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: 6Y4VZ

Calculation Name: 3D8H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D8H

Chain ID: A

ChEMBL ID:

UniProt ID: Q5CXZ9

Base Structure: X-ray

Registration Date: 2023-09-23

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2956180.757058
FMO2-HF: Nuclear repulsion 2864588.686554
FMO2-HF: Total energy -91592.070504
FMO2-MP2: Total energy -91858.948374


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:20:THR)


Summations of interaction energy for fragment #1(A:20:THR)
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.
-22.366-13.485.448-6.155-8.175-0.051
Interaction energy analysis for fragmet #1(A:20:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.015
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].
3A22LYS10.9460.9613.831-1.4520.363-0.020-1.010-0.7840.005
4A23LEU0-0.0110.0126.775-0.682-0.6820.0000.0000.0000.000
5A24THR00.0100.0129.8490.1450.1450.0000.0000.0000.000
6A25LEU00.003-0.00113.101-0.164-0.1640.0000.0000.0000.000
7A26ILE00.0240.01615.9460.0350.0350.0000.0000.0000.000
8A27ARG10.9120.96519.545-0.294-0.2940.0000.0000.0000.000
9A28HIS00.0240.00422.7730.0040.0040.0000.0000.0000.000
10A29GLY00.0740.03026.1300.0070.0070.0000.0000.0000.000
11A30GLU-1-0.862-0.88128.7070.1420.1420.0000.0000.0000.000
12A31SER00.010-0.00332.041-0.004-0.0040.0000.0000.0000.000
13A32GLU-1-0.828-0.95034.1160.0930.0930.0000.0000.0000.000
14A33TRP00.0570.02036.719-0.006-0.0060.0000.0000.0000.000
15A34ASN0-0.063-0.02232.3480.0080.0080.0000.0000.0000.000
16A35LYS10.9531.00135.890-0.126-0.1260.0000.0000.0000.000
17A36GLU-1-0.940-0.97238.8160.0840.0840.0000.0000.0000.000
18A37ASN0-0.037-0.01238.552-0.001-0.0010.0000.0000.0000.000
19A38ARG10.9080.97138.808-0.077-0.0770.0000.0000.0000.000
20A39PHE0-0.037-0.01335.5990.0100.0100.0000.0000.0000.000
21A40THR00.0130.00633.542-0.003-0.0030.0000.0000.0000.000
22A41GLY0-0.0270.01432.167-0.009-0.0090.0000.0000.0000.000
23A42TRP00.015-0.01129.9590.0050.0050.0000.0000.0000.000
24A43THR0-0.005-0.00433.594-0.006-0.0060.0000.0000.0000.000
25A44ASP-1-0.805-0.90434.0610.0900.0900.0000.0000.0000.000
26A45VAL0-0.064-0.02034.531-0.002-0.0020.0000.0000.0000.000
27A46SER0-0.014-0.02534.5570.0060.0060.0000.0000.0000.000
28A47LEU0-0.023-0.01329.7820.0010.0010.0000.0000.0000.000
29A48SER0-0.068-0.06633.913-0.008-0.0080.0000.0000.0000.000
30A49GLU-1-0.883-0.95934.9800.1220.1220.0000.0000.0000.000
31A50GLN00.0130.01632.599-0.001-0.0010.0000.0000.0000.000
32A51GLY00.0250.01831.2670.0150.0150.0000.0000.0000.000
33A52VAL0-0.030-0.02230.3210.0150.0150.0000.0000.0000.000
34A53SER0-0.038-0.02430.9500.0120.0120.0000.0000.0000.000
35A54GLU-1-0.799-0.91028.1160.2410.2410.0000.0000.0000.000
36A55ALA0-0.013-0.00626.3630.0270.0270.0000.0000.0000.000
37A56ILE0-0.037-0.01526.3740.0180.0180.0000.0000.0000.000
38A57GLU-1-0.865-0.94027.4440.2740.2740.0000.0000.0000.000
39A58ALA0-0.020-0.00322.5960.0300.0300.0000.0000.0000.000
40A59GLY00.001-0.01522.4640.0400.0400.0000.0000.0000.000
41A60ARG10.8930.95323.183-0.211-0.2110.0000.0000.0000.000
42A61MET00.0110.02720.4110.0380.0380.0000.0000.0000.000
43A62LEU0-0.041-0.04017.2220.0600.0600.0000.0000.0000.000
44A63LEU0-0.012-0.00519.2660.0400.0400.0000.0000.0000.000
45A64GLU-1-0.965-0.97321.2490.4350.4350.0000.0000.0000.000
46A65LYS10.8660.93516.751-0.644-0.6440.0000.0000.0000.000
47A66GLY0-0.0010.01016.4790.1020.1020.0000.0000.0000.000
48A67PHE0-0.050-0.02212.7650.0740.0740.0000.0000.0000.000
49A68LYS10.9690.97715.472-0.340-0.3400.0000.0000.0000.000
50A69PHE0-0.033-0.01214.1580.0320.0320.0000.0000.0000.000
51A70ASP-1-0.773-0.88414.2500.1130.1130.0000.0000.0000.000
52A71VAL0-0.043-0.03515.817-0.058-0.0580.0000.0000.0000.000
53A72VAL0-0.013-0.00317.2240.0640.0640.0000.0000.0000.000
54A73TYR0-0.024-0.03216.080-0.047-0.0470.0000.0000.0000.000
55A74THR0-0.010-0.04020.1480.0410.0410.0000.0000.0000.000
56A75SER0-0.037-0.03022.996-0.027-0.0270.0000.0000.0000.000
57A76VAL0-0.019-0.02525.889-0.004-0.0040.0000.0000.0000.000
58A77LEU0-0.0210.00028.905-0.004-0.0040.0000.0000.0000.000
59A78LYS10.9780.98029.637-0.066-0.0660.0000.0000.0000.000
60A79ARG10.8360.93429.529-0.115-0.1150.0000.0000.0000.000
61A80ALA0-0.0010.01225.3280.0170.0170.0000.0000.0000.000
62A81ILE00.0370.02526.2660.0160.0160.0000.0000.0000.000
63A82MET00.0160.00728.0380.0080.0080.0000.0000.0000.000
64A83THR00.019-0.00524.6710.0100.0100.0000.0000.0000.000
65A84THR00.0140.00923.1590.0300.0300.0000.0000.0000.000
66A85TRP0-0.008-0.01125.0510.0080.0080.0000.0000.0000.000
67A86THR0-0.056-0.02927.892-0.004-0.0040.0000.0000.0000.000
68A87VAL00.0200.00621.6280.0060.0060.0000.0000.0000.000
69A88LEU00.001-0.00521.4650.0170.0170.0000.0000.0000.000
70A89LYS10.9450.96524.699-0.164-0.1640.0000.0000.0000.000
71A90GLU-1-0.930-0.95626.0500.2150.2150.0000.0000.0000.000
72A91LEU0-0.023-0.00720.1280.0100.0100.0000.0000.0000.000
73A92GLY0-0.0270.00623.6290.0020.0020.0000.0000.0000.000
74A93ASN0-0.088-0.05519.737-0.037-0.0370.0000.0000.0000.000
75A94ILE00.0320.01523.909-0.003-0.0030.0000.0000.0000.000
76A95ASN0-0.032-0.01724.9830.0050.0050.0000.0000.0000.000
77A96CYS0-0.0390.01520.224-0.012-0.0120.0000.0000.0000.000
78A97PRO0-0.0030.00520.913-0.003-0.0030.0000.0000.0000.000
79A98ILE00.0030.00021.7040.0240.0240.0000.0000.0000.000
80A99ILE0-0.0200.00020.399-0.023-0.0230.0000.0000.0000.000
81A100ASN00.0260.00523.3030.0270.0270.0000.0000.0000.000
82A101HIS00.005-0.00623.997-0.012-0.0120.0000.0000.0000.000
83A102TRP00.0930.03725.7440.0180.0180.0000.0000.0000.000
84A103ARG10.8910.96623.4560.0590.0590.0000.0000.0000.000
85A104LEU00.0410.02619.5260.0120.0120.0000.0000.0000.000
86A105ASN00.0440.02923.6190.0330.0330.0000.0000.0000.000
87A106GLU-1-0.809-0.90326.3180.1590.1590.0000.0000.0000.000
88A107ARG10.8720.94727.780-0.110-0.1100.0000.0000.0000.000
89A108HIS00.0280.01329.1470.0070.0070.0000.0000.0000.000
90A109TYR00.024-0.02230.8870.0030.0030.0000.0000.0000.000
91A110GLY00.0630.03335.385-0.001-0.0010.0000.0000.0000.000
92A111ALA0-0.036-0.02238.3850.0030.0030.0000.0000.0000.000
93A112LEU0-0.0070.00137.2320.0010.0010.0000.0000.0000.000
94A113GLN00.0270.01435.7860.0070.0070.0000.0000.0000.000
95A114GLY00.0380.01239.351-0.005-0.0050.0000.0000.0000.000
96A115LEU0-0.072-0.01541.315-0.002-0.0020.0000.0000.0000.000
97A116ASN00.0610.02241.3690.0100.0100.0000.0000.0000.000
98A117LYS10.9710.98140.498-0.086-0.0860.0000.0000.0000.000
99A118SER0-0.050-0.03542.247-0.003-0.0030.0000.0000.0000.000
100A119GLU-1-0.799-0.91245.5530.0580.0580.0000.0000.0000.000
101A120THR0-0.052-0.03541.386-0.003-0.0030.0000.0000.0000.000
102A121ALA00.006-0.00144.656-0.003-0.0030.0000.0000.0000.000
103A122SER0-0.0460.00546.337-0.003-0.0030.0000.0000.0000.000
104A123LYS10.9400.96947.287-0.052-0.0520.0000.0000.0000.000
105A124PHE00.0120.00244.650-0.003-0.0030.0000.0000.0000.000
106A125GLY00.0400.02346.2120.0010.0010.0000.0000.0000.000
107A126GLU-1-0.900-0.96844.3130.0700.0700.0000.0000.0000.000
108A127ASP-1-0.914-0.95242.8240.0670.0670.0000.0000.0000.000
109A128GLN0-0.029-0.03441.2650.0020.0020.0000.0000.0000.000
110A129VAL00.0390.02839.6470.0010.0010.0000.0000.0000.000
111A130LYS10.9130.94737.481-0.080-0.0800.0000.0000.0000.000
112A131ILE00.0220.01536.5520.0070.0070.0000.0000.0000.000
113A132TRP00.0600.05135.5000.0050.0050.0000.0000.0000.000
114A133ARG10.8960.95532.982-0.123-0.1230.0000.0000.0000.000
115A134ARG10.9120.95031.772-0.114-0.1140.0000.0000.0000.000
116A135SER00.0060.01231.8380.0020.0020.0000.0000.0000.000
117A136PHE00.0510.01124.4130.0050.0050.0000.0000.0000.000
118A137ASP-1-0.902-0.97229.6940.0330.0330.0000.0000.0000.000
119A138VAL00.0080.02032.205-0.008-0.0080.0000.0000.0000.000
120A139PRO0-0.0200.00034.8970.0090.0090.0000.0000.0000.000
121A140PRO0-0.021-0.00735.349-0.002-0.0020.0000.0000.0000.000
122A141PRO00.0070.01238.620-0.005-0.0050.0000.0000.0000.000
123A142VAL00.0250.00940.1450.0030.0030.0000.0000.0000.000
124A143LEU0-0.043-0.00639.6960.0010.0010.0000.0000.0000.000
125A144GLU-1-0.922-0.96343.0390.0080.0080.0000.0000.0000.000
126A145LYS10.9480.95242.5640.0110.0110.0000.0000.0000.000
127A146SER00.0000.00545.2460.0010.0010.0000.0000.0000.000
128A147ASP-1-0.799-0.90344.7570.0340.0340.0000.0000.0000.000
129A148PRO00.029-0.00544.7660.0000.0000.0000.0000.0000.000
130A149ARG10.7640.88441.144-0.042-0.0420.0000.0000.0000.000
131A150TRP0-0.0200.00638.9070.0020.0020.0000.0000.0000.000
132A151PRO00.0740.02536.130-0.001-0.0010.0000.0000.0000.000
133A152GLY0-0.043-0.02138.308-0.001-0.0010.0000.0000.0000.000
134A153ASN0-0.043-0.00340.276-0.006-0.0060.0000.0000.0000.000
135A154GLU-1-0.928-0.95837.4520.0450.0450.0000.0000.0000.000
136A155LEU0-0.011-0.02439.448-0.004-0.0040.0000.0000.0000.000
137A156ILE0-0.0040.00033.739-0.005-0.0050.0000.0000.0000.000
138A157TYR00.004-0.00331.872-0.003-0.0030.0000.0000.0000.000
139A158LYS10.9650.98335.812-0.002-0.0020.0000.0000.0000.000
140A159GLY0-0.008-0.00236.517-0.003-0.0030.0000.0000.0000.000
141A160ILE0-0.0130.00331.022-0.008-0.0080.0000.0000.0000.000
142A161CYS0-0.019-0.00732.8250.0020.0020.0000.0000.0000.000
143A162PRO00.0690.01934.5070.0040.0040.0000.0000.0000.000
144A163SER0-0.025-0.01634.0660.0050.0050.0000.0000.0000.000
145A164CYS0-0.045-0.01631.091-0.002-0.0020.0000.0000.0000.000
146A165LEU0-0.027-0.00532.4700.0080.0080.0000.0000.0000.000
147A166PRO00.0400.03632.404-0.003-0.0030.0000.0000.0000.000
148A167THR0-0.018-0.00535.2690.0030.0030.0000.0000.0000.000
149A168THR0-0.015-0.05036.4140.0080.0080.0000.0000.0000.000
150A169GLU-1-0.735-0.85729.8550.0420.0420.0000.0000.0000.000
151A170CYS0-0.093-0.01231.7010.0080.0080.0000.0000.0000.000
152A171LEU0-0.022-0.02724.2270.0000.0000.0000.0000.0000.000
153A172LYS10.9360.96526.3520.0120.0120.0000.0000.0000.000
154A173ASP-1-0.766-0.89626.7030.0080.0080.0000.0000.0000.000
155A174THR0-0.059-0.03124.560-0.003-0.0030.0000.0000.0000.000
156A175VAL00.014-0.00620.9240.0000.0000.0000.0000.0000.000
157A176GLU-1-0.897-0.94122.090-0.042-0.0420.0000.0000.0000.000
158A177ARG10.6650.83824.202-0.081-0.0810.0000.0000.0000.000
159A178VAL0-0.001-0.00819.203-0.008-0.0080.0000.0000.0000.000
160A179LYS10.9520.97818.0680.1500.1500.0000.0000.0000.000
161A180PRO00.0600.03718.054-0.021-0.0210.0000.0000.0000.000
162A181TYR0-0.014-0.01019.352-0.018-0.0180.0000.0000.0000.000
163A182PHE00.015-0.01010.2700.0010.0010.0000.0000.0000.000
164A183GLU-1-0.908-0.96214.684-0.284-0.2840.0000.0000.0000.000
165A184ASP-1-0.857-0.93215.179-0.350-0.3500.0000.0000.0000.000
166A185VAL0-0.083-0.03417.302-0.007-0.0070.0000.0000.0000.000
167A186ILE0-0.048-0.02713.086-0.009-0.0090.0000.0000.0000.000
168A187ALA00.0190.01111.1700.0090.0090.0000.0000.0000.000
169A188PRO00.0360.01610.896-0.146-0.1460.0000.0000.0000.000
170A189SER0-0.0210.01512.325-0.047-0.0470.0000.0000.0000.000
171A190ILE00.0120.0177.3960.0130.0130.0000.0000.0000.000
172A191MET0-0.0040.0057.473-0.168-0.1680.0000.0000.0000.000
173A192SER0-0.125-0.0708.467-0.160-0.1600.0000.0000.0000.000
174A193GLY00.0200.0098.3030.0200.0200.0000.0000.0000.000
175A194LYS10.8830.9589.3350.4240.4240.0000.0000.0000.000
176A195SER0-0.033-0.02410.6680.1370.1370.0000.0000.0000.000
177A196VAL00.007-0.00611.750-0.084-0.0840.0000.0000.0000.000
178A197LEU0-0.021-0.00213.2640.1500.1500.0000.0000.0000.000
179A198VAL0-0.013-0.01014.980-0.094-0.0940.0000.0000.0000.000
180A199SER0-0.016-0.00517.5120.0490.0490.0000.0000.0000.000
181A200ALA00.0330.02320.952-0.046-0.0460.0000.0000.0000.000
182A201HIS00.0020.01122.779-0.004-0.0040.0000.0000.0000.000
183A202GLY00.0100.00622.9270.0150.0150.0000.0000.0000.000
184A203ASN0-0.046-0.03723.0070.0160.0160.0000.0000.0000.000
185A204SER00.015-0.01321.973-0.003-0.0030.0000.0000.0000.000
186A205LEU00.0060.00717.847-0.003-0.0030.0000.0000.0000.000
187A206ARG10.9020.95718.186-0.170-0.1700.0000.0000.0000.000
188A207ALA00.0130.01219.495-0.001-0.0010.0000.0000.0000.000
189A208LEU00.0200.00215.225-0.024-0.0240.0000.0000.0000.000
190A209LEU00.0020.01314.4490.0100.0100.0000.0000.0000.000
191A210TYR00.0300.00315.474-0.004-0.0040.0000.0000.0000.000
192A211LEU0-0.032-0.00615.836-0.033-0.0330.0000.0000.0000.000
193A212LEU0-0.007-0.01110.514-0.064-0.0640.0000.0000.0000.000
194A213GLU-1-0.807-0.89411.3880.6390.6390.0000.0000.0000.000
195A214GLY0-0.085-0.02013.419-0.045-0.0450.0000.0000.0000.000
196A215MET0-0.0520.00116.113-0.012-0.0120.0000.0000.0000.000
197A216THR00.0540.02219.024-0.038-0.0380.0000.0000.0000.000
198A217PRO0-0.015-0.03922.7560.0220.0220.0000.0000.0000.000
199A218GLU-1-0.949-0.97825.3230.1210.1210.0000.0000.0000.000
200A219GLN00.1210.06619.253-0.020-0.0200.0000.0000.0000.000
201A220ILE00.004-0.00119.7080.0300.0300.0000.0000.0000.000
202A221LEU0-0.117-0.06322.5970.0120.0120.0000.0000.0000.000
203A222GLU-1-0.928-0.94324.2370.1970.1970.0000.0000.0000.000
204A223VAL0-0.060-0.01019.6820.0290.0290.0000.0000.0000.000
205A224ASN0-0.042-0.03422.813-0.026-0.0260.0000.0000.0000.000
206A225ILE0-0.0170.00019.4670.0260.0260.0000.0000.0000.000
207A226PRO00.0230.01721.182-0.041-0.0410.0000.0000.0000.000
208A227THR0-0.037-0.03023.0660.0230.0230.0000.0000.0000.000
209A228ALA00.0080.01123.8440.0080.0080.0000.0000.0000.000
210A229CYS0-0.0140.00421.3450.0270.0270.0000.0000.0000.000
211A230PRO0-0.006-0.00117.5310.0130.0130.0000.0000.0000.000
212A231LEU0-0.0060.00213.9140.0280.0280.0000.0000.0000.000
213A232VAL0-0.014-0.0069.566-0.037-0.0370.0000.0000.0000.000
214A233LEU0-0.011-0.0209.081-0.022-0.0220.0000.0000.0000.000
215A234GLU-1-0.879-0.9484.4504.4424.590-0.001-0.010-0.1370.000
216A235LEU0-0.051-0.0343.721-1.609-1.2760.000-0.089-0.2430.000
217A236ASP-1-0.870-0.9382.1980.4741.3483.507-1.800-2.580-0.022
218A237ASP-1-0.843-0.9282.628-24.106-18.5781.944-3.310-4.162-0.034
219A238TYR0-0.067-0.0473.2392.1482.2450.0190.068-0.1830.000
220A239LEU0-0.053-0.0225.1120.6510.6510.0000.0000.0000.000
221A240LYS10.8920.9456.5370.2430.2430.0000.0000.0000.000
222A241VAL00.006-0.0026.6900.3880.3880.0000.0000.0000.000
223A242THR00.0170.0244.322-0.254-0.163-0.001-0.004-0.0860.000
224A243LYS10.9070.9557.165-2.327-2.3270.0000.0000.0000.000
225A244LYS10.8440.9058.665-0.418-0.4180.0000.0000.0000.000
226A245TYR0-0.050-0.0209.255-0.353-0.3530.0000.0000.0000.000
227A246TYR00.0390.00614.1120.0220.0220.0000.0000.0000.000
228A247LEU0-0.045-0.00915.2400.0290.0290.0000.0000.0000.000
229A248ILE00.0200.00818.334-0.053-0.0530.0000.0000.0000.000