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: 2L2NR

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 OptHSide
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 -2224875.137509
FMO2-HF: Nuclear repulsion 2144098.016412
FMO2-HF: Total energy -80777.121097
FMO2-MP2: Total energy -81008.835153


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.
-7.964-6.825-0.006-0.566-0.5670.003
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 : 0.000 / q_NPA : -0.008
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].
3A618ARG10.9730.9923.8240.0801.146-0.005-0.565-0.4960.003
4A619LYS10.9490.9556.0360.8090.8090.0000.0000.0000.000
5A620ALA00.0030.0108.489-0.174-0.1740.0000.0000.0000.000
6A621ARG10.8560.91811.6670.3420.3420.0000.0000.0000.000
7A622ARG10.9730.97013.072-0.245-0.2450.0000.0000.0000.000
8A623ALA00.035-0.00315.518-0.047-0.0470.0000.0000.0000.000
9A624ARG10.9390.97118.847-0.072-0.0720.0000.0000.0000.000
10A625LEU00.0020.02214.4780.0080.0080.0000.0000.0000.000
11A626ASN00.0440.01718.178-0.011-0.0110.0000.0000.0000.000
12A627PRO00.025-0.00715.985-0.019-0.0190.0000.0000.0000.000
13A628LEU00.0550.04115.987-0.061-0.0610.0000.0000.0000.000
14A629VAL00.0130.00217.023-0.031-0.0310.0000.0000.0000.000
15A630LEU0-0.021-0.01312.2660.0000.0000.0000.0000.0000.000
16A631LEU0-0.0070.01012.508-0.122-0.1220.0000.0000.0000.000
17A632LEU00.0270.01113.898-0.086-0.0860.0000.0000.0000.000
18A633ASP-1-0.876-0.92612.941-0.304-0.3040.0000.0000.0000.000
19A634ALA0-0.047-0.0129.691-0.042-0.0420.0000.0000.0000.000
20A635ALA0-0.006-0.00610.858-0.146-0.1460.0000.0000.0000.000
21A636LEU0-0.0080.00713.5970.0120.0120.0000.0000.0000.000
22A637THR0-0.083-0.06410.337-0.023-0.0230.0000.0000.0000.000
23A638GLY00.0360.02810.4370.0410.0410.0000.0000.0000.000
24A639GLU-1-0.971-0.9694.967-2.917-2.844-0.001-0.001-0.0710.000
25A640LEU00.0430.0117.4640.2080.2080.0000.0000.0000.000
26A641GLU-1-0.855-0.9305.214-4.891-4.8910.0000.0000.0000.000
27A642VAL0-0.065-0.0426.1220.7500.7500.0000.0000.0000.000
28A643VAL00.0390.0238.6940.4290.4290.0000.0000.0000.000
29A644GLN0-0.040-0.02411.1960.0420.0420.0000.0000.0000.000
30A645GLN0-0.076-0.03611.0330.1790.1790.0000.0000.0000.000
31A646ALA0-0.010-0.01312.7840.1690.1690.0000.0000.0000.000
32A647VAL00.0360.00514.7890.1050.1050.0000.0000.0000.000
33A648LYS10.8830.95415.8420.6710.6710.0000.0000.0000.000
34A649GLU-1-0.881-0.90216.050-0.274-0.2740.0000.0000.0000.000
35A650MET0-0.070-0.00818.6930.0310.0310.0000.0000.0000.000
36A651ASN0-0.006-0.01520.6480.0000.0000.0000.0000.0000.000
37A652ASP-1-0.779-0.89423.439-0.260-0.2600.0000.0000.0000.000
38A653PRO0-0.008-0.01120.271-0.013-0.0130.0000.0000.0000.000
39A654SER0-0.040-0.02621.026-0.032-0.0320.0000.0000.0000.000
40A655GLN0-0.086-0.03921.9090.0290.0290.0000.0000.0000.000
41A656PRO00.0150.02322.402-0.025-0.0250.0000.0000.0000.000
42A657ASN0-0.013-0.01722.3050.0180.0180.0000.0000.0000.000
43A658GLU-1-0.941-0.99124.503-0.096-0.0960.0000.0000.0000.000
44A659GLU-1-0.899-0.92926.037-0.116-0.1160.0000.0000.0000.000
45A660GLY00.0030.01527.365-0.001-0.0010.0000.0000.0000.000
46A661ILE0-0.012-0.00121.593-0.014-0.0140.0000.0000.0000.000
47A662THR00.019-0.01821.980-0.018-0.0180.0000.0000.0000.000
48A663ALA00.012-0.02316.871-0.014-0.0140.0000.0000.0000.000
49A664LEU00.0400.01718.182-0.043-0.0430.0000.0000.0000.000
50A665HIS00.0560.05020.311-0.028-0.0280.0000.0000.0000.000
51A666ASN00.009-0.01817.0690.0390.0390.0000.0000.0000.000
52A667ALA0-0.0120.00016.229-0.017-0.0170.0000.0000.0000.000
53A668ILE0-0.028-0.00617.183-0.014-0.0140.0000.0000.0000.000
54A669CYS0-0.051-0.02020.2150.0190.0190.0000.0000.0000.000
55A670GLY0-0.021-0.00516.3680.0270.0270.0000.0000.0000.000
56A671ALA0-0.0140.00716.578-0.027-0.0270.0000.0000.0000.000
57A672ASN0-0.034-0.01613.394-0.091-0.0910.0000.0000.0000.000
58A673TYR0-0.012-0.05115.471-0.066-0.0660.0000.0000.0000.000
59A674SER0-0.0230.00113.169-0.065-0.0650.0000.0000.0000.000
60A675ILE0-0.014-0.02110.752-0.020-0.0200.0000.0000.0000.000
61A676VAL00.0250.01514.6870.0490.0490.0000.0000.0000.000
62A677ASP-1-0.854-0.91818.373-0.493-0.4930.0000.0000.0000.000
63A678PHE0-0.077-0.02915.0410.0220.0220.0000.0000.0000.000
64A679LEU00.003-0.01216.7660.0450.0450.0000.0000.0000.000
65A680ILE00.0290.02219.1470.0490.0490.0000.0000.0000.000
66A681THR0-0.051-0.03520.7720.0450.0450.0000.0000.0000.000
67A682ALA0-0.092-0.04519.5690.0260.0260.0000.0000.0000.000
68A683GLY0-0.0080.00021.7180.0240.0240.0000.0000.0000.000
69A684ALA0-0.066-0.02221.4380.0230.0230.0000.0000.0000.000
70A685ASN00.038-0.00223.5890.0160.0160.0000.0000.0000.000
71A686VAL00.0440.01725.433-0.004-0.0040.0000.0000.0000.000
72A687ASN0-0.030-0.02527.1530.0080.0080.0000.0000.0000.000
73A688SER0-0.068-0.02926.5240.0090.0090.0000.0000.0000.000
74A689PRO00.0160.00628.230-0.013-0.0130.0000.0000.0000.000
75A690ASP-1-0.847-0.91427.456-0.172-0.1720.0000.0000.0000.000
76A691SER0-0.032-0.03829.2440.0090.0090.0000.0000.0000.000
77A692HIS00.0080.00730.2700.0160.0160.0000.0000.0000.000
78A693GLY0-0.014-0.02532.4570.0060.0060.0000.0000.0000.000
79A694TRP0-0.021-0.01229.146-0.003-0.0030.0000.0000.0000.000
80A695THR00.009-0.00929.221-0.014-0.0140.0000.0000.0000.000
81A696PRO00.007-0.01024.797-0.001-0.0010.0000.0000.0000.000
82A697LEU00.0520.02326.494-0.010-0.0100.0000.0000.0000.000
83A698HIS00.0120.03829.036-0.008-0.0080.0000.0000.0000.000
84A699CYS0-0.032-0.00524.9390.0070.0070.0000.0000.0000.000
85A700ALA00.0330.01525.385-0.001-0.0010.0000.0000.0000.000
86A701ALA00.0640.02326.3330.0010.0010.0000.0000.0000.000
87A702SER0-0.052-0.00127.7230.0080.0080.0000.0000.0000.000
88A703CYS0-0.106-0.06124.6420.0070.0070.0000.0000.0000.000
89A704ASN0-0.061-0.05426.731-0.001-0.0010.0000.0000.0000.000
90A705ASP-1-0.750-0.85522.854-0.337-0.3370.0000.0000.0000.000
91A706THR00.012-0.04426.312-0.009-0.0090.0000.0000.0000.000
92A707VAL00.0210.01123.5490.0010.0010.0000.0000.0000.000
93A708ILE0-0.008-0.00520.525-0.013-0.0130.0000.0000.0000.000
94A709CYS0-0.038-0.01924.6430.0070.0070.0000.0000.0000.000
95A710MET0-0.0080.00428.2140.0070.0070.0000.0000.0000.000
96A711ALA00.0120.01924.4980.0070.0070.0000.0000.0000.000
97A712LEU00.0090.00324.5470.0000.0000.0000.0000.0000.000
98A713VAL00.0040.00027.6270.0120.0120.0000.0000.0000.000
99A714GLN0-0.072-0.05329.3210.0130.0130.0000.0000.0000.000
100A715HIS0-0.090-0.05526.311-0.001-0.0010.0000.0000.0000.000
101A716GLY00.0100.01629.561-0.005-0.0050.0000.0000.0000.000
102A717ALA0-0.0040.00929.9700.0050.0050.0000.0000.0000.000
103A718ALA0-0.009-0.01731.7440.0090.0090.0000.0000.0000.000
104A719ILE0-0.010-0.01634.462-0.001-0.0010.0000.0000.0000.000
105A720PHE00.001-0.00436.2520.0010.0010.0000.0000.0000.000
106A721ALA0-0.0230.00534.8280.0070.0070.0000.0000.0000.000
107A722THR00.007-0.00836.623-0.002-0.0020.0000.0000.0000.000
108A723THR0-0.107-0.05733.460-0.003-0.0030.0000.0000.0000.000
109A724LEU0-0.021-0.01735.5940.0080.0080.0000.0000.0000.000
110A725SER0-0.023-0.02235.8040.0060.0060.0000.0000.0000.000
111A726ASP-1-0.898-0.92837.082-0.118-0.1180.0000.0000.0000.000
112A727GLY00.0250.02239.4380.0020.0020.0000.0000.0000.000
113A728ALA00.0150.03237.0460.0010.0010.0000.0000.0000.000
114A729THR00.0380.00736.981-0.008-0.0080.0000.0000.0000.000
115A730ALA0-0.011-0.01932.488-0.002-0.0020.0000.0000.0000.000
116A731PHE00.0240.01234.080-0.002-0.0020.0000.0000.0000.000
117A732GLU-1-0.862-0.92836.381-0.107-0.1070.0000.0000.0000.000
118A733LYS10.7920.89432.3380.1330.1330.0000.0000.0000.000
119A734CYS0-0.075-0.00332.356-0.008-0.0080.0000.0000.0000.000
120A735ASP-1-0.738-0.87431.011-0.121-0.1210.0000.0000.0000.000
121A736PRO0-0.034-0.01732.941-0.004-0.0040.0000.0000.0000.000
122A737TYR0-0.088-0.04333.3300.0100.0100.0000.0000.0000.000
123A738ARG10.8140.90926.2320.1730.1730.0000.0000.0000.000
124A739GLU-1-0.946-0.97627.206-0.173-0.1730.0000.0000.0000.000
125A740GLY00.0560.01329.508-0.010-0.0100.0000.0000.0000.000
126A741TYR0-0.0120.01630.9900.0000.0000.0000.0000.0000.000
127A742ALA0-0.012-0.01433.495-0.001-0.0010.0000.0000.0000.000
128A743ASP-1-0.881-0.90431.481-0.183-0.1830.0000.0000.0000.000
129A744CYS00.0220.03830.071-0.002-0.0020.0000.0000.0000.000
130A745ALA00.0500.01432.7270.0000.0000.0000.0000.0000.000
131A746THR0-0.046-0.04135.9980.0070.0070.0000.0000.0000.000
132A747TYR00.0260.01731.712-0.001-0.0010.0000.0000.0000.000
133A748LEU00.0370.00132.0630.0010.0010.0000.0000.0000.000
134A749ALA00.0000.01435.9060.0050.0050.0000.0000.0000.000
135A750ASP-1-0.973-0.98838.505-0.128-0.1280.0000.0000.0000.000
136A751VAL0-0.019-0.01034.7660.0020.0020.0000.0000.0000.000
137A752GLU-1-0.875-0.95038.202-0.122-0.1220.0000.0000.0000.000
138A753GLN00.0010.00140.5230.0060.0060.0000.0000.0000.000
139A754SER0-0.065-0.02940.2140.0040.0040.0000.0000.0000.000
140A755MET00.0080.01239.7050.0000.0000.0000.0000.0000.000
141A756GLY00.0380.01442.9300.0050.0050.0000.0000.0000.000
142A757LEU0-0.075-0.03345.3170.0060.0060.0000.0000.0000.000
143A758MET0-0.011-0.01342.2420.0040.0040.0000.0000.0000.000
144A759ASN0-0.042-0.01941.4000.0010.0010.0000.0000.0000.000
145A760SER0-0.022-0.02443.7880.0010.0010.0000.0000.0000.000
146A761GLY00.0440.03046.2380.0040.0040.0000.0000.0000.000
147A762ALA0-0.063-0.02143.8890.0020.0020.0000.0000.0000.000
148A763VAL00.0050.00941.174-0.006-0.0060.0000.0000.0000.000
149A764TYR0-0.005-0.00837.7530.0040.0040.0000.0000.0000.000
150A765ALA00.0430.04938.859-0.004-0.0040.0000.0000.0000.000
151A766LEU0-0.024-0.00434.172-0.007-0.0070.0000.0000.0000.000
152A767TRP0-0.014-0.02334.004-0.011-0.0110.0000.0000.0000.000
153A768ASP-1-0.814-0.89438.565-0.111-0.1110.0000.0000.0000.000
154A769TYR0-0.052-0.06041.808-0.003-0.0030.0000.0000.0000.000
155A770SER0-0.057-0.04444.7750.0010.0010.0000.0000.0000.000
156A771ALA00.0130.01448.1800.0000.0000.0000.0000.0000.000
157A772GLU-1-0.966-0.98048.786-0.074-0.0740.0000.0000.0000.000
158A773PHE0-0.053-0.02752.5500.0050.0050.0000.0000.0000.000
159A774GLY0-0.041-0.02454.961-0.002-0.0020.0000.0000.0000.000
160A775ASP-1-0.935-0.96556.941-0.063-0.0630.0000.0000.0000.000
161A776GLU-1-0.741-0.85150.949-0.078-0.0780.0000.0000.0000.000
162A777LEU0-0.028-0.01749.4270.0010.0010.0000.0000.0000.000
163A778SER0-0.013-0.00548.495-0.002-0.0020.0000.0000.0000.000
164A779PHE0-0.004-0.00442.2020.0000.0000.0000.0000.0000.000
165A780ARG10.7530.87542.3440.0990.0990.0000.0000.0000.000
166A781GLU-1-0.808-0.90135.244-0.173-0.1730.0000.0000.0000.000
167A782GLY0-0.013-0.00937.7960.0000.0000.0000.0000.0000.000
168A783GLU-1-0.870-0.92838.607-0.102-0.1020.0000.0000.0000.000
169A784SER0-0.035-0.01841.820-0.004-0.0040.0000.0000.0000.000
170A785VAL00.0090.00043.4010.0060.0060.0000.0000.0000.000
171A786THR0-0.0010.00945.547-0.003-0.0030.0000.0000.0000.000
172A787VAL0-0.0080.00545.9240.0040.0040.0000.0000.0000.000
173A788LEU0-0.054-0.01848.8680.0010.0010.0000.0000.0000.000
174A789ARG10.7580.86052.4640.0690.0690.0000.0000.0000.000
175A790ARG10.8210.89845.8980.0960.0960.0000.0000.0000.000
176A791ASP-1-0.845-0.91350.163-0.085-0.0850.0000.0000.0000.000
177A792GLY0-0.0140.00352.1060.0030.0030.0000.0000.0000.000
178A793PRO0-0.033-0.02653.694-0.001-0.0010.0000.0000.0000.000
179A794GLU-1-0.933-0.96455.668-0.064-0.0640.0000.0000.0000.000
180A795GLU-1-0.916-0.96451.263-0.072-0.0720.0000.0000.0000.000
181A796THR00.0100.01149.363-0.001-0.0010.0000.0000.0000.000
182A797ASP-1-0.880-0.92345.701-0.095-0.0950.0000.0000.0000.000
183A798TRP0-0.022-0.01046.642-0.005-0.0050.0000.0000.0000.000
184A799TRP00.0100.00642.6740.0000.0000.0000.0000.0000.000
185A800TRP0-0.051-0.02349.6800.0000.0000.0000.0000.0000.000
186A801ALA00.014-0.01048.975-0.002-0.0020.0000.0000.0000.000
187A802ALA00.0390.01350.3780.0040.0040.0000.0000.0000.000
188A803LEU0-0.0060.00447.045-0.004-0.0040.0000.0000.0000.000
189A804HIS0-0.053-0.03547.6780.0060.0060.0000.0000.0000.000
190A805GLY0-0.046-0.02752.3300.0030.0030.0000.0000.0000.000
191A806GLN0-0.059-0.01353.4980.0050.0050.0000.0000.0000.000
192A807GLU-1-0.867-0.93853.600-0.071-0.0710.0000.0000.0000.000
193A808GLY00.0020.00153.4350.0030.0030.0000.0000.0000.000
194A809TYR00.0100.01251.462-0.003-0.0030.0000.0000.0000.000
195A810VAL0-0.024-0.00146.2840.0000.0000.0000.0000.0000.000
196A811PRO00.0650.04744.0250.0000.0000.0000.0000.0000.000
197A812ARG10.9550.95343.1270.0940.0940.0000.0000.0000.000
198A813ASN0-0.019-0.01039.211-0.003-0.0030.0000.0000.0000.000
199A814TYR0-0.032-0.01838.598-0.008-0.0080.0000.0000.0000.000
200A815PHE0-0.013-0.01439.257-0.004-0.0040.0000.0000.0000.000
201A816GLY00.0600.03136.004-0.004-0.0040.0000.0000.0000.000
202A817LEU0-0.013-0.00336.0110.0060.0060.0000.0000.0000.000
203A818PHE0-0.012-0.00933.3930.0030.0030.0000.0000.0000.000
204A819PRO00.0040.00734.4430.0000.0000.0000.0000.0000.000
205A820ARG10.8250.91430.8690.1790.1790.0000.0000.0000.000
206A821VAL00.0120.01626.3990.0090.0090.0000.0000.0000.000
207A822LYS10.8000.89429.0760.1780.1780.0000.0000.0000.000