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: JM859

Calculation Name: 1ZQ7-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZQ7

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PZK8

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 205
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2237727.922275
FMO2-HF: Nuclear repulsion 2158131.954509
FMO2-HF: Total energy -79595.967766
FMO2-MP2: Total energy -79826.927765


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.
-31.109-32.10826.864-10.953-14.91-0.011
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 : -0.031 / q_NPA : -0.011
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].
3A3THR 0-0.011-0.0113.698-0.5140.9420.002-0.689-0.769-0.001
4A4GLU -1-0.843-0.9386.0080.1270.1270.0000.0000.0000.000
5A5THR 0-0.052-0.0278.5350.1430.1430.0000.0000.0000.000
6A6GLU -1-0.794-0.8806.594-0.584-0.5840.0000.0000.0000.000
7A7GLY 00.0570.0308.1550.2580.2580.0000.0000.0000.000
8A8ARG 10.9340.9598.776-0.079-0.0790.0000.0000.0000.000
9A9ALA 0-0.005-0.01111.9010.0160.0160.0000.0000.0000.000
10A10ALA 00.0610.0249.4490.0230.0230.0000.0000.0000.000
11A11VAL 00.0260.01111.572-0.015-0.0150.0000.0000.0000.000
12A12LYS 10.8550.94413.977-0.330-0.3300.0000.0000.0000.000
13A13LEU 00.0080.02613.850-0.045-0.0450.0000.0000.0000.000
14A14ALA 00.0200.03214.937-0.030-0.0300.0000.0000.0000.000
15A15ARG 10.8770.93416.785-0.298-0.2980.0000.0000.0000.000
16A16LYS 10.9730.97619.557-0.272-0.2720.0000.0000.0000.000
17A17THR 0-0.062-0.04418.709-0.027-0.0270.0000.0000.0000.000
18A18ILE 00.0000.00220.022-0.026-0.0260.0000.0000.0000.000
19A19GLU -1-0.903-0.95723.0810.2130.2130.0000.0000.0000.000
20A20ILE 0-0.028-0.01023.923-0.026-0.0260.0000.0000.0000.000
21A21PHE 0-0.057-0.02125.254-0.020-0.0200.0000.0000.0000.000
22A22LEU 0-0.009-0.00126.794-0.016-0.0160.0000.0000.0000.000
23A23SER 0-0.0590.01128.856-0.021-0.0210.0000.0000.0000.000
24A24LYS 10.8680.91729.931-0.207-0.2070.0000.0000.0000.000
25A25GLY 00.0250.01630.674-0.003-0.0030.0000.0000.0000.000
26A26LYS 10.9070.94128.514-0.225-0.2250.0000.0000.0000.000
27A27SER 00.0580.00624.117-0.010-0.0100.0000.0000.0000.000
28A28PRO 0-0.093-0.02423.522-0.005-0.0050.0000.0000.0000.000
29A29ARG 00.1300.04219.8920.0970.0970.0000.0000.0000.000
30A30PRO 0-0.096-0.08522.573-0.025-0.0250.0000.0000.0000.000
31A31ASP -1-0.839-0.89722.0760.2190.2190.0000.0000.0000.000
32A32ALA 00.003-0.01423.3350.0070.0070.0000.0000.0000.000
33A33SER 0-0.0760.01320.349-0.004-0.0040.0000.0000.0000.000
34A34GLY 0-0.0270.00822.315-0.006-0.0060.0000.0000.0000.000
35A35VAL 0-0.070-0.03215.996-0.023-0.0230.0000.0000.0000.000
36A36GLU -1-0.934-0.96316.9740.1770.1770.0000.0000.0000.000
37A37LEU 0-0.038-0.01513.3250.0180.0180.0000.0000.0000.000
38A38SER 0-0.022-0.0339.4490.0510.0510.0000.0000.0000.000
39A39PRO 00.053-0.00410.1850.1080.1080.0000.0000.0000.000
40A40VAL 00.0420.0435.1690.1750.1750.0000.0000.0000.000
41A41PHE 0-0.056-0.0397.9390.6070.6070.0000.0000.0000.000
42A42GLU -1-0.877-0.94110.5390.6420.6420.0000.0000.0000.000
43A43GLU -1-0.928-0.9615.2522.5532.5530.0000.0000.0000.000
44A44TYR 0-0.049-0.0159.3620.0570.0570.0000.0000.0000.000
45A45ARG 10.8260.8821.901-20.371-26.74213.833-4.024-3.4390.029
46A46GLY 00.0190.0359.068-0.375-0.3750.0000.0000.0000.000
47A47VAL 0-0.009-0.0238.9060.6080.6080.0000.0000.0000.000
48A48PHE 00.0020.00610.881-0.340-0.3400.0000.0000.0000.000
49A49VAL 0-0.0050.01212.7060.0910.0910.0000.0000.0000.000
50A50THR 0-0.002-0.02415.331-0.055-0.0550.0000.0000.0000.000
51A51LEU 00.0160.02517.515-0.005-0.0050.0000.0000.0000.000
52A52THR 00.0280.01619.762-0.032-0.0320.0000.0000.0000.000
53A53GLU -1-0.838-0.94022.5610.1720.1720.0000.0000.0000.000
54A54GLY 0-0.010-0.00226.089-0.011-0.0110.0000.0000.0000.000
55A55GLY 0-0.041-0.01924.024-0.013-0.0130.0000.0000.0000.000
56A56LEU 0-0.026-0.00924.443-0.006-0.0060.0000.0000.0000.000
57A57LEU 0-0.034-0.00720.3210.0140.0140.0000.0000.0000.000
58A58ARG 10.7740.88323.119-0.226-0.2260.0000.0000.0000.000
59A59GLY 00.0340.02122.806-0.010-0.0100.0000.0000.0000.000
60A60CYS 0-0.086-0.04616.8890.0270.0270.0000.0000.0000.000
61A61ILE 0-0.0200.00018.418-0.038-0.0380.0000.0000.0000.000
62A62GLY 00.0360.00015.4790.0650.0650.0000.0000.0000.000
63A63HIS 0-0.075-0.01114.561-0.060-0.0600.0000.0000.0000.000
64A64PRO 0-0.013-0.01013.2600.2050.2050.0000.0000.0000.000
65A65TYR 00.0410.02112.6340.1560.1560.0000.0000.0000.000
66A66PRO 0-0.0080.02010.5370.0640.0640.0000.0000.0000.000
67A67ASP -1-0.897-0.96312.4380.6970.6970.0000.0000.0000.000
68A68SER 0-0.055-0.03314.465-0.159-0.1590.0000.0000.0000.000
69A69THR 00.0320.01812.3450.2280.2280.0000.0000.0000.000
70A70LEU 00.0470.0217.126-0.095-0.0950.0000.0000.0000.000
71A71LYN 0-0.037-0.03211.046-0.139-0.1390.0000.0000.0000.000
72A72GLH 00.021-0.02313.887-0.125-0.1250.0000.0000.0000.000
73A73ALA 00.0340.03112.742-0.084-0.0840.0000.0000.0000.000
74A74ILE 00.0030.01210.388-0.087-0.0870.0000.0000.0000.000
75A75LEU 0-0.041-0.02614.407-0.120-0.1200.0000.0000.0000.000
76A76ASP -1-0.859-0.94018.0500.5030.5030.0000.0000.0000.000
77A77SER 00.009-0.01115.704-0.063-0.0630.0000.0000.0000.000
78A78ALA 00.013-0.00117.250-0.064-0.0640.0000.0000.0000.000
79A79ILE 0-0.012-0.00618.698-0.065-0.0650.0000.0000.0000.000
80A80SER 0-0.038-0.01721.050-0.065-0.0650.0000.0000.0000.000
81A81ALA 0-0.0260.00019.441-0.041-0.0410.0000.0000.0000.000
82A82ALA 00.0350.02221.587-0.036-0.0360.0000.0000.0000.000
83A83THR 0-0.060-0.04924.386-0.035-0.0350.0000.0000.0000.000
84A84ARG 10.8680.93423.772-0.389-0.3890.0000.0000.0000.000
85A85ASP -1-0.688-0.83223.7150.3200.3200.0000.0000.0000.000
86A86PRO 0-0.040-0.02325.909-0.022-0.0220.0000.0000.0000.000
87A87ARG 10.8030.89421.360-0.313-0.3130.0000.0000.0000.000
88A88PHE 0-0.031-0.01224.236-0.018-0.0180.0000.0000.0000.000
89A89PRO 0-0.0170.01129.4800.0040.0040.0000.0000.0000.000
90A90THR 00.016-0.01429.1100.0140.0140.0000.0000.0000.000
91A91VAL 0-0.0320.00325.710-0.012-0.0120.0000.0000.0000.000
92A92GLU -1-0.917-0.96229.0020.1680.1680.0000.0000.0000.000
93A93GLN 0-0.029-0.04029.8170.0090.0090.0000.0000.0000.000
94A94ASP -1-0.954-0.98729.8860.1470.1470.0000.0000.0000.000
95A95GLU -1-0.705-0.85228.9090.1770.1770.0000.0000.0000.000
96A96MET 00.0370.03322.1020.0060.0060.0000.0000.0000.000
97A97LYS 10.8300.93525.486-0.116-0.1160.0000.0000.0000.000
98A98ASN 0-0.038-0.02727.755-0.015-0.0150.0000.0000.0000.000
99A99ILE 00.0280.02522.2760.0000.0000.0000.0000.0000.000
100A100LEU 0-0.066-0.02520.038-0.001-0.0010.0000.0000.0000.000
101A101VAL 0-0.001-0.01615.9050.0240.0240.0000.0000.0000.000
102A102GLU -1-0.938-0.98214.4250.4000.4000.0000.0000.0000.000
103A103VAL 00.002-0.0019.860-0.003-0.0030.0000.0000.0000.000
104A104THR 0-0.020-0.0048.4980.0210.0210.0000.0000.0000.000
105A105ILE 0-0.017-0.0104.837-0.173-0.1730.0000.0000.0000.000
106A106LEU 0-0.0080.0015.3031.0411.0410.0000.0000.0000.000
107A107THR 00.005-0.0062.4170.8870.5844.904-1.245-3.3540.005
108A108GLN 0-0.029-0.0154.426-3.224-3.1030.002-0.072-0.0520.000
109A109PRO 0-0.036-0.0196.837-0.578-0.5780.0000.0000.0000.000
110A110GLU -1-0.903-0.9406.818-0.807-0.8070.0000.0000.0000.000
111A111LYS 10.8410.92310.253-0.245-0.2450.0000.0000.0000.000
112A112ILE 00.0410.02612.472-0.091-0.0910.0000.0000.0000.000
113A113ASN 0-0.074-0.04814.5630.0860.0860.0000.0000.0000.000
114A114ALA 00.0260.01117.580-0.039-0.0390.0000.0000.0000.000
115A115SER 0-0.027-0.00219.6410.0370.0370.0000.0000.0000.000
116A116PRO 00.0660.00621.616-0.019-0.0190.0000.0000.0000.000
117A117LYS 10.8620.91822.5370.0670.0670.0000.0000.0000.000
118A118GLU -1-0.834-0.92119.802-0.206-0.2060.0000.0000.0000.000
119A119LEU 0-0.0170.00816.940-0.035-0.0350.0000.0000.0000.000
120A120PRO 00.004-0.00616.958-0.035-0.0350.0000.0000.0000.000
121A121ASP -1-0.899-0.94017.533-0.286-0.2860.0000.0000.0000.000
122A122LYS 10.8320.91313.9880.3060.3060.0000.0000.0000.000
123A123VAL 0-0.0200.00312.494-0.083-0.0830.0000.0000.0000.000
124A124GLU -1-0.864-0.9299.661-1.308-1.3080.0000.0000.0000.000
125A125ILE 00.0120.00110.711-0.069-0.0690.0000.0000.0000.000
126A126GLY 00.0100.00110.844-0.051-0.0510.0000.0000.0000.000
127A127LYS 10.8480.9455.2032.1532.1530.0000.0000.0000.000
128A128HIS 00.0280.0026.3610.1310.1310.0000.0000.0000.000
129A129GLY 00.0360.0328.4750.1290.1290.0000.0000.0000.000
130A130LEU 0-0.047-0.03110.141-0.027-0.0270.0000.0000.0000.000
131A131ILE 00.0400.01212.8430.0760.0760.0000.0000.0000.000
132A132VAL 0-0.027-0.00315.060-0.055-0.0550.0000.0000.0000.000
133A133LYS 10.9160.95118.350-0.271-0.2710.0000.0000.0000.000
134A134GLN 00.0170.00020.405-0.049-0.0490.0000.0000.0000.000
135A135GLY 0-0.014-0.00124.059-0.005-0.0050.0000.0000.0000.000
136A136TYR 0-0.020-0.03123.7400.0260.0260.0000.0000.0000.000
137A137CYS 0-0.0250.00724.6140.0110.0110.0000.0000.0000.000
138A138GLN 00.0590.00417.6980.0390.0390.0000.0000.0000.000
139A139GLY 00.0170.00619.307-0.011-0.0110.0000.0000.0000.000
140A140LEU 0-0.034-0.00413.437-0.007-0.0070.0000.0000.0000.000
141A141LEU 0-0.046-0.01114.845-0.010-0.0100.0000.0000.0000.000
142A142LEU 00.013-0.00311.3610.0210.0210.0000.0000.0000.000
143A143PRO 00.0550.0167.413-0.014-0.0140.0000.0000.0000.000
144A144GLN 00.0600.04310.214-0.090-0.0900.0000.0000.0000.000
145A145VAL 0-0.059-0.03012.604-0.003-0.0030.0000.0000.0000.000
146A146ALA 00.0380.01214.139-0.009-0.0090.0000.0000.0000.000
147A147PRO 00.0040.00812.4350.0000.0000.0000.0000.0000.000
148A148GLU -1-0.839-0.92615.4150.0440.0440.0000.0000.0000.000
149A149ASN 0-0.156-0.09217.6660.0300.0300.0000.0000.0000.000
150A150ASP -1-0.981-0.97319.632-0.116-0.1160.0000.0000.0000.000
151A151MET 0-0.0510.00618.1370.0260.0260.0000.0000.0000.000
152A152ASP -1-0.808-0.90517.997-0.179-0.1790.0000.0000.0000.000
153A153SER 00.014-0.02716.7600.0160.0160.0000.0000.0000.000
154A154ILE 0-0.048-0.01918.0940.0320.0320.0000.0000.0000.000
155A155ASP -1-0.837-0.91220.632-0.051-0.0510.0000.0000.0000.000
156A156PHE 00.0040.00312.3960.0470.0470.0000.0000.0000.000
157A157LEU 00.0000.00516.9510.0530.0530.0000.0000.0000.000
158A158SER 00.0040.00619.0870.0420.0420.0000.0000.0000.000
159A159HIS 00.0320.00220.2430.0210.0210.0000.0000.0000.000
160A160THR 00.004-0.00916.6140.0440.0440.0000.0000.0000.000
161A161CYS 0-0.101-0.02219.4400.0350.0350.0000.0000.0000.000
162A162MET 00.0080.01522.2980.0140.0140.0000.0000.0000.000
163A163LYS 10.9030.97119.527-0.280-0.2800.0000.0000.0000.000
164A164ALA 0-0.028-0.01721.2700.0270.0270.0000.0000.0000.000
165A165GLY 0-0.035-0.00922.9350.0010.0010.0000.0000.0000.000
166A166LEU 0-0.087-0.04123.470-0.016-0.0160.0000.0000.0000.000
167A167SER 0-0.026-0.03826.841-0.006-0.0060.0000.0000.0000.000
168A168PRO 00.0770.02225.4750.0020.0020.0000.0000.0000.000
169A169ASP -1-0.865-0.90725.0000.0200.0200.0000.0000.0000.000
170A170ALA 00.016-0.00824.516-0.007-0.0070.0000.0000.0000.000
171A171TRP 00.043-0.01121.029-0.007-0.0070.0000.0000.0000.000
172A172VAL 0-0.054-0.01822.878-0.018-0.0180.0000.0000.0000.000
173A173LYS 10.8490.91125.578-0.031-0.0310.0000.0000.0000.000
174A174GLY 0-0.012-0.00124.2760.0060.0060.0000.0000.0000.000
175A175ALA 0-0.0230.01322.5820.0130.0130.0000.0000.0000.000
176A176GLU -1-0.926-0.97718.8360.1890.1890.0000.0000.0000.000
177A177VAL 00.0390.01614.6700.0330.0330.0000.0000.0000.000
178A178TYR 0-0.061-0.02612.440-0.045-0.0450.0000.0000.0000.000
179A179CYS 00.0050.0179.0730.0450.0450.0000.0000.0000.000
180A180PHE 00.0110.0086.4730.1470.1470.0000.0000.0000.000
181A181GLU -1-0.840-0.9322.419-8.854-7.4961.959-1.271-2.045-0.011
182A182GLY 00.019-0.0073.3562.1952.7160.021-0.151-0.391-0.001
183A183GLN 00.0390.0462.315-6.028-3.8656.143-3.490-4.816-0.032
184A184ILE 00.0200.0095.1800.1170.1730.000-0.011-0.0440.000
185A185PHE 00.0350.0375.509-0.216-0.2160.0000.0000.0000.000
186A186LYS 10.9630.96910.684-0.254-0.2540.0000.0000.0000.000
187A187GLU -1-0.812-0.91114.4470.2360.2360.0000.0000.0000.000
188A188LYS 10.8760.94517.664-0.066-0.0660.0000.0000.0000.000
189A189GLU -1-0.942-0.99019.8780.0680.0680.0000.0000.0000.000
190A190PRO 00.0200.02321.3830.0230.0230.0000.0000.0000.000
191A191ASP -1-0.983-0.98921.1670.1800.1800.0000.0000.0000.000
192A192GLY 0-0.0130.00821.481-0.020-0.0200.0000.0000.0000.000
193A193GLU -1-0.982-1.01517.6740.0660.0660.0000.0000.0000.000
194A194VAL 0-0.045-0.01812.5420.0250.0250.0000.0000.0000.000
195A195ILE 0-0.0040.00713.551-0.044-0.0440.0000.0000.0000.000
196A196GLU -1-0.884-0.9676.1630.9760.9760.0000.0000.0000.000
197A197GLU -1-0.949-0.95010.312-0.211-0.2110.0000.0000.0000.000
198A198LYS 10.8900.9217.2020.6570.6570.0000.0000.0000.000
199A199PHE 0-0.059-0.0197.171-0.338-0.3380.0000.0000.0000.000
200A200LEU 0-0.020-0.0116.0690.2290.2290.0000.0000.0000.000
201A201GLU -1-0.912-0.9549.542-0.348-0.3480.0000.0000.0000.000
202A202HIS 0-0.051-0.01512.534-0.036-0.0360.0000.0000.0000.000
203A203HIS 0-0.057-0.03515.843-0.026-0.0260.0000.0000.0000.000
204A204HIS 0-0.021-0.01913.1280.0410.0410.0000.0000.0000.000
205A205NME 00.0070.02216.739-0.013-0.0130.0000.0000.0000.000