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: N144Q

Calculation Name: 2QVA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QVA

Chain ID: A

ChEMBL ID:

UniProt ID: Q7JVK6

Base Structure: X-ray

Registration Date: 2023-06-20

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1898599.198663
FMO2-HF: Nuclear repulsion 1825971.159972
FMO2-HF: Total energy -72628.038691
FMO2-MP2: Total energy -72842.506937


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:5:VAL)


Summations of interaction energy for fragment #1(A:5:VAL)
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.
-0.691.471-0.035-0.978-1.1480.001
Interaction energy analysis for fragmet #1(A:5:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.010
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].
3A7LEU00.0560.0243.784-0.9891.172-0.035-0.978-1.1480.001
4A8ASP-1-0.878-0.9566.1060.1910.1910.0000.0000.0000.000
5A9ILE0-0.063-0.0295.2390.2000.2000.0000.0000.0000.000
6A10PHE0-0.021-0.0134.925-0.013-0.0130.0000.0000.0000.000
7A11SER00.0050.0179.253-0.061-0.0610.0000.0000.0000.000
8A12ASN0-0.067-0.03711.6570.0100.0100.0000.0000.0000.000
9A13TYR00.0020.00310.754-0.021-0.0210.0000.0000.0000.000
10A14GLN00.0290.01814.210-0.023-0.0230.0000.0000.0000.000
11A15LYS10.9890.98415.731-0.088-0.0880.0000.0000.0000.000
12A16TYR00.0270.02217.337-0.004-0.0040.0000.0000.0000.000
13A17ILE0-0.003-0.00815.358-0.010-0.0100.0000.0000.0000.000
14A18ASP-1-0.890-0.95018.856-0.009-0.0090.0000.0000.0000.000
15A19ASN0-0.018-0.00421.031-0.014-0.0140.0000.0000.0000.000
16A20GLU-1-0.849-0.90722.1690.1210.1210.0000.0000.0000.000
17A21GLN0-0.035-0.02621.3520.0000.0000.0000.0000.0000.000
18A22GLU-1-0.946-0.95724.4260.0360.0360.0000.0000.0000.000
19A23VAL00.0370.01727.052-0.003-0.0030.0000.0000.0000.000
20A24ARG10.8500.91323.854-0.095-0.0950.0000.0000.0000.000
21A25GLU-1-0.924-0.93528.6910.0140.0140.0000.0000.0000.000
22A26ASN00.012-0.00730.330-0.006-0.0060.0000.0000.0000.000
23A27ILE0-0.037-0.01031.539-0.002-0.0020.0000.0000.0000.000
24A28ARG10.9390.96727.809-0.034-0.0340.0000.0000.0000.000
25A29ILE0-0.034-0.01334.156-0.004-0.0040.0000.0000.0000.000
26A30VAL00.0240.00736.728-0.002-0.0020.0000.0000.0000.000
27A31VAL00.0140.00336.669-0.002-0.0020.0000.0000.0000.000
28A32ARG10.9330.97037.797-0.015-0.0150.0000.0000.0000.000
29A33GLU-1-0.883-0.92639.8330.0170.0170.0000.0000.0000.000
30A34ILE00.0090.00541.525-0.002-0.0020.0000.0000.0000.000
31A35GLU-1-0.890-0.94041.3380.0160.0160.0000.0000.0000.000
32A36HIS00.0160.00643.606-0.001-0.0010.0000.0000.0000.000
33A37LEU00.010-0.00745.946-0.001-0.0010.0000.0000.0000.000
34A38SER00.0150.00746.5070.0000.0000.0000.0000.0000.000
35A39LYS10.9110.97246.299-0.014-0.0140.0000.0000.0000.000
36A40GLU-1-0.922-0.96948.9580.0100.0100.0000.0000.0000.000
37A41ALA00.0270.01251.817-0.001-0.0010.0000.0000.0000.000
38A42GLN0-0.014-0.01849.0110.0000.0000.0000.0000.0000.000
39A43ILE0-0.022-0.00951.564-0.001-0.0010.0000.0000.0000.000
40A44LYS10.9220.96754.460-0.010-0.0100.0000.0000.0000.000
41A45LEU00.0260.00355.427-0.001-0.0010.0000.0000.0000.000
42A46GLN0-0.0010.00954.7260.0000.0000.0000.0000.0000.000
43A47ILE00.0080.00058.3450.0000.0000.0000.0000.0000.000
44A48ILE00.0070.02060.6110.0000.0000.0000.0000.0000.000
45A49HIS0-0.067-0.04658.314-0.001-0.0010.0000.0000.0000.000
46A50SER0-0.054-0.03163.016-0.001-0.0010.0000.0000.0000.000
47A51ASP-1-0.830-0.92265.6000.0080.0080.0000.0000.0000.000
48A52LEU00.0580.00866.8700.0010.0010.0000.0000.0000.000
49A53SER0-0.077-0.02268.6720.0010.0010.0000.0000.0000.000
50A54GLN0-0.026-0.02365.1690.0000.0000.0000.0000.0000.000
51A55ILE00.0360.03364.1320.0000.0000.0000.0000.0000.000
52A56SER00.0300.00864.1020.0010.0010.0000.0000.0000.000
53A57ALA00.0010.00764.9350.0000.0000.0000.0000.0000.000
54A58ALA0-0.014-0.00860.4990.0000.0000.0000.0000.0000.000
55A59CYS0-0.0040.00059.8820.0010.0010.0000.0000.0000.000
56A60GLY00.0240.02460.3470.0010.0010.0000.0000.0000.000
57A61LEU0-0.051-0.02957.8720.0000.0000.0000.0000.0000.000
58A62ALA00.002-0.01855.8890.0000.0000.0000.0000.0000.000
59A63ARG10.8340.89855.433-0.020-0.0200.0000.0000.0000.000
60A64LYS10.9841.00556.419-0.013-0.0130.0000.0000.0000.000
61A65GLN0-0.006-0.00552.3520.0010.0010.0000.0000.0000.000
62A66VAL00.0090.00251.3260.0010.0010.0000.0000.0000.000
63A67GLU-1-0.917-0.95851.0580.0220.0220.0000.0000.0000.000
64A68LEU0-0.029-0.01251.1380.0000.0000.0000.0000.0000.000
65A69CYS0-0.143-0.08046.6550.0000.0000.0000.0000.0000.000
66A70ALA00.0960.05846.8880.0020.0020.0000.0000.0000.000
67A71GLN0-0.014-0.01547.3330.0010.0010.0000.0000.0000.000
68A72LYS10.7870.89443.568-0.020-0.0200.0000.0000.0000.000
69A73TYR00.009-0.05042.2180.0010.0010.0000.0000.0000.000
70A74GLN00.0120.02042.5150.0050.0050.0000.0000.0000.000
71A75LYS10.9430.98140.141-0.027-0.0270.0000.0000.0000.000
72A76LEU0-0.047-0.03536.9630.0020.0020.0000.0000.0000.000
73A77ALA0-0.0100.00037.5140.0040.0040.0000.0000.0000.000
74A78GLU-1-0.933-0.96538.1340.0470.0470.0000.0000.0000.000
75A79LEU0-0.070-0.03334.1960.0020.0020.0000.0000.0000.000
76A80VAL0-0.0050.00532.9000.0050.0050.0000.0000.0000.000
77A81PRO0-0.0040.01729.1970.0000.0000.0000.0000.0000.000
78A82ALA0-0.018-0.02930.9350.0050.0050.0000.0000.0000.000
79A83GLY00.0370.02932.085-0.007-0.0070.0000.0000.0000.000
80A84GLN0-0.017-0.03327.1150.0130.0130.0000.0000.0000.000
81A85TYR00.0700.03231.0400.0000.0000.0000.0000.0000.000
82A86TYR0-0.002-0.02332.2640.0010.0010.0000.0000.0000.000
83A87ARG10.8380.96322.407-0.149-0.1490.0000.0000.0000.000
84A88TYR0-0.057-0.06726.037-0.002-0.0020.0000.0000.0000.000
85A89SER00.0560.01831.012-0.005-0.0050.0000.0000.0000.000
86A90ASP-1-0.870-0.92430.7990.0710.0710.0000.0000.0000.000
87A91HIS0-0.122-0.07229.797-0.001-0.0010.0000.0000.0000.000
88A92TRP0-0.010-0.00134.332-0.005-0.0050.0000.0000.0000.000
89A93THR00.0590.04837.012-0.001-0.0010.0000.0000.0000.000
90A94PHE00.0210.00436.292-0.003-0.0030.0000.0000.0000.000
91A95ILE0-0.018-0.00940.375-0.003-0.0030.0000.0000.0000.000
92A96THR00.0760.06241.477-0.002-0.0020.0000.0000.0000.000
93A97GLN0-0.0020.01241.3170.0010.0010.0000.0000.0000.000
94A98ARG10.8650.93644.894-0.025-0.0250.0000.0000.0000.000
95A99LEU00.0120.01446.258-0.002-0.0020.0000.0000.0000.000
96A100ILE00.0020.02745.734-0.001-0.0010.0000.0000.0000.000
97A101PHE0-0.067-0.01849.310-0.002-0.0020.0000.0000.0000.000
98A102ILE00.006-0.00349.819-0.001-0.0010.0000.0000.0000.000
99A103ILE00.0140.00051.004-0.001-0.0010.0000.0000.0000.000
100A104ALA00.005-0.01553.639-0.001-0.0010.0000.0000.0000.000
101A105LEU0-0.004-0.00255.398-0.001-0.0010.0000.0000.0000.000
102A106VAL00.004-0.00656.642-0.001-0.0010.0000.0000.0000.000
103A107ILE00.013-0.00258.033-0.001-0.0010.0000.0000.0000.000
104A108TYR0-0.0240.00059.561-0.001-0.0010.0000.0000.0000.000
105A109LEU0-0.078-0.05560.742-0.001-0.0010.0000.0000.0000.000
106A110GLU-1-0.845-0.89462.6630.0190.0190.0000.0000.0000.000
107A111ALA0-0.034-0.02263.997-0.001-0.0010.0000.0000.0000.000
108A112GLY0-0.0070.01864.3220.0000.0000.0000.0000.0000.000
109A113PHE0-0.037-0.01760.6470.0000.0000.0000.0000.0000.000
110A114LEU00.005-0.00555.2340.0000.0000.0000.0000.0000.000
111A115VAL00.0140.03654.7350.0000.0000.0000.0000.0000.000
112A116THR00.0710.06055.1160.0010.0010.0000.0000.0000.000
113A117ARG10.9330.95946.462-0.050-0.0500.0000.0000.0000.000
114A118GLU-1-0.893-0.95651.0800.0410.0410.0000.0000.0000.000
115A119THR00.0410.02052.6610.0000.0000.0000.0000.0000.000
116A120VAL0-0.0230.00049.473-0.001-0.0010.0000.0000.0000.000
117A121ALA00.001-0.01148.5710.0000.0000.0000.0000.0000.000
118A122GLU-1-0.959-0.98349.6440.0320.0320.0000.0000.0000.000
119A123MET0-0.082-0.04852.431-0.001-0.0010.0000.0000.0000.000
120A124LEU0-0.037-0.01746.839-0.001-0.0010.0000.0000.0000.000
121A125GLY0-0.0320.00148.2680.0000.0000.0000.0000.0000.000
122A126LEU0-0.045-0.02243.4860.0020.0020.0000.0000.0000.000
123A127LYS10.9340.96444.491-0.051-0.0510.0000.0000.0000.000
124A128ILE00.0530.02245.8550.0010.0010.0000.0000.0000.000
125A129SER0-0.048-0.03444.3170.0020.0020.0000.0000.0000.000
126A130GLN00.0700.02836.5340.0010.0010.0000.0000.0000.000
127A131SER0-0.023-0.01640.3900.0020.0020.0000.0000.0000.000
128A132GLU-1-0.907-0.96241.3970.0560.0560.0000.0000.0000.000
129A133GLY0-0.016-0.00241.270-0.003-0.0030.0000.0000.0000.000
130A134PHE00.0310.02537.5760.0020.0020.0000.0000.0000.000
131A135HIS0-0.041-0.00938.246-0.005-0.0050.0000.0000.0000.000
132A136LEU00.0070.00641.9480.0000.0000.0000.0000.0000.000
133A137ASP-1-0.791-0.89939.6610.0670.0670.0000.0000.0000.000
134A138VAL0-0.029-0.01542.740-0.004-0.0040.0000.0000.0000.000
135A139GLU-1-0.843-0.93341.3540.0600.0600.0000.0000.0000.000
136A140ASP-1-0.843-0.92141.1120.0510.0510.0000.0000.0000.000
137A141TYR0-0.058-0.09343.738-0.003-0.0030.0000.0000.0000.000
138A142LEU00.002-0.00646.283-0.003-0.0030.0000.0000.0000.000
139A143LEU00.011-0.00142.437-0.003-0.0030.0000.0000.0000.000
140A144GLY0-0.025-0.00446.534-0.002-0.0020.0000.0000.0000.000
141A145ILE00.002-0.01148.435-0.003-0.0030.0000.0000.0000.000
142A146LEU0-0.030-0.01047.707-0.002-0.0020.0000.0000.0000.000
143A147GLN0-0.034-0.02246.9500.0000.0000.0000.0000.0000.000
144A148LEU0-0.0060.01350.791-0.002-0.0020.0000.0000.0000.000
145A149ALA00.0420.02254.138-0.002-0.0020.0000.0000.0000.000
146A150SER0-0.043-0.01652.618-0.002-0.0020.0000.0000.0000.000
147A151GLU-1-0.851-0.93854.4550.0160.0160.0000.0000.0000.000
148A152LEU00.013-0.00456.008-0.001-0.0010.0000.0000.0000.000
149A153SER00.0340.01657.664-0.001-0.0010.0000.0000.0000.000
150A154ARG10.8690.96352.786-0.018-0.0180.0000.0000.0000.000
151A155PHE00.003-0.00759.854-0.001-0.0010.0000.0000.0000.000
152A156ALA00.0160.00562.151-0.001-0.0010.0000.0000.0000.000
153A157THR0-0.001-0.00362.930-0.001-0.0010.0000.0000.0000.000
154A158ASN0-0.022-0.04561.578-0.001-0.0010.0000.0000.0000.000
155A159SER0-0.0040.00765.514-0.001-0.0010.0000.0000.0000.000
156A160VAL0-0.021-0.00268.0450.0000.0000.0000.0000.0000.000
157A161THR0-0.034-0.00467.150-0.001-0.0010.0000.0000.0000.000
158A162MET0-0.100-0.02866.543-0.001-0.0010.0000.0000.0000.000
159A163GLY0-0.013-0.01071.0010.0000.0000.0000.0000.0000.000
160A164ASP-1-0.866-0.94270.9500.0120.0120.0000.0000.0000.000
161A165TYR00.005-0.01071.4310.0010.0010.0000.0000.0000.000
162A166GLU-1-0.915-0.96272.2260.0140.0140.0000.0000.0000.000
163A167ARG10.9670.99466.944-0.013-0.0130.0000.0000.0000.000
164A168SER0-0.078-0.02867.5700.0010.0010.0000.0000.0000.000
165A169LEU00.003-0.00767.5740.0010.0010.0000.0000.0000.000
166A170ASN00.0030.00568.3910.0010.0010.0000.0000.0000.000
167A171ILE0-0.037-0.00562.8890.0010.0010.0000.0000.0000.000
168A172SER00.0130.00263.9380.0010.0010.0000.0000.0000.000
169A173HIS0-0.0040.00164.2060.0010.0010.0000.0000.0000.000
170A174PHE00.0340.03058.9390.0010.0010.0000.0000.0000.000
171A175ILE0-0.018-0.01558.6740.0010.0010.0000.0000.0000.000
172A176GLY0-0.0020.00259.7760.0010.0010.0000.0000.0000.000
173A177ASP-1-0.888-0.94261.0370.0250.0250.0000.0000.0000.000
174A178LEU0-0.031-0.00855.9230.0020.0020.0000.0000.0000.000
175A179ASN0-0.035-0.01956.4220.0020.0020.0000.0000.0000.000
176A180THR0-0.058-0.04156.8090.0010.0010.0000.0000.0000.000
177A181GLY00.0070.00556.7290.0010.0010.0000.0000.0000.000
178A182PHE0-0.001-0.00749.8840.0020.0020.0000.0000.0000.000
179A183ARG10.9680.97552.664-0.027-0.0270.0000.0000.0000.000
180A184LEU0-0.071-0.02754.2310.0010.0010.0000.0000.0000.000
181A185LEU0-0.057-0.01449.5440.0020.0020.0000.0000.0000.000
182A186ASN0-0.043-0.00547.3010.0030.0030.0000.0000.0000.000