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: R9M98

Calculation Name: 1VK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FNG3

Base Structure: X-ray

Registration Date: 2023-06-22

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2376942.213157
FMO2-HF: Nuclear repulsion 2297029.726173
FMO2-HF: Total energy -79912.486984
FMO2-MP2: Total energy -80150.864639


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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-0.5170.568-0.005-0.447-0.6330.002
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / 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].
3A3SER00.0170.0063.869-0.0651.020-0.005-0.447-0.6330.002
4A4PHE00.015-0.0116.2300.3400.3400.0000.0000.0000.000
5A5ASP-1-0.906-0.9456.995-2.254-2.2540.0000.0000.0000.000
6A6GLY00.0240.0249.6240.1410.1410.0000.0000.0000.000
7A7PRO00.0200.00812.778-0.042-0.0420.0000.0000.0000.000
8A8LYS10.9300.98714.7790.6630.6630.0000.0000.0000.000
9A9PHE00.0530.01817.2770.0310.0310.0000.0000.0000.000
10A10LYS10.9180.97920.9940.2440.2440.0000.0000.0000.000
11A11MET00.0230.01622.5390.0270.0270.0000.0000.0000.000
12A12THR0-0.009-0.01925.675-0.002-0.0020.0000.0000.0000.000
13A13ASP-1-0.799-0.88026.041-0.208-0.2080.0000.0000.0000.000
14A14GLY0-0.106-0.05726.3200.0000.0000.0000.0000.0000.000
15A15SER0-0.050-0.02821.837-0.033-0.0330.0000.0000.0000.000
16A16TYR0-0.018-0.03318.4430.0040.0040.0000.0000.0000.000
17A17VAL00.0410.03618.212-0.016-0.0160.0000.0000.0000.000
18A18GLN0-0.041-0.02411.0590.0790.0790.0000.0000.0000.000
19A19THR0-0.038-0.03314.6570.0640.0640.0000.0000.0000.000
20A20LYS10.9050.9507.9731.4091.4090.0000.0000.0000.000
21A21THR00.0250.01412.8130.1330.1330.0000.0000.0000.000
22A22ILE0-0.044-0.02411.270-0.057-0.0570.0000.0000.0000.000
23A23ASP-1-0.837-0.89914.083-0.126-0.1260.0000.0000.0000.000
24A24VAL0-0.046-0.02615.7070.0380.0380.0000.0000.0000.000
25A25GLY00.0420.01516.807-0.016-0.0160.0000.0000.0000.000
26A26SER0-0.029-0.02018.4170.0300.0300.0000.0000.0000.000
27A27SER0-0.011-0.01216.0310.0110.0110.0000.0000.0000.000
28A28THR0-0.0030.01612.5360.0800.0800.0000.0000.0000.000
29A29ASP-1-0.758-0.8589.7591.0111.0110.0000.0000.0000.000
30A30ILE00.0280.00210.2910.0340.0340.0000.0000.0000.000
31A31SER0-0.030-0.02411.3750.0010.0010.0000.0000.0000.000
32A32PRO0-0.0100.0006.289-0.029-0.0290.0000.0000.0000.000
33A33TYR00.0160.0066.613-0.435-0.4350.0000.0000.0000.000
34A34LEU00.0220.01110.420-0.089-0.0890.0000.0000.0000.000
35A35SER0-0.091-0.05910.051-0.093-0.0930.0000.0000.0000.000
36A36LEU00.0420.0296.415-0.097-0.0970.0000.0000.0000.000
37A37ILE00.0180.02910.749-0.083-0.0830.0000.0000.0000.000
38A38ARG10.9250.95714.337-0.380-0.3800.0000.0000.0000.000
39A39GLU-1-0.986-0.99210.5370.1140.1140.0000.0000.0000.000
40A40ASP-1-0.761-0.87613.694-0.289-0.2890.0000.0000.0000.000
41A41SER00.0310.00415.243-0.002-0.0020.0000.0000.0000.000
42A42ILE0-0.109-0.06417.8470.0030.0030.0000.0000.0000.000
43A43LEU0-0.062-0.02314.6500.0000.0000.0000.0000.0000.000
44A44ASN0-0.031-0.01716.0830.0040.0040.0000.0000.0000.000
45A45GLY00.0020.01319.633-0.012-0.0120.0000.0000.0000.000
46A46ASN00.0100.00821.5010.0140.0140.0000.0000.0000.000
47A47ARG10.8430.91322.064-0.061-0.0610.0000.0000.0000.000
48A48ALA00.0700.05923.0810.0130.0130.0000.0000.0000.000
49A49VAL0-0.038-0.02119.665-0.010-0.0100.0000.0000.0000.000
50A50ILE0-0.0050.01222.1290.0140.0140.0000.0000.0000.000
51A51PHE0-0.041-0.03522.543-0.007-0.0070.0000.0000.0000.000
52A52ASP-1-0.868-0.92924.427-0.077-0.0770.0000.0000.0000.000
53A53VAL0-0.069-0.03824.9310.0030.0030.0000.0000.0000.000
54A54TYR00.0270.02423.829-0.011-0.0110.0000.0000.0000.000
55A55TRP0-0.010-0.03027.6230.0100.0100.0000.0000.0000.000
56A56ASP-1-0.952-0.98029.784-0.031-0.0310.0000.0000.0000.000
57A57VAL00.0110.02031.4870.0080.0080.0000.0000.0000.000
58A58GLY00.0560.02735.242-0.001-0.0010.0000.0000.0000.000
59A59PHE0-0.036-0.02937.0090.0000.0000.0000.0000.0000.000
60A60PRO0-0.103-0.07239.2910.0030.0030.0000.0000.0000.000
61A61GLU-1-0.776-0.84740.0540.0110.0110.0000.0000.0000.000
62A62THR00.033-0.00439.3410.0000.0000.0000.0000.0000.000
63A63GLU-1-0.831-0.90041.6680.0320.0320.0000.0000.0000.000
64A64THR0-0.055-0.05643.039-0.002-0.0020.0000.0000.0000.000
65A65LYS10.7850.90145.164-0.017-0.0170.0000.0000.0000.000
66A66THR00.0300.02341.357-0.004-0.0040.0000.0000.0000.000
67A67LYS10.9010.90342.147-0.006-0.0060.0000.0000.0000.000
68A68THR00.0500.04838.838-0.002-0.0020.0000.0000.0000.000
69A69SER0-0.0350.01437.7110.0010.0010.0000.0000.0000.000
70A70GLY00.020-0.00336.6530.0040.0040.0000.0000.0000.000
71A71TRP0-0.0290.00534.098-0.004-0.0040.0000.0000.0000.000
72A72SER0-0.023-0.00130.5180.0080.0080.0000.0000.0000.000
73A73LEU0-0.011-0.01724.968-0.008-0.0080.0000.0000.0000.000
74A74SER0-0.042-0.00826.0310.0040.0040.0000.0000.0000.000
75A75SER0-0.031-0.03321.866-0.013-0.0130.0000.0000.0000.000
76A76VAL00.0300.01720.6310.0120.0120.0000.0000.0000.000
77A77LYS10.9040.96920.4880.1250.1250.0000.0000.0000.000
78A78LEU0-0.041-0.02417.6090.0350.0350.0000.0000.0000.000
79A79SER00.017-0.00618.342-0.045-0.0450.0000.0000.0000.000
80A80THR0-0.049-0.03916.8050.0300.0300.0000.0000.0000.000
81A81ARG10.8600.90619.5260.1360.1360.0000.0000.0000.000
82A82ASN0-0.008-0.01815.633-0.020-0.0200.0000.0000.0000.000
83A83LEU0-0.0260.00712.239-0.094-0.0940.0000.0000.0000.000
84A84CYS0-0.0010.01015.7770.0930.0930.0000.0000.0000.000
85A85LEU0-0.049-0.01912.944-0.080-0.0800.0000.0000.0000.000
86A86PHE00.0340.00915.9880.0680.0680.0000.0000.0000.000
87A87LEU0-0.020-0.01415.099-0.021-0.0210.0000.0000.0000.000
88A88ARG10.9050.92917.9340.1920.1920.0000.0000.0000.000
89A89LEU0-0.0130.00319.5110.0180.0180.0000.0000.0000.000
90A90PRO00.0160.01820.625-0.011-0.0110.0000.0000.0000.000
91A91LYS10.9590.97323.503-0.008-0.0080.0000.0000.0000.000
92A92PRO0-0.037-0.01225.9010.0010.0010.0000.0000.0000.000
93A93PHE00.0430.01723.6720.0100.0100.0000.0000.0000.000
94A94HIS00.0420.00921.5390.0040.0040.0000.0000.0000.000
95A95ASP-1-0.874-0.95621.2210.2170.2170.0000.0000.0000.000
96A96ASN0-0.061-0.03516.248-0.005-0.0050.0000.0000.0000.000
97A97LEU00.0400.01817.4830.0200.0200.0000.0000.0000.000
98A98LYS10.9030.95819.899-0.214-0.2140.0000.0000.0000.000
99A99ASP-1-0.829-0.90215.3020.4740.4740.0000.0000.0000.000
100A100LEU00.0080.01818.159-0.008-0.0080.0000.0000.0000.000
101A101TYR0-0.046-0.04719.650-0.014-0.0140.0000.0000.0000.000
102A102ARG10.8190.87818.303-0.341-0.3410.0000.0000.0000.000
103A103PHE0-0.024-0.01216.7230.0050.0050.0000.0000.0000.000
104A104PHE00.0790.02920.155-0.016-0.0160.0000.0000.0000.000
105A105ALA00.0080.02323.361-0.015-0.0150.0000.0000.0000.000
106A106SER0-0.0250.00121.510-0.006-0.0060.0000.0000.0000.000
107A107LYS10.9800.97823.935-0.103-0.1030.0000.0000.0000.000
108A108PHE0-0.074-0.03219.660-0.004-0.0040.0000.0000.0000.000
109A109VAL00.0370.02420.504-0.006-0.0060.0000.0000.0000.000
110A110THR00.0270.02023.7570.0150.0150.0000.0000.0000.000
111A111PHE0-0.045-0.01421.342-0.011-0.0110.0000.0000.0000.000
112A112VAL00.0270.00925.9250.0040.0040.0000.0000.0000.000
113A113GLY00.0580.02827.085-0.011-0.0110.0000.0000.0000.000
114A114VAL0-0.011-0.02729.4270.0020.0020.0000.0000.0000.000
115A115GLN0-0.079-0.03732.3740.0030.0030.0000.0000.0000.000
116A116ILE00.0470.01530.2600.0010.0010.0000.0000.0000.000
117A117GLU-1-1.000-0.99633.4670.0010.0010.0000.0000.0000.000
118A118GLU-1-0.856-0.93536.4760.0000.0000.0000.0000.0000.000
119A119ASP-1-0.794-0.89231.196-0.022-0.0220.0000.0000.0000.000
120A120LEU0-0.073-0.05230.8060.0090.0090.0000.0000.0000.000
121A121ASP-1-0.848-0.91733.0480.0240.0240.0000.0000.0000.000
122A122LEU00.0540.03633.7880.0060.0060.0000.0000.0000.000
123A123LEU0-0.060-0.02827.7630.0080.0080.0000.0000.0000.000
124A124ARG10.8510.93031.170-0.023-0.0230.0000.0000.0000.000
125A125GLU-1-0.987-1.00333.1680.0280.0280.0000.0000.0000.000
126A126ASN0-0.051-0.04132.9800.0060.0060.0000.0000.0000.000
127A127HIS0-0.0210.00928.290-0.005-0.0050.0000.0000.0000.000
128A128GLY00.0490.06129.3480.0130.0130.0000.0000.0000.000
129A129LEU0-0.077-0.03624.3750.0150.0150.0000.0000.0000.000
130A130VAL0-0.020-0.01828.257-0.010-0.0100.0000.0000.0000.000
131A131ILE00.0360.02026.5220.0120.0120.0000.0000.0000.000
132A132ARG10.7670.85826.524-0.117-0.1170.0000.0000.0000.000
133A133ASN0-0.042-0.01127.304-0.008-0.0080.0000.0000.0000.000
134A134ALA00.0260.02028.207-0.003-0.0030.0000.0000.0000.000
135A135ILE00.0180.01329.9690.0010.0010.0000.0000.0000.000
136A136ASN00.0310.02931.386-0.010-0.0100.0000.0000.0000.000
137A137VAL00.0460.00431.4400.0020.0020.0000.0000.0000.000
138A138GLY00.0350.02233.767-0.001-0.0010.0000.0000.0000.000
139A139LYS10.9540.97736.8340.0110.0110.0000.0000.0000.000
140A140LEU00.0390.03034.1370.0010.0010.0000.0000.0000.000
141A141ALA00.0450.01536.4360.0000.0000.0000.0000.0000.000
142A142ALA0-0.041-0.01038.125-0.001-0.0010.0000.0000.0000.000
143A143GLU-1-0.974-1.00341.137-0.011-0.0110.0000.0000.0000.000
144A144ALA0-0.046-0.01238.8520.0010.0010.0000.0000.0000.000
145A145ARG10.8480.91637.9530.0550.0550.0000.0000.0000.000
146A146GLY00.0180.02842.5180.0000.0000.0000.0000.0000.000
147A147THR0-0.111-0.05343.380-0.001-0.0010.0000.0000.0000.000
148A148LEU00.0480.00643.860-0.001-0.0010.0000.0000.0000.000
149A149VAL00.022-0.00443.6320.0000.0000.0000.0000.0000.000
150A150LEU0-0.0020.00439.486-0.002-0.0020.0000.0000.0000.000
151A151GLU-1-0.895-0.93839.333-0.021-0.0210.0000.0000.0000.000
152A152PHE0-0.072-0.03040.0730.0000.0000.0000.0000.0000.000
153A153LEU0-0.056-0.00738.599-0.002-0.0020.0000.0000.0000.000
154A154GLY00.0780.03036.2390.0020.0020.0000.0000.0000.000
155A155THR00.010-0.00429.7990.0030.0030.0000.0000.0000.000
156A156ARG10.8800.90533.1450.0900.0900.0000.0000.0000.000
157A157GLU-1-0.814-0.91634.172-0.071-0.0710.0000.0000.0000.000
158A158LEU00.0360.01533.6180.0020.0020.0000.0000.0000.000
159A159ALA00.0380.01232.2800.0010.0010.0000.0000.0000.000
160A160HIS0-0.091-0.04134.126-0.001-0.0010.0000.0000.0000.000
161A161ARG10.8540.92837.1630.0590.0590.0000.0000.0000.000
162A162VAL00.0060.01534.8860.0050.0050.0000.0000.0000.000
163A163LEU0-0.010-0.01731.1850.0000.0000.0000.0000.0000.000
164A164TRP0-0.105-0.02735.619-0.001-0.0010.0000.0000.0000.000
165A165SER00.0030.00632.179-0.001-0.0010.0000.0000.0000.000
166A166ASP-1-0.917-0.96234.052-0.121-0.1210.0000.0000.0000.000
167A167LEU00.028-0.00232.667-0.010-0.0100.0000.0000.0000.000
168A168GLY00.0200.01834.4100.0010.0010.0000.0000.0000.000
169A169GLN0-0.044-0.03327.7090.0160.0160.0000.0000.0000.000
170A170LEU00.0000.00029.027-0.003-0.0030.0000.0000.0000.000
171A171ASP-1-0.775-0.85731.378-0.099-0.0990.0000.0000.0000.000
172A172SER0-0.057-0.01433.2050.0080.0080.0000.0000.0000.000
173A173ILE0-0.012-0.00327.6130.0050.0050.0000.0000.0000.000
174A174GLH0-0.077-0.10130.9650.0080.0080.0000.0000.0000.000
175A175ALA0-0.036-0.01133.4120.0080.0080.0000.0000.0000.000
176A176LYS10.8460.93832.1970.1470.1470.0000.0000.0000.000
177A177TRP00.0580.03927.587-0.008-0.0080.0000.0000.0000.000
178A178GLU-1-0.887-0.95732.039-0.093-0.0930.0000.0000.0000.000
179A179LYS10.8560.92333.4460.0850.0850.0000.0000.0000.000
180A180ALA0-0.0110.02629.386-0.006-0.0060.0000.0000.0000.000
181A181GLY00.0140.01127.5090.0040.0040.0000.0000.0000.000
182A182PRO00.017-0.01222.776-0.005-0.0050.0000.0000.0000.000
183A183GLU-1-0.925-0.96920.606-0.377-0.3770.0000.0000.0000.000
184A184GLU-1-0.844-0.93922.797-0.182-0.1820.0000.0000.0000.000
185A185GLN0-0.045-0.01125.561-0.001-0.0010.0000.0000.0000.000
186A186LEU0-0.017-0.01018.2320.0040.0040.0000.0000.0000.000
187A187GLU-1-0.871-0.92722.471-0.253-0.2530.0000.0000.0000.000
188A188ALA0-0.003-0.00623.5540.0040.0040.0000.0000.0000.000
189A189ALA00.0200.02623.1270.0110.0110.0000.0000.0000.000
190A190ALA00.015-0.00820.4970.0090.0090.0000.0000.0000.000
191A191ILE00.001-0.00322.3410.0100.0100.0000.0000.0000.000
192A192GLU-1-0.839-0.89525.554-0.103-0.1030.0000.0000.0000.000
193A193GLY0-0.025-0.01523.3300.0160.0160.0000.0000.0000.000
194A194TRP00.0250.01422.7230.0200.0200.0000.0000.0000.000
195A195LEU0-0.004-0.00524.4770.0150.0150.0000.0000.0000.000
196A196ILE0-0.0020.00927.2470.0120.0120.0000.0000.0000.000
197A197VAL0-0.011-0.00422.5110.0100.0100.0000.0000.0000.000
198A198ASN00.000-0.01525.8280.0160.0160.0000.0000.0000.000
199A199VAL0-0.027-0.00628.4020.0090.0090.0000.0000.0000.000
200A200TRP00.006-0.01427.1150.0120.0120.0000.0000.0000.000
201A201ASP-1-0.833-0.90926.112-0.096-0.0960.0000.0000.0000.000
202A202GLN0-0.058-0.01929.3510.0090.0090.0000.0000.0000.000
203A203LEU0-0.009-0.02033.0040.0060.0060.0000.0000.0000.000
204A204SER0-0.066-0.02530.6360.0080.0080.0000.0000.0000.000
205A205ASP-1-1.003-0.99431.422-0.046-0.0460.0000.0000.0000.000
206A206GLU-1-0.957-0.96034.248-0.046-0.0460.0000.0000.0000.000