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: 6YVJZ

Calculation Name: 3CKF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q45040

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2225103.237201
FMO2-HF: Nuclear repulsion 2144239.890942
FMO2-HF: Total energy -80863.346258
FMO2-MP2: Total energy -81103.074225


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:28:ASN)


Summations of interaction energy for fragment #1(A:28:ASN)
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.
1.1954.9460.162-1.813-2.10.002
Interaction energy analysis for fragmet #1(A:28:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.014
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].
3A30VAL0-0.035-0.0173.7162.2804.7200.012-1.313-1.1390.001
4A31SER00.0000.0106.409-0.554-0.5540.0000.0000.0000.000
5A32VAL0-0.024-0.0088.836-0.192-0.1920.0000.0000.0000.000
6A33ASP-1-0.806-0.89212.2791.1611.1610.0000.0000.0000.000
7A34LEU0-0.004-0.00215.239-0.113-0.1130.0000.0000.0000.000
8A35PRO00.0120.00218.2930.0170.0170.0000.0000.0000.000
9A36GLY00.009-0.00521.6760.0060.0060.0000.0000.0000.000
10A37SER0-0.069-0.02619.698-0.005-0.0050.0000.0000.0000.000
11A38MET0-0.0020.02617.6910.0640.0640.0000.0000.0000.000
12A39LYS10.8190.87412.388-1.259-1.2590.0000.0000.0000.000
13A40VAL0-0.0130.00412.054-0.110-0.1100.0000.0000.0000.000
14A41LEU0-0.0150.0005.8210.4120.4120.0000.0000.0000.000
15A42VAL00.0240.0178.634-0.451-0.4510.0000.0000.0000.000
16A43SER00.014-0.0075.0000.6070.6070.0000.0000.0000.000
17A44LYS10.9260.9522.6720.4991.6440.151-0.488-0.8090.001
18A45SER0-0.064-0.0484.6870.5170.683-0.001-0.012-0.1520.000
19A46SER00.0250.0426.560-0.357-0.3570.0000.0000.0000.000
20A47ASN00.003-0.0219.010-0.194-0.1940.0000.0000.0000.000
21A48ALA0-0.004-0.01610.4730.1310.1310.0000.0000.0000.000
22A49ASP-1-0.890-0.92113.763-0.652-0.6520.0000.0000.0000.000
23A50GLY0-0.034-0.01513.7390.1030.1030.0000.0000.0000.000
24A51LYS10.8390.90813.5480.4650.4650.0000.0000.0000.000
25A52TYR0-0.008-0.0038.636-0.283-0.2830.0000.0000.0000.000
26A53ASP-1-0.882-0.9417.611-1.593-1.5930.0000.0000.0000.000
27A54LEU0-0.040-0.0279.2520.0810.0810.0000.0000.0000.000
28A55ILE00.0120.0008.779-0.078-0.0780.0000.0000.0000.000
29A56ALA00.0330.00311.2830.2610.2610.0000.0000.0000.000
30A57THR0-0.015-0.00413.767-0.079-0.0790.0000.0000.0000.000
31A58VAL0-0.030-0.02515.9170.0400.0400.0000.0000.0000.000
32A59ASP-1-0.839-0.90919.4270.2710.2710.0000.0000.0000.000
33A60ALA0-0.041-0.02120.209-0.032-0.0320.0000.0000.0000.000
34A61LEU0-0.0220.00520.025-0.006-0.0060.0000.0000.0000.000
35A62GLU-1-0.841-0.91612.2450.7640.7640.0000.0000.0000.000
36A63LEU0-0.065-0.02215.794-0.099-0.0990.0000.0000.0000.000
37A64SER00.002-0.00913.4820.0420.0420.0000.0000.0000.000
38A65GLY00.0290.00913.4020.0160.0160.0000.0000.0000.000
39A66THR0-0.0120.00612.271-0.088-0.0880.0000.0000.0000.000
40A67SER0-0.024-0.01713.6100.1000.1000.0000.0000.0000.000
41A68ASP-1-0.850-0.91114.422-0.386-0.3860.0000.0000.0000.000
42A69LYS10.8020.90815.3360.1170.1170.0000.0000.0000.000
43A70ASN00.0270.01010.8930.0340.0340.0000.0000.0000.000
44A71ASN0-0.0030.01411.5480.0540.0540.0000.0000.0000.000
45A72GLY00.0560.01813.0150.1330.1330.0000.0000.0000.000
46A73SER0-0.019-0.01113.8300.0060.0060.0000.0000.0000.000
47A74GLY00.0410.02216.255-0.087-0.0870.0000.0000.0000.000
48A75VAL0-0.041-0.02517.7720.0580.0580.0000.0000.0000.000
49A76LEU0-0.0180.00513.853-0.048-0.0480.0000.0000.0000.000
50A77GLU-1-0.851-0.93217.700-0.007-0.0070.0000.0000.0000.000
51A78GLY00.0730.03118.4330.0060.0060.0000.0000.0000.000
52A79VAL0-0.066-0.03220.667-0.014-0.0140.0000.0000.0000.000
53A80LYS10.8960.96523.158-0.128-0.1280.0000.0000.0000.000
54A81ALA00.0430.01325.335-0.020-0.0200.0000.0000.0000.000
55A82ASP-1-0.862-0.90427.1680.1120.1120.0000.0000.0000.000
56A83ALA00.007-0.00628.165-0.012-0.0120.0000.0000.0000.000
57A84SER0-0.039-0.04728.068-0.012-0.0120.0000.0000.0000.000
58A85LYS10.8560.92825.8670.0240.0240.0000.0000.0000.000
59A86VAL0-0.021-0.01422.5540.0090.0090.0000.0000.0000.000
60A87LYS10.8470.93022.189-0.002-0.0020.0000.0000.0000.000
61A88LEU00.0150.00917.4860.0240.0240.0000.0000.0000.000
62A89THR0-0.0050.00020.369-0.044-0.0440.0000.0000.0000.000
63A90ILE0-0.0050.00516.6160.0360.0360.0000.0000.0000.000
64A91SER0-0.002-0.02920.442-0.033-0.0330.0000.0000.0000.000
65A92ASP-1-0.792-0.91920.560-0.035-0.0350.0000.0000.0000.000
66A93ASP-1-0.856-0.90520.5410.1180.1180.0000.0000.0000.000
67A94LEU0-0.042-0.01816.9070.0360.0360.0000.0000.0000.000
68A95GLY0-0.0020.01221.0180.0370.0370.0000.0000.0000.000
69A96GLN0-0.029-0.03323.832-0.003-0.0030.0000.0000.0000.000
70A97THR00.0200.01120.1420.0150.0150.0000.0000.0000.000
71A98THR0-0.036-0.02123.1800.0000.0000.0000.0000.0000.000
72A99LEU00.0180.01721.919-0.008-0.0080.0000.0000.0000.000
73A100GLU-1-0.873-0.94424.7320.0470.0470.0000.0000.0000.000
74A101VAL00.0100.00725.9890.0060.0060.0000.0000.0000.000
75A102PHE00.012-0.00427.393-0.008-0.0080.0000.0000.0000.000
76A103LYS10.9300.95430.262-0.025-0.0250.0000.0000.0000.000
77A104SER00.0710.03930.154-0.005-0.0050.0000.0000.0000.000
78A105ASP-1-0.792-0.86130.5590.0010.0010.0000.0000.0000.000
79A106GLY00.0100.00230.236-0.012-0.0120.0000.0000.0000.000
80A107SER0-0.081-0.05330.9590.0010.0010.0000.0000.0000.000
81A108THR0-0.024-0.01834.1250.0010.0010.0000.0000.0000.000
82A109LEU00.0090.01930.5470.0050.0050.0000.0000.0000.000
83A110VAL0-0.029-0.01832.457-0.003-0.0030.0000.0000.0000.000
84A111SER0-0.026-0.03230.3450.0050.0050.0000.0000.0000.000
85A112LYS10.8510.92229.127-0.079-0.0790.0000.0000.0000.000
86A113LYS10.8020.89924.738-0.288-0.2880.0000.0000.0000.000
87A114VAL00.0160.00926.8490.0080.0080.0000.0000.0000.000
88A115THR0-0.0030.00123.927-0.015-0.0150.0000.0000.0000.000
89A116ARG10.8230.89426.126-0.183-0.1830.0000.0000.0000.000
90A117ALA00.0790.03624.7500.0250.0250.0000.0000.0000.000
91A118ASP-1-0.749-0.82525.2280.2410.2410.0000.0000.0000.000
92A119GLY00.0010.00725.3860.0170.0170.0000.0000.0000.000
93A120THR0-0.109-0.05626.2640.0010.0010.0000.0000.0000.000
94A121ARG10.8380.89227.272-0.251-0.2510.0000.0000.0000.000
95A122LEU0-0.0020.01129.696-0.008-0.0080.0000.0000.0000.000
96A123GLU-1-0.814-0.90629.7900.2280.2280.0000.0000.0000.000
97A124TYR00.0150.00332.631-0.007-0.0070.0000.0000.0000.000
98A125THR00.010-0.01633.6520.0020.0020.0000.0000.0000.000
99A126GLY00.0180.01235.926-0.006-0.0060.0000.0000.0000.000
100A127ILE0-0.0250.01534.027-0.006-0.0060.0000.0000.0000.000
101A128LYS10.8370.90338.081-0.066-0.0660.0000.0000.0000.000
102A129SER00.0330.01040.1890.0000.0000.0000.0000.0000.000
103A130ASP-1-0.832-0.88541.7890.0380.0380.0000.0000.0000.000
104A131GLY0-0.013-0.00839.361-0.001-0.0010.0000.0000.0000.000
105A132SER0-0.061-0.04439.8830.0070.0070.0000.0000.0000.000
106A133GLY00.029-0.00739.3730.0010.0010.0000.0000.0000.000
107A134LYS10.9050.96339.458-0.084-0.0840.0000.0000.0000.000
108A135ALA00.000-0.00137.2400.0030.0030.0000.0000.0000.000
109A136LYS10.8360.91234.351-0.151-0.1510.0000.0000.0000.000
110A137GLU-1-0.735-0.84334.1580.1430.1430.0000.0000.0000.000
111A138VAL0-0.019-0.01131.307-0.002-0.0020.0000.0000.0000.000
112A139LEU0-0.008-0.00831.9540.0120.0120.0000.0000.0000.000
113A140LYS10.8580.89828.397-0.247-0.2470.0000.0000.0000.000
114A141GLY00.0540.03633.288-0.008-0.0080.0000.0000.0000.000
115A142TYR0-0.088-0.04335.758-0.012-0.0120.0000.0000.0000.000
116A143VAL0-0.011-0.00435.3560.0100.0100.0000.0000.0000.000
117A144LEU0-0.0190.00637.614-0.010-0.0100.0000.0000.0000.000
118A145GLU-1-0.764-0.87538.5820.1430.1430.0000.0000.0000.000
119A146GLY00.0110.00041.023-0.006-0.0060.0000.0000.0000.000
120A147THR0-0.053-0.01941.8720.0010.0010.0000.0000.0000.000
121A148LEU0-0.021-0.00236.7740.0020.0020.0000.0000.0000.000
122A149THR0-0.013-0.02040.726-0.005-0.0050.0000.0000.0000.000
123A150ALA00.0280.00640.8660.0020.0020.0000.0000.0000.000
124A151GLU-1-0.942-0.95841.1840.0420.0420.0000.0000.0000.000
125A152LYS10.8690.92940.691-0.056-0.0560.0000.0000.0000.000
126A153THR00.0180.02637.8480.0020.0020.0000.0000.0000.000
127A154THR0-0.008-0.01540.370-0.003-0.0030.0000.0000.0000.000
128A155LEU0-0.034-0.00537.8550.0020.0020.0000.0000.0000.000
129A156VAL0-0.013-0.01342.391-0.003-0.0030.0000.0000.0000.000
130A157VAL00.0020.00344.4330.0050.0050.0000.0000.0000.000
131A158LYS10.9170.95046.956-0.073-0.0730.0000.0000.0000.000
132A159GLU-1-0.843-0.92850.5170.0920.0920.0000.0000.0000.000
133A160GLY0-0.0040.00753.021-0.003-0.0030.0000.0000.0000.000
134A161THR0-0.039-0.03556.1790.0010.0010.0000.0000.0000.000
135A162VAL0-0.0070.01452.639-0.002-0.0020.0000.0000.0000.000
136A163THR0-0.021-0.01650.6490.0030.0030.0000.0000.0000.000
137A164LEU00.0230.03045.721-0.003-0.0030.0000.0000.0000.000
138A165SER00.008-0.01346.0060.0040.0040.0000.0000.0000.000
139A166LYS10.8680.93636.346-0.133-0.1330.0000.0000.0000.000
140A167ASN0-0.017-0.01142.1270.0020.0020.0000.0000.0000.000
141A168ILE00.0160.00136.0760.0040.0040.0000.0000.0000.000
142A169SER00.0540.03339.1200.0000.0000.0000.0000.0000.000
143A170LYS11.0010.99536.044-0.022-0.0220.0000.0000.0000.000
144A171SER0-0.031-0.01434.7860.0020.0020.0000.0000.0000.000
145A172GLY0-0.004-0.00234.1460.0050.0050.0000.0000.0000.000
146A173GLU-1-0.974-0.98135.1250.0610.0610.0000.0000.0000.000
147A174VAL0-0.002-0.00536.980-0.002-0.0020.0000.0000.0000.000
148A175SER00.0070.00339.652-0.005-0.0050.0000.0000.0000.000
149A176VAL0-0.029-0.01543.4120.0040.0040.0000.0000.0000.000
150A177GLU-1-0.845-0.90145.7960.0550.0550.0000.0000.0000.000
151A178LEU0-0.013-0.02048.9910.0050.0050.0000.0000.0000.000
152A179ASN0-0.0220.00551.713-0.006-0.0060.0000.0000.0000.000
153A180ASP-1-0.710-0.86554.6230.0610.0610.0000.0000.0000.000
154A181THR0-0.019-0.02157.357-0.002-0.0020.0000.0000.0000.000
155A182ASP-1-0.794-0.86560.3230.0500.0500.0000.0000.0000.000
156A183SER00.001-0.00362.446-0.001-0.0010.0000.0000.0000.000
157A184SER0-0.042-0.01565.457-0.003-0.0030.0000.0000.0000.000
158A185ALA00.032-0.00265.2170.0020.0020.0000.0000.0000.000
159A186ALA0-0.011-0.00165.5750.0010.0010.0000.0000.0000.000
160A187THR0-0.058-0.05162.6510.0010.0010.0000.0000.0000.000
161A188LYS10.8480.94160.804-0.046-0.0460.0000.0000.0000.000
162A189LYS10.8430.92455.706-0.063-0.0630.0000.0000.0000.000
163A190THR0-0.039-0.01757.054-0.002-0.0020.0000.0000.0000.000
164A191ALA00.014-0.01052.1280.0020.0020.0000.0000.0000.000
165A192ALA0-0.0010.00952.791-0.003-0.0030.0000.0000.0000.000
166A193TRP00.0290.02242.5500.0040.0040.0000.0000.0000.000
167A194ASN00.0230.01448.137-0.006-0.0060.0000.0000.0000.000
168A195SER00.0400.01144.5830.0040.0040.0000.0000.0000.000
169A196GLY00.0230.01743.6000.0030.0030.0000.0000.0000.000
170A197THR0-0.036-0.03143.6290.0000.0000.0000.0000.0000.000
171A198SER0-0.0040.01140.9060.0060.0060.0000.0000.0000.000
172A199THR0-0.031-0.01542.9300.0070.0070.0000.0000.0000.000
173A200LEU0-0.037-0.01445.838-0.005-0.0050.0000.0000.0000.000
174A201THR00.001-0.01848.4450.0010.0010.0000.0000.0000.000
175A202ILE0-0.020-0.01050.322-0.002-0.0020.0000.0000.0000.000
176A203THR00.004-0.00153.8380.0000.0000.0000.0000.0000.000
177A204VAL00.014-0.00257.6500.0000.0000.0000.0000.0000.000
178A205ASN0-0.0010.00860.596-0.002-0.0020.0000.0000.0000.000
179A206SER0-0.033-0.01463.593-0.001-0.0010.0000.0000.0000.000
180A207LYS10.8730.95161.537-0.049-0.0490.0000.0000.0000.000
181A208LYS10.8670.93953.641-0.057-0.0570.0000.0000.0000.000
182A209THR0-0.034-0.03355.7640.0010.0010.0000.0000.0000.000
183A210LYS10.8720.92950.945-0.075-0.0750.0000.0000.0000.000
184A211ASP-1-0.743-0.81348.4560.0660.0660.0000.0000.0000.000
185A212LEU0-0.029-0.01745.5750.0040.0040.0000.0000.0000.000
186A213VAL00.0160.01441.469-0.003-0.0030.0000.0000.0000.000
187A214PHE0-0.009-0.01940.1090.0080.0080.0000.0000.0000.000
188A215THR00.016-0.00836.289-0.003-0.0030.0000.0000.0000.000
189A216SER00.0600.01833.727-0.001-0.0010.0000.0000.0000.000
190A217SER0-0.042-0.02431.8260.0070.0070.0000.0000.0000.000
191A218ASN0-0.062-0.04631.7620.0010.0010.0000.0000.0000.000
192A219THR0-0.034-0.00834.2150.0000.0000.0000.0000.0000.000
193A220ILE0-0.0010.00036.568-0.010-0.0100.0000.0000.0000.000
194A221THR0-0.0010.01040.1420.0030.0030.0000.0000.0000.000
195A222VAL0-0.003-0.01542.588-0.007-0.0070.0000.0000.0000.000
196A223GLN00.0040.00146.4070.0050.0050.0000.0000.0000.000
197A224GLN00.0360.00849.148-0.005-0.0050.0000.0000.0000.000
198A225TYR0-0.037-0.04252.502-0.002-0.0020.0000.0000.0000.000
199A226ASP-1-0.689-0.82955.7570.0550.0550.0000.0000.0000.000
200A227SER0-0.015-0.00358.902-0.002-0.0020.0000.0000.0000.000
201A228ASN0-0.063-0.04761.817-0.003-0.0030.0000.0000.0000.000
202A229GLY00.0110.01658.712-0.002-0.0020.0000.0000.0000.000
203A230THR0-0.103-0.07158.976-0.001-0.0010.0000.0000.0000.000
204A231SER0-0.019-0.01756.408-0.001-0.0010.0000.0000.0000.000
205A232LEU0-0.0260.00449.7800.0000.0000.0000.0000.0000.000
206A233GLU-1-0.908-0.95553.6240.0690.0690.0000.0000.0000.000
207A234GLY0-0.016-0.00251.8340.0030.0030.0000.0000.0000.000
208A235SER0-0.003-0.01246.439-0.001-0.0010.0000.0000.0000.000
209A236ALA0-0.0150.00144.2030.0000.0000.0000.0000.0000.000
210A237VAL0-0.016-0.00743.7900.0050.0050.0000.0000.0000.000
211A238GLU-1-0.868-0.91836.4480.1660.1660.0000.0000.0000.000
212A239ILE0-0.055-0.02141.157-0.001-0.0010.0000.0000.0000.000
213A240THR0-0.002-0.02138.5620.0090.0090.0000.0000.0000.000
214A241LYS10.8450.87538.659-0.125-0.1250.0000.0000.0000.000
215A242LEU00.0450.01841.028-0.008-0.0080.0000.0000.0000.000
216A243ASP-1-0.854-0.91843.1450.1180.1180.0000.0000.0000.000
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