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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 49VRN

Calculation Name: 1BPL-A-Xray372

Preferred Name: Alpha-amylase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1BPL

Chain ID: A

ChEMBL ID: CHEMBL4215

UniProt ID: P06278

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1823606.842217
FMO2-HF: Nuclear repulsion 1752495.730288
FMO2-HF: Total energy -71111.111929
FMO2-MP2: Total energy -71323.149457


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-4.0390.0970.59-1.816-2.91-0.003
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.018
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A5GLY00.0190.0202.994-2.8490.1240.231-1.542-1.662-0.002
4A6THR0-0.025-0.0114.6710.7950.943-0.001-0.010-0.1370.000
5A7LEU0-0.037-0.0126.701-0.021-0.0210.0000.0000.0000.000
6A8MET00.0190.01510.0680.0890.0890.0000.0000.0000.000
7A9GLN00.0070.01212.872-0.005-0.0050.0000.0000.0000.000
8A10TYR0-0.058-0.06214.5540.0420.0420.0000.0000.0000.000
9A11PHE0-0.034-0.03817.0410.0430.0430.0000.0000.0000.000
10A12GLU-1-0.747-0.87720.802-0.188-0.1880.0000.0000.0000.000
11A13TRP0-0.011-0.00323.6950.0020.0020.0000.0000.0000.000
12A14TYR0-0.039-0.05027.3210.0120.0120.0000.0000.0000.000
13A15MET0-0.0400.02222.7090.0060.0060.0000.0000.0000.000
14A16PRO00.0270.01627.0290.0040.0040.0000.0000.0000.000
15A17ASN00.0400.00628.831-0.013-0.0130.0000.0000.0000.000
16A18ASP-1-0.796-0.87427.977-0.123-0.1230.0000.0000.0000.000
17A19GLY0-0.0120.00228.6390.0070.0070.0000.0000.0000.000
18A20GLN00.002-0.01126.422-0.001-0.0010.0000.0000.0000.000
19A21HIS0-0.016-0.01420.1780.0180.0180.0000.0000.0000.000
20A22TRP00.0210.01520.562-0.021-0.0210.0000.0000.0000.000
21A23LYS10.8600.92020.5590.1120.1120.0000.0000.0000.000
22A24ARG10.8290.89720.5120.1510.1510.0000.0000.0000.000
23A25LEU00.0570.03614.4750.0030.0030.0000.0000.0000.000
24A26GLN0-0.059-0.03415.926-0.020-0.0200.0000.0000.0000.000
25A27ASN0-0.043-0.00616.619-0.001-0.0010.0000.0000.0000.000
26A28ASP-1-0.781-0.87515.311-0.258-0.2580.0000.0000.0000.000
27A29SER0-0.026-0.01612.255-0.013-0.0130.0000.0000.0000.000
28A30ALA0-0.015-0.00810.791-0.047-0.0470.0000.0000.0000.000
29A31TYR00.0220.03310.793-0.007-0.0070.0000.0000.0000.000
30A32LEU00.005-0.0129.708-0.030-0.0300.0000.0000.0000.000
31A33ALA00.0120.0086.585-0.151-0.1510.0000.0000.0000.000
32A34GLU-1-0.943-0.9715.980-0.062-0.0620.0000.0000.0000.000
33A35HIS0-0.086-0.0427.2010.1390.1390.0000.0000.0000.000
34A36GLY00.0020.0123.775-0.209-0.0520.007-0.046-0.1180.000
35A37ILE0-0.042-0.0264.397-0.770-0.688-0.001-0.011-0.0700.000
36A38THR00.0180.0072.845-0.887-0.1110.354-0.207-0.923-0.001
37A39ALA0-0.006-0.0015.4110.2460.2460.0000.0000.0000.000
38A40VAL00.0150.0079.2650.0450.0450.0000.0000.0000.000
39A41TRP0-0.020-0.00212.6340.0170.0170.0000.0000.0000.000
40A42ILE0-0.015-0.01016.0290.0320.0320.0000.0000.0000.000
41A43PRO00.0090.01518.6470.0010.0010.0000.0000.0000.000
42A44PRO0-0.027-0.01522.340-0.001-0.0010.0000.0000.0000.000
43A45ALA00.0110.00323.5070.0160.0160.0000.0000.0000.000
44A46TYR0-0.051-0.03725.3360.0190.0190.0000.0000.0000.000
45A47LYS10.7560.88628.9790.1160.1160.0000.0000.0000.000
46A48GLY00.0220.02232.417-0.001-0.0010.0000.0000.0000.000
47A49THR0-0.040-0.06633.4310.0090.0090.0000.0000.0000.000
48A50SER0-0.005-0.00335.6270.0070.0070.0000.0000.0000.000
49A51GLN00.003-0.01433.530-0.006-0.0060.0000.0000.0000.000
50A52ALA0-0.004-0.00232.572-0.006-0.0060.0000.0000.0000.000
51A53ASP-1-0.794-0.86032.033-0.150-0.1500.0000.0000.0000.000
52A54VAL00.0110.00626.984-0.004-0.0040.0000.0000.0000.000
53A55GLY00.0780.04427.234-0.016-0.0160.0000.0000.0000.000
54A56TYR0-0.051-0.06523.9470.0090.0090.0000.0000.0000.000
55A57GLY00.0100.02230.2390.0050.0050.0000.0000.0000.000
56A58ALA0-0.017-0.01031.2560.0070.0070.0000.0000.0000.000
57A59TYR0-0.002-0.01732.7080.0050.0050.0000.0000.0000.000
58A60ASP-1-0.784-0.89633.947-0.117-0.1170.0000.0000.0000.000
59A61LEU00.0110.00329.154-0.002-0.0020.0000.0000.0000.000
60A62TYR0-0.013-0.00129.528-0.010-0.0100.0000.0000.0000.000
61A63ASP-1-0.715-0.84031.776-0.113-0.1130.0000.0000.0000.000
62A64LEU00.0070.00225.482-0.003-0.0030.0000.0000.0000.000
63A65GLY0-0.0080.00727.959-0.004-0.0040.0000.0000.0000.000
64A66GLU-1-0.805-0.88630.418-0.122-0.1220.0000.0000.0000.000
65A67PHE00.0330.01432.5890.0080.0080.0000.0000.0000.000
66A68HIS0-0.038-0.02436.233-0.003-0.0030.0000.0000.0000.000
67A69GLN0-0.019-0.03336.2480.0080.0080.0000.0000.0000.000
68A70LYS10.8070.90537.6070.0930.0930.0000.0000.0000.000
69A71GLY00.0460.03038.980-0.002-0.0020.0000.0000.0000.000
70A72THR0-0.059-0.03934.4330.0040.0040.0000.0000.0000.000
71A73VAL00.0250.03133.655-0.002-0.0020.0000.0000.0000.000
72A74ARG10.8400.92030.5020.1090.1090.0000.0000.0000.000
73A75THR00.0610.03727.8970.0070.0070.0000.0000.0000.000
74A76LYS10.9030.97327.8760.1650.1650.0000.0000.0000.000
75A77TYR0-0.022-0.04124.1020.0050.0050.0000.0000.0000.000
76A78GLY00.0380.02225.528-0.001-0.0010.0000.0000.0000.000
77A79THR0-0.050-0.04127.359-0.001-0.0010.0000.0000.0000.000
78A80LYS10.8610.93026.1890.1260.1260.0000.0000.0000.000
79A81GLY00.0400.02025.113-0.010-0.0100.0000.0000.0000.000
80A82GLU-1-0.813-0.89324.293-0.133-0.1330.0000.0000.0000.000
81A83LEU00.0380.02620.119-0.011-0.0110.0000.0000.0000.000
82A84GLN00.004-0.00920.312-0.015-0.0150.0000.0000.0000.000
83A85SER0-0.016-0.01120.252-0.003-0.0030.0000.0000.0000.000
84A86ALA00.0050.00618.067-0.001-0.0010.0000.0000.0000.000
85A87ILE00.0090.00516.037-0.022-0.0220.0000.0000.0000.000
86A88LYS10.9540.98315.2860.0870.0870.0000.0000.0000.000
87A89SER0-0.023-0.02315.5470.0130.0130.0000.0000.0000.000
88A90LEU0-0.0070.00811.8780.0110.0110.0000.0000.0000.000
89A91HIS0-0.012-0.02510.750-0.007-0.0070.0000.0000.0000.000
90A92SER0-0.141-0.06911.5680.0260.0260.0000.0000.0000.000
91A93ARG10.8870.9348.7210.2790.2790.0000.0000.0000.000
92A94ASP-1-0.891-0.9356.101-0.433-0.4330.0000.0000.0000.000
93A95ILE0-0.063-0.0066.786-0.262-0.2620.0000.0000.0000.000
94A96ASN0-0.028-0.0207.1520.3470.3470.0000.0000.0000.000
95A97VAL0-0.006-0.02010.2580.0110.0110.0000.0000.0000.000
96A98TYR0-0.0020.00110.3590.0290.0290.0000.0000.0000.000
97A99GLY00.0190.00416.0070.0170.0170.0000.0000.0000.000
98A100ASP-1-0.763-0.86719.729-0.296-0.2960.0000.0000.0000.000
99A101VAL0-0.0110.00822.3060.0180.0180.0000.0000.0000.000
100A102VAL00.001-0.00124.9760.0060.0060.0000.0000.0000.000
101A103ILE0-0.013-0.01728.1340.0130.0130.0000.0000.0000.000
102A104ASN0-0.056-0.02130.6100.0070.0070.0000.0000.0000.000
103A105HIS0-0.0040.00632.1150.0090.0090.0000.0000.0000.000
104A106LYS10.8310.91034.1600.1250.1250.0000.0000.0000.000
105A107GLY00.0380.03036.4630.0060.0060.0000.0000.0000.000
106A108GLY00.001-0.01138.093-0.001-0.0010.0000.0000.0000.000
107A109ALA00.0210.01740.3780.0000.0000.0000.0000.0000.000
108A110ASP-1-0.809-0.89242.356-0.090-0.0900.0000.0000.0000.000
109A111ALA0-0.022-0.01144.4940.0040.0040.0000.0000.0000.000
110A112THR0-0.011-0.00146.937-0.002-0.0020.0000.0000.0000.000
111A113GLU-1-0.795-0.86447.456-0.076-0.0760.0000.0000.0000.000
112A114ASP-1-0.836-0.90250.799-0.059-0.0590.0000.0000.0000.000
113A115VAL0-0.023-0.01049.174-0.001-0.0010.0000.0000.0000.000
114A116THR00.0140.00952.5800.0010.0010.0000.0000.0000.000
115A117ALA0-0.003-0.00251.202-0.003-0.0030.0000.0000.0000.000
116A118VAL00.0170.01351.5290.0030.0030.0000.0000.0000.000
117A119GLU-1-0.835-0.90951.122-0.069-0.0690.0000.0000.0000.000
118A120VAL0-0.033-0.01846.8000.0020.0020.0000.0000.0000.000
119A121ASP-1-0.810-0.89949.358-0.075-0.0750.0000.0000.0000.000
120A122PRO0-0.028-0.01946.446-0.003-0.0030.0000.0000.0000.000
121A123ALA0-0.044-0.01744.943-0.005-0.0050.0000.0000.0000.000
122A124ASP-1-0.831-0.91744.877-0.089-0.0890.0000.0000.0000.000
123A125ARG10.8420.88841.9810.1050.1050.0000.0000.0000.000
124A126ASN0-0.064-0.04343.807-0.003-0.0030.0000.0000.0000.000
125A127ARG10.8600.92747.2660.0700.0700.0000.0000.0000.000
126A128VAL00.0070.00450.7020.0000.0000.0000.0000.0000.000
127A129ILE0-0.061-0.03052.5910.0020.0020.0000.0000.0000.000
128A130SER0-0.019-0.00755.1470.0010.0010.0000.0000.0000.000
129A131GLY00.0300.01856.8370.0000.0000.0000.0000.0000.000
130A132GLU-1-0.846-0.92255.839-0.064-0.0640.0000.0000.0000.000
131A133HIS0-0.094-0.04255.2480.0020.0020.0000.0000.0000.000
132A134LEU00.0200.01655.928-0.002-0.0020.0000.0000.0000.000
133A135ILE00.0020.02050.1720.0010.0010.0000.0000.0000.000
134A136LYS10.8360.89852.2970.0590.0590.0000.0000.0000.000
135A137ALA00.0380.02847.158-0.001-0.0010.0000.0000.0000.000
136A138TRP0-0.035-0.03844.4170.0010.0010.0000.0000.0000.000
137A139THR00.009-0.02443.599-0.004-0.0040.0000.0000.0000.000
138A140HIS00.0340.04043.887-0.005-0.0050.0000.0000.0000.000
139A141PHE0-0.031-0.01538.512-0.002-0.0020.0000.0000.0000.000
140A142HIS0-0.026-0.04242.0970.0010.0010.0000.0000.0000.000
141A143PHE0-0.0210.00837.3180.0010.0010.0000.0000.0000.000
142A144PRO00.0140.00540.8110.0010.0010.0000.0000.0000.000
143A145GLY0-0.0010.00840.6020.0040.0040.0000.0000.0000.000
144A146ARG10.7880.87334.7790.1100.1100.0000.0000.0000.000
145A147GLY00.0230.01938.7760.0020.0020.0000.0000.0000.000
146A148SER0-0.013-0.02639.950-0.002-0.0020.0000.0000.0000.000
147A149THR0-0.0070.00735.2820.0010.0010.0000.0000.0000.000
148A150TYR0-0.100-0.07631.884-0.005-0.0050.0000.0000.0000.000
149A151SER00.0020.00834.296-0.004-0.0040.0000.0000.0000.000
150A152ASP-1-0.862-0.92836.620-0.088-0.0880.0000.0000.0000.000
151A153PHE0-0.0080.00537.9630.0040.0040.0000.0000.0000.000
152A154LYS10.7970.90239.9520.0860.0860.0000.0000.0000.000
153A155TRP00.001-0.00235.2500.0010.0010.0000.0000.0000.000
154A156HIS10.8780.91441.9970.0830.0830.0000.0000.0000.000
155A157TRP00.0550.01644.130-0.005-0.0050.0000.0000.0000.000
156A158TYR00.0110.01245.281-0.003-0.0030.0000.0000.0000.000
157A159HIS0-0.042-0.00440.632-0.001-0.0010.0000.0000.0000.000
158A160PHE0-0.040-0.01538.381-0.007-0.0070.0000.0000.0000.000
159A161ASP-1-0.761-0.86741.359-0.099-0.0990.0000.0000.0000.000
160A162GLY00.0450.00743.0480.0050.0050.0000.0000.0000.000
161A163THR0-0.080-0.03043.339-0.005-0.0050.0000.0000.0000.000
162A164ASP-1-0.760-0.85142.979-0.099-0.0990.0000.0000.0000.000
163A165TRP0-0.051-0.04945.2670.0020.0020.0000.0000.0000.000
164A166ASP-1-0.711-0.80247.744-0.065-0.0650.0000.0000.0000.000
165A167GLU-1-0.803-0.87849.622-0.069-0.0690.0000.0000.0000.000
166A168SER0-0.123-0.09251.7730.0030.0030.0000.0000.0000.000
167A169ARG10.8310.88355.0180.0610.0610.0000.0000.0000.000
168A170LYS10.8490.91852.2070.0640.0640.0000.0000.0000.000
169A171LEU00.0120.02552.5220.0000.0000.0000.0000.0000.000
170A172ASN0-0.016-0.00945.423-0.002-0.0020.0000.0000.0000.000
171A173ARG10.8820.93848.6010.0690.0690.0000.0000.0000.000
172A174ILE0-0.0100.01045.043-0.002-0.0020.0000.0000.0000.000
173A175TYR0-0.018-0.02547.5730.0020.0020.0000.0000.0000.000
174A176LYS10.8530.91743.2130.0950.0950.0000.0000.0000.000
175A177PHE0-0.033-0.02744.3550.0040.0040.0000.0000.0000.000
176A178GLN00.001-0.01148.839-0.004-0.0040.0000.0000.0000.000
177A179GLY0-0.011-0.01750.965-0.001-0.0010.0000.0000.0000.000
178A180LYS10.8820.94647.9510.0750.0750.0000.0000.0000.000
179A181ALA0-0.028-0.01244.821-0.002-0.0020.0000.0000.0000.000