00   0.0  0
 DI3  CONST_10  H22   C22  C17  C18   180.00   0.0  0
 DI3  CONST_11  H20   C20  C19  C18   180.00   0.0  0
 DI3  CONST_12  H17   C17  C18  C19   180.00   0.0  0
 DI3  CONST_13  H18   C18  C19  C20   180.00   0.0  0
 DI3  CONST_14  C14   C12  N3   C7    180.00   0.0  0
 DI3  CONST_15  O3    C12  N3   C7      0.00   0.0  0
 DI3  CONST_16  C14   C12  N3   C11     0.00   0.0  0
 DI3  CONST_17  O3    C12  N3   C11   180.00   0.0  0
 DI3  CONST_18  C7    C8   N    C     180.00   0.0  0
 DI3  CONST_19  HN    N    C8   C7      0.00   0.0  0
 DI3  CONST_20  O2    C8   N    C       0.00   0.0  0
 DI3  CONST_21  C16   C15  N4   C14   180.00   0.0  0
 DI3  CONST_22  O4    C15  N4   C14     0.00   0.0  0
 DI3  CONST_23  HN4   N4   C15  C16     0.00   0.0  0
 DI3  CONST_24  HN1   N1   C6   C5    180.00   0.0  0
 DI3  Var_01    C11   C10  C9   C7     36.21  30.0  1
 DI3  Var_02    C10   C11  N3   C7     24.09  30.0  1
 DI3  Var_03    N3    C11  C10  C9    -36.51  30.0  1
 DI3  Var_04    C20   C21  C13  C14    79.48  30.0  2
 DI3  Var_05    C4    C3   C2   C     175.05  30.0  3
 DI3  Var_06    C5    C4   C3   C2   -178.11  30.0  3
 DI3  Var_07    C6    C5   C4   C3   -177.77  30.0  3
 DI3  Var_08    N1    C6   C5   C4     11.32  30.0  3
 DI3  Var_09    H161  C16  C15  N4    174.04  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
 DI3  chir_01  C    B1  C2   N    positiv
 DI3  chir_02  C7   N3  C8   C9   positiv
 DI3  chir_03  C14  N4  C12  C13  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
 DI3  plan-1  C13   0.020
 DI3  plan-1  C17   0.020
 DI3  plan-1  C18   0.020
 DI3  plan-1  C19   0.020
 DI3  plan-1  C20   0.020
 DI3  plan-1  C21   0.020
 DI3  plan-1  C22   0.020
 DI3  plan-1  H17   0.020
 DI3  plan-1  H18   0.020
 DI3  plan-1  H19   0.020
 DI3  plan-1  H20   0.020
 DI3  plan-1  H22   0.020
 DI3  plan-2  C7    0.020
 DI3  plan-2  C11   0.020
 DI3  plan-2  C14   0.020
 DI3  plan-2  N3    0.020
 DI3  plan-2  C12   0.020
 DI3  plan-2  O3    0.020
 DI3  plan-3  C14   0.020
 DI3  plan-3  C16   0.020
 DI3  plan-3  N4    0.020
 DI3  plan-3  O4    0.020
 DI3  plan-3  HN4   0.020
 DI3  plan-3  C15   0.020
 DI3  plan-4  C     0.020
 DI3  plan-4  C7    0.020
 DI3  plan-4  N     0.020
 DI3  plan-4  HN    0.020
 DI3  plan-4  C8    0.020
 DI3  plan-4  O2    0.020
 DI3  plan-5  C5    0.020
 DI3  plan-5  C6    0.020
 DI3  plan-5  N1    0.020
 DI3  plan-5  N2    0.020
 DI3  plan-5  HN1   0.020
 DI3  plan-5  HN21  0.020
 DI3  plan-5  HN22  0.020

