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: 6G6YZ

Calculation Name: 2VGE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VGE

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WUF5

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptAll
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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2227752.627065
FMO2-HF: Nuclear repulsion 2146975.177991
FMO2-HF: Total energy -80777.449074
FMO2-MP2: Total energy -81009.098751


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:616:SER)


Summations of interaction energy for fragment #1(A:616: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.
-12.651-11.366-0.015-0.623-0.6470.002
Interaction energy analysis for fragmet #1(A:616:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.009
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].
3A618ARG10.9700.9843.8820.5481.689-0.014-0.589-0.5380.002
4A619LYS10.9390.9575.233-0.630-0.6300.0000.0000.0000.000
5A620ALA00.0090.0108.504-0.244-0.2440.0000.0000.0000.000
6A621ARG10.8580.91811.3600.1950.1950.0000.0000.0000.000
7A622ARG10.9710.96812.915-0.450-0.4500.0000.0000.0000.000
8A623ALA00.0370.00415.486-0.065-0.0650.0000.0000.0000.000
9A624ARG10.9330.96918.611-0.124-0.1240.0000.0000.0000.000
10A625LEU0-0.0060.01113.815-0.004-0.0040.0000.0000.0000.000
11A626ASN00.0560.02017.5570.0060.0060.0000.0000.0000.000
12A627PRO00.013-0.00315.597-0.027-0.0270.0000.0000.0000.000
13A628LEU00.0500.03015.647-0.066-0.0660.0000.0000.0000.000
14A629VAL00.0120.01216.292-0.034-0.0340.0000.0000.0000.000
15A630LEU0-0.016-0.01711.818-0.015-0.0150.0000.0000.0000.000
16A631LEU00.0030.01312.033-0.157-0.1570.0000.0000.0000.000
17A632LEU00.0180.01813.853-0.107-0.1070.0000.0000.0000.000
18A633ASP-1-0.871-0.93312.382-0.477-0.4770.0000.0000.0000.000
19A634ALA0-0.053-0.0159.576-0.126-0.1260.0000.0000.0000.000
20A635ALA0-0.009-0.01110.465-0.202-0.2020.0000.0000.0000.000
21A636LEU00.0020.01313.360-0.004-0.0040.0000.0000.0000.000
22A637THR0-0.090-0.0699.693-0.083-0.0830.0000.0000.0000.000
23A638GLY00.0640.0399.777-0.059-0.0590.0000.0000.0000.000
24A639GLU-1-0.974-0.9734.255-6.090-5.946-0.001-0.034-0.1090.000
25A640LEU00.0450.0217.0360.6020.6020.0000.0000.0000.000
26A641GLU-1-0.851-0.9345.024-4.410-4.4100.0000.0000.0000.000
27A642VAL0-0.070-0.0476.0540.8590.8590.0000.0000.0000.000
28A643VAL00.0420.0228.6740.4210.4210.0000.0000.0000.000
29A644GLN0-0.051-0.02411.1940.1740.1740.0000.0000.0000.000
30A645GLN0-0.075-0.04411.0430.2100.2100.0000.0000.0000.000
31A646ALA0-0.0030.00012.7480.1360.1360.0000.0000.0000.000
32A647VAL00.037-0.00214.8320.0880.0880.0000.0000.0000.000
33A648LYS10.8790.94616.2220.5130.5130.0000.0000.0000.000
34A649GLU-1-0.873-0.88115.764-0.066-0.0660.0000.0000.0000.000
35A650MET0-0.060-0.00418.5160.0240.0240.0000.0000.0000.000
36A651ASN0-0.018-0.02620.743-0.002-0.0020.0000.0000.0000.000
37A652ASP-1-0.765-0.86923.060-0.249-0.2490.0000.0000.0000.000
38A653PRO0-0.018-0.01420.041-0.012-0.0120.0000.0000.0000.000
39A654SER0-0.039-0.04320.949-0.042-0.0420.0000.0000.0000.000
40A655GLN0-0.103-0.04321.6310.0230.0230.0000.0000.0000.000
41A656PRO00.0320.03322.297-0.028-0.0280.0000.0000.0000.000
42A657ASN0-0.031-0.02121.7100.0290.0290.0000.0000.0000.000
43A658GLU-1-0.927-0.97924.487-0.110-0.1100.0000.0000.0000.000
44A659GLU-1-0.884-0.90525.975-0.158-0.1580.0000.0000.0000.000
45A660GLY00.0140.00727.477-0.007-0.0070.0000.0000.0000.000
46A661ILE0-0.019-0.00321.514-0.016-0.0160.0000.0000.0000.000
47A662THR00.026-0.01321.777-0.010-0.0100.0000.0000.0000.000
48A663ALA00.008-0.02116.891-0.031-0.0310.0000.0000.0000.000
49A664LEU00.0350.02017.885-0.073-0.0730.0000.0000.0000.000
50A665HIS00.0570.04620.326-0.043-0.0430.0000.0000.0000.000
51A666ASN0-0.001-0.01816.5670.0350.0350.0000.0000.0000.000
52A667ALA0-0.010-0.00516.013-0.044-0.0440.0000.0000.0000.000
53A668ILE0-0.034-0.00716.999-0.037-0.0370.0000.0000.0000.000
54A669CYS0-0.041-0.02719.8910.0150.0150.0000.0000.0000.000
55A670GLY0-0.027-0.00616.1210.0230.0230.0000.0000.0000.000
56A671ALA0-0.0060.00616.328-0.068-0.0680.0000.0000.0000.000
57A672ASN0-0.024-0.00313.141-0.162-0.1620.0000.0000.0000.000
58A673TYR0-0.025-0.04815.369-0.054-0.0540.0000.0000.0000.000
59A674SER00.0060.00113.161-0.009-0.0090.0000.0000.0000.000
60A675ILE0-0.068-0.03311.072-0.022-0.0220.0000.0000.0000.000
61A676VAL00.0290.01914.7860.0870.0870.0000.0000.0000.000
62A677ASP-1-0.855-0.92417.955-0.584-0.5840.0000.0000.0000.000
63A678PHE0-0.072-0.02515.0100.0600.0600.0000.0000.0000.000
64A679LEU0-0.006-0.01316.7160.0660.0660.0000.0000.0000.000
65A680ILE00.0290.01919.2680.0580.0580.0000.0000.0000.000
66A681THR0-0.055-0.04320.2810.0530.0530.0000.0000.0000.000
67A682ALA0-0.099-0.04919.7200.0370.0370.0000.0000.0000.000
68A683GLY0-0.008-0.00221.8490.0300.0300.0000.0000.0000.000
69A684ALA0-0.042-0.01121.7110.0260.0260.0000.0000.0000.000
70A685ASN00.0430.00323.8710.0060.0060.0000.0000.0000.000
71A686VAL00.0310.01125.475-0.005-0.0050.0000.0000.0000.000
72A687ASN0-0.046-0.02127.1880.0000.0000.0000.0000.0000.000
73A688SER0-0.043-0.02226.2250.0110.0110.0000.0000.0000.000
74A689PRO00.0110.01428.137-0.017-0.0170.0000.0000.0000.000
75A690ASP-1-0.826-0.90927.244-0.221-0.2210.0000.0000.0000.000
76A691SER0-0.050-0.06928.8940.0100.0100.0000.0000.0000.000
77A692HIS0-0.0150.00129.8660.0210.0210.0000.0000.0000.000
78A693GLY0-0.010-0.01132.2450.0060.0060.0000.0000.0000.000
79A694TRP0-0.042-0.02929.052-0.007-0.0070.0000.0000.0000.000
80A695THR00.026-0.00728.737-0.017-0.0170.0000.0000.0000.000
81A696PRO00.000-0.00424.914-0.008-0.0080.0000.0000.0000.000
82A697LEU00.0630.03226.251-0.018-0.0180.0000.0000.0000.000
83A698HIS00.0320.05028.895-0.014-0.0140.0000.0000.0000.000
84A699CYS0-0.046-0.01324.6430.0010.0010.0000.0000.0000.000
85A700ALA00.0300.01125.193-0.008-0.0080.0000.0000.0000.000
86A701ALA00.0500.01426.141-0.005-0.0050.0000.0000.0000.000
87A702SER0-0.056-0.00927.5340.0040.0040.0000.0000.0000.000
88A703CYS0-0.111-0.06824.159-0.005-0.0050.0000.0000.0000.000
89A704ASN0-0.056-0.04426.214-0.004-0.0040.0000.0000.0000.000
90A705ASP-1-0.743-0.84622.861-0.469-0.4690.0000.0000.0000.000
91A706THR00.028-0.03626.188-0.002-0.0020.0000.0000.0000.000
92A707VAL00.0030.01323.5160.0100.0100.0000.0000.0000.000
93A708ILE0-0.001-0.01020.383-0.005-0.0050.0000.0000.0000.000
94A709CYS0-0.046-0.02124.5060.0180.0180.0000.0000.0000.000
95A710MET0-0.020-0.00627.9220.0120.0120.0000.0000.0000.000
96A711ALA00.0010.00724.0220.0140.0140.0000.0000.0000.000
97A712LEU00.0110.00824.6240.0050.0050.0000.0000.0000.000
98A713VAL00.008-0.00327.5330.0200.0200.0000.0000.0000.000
99A714GLN0-0.057-0.04328.9900.0140.0140.0000.0000.0000.000
100A715HIS0-0.097-0.05325.8930.0100.0100.0000.0000.0000.000
101A716GLY00.0220.02529.531-0.001-0.0010.0000.0000.0000.000
102A717ALA0-0.017-0.00430.1980.0070.0070.0000.0000.0000.000
103A718ALA00.007-0.01031.8600.0110.0110.0000.0000.0000.000
104A719ILE0-0.026-0.01534.255-0.002-0.0020.0000.0000.0000.000
105A720PHE00.006-0.00135.994-0.001-0.0010.0000.0000.0000.000
106A721ALA0-0.014-0.00534.5970.0090.0090.0000.0000.0000.000
107A722THR0-0.012-0.00436.427-0.004-0.0040.0000.0000.0000.000
108A723THR0-0.087-0.04533.250-0.001-0.0010.0000.0000.0000.000
109A724LEU00.004-0.01135.2090.0100.0100.0000.0000.0000.000
110A725SER0-0.017-0.02935.0680.0060.0060.0000.0000.0000.000
111A726ASP-1-0.881-0.90436.334-0.168-0.1680.0000.0000.0000.000
112A727GLY00.0130.01438.8640.0050.0050.0000.0000.0000.000
113A728ALA0-0.0040.02036.6540.0000.0000.0000.0000.0000.000
114A729THR00.005-0.03436.757-0.009-0.0090.0000.0000.0000.000
115A730ALA0-0.002-0.01132.589-0.006-0.0060.0000.0000.0000.000
116A731PHE00.0150.00733.883-0.007-0.0070.0000.0000.0000.000
117A732GLU-1-0.877-0.93036.157-0.148-0.1480.0000.0000.0000.000
118A733LYS10.7930.89332.1880.1860.1860.0000.0000.0000.000
119A734CYS0-0.0620.00032.198-0.016-0.0160.0000.0000.0000.000
120A735ASP-1-0.758-0.87730.719-0.206-0.2060.0000.0000.0000.000
121A736PRO0-0.030-0.01632.654-0.008-0.0080.0000.0000.0000.000
122A737TYR0-0.100-0.04732.8170.0110.0110.0000.0000.0000.000
123A738ARG10.8300.90925.9880.2750.2750.0000.0000.0000.000
124A739GLU-1-0.924-0.96127.428-0.296-0.2960.0000.0000.0000.000
125A740GLY00.0550.02029.648-0.009-0.0090.0000.0000.0000.000
126A741TYR0-0.0270.00030.6220.0100.0100.0000.0000.0000.000
127A742ALA0-0.002-0.00733.2430.0030.0030.0000.0000.0000.000
128A743ASP-1-0.888-0.89731.529-0.250-0.2500.0000.0000.0000.000
129A744CYS00.0180.03229.9590.0050.0050.0000.0000.0000.000
130A745ALA00.0390.00632.5850.0050.0050.0000.0000.0000.000
131A746THR0-0.048-0.04235.8610.0130.0130.0000.0000.0000.000
132A747TYR00.0240.00531.5960.0010.0010.0000.0000.0000.000
133A748LEU00.026-0.00231.6900.0040.0040.0000.0000.0000.000
134A749ALA00.0070.01735.7260.0080.0080.0000.0000.0000.000
135A750ASP-1-0.973-0.98338.255-0.163-0.1630.0000.0000.0000.000
136A751VAL00.008-0.00234.7100.0060.0060.0000.0000.0000.000
137A752GLU-1-0.823-0.90538.108-0.157-0.1570.0000.0000.0000.000
138A753GLN0-0.002-0.00140.2570.0100.0100.0000.0000.0000.000
139A754SER0-0.064-0.04239.9240.0060.0060.0000.0000.0000.000
140A755MET00.0060.01439.7580.0030.0030.0000.0000.0000.000
141A756GLY00.0290.00742.7800.0060.0060.0000.0000.0000.000
142A757LEU0-0.062-0.02245.2690.0070.0070.0000.0000.0000.000
143A758MET0-0.013-0.01241.7570.0050.0050.0000.0000.0000.000
144A759ASN0-0.059-0.03741.4070.0030.0030.0000.0000.0000.000
145A760SER0-0.021-0.02043.6060.0020.0020.0000.0000.0000.000
146A761GLY00.0530.03446.3490.0050.0050.0000.0000.0000.000
147A762ALA0-0.052-0.01144.1780.0010.0010.0000.0000.0000.000
148A763VAL00.0110.01241.173-0.008-0.0080.0000.0000.0000.000
149A764TYR0-0.014-0.00937.8180.0070.0070.0000.0000.0000.000
150A765ALA00.0460.04138.757-0.006-0.0060.0000.0000.0000.000
151A766LEU0-0.030-0.00234.156-0.006-0.0060.0000.0000.0000.000
152A767TRP0-0.022-0.02133.880-0.010-0.0100.0000.0000.0000.000
153A768ASP-1-0.824-0.90438.350-0.110-0.1100.0000.0000.0000.000
154A769TYR0-0.052-0.04441.560-0.003-0.0030.0000.0000.0000.000
155A770SER0-0.054-0.04244.6690.0010.0010.0000.0000.0000.000
156A771ALA00.0030.01348.2110.0000.0000.0000.0000.0000.000
157A772GLU-1-0.975-0.97348.786-0.080-0.0800.0000.0000.0000.000
158A773PHE0-0.049-0.02452.4320.0060.0060.0000.0000.0000.000
159A774GLY0-0.053-0.03754.968-0.002-0.0020.0000.0000.0000.000
160A775ASP-1-0.904-0.95256.810-0.071-0.0710.0000.0000.0000.000
161A776GLU-1-0.744-0.84750.688-0.087-0.0870.0000.0000.0000.000
162A777LEU0-0.030-0.01049.4460.0030.0030.0000.0000.0000.000
163A778SER0-0.016-0.01048.484-0.003-0.0030.0000.0000.0000.000
164A779PHE00.0050.00542.1200.0010.0010.0000.0000.0000.000
165A780ARG10.7510.85242.2800.1010.1010.0000.0000.0000.000
166A781GLU-1-0.800-0.88535.011-0.178-0.1780.0000.0000.0000.000
167A782GLY0-0.022-0.01137.7070.0020.0020.0000.0000.0000.000
168A783GLU-1-0.851-0.91538.459-0.103-0.1030.0000.0000.0000.000
169A784SER0-0.036-0.02241.488-0.005-0.0050.0000.0000.0000.000
170A785VAL00.0040.00343.3320.0070.0070.0000.0000.0000.000
171A786THR00.0000.00845.702-0.005-0.0050.0000.0000.0000.000
172A787VAL0-0.0110.00046.2810.0050.0050.0000.0000.0000.000
173A788LEU0-0.055-0.02449.0630.0010.0010.0000.0000.0000.000
174A789ARG10.7240.83352.4060.0810.0810.0000.0000.0000.000
175A790ARG10.8120.88945.8430.1190.1190.0000.0000.0000.000
176A791ASP-1-0.857-0.89650.086-0.106-0.1060.0000.0000.0000.000
177A792GLY00.0070.00351.8680.0040.0040.0000.0000.0000.000
178A793PRO0-0.049-0.02853.715-0.001-0.0010.0000.0000.0000.000
179A794GLU-1-0.869-0.92856.019-0.076-0.0760.0000.0000.0000.000
180A795GLU-1-0.915-0.96451.094-0.088-0.0880.0000.0000.0000.000
181A796THR0-0.004-0.01049.0820.0000.0000.0000.0000.0000.000
182A797ASP-1-0.847-0.88845.453-0.119-0.1190.0000.0000.0000.000
183A798TRP0-0.040-0.01446.364-0.005-0.0050.0000.0000.0000.000
184A799TRP00.0120.00242.358-0.001-0.0010.0000.0000.0000.000
185A800TRP0-0.033-0.01749.4760.0010.0010.0000.0000.0000.000
186A801ALA00.008-0.00148.888-0.003-0.0030.0000.0000.0000.000
187A802ALA00.0420.01850.4020.0040.0040.0000.0000.0000.000
188A803LEU00.0040.00346.970-0.005-0.0050.0000.0000.0000.000
189A804HIS0-0.059-0.03647.6030.0070.0070.0000.0000.0000.000
190A805GLY0-0.040-0.01952.3090.0040.0040.0000.0000.0000.000
191A806GLN0-0.068-0.02653.6180.0050.0050.0000.0000.0000.000
192A807GLU-1-0.883-0.95053.849-0.078-0.0780.0000.0000.0000.000
193A808GLY00.0180.00853.4990.0030.0030.0000.0000.0000.000
194A809TYR0-0.006-0.00651.223-0.004-0.0040.0000.0000.0000.000
195A810VAL0-0.026-0.00846.1500.0010.0010.0000.0000.0000.000
196A811PRO00.0590.04943.994-0.001-0.0010.0000.0000.0000.000
197A812ARG10.8920.91642.9100.1190.1190.0000.0000.0000.000
198A813ASN00.0180.00738.981-0.002-0.0020.0000.0000.0000.000
199A814TYR0-0.045-0.02438.364-0.009-0.0090.0000.0000.0000.000
200A815PHE00.009-0.00239.154-0.001-0.0010.0000.0000.0000.000
201A816GLY00.0640.02635.955-0.007-0.0070.0000.0000.0000.000
202A817LEU0-0.024-0.01135.9490.0080.0080.0000.0000.0000.000
203A818PHE0-0.0060.00033.4230.0040.0040.0000.0000.0000.000
204A819PRO00.0180.00734.5460.0000.0000.0000.0000.0000.000
205A820ARG10.8360.91330.6750.1910.1910.0000.0000.0000.000
206A821VAL00.0060.01626.2290.0140.0140.0000.0000.0000.000
207A822LYS10.7670.86929.5740.1880.1880.0000.0000.0000.000