Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: L7N19

Calculation Name: 3B02-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B02

Chain ID: A

ChEMBL ID:

UniProt ID: Q53W63

Base Structure: X-ray

Registration Date: 2023-09-27

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2205462.699773
FMO2-HF: Nuclear repulsion 2128547.585216
FMO2-HF: Total energy -76915.114558
FMO2-MP2: Total energy -77142.41825


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-12.579-15.04628.015-10.829-14.72-0.06
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.021
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].
3A3ARG10.9510.9783.806-0.1742.286-0.029-1.247-1.1850.002
4A4PHE0-0.008-0.0065.677-0.081-0.0810.0000.0000.0000.000
5A5ALA00.0720.0449.0550.1330.1330.0000.0000.0000.000
6A6ARG10.7660.85412.2900.0740.0740.0000.0000.0000.000
7A7LYS10.8590.90914.8980.0420.0420.0000.0000.0000.000
8A8GLU-1-0.855-0.88912.082-0.512-0.5120.0000.0000.0000.000
9A9THR0-0.015-0.02214.0590.0310.0310.0000.0000.0000.000
10A10ILE0-0.066-0.0248.931-0.059-0.0590.0000.0000.0000.000
11A11TYR00.0010.00611.424-0.044-0.0440.0000.0000.0000.000
12A12LEU00.0140.00214.0650.0410.0410.0000.0000.0000.000
13A13ARG10.9600.98017.8610.0260.0260.0000.0000.0000.000
14A14GLY0-0.043-0.02820.733-0.009-0.0090.0000.0000.0000.000
15A15GLU-1-0.928-0.95317.012-0.210-0.2100.0000.0000.0000.000
16A16GLU-1-0.824-0.88716.752-0.102-0.1020.0000.0000.0000.000
17A17ALA0-0.013-0.00315.527-0.029-0.0290.0000.0000.0000.000
18A18ARG10.7830.85313.1940.1990.1990.0000.0000.0000.000
19A19THR0-0.028-0.0117.8550.0400.0400.0000.0000.0000.000
20A20LEU00.0380.05310.3520.0020.0020.0000.0000.0000.000
21A21TYR00.018-0.0066.154-0.112-0.1120.0000.0000.0000.000
22A22ARG10.8460.9194.536-1.868-1.787-0.001-0.007-0.0730.000
23A23LEU0-0.0280.0006.0850.7770.927-0.001-0.006-0.1430.000
24A24GLU-1-0.865-0.9262.6151.7370.1185.399-1.428-2.352-0.002
25A25GLU-1-0.934-0.9755.956-0.480-0.475-0.001-0.0090.0050.000
26A26GLY00.0370.0168.382-0.059-0.0590.0000.0000.0000.000
27A27LEU0-0.003-0.01411.0530.0680.0680.0000.0000.0000.000
28A28VAL00.0200.02110.818-0.070-0.0700.0000.0000.0000.000
29A29ARG10.7320.85013.8550.0220.0220.0000.0000.0000.000
30A30VAL00.0110.00216.334-0.021-0.0210.0000.0000.0000.000
31A31VAL0-0.010-0.01518.4210.0030.0030.0000.0000.0000.000
32A32GLU-1-0.810-0.90621.491-0.001-0.0010.0000.0000.0000.000
33A33LEU0-0.0250.00324.4070.0000.0000.0000.0000.0000.000
34A34LEU0-0.023-0.03226.7050.0010.0010.0000.0000.0000.000
35A35PRO00.002-0.01530.219-0.005-0.0050.0000.0000.0000.000
36A36ASP-1-0.834-0.90233.256-0.011-0.0110.0000.0000.0000.000
37A37GLY00.0040.00731.363-0.001-0.0010.0000.0000.0000.000
38A38ARG10.8530.91830.273-0.003-0.0030.0000.0000.0000.000
39A39LEU00.0060.02422.788-0.002-0.0020.0000.0000.0000.000
40A40ILE0-0.011-0.00225.9450.0040.0040.0000.0000.0000.000
41A41THR00.005-0.00821.442-0.003-0.0030.0000.0000.0000.000
42A42LEU0-0.009-0.00121.9350.0040.0040.0000.0000.0000.000
43A43ARG10.8110.88316.154-0.201-0.2010.0000.0000.0000.000
44A44HIS00.0280.04418.245-0.022-0.0220.0000.0000.0000.000
45A45VAL0-0.024-0.01012.3210.0080.0080.0000.0000.0000.000
46A46LEU00.028-0.00913.790-0.010-0.0100.0000.0000.0000.000
47A47PRO00.0090.0079.9930.0740.0740.0000.0000.0000.000
48A48GLY0-0.014-0.0119.391-0.147-0.1470.0000.0000.0000.000
49A49ASP-1-0.815-0.86710.4380.3440.3440.0000.0000.0000.000
50A50TYR0-0.011-0.01410.2390.2130.2130.0000.0000.0000.000
51A51PHE00.013-0.0058.906-0.109-0.1090.0000.0000.0000.000
52A52GLY00.0910.04512.0220.0190.0190.0000.0000.0000.000
53A53GLU-1-0.811-0.92113.6720.1640.1640.0000.0000.0000.000
54A54GLU-1-0.704-0.85116.1470.0540.0540.0000.0000.0000.000
55A55ALA0-0.0170.01014.046-0.011-0.0110.0000.0000.0000.000
56A56LEU0-0.119-0.07215.5320.0060.0060.0000.0000.0000.000
57A57GLU-1-1.000-1.00017.7350.0540.0540.0000.0000.0000.000
58A58GLY00.0300.03320.278-0.009-0.0090.0000.0000.0000.000
59A59LYS10.8820.92120.202-0.008-0.0080.0000.0000.0000.000
60A60ALA00.0100.00619.451-0.018-0.0180.0000.0000.0000.000
61A61TYR0-0.0260.00012.569-0.007-0.0070.0000.0000.0000.000
62A62ARG10.8040.88118.811-0.023-0.0230.0000.0000.0000.000
63A63TYR0-0.031-0.02419.429-0.005-0.0050.0000.0000.0000.000
64A64THR00.0250.01417.575-0.014-0.0140.0000.0000.0000.000
65A65ALA0-0.0060.02613.5040.0310.0310.0000.0000.0000.000
66A66GLU-1-0.819-0.90414.563-0.109-0.1090.0000.0000.0000.000
67A67ALA00.0440.03511.5140.0660.0660.0000.0000.0000.000
68A68MET0-0.0050.00213.348-0.031-0.0310.0000.0000.0000.000
69A69THR0-0.028-0.03111.9670.0030.0030.0000.0000.0000.000
70A70GLU-1-0.917-0.95610.230-0.357-0.3570.0000.0000.0000.000
71A71ALA0-0.0060.0048.3670.1190.1190.0000.0000.0000.000
72A72VAL00.0080.0172.439-1.367-1.1501.870-0.474-1.6130.000
73A73VAL00.0180.0163.8420.5861.2810.005-0.204-0.4960.000
74A74GLN00.1030.0441.777-9.857-14.21620.699-7.963-8.378-0.061
75A75GLY0-0.0120.0023.077-0.771-0.9850.0750.513-0.3740.001
76A76LEU0-0.054-0.0394.9030.0320.149-0.001-0.004-0.1110.000
77A77GLU-1-0.866-0.9387.688-0.074-0.0740.0000.0000.0000.000
78A78PRO0-0.002-0.02010.7640.0550.0550.0000.0000.0000.000
79A79ARG10.9370.94013.798-0.037-0.0370.0000.0000.0000.000
80A80ALA00.0020.02412.228-0.012-0.0120.0000.0000.0000.000
81A81MET0-0.0630.00612.5800.0620.0620.0000.0000.0000.000
82A82ASP-1-0.790-0.88214.6770.2480.2480.0000.0000.0000.000
83A83HIS00.0370.00017.1680.0130.0130.0000.0000.0000.000
84A84GLU-1-0.931-0.96514.4170.2750.2750.0000.0000.0000.000
85A85ALA0-0.051-0.03813.1310.0250.0250.0000.0000.0000.000
86A86LEU00.0540.01514.3070.0230.0230.0000.0000.0000.000
87A87HIS00.0080.01317.307-0.004-0.0040.0000.0000.0000.000
88A88ARG10.8910.94710.266-0.474-0.4740.0000.0000.0000.000
89A89VAL00.0130.01513.6700.0140.0140.0000.0000.0000.000
90A90ALA00.0360.02415.632-0.015-0.0150.0000.0000.0000.000
91A91ARG10.9350.96317.786-0.212-0.2120.0000.0000.0000.000
92A92ASN0-0.036-0.02814.705-0.009-0.0090.0000.0000.0000.000
93A93LEU00.0610.03416.819-0.009-0.0090.0000.0000.0000.000
94A94ALA00.0140.01618.909-0.023-0.0230.0000.0000.0000.000
95A95ARG10.8990.94216.959-0.262-0.2620.0000.0000.0000.000
96A96GLN0-0.006-0.02715.083-0.041-0.0410.0000.0000.0000.000
97A97MET0-0.0070.01519.947-0.021-0.0210.0000.0000.0000.000
98A98ARG10.8950.93022.281-0.160-0.1600.0000.0000.0000.000
99A99ARG10.8080.86816.610-0.280-0.2800.0000.0000.0000.000
100A100VAL0-0.019-0.00222.523-0.011-0.0110.0000.0000.0000.000
101A101GLN00.0590.02824.194-0.004-0.0040.0000.0000.0000.000
102A102ALA00.0130.01626.507-0.009-0.0090.0000.0000.0000.000
103A103TYR0-0.071-0.04224.920-0.008-0.0080.0000.0000.0000.000
104A104GLU-1-0.899-0.96527.0450.0560.0560.0000.0000.0000.000
105A105ALA00.0010.00429.563-0.008-0.0080.0000.0000.0000.000
106A106HIS0-0.0330.00528.675-0.006-0.0060.0000.0000.0000.000
107A107LEU0-0.065-0.03228.467-0.007-0.0070.0000.0000.0000.000
108A108GLN0-0.072-0.02732.154-0.008-0.0080.0000.0000.0000.000
109A109THR0-0.0080.00334.786-0.002-0.0020.0000.0000.0000.000
110A110GLY00.0150.00235.9680.0010.0010.0000.0000.0000.000
111A111GLU-1-0.869-0.93538.0660.0180.0180.0000.0000.0000.000
112A112LEU0-0.026-0.01933.9780.0020.0020.0000.0000.0000.000
113A113ARG10.7320.81735.335-0.014-0.0140.0000.0000.0000.000
114A114ALA00.0590.04135.7220.0010.0010.0000.0000.0000.000
115A115ARG10.8310.91332.578-0.023-0.0230.0000.0000.0000.000
116A116ILE00.013-0.01031.1760.0040.0040.0000.0000.0000.000
117A117ALA00.0110.01530.6930.0030.0030.0000.0000.0000.000
118A118ARG10.8200.89729.814-0.044-0.0440.0000.0000.0000.000
119A119TYR0-0.029-0.04122.4080.0020.0020.0000.0000.0000.000
120A120LEU0-0.027-0.02026.1390.0060.0060.0000.0000.0000.000
121A121LEU00.007-0.00426.4760.0040.0040.0000.0000.0000.000
122A122PHE0-0.0140.01520.5010.0080.0080.0000.0000.0000.000
123A123LEU0-0.015-0.01521.0380.0120.0120.0000.0000.0000.000
124A124ALA0-0.023-0.01421.8280.0060.0060.0000.0000.0000.000
125A125ASP-1-0.931-0.94021.9950.1010.1010.0000.0000.0000.000
126A126THR0-0.053-0.03517.8120.0280.0280.0000.0000.0000.000
127A127PRO0-0.041-0.03613.731-0.025-0.0250.0000.0000.0000.000
128A128LEU0-0.0170.00516.198-0.026-0.0260.0000.0000.0000.000
129A129SER0-0.070-0.02218.557-0.028-0.0280.0000.0000.0000.000
130A130ALA00.0210.01219.9090.0030.0030.0000.0000.0000.000
131A131ARG10.9510.96622.249-0.035-0.0350.0000.0000.0000.000
132A132ASP-1-0.799-0.86325.325-0.005-0.0050.0000.0000.0000.000
133A133ARG10.9330.94928.0610.0030.0030.0000.0000.0000.000
134A134GLN0-0.064-0.02231.2010.0030.0030.0000.0000.0000.000
135A135GLY00.0580.03130.5310.0020.0020.0000.0000.0000.000
136A136ILE0-0.002-0.00725.877-0.002-0.0020.0000.0000.0000.000
137A137TYR0-0.016-0.00922.521-0.005-0.0050.0000.0000.0000.000
138A138VAL00.0560.03622.9650.0070.0070.0000.0000.0000.000
139A139THR0-0.048-0.02820.398-0.016-0.0160.0000.0000.0000.000
140A140VAL00.0240.01721.2020.0040.0040.0000.0000.0000.000
141A141SER0-0.068-0.03523.516-0.007-0.0070.0000.0000.0000.000
142A142HIS00.010-0.04225.9000.0050.0050.0000.0000.0000.000
143A143GLU-1-0.887-0.94826.674-0.014-0.0140.0000.0000.0000.000
144A144GLU-1-0.780-0.87120.747-0.006-0.0060.0000.0000.0000.000
145A145ILE00.0250.01425.0020.0080.0080.0000.0000.0000.000
146A146ALA0-0.0280.00127.4920.0050.0050.0000.0000.0000.000
147A147ASP-1-0.754-0.87625.263-0.001-0.0010.0000.0000.0000.000
148A148ALA0-0.034-0.00724.7870.0060.0060.0000.0000.0000.000
149A149THR0-0.025-0.03026.8620.0040.0040.0000.0000.0000.000
150A150ALA00.0280.03230.301-0.002-0.0020.0000.0000.0000.000
151A151SER0-0.045-0.02531.948-0.003-0.0030.0000.0000.0000.000
152A152ILE00.0680.04132.465-0.001-0.0010.0000.0000.0000.000
153A153ARG10.9670.97030.8740.0240.0240.0000.0000.0000.000
154A154GLU-1-0.871-0.94233.058-0.014-0.0140.0000.0000.0000.000
155A155SER00.006-0.00736.4690.0010.0010.0000.0000.0000.000
156A156VAL00.0400.03031.0370.0020.0020.0000.0000.0000.000
157A157SER0-0.036-0.01734.3740.0000.0000.0000.0000.0000.000
158A158LYS10.9270.97635.477-0.004-0.0040.0000.0000.0000.000
159A159VAL00.0350.02436.2010.0000.0000.0000.0000.0000.000
160A160LEU00.0250.01131.3030.0010.0010.0000.0000.0000.000
161A161ALA0-0.066-0.04035.7030.0000.0000.0000.0000.0000.000
162A162ASP-1-0.866-0.92838.8230.0040.0040.0000.0000.0000.000
163A163LEU00.0370.01234.9310.0000.0000.0000.0000.0000.000
164A164ARG10.8810.94534.5380.0050.0050.0000.0000.0000.000
165A165ARG10.8300.91938.414-0.002-0.0020.0000.0000.0000.000
166A166GLU-1-0.821-0.89141.0650.0120.0120.0000.0000.0000.000
167A167GLY00.0050.01939.7530.0010.0010.0000.0000.0000.000
168A168LEU00.0170.01236.4100.0010.0010.0000.0000.0000.000
169A169ILE0-0.024-0.00832.8300.0020.0020.0000.0000.0000.000
170A170ALA00.0360.01933.092-0.003-0.0030.0000.0000.0000.000
171A171THR0-0.0130.00331.1150.0020.0020.0000.0000.0000.000
172A172ALA0-0.006-0.01330.018-0.002-0.0020.0000.0000.0000.000
173A173TYR00.0210.00926.9200.0000.0000.0000.0000.0000.000
174A174ARG10.9190.95921.3420.0630.0630.0000.0000.0000.000
175A175ARG10.9190.97823.7890.0210.0210.0000.0000.0000.000
176A176VAL00.0180.00726.463-0.004-0.0040.0000.0000.0000.000
177A177TYR0-0.069-0.06527.8610.0030.0030.0000.0000.0000.000
178A178LEU0-0.012-0.01327.806-0.001-0.0010.0000.0000.0000.000
179A179LEU0-0.032-0.02131.3020.0010.0010.0000.0000.0000.000
180A180ASP-1-0.859-0.91834.6120.0230.0230.0000.0000.0000.000
181A181LEU00.015-0.00830.4170.0010.0010.0000.0000.0000.000
182A182ALA00.0830.04834.1910.0020.0020.0000.0000.0000.000
183A183ALA0-0.049-0.02937.1730.0010.0010.0000.0000.0000.000
184A184LEU00.018-0.00132.1320.0000.0000.0000.0000.0000.000
185A185GLU-1-0.929-0.96633.1060.0480.0480.0000.0000.0000.000
186A186ARG10.8950.95135.141-0.025-0.0250.0000.0000.0000.000
187A187GLU-1-0.879-0.92136.7440.0210.0210.0000.0000.0000.000
188A188ALA0-0.025-0.00633.2030.0000.0000.0000.0000.0000.000
189A189GLY0-0.0060.01035.2340.0010.0010.0000.0000.0000.000
190A190SER0-0.028-0.00933.3180.0000.0000.0000.0000.0000.000
191A191ALA00.0250.00029.422-0.001-0.0010.0000.0000.0000.000
192A192LEU0-0.007-0.00225.610-0.001-0.0010.0000.0000.0000.000
193A193GLU-1-0.897-0.96024.7230.1160.1160.0000.0000.0000.000
194A194ALA00.0750.03622.1880.0070.0070.0000.0000.0000.000
195A195ALA0-0.0350.00519.8390.0060.0060.0000.0000.0000.000