# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 16:35:59 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: N-acetyl-D-phenylalanyl-N-[(1R)-6-amino-1-(dihydroxyboranyl)hexyl]-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](CCCCCN)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
 DI4  DI4  N-acetyl-D-phenylalanyl-N-[(1R)-6-amino-1-(dihydroxyboranyl)hexyl]-L-prolinamide  ligand  67  32  .  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_DI4
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
 DI4  B1    B  B     0   0.507  -0.9599   1.5598   -3.4161
 DI4  C     C  CH1   0  -0.235  -0.1489   0.1934   -3.2328
 DI4  C2    C  CH2   0  -0.482  -0.1398  -0.6316   -4.5216
 DI4  C3    C  CH2   0  -0.439   0.5895   0.0639   -5.6645
 DI4  C4    C  CH2   0  -0.416   0.7247  -0.8201   -6.8979
 DI4  C5    C  CH2   0  -0.426   1.4697  -0.1392   -8.0382
 DI4  C6    C  CH2   0  -0.273   1.6187  -1.0318   -9.2602
 DI4  C7    C  CH1   0  -0.162  -1.7943  -0.9015   -0.0033
 DI4  C9    C  CH2   0  -0.483  -3.3302  -0.8363   -0.0365
 DI4  C10   C  CH2   0  -0.467  -3.7301  -0.9060    1.4332
 DI4  C11   C  CH2   0  -0.290  -2.6350  -0.1075    2.1210
 DI4  C13   C  CH2   0  -0.552   0.0299  -1.0137    4.0866
 DI4  C14   C  CH1   0  -0.187   0.1240   0.1705    3.1036
 DI4  C16   C  CH3   0  -0.783   3.6887   1.4681    3.1238
 DI4  C17   C  CR16  0  -0.241   1.5220  -0.2423    7.4976
 DI4  C18   C  CR16  0  -0.271   0.4379   0.3205    8.1572
 DI4  C19   C  CR16  0  -0.240  -0.7795   0.4373    7.4977
 DI4  C20   C  CR16  0  -0.310  -0.9051  -0.0042    6.1881
 DI4  C21   C  CR6   0   0.151   0.1776  -0.5664    5.5139
 DI4  C22   C  CR16  0  -0.315   1.3912  -0.6817    6.1863
 DI4  N     N  NH1   0  -0.649  -0.7392  -0.5866   -2.1595
 DI4  N1    N  NH2   0  -0.801   2.3507  -0.3505  -10.3191
 DI4  N2    N  NT    0  -0.481  -1.4539  -0.4502    1.3360
 DI4  N3    N  NH1   0  -0.627   1.3640   0.8992    3.1767
 DI4  O     O  OH1   0  -0.629  -2.2881   1.4657   -3.7048
 DI4  O1    O  OH1   0  -0.621  -0.3446   2.7770   -3.5104
 DI4  O4    O  O     0  -0.492   2.8827  -0.7885    3.0475
 DI4  H     H  HCH1  0   0.233   0.8988   0.4071   -2.9730
 DI4  H21   H  HCH2  0   0.228   0.3518  -1.5923   -4.3266
 DI4  H22A  H  HCH2  0   0.231  -1.1645  -0.8672   -4.8230
 DI4  H31   H  HCH2  0   0.228   0.0670   0.9855   -5.9428
 DI4  H32   H  HCH2  0   0.215   1.5863   0.3680   -5.3276
 DI4  H41   H  HCH2  0   0.212   1.2463  -1.7435   -6.6233
 DI4  H42   H  HCH2  0   0.212  -0.2708  -1.1235   -7.2394
 DI4  H51   H  HCH2  0   0.211   0.9403   0.7779   -8.3213
 DI4  H52   H  HCH2  0   0.212   2.4631   0.1700   -7.6981
 DI4  H61   H  HCH2  0   0.210   2.1782  -1.9286   -8.9787
 DI4  H62   H  HCH2  0   0.186   0.6217  -1.3784   -9.5704
 DI4  H7    H  HCH1  0   0.279  -1.4493  -1.9297   -0.1507
 DI4  H91   H  HCH2  0   0.267  -3.7511  -1.6416   -0.6357
 DI4  H92   H  HCH2  0   0.253  -3.6607   0.1110   -0.4666
 DI4  H101  H  HCH2  0   0.246  -3.7157  -1.9387    1.7862
 DI4  H102  H  HCH2  0   0.259  -4.7213  -0.4974    1.6238
 DI4  H111  H  HCH2  0   0.257  -2.5257  -0.3811    3.1690
 DI4  H112  H  HCH2  0   0.253  -2.8351   0.9668    2.0706
 DI4  H131  H  HCH2  0   0.266  -0.9437  -1.4911    3.9547
 DI4  H132  H  HCH2  0   0.282   0.7807  -1.7604    3.8391
 DI4  H14   H  HCH1  0   0.293  -0.6422   0.8962    3.3874
 DI4  H161  H  HCH3  0   0.260   4.6746   1.0116    3.1450
 DI4  H162  H  HCH3  0   0.265   3.6159   2.0993    2.2369
 DI4  H163  H  HCH3  0   0.262   3.5826   2.1164    3.9944
 DI4  H17   H  HCR6  0   0.253   2.4736  -0.3414    8.0044
 DI4  H18   H  HCR6  0   0.254   0.5399   0.6621    9.1792
 DI4  H19   H  HCR6  0   0.254  -1.6335   0.8683    8.0044
 DI4  H20   H  HCR6  0   0.248  -1.8621   0.0849    5.6851
 DI4  H22   H  HCR6  0   0.246   2.2410  -1.1220    5.6801
 DI4  HN    H  HNH1  0   0.393  -0.6226  -1.5883   -2.1628
 DI4  HN11  H  HNH2  0   0.344   2.4511  -0.9704  -11.1127
 DI4  HN12  H  HNH2  0   0.336   1.7968   0.4287  -10.6543
 DI4  HN3   H  HNH1  0   0.406   1.2753   1.9018    3.1945
 DI4  HO    H  HOH1  0   0.481  -2.7078   2.3165   -3.8680
 DI4  HO1   H  HOH1  0   0.474   0.5937   2.7362   -3.3064
 DI4  C8    C  C     0   0.593  -1.1959   0.0109   -1.0608
 DI4  C12   C  C     0   0.571  -0.1630  -0.2912    1.6726
 DI4  O2    O  O     0  -0.504  -1.2119   1.2320   -0.9388
 DI4  C15   C  C     0   0.518   2.6167   0.4014    3.1049
 DI4  O3    O  O     0  -0.478   0.7347  -0.5233    0.8779

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
 DI4  B1   C     single    1.599  0.020  1.599
 DI4  B1   O     single    1.362  0.020  1.362
 DI4  B1   O1    single    1.367  0.020  1.367
 DI4  C    C2    single    1.530  0.020  1.530
 DI4  C    N     single    1.452  0.020  1.452
 DI4  C    H     single    0.970  0.020  1.090
 DI4  C2   C3    single    1.524  0.020  1.524
 DI4  C2   H21   single    0.970  0.020  1.090
 DI4  C2   H22A  single    0.970  0.020  1.090
 DI4  C3   C4    single    1.523  0.020  1.523
 DI4  C3   H31   single    0.970  0.020  1.090
 DI4  C3   H32   single    0.970  0.020  1.090
 DI4  C4   C5    single    1.523  0.020  1.523
 DI4  C4   H41   single    0.970  0.020  1.090
 DI4  C4   H42   single    0.970  0.020  1.090
 DI4  C5   C6    single    1.521  0.020  1.521
 DI4  C5   H51   single    0.970  0.020  1.090
 DI4  C5   H52   single    0.970  0.020  1.090
 DI4  C6   N1    single    1.457  0.020  1.457
 DI4  C6   H61   single    0.970  0.020  1.090
 DI4  C6   H62   single    0.970  0.020  1.090
 DI4  C7   C8    single    1.519  0.020  1.519
 DI4  C7   C9    single    1.538  0.020  1.538
 DI4  C7   N2    single    1.454  0.020  1.454
 DI4  C7   H7    single    0.970  0.020  1.090
 DI4  C8   N     single    1.331  0.020  1.331
 DI4  C8   O2    double    1.227  0.020  1.227
 DI4  C9   C10   single    1.525  0.020  1.525
 DI4  C9   H91   single    0.970  0.020  1.090
 DI4  C9   H92   single    0.970  0.020  1.090
 DI4  C10  C11   single    1.520  0.020  1.520
 DI4  C10  H101  single    0.970  0.020  1.090
 DI4  C10  H102  single    0.970  0.020  1.090
 DI4  C11  N2    single    1.459  0.020  1.459
 DI4  C11  H111  single    0.970  0.020  1.090
 DI4  C11  H112  single    0.970  0.020  1.090
 DI4  C12  C14   single    1.531  0.020  1.531
 DI4  C12  N2    single    1.344  0.020  1.344
 DI4  C12  O3    double    1.221  0.020  1.221
 DI4  C13  C14   single    1.542  0.020  1.542
 DI4  C13  C21   single    1.503  0.020  1.503
 DI4  C13  H131  single    0.970  0.020  1.090
 DI4  C13  H132  single    0.970  0.020  1.090
 DI4  C14  N3    single    1.440  0.020  1.440
 DI4  C14  H14   single    0.970  0.020  1.090
 DI4  C15  C16   single    1.512  0.020  1.512
 DI4  C15  N3    single    1.350  0.020  1.350
 DI4  C15  O4    double    1.221  0.020  1.221
 DI4  C16  H161  single    0.970  0.020  1.090
 DI4  C16  H162  single    0.970  0.020  1.090
 DI4  C16  H163  single    0.970  0.020  1.090
 DI4  C17  C18   aromatic  1.388  0.020  1.388
 DI4  C17  C22   aromatic  1.389  0.020  1.389
 DI4  C17  H17   single    0.930  0.020  1.080
 DI4  C18  C19   aromatic  1.389  0.020  1.389
 DI4  C18  H18   single    0.930  0.020  1.080
 DI4  C19  C20   aromatic  1.388  0.020  1.388
 DI4  C19  H19   single    0.930  0.020  1.080
 DI4  C20  C21   aromatic  1.394  0.020  1.394
 DI4  C20  H20   single    0.930  0.020  1.080
 DI4  C21  C22   aromatic  1.392  0.020  1.392
 DI4  C22  H22   single    0.930  0.020  1.080
 DI4  N    HN    single    0.860  0.020  1.020
 DI4  N1   HN11  single    0.890  0.020  1.040
 DI4  N1   HN12  single    0.890  0.020  1.040
 DI4  N3   HN3   single    0.860  0.020  1.020
 DI4  O    HO    single    0.850  0.020  0.980
 DI4  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
 DI4  O1    B1   O     119.05  3.000
 DI4  O1    B1   C     122.70  3.000
 DI4  O     B1   C     117.36  3.000
 DI4  H     C    N     108.47  3.000
 DI4  H     C    C2    107.33  3.000
 DI4  N     C    C2    109.59  3.000
 DI4  H     C    B1    110.12  3.000
 DI4  N     C    B1    109.72  3.000
 DI4  C2    C    B1    111.53  3.000
 DI4  H22A  C2   H21   106.28  3.000
 DI4  H22A  C2   C3    109.88  3.000
 DI4  H21   C2   C3    108.59  3.000
 DI4  H22A  C2   C     110.03  3.000
 DI4  H21   C2   C     108.98  3.000
 DI4  C3    C2   C     112.86  3.000
 DI4  H32   C3   H31   106.19  3.000
 DI4  H32   C3   C4    109.22  3.000
 DI4  H31   C3   C4    108.96  3.000
 DI4  H32   C3   C2    109.37  3.000
 DI4  H31   C3   C2    110.27  3.000
 DI4  C4    C3   C2    112.63  3.000
 DI4  H42   C4   H41   106.10  3.000
 DI4  H42   C4   C5    109.57  3.000
 DI4  H41   C4   C5    109.37  3.000
 DI4  H42   C4   C3    109.42  3.000
 DI4  H41   C4   C3    109.17  3.000
 DI4  C5    C4   C3    112.97  3.000
 DI4  H52   C5   H51   106.39  3.000
 DI4  H52   C5   C6    109.07  3.000
 DI4  H51   C5   C6    109.33  3.000
 DI4  H52   C5   C4    109.73  3.000
 DI4  H51   C5   C4    109.34  3.000
 DI4  C6    C5   C4    112.79  3.000
 DI4  H62   C6   H61   106.13  3.000
 DI4  H62   C6   N1    113.44  3.000
 DI4  H61   C6   N1    108.27  3.000
 DI4  H62   C6   C5    108.83  3.000
 DI4  H61   C6   C5    108.94  3.000
 DI4  N1    C6   C5    111.03  3.000
 DI4  H7    C7   N2    110.00  3.000
 DI4  H7    C7   C9    110.60  3.000
 DI4  N2    C7   C9    103.92  3.000
 DI4  H7    C7   C8    110.25  3.000
 DI4  N2    C7   C8    111.26  3.000
 DI4  C9    C7   C8    110.66  3.000
 DI4  H92   C9   H91   107.94  3.000
 DI4  H92   C9   C10   109.88  3.000
 DI4  H91   C9   C10   113.29  3.000
 DI4  H92   C9   C7    110.35  3.000
 DI4  H91   C9   C7    111.52  3.000
 DI4  C10   C9   C7    103.84  3.000
 DI4  H102  C10  H101  108.09  3.000
 DI4  H102  C10  C11   112.30  3.000
 DI4  H101  C10  C11   109.95  3.000
 DI4  H102  C10  C9    112.98  3.000
 DI4  H101  C10  C9    110.58  3.000
 DI4  C11   C10  C9    102.90  3.000
 DI4  H112  C11  H111  108.03  3.000
 DI4  H112  C11  N2    110.73  3.000
 DI4  H111  C11  N2    112.19  3.000
 DI4  H112  C11  C10   111.30  3.000
 DI4  H111  C11  C10   112.09  3.000
 DI4  N2    C11  C10   102.50  3.000
 DI4  H132  C13  H131  106.73  3.000
 DI4  H132  C13  C21   110.65  3.000
 DI4  H131  C13  C21   109.41  3.000
 DI4  H132  C13  C14   109.88  3.000
 DI4  H131  C13  C14   108.24  3.000
 DI4  C21   C13  C14   111.77  3.000
 DI4  H14   C14  N3    104.74  3.000
 DI4  H14   C14  C13   107.56  3.000
 DI4  N3    C14  C13   114.13  3.000
 DI4  H14   C14  C12   108.15  3.000
 DI4  N3    C14  C12   111.19  3.000
 DI4  C13   C14  C12   110.66  3.000
 DI4  H163  C16  H162  107.37  3.000
 DI4  H163  C16  H161  108.81  3.000
 DI4  H162  C16  H161  108.63  3.000
 DI4  H163  C16  C15   111.12  3.000
 DI4  H162  C16  C15   110.53  3.000
 DI4  H161  C16  C15   110.30  3.000
 DI4  H17   C17  C22   119.72  3.000
 DI4  H17   C17  C18   120.07  3.000
 DI4  C22   C17  C18   120.21  3.000
 DI4  H18   C18  C19   120.28  3.000
 DI4  H18   C18  C17   120.20  3.000
 DI4  C19   C18  C17   119.52  3.000
 DI4  H19   C19  C20   119.80  3.000
 DI4  H19   C19  C18   120.16  3.000
 DI4  C20   C19  C18   120.03  3.000
 DI4  H20   C20  C21   119.61  3.000
 DI4  H20   C20  C19   119.42  3.000
 DI4  C21   C20  C19   120.97  3.000
 DI4  C22   C21  C20   118.48  3.000
 DI4  C22   C21  C13   121.31  3.000
 DI4  C20   C21  C13   120.20  3.000
 DI4  H22   C22  C21   119.48  3.000
 DI4  H22   C22  C17   119.74  3.000
 DI4  C21   C22  C17   120.78  3.000
 DI4  HN    N    C8    119.22  3.000
 DI4  HN    N    C     118.96  3.000
 DI4  C8    N    C     120.55  3.000
 DI4  HN12  N1   HN11  105.42  3.000
 DI4  HN12  N1   C6    109.00  3.000
 DI4  HN11  N1   C6    109.48  3.000
 DI4  C12   N2   C11   127.97  3.000
 DI4  C12   N2   C7    119.50  3.000
 DI4  C11   N2   C7    112.28  3.000
 DI4  HN3   N3   C15   116.74  3.000
 DI4  HN3   N3   C14   115.41  3.000
 DI4  C15   N3   C14   127.57  3.000
 DI4  HO    O    B1    113.57  3.000
 DI4  HO1   O1   B1    112.77  3.000
 DI4  O2    C8   N     122.21  3.000
 DI4  O2    C8   C7    121.54  3.000
 DI4  N     C8   C7    116.10  3.000
 DI4  O3    C12  N2    121.39  3.000
 DI4  O3    C12  C14   121.86  3.000
 DI4  N2    C12  C14   116.74  3.000
 DI4  O4    C15  N3    124.35  3.000
 DI4  O4    C15  C16   122.26  3.000
 DI4  N3    C15  C16   113.39  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
 DI4  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 DI4  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 DI4  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 DI4  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 DI4  CONST_05  C22   C17  C18  C19     0.00   0.0  0
 DI4  CONST_06  C22   C21  C20  C19     0.00   0.0  0
 DI4  CONST_07  C19   C20  C21  C13   180.00   0.0  0
 DI4  CONST_08  C17   C22  C21  C13   180.00   0.0  0
 DI4  CONST_09  H19   C19  C18  C17   180.00   0.0  0
 DI4  CONST_10  H22   C22  C17  C18   180.00   0.0  0
 DI4  CONST_11  H20   C20  C19  C18   180.00   0.0  0
 DI4  CONST_12  H17   C17  C18  C19   180.00   0.0  0
 DI4  CONST_13  H18   C18  C19  C20   180.00   0.0  0
 DI4  CONST_14  C14   C12  N2   C7    180.00   0.0  0
 DI4  CONST_15  O3    C12  N2   C7      0.00   0.0  0
 DI4  CONST_16  C14   C12  N2   C11     0.00   0.0  0
 DI4  CONST_17  O3    C12  N2   C11   180.00   0.0  0
 DI4  CONST_18  C7    C8   N    C     180.00   0.0  0
 DI4  CONST_19  HN    N    C8   C7      0.00   0.0  0
 DI4  CONST_20  O2    C8   N    C       0.00   0.0  0
 DI4  CONST_21  C16   C15  N3   C14   180.00   0.0  0
 DI4  CONST_22  O4    C15  N3   C14     0.00   0.0  0
 DI4  CONST_23  HN3   N3   C15  C16     0.00   0.0  0
 DI4  Var_01    C11   C10  C9   C7     36.52  30.0  1
 DI4  Var_02    C10   C11  N2   C7     23.14  30.0  1
 DI4  Var_03    N2    C11  C10  C9    -36.14  30.0  1
 DI4  Var_04    C20   C21  C13  C14    79.91  30.0  2
 DI4  Var_05    C4    C3   C2   C     173.91  30.0  3
 DI4  Var_06    C5    C4   C3   C2   -179.19  30.0  3
 DI4  Var_07    C6    C5   C4   C3    179.23  30.0  3
 DI4  Var_08    N1    C6   C5   C4   -179.25  30.0  3
 DI4  Var_09    HN11  N1   C6   C5    178.95  30.0  3
 DI4  Var_10    H161  C16  C15  N3    175.44  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
 DI4  chir_01  C    B1  C2   N    positiv
 DI4  chir_02  C7   N2  C8   C9   positiv
 DI4  chir_03  C14  N3  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
 DI4  plan-1  C13  0.020
 DI4  plan-1  C17  0.020
 DI4  plan-1  C18  0.020
 DI4  plan-1  C19  0.020
 DI4  plan-1  C20  0.020
 DI4  plan-1  C21  0.020
 DI4  plan-1  C22  0.020
 DI4  plan-1  H17  0.020
 DI4  plan-1  H18  0.020
 DI4  plan-1  H19  0.020
 DI4  plan-1  H20  0.020
 DI4  plan-1  H22  0.020
 DI4  plan-2  C7   0.020
 DI4  plan-2  C11  0.020
 DI4  plan-2  C14  0.020
 DI4  plan-2  N2   0.020
 DI4  plan-2  C12  0.020
 DI4  plan-2  O3   0.020
 DI4  plan-3  C14  0.020
 DI4  plan-3  C16  0.020
 DI4  plan-3  N3   0.020
 DI4  plan-3  O4   0.020
 DI4  plan-3  HN3  0.020
 DI4  plan-3  C15  0.020
 DI4  plan-4  C    0.020
 DI4  plan-4  C7   0.020
 DI4  plan-4  N    0.020
 DI4  plan-4  HN   0.020
 DI4  plan-4  C8   0.020
 DI4  plan-4  O2   0.020

