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: 7MGNK

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 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 297
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3551577.585509
FMO2-HF: Nuclear repulsion 3441317.584725
FMO2-HF: Total energy -110260.000784
FMO2-MP2: Total energy -110567.92775


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.
-1.0270.2872.323-1.24-2.3990.003
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 : -0.038 / q_NPA : -0.040
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].
3A6LYS10.8880.9642.1012.5183.4972.325-1.205-2.1000.003
4A7ILE00.0240.0156.0590.7010.7010.0000.0000.0000.000
5A8GLY00.0560.0339.1830.0110.0110.0000.0000.0000.000
6A9PHE0-0.031-0.02112.4380.0820.0820.0000.0000.0000.000
7A10ILE00.0030.00615.8600.0150.0150.0000.0000.0000.000
8A11GLY00.0050.00719.2020.0320.0320.0000.0000.0000.000
9A12LEU0-0.064-0.04816.872-0.016-0.0160.0000.0000.0000.000
10A13GLY00.0300.01620.8930.0180.0180.0000.0000.0000.000
11A14ALA0-0.009-0.02323.015-0.001-0.0010.0000.0000.0000.000
12A15MET0-0.0010.00822.2070.0080.0080.0000.0000.0000.000
13A16GLY00.0590.01419.006-0.001-0.0010.0000.0000.0000.000
14A17LYS10.9921.01017.8200.0910.0910.0000.0000.0000.000
15A18PRO0-0.012-0.00617.894-0.011-0.0110.0000.0000.0000.000
16A19MET00.0100.02316.1390.0160.0160.0000.0000.0000.000
17A20ALA00.0530.02513.522-0.002-0.0020.0000.0000.0000.000
18A21ILE0-0.006-0.00913.006-0.014-0.0140.0000.0000.0000.000
19A22ASN0-0.025-0.01914.1740.0220.0220.0000.0000.0000.000
20A23LEU00.0370.0319.7290.0370.0370.0000.0000.0000.000
21A24LEU0-0.027-0.0049.4760.0270.0270.0000.0000.0000.000
22A25LYS10.8320.91210.7160.0520.0520.0000.0000.0000.000
23A26GLU-1-0.930-0.9489.4540.2170.2170.0000.0000.0000.000
24A27GLY0-0.058-0.0207.7050.1550.1550.0000.0000.0000.000
25A28VAL0-0.029-0.0034.712-0.235-0.101-0.001-0.007-0.1270.000
26A29THR0-0.057-0.0424.355-0.267-0.066-0.001-0.028-0.1720.000
27A30VAL00.0250.0186.044-0.246-0.2460.0000.0000.0000.000
28A31TYR00.0170.0007.3520.0350.0350.0000.0000.0000.000
29A32ALA0-0.012-0.02411.8060.0270.0270.0000.0000.0000.000
30A33PHE00.0290.01615.5590.0240.0240.0000.0000.0000.000
31A34ASP-1-0.813-0.91019.077-0.167-0.1670.0000.0000.0000.000
32A35LEU00.0030.01022.5400.0050.0050.0000.0000.0000.000
33A36MET0-0.049-0.02026.0390.0140.0140.0000.0000.0000.000
34A37GLU-1-0.864-0.94124.441-0.122-0.1220.0000.0000.0000.000
35A38ALA0-0.011-0.01723.770-0.008-0.0080.0000.0000.0000.000
36A39ASN0-0.022-0.00522.3940.0100.0100.0000.0000.0000.000
37A40VAL00.0510.02518.370-0.012-0.0120.0000.0000.0000.000
38A41ALA00.012-0.00919.205-0.012-0.0120.0000.0000.0000.000
39A42ALA0-0.034-0.01920.6160.0040.0040.0000.0000.0000.000
40A43VAL00.010-0.00815.8290.0100.0100.0000.0000.0000.000
41A44VAL0-0.0030.01215.846-0.012-0.0120.0000.0000.0000.000
42A45ALA0-0.051-0.01016.6420.0050.0050.0000.0000.0000.000
43A46GLN0-0.077-0.03815.2970.0330.0330.0000.0000.0000.000
44A47GLY00.0090.01312.6070.0030.0030.0000.0000.0000.000
45A48ALA0-0.049-0.01211.611-0.067-0.0670.0000.0000.0000.000
46A49GLN0-0.016-0.0168.3490.1060.1060.0000.0000.0000.000
47A50ALA00.0160.00112.739-0.041-0.0410.0000.0000.0000.000
48A51CYS0-0.059-0.01914.399-0.036-0.0360.0000.0000.0000.000
49A52GLU-1-0.916-0.96417.008-0.154-0.1540.0000.0000.0000.000
50A53ASN00.0110.00519.472-0.001-0.0010.0000.0000.0000.000
51A54ASN00.0850.01818.941-0.041-0.0410.0000.0000.0000.000
52A55GLN00.0110.01218.029-0.035-0.0350.0000.0000.0000.000
53A56LYN00.0130.01215.961-0.041-0.0410.0000.0000.0000.000
54A57VAL0-0.016-0.00113.868-0.067-0.0670.0000.0000.0000.000
55A58ALA0-0.025-0.02313.091-0.122-0.1220.0000.0000.0000.000
56A59ALA0-0.0040.00113.264-0.070-0.0700.0000.0000.0000.000
57A60ALA0-0.065-0.02210.081-0.034-0.0340.0000.0000.0000.000
58A61SER0-0.073-0.0428.398-0.400-0.4000.0000.0000.0000.000
59A62ASP-1-0.823-0.9115.401-3.619-3.6190.0000.0000.0000.000
60A63ILE0-0.019-0.0148.9530.3380.3380.0000.0000.0000.000
61A64ILE0-0.0100.00211.393-0.065-0.0650.0000.0000.0000.000
62A65PHE00.0130.00712.1610.0830.0830.0000.0000.0000.000
63A66THR0-0.006-0.01016.610-0.002-0.0020.0000.0000.0000.000
64A67SER0-0.018-0.00620.2130.0210.0210.0000.0000.0000.000
65A68LEU00.0030.00523.4680.0060.0060.0000.0000.0000.000
66A69PRO00.008-0.00226.5280.0090.0090.0000.0000.0000.000
67A70ASN0-0.003-0.02130.2350.0070.0070.0000.0000.0000.000
68A71ALA00.1420.06330.219-0.008-0.0080.0000.0000.0000.000
69A72GLY00.0340.03330.717-0.004-0.0040.0000.0000.0000.000
70A73ILE0-0.017-0.02228.057-0.003-0.0030.0000.0000.0000.000
71A74VAL00.0470.02925.329-0.010-0.0100.0000.0000.0000.000
72A75GLU-1-0.918-0.96126.392-0.110-0.1100.0000.0000.0000.000
73A76THR0-0.061-0.02528.086-0.003-0.0030.0000.0000.0000.000
74A77VAL0-0.039-0.01623.007-0.006-0.0060.0000.0000.0000.000
75A78MET0-0.036-0.00720.147-0.021-0.0210.0000.0000.0000.000
76A79ASN00.010-0.02423.842-0.018-0.0180.0000.0000.0000.000
77A80GLY0-0.0180.02126.5250.0090.0090.0000.0000.0000.000
78A81PRO0-0.027-0.04027.101-0.009-0.0090.0000.0000.0000.000
79A82GLY0-0.0240.00425.355-0.001-0.0010.0000.0000.0000.000
80A83GLY00.0500.05024.095-0.011-0.0110.0000.0000.0000.000
81A84VAL00.034-0.00818.136-0.015-0.0150.0000.0000.0000.000
82A85LEU00.014-0.00419.072-0.028-0.0280.0000.0000.0000.000
83A86SER0-0.129-0.06019.837-0.004-0.0040.0000.0000.0000.000
84A87ALA00.0170.01517.9860.0080.0080.0000.0000.0000.000
85A88CYS0-0.0330.00815.097-0.055-0.0550.0000.0000.0000.000
86A89LYS10.9640.99512.0010.4070.4070.0000.0000.0000.000
87A90ALA00.0300.01614.360-0.023-0.0230.0000.0000.0000.000
88A91GLY0-0.034-0.02513.256-0.048-0.0480.0000.0000.0000.000
89A92THR0-0.052-0.03511.916-0.096-0.0960.0000.0000.0000.000
90A93VAL0-0.009-0.00612.6440.1100.1100.0000.0000.0000.000
91A94ILE0-0.031-0.02514.256-0.069-0.0690.0000.0000.0000.000
92A95VAL00.007-0.00715.6350.0460.0460.0000.0000.0000.000
93A96ASP-1-0.756-0.83918.284-0.167-0.1670.0000.0000.0000.000
94A97MET0-0.054-0.03318.4740.0250.0250.0000.0000.0000.000
95A98SER0-0.031-0.04522.9570.0140.0140.0000.0000.0000.000
96A99SER0-0.053-0.01126.1190.0070.0070.0000.0000.0000.000
97A100VAL0-0.013-0.01828.1950.0030.0030.0000.0000.0000.000
98A101SER00.0400.02530.8990.0010.0010.0000.0000.0000.000
99A102PRO00.0420.00830.436-0.006-0.0060.0000.0000.0000.000
100A103SER0-0.018-0.04330.454-0.008-0.0080.0000.0000.0000.000
101A104SER0-0.055-0.02829.217-0.006-0.0060.0000.0000.0000.000
102A105THR00.010-0.01825.116-0.011-0.0110.0000.0000.0000.000
103A106LEU0-0.017-0.00526.741-0.009-0.0090.0000.0000.0000.000
104A107LYS10.9060.95228.4760.0800.0800.0000.0000.0000.000
105A108MET0-0.0060.00924.708-0.004-0.0040.0000.0000.0000.000
106A109ALA00.0820.02723.722-0.013-0.0130.0000.0000.0000.000
107A110LYS10.9010.95924.4090.0750.0750.0000.0000.0000.000
108A111VAL00.0160.01224.8930.0000.0000.0000.0000.0000.000
109A112ALA0-0.032-0.01020.816-0.007-0.0070.0000.0000.0000.000
110A113ALA00.0400.01821.567-0.012-0.0120.0000.0000.0000.000
111A114GLU-1-1.006-0.99122.831-0.115-0.1150.0000.0000.0000.000
112A115LYS10.8800.94020.7270.1880.1880.0000.0000.0000.000
113A116GLY0-0.019-0.01019.049-0.024-0.0240.0000.0000.0000.000
114A117ILE0-0.074-0.01716.696-0.034-0.0340.0000.0000.0000.000
115A118ASP-1-0.888-0.93716.570-0.180-0.1800.0000.0000.0000.000
116A119TYR0-0.058-0.07017.826-0.044-0.0440.0000.0000.0000.000
117A120VAL00.005-0.00218.5070.0260.0260.0000.0000.0000.000
118A121ASP-1-0.726-0.82621.139-0.104-0.1040.0000.0000.0000.000
119A122ALA00.004-0.02220.2370.0130.0130.0000.0000.0000.000
120A123PRO00.0330.04022.045-0.004-0.0040.0000.0000.0000.000
121A124VAL00.0600.02921.2410.0120.0120.0000.0000.0000.000
122A125SER0-0.047-0.02524.512-0.001-0.0010.0000.0000.0000.000
123A126GLY00.0870.04025.7490.0030.0030.0000.0000.0000.000
124A127GLY0-0.027-0.00727.0810.0030.0030.0000.0000.0000.000
125A128THR00.0760.00725.1950.0000.0000.0000.0000.0000.000
126A129LYS10.9890.99724.8630.0280.0280.0000.0000.0000.000
127A130GLY00.0440.03124.8700.0040.0040.0000.0000.0000.000
128A131ALA00.008-0.00321.3640.0030.0030.0000.0000.0000.000
129A132GLU-1-0.994-1.01220.254-0.054-0.0540.0000.0000.0000.000
130A133ALA0-0.060-0.02520.8020.0030.0030.0000.0000.0000.000
131A134GLY00.0470.04118.9220.0120.0120.0000.0000.0000.000
132A135THR0-0.065-0.04419.6790.0110.0110.0000.0000.0000.000
133A136LEU0-0.039-0.01120.2180.0000.0000.0000.0000.0000.000
134A137THR00.0020.01522.3040.0120.0120.0000.0000.0000.000
135A138ILE0-0.002-0.00718.606-0.013-0.0130.0000.0000.0000.000
136A139MET0-0.061-0.01622.6830.0140.0140.0000.0000.0000.000
137A140VAL00.0190.00019.879-0.012-0.0120.0000.0000.0000.000
138A141GLY0-0.0040.00723.0170.0140.0140.0000.0000.0000.000
139A142ALA0-0.020-0.02220.513-0.017-0.0170.0000.0000.0000.000
140A143SER00.0770.03620.6150.0180.0180.0000.0000.0000.000
141A144GLU-1-0.891-0.95820.7660.0210.0210.0000.0000.0000.000
142A145ALA00.0350.01417.8980.0090.0090.0000.0000.0000.000
143A146VAL0-0.002-0.00216.3010.0070.0070.0000.0000.0000.000
144A147PHE00.004-0.00316.023-0.012-0.0120.0000.0000.0000.000
145A148GLU-1-0.897-0.95915.6490.0890.0890.0000.0000.0000.000
146A149LYS10.8990.96111.1210.3710.3710.0000.0000.0000.000
147A150ILE00.002-0.00711.4310.0380.0380.0000.0000.0000.000
148A151GLN00.0020.01313.2910.0480.0480.0000.0000.0000.000
149A152PRO00.0140.00610.1160.0000.0000.0000.0000.0000.000
150A153VAL00.0000.0038.7130.0230.0230.0000.0000.0000.000
151A154LEU00.014-0.01911.321-0.042-0.0420.0000.0000.0000.000
152A155SER0-0.055-0.04114.516-0.016-0.0160.0000.0000.0000.000
153A156VAL0-0.0270.02511.494-0.004-0.0040.0000.0000.0000.000
154A157ILE0-0.049-0.02813.810-0.029-0.0290.0000.0000.0000.000
155A158GLY0-0.025-0.01416.249-0.017-0.0170.0000.0000.0000.000
156A159LYS10.9420.98618.698-0.015-0.0150.0000.0000.0000.000
157A160ASP-1-0.926-0.95821.3730.0370.0370.0000.0000.0000.000
158A161ILE0-0.011-0.00418.289-0.018-0.0180.0000.0000.0000.000
159A162TYR00.000-0.00721.6060.0110.0110.0000.0000.0000.000
160A163HIS10.8510.94222.1340.0060.0060.0000.0000.0000.000
161A164VAL0-0.036-0.01823.7840.0060.0060.0000.0000.0000.000
162A165GLY00.0120.00626.1470.0030.0030.0000.0000.0000.000
163A166ASP-1-0.851-0.91525.654-0.063-0.0630.0000.0000.0000.000
164A167THR0-0.055-0.04425.011-0.005-0.0050.0000.0000.0000.000
165A168GLY0-0.008-0.01126.4400.0060.0060.0000.0000.0000.000
166A169ALA0-0.007-0.00327.8820.0040.0040.0000.0000.0000.000
167A170GLY00.0310.00726.0840.0080.0080.0000.0000.0000.000
168A171ASP-1-0.791-0.91827.118-0.091-0.0910.0000.0000.0000.000
169A172ALA0-0.047-0.01729.1190.0050.0050.0000.0000.0000.000
170A173VAL0-0.017-0.00829.2460.0040.0040.0000.0000.0000.000
171A174LYS10.8670.92128.2940.0600.0600.0000.0000.0000.000
172A175ILE00.0010.00831.3940.0030.0030.0000.0000.0000.000
173A176VAL0-0.006-0.00434.3400.0030.0030.0000.0000.0000.000
174A177ASN0-0.029-0.01633.7900.0060.0060.0000.0000.0000.000
175A178ASN00.011-0.01332.7530.0050.0050.0000.0000.0000.000
176A179LEU0-0.0020.01836.5420.0010.0010.0000.0000.0000.000
177A180LEU00.0150.00738.9200.0020.0020.0000.0000.0000.000
178A181LEU0-0.039-0.00137.1690.0020.0020.0000.0000.0000.000
179A182GLY00.0520.01940.3780.0010.0010.0000.0000.0000.000
180A183CYS0-0.018-0.01442.2410.0010.0010.0000.0000.0000.000
181A184ASN0-0.021-0.01042.6730.0010.0010.0000.0000.0000.000
182A185MET0-0.0080.01843.8960.0010.0010.0000.0000.0000.000
183A186ALA00.0050.00045.8200.0010.0010.0000.0000.0000.000
184A187SER0-0.001-0.00648.2410.0010.0010.0000.0000.0000.000
185A188LEU0-0.018-0.00147.3860.0010.0010.0000.0000.0000.000
186A189ALA0-0.007-0.00549.8500.0010.0010.0000.0000.0000.000
187A190GLU-1-0.924-0.96651.460-0.017-0.0170.0000.0000.0000.000
188A191ALA0-0.009-0.00253.3730.0010.0010.0000.0000.0000.000
189A192LEU0-0.003-0.01751.0410.0010.0010.0000.0000.0000.000
190A193VAL00.0570.02755.2820.0010.0010.0000.0000.0000.000
191A194LEU0-0.014-0.00157.6670.0010.0010.0000.0000.0000.000
192A195GLY00.0340.00158.6060.0010.0010.0000.0000.0000.000
193A196VAL00.0070.01158.1010.0010.0010.0000.0000.0000.000
194A197LYS10.9190.97560.8970.0130.0130.0000.0000.0000.000
195A198CYS0-0.126-0.06663.0890.0000.0000.0000.0000.0000.000
196A199GLY0-0.018-0.00464.2550.0010.0010.0000.0000.0000.000
197A200LEU0-0.071-0.02959.8220.0010.0010.0000.0000.0000.000
198A201LYS10.9780.98859.7720.0070.0070.0000.0000.0000.000
199A202PRO00.0930.02554.7570.0000.0000.0000.0000.0000.000
200A203GLU-1-0.821-0.92854.958-0.009-0.0090.0000.0000.0000.000
201A204THR0-0.024-0.00555.7310.0000.0000.0000.0000.0000.000
202A205MET0-0.0200.01055.0240.0000.0000.0000.0000.0000.000
203A206GLN0-0.016-0.02548.2950.0000.0000.0000.0000.0000.000
204A207GLU-1-0.982-0.98251.959-0.004-0.0040.0000.0000.0000.000
205A208ILE00.002-0.00853.6810.0010.0010.0000.0000.0000.000
206A209ILE00.0030.00851.0980.0010.0010.0000.0000.0000.000
207A210GLY00.0540.03449.3900.0000.0000.0000.0000.0000.000
208A211LYS10.8740.94249.2360.0040.0040.0000.0000.0000.000
209A212SER0-0.045-0.03951.6670.0010.0010.0000.0000.0000.000
210A213SER0-0.034-0.03350.7550.0000.0000.0000.0000.0000.000
211A214GLY00.0140.01450.4110.0000.0000.0000.0000.0000.000
212A215ARG10.8740.97146.3240.0030.0030.0000.0000.0000.000
213A216SER00.0410.00544.075-0.001-0.0010.0000.0000.0000.000
214A217TYR00.0910.04636.893-0.001-0.0010.0000.0000.0000.000
215A218ALA0-0.0080.00141.731-0.001-0.0010.0000.0000.0000.000
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