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: K9L73

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 OptHSide
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 -1819342.466871
FMO2-HF: Nuclear repulsion 1748231.715565
FMO2-HF: Total energy -71110.751307
FMO2-MP2: Total energy -71322.806352


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.
-6.154-1.7671.206-2.379-3.214-0.008
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 : 0.017 / q_NPA : 0.012
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].
3A5GLY00.0240.0222.521-4.846-1.3681.127-2.201-2.404-0.008
4A6THR0-0.003-0.0084.7210.8080.927-0.001-0.009-0.1080.000
5A7LEU0-0.029-0.0057.147-0.015-0.0150.0000.0000.0000.000
6A8MET00.0190.00710.4170.0870.0870.0000.0000.0000.000
7A9GLN0-0.0100.01313.004-0.001-0.0010.0000.0000.0000.000
8A10TYR0-0.061-0.07114.8880.0450.0450.0000.0000.0000.000
9A11PHE0-0.007-0.02817.3900.0420.0420.0000.0000.0000.000
10A12GLU-1-0.788-0.89021.109-0.217-0.2170.0000.0000.0000.000
11A13TRP00.006-0.00723.8170.0030.0030.0000.0000.0000.000
12A14TYR0-0.071-0.05427.3990.0130.0130.0000.0000.0000.000
13A15MET0-0.0140.04023.0510.0040.0040.0000.0000.0000.000
14A16PRO00.0210.00527.1010.0060.0060.0000.0000.0000.000
15A17ASN00.0280.00129.000-0.014-0.0140.0000.0000.0000.000
16A18ASP-1-0.797-0.87928.587-0.145-0.1450.0000.0000.0000.000
17A19GLY0-0.025-0.01029.1730.0060.0060.0000.0000.0000.000
18A20GLN00.0070.00026.552-0.003-0.0030.0000.0000.0000.000
19A21HIS0-0.008-0.00820.5260.0180.0180.0000.0000.0000.000
20A22TRP00.0220.01920.870-0.023-0.0230.0000.0000.0000.000
21A23LYS10.8500.92220.8270.1360.1360.0000.0000.0000.000
22A24ARG10.8540.90220.9530.1750.1750.0000.0000.0000.000
23A25LEU00.0670.03914.886-0.004-0.0040.0000.0000.0000.000
24A26GLN0-0.071-0.03416.373-0.022-0.0220.0000.0000.0000.000
25A27ASN0-0.076-0.05217.106-0.001-0.0010.0000.0000.0000.000
26A28ASP-1-0.786-0.86215.602-0.320-0.3200.0000.0000.0000.000
27A29SER0-0.028-0.00512.473-0.027-0.0270.0000.0000.0000.000
28A30ALA0-0.021-0.01510.942-0.064-0.0640.0000.0000.0000.000
29A31TYR00.0380.04010.738-0.025-0.0250.0000.0000.0000.000
30A32LEU00.0250.0029.816-0.036-0.0360.0000.0000.0000.000
31A33ALA00.0120.0036.559-0.158-0.1580.0000.0000.0000.000
32A34GLU-1-0.961-0.9795.899-0.173-0.1730.0000.0000.0000.000
33A35HIS0-0.092-0.0487.4820.1600.1600.0000.0000.0000.000
34A36GLY0-0.0010.0103.817-0.147-0.0140.004-0.035-0.1020.000
35A37ILE0-0.065-0.0244.666-0.686-0.640-0.001-0.006-0.0390.000
36A38THR00.0710.0263.229-0.762-0.1510.077-0.128-0.5610.000
37A39ALA0-0.051-0.0165.9140.2440.2440.0000.0000.0000.000
38A40VAL00.0290.0199.6980.0390.0390.0000.0000.0000.000
39A41TRP0-0.029-0.00312.8810.0130.0130.0000.0000.0000.000
40A42ILE0-0.027-0.02116.3070.0310.0310.0000.0000.0000.000
41A43PRO00.0070.01219.0040.0020.0020.0000.0000.0000.000
42A44PRO0-0.018-0.00622.6470.0000.0000.0000.0000.0000.000
43A45ALA00.0180.00223.8030.0150.0150.0000.0000.0000.000
44A46TYR0-0.065-0.05225.6900.0210.0210.0000.0000.0000.000
45A47LYS10.7500.88129.2230.1340.1340.0000.0000.0000.000
46A48GLY00.0280.02432.651-0.001-0.0010.0000.0000.0000.000
47A49THR0-0.053-0.06533.7710.0100.0100.0000.0000.0000.000
48A50SER00.006-0.00235.8550.0080.0080.0000.0000.0000.000
49A51GLN0-0.004-0.01333.693-0.008-0.0080.0000.0000.0000.000
50A52ALA00.007-0.00432.775-0.008-0.0080.0000.0000.0000.000
51A53ASP-1-0.775-0.85032.485-0.170-0.1700.0000.0000.0000.000
52A54VAL00.0070.00527.335-0.005-0.0050.0000.0000.0000.000
53A55GLY00.0560.02827.687-0.017-0.0170.0000.0000.0000.000
54A56TYR0-0.035-0.05024.3560.0040.0040.0000.0000.0000.000
55A57GLY0-0.0020.01430.7570.0070.0070.0000.0000.0000.000
56A58ALA0-0.044-0.02831.5040.0060.0060.0000.0000.0000.000
57A59TYR0-0.005-0.01733.1620.0070.0070.0000.0000.0000.000
58A60ASP-1-0.805-0.90834.359-0.133-0.1330.0000.0000.0000.000
59A61LEU00.0270.01229.640-0.003-0.0030.0000.0000.0000.000
60A62TYR00.0030.00829.908-0.012-0.0120.0000.0000.0000.000
61A63ASP-1-0.742-0.84231.972-0.133-0.1330.0000.0000.0000.000
62A64LEU00.0060.00425.866-0.004-0.0040.0000.0000.0000.000
63A65GLY0-0.0030.00328.712-0.005-0.0050.0000.0000.0000.000
64A66GLU-1-0.812-0.89131.170-0.140-0.1400.0000.0000.0000.000
65A67PHE00.0430.02333.1750.0090.0090.0000.0000.0000.000
66A68HIS0-0.027-0.01936.583-0.003-0.0030.0000.0000.0000.000
67A69GLN0-0.027-0.03536.6270.0100.0100.0000.0000.0000.000
68A70LYS10.8370.91637.6930.1070.1070.0000.0000.0000.000
69A71GLY00.0330.02539.335-0.002-0.0020.0000.0000.0000.000
70A72THR0-0.035-0.01334.9390.0040.0040.0000.0000.0000.000
71A73VAL00.0060.01334.237-0.001-0.0010.0000.0000.0000.000
72A74ARG10.8550.94430.9380.1300.1300.0000.0000.0000.000
73A75THR00.0740.03428.0080.0090.0090.0000.0000.0000.000
74A76LYS10.9180.97728.3740.1910.1910.0000.0000.0000.000
75A77TYR0-0.042-0.06524.6610.0050.0050.0000.0000.0000.000
76A78GLY00.0510.02926.105-0.002-0.0020.0000.0000.0000.000
77A79THR0-0.034-0.02127.955-0.001-0.0010.0000.0000.0000.000
78A80LYS10.8790.93826.7920.1440.1440.0000.0000.0000.000
79A81GLY00.0440.02525.726-0.011-0.0110.0000.0000.0000.000
80A82GLU-1-0.827-0.91724.831-0.162-0.1620.0000.0000.0000.000
81A83LEU00.0310.02320.850-0.014-0.0140.0000.0000.0000.000
82A84GLN0-0.002-0.01620.965-0.015-0.0150.0000.0000.0000.000
83A85SER0-0.038-0.01820.693-0.005-0.0050.0000.0000.0000.000
84A86ALA00.0110.00018.669-0.006-0.0060.0000.0000.0000.000
85A87ILE00.0140.00216.386-0.029-0.0290.0000.0000.0000.000
86A88LYS10.9680.99715.6510.1220.1220.0000.0000.0000.000
87A89SER0-0.023-0.00915.7890.0100.0100.0000.0000.0000.000
88A90LEU00.0140.01212.123-0.003-0.0030.0000.0000.0000.000
89A91HIS0-0.018-0.01411.203-0.014-0.0140.0000.0000.0000.000
90A92SER0-0.111-0.05011.5260.0100.0100.0000.0000.0000.000
91A93ARG10.8980.9329.1700.3450.3450.0000.0000.0000.000
92A94ASP-1-0.911-0.9396.412-0.556-0.5560.0000.0000.0000.000
93A95ILE0-0.056-0.0126.620-0.328-0.3280.0000.0000.0000.000
94A96ASN0-0.058-0.0467.6640.3850.3850.0000.0000.0000.000
95A97VAL00.009-0.00810.569-0.001-0.0010.0000.0000.0000.000
96A98TYR0-0.023-0.01011.0570.0050.0050.0000.0000.0000.000
97A99GLY00.0240.00316.1950.0220.0220.0000.0000.0000.000
98A100ASP-1-0.770-0.87119.901-0.335-0.3350.0000.0000.0000.000
99A101VAL0-0.0020.01822.4650.0250.0250.0000.0000.0000.000
100A102VAL0-0.010-0.00425.2700.0030.0030.0000.0000.0000.000
101A103ILE0-0.016-0.02528.6730.0130.0130.0000.0000.0000.000
102A104ASN0-0.0390.00231.1170.0070.0070.0000.0000.0000.000
103A105HIS0-0.004-0.00332.7930.0110.0110.0000.0000.0000.000
104A106LYS10.8590.93934.6220.1380.1380.0000.0000.0000.000
105A107GLY00.0430.02436.7410.0060.0060.0000.0000.0000.000
106A108GLY0-0.002-0.02038.300-0.002-0.0020.0000.0000.0000.000
107A109ALA0-0.0050.01240.7100.0010.0010.0000.0000.0000.000
108A110ASP-1-0.797-0.89042.955-0.101-0.1010.0000.0000.0000.000
109A111ALA0-0.013-0.00745.0730.0040.0040.0000.0000.0000.000
110A112THR00.000-0.00347.458-0.003-0.0030.0000.0000.0000.000
111A113GLU-1-0.805-0.86447.923-0.085-0.0850.0000.0000.0000.000
112A114ASP-1-0.861-0.90451.383-0.066-0.0660.0000.0000.0000.000
113A115VAL0-0.014-0.00249.5000.0000.0000.0000.0000.0000.000
114A116THR00.0210.01152.9410.0020.0020.0000.0000.0000.000
115A117ALA0-0.0150.00251.296-0.003-0.0030.0000.0000.0000.000
116A118VAL00.0300.03051.5860.0040.0040.0000.0000.0000.000
117A119GLU-1-0.846-0.93451.417-0.075-0.0750.0000.0000.0000.000
118A120VAL0-0.020-0.01846.9040.0010.0010.0000.0000.0000.000
119A121ASP-1-0.811-0.90649.639-0.079-0.0790.0000.0000.0000.000
120A122PRO0-0.040-0.02146.675-0.004-0.0040.0000.0000.0000.000
121A123ALA0-0.045-0.01245.321-0.005-0.0050.0000.0000.0000.000
122A124ASP-1-0.862-0.92845.190-0.093-0.0930.0000.0000.0000.000
123A125ARG10.8660.92442.2470.1140.1140.0000.0000.0000.000
124A126ASN0-0.064-0.05644.215-0.005-0.0050.0000.0000.0000.000
125A127ARG10.8560.92847.5950.0740.0740.0000.0000.0000.000
126A128VAL00.0220.01650.983-0.001-0.0010.0000.0000.0000.000
127A129ILE0-0.076-0.03652.8020.0030.0030.0000.0000.0000.000
128A130SER00.002-0.00555.3570.0010.0010.0000.0000.0000.000
129A131GLY00.0240.02356.594-0.001-0.0010.0000.0000.0000.000
130A132GLU-1-0.868-0.95156.381-0.067-0.0670.0000.0000.0000.000
131A133HIS0-0.079-0.03455.5630.0020.0020.0000.0000.0000.000
132A134LEU00.0250.01956.156-0.002-0.0020.0000.0000.0000.000
133A135ILE0-0.0190.01950.7980.0010.0010.0000.0000.0000.000
134A136LYS10.8630.90652.9050.0650.0650.0000.0000.0000.000
135A137ALA00.0370.02747.633-0.002-0.0020.0000.0000.0000.000
136A138TRP0-0.048-0.03045.0060.0010.0010.0000.0000.0000.000
137A139THR00.010-0.03744.271-0.005-0.0050.0000.0000.0000.000
138A140HIS00.0210.03044.405-0.005-0.0050.0000.0000.0000.000
139A141PHE0-0.033-0.01639.055-0.002-0.0020.0000.0000.0000.000
140A142HIS0-0.024-0.03842.7020.0020.0020.0000.0000.0000.000
141A143PHE0-0.0330.00237.9080.0000.0000.0000.0000.0000.000
142A144PRO00.0170.00641.2570.0010.0010.0000.0000.0000.000
143A145GLY0-0.0030.00440.8290.0030.0030.0000.0000.0000.000
144A146ARG10.7920.88335.2930.1260.1260.0000.0000.0000.000
145A147GLY00.0320.01839.4440.0030.0030.0000.0000.0000.000
146A148SER0-0.005-0.03240.368-0.003-0.0030.0000.0000.0000.000
147A149THR0-0.0180.01035.8670.0010.0010.0000.0000.0000.000
148A150TYR0-0.107-0.07832.397-0.006-0.0060.0000.0000.0000.000
149A151SER00.0070.00334.977-0.004-0.0040.0000.0000.0000.000
150A152ASP-1-0.872-0.93337.153-0.097-0.0970.0000.0000.0000.000
151A153PHE0-0.0040.01438.3320.0050.0050.0000.0000.0000.000
152A154LYS10.8050.91340.1350.0960.0960.0000.0000.0000.000
153A155TRP0-0.013-0.01635.9250.0000.0000.0000.0000.0000.000
154A156HIS10.8800.91042.5240.0920.0920.0000.0000.0000.000
155A157TRP00.0590.01344.683-0.005-0.0050.0000.0000.0000.000
156A158TYR00.0060.00845.595-0.003-0.0030.0000.0000.0000.000
157A159HIS0-0.059-0.02040.946-0.002-0.0020.0000.0000.0000.000
158A160PHE0-0.063-0.03939.097-0.007-0.0070.0000.0000.0000.000
159A161ASP-1-0.780-0.87941.852-0.107-0.1070.0000.0000.0000.000
160A162GLY00.028-0.00243.4360.0060.0060.0000.0000.0000.000
161A163THR0-0.079-0.02643.431-0.006-0.0060.0000.0000.0000.000
162A164ASP-1-0.747-0.87543.311-0.107-0.1070.0000.0000.0000.000
163A165TRP0-0.051-0.04945.8100.0020.0020.0000.0000.0000.000
164A166ASP-1-0.700-0.79348.177-0.071-0.0710.0000.0000.0000.000
165A167GLU-1-0.791-0.88750.104-0.077-0.0770.0000.0000.0000.000
166A168SER0-0.126-0.08552.1560.0030.0030.0000.0000.0000.000
167A169ARG10.8180.87355.8240.0660.0660.0000.0000.0000.000
168A170LYS10.8470.92552.3760.0730.0730.0000.0000.0000.000
169A171LEU00.0040.01552.8890.0000.0000.0000.0000.0000.000
170A172ASN0-0.0160.00345.919-0.002-0.0020.0000.0000.0000.000
171A173ARG10.8930.94849.1780.0750.0750.0000.0000.0000.000
172A174ILE0-0.0060.01045.196-0.003-0.0030.0000.0000.0000.000
173A175TYR0-0.022-0.02347.3780.0030.0030.0000.0000.0000.000
174A176LYS10.8840.93943.0280.1040.1040.0000.0000.0000.000
175A177PHE0-0.029-0.02245.1600.0040.0040.0000.0000.0000.000
176A178GLN00.008-0.01349.438-0.004-0.0040.0000.0000.0000.000
177A179GLY0-0.002-0.00751.8520.0000.0000.0000.0000.0000.000
178A180LYS10.8860.94348.4820.0800.0800.0000.0000.0000.000
179A181ALA00.0240.03244.788-0.001-0.0010.0000.0000.0000.000