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: MVV9Z

Calculation Name: 4KEJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KEJ

Chain ID: A

ChEMBL ID:

UniProt ID: E9Q401

Base Structure: X-ray

Registration Date: 2023-06-21

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973495.388775
FMO2-HF: Nuclear repulsion 1900605.967775
FMO2-HF: Total energy -72889.421
FMO2-MP2: Total energy -73098.583281


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:12:GLN)


Summations of interaction energy for fragment #1(A:12:GLN)
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.
-50.372-52.45422.91-9.184-11.6420.016
Interaction energy analysis for fragmet #1(A:12:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.004
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].
3A14LEU00.0320.0242.062-9.083-6.9434.978-3.246-3.872-0.033
4A15ARG10.8140.8931.878-26.638-33.29416.719-4.849-5.2140.054
5A16THR0-0.004-0.0205.342-0.586-0.572-0.0010.000-0.0120.000
6A17ASP-1-0.943-0.9688.590-0.086-0.0860.0000.0000.0000.000
7A18ASP-1-0.938-0.9525.222-3.706-3.7060.0000.0000.0000.000
8A19GLU-1-0.847-0.9118.851-0.966-0.9660.0000.0000.0000.000
9A20VAL0-0.074-0.0567.419-0.715-0.7150.0000.0000.0000.000
10A21VAL00.0510.01510.0060.4840.4840.0000.0000.0000.000
11A22LEU0-0.012-0.00111.837-0.278-0.2780.0000.0000.0000.000
12A23GLN00.0380.00213.7210.2090.2090.0000.0000.0000.000
13A24CYS00.0190.03115.580-0.034-0.0340.0000.0000.0000.000
14A25THR0-0.024-0.00618.117-0.002-0.0020.0000.0000.0000.000
15A26ALA00.0450.03420.3090.0550.0550.0000.0000.0000.000
16A27THR0-0.015-0.02624.0430.0010.0010.0000.0000.0000.000
17A28ILE00.0150.01226.6290.0260.0260.0000.0000.0000.000
18A29HIS00.0380.01930.3500.0050.0050.0000.0000.0000.000
19A30LYS10.8630.93729.9800.4150.4150.0000.0000.0000.000
20A31GLU-1-0.892-0.93128.363-0.528-0.5280.0000.0000.0000.000
21A32GLN0-0.048-0.03621.466-0.087-0.0870.0000.0000.0000.000
22A33GLN00.0520.04522.868-0.032-0.0320.0000.0000.0000.000
23A34LYS10.8990.94715.5411.3291.3290.0000.0000.0000.000
24A35LEU00.0060.01119.7920.0540.0540.0000.0000.0000.000
25A36CYS0-0.0270.00117.181-0.183-0.1830.0000.0000.0000.000
26A37LEU00.0150.00917.5780.1260.1260.0000.0000.0000.000
27A38ALA00.0200.01318.540-0.078-0.0780.0000.0000.0000.000
28A39ALA00.028-0.00121.0190.0570.0570.0000.0000.0000.000
29A40GLU-1-0.887-0.94123.658-0.515-0.5150.0000.0000.0000.000
30A41GLY00.011-0.00926.1240.0170.0170.0000.0000.0000.000
31A42PHE0-0.030-0.02127.5360.0350.0350.0000.0000.0000.000
32A43GLY00.0000.00331.112-0.009-0.0090.0000.0000.0000.000
33A44ASN0-0.028-0.02531.644-0.013-0.0130.0000.0000.0000.000
34A45ARG10.9971.00128.6400.3430.3430.0000.0000.0000.000
35A46LEU0-0.040-0.01227.256-0.028-0.0280.0000.0000.0000.000
36A47CYS0-0.0150.01021.971-0.001-0.0010.0000.0000.0000.000
37A48PHE0-0.040-0.00923.9860.0430.0430.0000.0000.0000.000
38A49LEU0-0.011-0.01521.144-0.072-0.0720.0000.0000.0000.000
39A50GLU-1-0.815-0.91021.653-0.763-0.7630.0000.0000.0000.000
40A51SER0-0.014-0.03821.841-0.059-0.0590.0000.0000.0000.000
41A52THR0-0.046-0.03918.302-0.041-0.0410.0000.0000.0000.000
42A53SER0-0.100-0.05121.0150.0370.0370.0000.0000.0000.000
43A54ASN00.0310.01822.2040.0240.0240.0000.0000.0000.000
44A55SER00.0550.02120.3030.0240.0240.0000.0000.0000.000
45A56LYS10.8800.93215.0691.3101.3100.0000.0000.0000.000
46A57ASN0-0.055-0.04414.663-0.031-0.0310.0000.0000.0000.000
47A58VAL00.0470.02816.139-0.184-0.1840.0000.0000.0000.000
48A59PRO00.0580.05317.5370.0780.0780.0000.0000.0000.000
49A60PRO0-0.055-0.02120.6270.0120.0120.0000.0000.0000.000
50A61ASP-1-0.836-0.92222.815-0.660-0.6600.0000.0000.0000.000
51A62LEU00.004-0.00515.490-0.069-0.0690.0000.0000.0000.000
52A63SER0-0.056-0.02217.960-0.071-0.0710.0000.0000.0000.000
53A64ILE0-0.0040.00719.477-0.037-0.0370.0000.0000.0000.000
54A65CYS0-0.016-0.00317.263-0.035-0.0350.0000.0000.0000.000
55A66THR0-0.0470.00014.005-0.153-0.1530.0000.0000.0000.000
56A67PHE00.014-0.00813.7000.1910.1910.0000.0000.0000.000
57A68VAL00.0120.00112.501-0.253-0.2530.0000.0000.0000.000
58A69LEU0-0.063-0.0137.8500.1800.1800.0000.0000.0000.000
59A70GLU-1-0.763-0.87311.970-0.299-0.2990.0000.0000.0000.000
60A71GLN0-0.028-0.01514.6870.1870.1870.0000.0000.0000.000
61A72SER0-0.008-0.01612.220-0.087-0.0870.0000.0000.0000.000
62A73LEU0-0.010-0.00114.2980.1680.1680.0000.0000.0000.000
63A74SER00.0360.02817.245-0.068-0.0680.0000.0000.0000.000
64A75VAL00.1280.04919.150-0.007-0.0070.0000.0000.0000.000
65A76ARG10.8390.92122.073-0.034-0.0340.0000.0000.0000.000
66A77ALA00.001-0.01220.9340.0050.0050.0000.0000.0000.000
67A78LEU00.0320.01721.2460.0070.0070.0000.0000.0000.000
68A79GLN00.0420.00123.0290.0220.0220.0000.0000.0000.000
69A80GLU-1-0.935-0.94125.9800.0810.0810.0000.0000.0000.000
70A81MET0-0.028-0.02121.583-0.005-0.0050.0000.0000.0000.000
71A82LEU00.0260.02125.9400.0000.0000.0000.0000.0000.000
72A83ALA00.0210.01328.8560.0000.0000.0000.0000.0000.000
73A84ASN0-0.044-0.02729.9200.0030.0030.0000.0000.0000.000
74A85THR0-0.104-0.03929.9850.0010.0010.0000.0000.0000.000
75A86VAL0-0.048-0.00533.065-0.004-0.0040.0000.0000.0000.000
76A110HIS00.0490.0318.263-0.266-0.2660.0000.0000.0000.000
77A111ARG10.9010.9598.5560.4200.4200.0000.0000.0000.000
78A112THR0-0.034-0.0306.3560.2900.2900.0000.0000.0000.000
79A113LEU00.0240.0277.2330.0450.0450.0000.0000.0000.000
80A114LEU0-0.057-0.0389.1470.2660.2660.0000.0000.0000.000
81A115TYR00.0090.00810.580-0.220-0.2200.0000.0000.0000.000
82A116GLY00.0690.04214.1470.1690.1690.0000.0000.0000.000
83A117HIS0-0.137-0.07513.9180.1510.1510.0000.0000.0000.000
84A118ALA00.0540.02915.943-0.122-0.1220.0000.0000.0000.000
85A119ILE0-0.070-0.04812.2750.0360.0360.0000.0000.0000.000
86A120LEU00.0140.02415.1240.0220.0220.0000.0000.0000.000
87A121LEU0-0.008-0.01513.384-0.108-0.1080.0000.0000.0000.000
88A122ARG10.9470.99516.1750.7010.7010.0000.0000.0000.000
89A123HIS00.0030.00216.951-0.077-0.0770.0000.0000.0000.000
90A124SER0-0.057-0.04616.0100.0970.0970.0000.0000.0000.000
91A125TYR0-0.036-0.00618.7610.0880.0880.0000.0000.0000.000
92A126SER00.002-0.01222.1830.0620.0620.0000.0000.0000.000
93A127GLY0-0.039-0.00921.7700.0520.0520.0000.0000.0000.000
94A128MET0-0.068-0.02222.8020.0430.0430.0000.0000.0000.000
95A129TYR0-0.042-0.06419.371-0.061-0.0610.0000.0000.0000.000
96A130LEU00.0080.01117.9280.0380.0380.0000.0000.0000.000
97A131CYS0-0.064-0.01921.1610.0260.0260.0000.0000.0000.000
98A132CYS00.0120.01023.804-0.021-0.0210.0000.0000.0000.000
99A133LEU0-0.0180.00026.0740.0430.0430.0000.0000.0000.000
100A134SER00.023-0.00229.6590.0050.0050.0000.0000.0000.000
101A135THR0-0.056-0.01432.2200.0290.0290.0000.0000.0000.000
102A136SER0-0.041-0.03432.648-0.010-0.0100.0000.0000.0000.000
103A137ARG10.8110.92133.6540.3310.3310.0000.0000.0000.000
104A138SER00.0580.01229.851-0.028-0.0280.0000.0000.0000.000
105A139SER0-0.097-0.04431.8560.0250.0250.0000.0000.0000.000
106A140THR0-0.027-0.04232.428-0.003-0.0030.0000.0000.0000.000
107A141ASP-1-0.691-0.84132.998-0.314-0.3140.0000.0000.0000.000
108A142LYS10.7930.88134.9390.2670.2670.0000.0000.0000.000
109A143LEU0-0.084-0.04535.1440.0160.0160.0000.0000.0000.000
110A144ALA00.0490.05330.139-0.001-0.0010.0000.0000.0000.000
111A145PHE0-0.032-0.02129.3230.0250.0250.0000.0000.0000.000
112A146ASP-1-0.709-0.83129.084-0.419-0.4190.0000.0000.0000.000
113A147VAL00.008-0.00322.7150.0080.0080.0000.0000.0000.000
114A148GLY00.0460.01625.601-0.008-0.0080.0000.0000.0000.000
115A149LEU0-0.0350.01122.038-0.020-0.0200.0000.0000.0000.000
116A150GLN0-0.006-0.03425.0370.0470.0470.0000.0000.0000.000
117A151GLU-1-0.919-0.95425.225-0.300-0.3000.0000.0000.0000.000
118A152ASP-1-0.844-0.90126.237-0.218-0.2180.0000.0000.0000.000
119A153THR00.026-0.01122.960-0.022-0.0220.0000.0000.0000.000
120A154THR0-0.108-0.04224.3280.0080.0080.0000.0000.0000.000
121A155GLY00.0390.01526.989-0.013-0.0130.0000.0000.0000.000
122A156GLU-1-0.882-0.97525.065-0.222-0.2220.0000.0000.0000.000
123A157ALA00.000-0.00624.365-0.035-0.0350.0000.0000.0000.000
124A158CYS0-0.067-0.02321.976-0.039-0.0390.0000.0000.0000.000
125A159TRP00.0170.01917.467-0.066-0.0660.0000.0000.0000.000
126A160TRP00.007-0.00617.3910.0160.0160.0000.0000.0000.000
127A161THR0-0.001-0.00216.992-0.051-0.0510.0000.0000.0000.000
128A162ILE0-0.0120.01011.182-0.081-0.0810.0000.0000.0000.000
129A163HIS00.0150.00315.3980.1250.1250.0000.0000.0000.000
130A164PRO00.0260.01414.568-0.202-0.2020.0000.0000.0000.000
131A165ALA00.0240.01514.7270.0830.0830.0000.0000.0000.000
132A166SER0-0.030-0.02916.1570.1180.1180.0000.0000.0000.000
133A167LYS10.9520.98417.1540.0910.0910.0000.0000.0000.000
134A168GLN0-0.035-0.02913.9440.1190.1190.0000.0000.0000.000
135A169GLN0-0.047-0.03310.4290.1750.1750.0000.0000.0000.000
136A170SER00.0070.00913.580-0.081-0.0810.0000.0000.0000.000
137A171GLU-1-0.843-0.92115.652-0.286-0.2860.0000.0000.0000.000
138A172GLY0-0.035-0.01516.0270.0930.0930.0000.0000.0000.000
139A173GLU-1-0.949-0.97312.3060.5820.5820.0000.0000.0000.000
140A174LYS10.9240.9517.969-3.437-3.4370.0000.0000.0000.000
141A175VAL00.0500.0377.6140.0550.0550.0000.0000.0000.000
142A176ARG10.9290.9664.297-1.946-1.768-0.001-0.037-0.1400.000
143A177VAL00.0330.0012.354-2.487-0.4531.217-1.025-2.225-0.005
144A178GLY0-0.030-0.0174.4760.1700.254-0.001-0.014-0.0690.000
145A179ASP-1-0.820-0.8957.287-0.823-0.8230.0000.0000.0000.000
146A180ASP-1-0.919-0.9589.430-1.934-1.9340.0000.0000.0000.000
147A181LEU0-0.066-0.04110.0570.1990.1990.0000.0000.0000.000
148A182ILE00.0040.00514.2730.0420.0420.0000.0000.0000.000
149A183LEU0-0.013-0.01514.340-0.002-0.0020.0000.0000.0000.000
150A184VAL00.0160.01518.2670.0320.0320.0000.0000.0000.000
151A185SER0-0.036-0.00920.898-0.002-0.0020.0000.0000.0000.000
152A186VAL00.0340.00121.4120.0380.0380.0000.0000.0000.000
153A187SER0-0.0070.01924.0730.0330.0330.0000.0000.0000.000
154A188SER0-0.054-0.04626.9820.0190.0190.0000.0000.0000.000
155A189GLU-1-0.895-0.94725.585-0.276-0.2760.0000.0000.0000.000
156A190ARG10.7630.88026.5100.3330.3330.0000.0000.0000.000
157A191TYR00.011-0.00322.209-0.023-0.0230.0000.0000.0000.000
158A192LEU00.0090.01818.1400.0320.0320.0000.0000.0000.000
159A193HIS0-0.081-0.04321.511-0.054-0.0540.0000.0000.0000.000
160A194LEU0-0.004-0.00522.588-0.002-0.0020.0000.0000.0000.000
161A195SER0-0.0010.00224.3220.0460.0460.0000.0000.0000.000
162A196TYR00.032-0.00228.062-0.013-0.0130.0000.0000.0000.000
163A197GLY00.0140.03030.6480.0260.0260.0000.0000.0000.000
164A198ASN0-0.064-0.03333.6850.0130.0130.0000.0000.0000.000
165A199SER00.008-0.00834.8960.0010.0010.0000.0000.0000.000
166A200SER0-0.031-0.00830.352-0.018-0.0180.0000.0000.0000.000
167A201TRP00.0260.01326.1740.0080.0080.0000.0000.0000.000
168A202HIS0-0.007-0.01227.1020.0100.0100.0000.0000.0000.000
169A203VAL00.0290.01421.947-0.030-0.0300.0000.0000.0000.000
170A204ASP-1-0.843-0.93025.112-0.477-0.4770.0000.0000.0000.000
171A205ALA00.0490.02225.045-0.042-0.0420.0000.0000.0000.000
172A206ALA0-0.0080.00226.4220.0580.0580.0000.0000.0000.000
173A207PHE00.025-0.01227.550-0.007-0.0070.0000.0000.0000.000
174A208GLN0-0.028-0.00427.664-0.004-0.0040.0000.0000.0000.000
175A209GLN00.0670.03822.157-0.002-0.0020.0000.0000.0000.000
176A210THR0-0.028-0.02219.9000.0330.0330.0000.0000.0000.000
177A211LEU0-0.036-0.00116.702-0.009-0.0090.0000.0000.0000.000
178A212TRP0-0.021-0.02314.833-0.030-0.0300.0000.0000.0000.000
179A213SER0-0.018-0.01511.918-0.107-0.1070.0000.0000.0000.000
180A214VAL0-0.019-0.0058.570-0.031-0.0310.0000.0000.0000.000
181A215ALA0-0.028-0.0156.760-0.920-0.9200.0000.0000.0000.000
182A216PRO00.0210.0193.9490.5120.636-0.001-0.013-0.1100.000
183A217ILE0-0.019-0.0037.1830.1970.1970.0000.0000.0000.000