Manual

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: QYG7Y

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 OptH
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 -1819596.288067
FMO2-HF: Nuclear repulsion 1748486.369791
FMO2-HF: Total energy -71109.918276
FMO2-MP2: Total energy -71321.99503


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.
-6.853-3.3754.101-3.115-4.463-0.014
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 : 0.029 / q_NPA : 0.015
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].
3A5GLY00.0280.0232.228-5.166-2.9253.741-2.791-3.191-0.014
4A6THR0-0.003-0.0124.4440.9981.153-0.001-0.015-0.1390.000
5A7LEU0-0.0230.0006.948-0.016-0.0160.0000.0000.0000.000
6A8MET00.0270.0099.9340.0960.0960.0000.0000.0000.000
7A9GLN0-0.0140.01112.330-0.004-0.0040.0000.0000.0000.000
8A10TYR0-0.068-0.08114.5290.0460.0460.0000.0000.0000.000
9A11PHE0-0.026-0.03516.8590.0470.0470.0000.0000.0000.000
10A12GLU-1-0.792-0.89020.556-0.243-0.2430.0000.0000.0000.000
11A13TRP00.012-0.01423.2030.0040.0040.0000.0000.0000.000
12A14TYR0-0.063-0.04426.7760.0140.0140.0000.0000.0000.000
13A15MET0-0.0080.04122.7640.0040.0040.0000.0000.0000.000
14A16PRO00.0300.01226.7900.0060.0060.0000.0000.0000.000
15A17ASN00.0180.00128.599-0.016-0.0160.0000.0000.0000.000
16A18ASP-1-0.768-0.87828.419-0.161-0.1610.0000.0000.0000.000
17A19GLY0-0.025-0.01328.8970.0060.0060.0000.0000.0000.000
18A20GLN00.0020.01726.3720.0000.0000.0000.0000.0000.000
19A21HIS0-0.0140.00020.1470.0200.0200.0000.0000.0000.000
20A22TRP00.0450.02420.378-0.025-0.0250.0000.0000.0000.000
21A23LYS10.8510.91220.6960.1490.1490.0000.0000.0000.000
22A24ARG10.8410.90320.6990.1970.1970.0000.0000.0000.000
23A25LEU00.0780.04814.693-0.004-0.0040.0000.0000.0000.000
24A26GLN0-0.034-0.02516.259-0.026-0.0260.0000.0000.0000.000
25A27ASN0-0.068-0.03417.1530.0010.0010.0000.0000.0000.000
26A28ASP-1-0.788-0.85615.010-0.336-0.3360.0000.0000.0000.000
27A29SER0-0.064-0.03512.426-0.034-0.0340.0000.0000.0000.000
28A30ALA0-0.038-0.02410.993-0.068-0.0680.0000.0000.0000.000
29A31TYR00.0730.04410.836-0.030-0.0300.0000.0000.0000.000
30A32LEU0-0.008-0.0109.536-0.039-0.0390.0000.0000.0000.000
31A33ALA00.0120.0046.583-0.187-0.1870.0000.0000.0000.000
32A34GLU-1-0.976-0.9825.995-0.180-0.1800.0000.0000.0000.000
33A35HIS0-0.079-0.0387.6030.1750.1750.0000.0000.0000.000
34A36GLY00.0000.0113.473-0.198-0.0070.017-0.058-0.1500.000
35A37ILE0-0.057-0.0194.039-1.020-0.8650.001-0.050-0.1050.000
36A38THR00.0710.0262.723-0.971-0.2350.343-0.201-0.8780.000
37A39ALA0-0.055-0.0155.5260.3210.3210.0000.0000.0000.000
38A40VAL00.0230.0179.2280.0330.0330.0000.0000.0000.000
39A41TRP0-0.031-0.00712.4140.0170.0170.0000.0000.0000.000
40A42ILE0-0.036-0.02415.7870.0340.0340.0000.0000.0000.000
41A43PRO00.0070.00818.5620.0020.0020.0000.0000.0000.000
42A44PRO0-0.0060.00422.1620.0010.0010.0000.0000.0000.000
43A45ALA00.011-0.00123.4560.0160.0160.0000.0000.0000.000
44A46TYR0-0.056-0.05025.2940.0220.0220.0000.0000.0000.000
45A47LYS10.7540.88728.8440.1490.1490.0000.0000.0000.000
46A48GLY00.0400.03032.294-0.002-0.0020.0000.0000.0000.000
47A49THR0-0.054-0.05433.3410.0120.0120.0000.0000.0000.000
48A50SER00.006-0.00235.4140.0090.0090.0000.0000.0000.000
49A51GLN0-0.001-0.02233.461-0.007-0.0070.0000.0000.0000.000
50A52ALA00.003-0.00332.374-0.009-0.0090.0000.0000.0000.000
51A53ASP-1-0.784-0.86731.940-0.190-0.1900.0000.0000.0000.000
52A54VAL00.0180.01326.580-0.005-0.0050.0000.0000.0000.000
53A55GLY00.0290.02427.180-0.019-0.0190.0000.0000.0000.000
54A56TYR0-0.024-0.03423.8480.0030.0030.0000.0000.0000.000
55A57GLY00.0060.01230.2010.0080.0080.0000.0000.0000.000
56A58ALA0-0.045-0.03031.0940.0070.0070.0000.0000.0000.000
57A59TYR0-0.018-0.00632.7040.0070.0070.0000.0000.0000.000
58A60ASP-1-0.810-0.92633.950-0.145-0.1450.0000.0000.0000.000
59A61LEU00.0240.00729.258-0.004-0.0040.0000.0000.0000.000
60A62TYR00.0060.00729.568-0.010-0.0100.0000.0000.0000.000
61A63ASP-1-0.738-0.86131.661-0.147-0.1470.0000.0000.0000.000
62A64LEU0-0.001-0.00325.844-0.005-0.0050.0000.0000.0000.000
63A65GLY0-0.0070.00328.421-0.005-0.0050.0000.0000.0000.000
64A66GLU-1-0.832-0.91630.946-0.150-0.1500.0000.0000.0000.000
65A67PHE00.0450.01932.9220.0090.0090.0000.0000.0000.000
66A68HIS0-0.024-0.01836.307-0.004-0.0040.0000.0000.0000.000
67A69GLN0-0.001-0.00536.4710.0110.0110.0000.0000.0000.000
68A70LYS10.8360.91637.2450.1200.1200.0000.0000.0000.000
69A71GLY00.0280.02238.983-0.002-0.0020.0000.0000.0000.000
70A72THR0-0.0270.00434.7390.0040.0040.0000.0000.0000.000
71A73VAL00.0270.02633.838-0.001-0.0010.0000.0000.0000.000
72A74ARG10.8370.94530.6640.1460.1460.0000.0000.0000.000
73A75THR00.0550.02927.7480.0100.0100.0000.0000.0000.000
74A76LYS10.9270.96527.5260.2120.2120.0000.0000.0000.000
75A77TYR0-0.045-0.08424.2940.0060.0060.0000.0000.0000.000
76A78GLY00.0590.03525.849-0.002-0.0020.0000.0000.0000.000
77A79THR0-0.026-0.01127.739-0.001-0.0010.0000.0000.0000.000
78A80LYS10.9150.96826.5310.1620.1620.0000.0000.0000.000
79A81GLY00.0400.02225.526-0.012-0.0120.0000.0000.0000.000
80A82GLU-1-0.869-0.95324.733-0.178-0.1780.0000.0000.0000.000
81A83LEU00.0200.01620.745-0.016-0.0160.0000.0000.0000.000
82A84GLN0-0.015-0.02420.825-0.013-0.0130.0000.0000.0000.000
83A85SER0-0.042-0.01420.581-0.006-0.0060.0000.0000.0000.000
84A86ALA00.0040.00018.521-0.006-0.0060.0000.0000.0000.000
85A87ILE00.0160.00316.025-0.031-0.0310.0000.0000.0000.000
86A88LYS10.9730.99615.5410.1320.1320.0000.0000.0000.000
87A89SER0-0.020-0.00515.8010.0120.0120.0000.0000.0000.000
88A90LEU00.0080.00212.130-0.002-0.0020.0000.0000.0000.000
89A91HIS00.003-0.00211.149-0.009-0.0090.0000.0000.0000.000
90A92SER0-0.124-0.04911.6190.0160.0160.0000.0000.0000.000
91A93ARG10.9260.9489.4770.3580.3580.0000.0000.0000.000
92A94ASP-1-0.902-0.9336.338-0.534-0.5340.0000.0000.0000.000
93A95ILE0-0.074-0.0166.538-0.337-0.3370.0000.0000.0000.000
94A96ASN0-0.013-0.0298.3590.3510.3510.0000.0000.0000.000
95A97VAL0-0.020-0.02110.279-0.007-0.0070.0000.0000.0000.000
96A98TYR0-0.029-0.01010.6430.0130.0130.0000.0000.0000.000
97A99GLY00.022-0.00115.7700.0230.0230.0000.0000.0000.000
98A100ASP-1-0.768-0.87719.487-0.379-0.3790.0000.0000.0000.000
99A101VAL0-0.0090.02021.9940.0280.0280.0000.0000.0000.000
100A102VAL0-0.012-0.01124.8110.0020.0020.0000.0000.0000.000
101A103ILE0-0.024-0.02928.1130.0150.0150.0000.0000.0000.000
102A104ASN0-0.0100.01430.6500.0090.0090.0000.0000.0000.000
103A105HIS0-0.028-0.01032.4160.0110.0110.0000.0000.0000.000
104A106LYS10.9110.97734.1480.1510.1510.0000.0000.0000.000
105A107GLY00.0320.01836.2710.0070.0070.0000.0000.0000.000
106A108GLY0-0.023-0.03337.848-0.002-0.0020.0000.0000.0000.000
107A109ALA00.0270.02240.2460.0010.0010.0000.0000.0000.000
108A110ASP-1-0.812-0.90442.533-0.110-0.1100.0000.0000.0000.000
109A111ALA0-0.023-0.01444.6620.0050.0050.0000.0000.0000.000
110A112THR0-0.040-0.02147.019-0.002-0.0020.0000.0000.0000.000
111A113GLU-1-0.769-0.86647.716-0.093-0.0930.0000.0000.0000.000
112A114ASP-1-0.847-0.90950.939-0.074-0.0740.0000.0000.0000.000
113A115VAL0-0.028-0.01049.1290.0000.0000.0000.0000.0000.000
114A116THR00.0180.01252.4730.0020.0020.0000.0000.0000.000
115A117ALA0-0.028-0.00950.884-0.003-0.0030.0000.0000.0000.000
116A118VAL00.0280.03251.3400.0040.0040.0000.0000.0000.000
117A119GLU-1-0.919-0.97251.145-0.082-0.0820.0000.0000.0000.000
118A120VAL0-0.025-0.02146.7130.0010.0010.0000.0000.0000.000
119A121ASP-1-0.837-0.94149.251-0.087-0.0870.0000.0000.0000.000
120A122PRO0-0.049-0.02246.440-0.004-0.0040.0000.0000.0000.000
121A123ALA0-0.043-0.00645.073-0.005-0.0050.0000.0000.0000.000
122A124ASP-1-0.864-0.93344.924-0.102-0.1020.0000.0000.0000.000
123A125ARG10.9170.96141.8610.1280.1280.0000.0000.0000.000
124A126ASN0-0.044-0.04043.838-0.003-0.0030.0000.0000.0000.000
125A127ARG10.8730.95247.3470.0820.0820.0000.0000.0000.000
126A128VAL00.0190.01750.729-0.001-0.0010.0000.0000.0000.000
127A129ILE0-0.074-0.03852.5090.0030.0030.0000.0000.0000.000
128A130SER00.0110.00655.1210.0010.0010.0000.0000.0000.000
129A131GLY00.0320.02456.375-0.001-0.0010.0000.0000.0000.000
130A132GLU-1-0.907-0.98155.713-0.073-0.0730.0000.0000.0000.000
131A133HIS0-0.073-0.03855.1560.0020.0020.0000.0000.0000.000
132A134LEU00.0290.01855.674-0.002-0.0020.0000.0000.0000.000
133A135ILE0-0.0270.02149.9900.0010.0010.0000.0000.0000.000
134A136LYS10.8700.92652.4250.0720.0720.0000.0000.0000.000
135A137ALA00.0440.02947.078-0.002-0.0020.0000.0000.0000.000
136A138TRP0-0.054-0.02844.5100.0010.0010.0000.0000.0000.000
137A139THR00.005-0.03643.818-0.005-0.0050.0000.0000.0000.000
138A140HIS00.0190.02543.976-0.005-0.0050.0000.0000.0000.000
139A141PHE0-0.023-0.00438.431-0.002-0.0020.0000.0000.0000.000
140A142HIS0-0.028-0.04042.3080.0010.0010.0000.0000.0000.000
141A143PHE0-0.047-0.00737.8120.0000.0000.0000.0000.0000.000
142A144PRO00.0070.01240.9150.0010.0010.0000.0000.0000.000
143A145GLY00.005-0.00140.5420.0030.0030.0000.0000.0000.000
144A146ARG10.7950.89735.0080.1390.1390.0000.0000.0000.000
145A147GLY00.0180.00639.1670.0030.0030.0000.0000.0000.000
146A148SER00.003-0.02840.130-0.003-0.0030.0000.0000.0000.000
147A149THR0-0.0150.01435.5200.0010.0010.0000.0000.0000.000
148A150TYR0-0.119-0.07432.266-0.007-0.0070.0000.0000.0000.000
149A151SER0-0.010-0.01234.747-0.002-0.0020.0000.0000.0000.000
150A152ASP-1-0.890-0.93936.896-0.105-0.1050.0000.0000.0000.000
151A153PHE00.0050.01438.0110.0050.0050.0000.0000.0000.000
152A154LYS10.8300.92139.8040.1040.1040.0000.0000.0000.000
153A155TRP0-0.016-0.01135.7640.0000.0000.0000.0000.0000.000
154A156HIS10.8830.92542.1330.1000.1000.0000.0000.0000.000
155A157TRP00.0420.00944.259-0.005-0.0050.0000.0000.0000.000
156A158TYR00.0150.00945.467-0.003-0.0030.0000.0000.0000.000
157A159HIS0-0.055-0.02040.518-0.002-0.0020.0000.0000.0000.000
158A160PHE0-0.066-0.03738.534-0.008-0.0080.0000.0000.0000.000
159A161ASP-1-0.790-0.89241.308-0.123-0.1230.0000.0000.0000.000
160A162GLY0-0.038-0.03942.9570.0060.0060.0000.0000.0000.000
161A163THR0-0.090-0.03442.953-0.007-0.0070.0000.0000.0000.000
162A164ASP-1-0.788-0.90743.044-0.118-0.1180.0000.0000.0000.000
163A165TRP0-0.051-0.04345.5000.0020.0020.0000.0000.0000.000
164A166ASP-1-0.728-0.80947.734-0.079-0.0790.0000.0000.0000.000
165A167GLU-1-0.808-0.92849.600-0.086-0.0860.0000.0000.0000.000
166A168SER0-0.141-0.09551.6010.0030.0030.0000.0000.0000.000
167A169ARG10.8310.89255.3590.0730.0730.0000.0000.0000.000
168A170LYS10.8770.95451.2900.0820.0820.0000.0000.0000.000
169A171LEU00.0100.01452.4200.0000.0000.0000.0000.0000.000
170A172ASN00.0150.01446.747-0.005-0.0050.0000.0000.0000.000
171A173ARG10.8680.93648.8170.0840.0840.0000.0000.0000.000
172A174ILE00.0170.02644.807-0.003-0.0030.0000.0000.0000.000
173A175TYR00.022-0.00147.1360.0030.0030.0000.0000.0000.000
174A176LYS10.9190.96943.0150.1120.1120.0000.0000.0000.000
175A177PHE0-0.002-0.00544.9930.0040.0040.0000.0000.0000.000
176A178GLN00.0540.01548.958-0.004-0.0040.0000.0000.0000.000
177A179GLY00.006-0.00451.3910.0000.0000.0000.0000.0000.000
178A180LYS10.8780.94048.2850.0870.0870.0000.0000.0000.000
179A181ALA00.0310.03544.411-0.001-0.0010.0000.0000.0000.000