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: 82R9Y

Calculation Name: 2ZZ8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZZ8

Chain ID: A

ChEMBL ID:

UniProt ID: O34094

Base Structure: X-ray

Registration Date: 2023-06-19

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2739167.29126
FMO2-HF: Nuclear repulsion 2651212.416502
FMO2-HF: Total energy -87954.874758
FMO2-MP2: Total energy -88214.36002


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:6:GLY)


Summations of interaction energy for fragment #1(A:6:GLY)
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.
3.5754.45-0.011-0.413-0.4520.002
Interaction energy analysis for fragmet #1(A:6:GLY)
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 : 0.017
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].
3A8PRO00.0250.0153.7821.3422.161-0.010-0.410-0.4000.002
4A9SER00.0400.0176.6780.1590.1590.0000.0000.0000.000
5A10LEU00.0030.0118.642-0.121-0.1210.0000.0000.0000.000
6A11LYS10.9070.96411.1400.1050.1050.0000.0000.0000.000
7A12SER00.0420.01214.526-0.037-0.0370.0000.0000.0000.000
8A13SER0-0.138-0.11317.939-0.008-0.0080.0000.0000.0000.000
9A14PHE00.0470.02520.9190.0030.0030.0000.0000.0000.000
10A15VAL0-0.041-0.02720.9120.0020.0020.0000.0000.0000.000
11A16LEU0-0.029-0.01019.0870.0060.0060.0000.0000.0000.000
12A17SER00.0160.00022.1920.0090.0090.0000.0000.0000.000
13A18GLU-1-0.858-0.90723.354-0.037-0.0370.0000.0000.0000.000
14A19ASP-1-0.875-0.91523.9740.0580.0580.0000.0000.0000.000
15A20THR0-0.004-0.00725.850-0.011-0.0110.0000.0000.0000.000
16A21ILE00.016-0.00524.6590.0090.0090.0000.0000.0000.000
17A22PRO00.0120.00326.343-0.002-0.0020.0000.0000.0000.000
18A23GLY0-0.023-0.01029.360-0.005-0.0050.0000.0000.0000.000
19A24THR0-0.0370.00429.818-0.004-0.0040.0000.0000.0000.000
20A25ASN0-0.067-0.04331.9290.0010.0010.0000.0000.0000.000
21A26GLU-1-0.898-0.95227.696-0.059-0.0590.0000.0000.0000.000
22A27THR0-0.020-0.00426.9490.0080.0080.0000.0000.0000.000
23A28VAL0-0.001-0.00220.389-0.017-0.0170.0000.0000.0000.000
24A29LYS10.8280.89722.4700.0580.0580.0000.0000.0000.000
25A30THR00.0060.00717.890-0.014-0.0140.0000.0000.0000.000
26A31LEU0-0.044-0.02717.0510.0030.0030.0000.0000.0000.000
27A32LEU00.0390.01917.0380.0270.0270.0000.0000.0000.000
28A33PRO0-0.0160.00612.876-0.046-0.0460.0000.0000.0000.000
29A34TYR0-0.012-0.03613.908-0.005-0.0050.0000.0000.0000.000
30A35GLY00.0090.01313.9530.0380.0380.0000.0000.0000.000
31A36SER00.0010.00014.8870.0360.0360.0000.0000.0000.000
32A37VAL0-0.016-0.0149.694-0.071-0.0710.0000.0000.0000.000
33A38ILE00.0310.03311.3900.0680.0680.0000.0000.0000.000
34A39ASN0-0.030-0.0067.003-0.371-0.3710.0000.0000.0000.000
35A40TYR00.0200.0139.8970.0730.0730.0000.0000.0000.000
36A41TYR00.0650.0244.4280.0070.063-0.001-0.003-0.0520.000
37A42GLY0-0.009-0.00811.2590.0840.0840.0000.0000.0000.000
38A43TYR0-0.014-0.02514.214-0.057-0.0570.0000.0000.0000.000
39A44VAL0-0.0410.00416.8670.0340.0340.0000.0000.0000.000
40A45LYS11.0011.00320.1320.1020.1020.0000.0000.0000.000
41A46PRO00.0500.00422.5600.0010.0010.0000.0000.0000.000
42A47GLY0-0.018-0.00225.3670.0090.0090.0000.0000.0000.000
43A48GLN00.0050.01522.6440.0040.0040.0000.0000.0000.000
44A49ALA00.0080.00226.807-0.008-0.0080.0000.0000.0000.000
45A50PRO0-0.048-0.02027.048-0.005-0.0050.0000.0000.0000.000
46A51ASP-1-0.792-0.88525.150-0.110-0.1100.0000.0000.0000.000
47A52GLY0-0.029-0.01428.3550.0110.0110.0000.0000.0000.000
48A53LEU0-0.022-0.00829.451-0.010-0.0100.0000.0000.0000.000
49A54VAL00.000-0.00927.5870.0050.0050.0000.0000.0000.000
50A55ASP-1-0.827-0.91130.687-0.123-0.1230.0000.0000.0000.000
51A56GLY0-0.0040.01433.0010.0020.0020.0000.0000.0000.000
52A57ASN0-0.002-0.00132.561-0.001-0.0010.0000.0000.0000.000
53A58LYS10.7690.88927.7540.1370.1370.0000.0000.0000.000
54A59LYS10.9590.97727.0660.1500.1500.0000.0000.0000.000
55A60ALA00.0090.02925.198-0.017-0.0170.0000.0000.0000.000
56A61TYR0-0.016-0.01321.8870.0080.0080.0000.0000.0000.000
57A62TYR0-0.035-0.03922.873-0.011-0.0110.0000.0000.0000.000
58A63LEU0-0.0080.00316.241-0.002-0.0020.0000.0000.0000.000
59A64TYR0-0.024-0.01020.9700.0030.0030.0000.0000.0000.000
60A65VAL00.0360.00419.2240.0020.0020.0000.0000.0000.000
61A66TRP0-0.020-0.01021.561-0.006-0.0060.0000.0000.0000.000
62A67ILE00.001-0.00621.5180.0090.0090.0000.0000.0000.000
63A68PRO00.0600.02322.138-0.004-0.0040.0000.0000.0000.000
64A69ALA00.012-0.00125.0010.0030.0030.0000.0000.0000.000
65A70VAL0-0.0030.00125.630-0.006-0.0060.0000.0000.0000.000
66A71ILE0-0.027-0.00622.0500.0080.0080.0000.0000.0000.000
67A72ALA00.002-0.01423.871-0.006-0.0060.0000.0000.0000.000
68A73GLU-1-0.760-0.85120.328-0.081-0.0810.0000.0000.0000.000
69A74MET00.0220.03318.6320.0150.0150.0000.0000.0000.000
70A75GLY0-0.0090.00916.853-0.011-0.0110.0000.0000.0000.000
71A76VAL00.0050.00115.6550.0010.0010.0000.0000.0000.000
72A77ARG10.8770.9267.5020.9520.9520.0000.0000.0000.000
73A78MET0-0.0400.00013.213-0.020-0.0200.0000.0000.0000.000
74A79ILE0-0.017-0.0038.315-0.009-0.0090.0000.0000.0000.000
75A80SER0-0.0480.00611.5960.0300.0300.0000.0000.0000.000
76A81PRO00.0270.01712.6780.0120.0120.0000.0000.0000.000
77A82THR0-0.065-0.0677.988-0.084-0.0840.0000.0000.0000.000
78A83GLY00.0260.0328.079-0.202-0.2020.0000.0000.0000.000
79A84GLU-1-0.952-0.9939.692-0.237-0.2370.0000.0000.0000.000
80A85ILE0-0.030-0.0295.776-0.240-0.2400.0000.0000.0000.000
81A86GLY0-0.0230.0075.8240.1670.1670.0000.0000.0000.000
82A87GLU-1-0.936-0.9828.2510.3260.3260.0000.0000.0000.000
83A88PRO0-0.068-0.0257.7050.2260.2260.0000.0000.0000.000
84A89GLY00.0440.0157.1260.0750.0750.0000.0000.0000.000
85A90ASP-1-0.949-0.9828.0380.5530.5530.0000.0000.0000.000
86A91GLY00.0320.0279.178-0.125-0.1250.0000.0000.0000.000
87A92ASP-1-0.860-0.9276.5710.5800.5800.0000.0000.0000.000
88A93LEU0-0.022-0.0089.767-0.007-0.0070.0000.0000.0000.000
89A94VAL00.008-0.00410.383-0.066-0.0660.0000.0000.0000.000
90A95SER0-0.0110.00413.0830.0230.0230.0000.0000.0000.000
91A96ASP-1-0.813-0.92216.368-0.028-0.0280.0000.0000.0000.000
92A97ALA0-0.109-0.06218.883-0.005-0.0050.0000.0000.0000.000
93A98PHE00.012-0.0079.7660.0130.0130.0000.0000.0000.000
94A99LYS10.9520.96514.534-0.061-0.0610.0000.0000.0000.000
95A100ALA0-0.049-0.01516.2120.0040.0040.0000.0000.0000.000
96A101ALA0-0.0290.01916.353-0.001-0.0010.0000.0000.0000.000
97A102THR00.0350.00317.056-0.005-0.0050.0000.0000.0000.000
98A103PRO00.034-0.00114.587-0.029-0.0290.0000.0000.0000.000
99A104GLU-1-0.908-0.93915.184-0.256-0.2560.0000.0000.0000.000
100A105GLU-1-0.883-0.94417.519-0.205-0.2050.0000.0000.0000.000
101A106LYS10.8030.92012.1150.2070.2070.0000.0000.0000.000
102A107SER00.021-0.01013.098-0.126-0.1260.0000.0000.0000.000
103A108MET0-0.0220.01314.430-0.015-0.0150.0000.0000.0000.000
104A109PRO0-0.025-0.01116.370-0.013-0.0130.0000.0000.0000.000
105A110HIS00.0390.01517.3290.0570.0570.0000.0000.0000.000
106A111TRP0-0.073-0.06816.6000.0330.0330.0000.0000.0000.000
107A112PHE00.0520.01717.444-0.031-0.0310.0000.0000.0000.000
108A113ASP-1-0.813-0.87017.863-0.295-0.2950.0000.0000.0000.000
109A114THR00.0380.04017.5900.0240.0240.0000.0000.0000.000
110A115TRP0-0.080-0.02720.1950.0070.0070.0000.0000.0000.000
111A116ILE00.003-0.01617.926-0.001-0.0010.0000.0000.0000.000
112A117ARG10.8740.93122.5160.1270.1270.0000.0000.0000.000
113A118VAL0-0.0050.00322.175-0.006-0.0060.0000.0000.0000.000
114A119GLU-1-0.860-0.92124.913-0.083-0.0830.0000.0000.0000.000
115A120ARG10.9010.96727.5080.0350.0350.0000.0000.0000.000
116A121MET0-0.027-0.01328.441-0.002-0.0020.0000.0000.0000.000
117A122SER0-0.011-0.01930.9490.0040.0040.0000.0000.0000.000
118A123ALA0-0.037-0.01030.7040.0020.0020.0000.0000.0000.000
119A124ILE0-0.0090.00131.752-0.001-0.0010.0000.0000.0000.000
120A125MET00.0200.02532.0850.0060.0060.0000.0000.0000.000
121A126PRO00.1030.05228.888-0.007-0.0070.0000.0000.0000.000
122A127ASP-1-0.850-0.91930.4260.0010.0010.0000.0000.0000.000
123A128GLN0-0.005-0.02133.029-0.001-0.0010.0000.0000.0000.000
124A129ILE00.0270.02226.660-0.006-0.0060.0000.0000.0000.000
125A130ALA00.0110.00130.541-0.006-0.0060.0000.0000.0000.000
126A131LYS10.7870.88531.4560.0070.0070.0000.0000.0000.000
127A132ALA00.0180.01331.775-0.004-0.0040.0000.0000.0000.000
128A133ALA0-0.016-0.00529.099-0.004-0.0040.0000.0000.0000.000
129A134LYS10.9300.97130.8300.0290.0290.0000.0000.0000.000
130A135ALA0-0.045-0.00433.8750.0000.0000.0000.0000.0000.000
131A136LYS10.8680.92434.0580.0360.0360.0000.0000.0000.000
132A137PRO00.0390.00531.4180.0040.0040.0000.0000.0000.000
133A138VAL0-0.039-0.01233.0260.0040.0040.0000.0000.0000.000
134A139GLN00.0270.02834.427-0.001-0.0010.0000.0000.0000.000
135A147GLY00.0520.02432.2630.0030.0030.0000.0000.0000.000
136A148ASP-1-0.832-0.91926.629-0.081-0.0810.0000.0000.0000.000
137A149ASP-1-0.856-0.92627.482-0.041-0.0410.0000.0000.0000.000
138A150THR0-0.039-0.01528.4780.0070.0070.0000.0000.0000.000
139A151TYR0-0.002-0.01629.418-0.005-0.0050.0000.0000.0000.000
140A152LYS10.9681.01524.6700.1190.1190.0000.0000.0000.000
141A153GLU-1-0.798-0.90026.173-0.129-0.1290.0000.0000.0000.000
142A154GLU-1-0.892-0.93822.569-0.156-0.1560.0000.0000.0000.000
143A155ARG10.8970.95023.8440.1050.1050.0000.0000.0000.000
144A156HIS10.8120.89723.1410.1980.1980.0000.0000.0000.000
145A157ASN00.0390.04017.9640.0050.0050.0000.0000.0000.000
146A158LYS10.9880.99917.5710.2420.2420.0000.0000.0000.000
147A159TYR00.013-0.00714.9950.0320.0320.0000.0000.0000.000
148A160ASN00.0230.0149.894-0.010-0.0100.0000.0000.0000.000
149A161SER00.0040.00913.2410.0140.0140.0000.0000.0000.000
150A162LEU0-0.044-0.02613.536-0.024-0.0240.0000.0000.0000.000
151A163THR00.0150.01017.0370.0320.0320.0000.0000.0000.000
152A164ARG10.7930.88016.8760.1730.1730.0000.0000.0000.000
153A165ILE0-0.0030.00321.0940.0020.0020.0000.0000.0000.000
154A166LYS10.9470.95023.3160.0950.0950.0000.0000.0000.000
155A167ILE00.0370.02725.6920.0010.0010.0000.0000.0000.000
156A168PRO0-0.003-0.01628.819-0.003-0.0030.0000.0000.0000.000
157A169ASN0-0.034-0.01731.994-0.006-0.0060.0000.0000.0000.000
158A170PRO0-0.029-0.00127.4000.0060.0060.0000.0000.0000.000
159A171PRO00.0440.03828.692-0.003-0.0030.0000.0000.0000.000
160A172LYS10.9600.97027.1790.0260.0260.0000.0000.0000.000
161A173SER00.0190.00826.9760.0010.0010.0000.0000.0000.000
162A174PHE00.0690.01523.046-0.002-0.0020.0000.0000.0000.000
163A175ASP-1-0.872-0.94425.7090.0610.0610.0000.0000.0000.000
164A176ASP-1-0.868-0.94128.1230.0210.0210.0000.0000.0000.000
165A177LEU0-0.120-0.06125.369-0.005-0.0050.0000.0000.0000.000
166A178LYS10.9260.96829.281-0.065-0.0650.0000.0000.0000.000
167A179ASN0-0.030-0.01531.461-0.001-0.0010.0000.0000.0000.000
168A180ILE0-0.0210.00730.235-0.005-0.0050.0000.0000.0000.000
169A181ASP-1-0.875-0.94733.5090.0060.0060.0000.0000.0000.000
170A182THR00.0330.00432.783-0.004-0.0040.0000.0000.0000.000
171A183LYS10.9450.97933.0160.0010.0010.0000.0000.0000.000
172A184LYS10.9020.93932.496-0.001-0.0010.0000.0000.0000.000
173A185LEU0-0.053-0.00827.731-0.004-0.0040.0000.0000.0000.000
174A186LEU0-0.0030.01024.606-0.003-0.0030.0000.0000.0000.000
175A187VAL0-0.033-0.01827.9700.0080.0080.0000.0000.0000.000
176A188ARG10.8660.94227.093-0.024-0.0240.0000.0000.0000.000
177A189GLY00.012-0.00426.835-0.003-0.0030.0000.0000.0000.000
178A190LEU0-0.0070.00725.3960.0000.0000.0000.0000.0000.000
179A191TYR0-0.046-0.03823.510-0.007-0.0070.0000.0000.0000.000
180A192ARG10.8870.93223.9740.0850.0850.0000.0000.0000.000
181A193ILE00.0080.00318.611-0.004-0.0040.0000.0000.0000.000
182A194SER0-0.041-0.02022.5020.0010.0010.0000.0000.0000.000
183A195PHE00.012-0.00318.716-0.014-0.0140.0000.0000.0000.000
184A196THR00.023-0.02921.8870.0120.0120.0000.0000.0000.000
185A197THR0-0.022-0.00821.788-0.020-0.0200.0000.0000.0000.000
186A198TYR0-0.072-0.07623.8070.0340.0340.0000.0000.0000.000
187A199LYS10.8950.97225.7690.1610.1610.0000.0000.0000.000
188A200PRO00.005-0.01126.2680.0020.0020.0000.0000.0000.000
189A201GLY00.0600.03423.441-0.004-0.0040.0000.0000.0000.000
190A202GLU-1-0.972-1.02022.767-0.161-0.1610.0000.0000.0000.000
191A203VAL0-0.0100.00619.705-0.023-0.0230.0000.0000.0000.000
192A204LYS10.9220.95919.9580.2170.2170.0000.0000.0000.000
193A205GLY00.0530.03317.787-0.032-0.0320.0000.0000.0000.000
194A206SER0-0.015-0.00412.4650.0010.0010.0000.0000.0000.000
195A207PHE00.021-0.00812.305-0.016-0.0160.0000.0000.0000.000
196A208VAL00.0220.0127.4360.0390.0390.0000.0000.0000.000
197A209ALA0-0.049-0.02210.517-0.068-0.0680.0000.0000.0000.000
198A210SER0-0.039-0.0268.752-0.040-0.0400.0000.0000.0000.000
199A211VAL00.007-0.00111.479-0.003-0.0030.0000.0000.0000.000
200A212GLY00.001-0.00413.7960.0440.0440.0000.0000.0000.000
201A213LEU0-0.006-0.00714.902-0.020-0.0200.0000.0000.0000.000
202A214LEU0-0.022-0.01517.7240.0250.0250.0000.0000.0000.000
203A215PHE00.0450.02919.677-0.013-0.0130.0000.0000.0000.000
204A216PRO00.006-0.00122.9160.0040.0040.0000.0000.0000.000
205A217PRO00.0240.00825.1190.0110.0110.0000.0000.0000.000
206A218GLY0-0.021-0.00425.319-0.005-0.0050.0000.0000.0000.000
207A219ILE0-0.035-0.00824.864-0.001-0.0010.0000.0000.0000.000
208A220PRO0-0.0070.00022.7430.0060.0060.0000.0000.0000.000
209A221GLY00.004-0.00319.513-0.013-0.0130.0000.0000.0000.000
210A222VAL00.0220.00820.5870.0070.0070.0000.0000.0000.000
211A223SER0-0.019-0.01016.165-0.009-0.0090.0000.0000.0000.000
212A224PRO00.0100.01616.063-0.009-0.0090.0000.0000.0000.000
213A225LEU00.0220.02417.6430.0110.0110.0000.0000.0000.000
214A226ILE00.018-0.00714.972-0.021-0.0210.0000.0000.0000.000
215A227HIS00.0400.02818.744-0.003-0.0030.0000.0000.0000.000
216A228SER00.0330.02120.019-0.003-0.0030.0000.0000.0000.000
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218A230PRO00.0410.00524.6550.0090.0090.0000.0000.0000.000
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