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: 7MG6K

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2225079.254083
FMO2-HF: Nuclear repulsion 2144303.017492
FMO2-HF: Total energy -80776.23659
FMO2-MP2: Total energy -81008.030266


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.
-4.678-3.362-0.007-0.581-0.7280.003
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 : 0.003 / 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].
3A618ARG11.0211.0223.8240.4671.578-0.005-0.570-0.5370.003
4A619LYS10.9450.9596.2270.7910.7910.0000.0000.0000.000
5A620ALA00.0120.0108.496-0.116-0.1160.0000.0000.0000.000
6A621ARG10.9350.98011.6640.2720.2720.0000.0000.0000.000
7A622ARG10.9710.97313.116-0.212-0.2120.0000.0000.0000.000
8A623ALA00.038-0.00415.504-0.036-0.0360.0000.0000.0000.000
9A624ARG10.9320.96718.837-0.076-0.0760.0000.0000.0000.000
10A625LEU00.0050.02514.6900.0090.0090.0000.0000.0000.000
11A626ASN00.0410.01218.350-0.015-0.0150.0000.0000.0000.000
12A627PRO00.027-0.00615.964-0.008-0.0080.0000.0000.0000.000
13A628LEU00.0670.04815.943-0.046-0.0460.0000.0000.0000.000
14A629VAL00.0080.00317.025-0.021-0.0210.0000.0000.0000.000
15A630LEU0-0.024-0.01612.3470.0070.0070.0000.0000.0000.000
16A631LEU0-0.0080.01112.559-0.080-0.0800.0000.0000.0000.000
17A632LEU00.0280.00913.849-0.059-0.0590.0000.0000.0000.000
18A633ASP-1-0.876-0.92813.174-0.138-0.1380.0000.0000.0000.000
19A634ALA0-0.040-0.0219.6040.0030.0030.0000.0000.0000.000
20A635ALA0-0.004-0.00410.902-0.099-0.0990.0000.0000.0000.000
21A636LEU0-0.0100.00413.5400.0090.0090.0000.0000.0000.000
22A637THR0-0.094-0.06010.2950.0120.0120.0000.0000.0000.000
23A638GLY00.0520.03210.4370.0620.0620.0000.0000.0000.000
24A639GLU-1-0.963-0.9664.869-1.407-1.345-0.001-0.002-0.0590.000
25A640LEU00.0410.0137.3530.0280.0280.0000.0000.0000.000
26A641GLU-1-0.837-0.9284.446-4.192-4.049-0.001-0.009-0.1320.000
27A642VAL0-0.071-0.0415.9870.6280.6280.0000.0000.0000.000
28A643VAL00.0400.0278.3730.3620.3620.0000.0000.0000.000
29A644GLN0-0.052-0.03110.6470.0820.0820.0000.0000.0000.000
30A645GLN0-0.084-0.04810.6620.1210.1210.0000.0000.0000.000
31A646ALA0-0.001-0.00612.3250.1540.1540.0000.0000.0000.000
32A647VAL00.0280.00114.4570.0910.0910.0000.0000.0000.000
33A648LYS10.8470.93915.0860.6900.6900.0000.0000.0000.000
34A649GLU-1-0.972-0.97216.266-0.247-0.2470.0000.0000.0000.000
35A650MET0-0.076-0.00618.3310.0310.0310.0000.0000.0000.000
36A651ASN0-0.003-0.01720.313-0.007-0.0070.0000.0000.0000.000
37A652ASP-1-0.807-0.90123.123-0.218-0.2180.0000.0000.0000.000
38A653PRO00.000-0.01319.972-0.008-0.0080.0000.0000.0000.000
39A654SER0-0.023-0.00420.746-0.020-0.0200.0000.0000.0000.000
40A655GLN0-0.071-0.02821.6930.0220.0220.0000.0000.0000.000
41A656PRO00.0130.02022.257-0.017-0.0170.0000.0000.0000.000
42A657ASN0-0.010-0.01022.3780.0120.0120.0000.0000.0000.000
43A658GLU-1-0.954-1.00624.504-0.063-0.0630.0000.0000.0000.000
44A659GLU-1-0.918-0.94726.084-0.070-0.0700.0000.0000.0000.000
45A660GLY0-0.0060.00427.364-0.001-0.0010.0000.0000.0000.000
46A661ILE0-0.0110.00121.513-0.013-0.0130.0000.0000.0000.000
47A662THR00.007-0.03721.871-0.015-0.0150.0000.0000.0000.000
48A663ALA00.013-0.02216.698-0.005-0.0050.0000.0000.0000.000
49A664LEU00.0330.01518.060-0.026-0.0260.0000.0000.0000.000
50A665HIS00.0540.06120.130-0.018-0.0180.0000.0000.0000.000
51A666ASN00.003-0.02317.1370.0270.0270.0000.0000.0000.000
52A667ALA0-0.015-0.00116.155-0.003-0.0030.0000.0000.0000.000
53A668ILE0-0.038-0.00517.097-0.005-0.0050.0000.0000.0000.000
54A669CYS0-0.040-0.01520.3500.0160.0160.0000.0000.0000.000
55A670GLY0-0.026-0.00816.4500.0250.0250.0000.0000.0000.000
56A671ALA00.0030.01516.651-0.011-0.0110.0000.0000.0000.000
57A672ASN0-0.043-0.01713.334-0.057-0.0570.0000.0000.0000.000
58A673TYR0-0.025-0.05415.365-0.065-0.0650.0000.0000.0000.000
59A674SER00.0080.01112.5410.0040.0040.0000.0000.0000.000
60A675ILE0-0.019-0.01210.795-0.039-0.0390.0000.0000.0000.000
61A676VAL00.0140.00714.3730.0290.0290.0000.0000.0000.000
62A677ASP-1-0.855-0.92217.999-0.412-0.4120.0000.0000.0000.000
63A678PHE0-0.071-0.03515.0220.0020.0020.0000.0000.0000.000
64A679LEU0-0.005-0.02016.2950.0330.0330.0000.0000.0000.000
65A680ILE00.0290.02718.7540.0380.0380.0000.0000.0000.000
66A681THR0-0.041-0.01620.2230.0360.0360.0000.0000.0000.000
67A682ALA0-0.089-0.04519.0820.0190.0190.0000.0000.0000.000
68A683GLY0-0.012-0.00321.2240.0200.0200.0000.0000.0000.000
69A684ALA0-0.068-0.02421.1050.0220.0220.0000.0000.0000.000
70A685ASN00.031-0.00523.2330.0130.0130.0000.0000.0000.000
71A686VAL00.0570.01925.2600.0000.0000.0000.0000.0000.000
72A687ASN0-0.030-0.02326.8740.0080.0080.0000.0000.0000.000
73A688SER0-0.077-0.03826.3250.0110.0110.0000.0000.0000.000
74A689PRO00.0060.00028.093-0.008-0.0080.0000.0000.0000.000
75A690ASP-1-0.814-0.89127.371-0.120-0.1200.0000.0000.0000.000
76A691SER00.012-0.00629.2170.0060.0060.0000.0000.0000.000
77A692HIS0-0.018-0.01231.2890.0070.0070.0000.0000.0000.000
78A693GLY0-0.005-0.01832.4370.0040.0040.0000.0000.0000.000
79A694TRP0-0.022-0.01228.715-0.002-0.0020.0000.0000.0000.000
80A695THR00.0130.00129.100-0.011-0.0110.0000.0000.0000.000
81A696PRO00.008-0.01124.6870.0020.0020.0000.0000.0000.000
82A697LEU00.0550.02426.359-0.005-0.0050.0000.0000.0000.000
83A698HIS00.0090.02828.896-0.003-0.0030.0000.0000.0000.000
84A699CYS0-0.043-0.00824.9430.0070.0070.0000.0000.0000.000
85A700ALA00.0410.02025.3320.0020.0020.0000.0000.0000.000
86A701ALA00.0600.01926.2690.0030.0030.0000.0000.0000.000
87A702SER0-0.0190.02027.6490.0080.0080.0000.0000.0000.000
88A703CYS0-0.096-0.04024.5770.0090.0090.0000.0000.0000.000
89A704ASN0-0.064-0.05326.791-0.002-0.0020.0000.0000.0000.000
90A705ASP-1-0.751-0.86522.774-0.241-0.2410.0000.0000.0000.000
91A706THR00.034-0.01226.255-0.009-0.0090.0000.0000.0000.000
92A707VAL00.0140.01123.290-0.002-0.0020.0000.0000.0000.000
93A708ILE0-0.013-0.00420.527-0.015-0.0150.0000.0000.0000.000
94A709CYS0-0.023-0.01024.4480.0030.0030.0000.0000.0000.000
95A710MET0-0.024-0.00127.9690.0040.0040.0000.0000.0000.000
96A711ALA00.0190.02424.1880.0030.0030.0000.0000.0000.000
97A712LEU0-0.0020.00724.319-0.002-0.0020.0000.0000.0000.000
98A713VAL00.0090.00627.3420.0080.0080.0000.0000.0000.000
99A714GLN0-0.073-0.05828.9750.0090.0090.0000.0000.0000.000
100A715HIS0-0.089-0.06326.435-0.011-0.0110.0000.0000.0000.000
101A716GLY00.0110.01729.176-0.005-0.0050.0000.0000.0000.000
102A717ALA0-0.0060.00729.7460.0050.0050.0000.0000.0000.000
103A718ALA0-0.017-0.02331.4710.0070.0070.0000.0000.0000.000
104A719ILE0-0.007-0.01234.2140.0000.0000.0000.0000.0000.000
105A720PHE00.0210.00336.0440.0020.0020.0000.0000.0000.000
106A721ALA0-0.0280.00134.6740.0060.0060.0000.0000.0000.000
107A722THR0-0.018-0.02136.511-0.002-0.0020.0000.0000.0000.000
108A723THR0-0.126-0.08433.529-0.002-0.0020.0000.0000.0000.000
109A724LEU0-0.013-0.01335.7820.0050.0050.0000.0000.0000.000
110A725SER0-0.032-0.00735.7040.0050.0050.0000.0000.0000.000
111A726ASP-1-0.882-0.92437.230-0.080-0.0800.0000.0000.0000.000
112A727GLY00.0360.02639.4500.0010.0010.0000.0000.0000.000
113A728ALA00.0270.03237.3160.0000.0000.0000.0000.0000.000
114A729THR00.0260.00236.910-0.007-0.0070.0000.0000.0000.000
115A730ALA0-0.006-0.02032.4280.0000.0000.0000.0000.0000.000
116A731PHE00.0320.01134.0320.0000.0000.0000.0000.0000.000
117A732GLU-1-0.858-0.92936.312-0.075-0.0750.0000.0000.0000.000
118A733LYS10.8140.91432.2690.0930.0930.0000.0000.0000.000
119A734CYS0-0.0650.00632.380-0.004-0.0040.0000.0000.0000.000
120A735ASP-1-0.802-0.92431.225-0.071-0.0710.0000.0000.0000.000
121A736PRO0-0.048-0.01633.053-0.002-0.0020.0000.0000.0000.000
122A737TYR0-0.082-0.03733.5570.0070.0070.0000.0000.0000.000
123A738ARG10.8550.92427.0430.1050.1050.0000.0000.0000.000
124A739GLU-1-0.951-0.97626.893-0.113-0.1130.0000.0000.0000.000
125A740GLY00.0560.01129.591-0.007-0.0070.0000.0000.0000.000
126A741TYR0-0.0050.01431.024-0.002-0.0020.0000.0000.0000.000
127A742ALA0-0.021-0.01633.535-0.001-0.0010.0000.0000.0000.000
128A743ASP-1-0.885-0.93731.323-0.136-0.1360.0000.0000.0000.000
129A744CYS00.0380.03630.828-0.005-0.0050.0000.0000.0000.000
130A745ALA00.0340.00732.655-0.001-0.0010.0000.0000.0000.000
131A746THR0-0.033-0.02035.9410.0040.0040.0000.0000.0000.000
132A747TYR00.0360.02031.514-0.002-0.0020.0000.0000.0000.000
133A748LEU00.014-0.00432.1100.0000.0000.0000.0000.0000.000
134A749ALA00.0150.01935.7560.0030.0030.0000.0000.0000.000
135A750ASP-1-0.963-0.98438.330-0.099-0.0990.0000.0000.0000.000
136A751VAL0-0.032-0.01234.5120.0010.0010.0000.0000.0000.000
137A752GLU-1-0.940-0.98037.974-0.091-0.0910.0000.0000.0000.000
138A753GLN0-0.017-0.00740.3220.0030.0030.0000.0000.0000.000
139A754SER0-0.073-0.04239.9710.0020.0020.0000.0000.0000.000
140A755MET00.0120.01339.1190.0000.0000.0000.0000.0000.000
141A756GLY00.0520.01442.6460.0040.0040.0000.0000.0000.000
142A757LEU0-0.105-0.04945.0050.0050.0050.0000.0000.0000.000
143A758MET0-0.014-0.00941.9240.0030.0030.0000.0000.0000.000
144A759ASN0-0.027-0.01340.9770.0010.0010.0000.0000.0000.000
145A760SER0-0.024-0.02443.3960.0010.0010.0000.0000.0000.000
146A761GLY00.0410.03045.8690.0030.0030.0000.0000.0000.000
147A762ALA0-0.051-0.01543.4960.0020.0020.0000.0000.0000.000
148A763VAL00.0010.00940.814-0.005-0.0050.0000.0000.0000.000
149A764TYR0-0.014-0.01737.3810.0020.0020.0000.0000.0000.000
150A765ALA00.0430.04838.510-0.002-0.0020.0000.0000.0000.000
151A766LEU0-0.043-0.01233.983-0.008-0.0080.0000.0000.0000.000
152A767TRP0-0.029-0.02233.774-0.009-0.0090.0000.0000.0000.000
153A768ASP-1-0.843-0.91138.236-0.098-0.0980.0000.0000.0000.000
154A769TYR0-0.043-0.04541.463-0.001-0.0010.0000.0000.0000.000
155A770SER0-0.071-0.05044.4620.0000.0000.0000.0000.0000.000
156A771ALA00.0060.01047.8690.0000.0000.0000.0000.0000.000
157A772GLU-1-0.961-0.97848.554-0.059-0.0590.0000.0000.0000.000
158A773PHE0-0.060-0.02452.2980.0040.0040.0000.0000.0000.000
159A774GLY0-0.044-0.03054.675-0.002-0.0020.0000.0000.0000.000
160A775ASP-1-0.932-0.96556.140-0.051-0.0510.0000.0000.0000.000
161A776GLU-1-0.755-0.86151.138-0.061-0.0610.0000.0000.0000.000
162A777LEU0-0.029-0.01949.0300.0010.0010.0000.0000.0000.000
163A778SER0-0.019-0.00948.164-0.002-0.0020.0000.0000.0000.000
164A779PHE0-0.006-0.01341.9060.0000.0000.0000.0000.0000.000
165A780ARG10.8110.91141.8300.0830.0830.0000.0000.0000.000
166A781GLU-1-0.901-0.97035.242-0.142-0.1420.0000.0000.0000.000
167A782GLY00.0040.00637.365-0.001-0.0010.0000.0000.0000.000
168A783GLU-1-0.940-0.96338.177-0.087-0.0870.0000.0000.0000.000
169A784SER0-0.041-0.01741.416-0.002-0.0020.0000.0000.0000.000
170A785VAL00.0260.00742.9810.0050.0050.0000.0000.0000.000
171A786THR0-0.028-0.00645.176-0.002-0.0020.0000.0000.0000.000
172A787VAL0-0.0030.00845.6150.0030.0030.0000.0000.0000.000
173A788LEU0-0.051-0.02048.5420.0010.0010.0000.0000.0000.000
174A789ARG10.8550.91952.1510.0550.0550.0000.0000.0000.000
175A790ARG10.9350.97846.5560.0760.0760.0000.0000.0000.000
176A791ASP-1-0.925-0.95950.003-0.065-0.0650.0000.0000.0000.000
177A792GLY0-0.036-0.00951.9020.0030.0030.0000.0000.0000.000
178A793PRO0-0.042-0.02553.510-0.001-0.0010.0000.0000.0000.000
179A794GLU-1-0.973-1.00255.520-0.048-0.0480.0000.0000.0000.000
180A795GLU-1-0.926-0.96051.212-0.054-0.0540.0000.0000.0000.000
181A796THR00.0080.00949.241-0.001-0.0010.0000.0000.0000.000
182A797ASP-1-0.952-0.97145.956-0.070-0.0700.0000.0000.0000.000
183A798TRP00.013-0.00146.448-0.005-0.0050.0000.0000.0000.000
184A799TRP00.0070.00242.3280.0000.0000.0000.0000.0000.000
185A800TRP0-0.054-0.01649.4240.0000.0000.0000.0000.0000.000
186A801ALA00.012-0.00748.696-0.002-0.0020.0000.0000.0000.000
187A802ALA00.0390.01250.0250.0030.0030.0000.0000.0000.000
188A803LEU00.0130.00946.625-0.004-0.0040.0000.0000.0000.000
189A804HIS0-0.018-0.01647.4790.0040.0040.0000.0000.0000.000
190A805GLY0-0.048-0.02651.8890.0020.0020.0000.0000.0000.000
191A806GLN0-0.045-0.00853.1480.0040.0040.0000.0000.0000.000
192A807GLU-1-0.870-0.94553.220-0.057-0.0570.0000.0000.0000.000
193A808GLY00.0090.00353.0980.0020.0020.0000.0000.0000.000
194A809TYR00.0000.00651.201-0.003-0.0030.0000.0000.0000.000
195A810VAL0-0.037-0.00445.990-0.001-0.0010.0000.0000.0000.000
196A811PRO00.0630.04843.6990.0000.0000.0000.0000.0000.000
197A812ARG11.0140.99242.9850.0710.0710.0000.0000.0000.000
198A813ASN0-0.016-0.00738.979-0.002-0.0020.0000.0000.0000.000
199A814TYR0-0.034-0.02538.369-0.007-0.0070.0000.0000.0000.000
200A815PHE0-0.012-0.01238.938-0.004-0.0040.0000.0000.0000.000
201A816GLY00.0600.03235.678-0.003-0.0030.0000.0000.0000.000
202A817LEU0-0.007-0.00335.6710.0050.0050.0000.0000.0000.000
203A818PHE0-0.024-0.01233.0140.0020.0020.0000.0000.0000.000
204A819PRO00.0000.00733.7960.0010.0010.0000.0000.0000.000
205A820ARG10.8470.91230.2800.1480.1480.0000.0000.0000.000
206A821VAL00.0280.02725.9420.0070.0070.0000.0000.0000.000
207A822LYS10.8890.95528.6140.1610.1610.0000.0000.0000.000