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: 2L2RR

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 OptHSide
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 -3552160.591384
FMO2-HF: Nuclear repulsion 3441899.213979
FMO2-HF: Total energy -110261.377404
FMO2-MP2: Total energy -110569.246068


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.
-11.581-7.7571.038-2.029-2.8330.012
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 : -0.026 / q_NPA : -0.022
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].
3A6LYS10.8490.9252.547-11.856-8.4701.038-1.952-2.4720.012
4A7ILE00.0190.0106.2410.2420.2420.0000.0000.0000.000
5A8GLY00.0580.0379.1540.0050.0050.0000.0000.0000.000
6A9PHE0-0.035-0.02112.520-0.003-0.0030.0000.0000.0000.000
7A10ILE0-0.0030.00515.8440.0030.0030.0000.0000.0000.000
8A11GLY00.0270.01819.190-0.005-0.0050.0000.0000.0000.000
9A12LEU0-0.063-0.03616.883-0.001-0.0010.0000.0000.0000.000
10A13GLY00.0410.02020.879-0.004-0.0040.0000.0000.0000.000
11A14ALA0-0.017-0.02822.990-0.002-0.0020.0000.0000.0000.000
12A15MET0-0.0060.00822.203-0.004-0.0040.0000.0000.0000.000
13A16GLY00.0470.01318.9520.0000.0000.0000.0000.0000.000
14A17LYS11.0021.01217.788-0.013-0.0130.0000.0000.0000.000
15A18PRO0-0.016-0.01117.870-0.006-0.0060.0000.0000.0000.000
16A19MET00.0080.01516.133-0.002-0.0020.0000.0000.0000.000
17A20ALA00.0540.02813.4900.0000.0000.0000.0000.0000.000
18A21ILE0-0.009-0.01212.982-0.019-0.0190.0000.0000.0000.000
19A22ASN0-0.025-0.03114.147-0.022-0.0220.0000.0000.0000.000
20A23LEU00.0270.0189.7800.0060.0060.0000.0000.0000.000
21A24LEU0-0.022-0.0059.437-0.022-0.0220.0000.0000.0000.000
22A25LYS10.8150.92510.709-0.024-0.0240.0000.0000.0000.000
23A26GLU-1-0.918-0.9519.447-0.010-0.0100.0000.0000.0000.000
24A27GLY0-0.044-0.0137.6980.0350.0350.0000.0000.0000.000
25A28VAL0-0.046-0.0144.681-0.433-0.286-0.001-0.007-0.1390.000
26A29THR0-0.038-0.0284.017-0.458-0.1670.001-0.070-0.2220.000
27A30VAL00.0170.0126.0700.0810.0810.0000.0000.0000.000
28A31TYR00.0100.0047.4290.0910.0910.0000.0000.0000.000
29A32ALA0-0.005-0.02311.684-0.014-0.0140.0000.0000.0000.000
30A33PHE00.0190.01415.4290.0080.0080.0000.0000.0000.000
31A34ASP-1-0.804-0.90618.9680.0410.0410.0000.0000.0000.000
32A35LEU00.0020.01122.4160.0010.0010.0000.0000.0000.000
33A36MET0-0.051-0.02125.937-0.003-0.0030.0000.0000.0000.000
34A37GLU-1-0.860-0.93924.2910.0420.0420.0000.0000.0000.000
35A38ALA0-0.015-0.02023.584-0.001-0.0010.0000.0000.0000.000
36A39ASN0-0.049-0.02422.390-0.008-0.0080.0000.0000.0000.000
37A40VAL00.0480.01818.215-0.004-0.0040.0000.0000.0000.000
38A41ALA00.0050.00519.012-0.005-0.0050.0000.0000.0000.000
39A42ALA0-0.036-0.02220.500-0.007-0.0070.0000.0000.0000.000
40A43VAL00.0210.00115.862-0.008-0.0080.0000.0000.0000.000
41A44VAL0-0.0030.00515.609-0.014-0.0140.0000.0000.0000.000
42A45ALA0-0.057-0.01416.392-0.008-0.0080.0000.0000.0000.000
43A46GLN0-0.078-0.04215.319-0.009-0.0090.0000.0000.0000.000
44A47GLY00.0120.01612.647-0.023-0.0230.0000.0000.0000.000
45A48ALA0-0.037-0.00711.368-0.018-0.0180.0000.0000.0000.000
46A49GLN0-0.019-0.0197.8850.0830.0830.0000.0000.0000.000
47A50ALA00.0190.00312.5710.0120.0120.0000.0000.0000.000
48A51CYS0-0.070-0.02814.2670.0350.0350.0000.0000.0000.000
49A52GLU-1-0.879-0.95116.9300.0980.0980.0000.0000.0000.000
50A53ASN0-0.025-0.02319.435-0.005-0.0050.0000.0000.0000.000
51A54ASN00.0730.01318.9130.0100.0100.0000.0000.0000.000
52A55GLN00.0170.01618.3610.0110.0110.0000.0000.0000.000
53A56LYN00.0130.02216.3620.0170.0170.0000.0000.0000.000
54A57VAL0-0.0090.00313.8650.0360.0360.0000.0000.0000.000
55A58ALA0-0.025-0.02013.4790.0260.0260.0000.0000.0000.000
56A59ALA0-0.0070.00214.2700.0190.0190.0000.0000.0000.000
57A60ALA0-0.062-0.02010.2190.0670.0670.0000.0000.0000.000
58A61SER0-0.065-0.0449.0820.1180.1180.0000.0000.0000.000
59A62ASP-1-0.830-0.9066.4500.3430.3430.0000.0000.0000.000
60A63ILE0-0.021-0.0169.441-0.011-0.0110.0000.0000.0000.000
61A64ILE0-0.0060.00711.626-0.021-0.0210.0000.0000.0000.000
62A65PHE00.0140.00612.093-0.002-0.0020.0000.0000.0000.000
63A66THR0-0.011-0.01916.563-0.002-0.0020.0000.0000.0000.000
64A67SER0-0.017-0.00720.172-0.003-0.0030.0000.0000.0000.000
65A68LEU0-0.0050.00923.422-0.003-0.0030.0000.0000.0000.000
66A69PRO0-0.005-0.01626.490-0.002-0.0020.0000.0000.0000.000
67A70ASN0-0.004-0.01430.195-0.001-0.0010.0000.0000.0000.000
68A71ALA00.1320.05730.2780.0030.0030.0000.0000.0000.000
69A72GLY00.0200.02331.1520.0020.0020.0000.0000.0000.000
70A73ILE0-0.016-0.01528.2450.0020.0020.0000.0000.0000.000
71A74VAL00.0520.03425.7600.0040.0040.0000.0000.0000.000
72A75GLU-1-0.837-0.92127.0120.0540.0540.0000.0000.0000.000
73A76THR0-0.072-0.03728.9580.0030.0030.0000.0000.0000.000
74A77VAL0-0.036-0.01523.5660.0040.0040.0000.0000.0000.000
75A78MET0-0.029-0.01020.3220.0080.0080.0000.0000.0000.000
76A79ASN00.012-0.01924.8470.0100.0100.0000.0000.0000.000
77A80GLY0-0.0110.02127.629-0.002-0.0020.0000.0000.0000.000
78A81PRO0-0.028-0.03928.0560.0050.0050.0000.0000.0000.000
79A82GLY0-0.0150.00426.2700.0000.0000.0000.0000.0000.000
80A83GLY00.0450.04924.8750.0040.0040.0000.0000.0000.000
81A84VAL00.009-0.02619.0090.0100.0100.0000.0000.0000.000
82A85LEU00.002-0.00120.1950.0140.0140.0000.0000.0000.000
83A86SER0-0.039-0.02021.0200.0040.0040.0000.0000.0000.000
84A87ALA0-0.047-0.01618.9830.0050.0050.0000.0000.0000.000
85A88CYS0-0.0420.00216.2310.0270.0270.0000.0000.0000.000
86A89LYS10.9620.99312.861-0.295-0.2950.0000.0000.0000.000
87A90ALA00.0380.02215.493-0.012-0.0120.0000.0000.0000.000
88A91GLY0-0.010-0.01014.2410.0190.0190.0000.0000.0000.000
89A92THR0-0.016-0.01313.0900.0110.0110.0000.0000.0000.000
90A93VAL0-0.031-0.02213.239-0.019-0.0190.0000.0000.0000.000
91A94ILE0-0.027-0.02014.7200.0060.0060.0000.0000.0000.000
92A95VAL00.005-0.01015.400-0.006-0.0060.0000.0000.0000.000
93A96ASP-1-0.742-0.82018.2510.0600.0600.0000.0000.0000.000
94A97MET0-0.041-0.02418.785-0.004-0.0040.0000.0000.0000.000
95A98SER0-0.021-0.04722.891-0.006-0.0060.0000.0000.0000.000
96A99SER0-0.0250.00526.061-0.001-0.0010.0000.0000.0000.000
97A100VAL00.007-0.01428.072-0.002-0.0020.0000.0000.0000.000
98A101SER00.0380.00330.8350.0010.0010.0000.0000.0000.000
99A102PRO00.0330.00730.4450.0020.0020.0000.0000.0000.000
100A103SER0-0.058-0.05630.6760.0030.0030.0000.0000.0000.000
101A104SER00.009-0.00129.6580.0020.0020.0000.0000.0000.000
102A105THR0-0.014-0.02825.3200.0040.0040.0000.0000.0000.000
103A106LEU0-0.018-0.00627.2340.0030.0030.0000.0000.0000.000
104A107LYS10.8140.90929.153-0.043-0.0430.0000.0000.0000.000
105A108MET0-0.0160.00525.4390.0020.0020.0000.0000.0000.000
106A109ALA00.0810.02924.5030.0050.0050.0000.0000.0000.000
107A110LYS10.9100.96525.234-0.042-0.0420.0000.0000.0000.000
108A111VAL00.0130.00826.4900.0010.0010.0000.0000.0000.000
109A112ALA00.0020.00121.9080.0040.0040.0000.0000.0000.000
110A113ALA00.0480.02222.7900.0060.0060.0000.0000.0000.000
111A114GLU-1-0.945-0.95023.8550.0660.0660.0000.0000.0000.000
112A115LYS10.7990.89421.981-0.081-0.0810.0000.0000.0000.000
113A116GLY0-0.015-0.00620.2630.0120.0120.0000.0000.0000.000
114A117ILE0-0.064-0.01417.9180.0080.0080.0000.0000.0000.000
115A118ASP-1-0.829-0.90916.3410.0840.0840.0000.0000.0000.000
116A119TYR0-0.043-0.06618.5220.0100.0100.0000.0000.0000.000
117A120VAL0-0.007-0.00718.465-0.006-0.0060.0000.0000.0000.000
118A121ASP-1-0.720-0.82421.2370.0550.0550.0000.0000.0000.000
119A122ALA00.008-0.01920.1210.0010.0010.0000.0000.0000.000
120A123PRO00.0270.03521.9650.0000.0000.0000.0000.0000.000
121A124VAL00.0450.02221.1050.0000.0000.0000.0000.0000.000
122A125SER0-0.028-0.02524.431-0.003-0.0030.0000.0000.0000.000
123A126GLY00.0570.02325.6670.0010.0010.0000.0000.0000.000
124A127GLY0-0.019-0.00327.026-0.003-0.0030.0000.0000.0000.000
125A128THR00.0830.00825.1470.0020.0020.0000.0000.0000.000
126A129LYS10.8300.90824.810-0.009-0.0090.0000.0000.0000.000
127A130GLY00.0470.03124.800-0.002-0.0020.0000.0000.0000.000
128A131ALA00.0180.00021.2980.0020.0020.0000.0000.0000.000
129A132GLU-1-0.872-0.93820.1950.0100.0100.0000.0000.0000.000
130A133ALA0-0.034-0.00820.749-0.003-0.0030.0000.0000.0000.000
131A134GLY00.0540.04918.849-0.001-0.0010.0000.0000.0000.000
132A135THR0-0.037-0.03619.6050.0040.0040.0000.0000.0000.000
133A136LEU0-0.070-0.02220.035-0.002-0.0020.0000.0000.0000.000
134A137THR0-0.0130.00722.2120.0030.0030.0000.0000.0000.000
135A138ILE00.009-0.00318.439-0.001-0.0010.0000.0000.0000.000
136A139MET0-0.055-0.01322.588-0.001-0.0010.0000.0000.0000.000
137A140VAL00.011-0.00619.8250.0010.0010.0000.0000.0000.000
138A141GLY00.0000.01123.017-0.005-0.0050.0000.0000.0000.000
139A142ALA0-0.015-0.01920.3800.0050.0050.0000.0000.0000.000
140A143SER00.0590.02720.681-0.004-0.0040.0000.0000.0000.000
141A144GLU-1-0.835-0.91720.6680.0490.0490.0000.0000.0000.000
142A145ALA00.0400.01917.8660.0060.0060.0000.0000.0000.000
143A146VAL0-0.005-0.00516.1970.0110.0110.0000.0000.0000.000
144A147PHE00.0050.00115.9250.0190.0190.0000.0000.0000.000
145A148GLU-1-0.905-0.96515.5160.0640.0640.0000.0000.0000.000
146A149LYS10.7640.88911.451-0.087-0.0870.0000.0000.0000.000
147A150ILE00.008-0.00211.3280.0640.0640.0000.0000.0000.000
148A151GLN0-0.0040.00713.2730.0260.0260.0000.0000.0000.000
149A152PRO00.0070.01110.126-0.009-0.0090.0000.0000.0000.000
150A153VAL00.0160.0078.6210.0070.0070.0000.0000.0000.000
151A154LEU00.008-0.01811.220-0.050-0.0500.0000.0000.0000.000
152A155SER0-0.052-0.04114.503-0.032-0.0320.0000.0000.0000.000
153A156VAL0-0.0340.01610.524-0.015-0.0150.0000.0000.0000.000
154A157ILE0-0.042-0.01913.763-0.029-0.0290.0000.0000.0000.000
155A158GLY0-0.021-0.01516.169-0.014-0.0140.0000.0000.0000.000
156A159LYS10.8930.95018.602-0.021-0.0210.0000.0000.0000.000
157A160ASP-1-0.886-0.92521.2680.0330.0330.0000.0000.0000.000
158A161ILE00.0090.00718.164-0.001-0.0010.0000.0000.0000.000
159A162TYR0-0.040-0.03021.553-0.002-0.0020.0000.0000.0000.000
160A163HIS10.8320.91922.073-0.045-0.0450.0000.0000.0000.000
161A164VAL0-0.028-0.01923.784-0.005-0.0050.0000.0000.0000.000
162A165GLY00.0080.00826.078-0.005-0.0050.0000.0000.0000.000
163A166ASP-1-0.867-0.91225.5550.0490.0490.0000.0000.0000.000
164A167THR0-0.054-0.05625.0810.0010.0010.0000.0000.0000.000
165A168GLY00.002-0.01126.365-0.004-0.0040.0000.0000.0000.000
166A169ALA0-0.019-0.00927.753-0.003-0.0030.0000.0000.0000.000
167A170GLY00.0350.00825.995-0.003-0.0030.0000.0000.0000.000
168A171ASP-1-0.812-0.91727.0270.0460.0460.0000.0000.0000.000
169A172ALA0-0.038-0.01729.037-0.003-0.0030.0000.0000.0000.000
170A173VAL0-0.022-0.00929.158-0.003-0.0030.0000.0000.0000.000
171A174LYS10.9010.95228.279-0.035-0.0350.0000.0000.0000.000
172A175ILE00.0040.00831.308-0.002-0.0020.0000.0000.0000.000
173A176VAL0-0.004-0.00334.258-0.002-0.0020.0000.0000.0000.000
174A177ASN0-0.035-0.02333.671-0.003-0.0030.0000.0000.0000.000
175A178ASN0-0.040-0.05133.069-0.002-0.0020.0000.0000.0000.000
176A179LEU00.0090.02436.460-0.001-0.0010.0000.0000.0000.000
177A180LEU00.0270.01438.893-0.001-0.0010.0000.0000.0000.000
178A181LEU0-0.037-0.00536.994-0.001-0.0010.0000.0000.0000.000
179A182GLY00.0580.02640.295-0.001-0.0010.0000.0000.0000.000
180A183CYS0-0.033-0.02342.163-0.001-0.0010.0000.0000.0000.000
181A184ASN0-0.021-0.00342.476-0.001-0.0010.0000.0000.0000.000
182A185MET0-0.0080.02143.836-0.001-0.0010.0000.0000.0000.000
183A186ALA0-0.008-0.00645.741-0.001-0.0010.0000.0000.0000.000
184A187SER00.002-0.01248.164-0.001-0.0010.0000.0000.0000.000
185A188LEU0-0.016-0.00647.335-0.001-0.0010.0000.0000.0000.000
186A189ALA0-0.006-0.00449.723-0.001-0.0010.0000.0000.0000.000
187A190GLU-1-0.921-0.96551.3850.0100.0100.0000.0000.0000.000
188A191ALA0-0.016-0.00753.270-0.001-0.0010.0000.0000.0000.000
189A192LEU00.002-0.01250.953-0.001-0.0010.0000.0000.0000.000
190A193VAL00.0530.02355.2030.0000.0000.0000.0000.0000.000
191A194LEU0-0.0120.00157.5930.0000.0000.0000.0000.0000.000
192A195GLY00.0420.00858.5240.0000.0000.0000.0000.0000.000
193A196VAL00.0060.00858.0940.0000.0000.0000.0000.0000.000
194A197LYS10.9150.97460.821-0.007-0.0070.0000.0000.0000.000
195A198CYS0-0.122-0.06563.0110.0000.0000.0000.0000.0000.000
196A199GLY0-0.018-0.00464.1650.0000.0000.0000.0000.0000.000
197A200LEU0-0.063-0.02959.9240.0000.0000.0000.0000.0000.000
198A201LYS10.9150.94459.875-0.004-0.0040.0000.0000.0000.000
199A202PRO00.0940.02854.6430.0000.0000.0000.0000.0000.000
200A203GLU-1-0.770-0.89054.8740.0050.0050.0000.0000.0000.000
201A204THR0-0.025-0.00755.6490.0000.0000.0000.0000.0000.000
202A205MET0-0.0160.01355.0010.0000.0000.0000.0000.0000.000
203A206GLN0-0.024-0.03248.4880.0000.0000.0000.0000.0000.000
204A207GLU-1-0.951-0.96851.8730.0030.0030.0000.0000.0000.000
205A208ILE00.0140.00553.5920.0000.0000.0000.0000.0000.000
206A209ILE00.0090.00751.2150.0000.0000.0000.0000.0000.000
207A210GLY00.0580.03849.3000.0000.0000.0000.0000.0000.000
208A211LYS10.8020.90049.143-0.004-0.0040.0000.0000.0000.000
209A212SER0-0.031-0.02851.5730.0000.0000.0000.0000.0000.000
210A213SER0-0.039-0.03350.6590.0000.0000.0000.0000.0000.000
211A214GLY00.0100.01250.3140.0000.0000.0000.0000.0000.000
212A215ARG10.8810.97246.098-0.006-0.0060.0000.0000.0000.000
213A216SER00.0420.00343.9800.0010.0010.0000.0000.0000.000
214A217TYR00.0790.04136.8550.0000.0000.0000.0000.0000.000
215A218ALA0-0.012-0.00241.6420.0000.0000.0000.0000.0000.000
216A219MET0-0.006-0.00542.8500.0000.0000.0000.0000.0000.000
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