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: 982R2

Calculation Name: 1VLW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VLW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WXS1

Base Structure: X-ray

Registration Date: 2023-09-23

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2339448.698504
FMO2-HF: Nuclear repulsion 2260859.88753
FMO2-HF: Total energy -78588.810974
FMO2-MP2: Total energy -78815.959159


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:HIS)


Summations of interaction energy for fragment #1(A:-1:HIS)
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.
-61.974-50.7114.184-9.824-15.622-0.024
Interaction energy analysis for fragmet #1(A:-1:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / 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].
3A1MET00.0290.0123.902-2.202-0.932-0.006-0.513-0.7510.001
4A2LYS10.9560.9882.286-27.645-27.8688.613-2.914-5.4760.031
5A3MET00.0090.0262.712-4.008-2.3591.043-0.637-2.0540.003
6A4GLU-1-0.767-0.8625.5210.3550.548-0.001-0.011-0.1800.000
7A5GLU-1-0.818-0.9038.4100.8720.8720.0000.0000.0000.000
8A6LEU0-0.0130.0024.494-0.625-0.473-0.001-0.012-0.1390.000
9A7PHE00.001-0.0127.695-0.071-0.0710.0000.0000.0000.000
10A8LYS10.8140.88910.966-1.018-1.0180.0000.0000.0000.000
11A9LYS10.8660.94411.5760.6990.6990.0000.0000.0000.000
12A10HIS00.0330.0039.1710.3470.3470.0000.0000.0000.000
13A11LYS10.9090.95913.5880.1330.1330.0000.0000.0000.000
14A12ILE00.0200.00615.0240.0720.0720.0000.0000.0000.000
15A13VAL0-0.0090.00012.069-0.163-0.1630.0000.0000.0000.000
16A14ALA00.0370.01814.4410.1800.1800.0000.0000.0000.000
17A15VAL0-0.052-0.02515.427-0.147-0.1470.0000.0000.0000.000
18A16LEU00.0450.02216.4790.1430.1430.0000.0000.0000.000
19A17ARG10.8640.94418.5730.7060.7060.0000.0000.0000.000
20A18ALA0-0.012-0.02021.5390.0220.0220.0000.0000.0000.000
21A19ASN0-0.031-0.02923.7760.0020.0020.0000.0000.0000.000
22A20SER0-0.007-0.01925.4180.0210.0210.0000.0000.0000.000
23A21VAL00.0780.03520.874-0.047-0.0470.0000.0000.0000.000
24A22GLU-1-0.802-0.90421.853-0.760-0.7600.0000.0000.0000.000
25A23GLU-1-0.733-0.83623.490-0.633-0.6330.0000.0000.0000.000
26A24ALA0-0.007-0.01419.222-0.022-0.0220.0000.0000.0000.000
27A25LYS10.7600.87818.9350.7610.7610.0000.0000.0000.000
28A26GLU-1-0.903-0.95419.804-0.656-0.6560.0000.0000.0000.000
29A27LYS10.7850.88620.8680.6790.6790.0000.0000.0000.000
30A28ALA0-0.002-0.00715.810-0.020-0.0200.0000.0000.0000.000
31A29LEU00.0120.00917.187-0.074-0.0740.0000.0000.0000.000
32A30ALA00.0270.02219.0630.0060.0060.0000.0000.0000.000
33A31VAL0-0.011-0.02716.5740.0410.0410.0000.0000.0000.000
34A32PHE0-0.036-0.00512.524-0.013-0.0130.0000.0000.0000.000
35A33GLU-1-0.837-0.91016.887-0.643-0.6430.0000.0000.0000.000
36A34GLY0-0.027-0.00520.1310.0830.0830.0000.0000.0000.000
37A35GLY0-0.028-0.01417.6800.0660.0660.0000.0000.0000.000
38A36VAL0-0.051-0.02514.937-0.037-0.0370.0000.0000.0000.000
39A37HIS0-0.015-0.02210.691-0.067-0.0670.0000.0000.0000.000
40A38LEU0-0.0360.0068.494-0.454-0.4540.0000.0000.0000.000
41A39ILE00.0240.00410.4110.4120.4120.0000.0000.0000.000
42A40GLU-1-0.797-0.89111.068-1.605-1.6050.0000.0000.0000.000
43A41ILE00.0320.01112.7060.2930.2930.0000.0000.0000.000
44A42THR0-0.062-0.05014.595-0.002-0.0020.0000.0000.0000.000
45A43PHE00.050-0.00313.8490.0450.0450.0000.0000.0000.000
46A44THR0-0.018-0.00418.2980.0800.0800.0000.0000.0000.000
47A45VAL0-0.065-0.01119.6590.0660.0660.0000.0000.0000.000
48A46PRO00.0070.00621.026-0.038-0.0380.0000.0000.0000.000
49A47ASP-1-0.884-0.95120.865-0.756-0.7560.0000.0000.0000.000
50A48ALA00.0140.01416.623-0.073-0.0730.0000.0000.0000.000
51A49ASP-1-0.792-0.90314.928-1.204-1.2040.0000.0000.0000.000
52A50THR00.0290.03215.705-0.141-0.1410.0000.0000.0000.000
53A51VAL00.0010.01616.395-0.046-0.0460.0000.0000.0000.000
54A52ILE0-0.041-0.02910.781-0.078-0.0780.0000.0000.0000.000
55A53LYS10.8680.93213.1441.1731.1730.0000.0000.0000.000
56A54GLU-1-0.791-0.89114.921-0.899-0.8990.0000.0000.0000.000
57A55LEU0-0.042-0.01313.9010.0510.0510.0000.0000.0000.000
58A56SER0-0.001-0.00512.231-0.156-0.1560.0000.0000.0000.000
59A57PHE00.0480.02313.168-0.104-0.1040.0000.0000.0000.000
60A58LEU0-0.0090.00413.9510.0870.0870.0000.0000.0000.000
61A59LYS10.8410.9074.7347.2077.246-0.0010.001-0.0380.000
62A60GLU-1-0.904-0.94410.267-1.347-1.3470.0000.0000.0000.000
63A61LYS10.7740.87312.5861.2881.2880.0000.0000.0000.000
64A62GLY00.0100.01210.1400.2090.2090.0000.0000.0000.000
65A63ALA0-0.032-0.0019.678-0.195-0.1950.0000.0000.0000.000
66A64ILE0-0.058-0.0364.669-0.666-0.584-0.001-0.003-0.0780.000
67A65ILE00.0180.0076.8690.8710.8710.0000.0000.0000.000
68A66GLY00.0260.0147.279-1.067-1.0670.0000.0000.0000.000
69A67ALA0-0.0150.0098.6380.5140.5140.0000.0000.0000.000
70A68GLY00.041-0.00111.5870.0030.0030.0000.0000.0000.000
71A69THR0-0.082-0.04314.2380.1230.1230.0000.0000.0000.000
72A70VAL00.0090.02012.9670.0670.0670.0000.0000.0000.000
73A71THR0-0.020-0.04016.2090.0590.0590.0000.0000.0000.000
74A72SER00.0550.02017.7120.0670.0670.0000.0000.0000.000
75A73VAL00.0620.02215.158-0.136-0.1360.0000.0000.0000.000
76A74GLU-1-0.815-0.90116.053-0.689-0.6890.0000.0000.0000.000
77A75GLN00.0140.03216.666-0.042-0.0420.0000.0000.0000.000
78A76CYS0-0.0190.00411.643-0.260-0.2600.0000.0000.0000.000
79A77ARG10.8880.94812.2770.4130.4130.0000.0000.0000.000
80A78LYS10.8830.93513.6700.7730.7730.0000.0000.0000.000
81A79ALA00.0070.00511.155-0.102-0.1020.0000.0000.0000.000
82A80VAL0-0.008-0.0088.259-0.313-0.3130.0000.0000.0000.000
83A81GLU-1-0.911-0.95910.071-1.107-1.1070.0000.0000.0000.000
84A82SER0-0.050-0.05212.1230.2760.2760.0000.0000.0000.000
85A83GLY0-0.0110.0148.8460.0460.0460.0000.0000.0000.000
86A84ALA0-0.064-0.0247.479-0.868-0.8680.0000.0000.0000.000
87A85GLU-1-0.789-0.8992.744-16.743-14.4280.197-1.167-1.345-0.010
88A86PHE0-0.071-0.0432.930-4.916-2.4810.158-1.223-1.370-0.014
89A87ILE00.0440.0235.6980.6170.6170.0000.0000.0000.000
90A88VAL00.005-0.0059.3000.2350.2350.0000.0000.0000.000
91A89SER0-0.0030.01012.443-0.014-0.0140.0000.0000.0000.000
92A90PRO0-0.034-0.00915.8510.0300.0300.0000.0000.0000.000
93A91HIS00.0140.00118.7040.0450.0450.0000.0000.0000.000
94A92LEU00.0150.02015.794-0.070-0.0700.0000.0000.0000.000
95A93ASP-1-0.799-0.88615.748-0.430-0.4300.0000.0000.0000.000
96A94GLU-1-0.799-0.92715.079-0.033-0.0330.0000.0000.0000.000
97A95GLU-1-0.891-0.93315.373-0.237-0.2370.0000.0000.0000.000
98A96ILE00.007-0.00711.823-0.056-0.0560.0000.0000.0000.000
99A97SER00.0000.00111.191-0.074-0.0740.0000.0000.0000.000
100A98GLN0-0.052-0.00910.7620.1970.1970.0000.0000.0000.000
101A99PHE00.0700.02110.9330.0340.0340.0000.0000.0000.000
102A100CYS0-0.024-0.0187.158-0.193-0.1930.0000.0000.0000.000
103A101LYS10.8320.9056.426-0.682-0.6820.0000.0000.0000.000
104A102GLU-1-0.878-0.9207.500-0.153-0.1530.0000.0000.0000.000
105A103LYS10.8140.8957.8750.6760.6760.0000.0000.0000.000
106A104GLY00.0000.0183.860-0.273-0.0680.001-0.060-0.1460.000
107A105VAL0-0.026-0.0082.250-9.602-7.7164.067-2.866-3.087-0.033
108A106PHE0-0.008-0.0132.9750.4701.5840.115-0.393-0.836-0.002
109A107TYR00.024-0.0224.236-0.223-0.0760.000-0.026-0.1220.000
110A108MET0-0.058-0.0118.0680.5950.5950.0000.0000.0000.000
111A109PRO00.0120.00510.861-0.074-0.0740.0000.0000.0000.000
112A110GLY00.0140.02014.2810.0330.0330.0000.0000.0000.000
113A111VAL0-0.070-0.04917.5150.0680.0680.0000.0000.0000.000
114A112MET00.0100.00320.305-0.024-0.0240.0000.0000.0000.000
115A113THR00.002-0.03723.8650.0360.0360.0000.0000.0000.000
116A114PRO00.056-0.00323.4480.0100.0100.0000.0000.0000.000
117A115THR0-0.0050.00423.5310.0370.0370.0000.0000.0000.000
118A116GLU-1-0.768-0.84421.025-0.105-0.1050.0000.0000.0000.000
119A117LEU00.0170.02219.1560.0160.0160.0000.0000.0000.000
120A118VAL00.019-0.00318.6260.0590.0590.0000.0000.0000.000
121A119LYS10.8330.92119.3390.0480.0480.0000.0000.0000.000
122A120ALA00.0490.01715.4270.0300.0300.0000.0000.0000.000
123A121MET0-0.023-0.01214.5060.0580.0580.0000.0000.0000.000
124A122LYS10.9150.96814.950-0.163-0.1630.0000.0000.0000.000
125A123LEU0-0.0150.01514.1800.0540.0540.0000.0000.0000.000
126A124GLY0-0.015-0.00511.026-0.030-0.0300.0000.0000.0000.000
127A125HIS10.7890.8929.1940.2470.2470.0000.0000.0000.000
128A126THR00.0410.01811.454-0.112-0.1120.0000.0000.0000.000
129A127ILE0-0.026-0.0038.759-0.068-0.0680.0000.0000.0000.000
130A128LEU0-0.007-0.00412.209-0.098-0.0980.0000.0000.0000.000
131A129LYS10.8330.90714.5720.9600.9600.0000.0000.0000.000
132A130LEU0-0.074-0.02316.0290.0530.0530.0000.0000.0000.000
133A131PHE0-0.012-0.00519.758-0.061-0.0610.0000.0000.0000.000
134A132PRO00.0710.03521.9270.0270.0270.0000.0000.0000.000
135A133GLY00.0260.00423.6400.0400.0400.0000.0000.0000.000
136A134GLU-1-0.856-0.94824.657-0.331-0.3310.0000.0000.0000.000
137A135VAL0-0.044-0.01327.5260.0220.0220.0000.0000.0000.000
138A136VAL0-0.040-0.01223.9210.0300.0300.0000.0000.0000.000
139A137GLY00.0620.02925.129-0.011-0.0110.0000.0000.0000.000
140A138PRO00.009-0.00725.6600.0260.0260.0000.0000.0000.000
141A139GLN00.0400.00226.5360.0330.0330.0000.0000.0000.000
142A140PHE00.0050.01522.6750.0290.0290.0000.0000.0000.000
143A141VAL00.0030.00221.5340.0290.0290.0000.0000.0000.000
144A142LYS10.8440.91523.838-0.026-0.0260.0000.0000.0000.000
145A143ALA0-0.0060.00026.5310.0290.0290.0000.0000.0000.000
146A144MET0-0.016-0.00823.0460.0300.0300.0000.0000.0000.000
147A145LYS10.8710.93420.449-0.326-0.3260.0000.0000.0000.000
148A146GLY00.0170.01224.3480.0380.0380.0000.0000.0000.000
149A147PRO0-0.014-0.00125.7460.0300.0300.0000.0000.0000.000
150A148PHE00.006-0.01120.8340.0280.0280.0000.0000.0000.000
151A149PRO00.0480.03820.8260.0160.0160.0000.0000.0000.000
152A150ASN0-0.024-0.01416.8560.0030.0030.0000.0000.0000.000
153A151VAL0-0.022-0.00616.1270.1090.1090.0000.0000.0000.000
154A152LYS10.8260.89412.282-1.140-1.1400.0000.0000.0000.000
155A153PHE00.0590.01914.849-0.044-0.0440.0000.0000.0000.000
156A154VAL00.0180.00913.0470.0110.0110.0000.0000.0000.000
157A155PRO00.0170.03116.348-0.055-0.0550.0000.0000.0000.000
158A156THR0-0.019-0.02417.825-0.155-0.1550.0000.0000.0000.000
159A157GLY00.0680.04720.1120.0340.0340.0000.0000.0000.000
160A158GLY0-0.012-0.02023.6180.0130.0130.0000.0000.0000.000
161A159VAL0-0.0290.01321.3160.0340.0340.0000.0000.0000.000
162A160ASN00.020-0.00224.602-0.026-0.0260.0000.0000.0000.000
163A161LEU00.0690.02225.7730.0120.0120.0000.0000.0000.000
164A162ASP-1-0.875-0.92227.621-0.212-0.2120.0000.0000.0000.000
165A163ASN0-0.002-0.00327.1320.0000.0000.0000.0000.0000.000
166A164VAL00.0210.01322.3700.0190.0190.0000.0000.0000.000
167A203CYS0-0.087-0.05623.6310.0610.0610.0000.0000.0000.000
168A166GLU-1-0.886-0.92026.519-0.055-0.0550.0000.0000.0000.000
169A167TRP00.006-0.00822.6070.0370.0370.0000.0000.0000.000
170A168PHE0-0.005-0.00818.5780.0300.0300.0000.0000.0000.000
171A169LYS10.8710.93723.5190.0950.0950.0000.0000.0000.000
172A170ALA0-0.049-0.01824.6970.0380.0380.0000.0000.0000.000
173A171GLY0-0.003-0.00322.4060.0420.0420.0000.0000.0000.000
174A172VAL0-0.078-0.02618.6840.0460.0460.0000.0000.0000.000
175A173LEU0-0.040-0.01411.4060.0500.0500.0000.0000.0000.000
176A174ALA0-0.014-0.01114.115-0.026-0.0260.0000.0000.0000.000
177A175VAL00.000-0.00516.0830.0610.0610.0000.0000.0000.000
178A176GLY00.0370.02516.533-0.130-0.1300.0000.0000.0000.000
179A177VAL0-0.038-0.02217.1900.1000.1000.0000.0000.0000.000
180A178GLY00.0910.05319.468-0.081-0.0810.0000.0000.0000.000
181A179SER0-0.013-0.01921.6570.0030.0030.0000.0000.0000.000
182A180ALA00.0260.01025.2580.0040.0040.0000.0000.0000.000
183A181LEU0-0.0120.02319.0000.0250.0250.0000.0000.0000.000
184A182VAL00.025-0.00319.8940.0080.0080.0000.0000.0000.000
185A183LYS10.9160.96423.0350.4050.4050.0000.0000.0000.000
186A184GLY00.0370.01926.6860.0250.0250.0000.0000.0000.000
187A185THR0-0.015-0.03327.813-0.034-0.0340.0000.0000.0000.000
188A186PRO00.0660.01825.128-0.010-0.0100.0000.0000.0000.000
189A187ASP-1-0.801-0.88625.507-0.491-0.4910.0000.0000.0000.000
190A188GLU-1-0.854-0.89827.614-0.407-0.4070.0000.0000.0000.000
191A189VAL0-0.063-0.02721.986-0.002-0.0020.0000.0000.0000.000
192A190ARG10.7990.88822.8510.5430.5430.0000.0000.0000.000
193A191GLU-1-0.789-0.88723.900-0.444-0.4440.0000.0000.0000.000
194A192LYS10.8300.90825.5640.5010.5010.0000.0000.0000.000
195A193ALA0-0.010-0.01020.2670.0090.0090.0000.0000.0000.000
196A194LYS10.8550.91721.8940.4610.4610.0000.0000.0000.000
197A195ALA0-0.008-0.00123.5810.0330.0330.0000.0000.0000.000
198A196PHE00.019-0.01521.4790.0380.0380.0000.0000.0000.000
199A197VAL0-0.024-0.00218.7900.0330.0330.0000.0000.0000.000
200A198GLU-1-0.841-0.87321.453-0.238-0.2380.0000.0000.0000.000
201A199LYS10.8330.88925.0160.2730.2730.0000.0000.0000.000
202A200ILE00.008-0.00219.4570.0380.0380.0000.0000.0000.000
203A201ARG10.7740.87222.0530.3450.3450.0000.0000.0000.000
204A202GLY00.0080.01723.3500.0380.0380.0000.0000.0000.000