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: 7J88K

Calculation Name: 2YVS-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YVS

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SM78

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 219
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2544019.88083
FMO2-HF: Nuclear repulsion 2461754.932074
FMO2-HF: Total energy -82264.948756
FMO2-MP2: Total energy -82513.414069


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.
-20.16-12.45921.091-8.372-20.421-0.029
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 : -0.016 / 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].
3A3VAL 00.002-0.0103.0770.6962.5850.028-0.677-1.2400.000
4A4HIS 0-0.0050.0115.076-0.269-0.1910.000-0.008-0.0690.000
5A5ALA 00.018-0.0138.7500.1530.1530.0000.0000.0000.000
6A6ALA 0-0.007-0.01010.4060.0200.0200.0000.0000.0000.000
7A7ASP -1-0.902-0.93812.4670.0450.0450.0000.0000.0000.000
8A8GLN 0-0.086-0.04511.6160.0150.0150.0000.0000.0000.000
9A9TYR 0-0.012-0.0058.2590.0900.0900.0000.0000.0000.000
10A10LEU 00.003-0.0092.413-1.218-0.6752.387-0.631-2.2990.000
11A11VAL 00.0060.0164.098-0.1410.1620.000-0.076-0.2270.000
12A12ALA 00.0230.0032.413-3.838-2.2734.349-2.511-3.403-0.022
13A13PRO 00.0850.0372.485-1.103-0.4130.824-0.138-1.3760.000
14A14GLY 0-0.028-0.0255.6350.2580.2580.0000.0000.0000.000
15A15GLU -1-0.996-1.0157.312-0.754-0.7540.0000.0000.0000.000
16A16ALA 0-0.0070.0312.529-0.498-0.1140.569-0.234-0.720-0.001
17A17ASP -1-0.867-0.9674.448-0.0470.0530.000-0.008-0.0920.000
18A18LEU 0-0.059-0.0564.158-0.424-0.2940.000-0.032-0.0990.000
19A19LEU 0-0.008-0.0246.0710.4770.4770.0000.0000.0000.000
20A20GLU -1-0.868-0.8842.152-5.269-3.4721.789-1.508-2.078-0.016
21A21VAL 0-0.022-0.0182.491-0.8930.4983.428-1.486-3.333-0.001
22A22HIS 0-0.044-0.0333.1272.5601.9670.0480.922-0.3770.000
23A23ALA 0-0.015-0.0016.1420.1070.1070.0000.0000.0000.000
24A24ARG 10.8890.9552.165-6.374-7.0787.669-1.954-5.0110.011
25A25LEU 00.0030.0005.248-0.885-0.7570.000-0.031-0.0970.000
26A26ALA 00.0180.0377.394-0.742-0.7420.0000.0000.0000.000
27A27GLY 0-0.015-0.00910.499-0.052-0.0520.0000.0000.0000.000
28A28THR 0-0.031-0.0398.659-0.168-0.1680.0000.0000.0000.000
29A29GLY 0-0.058-0.01812.059-0.143-0.1430.0000.0000.0000.000
30A30LEU 0-0.029-0.01510.216-0.157-0.1570.0000.0000.0000.000
31A31PHE 0-0.0030.00110.5190.2140.2140.0000.0000.0000.000
32A32PRO 00.0500.0377.551-0.095-0.0950.0000.0000.0000.000
33A33PRO 0-0.035-0.0159.608-0.265-0.2650.0000.0000.0000.000
34A34PHE 00.015-0.0296.121-0.146-0.1460.0000.0000.0000.000
35A35PRO 00.0300.02911.4430.1340.1340.0000.0000.0000.000
36A36PRO 0-0.0040.01110.8780.0270.0270.0000.0000.0000.000
37A37VAL 00.003-0.01411.589-0.094-0.0940.0000.0000.0000.000
38A38GLU -1-0.771-0.8738.336-0.038-0.0380.0000.0000.0000.000
39A39LEU 0-0.005-0.01711.216-0.009-0.0090.0000.0000.0000.000
40A40PRO 00.0240.00711.865-0.042-0.0420.0000.0000.0000.000
41A41GLY 0-0.015-0.02112.6580.0440.0440.0000.0000.0000.000
42A42GLY 00.1050.0828.389-0.041-0.0410.0000.0000.0000.000
43A43VAL 0-0.007-0.0145.4740.1890.1890.0000.0000.0000.000
44A44GLY 00.010-0.0048.3350.0400.0400.0000.0000.0000.000
45A45GLY 0-0.027-0.01110.6960.0190.0190.0000.0000.0000.000
46A46LEU 0-0.0120.00110.4100.0100.0100.0000.0000.0000.000
47A47VAL 00.000-0.00311.1670.0060.0060.0000.0000.0000.000
48A48ALA 00.0080.00113.874-0.025-0.0250.0000.0000.0000.000
49A49ARG 10.9300.99113.447-0.137-0.1370.0000.0000.0000.000
50A50GLY 00.0130.00317.004-0.002-0.0020.0000.0000.0000.000
51A51GLY 0-0.040-0.01214.9710.0180.0180.0000.0000.0000.000
52A52PHE 00.009-0.00714.526-0.052-0.0520.0000.0000.0000.000
53A53ALA 00.017-0.00316.1820.0580.0580.0000.0000.0000.000
54A54GLN 0-0.0370.00517.7590.0250.0250.0000.0000.0000.000
55A55THR 0-0.020-0.01819.251-0.033-0.0330.0000.0000.0000.000
56A56PHE 0-0.065-0.02416.085-0.025-0.0250.0000.0000.0000.000
57A57PHE 00.033-0.00921.2960.0010.0010.0000.0000.0000.000
58A58PHE 00.0370.01413.022-0.002-0.0020.0000.0000.0000.000
59A59PRO 00.0550.02116.7950.0370.0370.0000.0000.0000.000
60A60ALA 0-0.0130.00617.132-0.008-0.0080.0000.0000.0000.000
61A61GLU -1-0.798-0.86713.9610.5180.5180.0000.0000.0000.000
62A62VAL 0-0.0020.01512.0470.1190.1190.0000.0000.0000.000
63A63LEU 0-0.004-0.01411.770-0.096-0.0960.0000.0000.0000.000
64A64GLY 00.012-0.01012.036-0.087-0.0870.0000.0000.0000.000
65A65LEU 0-0.0270.02111.1820.0840.0840.0000.0000.0000.000
66A66THR 00.0250.01711.258-0.029-0.0290.0000.0000.0000.000
67A67PHE 00.0120.02012.539-0.019-0.0190.0000.0000.0000.000
68A68ARG 10.9710.99515.1990.2390.2390.0000.0000.0000.000
69A69THR 00.022-0.00417.5400.0110.0110.0000.0000.0000.000
70A70PRO 00.009-0.01021.075-0.018-0.0180.0000.0000.0000.000
71A71LYS 10.8330.91223.5450.0870.0870.0000.0000.0000.000
72A72GLY 0-0.0040.01021.968-0.001-0.0010.0000.0000.0000.000
73A73ARG 10.8200.92421.1390.1080.1080.0000.0000.0000.000
74A74ARG 10.8720.92213.9540.4170.4170.0000.0000.0000.000
75A75VAL 0-0.0030.00217.4630.0050.0050.0000.0000.0000.000
76A76ARG 10.9190.96810.5170.4360.4360.0000.0000.0000.000
77A77ALA 00.006-0.00815.1110.0240.0240.0000.0000.0000.000
78A78GLY 0-0.033-0.02614.9320.0080.0080.0000.0000.0000.000
79A79GLY 00.019-0.00813.727-0.045-0.0450.0000.0000.0000.000
80A80VAL 0-0.023-0.02112.900-0.002-0.0020.0000.0000.0000.000
81A81VAL 00.0070.01515.751-0.023-0.0230.0000.0000.0000.000
82A82VAL 00.0540.02817.710-0.022-0.0220.0000.0000.0000.000
83A83LYS 10.8930.95717.675-0.008-0.0080.0000.0000.0000.000
84A84ASN 0-0.019-0.01119.439-0.012-0.0120.0000.0000.0000.000
85A85VAL 00.0400.01923.1750.0090.0090.0000.0000.0000.000
86A86GLN 0-0.057-0.02623.269-0.008-0.0080.0000.0000.0000.000
87A87GLY 00.0880.04124.1360.0080.0080.0000.0000.0000.000
88A88TYR 0-0.038-0.02124.280-0.006-0.0060.0000.0000.0000.000
89A89ASP -1-0.784-0.87120.6730.0770.0770.0000.0000.0000.000
90A90LEU 00.0360.00419.9150.0070.0070.0000.0000.0000.000
91A91VAL 0-0.0120.00115.594-0.008-0.0080.0000.0000.0000.000
92A92ARG 10.8130.86717.210-0.144-0.1440.0000.0000.0000.000
93A93LEU 0-0.0460.01520.1290.0000.0000.0000.0000.0000.000
94A94PHE 00.0080.00515.210-0.003-0.0030.0000.0000.0000.000
95A95VAL 0-0.0080.00615.6600.0090.0090.0000.0000.0000.000
96A96GLY 00.0190.01118.063-0.004-0.0040.0000.0000.0000.000
97A97SER 0-0.089-0.05419.659-0.023-0.0230.0000.0000.0000.000
98A98PHE 0-0.006-0.03219.659-0.018-0.0180.0000.0000.0000.000
99A99GLY 00.0260.02719.126-0.013-0.0130.0000.0000.0000.000
100A100LEU 0-0.045-0.00419.960-0.021-0.0210.0000.0000.0000.000
101A101LEU 00.019-0.01321.158-0.010-0.0100.0000.0000.0000.000
102A102GLY 0-0.0070.00119.643-0.019-0.0190.0000.0000.0000.000
103A103ARG 10.9370.97010.6930.4610.4610.0000.0000.0000.000
104A104ALA 00.0060.00811.761-0.029-0.0290.0000.0000.0000.000
105A105GLU -1-0.844-0.91910.905-0.494-0.4940.0000.0000.0000.000
106A106GLU -1-0.879-0.9436.219-1.059-1.0590.0000.0000.0000.000
107A107VAL 0-0.025-0.0076.8710.0750.0750.0000.0000.0000.000
108A108VAL 00.0140.0086.6220.1160.1160.0000.0000.0000.000
109A109LEU 0-0.017-0.0167.503-0.088-0.0880.0000.0000.0000.000
110A110ARG 10.9490.9759.032-0.393-0.3930.0000.0000.0000.000
111A111LEU 0-0.0170.0067.3320.1520.1520.0000.0000.0000.000
112A112ARG 10.7550.84511.415-0.742-0.7420.0000.0000.0000.000
113A113PRO 00.0350.02214.0180.0940.0940.0000.0000.0000.000
114A114GLY 0-0.030-0.02916.111-0.059-0.0590.0000.0000.0000.000
115A115ARG 10.9110.95316.977-0.437-0.4370.0000.0000.0000.000
116A116ALA 00.0300.02419.335-0.029-0.0290.0000.0000.0000.000
117A117GLN 00.0500.01614.4250.0280.0280.0000.0000.0000.000
118A118ALA 00.016-0.00418.983-0.039-0.0390.0000.0000.0000.000
119A119PHE 0-0.0040.01016.4570.0280.0280.0000.0000.0000.000
120A120LEU 00.0180.03119.440-0.016-0.0160.0000.0000.0000.000
121A121ARG 10.8520.92222.567-0.157-0.1570.0000.0000.0000.000
122A122ARG 10.9150.96124.743-0.172-0.1720.0000.0000.0000.000
123A123PRO 00.0620.03828.2510.0030.0030.0000.0000.0000.000
124A124PHE 0-0.034-0.00828.6550.0030.0030.0000.0000.0000.000
125A125SER 00.020-0.00130.438-0.006-0.0060.0000.0000.0000.000
126A126GLY 00.0350.01832.296-0.008-0.0080.0000.0000.0000.000
127A127SER 0-0.069-0.02932.087-0.003-0.0030.0000.0000.0000.000
128A128PHE 00.0050.00125.2240.0060.0060.0000.0000.0000.000
129A129PRO 0-0.0090.01428.790-0.006-0.0060.0000.0000.0000.000
130A130ARG 10.9620.96929.696-0.137-0.1370.0000.0000.0000.000
131A131LEU 0-0.009-0.00327.507-0.005-0.0050.0000.0000.0000.000
132A132VAL 0-0.0170.01429.8940.0040.0040.0000.0000.0000.000
133A133PRO 00.027-0.00427.080-0.008-0.0080.0000.0000.0000.000
134A134THR 00.0150.00225.087-0.001-0.0010.0000.0000.0000.000
135A135PRO 0-0.0050.01421.9590.0170.0170.0000.0000.0000.000
136A136ARG 10.8900.95318.164-0.493-0.4930.0000.0000.0000.000
137A137PHE 0-0.002-0.00314.6150.0220.0220.0000.0000.0000.000
138A138LEU 0-0.006-0.01419.349-0.013-0.0130.0000.0000.0000.000
139A139PHE 0-0.026-0.01817.7600.0000.0000.0000.0000.0000.000
140A140ALA 00.0300.02322.2400.0020.0020.0000.0000.0000.000
141A141LEU 0-0.024-0.02820.3400.0000.0000.0000.0000.0000.000
142A142GLU -1-0.916-0.95223.9590.0860.0860.0000.0000.0000.000
143A143ASP -1-0.900-0.94224.3990.1290.1290.0000.0000.0000.000
144A144GLU -1-0.950-0.98427.1090.0580.0580.0000.0000.0000.000
145A145GLU -1-0.966-0.98029.1410.1120.1120.0000.0000.0000.000
146A146GLY 00.0510.03130.007-0.004-0.0040.0000.0000.0000.000
147A147PRO 0-0.035-0.01728.3160.0080.0080.0000.0000.0000.000
148A148TRP 00.0440.02425.3840.0100.0100.0000.0000.0000.000
149A149LEU 0-0.044-0.03525.4650.0040.0040.0000.0000.0000.000
150A150TYR 00.0500.01020.2330.0000.0000.0000.0000.0000.000
151A151ALA 00.001-0.00321.4580.0010.0010.0000.0000.0000.000
152A152TYR 0-0.036-0.01113.8020.0430.0430.0000.0000.0000.000
153A153HIS 00.0310.01218.8070.0280.0280.0000.0000.0000.000
154A154PHE 00.0350.01214.9340.0180.0180.0000.0000.0000.000
155A155GLY 00.007-0.00318.674-0.028-0.0280.0000.0000.0000.000
156A156HIS 00.0270.01320.2770.0290.0290.0000.0000.0000.000
157A157PRO 00.0620.01323.080-0.007-0.0070.0000.0000.0000.000
158A158LYS 10.9880.99424.655-0.191-0.1910.0000.0000.0000.000
159A159GLU -1-0.965-0.98524.4120.2390.2390.0000.0000.0000.000
160A160VAL 0-0.055-0.03321.291-0.009-0.0090.0000.0000.0000.000
161A161GLU -1-0.922-0.95124.4470.2190.2190.0000.0000.0000.000
162A162ARG 10.9940.99227.602-0.198-0.1980.0000.0000.0000.000
163A163PHE 0-0.028-0.00823.136-0.008-0.0080.0000.0000.0000.000
164A164ARG 10.8900.93321.702-0.330-0.3300.0000.0000.0000.000
165A165GLU -1-0.948-0.95427.4390.1500.1500.0000.0000.0000.000
166A166ALA 0-0.022-0.00330.343-0.011-0.0110.0000.0000.0000.000
167A167PHE 0-0.111-0.05425.813-0.009-0.0090.0000.0000.0000.000
168A168GLY 00.0630.04429.208-0.012-0.0120.0000.0000.0000.000
169A169GLY 0-0.044-0.03528.2530.0130.0130.0000.0000.0000.000
170A170GLU -1-0.851-0.90625.7360.1630.1630.0000.0000.0000.000
171A171GLU -1-0.877-0.95521.6720.3340.3340.0000.0000.0000.000
172A172ALA 00.0030.00320.349-0.019-0.0190.0000.0000.0000.000
173A173ARG 10.9410.95317.809-0.191-0.1910.0000.0000.0000.000
174A174PRO 0-0.010-0.01512.627-0.016-0.0160.0000.0000.0000.000
175A175LEU 0-0.0090.01614.457-0.047-0.0470.0000.0000.0000.000
176A176ASP -1-0.738-0.86513.5710.0440.0440.0000.0000.0000.000
177A177LEU 00.005-0.01514.671-0.017-0.0170.0000.0000.0000.000
178A178ARG 10.8790.92711.0060.1180.1180.0000.0000.0000.000
179A179PRO 0-0.005-0.00816.220-0.011-0.0110.0000.0000.0000.000
180A180ARG 10.8690.92719.390-0.093-0.0930.0000.0000.0000.000
181A181PHE 0-0.072-0.02518.5530.0060.0060.0000.0000.0000.000
182A182PRO 00.0400.02819.313-0.015-0.0150.0000.0000.0000.000
183A183ARG 10.8350.90820.649-0.011-0.0110.0000.0000.0000.000
184A184GLY 00.0020.00418.794-0.007-0.0070.0000.0000.0000.000
185A185LEU 0-0.040-0.03016.5440.0120.0120.0000.0000.0000.000
186A186GLY 00.0080.02119.4820.0060.0060.0000.0000.0000.000
187A187LEU 0-0.047-0.03522.6260.0170.0170.0000.0000.0000.000
188A188GLY 00.024-0.00725.348-0.012-0.0120.0000.0000.0000.000
189A189GLU -1-0.968-0.98327.7890.0560.0560.0000.0000.0000.000
190A190GLY 0-0.001-0.00326.160-0.004-0.0040.0000.0000.0000.000
191A191PRO 00.006-0.00123.8980.0050.0050.0000.0000.0000.000
192A192LEU 00.0110.02018.6090.0120.0120.0000.0000.0000.000
193A193TRP 0-0.0080.00223.285-0.009-0.0090.0000.0000.0000.000
194A194ASP -1-0.745-0.85020.1410.2210.2210.0000.0000.0000.000
195A195LEU 0-0.030-0.02723.086-0.016-0.0160.0000.0000.0000.000
196A196ARG 10.7870.91019.243-0.199-0.1990.0000.0000.0000.000
197A197PHE 0-0.016-0.00921.285-0.019-0.0190.0000.0000.0000.000
198A198ARG 10.9480.99124.298-0.064-0.0640.0000.0000.0000.000
199A199TYR 0-0.057-0.06319.661-0.010-0.0100.0000.0000.0000.000
200A200GLN 00.006-0.00123.509-0.003-0.0030.0000.0000.0000.000
201A201ASP -1-0.749-0.86122.735-0.009-0.0090.0000.0000.0000.000
202A202GLY 0-0.034-0.01522.951-0.002-0.0020.0000.0000.0000.000
203A203GLY 0-0.0360.00424.480-0.002-0.0020.0000.0000.0000.000
204A204ALA 00.0120.00325.123-0.007-0.0070.0000.0000.0000.000
205A205SER 00.0450.01424.2980.0100.0100.0000.0000.0000.000
206A206PRO 0-0.016-0.00124.067-0.003-0.0030.0000.0000.0000.000
207A207PRO 0-0.0090.00027.226-0.008-0.0080.0000.0000.0000.000
208A208PRO 00.0250.00527.4080.0060.0060.0000.0000.0000.000
209A209PRO 00.0310.02829.091-0.003-0.0030.0000.0000.0000.000
210A210PRO 00.0820.01031.833-0.006-0.0060.0000.0000.0000.000
211A211ALA 0-0.033-0.02732.093-0.006-0.0060.0000.0000.0000.000
212A212PHE 00.067-0.01524.051-0.007-0.0070.0000.0000.0000.000
213A213LEU 00.0300.02628.877-0.009-0.0090.0000.0000.0000.000
214A214ARG 10.9180.96230.9120.0030.0030.0000.0000.0000.000
215A215LEU 0-0.0210.02425.928-0.007-0.0070.0000.0000.0000.000
216A216ALA 00.0590.04026.607-0.009-0.0090.0000.0000.0000.000
217A217ARG 10.8690.95827.3080.0610.0610.0000.0000.0000.000
218A218VAL 0-0.037-0.03828.516-0.010-0.0100.0000.0000.0000.000
219A219LEU -1-0.758-0.86722.962-0.121-0.1210.0000.0000.0000.000