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: YZ7M2

Calculation Name: 3AAZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AAZ

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2435971.692466
FMO2-HF: Nuclear repulsion 2348798.430821
FMO2-HF: Total energy -87173.261645
FMO2-MP2: Total energy -87427.471917


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:GLN)


Summations of interaction energy for fragment #1(A:1: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.
-0.0574.0580.579-1.826-2.8670.004
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.034
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].
3A3THR00.0160.0062.421-1.5942.1490.583-1.755-2.5710.004
4A4LEU0-0.049-0.0375.130-0.571-0.546-0.001-0.002-0.0220.000
5A5LYS10.8840.9398.7691.0871.0870.0000.0000.0000.000
6A6GLU-1-0.749-0.86911.169-0.086-0.0860.0000.0000.0000.000
7A7SER0-0.058-0.03114.982-0.070-0.0700.0000.0000.0000.000
8A8GLY00.0490.02117.7010.0160.0160.0000.0000.0000.000
9A9PRO00.000-0.00221.5180.0040.0040.0000.0000.0000.000
10A10THR00.0120.00522.3530.0200.0200.0000.0000.0000.000
11A11LEU0-0.044-0.02024.1000.0280.0280.0000.0000.0000.000
12A12VAL0-0.0160.00227.963-0.020-0.0200.0000.0000.0000.000
13A13LYS10.8600.92930.4700.1030.1030.0000.0000.0000.000
14A14PRO00.038-0.00134.251-0.004-0.0040.0000.0000.0000.000
15A15THR0-0.007-0.00536.156-0.006-0.0060.0000.0000.0000.000
16A16GLN00.0130.02633.398-0.009-0.0090.0000.0000.0000.000
17A17THR00.005-0.00829.6970.0140.0140.0000.0000.0000.000
18A18LEU0-0.0100.01924.440-0.014-0.0140.0000.0000.0000.000
19A19THR00.010-0.00725.0100.0060.0060.0000.0000.0000.000
20A20LEU0-0.030-0.00419.874-0.021-0.0210.0000.0000.0000.000
21A21THR00.0170.00216.833-0.002-0.0020.0000.0000.0000.000
22A22CYS0-0.084-0.01913.561-0.056-0.0560.0000.0000.0000.000
23A23THR00.0230.01911.4350.0100.0100.0000.0000.0000.000
24A24PHE00.0360.0079.1440.0160.0160.0000.0000.0000.000
25A25SER0-0.015-0.0145.842-0.046-0.0460.0000.0000.0000.000
26A26GLY00.0610.0324.613-0.393-0.358-0.001-0.0490.0160.000
27A27PHE0-0.025-0.0195.3030.7940.898-0.001-0.007-0.0960.000
28A28SER00.0610.0348.3970.0620.0620.0000.0000.0000.000
29A29LEU00.0170.00712.1930.1770.1770.0000.0000.0000.000
30A30ARG10.9410.97015.1430.6900.6900.0000.0000.0000.000
31A31THR0-0.013-0.00514.6540.0720.0720.0000.0000.0000.000
32A32SER0-0.045-0.01713.1450.1120.1120.0000.0000.0000.000
33A33ARG10.9020.94515.2960.3350.3350.0000.0000.0000.000
34A34VAL0-0.040-0.01011.9940.0550.0550.0000.0000.0000.000
35A35GLY00.0140.01515.463-0.027-0.0270.0000.0000.0000.000
36A36VAL0-0.041-0.02214.542-0.007-0.0070.0000.0000.0000.000
37A37SER00.022-0.00216.8810.0050.0050.0000.0000.0000.000
38A38TRP00.0030.00317.4980.0060.0060.0000.0000.0000.000
39A39ILE0-0.045-0.02517.4680.0150.0150.0000.0000.0000.000
40A40ARG10.7870.87520.704-0.054-0.0540.0000.0000.0000.000
41A41GLN00.0250.01121.0950.0480.0480.0000.0000.0000.000
42A42PRO00.0560.03523.751-0.005-0.0050.0000.0000.0000.000
43A43PRO00.0250.00626.1140.0270.0270.0000.0000.0000.000
44A44GLY00.0220.02326.352-0.010-0.0100.0000.0000.0000.000
45A45LYS10.8590.93226.691-0.145-0.1450.0000.0000.0000.000
46A46ALA00.0570.02825.5650.0280.0280.0000.0000.0000.000
47A47LEU0-0.014-0.00719.685-0.019-0.0190.0000.0000.0000.000
48A48GLU-1-0.781-0.87323.7410.0620.0620.0000.0000.0000.000
49A49TRP0-0.030-0.02121.495-0.007-0.0070.0000.0000.0000.000
50A50LEU00.0010.00623.330-0.013-0.0130.0000.0000.0000.000
51A51ALA00.0280.00523.335-0.015-0.0150.0000.0000.0000.000
52A52HIS0-0.0120.01718.7170.0340.0340.0000.0000.0000.000
53A53ILE0-0.0210.01119.922-0.004-0.0040.0000.0000.0000.000
54A54TYR00.0270.00920.0970.0030.0030.0000.0000.0000.000
55A55TRP00.0790.02918.532-0.056-0.0560.0000.0000.0000.000
56A56ASP-1-0.862-0.94020.032-0.185-0.1850.0000.0000.0000.000
57A57ASP-1-0.785-0.85923.269-0.279-0.2790.0000.0000.0000.000
58A58ASP-1-0.764-0.83224.515-0.065-0.0650.0000.0000.0000.000
59A59LYS10.7520.84424.7940.1810.1810.0000.0000.0000.000
60A60ARG10.7870.86725.6640.0570.0570.0000.0000.0000.000
61A61TYR00.0620.01426.124-0.014-0.0140.0000.0000.0000.000
62A62ASN00.0250.02627.7760.0050.0050.0000.0000.0000.000
63A63PRO00.013-0.00529.350-0.013-0.0130.0000.0000.0000.000
64A64SER0-0.030-0.02032.159-0.007-0.0070.0000.0000.0000.000
65A65LEU00.0250.00329.185-0.006-0.0060.0000.0000.0000.000
66A66LYS10.9180.96331.3830.0440.0440.0000.0000.0000.000
67A67SER0-0.022-0.00732.391-0.011-0.0110.0000.0000.0000.000
68A68ARG10.8330.90831.9700.0310.0310.0000.0000.0000.000
69A69LEU00.005-0.00126.779-0.007-0.0070.0000.0000.0000.000
70A70THR0-0.035-0.02627.434-0.002-0.0020.0000.0000.0000.000
71A71ILE0-0.0170.01220.657-0.014-0.0140.0000.0000.0000.000
72A72SER00.000-0.01422.7360.0020.0020.0000.0000.0000.000
73A73LYS10.8270.89018.2260.3230.3230.0000.0000.0000.000
74A74ASP-1-0.733-0.81719.045-0.571-0.5710.0000.0000.0000.000
75A75THR0-0.019-0.02317.537-0.090-0.0900.0000.0000.0000.000
76A76SER0-0.068-0.04417.655-0.077-0.0770.0000.0000.0000.000
77A77LYS10.8890.91517.0410.5430.5430.0000.0000.0000.000
78A78ASN0-0.028-0.00310.8480.0900.0900.0000.0000.0000.000
79A79GLN00.009-0.01613.278-0.037-0.0370.0000.0000.0000.000
80A80VAL00.0000.00015.7490.0550.0550.0000.0000.0000.000
81A81VAL0-0.012-0.00817.752-0.014-0.0140.0000.0000.0000.000
82A82LEU0-0.002-0.00220.5930.0330.0330.0000.0000.0000.000
83A83THR00.0030.00423.162-0.012-0.0120.0000.0000.0000.000
84A84MET0-0.039-0.01926.6630.0150.0150.0000.0000.0000.000
85A85THR00.0350.00328.738-0.005-0.0050.0000.0000.0000.000
86A86ASN0-0.030-0.00532.3760.0090.0090.0000.0000.0000.000
87A87MET0-0.034-0.00328.2400.0080.0080.0000.0000.0000.000
88A88ASP-1-0.776-0.89532.939-0.007-0.0070.0000.0000.0000.000
89A89PRO00.009-0.00732.8660.0020.0020.0000.0000.0000.000
90A90VAL0-0.0050.00332.4480.0080.0080.0000.0000.0000.000
91A91ASP-1-0.766-0.84129.325-0.005-0.0050.0000.0000.0000.000
92A92THR0-0.033-0.00227.928-0.010-0.0100.0000.0000.0000.000
93A93ALA00.000-0.01024.5660.0230.0230.0000.0000.0000.000
94A94THR0-0.0120.00918.610-0.049-0.0490.0000.0000.0000.000
95A95TYR0-0.012-0.02420.4910.0240.0240.0000.0000.0000.000
96A96TYR00.020-0.01215.426-0.015-0.0150.0000.0000.0000.000
97A98ALA00.0400.01513.1960.1010.1010.0000.0000.0000.000
98A99ARG10.8390.9057.9750.2070.2070.0000.0000.0000.000
99A100ARG10.8550.92413.020-0.005-0.0050.0000.0000.0000.000
100A101GLY00.0280.02211.855-0.113-0.1130.0000.0000.0000.000
101A102PHE0-0.031-0.03612.8330.0690.0690.0000.0000.0000.000
102A103TYR0-0.064-0.0669.9720.0620.0620.0000.0000.0000.000
103A104GLY00.0590.03114.4910.0080.0080.0000.0000.0000.000
104A105ARG10.9170.96715.895-0.028-0.0280.0000.0000.0000.000
105A106LYS10.9080.95118.377-0.160-0.1600.0000.0000.0000.000
106A107TYR0-0.014-0.01616.7180.0050.0050.0000.0000.0000.000
107A108GLU-1-0.797-0.90719.5900.1520.1520.0000.0000.0000.000
108A109VAL00.0570.04217.1720.0150.0150.0000.0000.0000.000
109A110ASN00.0000.00516.389-0.018-0.0180.0000.0000.0000.000
110A111HIS10.8850.93812.427-0.661-0.6610.0000.0000.0000.000
111A112PHE00.0530.01314.806-0.028-0.0280.0000.0000.0000.000
112A113ASP-1-0.772-0.83110.1870.4220.4220.0000.0000.0000.000
113A114TYR00.0220.0224.327-0.725-0.517-0.001-0.013-0.1940.000
114A115TRP00.0470.0079.129-0.407-0.4070.0000.0000.0000.000
115A116GLY00.0200.0169.5860.2220.2220.0000.0000.0000.000
116A117GLN0-0.035-0.01410.3610.0100.0100.0000.0000.0000.000
117A118GLY00.0240.01511.9770.0230.0230.0000.0000.0000.000
118A119THR0-0.049-0.03315.422-0.069-0.0690.0000.0000.0000.000
119A120THR0-0.0130.00418.0940.0210.0210.0000.0000.0000.000
120A121VAL0-0.026-0.00421.482-0.040-0.0400.0000.0000.0000.000
121A122THR00.0210.00724.5790.0310.0310.0000.0000.0000.000
122A123VAL0-0.0070.00128.072-0.020-0.0200.0000.0000.0000.000
123A124SER00.0300.00431.3440.0110.0110.0000.0000.0000.000
124A125SER00.0490.01634.152-0.010-0.0100.0000.0000.0000.000
125A126ALA00.0180.03434.625-0.007-0.0070.0000.0000.0000.000
126A127SER00.016-0.02033.690-0.009-0.0090.0000.0000.0000.000
127A128THR0-0.0100.00128.8030.0120.0120.0000.0000.0000.000
128A129LYS10.8430.92430.9930.0580.0580.0000.0000.0000.000
129A130GLY00.0640.04229.0110.0040.0040.0000.0000.0000.000
130A131PRO0-0.035-0.01926.9340.0100.0100.0000.0000.0000.000
131A132SER0-0.029-0.00130.219-0.009-0.0090.0000.0000.0000.000
132A133VAL00.013-0.00228.2900.0100.0100.0000.0000.0000.000
133A134PHE00.019-0.00131.417-0.009-0.0090.0000.0000.0000.000
134A135PRO00.0220.01532.6580.0070.0070.0000.0000.0000.000
135A136LEU0-0.037-0.01432.0150.0010.0010.0000.0000.0000.000
136A137ALA00.0460.01634.2000.0070.0070.0000.0000.0000.000
137A138PRO00.0170.02334.3660.0050.0050.0000.0000.0000.000
138A139SER00.015-0.00636.605-0.007-0.0070.0000.0000.0000.000
139A140SER00.0080.00639.9710.0060.0060.0000.0000.0000.000
140A141LYS10.9380.96441.945-0.051-0.0510.0000.0000.0000.000
141A142SER0-0.023-0.00436.3870.0000.0000.0000.0000.0000.000
142A143THR00.008-0.02236.8840.0060.0060.0000.0000.0000.000
143A144SER0-0.011-0.00737.924-0.003-0.0030.0000.0000.0000.000
144A145GLY00.0220.01538.3080.0060.0060.0000.0000.0000.000
145A146GLY00.0270.01938.3260.0070.0070.0000.0000.0000.000
146A147THR0-0.0120.01232.8450.0060.0060.0000.0000.0000.000
147A148ALA0-0.003-0.01034.181-0.008-0.0080.0000.0000.0000.000
148A149ALA00.0070.01232.2630.0110.0110.0000.0000.0000.000
149A150LEU0-0.0010.02129.327-0.013-0.0130.0000.0000.0000.000
150A151GLY00.0510.00229.3660.0150.0150.0000.0000.0000.000
151A152CYS0-0.0530.00224.612-0.018-0.0180.0000.0000.0000.000
152A153LEU00.0270.04329.3060.0100.0100.0000.0000.0000.000
153A154VAL0-0.026-0.02426.517-0.016-0.0160.0000.0000.0000.000
154A155LYS10.9160.93029.7570.0130.0130.0000.0000.0000.000
155A156ASP-1-0.810-0.88632.327-0.025-0.0250.0000.0000.0000.000
156A157TYR0-0.015-0.02426.357-0.013-0.0130.0000.0000.0000.000
157A158PHE00.0460.02530.0440.0140.0140.0000.0000.0000.000
158A159PRO00.0110.01226.218-0.016-0.0160.0000.0000.0000.000
159A160GLU-1-0.756-0.86424.1030.0330.0330.0000.0000.0000.000
160A161PRO0-0.037-0.02120.290-0.012-0.0120.0000.0000.0000.000
161A162VAL0-0.024-0.01522.820-0.038-0.0380.0000.0000.0000.000
162A163THR0-0.048-0.02317.3400.0130.0130.0000.0000.0000.000
163A164VAL00.037-0.00620.206-0.030-0.0300.0000.0000.0000.000
164A165SER0-0.0250.00218.0720.0240.0240.0000.0000.0000.000
165A166TRP00.013-0.00320.083-0.023-0.0230.0000.0000.0000.000
166A167ASN00.013-0.01820.8270.0020.0020.0000.0000.0000.000
167A168SER0-0.032-0.01520.724-0.001-0.0010.0000.0000.0000.000
168A169GLY00.0230.01716.996-0.057-0.0570.0000.0000.0000.000
169A170ALA0-0.069-0.02415.3840.0370.0370.0000.0000.0000.000
170A171LEU00.0610.04517.3670.0570.0570.0000.0000.0000.000
171A172THR00.020-0.01917.987-0.005-0.0050.0000.0000.0000.000
172A173SER0-0.0070.00820.880-0.017-0.0170.0000.0000.0000.000
173A174GLY00.0320.01123.0940.0140.0140.0000.0000.0000.000
174A175VAL0-0.058-0.01421.639-0.028-0.0280.0000.0000.0000.000
175A176HIS00.0110.00723.4390.0330.0330.0000.0000.0000.000
176A177THR0-0.0010.00021.984-0.035-0.0350.0000.0000.0000.000
177A178PHE00.0040.01324.2920.0250.0250.0000.0000.0000.000
178A179PRO00.020-0.00925.613-0.015-0.0150.0000.0000.0000.000
179A180ALA0-0.0010.00226.763-0.009-0.0090.0000.0000.0000.000
180A181VAL0-0.021-0.00528.7310.0100.0100.0000.0000.0000.000
181A182LEU0-0.030-0.01132.273-0.011-0.0110.0000.0000.0000.000
182A183GLN00.0190.00234.1060.0100.0100.0000.0000.0000.000
183A184SER00.0330.00337.051-0.003-0.0030.0000.0000.0000.000
184A185SER0-0.014-0.00438.201-0.001-0.0010.0000.0000.0000.000
185A186GLY00.0150.01437.219-0.006-0.0060.0000.0000.0000.000
186A187LEU0-0.066-0.02233.872-0.007-0.0070.0000.0000.0000.000
187A188TYR00.0170.00429.4680.0040.0040.0000.0000.0000.000
188A189SER0-0.016-0.01631.186-0.015-0.0150.0000.0000.0000.000
189A190LEU00.0020.03224.7430.0090.0090.0000.0000.0000.000
190A191SER0-0.003-0.02128.785-0.015-0.0150.0000.0000.0000.000
191A192SER0-0.024-0.00524.0150.0160.0160.0000.0000.0000.000
192A193VAL00.0310.00526.759-0.019-0.0190.0000.0000.0000.000
193A194VAL00.0050.00525.5120.0180.0180.0000.0000.0000.000
194A195THR0-0.006-0.00227.636-0.011-0.0110.0000.0000.0000.000
195A196VAL0-0.014-0.00728.4590.0130.0130.0000.0000.0000.000
196A197PRO00.0760.02830.333-0.002-0.0020.0000.0000.0000.000
197A198SER00.001-0.01333.579-0.008-0.0080.0000.0000.0000.000
198A199SER0-0.046-0.02236.810-0.007-0.0070.0000.0000.0000.000
199A200SER00.0460.02132.731-0.001-0.0010.0000.0000.0000.000
200A201LEU0-0.047-0.01734.131-0.006-0.0060.0000.0000.0000.000
201A202GLY00.010-0.00834.820-0.006-0.0060.0000.0000.0000.000
202A203THR0-0.0090.00534.220-0.006-0.0060.0000.0000.0000.000
203A204GLN0-0.0140.00328.827-0.008-0.0080.0000.0000.0000.000
204A205THR0-0.0040.00629.230-0.006-0.0060.0000.0000.0000.000
205A206TYR00.0130.00727.6270.0090.0090.0000.0000.0000.000
206A207ILE00.005-0.00524.968-0.008-0.0080.0000.0000.0000.000
207A209ASN0-0.016-0.03120.9770.0010.0010.0000.0000.0000.000
208A210VAL00.0130.00921.7940.0120.0120.0000.0000.0000.000
209A211ASN0-0.021-0.02718.073-0.056-0.0560.0000.0000.0000.000
210A212HIS00.0250.03021.5040.0070.0070.0000.0000.0000.000
211A213LYS10.9970.98616.9600.3940.3940.0000.0000.0000.000
212A214PRO00.0040.01221.733-0.026-0.0260.0000.0000.0000.000
213A215SER0-0.007-0.02024.684-0.003-0.0030.0000.0000.0000.000
214A216ASN0-0.076-0.03623.439-0.029-0.0290.0000.0000.0000.000
215A217THR00.0240.02024.711-0.008-0.0080.0000.0000.0000.000
216A218LYS10.8640.92320.4050.2230.2230.0000.0000.0000.000
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