# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:00:35 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: N-acetyl-D-phenylalanyl-N-[(1R)-5-amino-1-(dihydroxyboranyl)pentyl]-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](CCCCN)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
 DI2  DI2  N-acetyl-D-phenylalanyl-N-[(1R)-5-amino-1-(dihydroxyboranyl)pentyl]-L-prolinamide  ligand  64  31  .  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_DI2
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
 DI2  B1    B  B     0   0.506  -0.7133   1.5359   -3.7782
 DI2  C     C  CH1   0  -0.235   0.0972   0.1732   -3.5642
 DI2  C2    C  CH2   0  -0.481   0.1530  -0.6548   -4.8501
 DI2  C3    C  CH2   0  -0.446   0.9124   0.0436   -5.9712
 DI2  C4    C  CH2   0  -0.424   1.0724  -0.8347   -7.2051
 DI2  C5    C  CH2   0  -0.271   1.8483  -0.1462   -8.3169
 DI2  C6    C  CH1   0  -0.162  -1.6799  -0.9216   -0.4051
 DI2  C8    C  CH2   0  -0.483  -3.2123  -0.8747   -0.5242
 DI2  C9    C  CH2   0  -0.467  -3.6927  -0.9395    0.9211
 DI2  C10   C  CH2   0  -0.288  -2.6472  -0.1221    1.6617
 DI2  C12   C  CH2   0  -0.551  -0.0929  -0.9830    3.7831
 DI2  C13   C  CH1   0  -0.192   0.0505   0.1930    2.7963
 DI2  C15   C  CH3   0  -0.776   3.6208   1.4778    2.9612
 DI2  C16   C  CR16  0  -0.242   1.2586  -0.2672    7.2634
 DI2  C17   C  CR16  0  -0.271   0.1808   0.3762    7.8562
 DI2  C18   C  CR16  0  -0.240  -0.9872   0.5684    7.1284
 DI2  C19   C  CR16  0  -0.308  -1.0710   0.1196    5.8181
 DI2  C20   C  CR6   0   0.152   0.0062  -0.5244    5.2114
 DI2  C21   C  CR16  0  -0.316   1.1706  -0.7120    5.9501
 DI2  N     N  NH1   0  -0.649  -0.5277  -0.6073   -2.5109
 DI2  N1    N  NH2   0  -0.801   1.9731  -1.0125   -9.4806
 DI2  N2    N  NT    0  -0.481  -1.4199  -0.4576    0.9475
 DI2  N3    N  NH1   0  -0.633   1.2821   0.9274    2.9345
 DI2  O     O  OH1   0  -0.629  -2.0282   1.4346   -4.1209
 DI2  O1    O  OH1   0  -0.621  -0.1012   2.7566   -3.8478
 DI2  O4    O  O     0  -0.496   2.8010  -0.7639    2.9019
 DI2  H     H  HCH1  0   0.233   1.1343   0.3917   -3.2688
 DI2  H21A  H  HCH2  0   0.229   0.6439  -1.6121   -4.6383
 DI2  H22   H  HCH2  0   0.231  -0.8604  -0.8970   -5.1829
 DI2  H31   H  HCH2  0   0.229   0.3985   0.9680   -6.2559
 DI2  H32   H  HCH2  0   0.216   1.9012   0.3437   -5.6077
 DI2  H41   H  HCH2  0   0.213   1.5870  -1.7609   -6.9250
 DI2  H42   H  HCH2  0   0.215   0.0883  -1.1294   -7.5826
 DI2  H51   H  HCH2  0   0.211   1.3120   0.7583   -8.6175
 DI2  H52   H  HCH2  0   0.187   2.8154   0.1916   -7.9157
 DI2  H6    H  HCH1  0   0.279  -1.3155  -1.9469   -0.5256
 DI2  H81   H  HCH2  0   0.267  -3.5908  -1.6872   -1.1416
 DI2  H82   H  HCH2  0   0.253  -3.5290   0.0669   -0.9769
 DI2  H91   H  HCH2  0   0.246  -3.6850  -1.9692    1.2832
 DI2  H92   H  HCH2  0   0.259  -4.6979  -0.5421    1.0528
 DI2  H101  H  HCH2  0   0.256  -2.5929  -0.3859    2.7160
 DI2  H102  H  HCH2  0   0.253  -2.8565   0.9492    1.5901
 DI2  H121  H  HCH2  0   0.266  -1.0663  -1.4499    3.6186
 DI2  H122  H  HCH2  0   0.282   0.6583  -1.7399    3.5713
 DI2  H13   H  HCH1  0   0.293  -0.7343   0.9162    3.0309
 DI2  H151  H  HCH3  0   0.260   4.4599   1.1236    3.5566
 DI2  H152  H  HCH3  0   0.269   3.9845   1.6415    1.9452
 DI2  H153  H  HCH3  0   0.250   3.2887   2.4360    3.3569
 DI2  H16   H  HCR6  0   0.253   2.1717  -0.4238    7.8238
 DI2  H17   H  HCR6  0   0.254   0.2492   0.7231    8.8794
 DI2  H18   H  HCR6  0   0.254  -1.8352   1.0645    7.5829
 DI2  H19   H  HCR6  0   0.248  -1.9902   0.2699    5.2613
 DI2  H21   H  HCR6  0   0.247   2.0165  -1.2089    5.4917
 DI2  HN    H  HNH1  0   0.393  -0.4115  -1.6090   -2.5100
 DI2  HN11  H  HNH2  0   0.345   2.4807  -0.5276  -10.2095
 DI2  HN12  H  HNH2  0   0.337   2.5481  -1.8106   -9.2380
 DI2  HN3   H  HNH1  0   0.405   1.1898   1.9294    2.9315
 DI2  HO    H  HOH1  0   0.481  -2.4460   2.2833   -4.2991
 DI2  HO1   H  HOH1  0   0.474   0.8292   2.7195   -3.6099
 DI2  C7    C  C     0   0.594  -1.0363  -0.0094   -1.4356
 DI2  C11   C  C     0   0.572  -0.1518  -0.2795    1.3539
 DI2  O2    O  O     0  -0.504  -1.0643   1.2121   -1.3188
 DI2  C14   C  C     0   0.531   2.5346   0.4276    2.9316
 DI2  O3    O  O     0  -0.478   0.7918  -0.5028    0.6113

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
 DI2  B1   C     single    1.600  0.020  1.600
 DI2  B1   O     single    1.363  0.020  1.363
 DI2  B1   O1    single    1.367  0.020  1.367
 DI2  C    C2    single    1.530  0.020  1.530
 DI2  C    N     single    1.452  0.020  1.452
 DI2  C    H     single    0.970  0.020  1.090
 DI2  C2   C3    single    1.524  0.020  1.524
 DI2  C2   H21A  single    0.970  0.020  1.090
 DI2  C2   H22   single    0.970  0.020  1.090
 DI2  C3   C4    single    1.523  0.020  1.523
 DI2  C3   H31   single    0.970  0.020  1.090
 DI2  C3   H32   single    0.970  0.020  1.090
 DI2  C4   C5    single    1.521  0.020  1.521
 DI2  C4   H41   single    0.970  0.020  1.090
 DI2  C4   H42   single    0.970  0.020  1.090
 DI2  C5   N1    single    1.456  0.020  1.456
 DI2  C5   H51   single    0.970  0.020  1.090
 DI2  C5   H52   single    0.970  0.020  1.090
 DI2  C6   C7    single    1.519  0.020  1.519
 DI2  C6   C8    single    1.538  0.020  1.538
 DI2  C6   N2    single    1.453  0.020  1.453
 DI2  C6   H6    single    0.970  0.020  1.090
 DI2  C7   N     single    1.331  0.020  1.331
 DI2  C7   O2    double    1.227  0.020  1.227
 DI2  C8   C9    single    1.524  0.020  1.524
 DI2  C8   H81   single    0.970  0.020  1.090
 DI2  C8   H82   single    0.970  0.020  1.090
 DI2  C9   C10   single    1.520  0.020  1.520
 DI2  C9   H91   single    0.970  0.020  1.090
 DI2  C9   H92   single    0.970  0.020  1.090
 DI2  C10  N2    single    1.459  0.020  1.459
 DI2  C10  H101  single    0.970  0.020  1.090
 DI2  C10  H102  single    0.970  0.020  1.090
 DI2  C11  C13   single    1.531  0.020  1.531
 DI2  C11  N2    single    1.344  0.020  1.344
 DI2  C11  O3    double    1.221  0.020  1.221
 DI2  C12  C13   single    1.542  0.020  1.542
 DI2  C12  C20   single    1.503  0.020  1.503
 DI2  C12  H121  single    0.970  0.020  1.090
 DI2  C12  H122  single    0.970  0.020  1.090
 DI2  C13  N3    single    1.441  0.020  1.441
 DI2  C13  H13   single    0.970  0.020  1.090
 DI2  C14  C15   single    1.511  0.020  1.511
 DI2  C14  N3    single    1.348  0.020  1.348
 DI2  C14  O4    double    1.221  0.020  1.221
 DI2  C15  H151  single    0.970  0.020  1.090
 DI2  C15  H152  single    0.970  0.020  1.090
 DI2  C15  H153  single    0.970  0.020  1.090
 DI2  C16  C17   aromatic  1.388  0.020  1.388
 DI2  C16  C21   aromatic  1.389  0.020  1.389
 DI2  C16  H16   single    0.930  0.020  1.080
 DI2  C17  C18   aromatic  1.390  0.020  1.390
 DI2  C17  H17   single    0.930  0.020  1.080
 DI2  C18  C19   aromatic  1.388  0.020  1.388
 DI2  C18  H18   single    0.930  0.020  1.080
 DI2  C19  C20   aromatic  1.394  0.020  1.394
 DI2  C19  H19   single    0.930  0.020  1.080
 DI2  C20  C21   aromatic  1.392  0.020  1.392
 DI2  C21  H21   single    0.930  0.020  1.080
 DI2  N    HN    single    0.860  0.020  1.020
 DI2  N1   HN11  single    0.890  0.020  1.040
 DI2  N1   HN12  single    0.890  0.020  1.040
 DI2  N3   HN3   single    0.860  0.020  1.020
 DI2  O    HO    single    0.850  0.020  0.980
 DI2  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
 DI2  O1    B1   O     119.05  3.000
 DI2  O1    B1   C     122.71  3.000
 DI2  O     B1   C     117.33  3.000
 DI2  H     C    N     108.52  3.000
 DI2  H     C    C2    107.38  3.000
 DI2  N     C    C2    109.53  3.000
 DI2  H     C    B1    110.13  3.000
 DI2  N     C    B1    109.68  3.000
 DI2  C2    C    B1    111.53  3.000
 DI2  H22   C2   H21A  106.28  3.000
 DI2  H22   C2   C3    109.84  3.000
 DI2  H21A  C2   C3    108.61  3.000
 DI2  H22   C2   C     109.98  3.000
 DI2  H21A  C2   C     109.05  3.000
 DI2  C3    C2   C     112.86  3.000
 DI2  H32   C3   H31   106.17  3.000
 DI2  H32   C3   C4    109.39  3.000
 DI2  H31   C3   C4    108.99  3.000
 DI2  H32   C3   C2    109.35  3.000
 DI2  H31   C3   C2    110.14  3.000
 DI2  C4    C3   C2    112.59  3.000
 DI2  H42   C4   H41   106.43  3.000
 DI2  H42   C4   C5    109.18  3.000
 DI2  H41   C4   C5    109.27  3.000
 DI2  H42   C4   C3    109.90  3.000
 DI2  H41   C4   C3    109.24  3.000
 DI2  C5    C4   C3    112.63  3.000
 DI2  H52   C5   H51   106.10  3.000
 DI2  H52   C5   N1    113.50  3.000
 DI2  H51   C5   N1    108.32  3.000
 DI2  H52   C5   C4    108.72  3.000
 DI2  H51   C5   C4    108.98  3.000
 DI2  N1    C5   C4    111.02  3.000
 DI2  H6    C6   N2    109.99  3.000
 DI2  H6    C6   C8    110.59  3.000
 DI2  N2    C6   C8    103.92  3.000
 DI2  H6    C6   C7    110.29  3.000
 DI2  N2    C6   C7    111.33  3.000
 DI2  C8    C6   C7    110.57  3.000
 DI2  H82   C8   H81   107.92  3.000
 DI2  H82   C8   C9    109.78  3.000
 DI2  H81   C8   C9    113.36  3.000
 DI2  H82   C8   C6    110.34  3.000
 DI2  H81   C8   C6    111.58  3.000
 DI2  C9    C8   C6    103.85  3.000
 DI2  H92   C9   H91   108.10  3.000
 DI2  H92   C9   C10   112.32  3.000
 DI2  H91   C9   C10   109.93  3.000
 DI2  H92   C9   C8    112.96  3.000
 DI2  H91   C9   C8    110.63  3.000
 DI2  C10   C9   C8    102.85  3.000
 DI2  H102  C10  H101  108.09  3.000
 DI2  H102  C10  N2    110.74  3.000
 DI2  H101  C10  N2    112.12  3.000
 DI2  H102  C10  C9    111.29  3.000
 DI2  H101  C10  C9    112.09  3.000
 DI2  N2    C10  C9    102.50  3.000
 DI2  H122  C12  H121  106.79  3.000
 DI2  H122  C12  C20   110.60  3.000
 DI2  H121  C12  C20   109.41  3.000
 DI2  H122  C12  C13   110.00  3.000
 DI2  H121  C12  C13   108.22  3.000
 DI2  C20   C12  C13   111.67  3.000
 DI2  H13   C13  N3    104.83  3.000
 DI2  H13   C13  C12   107.49  3.000
 DI2  N3    C13  C12   114.02  3.000
 DI2  H13   C13  C11   108.15  3.000
 DI2  N3    C13  C11   111.14  3.000
 DI2  C12   C13  C11   110.81  3.000
 DI2  H153  C15  H152  107.93  3.000
 DI2  H153  C15  H151  108.84  3.000
 DI2  H152  C15  H151  107.53  3.000
 DI2  H153  C15  C14   113.55  3.000
 DI2  H152  C15  C14   109.00  3.000
 DI2  H151  C15  C14   109.81  3.000
 DI2  H16   C16  C21   119.76  3.000
 DI2  H16   C16  C17   120.05  3.000
 DI2  C21   C16  C17   120.19  3.000
 DI2  H17   C17  C18   120.25  3.000
 DI2  H17   C17  C16   120.21  3.000
 DI2  C18   C17  C16   119.54  3.000
 DI2  H18   C18  C19   119.83  3.000
 DI2  H18   C18  C17   120.13  3.000
 DI2  C19   C18  C17   120.04  3.000
 DI2  H19   C19  C20   119.69  3.000
 DI2  H19   C19  C18   119.40  3.000
 DI2  C20   C19  C18   120.91  3.000
 DI2  C21   C20  C19   118.54  3.000
 DI2  C21   C20  C12   121.22  3.000
 DI2  C19   C20  C12   120.23  3.000
 DI2  H21   C21  C20   119.39  3.000
 DI2  H21   C21  C16   119.84  3.000
 DI2  C20   C21  C16   120.77  3.000
 DI2  HN    N    C7    119.30  3.000
 DI2  HN    N    C     119.00  3.000
 DI2  C7    N    C     120.59  3.000
 DI2  HN12  N1   HN11  105.39  3.000
 DI2  HN12  N1   C5    109.02  3.000
 DI2  HN11  N1   C5    109.48  3.000
 DI2  C11   N2   C10   127.98  3.000
 DI2  C11   N2   C6    119.52  3.000
 DI2  C10   N2   C6    112.24  3.000
 DI2  HN3   N3   C14   117.02  3.000
 DI2  HN3   N3   C13   115.40  3.000
 DI2  C14   N3   C13   127.22  3.000
 DI2  HO    O    B1    113.57  3.000
 DI2  HO1   O1   B1    112.73  3.000
 DI2  O2    C7   N     122.18  3.000
 DI2  O2    C7   C6    121.55  3.000
 DI2  N     C7   C6    116.10  3.000
 DI2  O3    C11  N2    121.40  3.000
 DI2  O3    C11  C13   121.81  3.000
 DI2  N2    C11  C13   116.78  3.000
 DI2  O4    C14  N3    124.35  3.000
 DI2  O4    C14  C15   121.44  3.000
 DI2  N3    C14  C15   114.20  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
 DI2  CONST_01  C19   C18  C17  C16     0.00   0.0  0
 DI2  CONST_02  C19   C20  C21  C16     0.00   0.0  0
 DI2  CONST_03  C20   C21  C16  C17     0.00   0.0  0
 DI2  CONST_04  C20   C19  C18  C17     0.00   0.0  0
 DI2  CONST_05  C21   C16  C17  C18     0.00   0.0  0
 DI2  CONST_06  C21   C20  C19  C18     0.00   0.0  0
 DI2  CONST_07  C18   C19  C20  C12   180.00   0.0  0
 DI2  CONST_08  C16   C21  C20  C12   180.00   0.0  0
 DI2  CONST_09  H18   C18  C17  C16   180.00   0.0  0
 DI2  CONST_10  H21   C21  C16  C17   180.00   0.0  0
 DI2  CONST_11  H19   C19  C18  C17   180.00   0.0  0
 DI2  CONST_12  H16   C16  C17  C18   180.00   0.0  0
 DI2  CONST_13  H17   C17  C18  C19   180.00   0.0  0
 DI2  CONST_14  C13   C11  N2   C6    180.00   0.0  0
 DI2  CONST_15  O3    C11  N2   C6      0.00   0.0  0
 DI2  CONST_16  C13   C11  N2   C10     0.00   0.0  0
 DI2  CONST_17  O3    C11  N2   C10   180.00   0.0  0
 DI2  CONST_18  C6    C7   N    C     180.00   0.0  0
 DI2  CONST_19  HN    N    C7   C6      0.00   0.0  0
 DI2  CONST_20  O2    C7   N    C       0.00   0.0  0
 DI2  CONST_21  C15   C14  N3   C13   180.00   0.0  0
 DI2  CONST_22  O4    C14  N3   C13     0.00   0.0  0
 DI2  CONST_23  HN3   N3   C14  C15     0.00   0.0  0
 DI2  Var_01    C10   C9   C8   C6     36.59  30.0  1
 DI2  Var_02    C9    C10  N2   C6     23.27  30.0  1
 DI2  Var_03    N2    C10  C9   C8    -36.26  30.0  1
 DI2  Var_04    C19   C20  C12  C13    76.47  30.0  2
 DI2  Var_05    C4    C3   C2   C     174.86  30.0  3
 DI2  Var_06    C5    C4   C3   C2   -179.14  30.0  3
 DI2  Var_07    N1    C5   C4   C3   -179.65  30.0  3
 DI2  Var_08    HN11  N1   C5   C4    179.20  30.0  3
 DI2  Var_09    H151  C15  C14  N3    144.29  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
 DI2  chir_01  C    B1  C2   N    positiv
 DI2  chir_02  C6   N2  C7   C8   positiv
 DI2  chir_03  C13  N3  C11  C12  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
 DI2  plan-1  C12  0.020
 DI2  plan-1  C16  0.020
 DI2  plan-1  C17  0.020
 DI2  plan-1  C18  0.020
 DI2  plan-1  C19  0.020
 DI2  plan-1  C20  0.020
 DI2  plan-1  C21  0.020
 DI2  plan-1  H16  0.020
 DI2  plan-1  H17  0.020
 DI2  plan-1  H18  0.020
 DI2  plan-1  H19  0.020
 DI2  plan-1  H21  0.020
 DI2  plan-2  C6   0.020
 DI2  plan-2  C10  0.020
 DI2  plan-2  C13  0.020
 DI2  plan-2  N2   0.020
 DI2  plan-2  C11  0.020
 DI2  plan-2  O3   0.020
 DI2  plan-3  C13  0.020
 DI2  plan-3  C15  0.020
 DI2  plan-3  N3   0.020
 DI2  plan-3  O4   0.020
 DI2  plan-3  HN3  0.020
 DI2  plan-3  C14  0.020
 DI2  plan-4  C    0.020
 DI2  plan-4  C6   0.020
 DI2  plan-4  N    0.020
 DI2  plan-4  HN   0.020
 DI2  plan-4  C7   0.020
 DI2  plan-4  O2   0.020

