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: R1RJ8

Calculation Name: 2QLZ-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QLZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U4J2

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2565772.347928
FMO2-HF: Nuclear repulsion 2474195.895002
FMO2-HF: Total energy -91576.452926
FMO2-MP2: Total energy -91842.190011


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:ACE )


Summations of interaction energy for fragment #1(A:1:ACE )
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.
-2.95-1.3340.053-0.782-0.888-0.002
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.071 / q_NPA : -0.051
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].
3A3PRO 0-0.0020.0113.6540.4691.8530.012-0.690-0.706-0.002
4A4ASP -1-0.811-0.9025.5740.2750.2750.0000.0000.0000.000
5A5LEU 00.008-0.0216.7780.0420.0420.0000.0000.0000.000
6A6PHE 00.0150.0379.4830.0090.0090.0000.0000.0000.000
7A7TYR 00.0210.01511.3570.0200.0200.0000.0000.0000.000
8A8ILE 0-0.076-0.03611.2600.0180.0180.0000.0000.0000.000
9A9LEU 00.025-0.00612.7250.0040.0040.0000.0000.0000.000
10A10GLY 0-0.0020.01815.1450.0040.0040.0000.0000.0000.000
11A11ASN 0-0.025-0.02117.213-0.008-0.0080.0000.0000.0000.000
12A12LYS 10.9780.97919.822-0.014-0.0140.0000.0000.0000.000
13A13VAL 00.0370.01822.5950.0070.0070.0000.0000.0000.000
14A14ARG 10.8910.95316.6480.0630.0630.0000.0000.0000.000
15A15ARG 10.9470.96618.262-0.050-0.0500.0000.0000.0000.000
16A16ASP -1-0.811-0.89119.7430.0490.0490.0000.0000.0000.000
17A17LEU 0-0.021-0.01220.6890.0030.0030.0000.0000.0000.000
18A18LEU 00.0210.00315.0910.0030.0030.0000.0000.0000.000
19A19SER 0-0.017-0.00519.0230.0110.0110.0000.0000.0000.000
20A20HIS 10.8110.90321.351-0.043-0.0430.0000.0000.0000.000
21A21LEU 0-0.033-0.02518.680-0.002-0.0020.0000.0000.0000.000
22A22THR 0-0.0100.00517.9740.0040.0040.0000.0000.0000.000
23A26CYS 0-0.094-0.03320.5880.0060.0060.0000.0000.0000.000
24A24MET 0-0.012-0.00121.777-0.012-0.0120.0000.0000.0000.000
25A25GLU -1-0.868-0.94524.9150.0650.0650.0000.0000.0000.000
26A27TYR 00.0220.02625.703-0.004-0.0040.0000.0000.0000.000
27A28PHE 00.0450.02429.670-0.003-0.0030.0000.0000.0000.000
28A29SER 0-0.048-0.03229.576-0.004-0.0040.0000.0000.0000.000
29A30LEU 0-0.003-0.01823.5290.0050.0050.0000.0000.0000.000
30A31LEU 0-0.036-0.02425.3510.0020.0020.0000.0000.0000.000
31A32SER 00.0080.00027.7700.0030.0030.0000.0000.0000.000
32A33SER 0-0.0250.00029.932-0.005-0.0050.0000.0000.0000.000
33A34LYS 10.8470.92132.443-0.036-0.0360.0000.0000.0000.000
34A35VAL 0-0.076-0.03227.944-0.002-0.0020.0000.0000.0000.000
35A36SER 00.0350.02731.221-0.002-0.0020.0000.0000.0000.000
36A37VAL 0-0.012-0.01627.046-0.003-0.0030.0000.0000.0000.000
37A38SER 00.0420.02230.4060.0000.0000.0000.0000.0000.000
38A39SER 00.0490.01029.342-0.002-0.0020.0000.0000.0000.000
39A40THR 0-0.0090.00328.407-0.004-0.0040.0000.0000.0000.000
40A41ALA 00.0430.00126.280-0.008-0.0080.0000.0000.0000.000
41A42VAL 00.0210.02724.580-0.005-0.0050.0000.0000.0000.000
42A43ALA 00.0260.00923.402-0.003-0.0030.0000.0000.0000.000
43A44LYS 10.9360.97920.2260.1240.1240.0000.0000.0000.000
44A45HIS 00.020-0.00520.083-0.023-0.0230.0000.0000.0000.000
45A46LEU 00.0270.01618.547-0.008-0.0080.0000.0000.0000.000
46A47LYS 10.9670.99018.0780.1110.1110.0000.0000.0000.000
47A48ILE 0-0.084-0.04315.505-0.028-0.0280.0000.0000.0000.000
48A49MET 00.0450.02213.892-0.028-0.0280.0000.0000.0000.000
49A50GLU -1-0.857-0.90813.272-0.110-0.1100.0000.0000.0000.000
50A51ARG 10.8840.93313.5680.1800.1800.0000.0000.0000.000
51A52GLU -1-0.871-0.9279.270-0.600-0.6000.0000.0000.0000.000
52A53GLY 00.0330.0298.776-0.114-0.1140.0000.0000.0000.000
53A54VAL 0-0.024-0.0129.3070.0960.0960.0000.0000.0000.000
54A55LEU 0-0.065-0.03211.1820.0580.0580.0000.0000.0000.000
55A56GLN 00.0360.02614.388-0.057-0.0570.0000.0000.0000.000
56A57SER 0-0.114-0.07516.5170.0270.0270.0000.0000.0000.000
57A58TYR 00.013-0.00218.194-0.001-0.0010.0000.0000.0000.000
58A59GLU -1-0.921-0.97023.204-0.049-0.0490.0000.0000.0000.000
59A60LYS 10.9120.96226.8250.0030.0030.0000.0000.0000.000
60A61GLU -1-0.772-0.88830.085-0.030-0.0300.0000.0000.0000.000
61A62GLU -1-0.875-0.92733.605-0.010-0.0100.0000.0000.0000.000
62A63ARG 10.7980.88436.8330.0200.0200.0000.0000.0000.000
63A64PHE 00.0270.01736.329-0.001-0.0010.0000.0000.0000.000
64A65ILE 0-0.023-0.02335.3970.0010.0010.0000.0000.0000.000
65A66GLY 00.0370.02436.0240.0020.0020.0000.0000.0000.000
66A67PRO 0-0.045-0.01536.244-0.003-0.0030.0000.0000.0000.000
67A68THR 0-0.038-0.02130.5700.0040.0040.0000.0000.0000.000
68A69LYS 10.9390.97430.3940.0060.0060.0000.0000.0000.000
69A70LYS 10.9921.00222.6070.0670.0670.0000.0000.0000.000
70A71TYR 0-0.043-0.01723.5320.0060.0060.0000.0000.0000.000
71A72TYR 00.026-0.01319.277-0.014-0.0140.0000.0000.0000.000
72A73LYS 10.9300.96817.997-0.020-0.0200.0000.0000.0000.000
73A74ILE 00.0180.00913.296-0.025-0.0250.0000.0000.0000.000
74A75SER 0-0.003-0.00710.9990.0250.0250.0000.0000.0000.000
75A76ILE 0-0.0280.0007.2560.0350.0350.0000.0000.0000.000
76A77ALA 00.0250.0059.553-0.062-0.0620.0000.0000.0000.000
77A78LYS 10.9190.9643.074-4.910-4.6780.041-0.092-0.1820.000
78A79SER 00.0360.0299.458-0.153-0.1530.0000.0000.0000.000
79A80TYR 0-0.017-0.0235.5270.3630.3630.0000.0000.0000.000
80A81VAL 00.0220.03510.446-0.126-0.1260.0000.0000.0000.000
81A82PHE 0-0.008-0.02211.2920.0530.0530.0000.0000.0000.000
82A83THR 0-0.018-0.00113.580-0.024-0.0240.0000.0000.0000.000
83A84LEU 00.007-0.00116.461-0.005-0.0050.0000.0000.0000.000
84A85THR 0-0.0040.00718.947-0.005-0.0050.0000.0000.0000.000
85A86PRO 0-0.003-0.01921.956-0.002-0.0020.0000.0000.0000.000
86A87GLU -1-0.887-0.93223.6750.0450.0450.0000.0000.0000.000
87A88MET 0-0.044-0.01818.6510.0120.0120.0000.0000.0000.000
88A89PHE 0-0.006-0.01512.5490.0060.0060.0000.0000.0000.000
89A90TRP 00.0130.01511.9630.0250.0250.0000.0000.0000.000
90A91TYR 00.0350.0036.721-0.023-0.0230.0000.0000.0000.000
91A92LYS 10.9560.9777.723-0.879-0.8790.0000.0000.0000.000
92A93GLY 0-0.017-0.0015.486-0.094-0.0940.0000.0000.0000.000
93A94LEU 0-0.068-0.0416.5010.1760.1760.0000.0000.0000.000
94A95ASP -1-0.885-0.9486.2321.9171.9170.0000.0000.0000.000
95A96LEU 0-0.043-0.0228.625-0.156-0.1560.0000.0000.0000.000
96A97GLY 0-0.013-0.02311.9370.0010.0010.0000.0000.0000.000
97A98ASP -1-0.939-0.95914.6180.1710.1710.0000.0000.0000.000
98A99ALA 0-0.044-0.02317.7940.0170.0170.0000.0000.0000.000
99A100GLU -1-0.918-0.94919.2480.2050.2050.0000.0000.0000.000
100A101LEU 0-0.067-0.04321.6110.0080.0080.0000.0000.0000.000
101A102ARG 10.9560.96820.394-0.229-0.2290.0000.0000.0000.000
102A103ASP -1-0.910-0.93924.8450.1450.1450.0000.0000.0000.000
103A104PHE 0-0.050-0.03020.5970.0070.0070.0000.0000.0000.000
104A105GLU -1-0.872-0.92025.5960.1060.1060.0000.0000.0000.000
105A106ILE 0-0.046-0.03222.8440.0070.0070.0000.0000.0000.000
106A107SER 0-0.009-0.01126.407-0.007-0.0070.0000.0000.0000.000
107A108LEU 0-0.012-0.02025.1420.0020.0020.0000.0000.0000.000
108A109SER 0-0.0250.00229.166-0.004-0.0040.0000.0000.0000.000
109A110GLY 00.009-0.00732.4670.0020.0020.0000.0000.0000.000
110A111LEU 0-0.085-0.04226.740-0.001-0.0010.0000.0000.0000.000
111A112ASP -1-0.857-0.93231.1570.0580.0580.0000.0000.0000.000
112A113THR 0-0.042-0.02932.4110.0020.0020.0000.0000.0000.000
113A114GLU -1-1.033-1.01434.1690.0420.0420.0000.0000.0000.000
114A115PRO 00.0520.06832.154-0.003-0.0030.0000.0000.0000.000
115A116SER 0-0.006-0.00935.388-0.004-0.0040.0000.0000.0000.000
116A117THR 0-0.047-0.03035.994-0.003-0.0030.0000.0000.0000.000
117A118LEU 00.0870.02629.6920.0030.0030.0000.0000.0000.000
118A119LYS 10.9410.96831.206-0.036-0.0360.0000.0000.0000.000
119A120GLU -1-0.849-0.91731.4470.0530.0530.0000.0000.0000.000
120A121MET 00.0840.05829.8750.0060.0060.0000.0000.0000.000
121A122ILE 0-0.031-0.01426.1370.0080.0080.0000.0000.0000.000
122A123THR 0-0.087-0.05926.7370.0090.0090.0000.0000.0000.000
123A124ASP -1-0.854-0.94827.7540.0820.0820.0000.0000.0000.000
124A125PHE 0-0.037-0.01120.2070.0100.0100.0000.0000.0000.000
125A126ILE 0-0.021-0.01622.6930.0160.0160.0000.0000.0000.000
126A127LYS 10.9310.97523.527-0.071-0.0710.0000.0000.0000.000
127A128ALA 00.0640.02723.8620.0120.0120.0000.0000.0000.000
128A129ASN 0-0.017-0.01819.3230.0200.0200.0000.0000.0000.000
129A130LYS 10.8370.91819.565-0.166-0.1660.0000.0000.0000.000
130A131GLU -1-0.779-0.88621.5930.1660.1660.0000.0000.0000.000
131A132LEU 00.0010.00416.4300.0190.0190.0000.0000.0000.000
132A133GLU -1-0.889-0.94316.0860.2840.2840.0000.0000.0000.000
133A134LYS 10.8300.90817.592-0.133-0.1330.0000.0000.0000.000
134A135VAL 00.0200.02118.4210.0100.0100.0000.0000.0000.000
135A136LEU 0-0.039-0.02312.7240.0320.0320.0000.0000.0000.000
136A137GLU -1-0.870-0.92915.0910.4570.4570.0000.0000.0000.000
137A138ALA 00.0350.04216.7350.0000.0000.0000.0000.0000.000
138A139PHE 0-0.029-0.04013.5800.0020.0020.0000.0000.0000.000
139A140LYS 10.9310.96611.966-0.587-0.5870.0000.0000.0000.000
140A141THR 0-0.016-0.01915.051-0.013-0.0130.0000.0000.0000.000
141A142ILE 0-0.007-0.00418.303-0.022-0.0220.0000.0000.0000.000
142A143GLU -1-0.807-0.88315.5660.2690.2690.0000.0000.0000.000
143A144SER 0-0.036-0.01415.7090.0000.0000.0000.0000.0000.000
144A145TYR 0-0.025-0.00717.139-0.034-0.0340.0000.0000.0000.000
145A146ARG 10.8850.91220.045-0.233-0.2330.0000.0000.0000.000
146A147SER 0-0.0060.00916.428-0.035-0.0350.0000.0000.0000.000
147A148SER 0-0.014-0.01519.258-0.030-0.0300.0000.0000.0000.000
148A149LEU 0-0.051-0.02121.264-0.020-0.0200.0000.0000.0000.000
149A150MET 00.0590.04221.884-0.021-0.0210.0000.0000.0000.000
150A151ARG 10.9010.95821.679-0.134-0.1340.0000.0000.0000.000
151A152LYS 10.9620.97523.624-0.141-0.1410.0000.0000.0000.000
152A153ILE 00.0360.02626.829-0.010-0.0100.0000.0000.0000.000
153A154LYS 10.8710.93522.443-0.112-0.1120.0000.0000.0000.000
154A155GLU -1-0.947-0.97326.3180.0770.0770.0000.0000.0000.000
155A156ALA 0-0.009-0.01429.536-0.007-0.0070.0000.0000.0000.000
156A157TYR 00.0350.00031.424-0.004-0.0040.0000.0000.0000.000
157A158LEU 0-0.034-0.00930.270-0.005-0.0050.0000.0000.0000.000
158A159LYS 10.8840.93431.153-0.065-0.0650.0000.0000.0000.000
159A160GLU -1-0.961-0.96235.6120.0540.0540.0000.0000.0000.000
160A161ILE 0-0.039-0.01336.347-0.003-0.0030.0000.0000.0000.000
161A162GLY 0-0.0020.00735.878-0.003-0.0030.0000.0000.0000.000
162A163ASP -1-0.867-0.93236.2450.0360.0360.0000.0000.0000.000
163A164MET 00.020-0.01131.3360.0060.0060.0000.0000.0000.000
164A165THR 0-0.039-0.01732.342-0.003-0.0030.0000.0000.0000.000
165A166GLN 00.0670.03633.7510.0050.0050.0000.0000.0000.000
166A167LEU 00.0210.01228.4560.0050.0050.0000.0000.0000.000
167A168ALA 0-0.032-0.01928.8080.0070.0070.0000.0000.0000.000
168A169ILE 00.0110.01429.2400.0060.0060.0000.0000.0000.000
169A170LEU 00.0330.02330.2480.0050.0050.0000.0000.0000.000
170A171HIS 00.003-0.01722.236-0.001-0.0010.0000.0000.0000.000
171A172TYR 0-0.045-0.03826.2810.0110.0110.0000.0000.0000.000
172A173LEU 0-0.031-0.03427.3270.0060.0060.0000.0000.0000.000
173A174LEU 00.0000.01426.7310.0040.0040.0000.0000.0000.000
174A175LEU 0-0.097-0.03621.4690.0130.0130.0000.0000.0000.000
175A176ASN 0-0.053-0.01224.3550.0160.0160.0000.0000.0000.000
176A177GLY 00.0330.02126.661-0.004-0.0040.0000.0000.0000.000
177A178ARG 10.9500.97129.859-0.078-0.0780.0000.0000.0000.000
178A179ALA 00.0270.00930.8130.0040.0040.0000.0000.0000.000
179A180THR 0-0.0010.03033.002-0.004-0.0040.0000.0000.0000.000
180A181VAL 00.020-0.00335.3480.0010.0010.0000.0000.0000.000
181A182GLU -1-0.866-0.92136.8080.0310.0310.0000.0000.0000.000
182A183GLU -1-0.944-0.99031.7270.0560.0560.0000.0000.0000.000
183A184LEU 0-0.009-0.01031.6070.0010.0010.0000.0000.0000.000
184A185SER 0-0.065-0.04033.426-0.002-0.0020.0000.0000.0000.000
185A186ASP -1-0.788-0.90631.5500.0290.0290.0000.0000.0000.000
186A187ARG 10.9030.96924.746-0.072-0.0720.0000.0000.0000.000
187A188LEU 0-0.023-0.01930.115-0.001-0.0010.0000.0000.0000.000
188A189ASN 0-0.071-0.02431.195-0.006-0.0060.0000.0000.0000.000
189A190LEU 0-0.0060.01134.758-0.002-0.0020.0000.0000.0000.000
190A191LYS 10.9840.99537.799-0.016-0.0160.0000.0000.0000.000
191A192GLU -1-0.826-0.94139.9220.0310.0310.0000.0000.0000.000
192A193ARG 10.7780.87941.274-0.023-0.0230.0000.0000.0000.000
193A194GLU -1-0.827-0.92540.7670.0230.0230.0000.0000.0000.000
194A195VAL 0-0.0030.00736.9510.0020.0020.0000.0000.0000.000
195A196ARG 10.8690.90739.341-0.030-0.0300.0000.0000.0000.000
196A197GLU -1-0.864-0.89842.1250.0250.0250.0000.0000.0000.000
197A198LYS 10.9270.96338.010-0.032-0.0320.0000.0000.0000.000
198A199ILE 00.0120.00537.5810.0020.0020.0000.0000.0000.000
199A200SER 0-0.061-0.02439.7430.0010.0010.0000.0000.0000.000
200A201GLU -1-0.902-0.95941.5830.0320.0320.0000.0000.0000.000
201A202MET 0-0.018-0.00434.1960.0000.0000.0000.0000.0000.000
202A203ALA 0-0.007-0.00939.4260.0020.0020.0000.0000.0000.000
203A204ARG 10.8880.96741.352-0.035-0.0350.0000.0000.0000.000
204A205PHE 0-0.022-0.02538.551-0.001-0.0010.0000.0000.0000.000
205A206VAL 0-0.0010.00535.0080.0040.0040.0000.0000.0000.000
206A207PRO 00.0330.02637.243-0.003-0.0030.0000.0000.0000.000
207A208VAL 00.0130.02536.4990.0040.0040.0000.0000.0000.000
208A209LYS 10.9480.98338.700-0.054-0.0540.0000.0000.0000.000
209A210ILE 0-0.006-0.00439.4140.0020.0020.0000.0000.0000.000
210A211ILE 0-0.016-0.01738.756-0.002-0.0020.0000.0000.0000.000
211A212ASN 00.009-0.02041.001-0.001-0.0010.0000.0000.0000.000
212A213ASP -1-0.831-0.88543.9450.0300.0300.0000.0000.0000.000
213A214ASN 0-0.019-0.02639.5540.0000.0000.0000.0000.0000.000
214A215THR 0-0.0170.00136.0200.0020.0020.0000.0000.0000.000
215A216VAL 0-0.0090.00135.731-0.001-0.0010.0000.0000.0000.000
216A217VAL 0-0.001-0.02734.2800.0040.0040.0000.0000.0000.000
217A218LEU 00.0360.02031.377-0.004-0.0040.0000.0000.0000.000
218A219ASP -1-0.938-0.98635.4880.0560.0560.0000.0000.0000.000
219A220GLU -1-0.888-0.96532.9610.0890.0890.0000.0000.0000.000
220A221ASP -1-0.869-0.92636.8940.0630.0630.0000.0000.0000.000
221A222GLN 0-0.050-0.01140.279-0.001-0.0010.0000.0000.0000.000
222A223ILE 0-0.038-0.02234.4930.0000.0000.0000.0000.0000.000
223A224LEU 0-0.051-0.02333.7750.0020.0020.0000.0000.0000.000
224A225ARG 10.7940.89037.873-0.068-0.0680.0000.0000.0000.000
225A226NME 00.0340.04041.666-0.002-0.0020.0000.0000.0000.000