Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VRVM1

Calculation Name: 1I39-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I39

Chain ID: A

ChEMBL ID:

UniProt ID: O29634

Base Structure: X-ray

Registration Date: 2023-03-13

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2261491.597415
FMO2-HF: Nuclear repulsion 2181905.948707
FMO2-HF: Total energy -79585.648708
FMO2-MP2: Total energy -79816.311878


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-12.58-5.2634.839-3.41-8.743-0.005
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.020
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].
3A3ALA00.027-0.0153.134-1.8111.5480.090-1.788-1.6610.003
4A4GLY0-0.0170.0125.690-0.072-0.0720.0000.0000.0000.000
5A5ILE0-0.027-0.0289.2060.1520.1520.0000.0000.0000.000
6A6ASP-1-0.791-0.87412.213-0.166-0.1660.0000.0000.0000.000
7A7GLU-1-0.794-0.90615.713-0.120-0.1200.0000.0000.0000.000
8A8ALA00.0140.01818.9520.0230.0230.0000.0000.0000.000
9A9GLY00.0380.01721.9710.0010.0010.0000.0000.0000.000
10A10LYS10.8820.92222.0180.1760.1760.0000.0000.0000.000
11A11GLY0-0.023-0.02125.955-0.002-0.0020.0000.0000.0000.000
12A12CYS0-0.103-0.01628.7640.0110.0110.0000.0000.0000.000
13A13VAL0-0.017-0.01230.654-0.008-0.0080.0000.0000.0000.000
14A14ILE00.0010.00132.817-0.001-0.0010.0000.0000.0000.000
15A15GLY00.0690.04729.9280.0020.0020.0000.0000.0000.000
16A16PRO0-0.013-0.01025.432-0.011-0.0110.0000.0000.0000.000
17A17LEU0-0.0510.00522.5620.0050.0050.0000.0000.0000.000
18A18VAL0-0.013-0.01618.9740.0000.0000.0000.0000.0000.000
19A19VAL00.0080.00015.878-0.010-0.0100.0000.0000.0000.000
20A20ALA00.002-0.00114.0460.0270.0270.0000.0000.0000.000
21A21GLY00.0420.01810.420-0.104-0.1040.0000.0000.0000.000
22A22VAL0-0.036-0.0177.4640.2060.2060.0000.0000.0000.000
23A23ALA00.0480.0302.891-1.344-0.8460.149-0.169-0.4780.001
24A24CYS0-0.023-0.0303.4870.5101.5260.103-0.257-0.861-0.001
25A25SER00.0380.0102.375-4.384-2.6214.290-2.116-3.936-0.009
26A26ASP-1-0.890-0.9533.3591.120-0.2220.1321.519-0.3090.001
27A27GLU-1-0.819-0.9146.650-0.341-0.3410.0000.0000.0000.000
28A28ASP-1-0.849-0.9068.3030.3490.3490.0000.0000.0000.000
29A29ARG10.9470.98210.209-1.560-1.5600.0000.0000.0000.000
30A30LEU0-0.004-0.0068.843-0.118-0.1180.0000.0000.0000.000
31A31ARG10.7580.84610.710-0.437-0.4370.0000.0000.0000.000
32A32LYS10.9460.99014.192-0.647-0.6470.0000.0000.0000.000
33A33LEU0-0.028-0.01013.399-0.059-0.0590.0000.0000.0000.000
34A34GLY00.0000.00916.855-0.053-0.0530.0000.0000.0000.000
35A35VAL0-0.006-0.01012.993-0.050-0.0500.0000.0000.0000.000
36A36LYS10.9540.98816.413-0.100-0.1000.0000.0000.0000.000
37A37ASP-1-0.860-0.91017.8580.1350.1350.0000.0000.0000.000
38A38SER00.042-0.00218.3470.0000.0000.0000.0000.0000.000
39A39LYS10.7620.84320.7400.0440.0440.0000.0000.0000.000
40A40LYS10.8490.92423.358-0.165-0.1650.0000.0000.0000.000
41A41LEU0-0.0280.00021.4010.0010.0010.0000.0000.0000.000
42A42SER00.0340.01625.403-0.010-0.0100.0000.0000.0000.000
43A43GLN00.027-0.00125.6510.0070.0070.0000.0000.0000.000
44A44GLY00.0380.01925.5160.0130.0130.0000.0000.0000.000
45A45ARG10.8630.90624.593-0.192-0.1920.0000.0000.0000.000
46A46ARG10.8420.91121.595-0.068-0.0680.0000.0000.0000.000
47A47GLU-1-0.821-0.89520.5600.2220.2220.0000.0000.0000.000
48A48GLU-1-0.826-0.89920.6200.2780.2780.0000.0000.0000.000
49A49LEU0-0.006-0.00116.7260.0480.0480.0000.0000.0000.000
50A50ALA00.0120.00016.3680.0820.0820.0000.0000.0000.000
51A51GLU-1-0.806-0.90815.4860.4700.4700.0000.0000.0000.000
52A52GLU-1-0.860-0.90915.5750.6930.6930.0000.0000.0000.000
53A53ILE0-0.031-0.02211.1520.1590.1590.0000.0000.0000.000
54A54ARG10.8570.92210.800-0.116-0.1160.0000.0000.0000.000
55A55LYS10.8290.91610.906-0.498-0.4980.0000.0000.0000.000
56A56ILE0-0.048-0.0269.3500.0790.0790.0000.0000.0000.000
57A57CYS0-0.0700.0086.0840.7030.7030.0000.0000.0000.000
58A58ARG10.8840.9504.704-0.523-0.357-0.001-0.013-0.1520.000
59A59THR0-0.031-0.0356.472-0.144-0.1440.0000.0000.0000.000
60A60GLU-1-0.806-0.8739.440-0.168-0.1680.0000.0000.0000.000
61A61VAL0-0.008-0.01611.969-0.038-0.0380.0000.0000.0000.000
62A62LEU00.0110.02415.683-0.005-0.0050.0000.0000.0000.000
63A63LYS10.8500.90818.447-0.039-0.0390.0000.0000.0000.000
64A64VAL00.0170.01422.122-0.006-0.0060.0000.0000.0000.000
65A65SER00.0600.02925.1110.0040.0040.0000.0000.0000.000
66A66PRO00.0350.00328.486-0.010-0.0100.0000.0000.0000.000
67A67GLU-1-0.906-0.93831.466-0.054-0.0540.0000.0000.0000.000
68A68ASN00.021-0.00328.401-0.013-0.0130.0000.0000.0000.000
69A69LEU0-0.060-0.02626.374-0.014-0.0140.0000.0000.0000.000
70A70ASP-1-0.764-0.88230.051-0.080-0.0800.0000.0000.0000.000
71A71GLU-1-0.967-0.96532.187-0.103-0.1030.0000.0000.0000.000
72A72ARG10.9150.93923.4310.1940.1940.0000.0000.0000.000
73A73MET0-0.051-0.03230.510-0.007-0.0070.0000.0000.0000.000
74A74ALA0-0.085-0.02232.4350.0030.0030.0000.0000.0000.000
75A75ALA0-0.004-0.00732.7700.0010.0010.0000.0000.0000.000
76A76LYS10.8670.93426.9450.2180.2180.0000.0000.0000.000
77A77THR0-0.010-0.03329.5560.0110.0110.0000.0000.0000.000
78A78ILE00.0390.00126.586-0.011-0.0110.0000.0000.0000.000
79A79ASN00.021-0.00325.0830.0000.0000.0000.0000.0000.000
80A80GLU-1-0.835-0.87824.074-0.244-0.2440.0000.0000.0000.000
81A81ILE00.0080.00624.104-0.023-0.0230.0000.0000.0000.000
82A82LEU00.0180.00820.295-0.012-0.0120.0000.0000.0000.000
83A83LYS10.8820.95619.9510.3130.3130.0000.0000.0000.000
84A84GLU-1-0.803-0.88019.232-0.307-0.3070.0000.0000.0000.000
85A85CYS0-0.080-0.04419.098-0.012-0.0120.0000.0000.0000.000
86A86TYR0-0.029-0.03515.710-0.008-0.0080.0000.0000.0000.000
87A87ALA00.0330.02314.416-0.098-0.0980.0000.0000.0000.000
88A88GLU-1-0.821-0.90314.565-0.362-0.3620.0000.0000.0000.000
89A89ILE00.000-0.00511.261-0.040-0.0400.0000.0000.0000.000
90A90ILE00.012-0.00110.063-0.102-0.1020.0000.0000.0000.000
91A91LEU00.0040.0059.789-0.295-0.2950.0000.0000.0000.000
92A92ARG10.7210.86210.8240.2100.2100.0000.0000.0000.000
93A93LEU0-0.057-0.0406.1770.0770.0770.0000.0000.0000.000
94A94LYS10.8910.9625.8000.5180.5180.0000.0000.0000.000
95A95PRO0-0.024-0.0023.760-0.713-0.4680.000-0.059-0.1860.000
96A96GLU-1-0.896-0.9562.932-4.416-2.9840.077-0.507-1.0020.000
97A97ILE0-0.029-0.0304.7261.5201.700-0.001-0.020-0.1580.000
98A98ALA0-0.018-0.0046.640-0.539-0.5390.0000.0000.0000.000
99A99TYR00.0010.0027.9020.1460.1460.0000.0000.0000.000
100A100VAL00.013-0.00711.3770.0940.0940.0000.0000.0000.000
101A101ASP-1-0.844-0.92214.253-0.234-0.2340.0000.0000.0000.000
102A102SER00.0330.01817.414-0.007-0.0070.0000.0000.0000.000
103A103PRO0-0.055-0.03220.6100.0410.0410.0000.0000.0000.000
104A104ASP-1-0.904-0.95323.767-0.250-0.2500.0000.0000.0000.000
105A105VAL0-0.007-0.01624.728-0.014-0.0140.0000.0000.0000.000
106A106ILE0-0.038-0.00525.877-0.005-0.0050.0000.0000.0000.000
107A107PRO00.0510.03920.581-0.012-0.0120.0000.0000.0000.000
108A108GLU-1-0.863-0.94421.439-0.388-0.3880.0000.0000.0000.000
109A109ARG10.8300.89321.9250.2550.2550.0000.0000.0000.000
110A110LEU00.0330.01819.160-0.009-0.0090.0000.0000.0000.000
111A111SER00.018-0.00117.544-0.058-0.0580.0000.0000.0000.000
112A112ARG10.9720.98817.8800.3420.3420.0000.0000.0000.000
113A113GLU-1-0.762-0.86419.795-0.362-0.3620.0000.0000.0000.000
114A114LEU00.0170.00615.3600.0040.0040.0000.0000.0000.000
115A115GLU-1-0.820-0.87814.466-1.029-1.0290.0000.0000.0000.000
116A116GLU-1-1.020-0.99016.186-0.458-0.4580.0000.0000.0000.000
117A117ILE0-0.011-0.00518.0020.0090.0090.0000.0000.0000.000
118A118THR0-0.092-0.06613.085-0.056-0.0560.0000.0000.0000.000
119A119GLY00.0290.02814.273-0.030-0.0300.0000.0000.0000.000
120A120LEU0-0.063-0.0298.219-0.098-0.0980.0000.0000.0000.000
121A121ARG10.8800.9279.6341.2521.2520.0000.0000.0000.000
122A122VAL0-0.038-0.03510.369-0.278-0.2780.0000.0000.0000.000
123A123VAL0-0.028-0.01712.7610.1310.1310.0000.0000.0000.000
124A124ALA0-0.0060.01314.3500.0020.0020.0000.0000.0000.000
125A125GLU-1-0.800-0.88416.207-0.493-0.4930.0000.0000.0000.000
126A126HIS00.013-0.00518.7480.0140.0140.0000.0000.0000.000
127A127LYS10.8720.94320.4850.2160.2160.0000.0000.0000.000
128A128ALA00.0540.02315.2880.0180.0180.0000.0000.0000.000
129A129ASP-1-0.814-0.90515.686-0.082-0.0820.0000.0000.0000.000
130A130GLU-1-0.927-0.93616.883-0.021-0.0210.0000.0000.0000.000
131A131LYS10.7980.88815.9370.4440.4440.0000.0000.0000.000
132A132TYR0-0.034-0.04011.296-0.034-0.0340.0000.0000.0000.000
133A133PRO00.0270.00910.9920.0250.0250.0000.0000.0000.000
134A134LEU00.0430.0185.1150.1090.1090.0000.0000.0000.000
135A135VAL0-0.0040.0099.4640.0390.0390.0000.0000.0000.000
136A136ALA00.0240.02612.3000.0490.0490.0000.0000.0000.000
137A137ALA0-0.013-0.01710.7490.0370.0370.0000.0000.0000.000
138A138ALA0-0.0040.00011.2660.0490.0490.0000.0000.0000.000
139A139SER00.029-0.00812.9120.0150.0150.0000.0000.0000.000
140A140ILE0-0.082-0.03215.6960.0030.0030.0000.0000.0000.000
141A141ILE0-0.0060.00113.020-0.007-0.0070.0000.0000.0000.000
142A142ALA00.0050.00016.290-0.014-0.0140.0000.0000.0000.000
143A143LYS10.9040.92618.226-0.004-0.0040.0000.0000.0000.000
144A144VAL00.0280.03319.785-0.007-0.0070.0000.0000.0000.000
145A145GLU-1-0.819-0.89818.8710.1230.1230.0000.0000.0000.000
146A146ARG10.8210.89321.674-0.014-0.0140.0000.0000.0000.000
147A147GLU-1-0.818-0.91724.1370.0460.0460.0000.0000.0000.000
148A148ARG10.7910.88519.888-0.219-0.2190.0000.0000.0000.000
149A149GLU-1-0.831-0.87526.3110.0180.0180.0000.0000.0000.000
150A150ILE0-0.062-0.03627.980-0.008-0.0080.0000.0000.0000.000
151A151GLU-1-0.840-0.93129.8640.0580.0580.0000.0000.0000.000
152A152ARG10.8680.90629.470-0.035-0.0350.0000.0000.0000.000
153A153LEU0-0.062-0.04531.456-0.007-0.0070.0000.0000.0000.000
154A154LYS10.8150.91733.767-0.034-0.0340.0000.0000.0000.000
155A155GLU-1-0.964-0.96134.3230.0610.0610.0000.0000.0000.000
156A156LYS10.8900.95736.533-0.018-0.0180.0000.0000.0000.000
157A157PHE0-0.080-0.07236.275-0.004-0.0040.0000.0000.0000.000
158A158GLY00.0510.04439.628-0.004-0.0040.0000.0000.0000.000
159A159ASP-1-0.818-0.90737.8750.0240.0240.0000.0000.0000.000
160A160PHE00.0100.00233.410-0.004-0.0040.0000.0000.0000.000
161A161GLY00.0150.01537.248-0.006-0.0060.0000.0000.0000.000
162A162SER0-0.060-0.06532.3860.0000.0000.0000.0000.0000.000
163A163GLY00.0500.02332.2100.0000.0000.0000.0000.0000.000
164A164TYR00.0380.00027.224-0.015-0.0150.0000.0000.0000.000
165A165ALA00.010-0.00833.9530.0040.0040.0000.0000.0000.000
166A166SER0-0.015-0.01235.8350.0000.0000.0000.0000.0000.000
167A167ASP-1-0.776-0.86836.1970.0020.0020.0000.0000.0000.000
168A168PRO0-0.009-0.02238.109-0.002-0.0020.0000.0000.0000.000
169A169ARG10.9550.96739.951-0.004-0.0040.0000.0000.0000.000
170A170THR0-0.015-0.01636.5410.0000.0000.0000.0000.0000.000
171A171ARG10.8780.95739.5190.0210.0210.0000.0000.0000.000
172A172GLU-1-0.886-0.92142.066-0.004-0.0040.0000.0000.0000.000
173A173VAL00.0450.02841.258-0.001-0.0010.0000.0000.0000.000
174A174LEU00.000-0.00538.141-0.002-0.0020.0000.0000.0000.000
175A175LYS10.9100.96042.4350.0160.0160.0000.0000.0000.000
176A176GLU-1-0.911-0.95845.995-0.004-0.0040.0000.0000.0000.000
177A177TRP00.0450.01038.541-0.002-0.0020.0000.0000.0000.000
178A178ILE0-0.035-0.01542.868-0.002-0.0020.0000.0000.0000.000
179A179ALA0-0.042-0.01646.295-0.001-0.0010.0000.0000.0000.000
180A180SER0-0.034-0.01747.2760.0010.0010.0000.0000.0000.000
181A181GLY0-0.0080.00148.6530.0010.0010.0000.0000.0000.000
182A182ARG10.8740.93246.3110.0060.0060.0000.0000.0000.000
183A183ILE00.0130.00640.5750.0020.0020.0000.0000.0000.000
184A184PRO00.0150.02338.676-0.001-0.0010.0000.0000.0000.000
185A185SER00.0610.01236.180-0.003-0.0030.0000.0000.0000.000
186A186CYS0-0.060-0.00833.660-0.006-0.0060.0000.0000.0000.000
187A187VAL00.0270.00533.954-0.002-0.0020.0000.0000.0000.000
188A188ARG10.7980.91427.4670.0700.0700.0000.0000.0000.000
189A189MET00.019-0.01034.8740.0010.0010.0000.0000.0000.000
190A190ARG10.8230.90735.3500.0940.0940.0000.0000.0000.000
191A191TRP00.0130.01329.463-0.005-0.0050.0000.0000.0000.000
192A192LYS10.9810.98736.3260.0820.0820.0000.0000.0000.000
193A193THR0-0.010-0.02237.5430.0020.0020.0000.0000.0000.000
194A194VAL00.0570.03538.3100.0050.0050.0000.0000.0000.000
195A195SER00.0210.01640.5420.0030.0030.0000.0000.0000.000
196A196ASN0-0.021-0.03142.5720.0010.0010.0000.0000.0000.000
197A197LEU0-0.032-0.01942.3480.0030.0030.0000.0000.0000.000
198A198ARG10.9550.98343.2930.0490.0490.0000.0000.0000.000
199A199GLN0-0.0210.00445.6240.0000.0000.0000.0000.0000.000
200A200LYS10.9120.98447.0800.0380.0380.0000.0000.0000.000