FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 6G67Z

Calculation Name: 3CKY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CKY

Chain ID: A

ChEMBL ID:

UniProt ID: Q0QLF5

Base Structure: X-ray

Registration Date: 2023-09-26

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 297
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3556108.487502
FMO2-HF: Nuclear repulsion 3445846.731907
FMO2-HF: Total energy -110261.755595
FMO2-MP2: Total energy -110569.543035


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:4:SER)


Summations of interaction energy for fragment #1(A:4:SER)
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.
-12.126-8.6061.099-1.884-2.7360.012
Interaction energy analysis for fragmet #1(A:4:SER)
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 : -0.017
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].
3A6LYS10.8590.9362.547-12.849-9.8991.097-1.742-2.3060.013
4A7ILE00.0250.0096.2730.2960.2960.0000.0000.0000.000
5A8GLY00.0500.0279.266-0.011-0.0110.0000.0000.0000.000
6A9PHE0-0.034-0.02412.5100.0040.0040.0000.0000.0000.000
7A10ILE00.0060.00715.8480.0010.0010.0000.0000.0000.000
8A11GLY00.0300.02719.1320.0020.0020.0000.0000.0000.000
9A12LEU0-0.064-0.03217.075-0.004-0.0040.0000.0000.0000.000
10A13GLY00.0510.01921.152-0.006-0.0060.0000.0000.0000.000
11A14ALA0-0.028-0.03322.896-0.003-0.0030.0000.0000.0000.000
12A15MET00.0050.02122.563-0.005-0.0050.0000.0000.0000.000
13A16GLY00.0560.02519.208-0.001-0.0010.0000.0000.0000.000
14A17LYS10.9971.00418.0090.0160.0160.0000.0000.0000.000
15A18PRO0-0.044-0.01818.088-0.014-0.0140.0000.0000.0000.000
16A19MET00.0300.01916.364-0.005-0.0050.0000.0000.0000.000
17A20ALA00.0320.01813.678-0.009-0.0090.0000.0000.0000.000
18A21ILE0-0.019-0.01813.125-0.038-0.0380.0000.0000.0000.000
19A22ASN0-0.054-0.04714.276-0.031-0.0310.0000.0000.0000.000
20A23LEU00.0260.0159.786-0.002-0.0020.0000.0000.0000.000
21A24LEU0-0.032-0.0059.606-0.046-0.0460.0000.0000.0000.000
22A25LYS10.7790.90610.4380.0160.0160.0000.0000.0000.000
23A26GLU-1-0.888-0.9389.484-0.108-0.1080.0000.0000.0000.000
24A27GLY0-0.032-0.0097.1670.0490.0490.0000.0000.0000.000
25A28VAL0-0.052-0.0164.230-0.702-0.513-0.001-0.015-0.1730.000
26A29THR0-0.043-0.0203.787-0.1930.1880.003-0.127-0.257-0.001
27A30VAL00.0160.0045.8190.1830.1830.0000.0000.0000.000
28A31TYR00.0100.0087.4760.0920.0920.0000.0000.0000.000
29A32ALA0-0.021-0.02311.486-0.004-0.0040.0000.0000.0000.000
30A33PHE00.0310.01515.1980.0070.0070.0000.0000.0000.000
31A34ASP-1-0.781-0.89918.8210.0200.0200.0000.0000.0000.000
32A35LEU00.0190.01922.2810.0000.0000.0000.0000.0000.000
33A36MET0-0.070-0.02925.459-0.004-0.0040.0000.0000.0000.000
34A37GLU-1-0.867-0.93823.8670.0100.0100.0000.0000.0000.000
35A38ALA0-0.006-0.00823.345-0.005-0.0050.0000.0000.0000.000
36A39ASN0-0.076-0.04822.219-0.011-0.0110.0000.0000.0000.000
37A40VAL00.0550.02118.140-0.009-0.0090.0000.0000.0000.000
38A41ALA00.0000.00118.858-0.013-0.0130.0000.0000.0000.000
39A42ALA0-0.042-0.02820.246-0.011-0.0110.0000.0000.0000.000
40A43VAL00.0140.00815.881-0.009-0.0090.0000.0000.0000.000
41A44VAL0-0.0030.00215.136-0.025-0.0250.0000.0000.0000.000
42A45ALA0-0.056-0.01815.874-0.019-0.0190.0000.0000.0000.000
43A46GLN0-0.060-0.03415.505-0.006-0.0060.0000.0000.0000.000
44A47GLY00.0130.01312.142-0.034-0.0340.0000.0000.0000.000
45A48ALA0-0.033-0.00710.936-0.043-0.0430.0000.0000.0000.000
46A49GLN0-0.014-0.0127.4760.1350.1350.0000.0000.0000.000
47A50ALA00.0250.00412.3560.0220.0220.0000.0000.0000.000
48A51CYS0-0.066-0.01814.1890.0340.0340.0000.0000.0000.000
49A52GLU-1-0.883-0.94716.8620.0720.0720.0000.0000.0000.000
50A53ASN0-0.010-0.02719.657-0.002-0.0020.0000.0000.0000.000
51A54ASN00.0660.00619.1020.0070.0070.0000.0000.0000.000
52A55GLN00.0020.00418.5890.0140.0140.0000.0000.0000.000
53A56LYN0-0.0040.02216.5680.0210.0210.0000.0000.0000.000
54A57VAL00.0040.00913.7780.0320.0320.0000.0000.0000.000
55A58ALA0-0.009-0.00513.4610.0320.0320.0000.0000.0000.000
56A59ALA0-0.0120.00014.4610.0300.0300.0000.0000.0000.000
57A60ALA0-0.060-0.01910.3250.0710.0710.0000.0000.0000.000
58A61SER0-0.028-0.0409.0200.0760.0760.0000.0000.0000.000
59A62ASP-1-0.842-0.9106.4950.7720.7720.0000.0000.0000.000
60A63ILE0-0.019-0.0129.400-0.018-0.0180.0000.0000.0000.000
61A64ILE0-0.008-0.00511.702-0.052-0.0520.0000.0000.0000.000
62A65PHE00.0320.01912.1190.0050.0050.0000.0000.0000.000
63A66THR0-0.007-0.02516.630-0.009-0.0090.0000.0000.0000.000
64A67SER0-0.042-0.04320.2860.0000.0000.0000.0000.0000.000
65A68LEU00.0000.00723.727-0.006-0.0060.0000.0000.0000.000
66A69PRO0-0.008-0.01726.9980.0000.0000.0000.0000.0000.000
67A70ASN00.001-0.01530.6520.0000.0000.0000.0000.0000.000
68A71ALA00.1320.06230.7470.0020.0020.0000.0000.0000.000
69A72GLY00.0280.03131.1730.0030.0030.0000.0000.0000.000
70A73ILE0-0.015-0.00728.5190.0020.0020.0000.0000.0000.000
71A74VAL00.0410.02525.8130.0030.0030.0000.0000.0000.000
72A75GLU-1-0.829-0.92927.1830.0680.0680.0000.0000.0000.000
73A76THR0-0.078-0.04629.0440.0030.0030.0000.0000.0000.000
74A77VAL0-0.044-0.02323.5590.0030.0030.0000.0000.0000.000
75A78MET0-0.018-0.00320.3870.0070.0070.0000.0000.0000.000
76A79ASN0-0.012-0.02324.6600.0140.0140.0000.0000.0000.000
77A80GLY00.0400.04727.494-0.004-0.0040.0000.0000.0000.000
78A81PRO0-0.035-0.04128.3090.0060.0060.0000.0000.0000.000
79A82GLY00.0130.01926.106-0.002-0.0020.0000.0000.0000.000
80A83GLY00.0070.02224.5980.0030.0030.0000.0000.0000.000
81A84VAL00.026-0.00418.8800.0090.0090.0000.0000.0000.000
82A85LEU00.009-0.00420.3020.0180.0180.0000.0000.0000.000
83A86SER0-0.077-0.04321.7640.0040.0040.0000.0000.0000.000
84A87ALA0-0.050-0.02418.9020.0010.0010.0000.0000.0000.000
85A88CYS0-0.0460.00216.1200.0250.0250.0000.0000.0000.000
86A89LYS10.9470.99212.860-0.342-0.3420.0000.0000.0000.000
87A90ALA00.0360.02915.398-0.003-0.0030.0000.0000.0000.000
88A91GLY0-0.002-0.00513.7450.0250.0250.0000.0000.0000.000
89A92THR0-0.034-0.02712.9670.0370.0370.0000.0000.0000.000
90A93VAL0-0.024-0.01213.142-0.024-0.0240.0000.0000.0000.000
91A94ILE0-0.021-0.01114.977-0.005-0.0050.0000.0000.0000.000
92A95VAL00.014-0.00315.251-0.001-0.0010.0000.0000.0000.000
93A96ASP-1-0.749-0.82618.1530.0660.0660.0000.0000.0000.000
94A97MET0-0.026-0.01018.673-0.002-0.0020.0000.0000.0000.000
95A98SER0-0.011-0.02022.985-0.010-0.0100.0000.0000.0000.000
96A99SER0-0.0440.01026.2800.0000.0000.0000.0000.0000.000
97A100VAL00.005-0.01828.465-0.003-0.0030.0000.0000.0000.000
98A101SER00.0430.00831.2680.0010.0010.0000.0000.0000.000
99A102PRO00.0360.00630.7990.0030.0030.0000.0000.0000.000
100A103SER0-0.065-0.05530.9460.0050.0050.0000.0000.0000.000
101A104SER0-0.019-0.01329.4170.0010.0010.0000.0000.0000.000
102A105THR0-0.003-0.02125.2420.0040.0040.0000.0000.0000.000
103A106LEU0-0.011-0.00627.3100.0060.0060.0000.0000.0000.000
104A107LYS10.8120.90629.188-0.057-0.0570.0000.0000.0000.000
105A108MET0-0.0080.01725.3710.0020.0020.0000.0000.0000.000
106A109ALA00.0710.02324.4030.0070.0070.0000.0000.0000.000
107A110LYS10.8840.94525.318-0.072-0.0720.0000.0000.0000.000
108A111VAL00.0130.00826.8350.0000.0000.0000.0000.0000.000
109A112ALA00.0370.03321.7440.0040.0040.0000.0000.0000.000
110A113ALA00.0420.01622.5860.0090.0090.0000.0000.0000.000
111A114GLU-1-0.945-0.95323.5600.0970.0970.0000.0000.0000.000
112A115LYS10.7960.88822.231-0.110-0.1100.0000.0000.0000.000
113A116GLY0-0.010-0.00220.0170.0150.0150.0000.0000.0000.000
114A117ILE0-0.067-0.02417.7830.0230.0230.0000.0000.0000.000
115A118ASP-1-0.793-0.88716.2890.1980.1980.0000.0000.0000.000
116A119TYR0-0.057-0.08318.6770.0050.0050.0000.0000.0000.000
117A120VAL0-0.0200.00018.727-0.005-0.0050.0000.0000.0000.000
118A121ASP-1-0.725-0.83421.4600.0850.0850.0000.0000.0000.000
119A122ALA00.028-0.00620.2750.0060.0060.0000.0000.0000.000
120A123PRO00.0260.02622.107-0.005-0.0050.0000.0000.0000.000
121A124VAL00.0430.02221.5360.0010.0010.0000.0000.0000.000
122A125SER0-0.020-0.02324.835-0.004-0.0040.0000.0000.0000.000
123A126GLY00.0630.02725.8390.0020.0020.0000.0000.0000.000
124A127GLY0-0.0140.00027.323-0.004-0.0040.0000.0000.0000.000
125A128THR00.028-0.02425.1010.0020.0020.0000.0000.0000.000
126A129LYS10.8300.89924.4870.0050.0050.0000.0000.0000.000
127A130GLY00.0500.03624.464-0.003-0.0030.0000.0000.0000.000
128A131ALA00.0290.00820.8800.0020.0020.0000.0000.0000.000
129A132GLU-1-0.833-0.90019.924-0.015-0.0150.0000.0000.0000.000
130A133ALA0-0.025-0.00120.831-0.008-0.0080.0000.0000.0000.000
131A134GLY00.0560.05018.524-0.002-0.0020.0000.0000.0000.000
132A135THR0-0.055-0.03919.2610.0090.0090.0000.0000.0000.000
133A136LEU0-0.058-0.01820.2740.0000.0000.0000.0000.0000.000
134A137THR00.0030.00822.3490.0050.0050.0000.0000.0000.000
135A138ILE0-0.027-0.02618.582-0.004-0.0040.0000.0000.0000.000
136A139MET0-0.050-0.01522.6690.0040.0040.0000.0000.0000.000
137A140VAL00.004-0.01420.0040.0000.0000.0000.0000.0000.000
138A141GLY0-0.0070.00423.173-0.003-0.0030.0000.0000.0000.000
139A142ALA0-0.002-0.01820.3910.0070.0070.0000.0000.0000.000
140A143SER00.0410.02821.481-0.002-0.0020.0000.0000.0000.000
141A144GLU-1-0.841-0.91020.6750.1220.1220.0000.0000.0000.000
142A145ALA00.0600.03017.6620.0140.0140.0000.0000.0000.000
143A146VAL0-0.028-0.01116.2000.0340.0340.0000.0000.0000.000
144A147PHE00.0070.00316.3730.0200.0200.0000.0000.0000.000
145A148GLU-1-0.911-0.97115.6710.1970.1970.0000.0000.0000.000
146A149LYS10.7490.87111.615-0.253-0.2530.0000.0000.0000.000
147A150ILE0-0.002-0.00511.4320.0770.0770.0000.0000.0000.000
148A151GLN00.0020.01113.4000.0120.0120.0000.0000.0000.000
149A152PRO00.0010.00310.570-0.033-0.0330.0000.0000.0000.000
150A153VAL00.0170.0088.638-0.023-0.0230.0000.0000.0000.000
151A154LEU00.032-0.00511.260-0.073-0.0730.0000.0000.0000.000
152A155SER0-0.057-0.04014.534-0.041-0.0410.0000.0000.0000.000
153A156VAL0-0.0030.01610.718-0.014-0.0140.0000.0000.0000.000
154A157ILE0-0.055-0.02513.985-0.036-0.0360.0000.0000.0000.000
155A158GLY0-0.032-0.02616.445-0.011-0.0110.0000.0000.0000.000
156A159LYS10.8830.94918.458-0.029-0.0290.0000.0000.0000.000
157A160ASP-1-0.867-0.90421.1630.0530.0530.0000.0000.0000.000
158A161ILE0-0.0040.00418.023-0.003-0.0030.0000.0000.0000.000
159A162TYR0-0.018-0.02921.2860.0060.0060.0000.0000.0000.000
160A163HIS10.8240.90522.102-0.107-0.1070.0000.0000.0000.000
161A164VAL0-0.028-0.01523.854-0.006-0.0060.0000.0000.0000.000
162A165GLY00.0060.00326.305-0.007-0.0070.0000.0000.0000.000
163A166ASP-1-0.843-0.90125.4790.1080.1080.0000.0000.0000.000
164A167THR0-0.054-0.05525.055-0.002-0.0020.0000.0000.0000.000
165A168GLY0-0.004-0.01226.331-0.006-0.0060.0000.0000.0000.000
166A169ALA0-0.034-0.01028.005-0.006-0.0060.0000.0000.0000.000
167A170GLY00.0300.01426.321-0.004-0.0040.0000.0000.0000.000
168A171ASP-1-0.808-0.90827.3470.0640.0640.0000.0000.0000.000
169A172ALA0-0.021-0.00729.523-0.005-0.0050.0000.0000.0000.000
170A173VAL0-0.019-0.00929.313-0.005-0.0050.0000.0000.0000.000
171A174LYS10.8980.95328.707-0.045-0.0450.0000.0000.0000.000
172A175ILE0-0.021-0.00731.135-0.004-0.0040.0000.0000.0000.000
173A176VAL00.003-0.00334.366-0.004-0.0040.0000.0000.0000.000
174A177ASN0-0.024-0.01633.591-0.003-0.0030.0000.0000.0000.000
175A178ASN0-0.037-0.03533.401-0.002-0.0020.0000.0000.0000.000
176A179LEU0-0.0050.01236.513-0.002-0.0020.0000.0000.0000.000
177A180LEU00.0290.01038.935-0.002-0.0020.0000.0000.0000.000
178A181LEU0-0.039-0.00437.008-0.002-0.0020.0000.0000.0000.000
179A182GLY00.0610.02840.364-0.002-0.0020.0000.0000.0000.000
180A183CYS0-0.039-0.02442.361-0.001-0.0010.0000.0000.0000.000
181A184ASN0-0.0160.00442.636-0.001-0.0010.0000.0000.0000.000
182A185MET0-0.0040.02144.037-0.001-0.0010.0000.0000.0000.000
183A186ALA0-0.018-0.00845.934-0.001-0.0010.0000.0000.0000.000
184A187SER00.017-0.01048.371-0.001-0.0010.0000.0000.0000.000
185A188LEU0-0.021-0.01047.423-0.001-0.0010.0000.0000.0000.000
186A189ALA0-0.0030.00249.934-0.001-0.0010.0000.0000.0000.000
187A190GLU-1-0.910-0.96251.6220.0140.0140.0000.0000.0000.000
188A191ALA0-0.017-0.00453.452-0.001-0.0010.0000.0000.0000.000
189A192LEU00.014-0.00851.111-0.001-0.0010.0000.0000.0000.000
190A193VAL00.0320.01755.377-0.001-0.0010.0000.0000.0000.000
191A194LEU0-0.0050.00057.684-0.001-0.0010.0000.0000.0000.000
192A195GLY00.0420.00758.5280.0000.0000.0000.0000.0000.000
193A196VAL0-0.005-0.00258.2590.0000.0000.0000.0000.0000.000
194A197LYS10.8530.94160.958-0.008-0.0080.0000.0000.0000.000
195A198CYS0-0.095-0.04663.0440.0000.0000.0000.0000.0000.000
196A199GLY0-0.0100.00164.1350.0000.0000.0000.0000.0000.000
197A200LEU0-0.063-0.03259.7940.0000.0000.0000.0000.0000.000
198A201LYS10.9100.93259.882-0.004-0.0040.0000.0000.0000.000
199A202PRO00.0770.03054.8160.0000.0000.0000.0000.0000.000
200A203GLU-1-0.758-0.87954.6050.0050.0050.0000.0000.0000.000
201A204THR0-0.028-0.00855.2880.0000.0000.0000.0000.0000.000
202A205MET0-0.0290.01054.9270.0000.0000.0000.0000.0000.000
203A206GLN0-0.017-0.03349.0790.0010.0010.0000.0000.0000.000
204A207GLU-1-0.891-0.93851.7390.0060.0060.0000.0000.0000.000
205A208ILE00.0080.00053.6480.0000.0000.0000.0000.0000.000
206A209ILE00.0150.01451.0210.0000.0000.0000.0000.0000.000
207A210GLY00.0460.02349.1840.0010.0010.0000.0000.0000.000
208A211LYS10.7760.88649.085-0.006-0.0060.0000.0000.0000.000
209A212SER0-0.048-0.02651.5060.0000.0000.0000.0000.0000.000
210A213SER0-0.047-0.04250.6330.0000.0000.0000.0000.0000.000
211A214GLY00.0190.01750.2870.0010.0010.0000.0000.0000.000
212A215ARG10.8730.96746.027-0.012-0.0120.0000.0000.0000.000
213A216SER00.0470.00843.7050.0010.0010.0000.0000.0000.000
214A217TYR00.0640.03836.584-0.001-0.0010.0000.0000.0000.000
215A218ALA0-0.014-0.00841.489-0.001-0.0010.0000.0000.0000.000
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