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: RY938

Calculation Name: 1B6U-A-Xray372

Preferred Name: Killer cell immunoglobulin-like receptor 2DL3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1B6U

Chain ID: A

ChEMBL ID: CHEMBL3713026

UniProt ID: P43628

Base Structure: X-ray

Registration Date: 2023-09-27

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2015070.284487
FMO2-HF: Nuclear repulsion 1937985.450834
FMO2-HF: Total energy -77084.833653
FMO2-MP2: Total energy -77308.819799


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:5:HIS)


Summations of interaction energy for fragment #1(A:5:HIS)
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.
-29.185-21.38111.736-6.877-12.667-0.056
Interaction energy analysis for fragmet #1(A:5:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.037
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].
3A7LYS10.8610.9373.853-1.372-0.039-0.013-0.635-0.6850.002
4A8PRO0-0.042-0.0106.8150.7960.7960.0000.0000.0000.000
5A9SER0-0.012-0.0089.121-0.250-0.2500.0000.0000.0000.000
6A10LEU00.006-0.01112.583-0.119-0.1190.0000.0000.0000.000
7A11LEU0-0.0190.00415.3550.0180.0180.0000.0000.0000.000
8A12ALA00.0250.00518.886-0.065-0.0650.0000.0000.0000.000
9A13HIS0-0.0330.00121.4550.0720.0720.0000.0000.0000.000
10A14PRO00.0550.01624.664-0.027-0.0270.0000.0000.0000.000
11A15GLY00.0250.00325.5960.0330.0330.0000.0000.0000.000
12A16PRO00.016-0.00124.286-0.026-0.0260.0000.0000.0000.000
13A17LEU00.0010.01826.285-0.030-0.0300.0000.0000.0000.000
14A18VAL0-0.0030.01327.2000.0100.0100.0000.0000.0000.000
15A19LYS10.8270.90130.381-0.020-0.0200.0000.0000.0000.000
16A20SER00.043-0.01332.904-0.011-0.0110.0000.0000.0000.000
17A21GLU-1-0.892-0.90934.111-0.063-0.0630.0000.0000.0000.000
18A22GLU-1-0.879-0.93331.0260.0110.0110.0000.0000.0000.000
19A23THR0-0.064-0.04927.072-0.016-0.0160.0000.0000.0000.000
20A24VAL0-0.003-0.00224.0260.0270.0270.0000.0000.0000.000
21A25ILE0-0.014-0.01120.747-0.032-0.0320.0000.0000.0000.000
22A26LEU00.0220.00117.9610.0480.0480.0000.0000.0000.000
23A27GLN0-0.0010.00317.072-0.042-0.0420.0000.0000.0000.000
24A28CYS0-0.0280.00611.356-0.035-0.0350.0000.0000.0000.000
25A29TRP00.004-0.00611.8820.0350.0350.0000.0000.0000.000
26A30SER0-0.020-0.0187.7060.6010.6010.0000.0000.0000.000
27A31ASP-1-0.706-0.8098.6033.9133.9130.0000.0000.0000.000
28A32VAL0-0.0270.0064.371-0.249-0.028-0.001-0.027-0.1930.000
29A33ARG10.9360.9747.503-2.064-2.0640.0000.0000.0000.000
30A34PHE0-0.023-0.0112.291-1.733-0.8290.931-0.529-1.3070.003
31A35GLN0-0.021-0.0146.6170.0660.0660.0000.0000.0000.000
32A36HIS0-0.0030.0117.5200.2970.2970.0000.0000.0000.000
33A37PHE00.0370.0137.365-0.254-0.2540.0000.0000.0000.000
34A38LEU0-0.016-0.0118.940-0.057-0.0570.0000.0000.0000.000
35A39LEU0-0.001-0.00311.3570.0970.0970.0000.0000.0000.000
36A40HIS00.0130.02814.1470.0460.0460.0000.0000.0000.000
37A41ARG10.8270.90715.6470.4890.4890.0000.0000.0000.000
38A42GLU-1-0.838-0.91319.010-0.653-0.6530.0000.0000.0000.000
39A43GLY00.001-0.00720.5660.0640.0640.0000.0000.0000.000
40A44LYS10.7490.85624.2960.1850.1850.0000.0000.0000.000
41A45PHE00.0110.02325.035-0.010-0.0100.0000.0000.0000.000
42A46LYS10.8180.89318.9260.6820.6820.0000.0000.0000.000
43A47ASP-1-0.798-0.87320.319-0.545-0.5450.0000.0000.0000.000
44A48THR0-0.094-0.07813.941-0.116-0.1160.0000.0000.0000.000
45A49LEU00.0200.04016.4180.0020.0020.0000.0000.0000.000
46A50HIS0-0.007-0.03111.569-0.054-0.0540.0000.0000.0000.000
47A51LEU00.0010.00912.8720.1590.1590.0000.0000.0000.000
48A52ILE0-0.007-0.00112.136-0.125-0.1250.0000.0000.0000.000
49A53GLY0-0.0030.00311.2130.0930.0930.0000.0000.0000.000
50A54GLU-1-0.798-0.87912.1680.2740.2740.0000.0000.0000.000
51A55HIS0-0.054-0.05410.4650.3950.3950.0000.0000.0000.000
52A56HIS0-0.033-0.00515.083-0.029-0.0290.0000.0000.0000.000
53A57ASP-1-0.871-0.94616.3620.9880.9880.0000.0000.0000.000
54A58GLY0-0.034-0.01315.0720.0050.0050.0000.0000.0000.000
55A59VAL0-0.059-0.03012.7800.2910.2910.0000.0000.0000.000
56A60SER0-0.023-0.0099.222-0.315-0.3150.0000.0000.0000.000
57A61LYS10.7790.84711.772-0.205-0.2050.0000.0000.0000.000
58A62ALA00.0320.01712.877-0.134-0.1340.0000.0000.0000.000
59A63ASN0-0.0020.00314.4770.0510.0510.0000.0000.0000.000
60A64PHE00.0420.01713.010-0.040-0.0400.0000.0000.0000.000
61A65SER0-0.0030.00218.6220.0350.0350.0000.0000.0000.000
62A66ILE0-0.0010.01420.354-0.046-0.0460.0000.0000.0000.000
63A67GLY00.0410.03823.8310.0350.0350.0000.0000.0000.000
64A68PRO0-0.013-0.01027.3050.0080.0080.0000.0000.0000.000
65A69MET0-0.0230.00625.973-0.015-0.0150.0000.0000.0000.000
66A70MET00.0070.00229.7910.0140.0140.0000.0000.0000.000
67A71GLN00.0670.00729.907-0.013-0.0130.0000.0000.0000.000
68A72ASP-1-0.878-0.94528.754-0.248-0.2480.0000.0000.0000.000
69A73LEU00.0100.00825.427-0.034-0.0340.0000.0000.0000.000
70A74ALA00.0120.03024.973-0.008-0.0080.0000.0000.0000.000
71A75GLY00.0490.01023.919-0.023-0.0230.0000.0000.0000.000
72A76THR0-0.064-0.03719.3440.0210.0210.0000.0000.0000.000
73A77TYR00.013-0.01017.862-0.097-0.0970.0000.0000.0000.000
74A78ARG10.9320.96513.4800.5550.5550.0000.0000.0000.000
75A80TYR00.0150.0076.7720.2500.2500.0000.0000.0000.000
76A81GLY00.0710.0325.5750.5560.5560.0000.0000.0000.000
77A82SER0-0.027-0.0252.906-3.189-2.6610.074-0.222-0.381-0.001
78A83VAL00.0310.0043.1432.1182.4860.022-0.046-0.3450.000
79A84THR00.0320.0065.536-0.535-0.5350.0000.0000.0000.000
80A85HIS00.0120.0146.279-0.811-0.8110.0000.0000.0000.000
81A86SER0-0.032-0.0215.935-0.371-0.3710.0000.0000.0000.000
82A87PRO00.0220.0235.528-1.989-1.9890.0000.0000.0000.000
83A88TYR00.0410.0207.213-0.121-0.1210.0000.0000.0000.000
84A89GLN0-0.0190.0042.529-0.8690.6870.297-0.645-1.2080.001
85A90LEU0-0.008-0.0051.947-17.678-16.8905.908-3.558-3.138-0.055
86A91SER0-0.014-0.0062.638-8.436-5.3404.427-2.918-4.605-0.007
87A92ALA0-0.0040.0013.503-0.415-1.4050.0911.703-0.8050.001
88A93PRO00.0040.0095.9190.5150.5150.0000.0000.0000.000
89A94SER00.012-0.0039.5290.3240.3240.0000.0000.0000.000
90A95ASP-1-0.857-0.91411.6880.3950.3950.0000.0000.0000.000
91A96PRO0-0.046-0.02814.622-0.057-0.0570.0000.0000.0000.000
92A97LEU00.0160.00917.6050.0700.0700.0000.0000.0000.000
93A98ASP-1-0.852-0.90620.091-0.176-0.1760.0000.0000.0000.000
94A99ILE0-0.058-0.02022.0720.0440.0440.0000.0000.0000.000
95A100VAL0-0.013-0.01224.985-0.035-0.0350.0000.0000.0000.000
96A101ILE0-0.0050.01028.7370.0100.0100.0000.0000.0000.000
97A102THR0-0.042-0.01831.9300.0040.0040.0000.0000.0000.000
98A103GLY00.002-0.02435.115-0.001-0.0010.0000.0000.0000.000
99A104LEU0-0.0320.00334.721-0.003-0.0030.0000.0000.0000.000
100A105TYR0-0.012-0.03736.278-0.005-0.0050.0000.0000.0000.000
101A106GLU-1-0.872-0.91742.174-0.013-0.0130.0000.0000.0000.000
102A107LYS10.8370.92643.005-0.010-0.0100.0000.0000.0000.000
103A108PRO0-0.040-0.01041.381-0.001-0.0010.0000.0000.0000.000
104A109SER0-0.011-0.01044.6750.0050.0050.0000.0000.0000.000
105A110LEU0-0.036-0.02541.843-0.001-0.0010.0000.0000.0000.000
106A111SER0-0.051-0.02445.5260.0010.0010.0000.0000.0000.000
107A112ALA00.044-0.00145.7750.0040.0040.0000.0000.0000.000
108A113GLN0-0.0080.01047.128-0.004-0.0040.0000.0000.0000.000
109A114PRO00.0600.01847.4760.0040.0040.0000.0000.0000.000
110A115GLY00.0100.01149.885-0.005-0.0050.0000.0000.0000.000
111A116PRO0-0.0010.00648.0150.0040.0040.0000.0000.0000.000
112A117THR0-0.037-0.02548.4780.0040.0040.0000.0000.0000.000
113A118VAL0-0.0020.02247.321-0.001-0.0010.0000.0000.0000.000
114A119LEU00.016-0.00749.8400.0040.0040.0000.0000.0000.000
115A120ALA00.005-0.00646.8570.0020.0020.0000.0000.0000.000
116A121GLY0-0.031-0.00945.333-0.002-0.0020.0000.0000.0000.000
117A122GLU-1-0.844-0.92246.3600.0770.0770.0000.0000.0000.000
118A123SER0-0.058-0.03144.6310.0060.0060.0000.0000.0000.000
119A124VAL00.0050.00843.550-0.007-0.0070.0000.0000.0000.000
120A125THR0-0.026-0.01743.0840.0040.0040.0000.0000.0000.000
121A126LEU0-0.0040.01040.437-0.005-0.0050.0000.0000.0000.000
122A127SER0-0.017-0.03142.915-0.003-0.0030.0000.0000.0000.000
123A128CYS0-0.047-0.01338.3200.0040.0040.0000.0000.0000.000
124A129SER00.0170.01144.014-0.005-0.0050.0000.0000.0000.000
125A130SER00.0700.03845.3580.0020.0020.0000.0000.0000.000
126A131ARG10.9310.95747.1170.0210.0210.0000.0000.0000.000
127A132SER0-0.0050.00444.394-0.003-0.0030.0000.0000.0000.000
128A133SER0-0.004-0.01643.2480.0040.0040.0000.0000.0000.000
129A134TYR0-0.049-0.04140.301-0.007-0.0070.0000.0000.0000.000
130A135ASP-1-0.776-0.87937.772-0.067-0.0670.0000.0000.0000.000
131A136MET0-0.064-0.00733.1340.0110.0110.0000.0000.0000.000
132A137TYR00.015-0.01636.834-0.004-0.0040.0000.0000.0000.000
133A138HIS0-0.026-0.01430.681-0.006-0.0060.0000.0000.0000.000
134A139LEU00.0000.00735.004-0.002-0.0020.0000.0000.0000.000
135A140SER00.034-0.03132.8160.0040.0040.0000.0000.0000.000
136A141ARG10.8170.90234.575-0.164-0.1640.0000.0000.0000.000
137A142GLU-1-0.796-0.88334.4920.1050.1050.0000.0000.0000.000
138A143GLY0-0.0050.00732.1670.0090.0090.0000.0000.0000.000
139A144GLU-1-0.877-0.92431.4700.1930.1930.0000.0000.0000.000
140A145ALA0-0.044-0.02826.596-0.007-0.0070.0000.0000.0000.000
141A146HIS00.0010.00122.923-0.016-0.0160.0000.0000.0000.000
142A147GLU-1-0.835-0.87828.1710.1000.1000.0000.0000.0000.000
143A148ARG10.8700.93229.815-0.127-0.1270.0000.0000.0000.000
144A149ARG10.9460.98726.9840.0040.0040.0000.0000.0000.000
145A150PHE00.001-0.00633.0160.0090.0090.0000.0000.0000.000
146A151SER0-0.002-0.02235.511-0.010-0.0100.0000.0000.0000.000
147A152ALA0-0.039-0.01337.4800.0070.0070.0000.0000.0000.000
148A153GLY00.0290.02141.121-0.003-0.0030.0000.0000.0000.000
149A154PRO0-0.069-0.06743.2590.0010.0010.0000.0000.0000.000
150A155LYS10.8940.96246.0170.0510.0510.0000.0000.0000.000
151A156VAL00.0580.04348.8710.0000.0000.0000.0000.0000.000
152A157ASN00.0080.00651.3900.0010.0010.0000.0000.0000.000
153A158GLY0-0.025-0.01652.6390.0000.0000.0000.0000.0000.000
154A159THR0-0.018-0.01149.333-0.004-0.0040.0000.0000.0000.000
155A160PHE00.0050.02544.581-0.004-0.0040.0000.0000.0000.000
156A161GLN0-0.025-0.02144.681-0.002-0.0020.0000.0000.0000.000
157A162ALA00.0390.01939.985-0.005-0.0050.0000.0000.0000.000
158A163ASP-1-0.810-0.86041.7790.0310.0310.0000.0000.0000.000
159A164PHE0-0.009-0.02435.9590.0020.0020.0000.0000.0000.000
160A165PRO0-0.004-0.01139.5590.0050.0050.0000.0000.0000.000
161A166LEU0-0.031-0.01338.2610.0060.0060.0000.0000.0000.000
162A167GLY00.0090.02238.7810.0120.0120.0000.0000.0000.000
163A168PRO0-0.020-0.01440.159-0.007-0.0070.0000.0000.0000.000
164A169ALA00.018-0.00341.5020.0080.0080.0000.0000.0000.000
165A170THR0-0.022-0.00538.3640.0010.0010.0000.0000.0000.000
166A171HIS00.0320.00338.707-0.005-0.0050.0000.0000.0000.000
167A172GLY00.0090.01241.658-0.005-0.0050.0000.0000.0000.000
168A173GLY00.0010.00440.3590.0130.0130.0000.0000.0000.000
169A174THR0-0.0140.00440.377-0.008-0.0080.0000.0000.0000.000
170A175TYR00.0220.00838.1280.0120.0120.0000.0000.0000.000
171A176ARG10.8160.86738.299-0.080-0.0800.0000.0000.0000.000
172A178PHE00.0350.02835.222-0.007-0.0070.0000.0000.0000.000
173A179GLY00.0450.00938.2310.0050.0050.0000.0000.0000.000
174A180SER00.0120.00334.398-0.004-0.0040.0000.0000.0000.000
175A181PHE00.0190.00336.4040.0100.0100.0000.0000.0000.000
176A182ARG10.7990.88134.5310.0740.0740.0000.0000.0000.000
177A183ASP-1-0.914-0.95333.171-0.137-0.1370.0000.0000.0000.000
178A184SER0-0.004-0.02331.273-0.017-0.0170.0000.0000.0000.000
179A185PRO0-0.006-0.00428.9640.0140.0140.0000.0000.0000.000
180A186TYR0-0.063-0.02423.9930.0070.0070.0000.0000.0000.000
181A187GLU-1-0.794-0.87829.632-0.159-0.1590.0000.0000.0000.000
182A188TRP0-0.040-0.02230.2570.0120.0120.0000.0000.0000.000
183A189SER00.007-0.00835.736-0.003-0.0030.0000.0000.0000.000
184A190ASN0-0.036-0.02038.1310.0080.0080.0000.0000.0000.000
185A191SER00.014-0.00139.1660.0030.0030.0000.0000.0000.000
186A192SER0-0.0160.00440.451-0.001-0.0010.0000.0000.0000.000
187A193ASP-1-0.818-0.89442.8440.0230.0230.0000.0000.0000.000
188A194PRO0-0.037-0.02243.0880.0030.0030.0000.0000.0000.000
189A195LEU00.0210.02543.6650.0000.0000.0000.0000.0000.000
190A196LEU0-0.013-0.01743.7630.0070.0070.0000.0000.0000.000
191A197VAL0-0.0020.00843.499-0.005-0.0050.0000.0000.0000.000
192A198SER0-0.057-0.04245.0610.0060.0060.0000.0000.0000.000
193A199VAL00.0240.01744.114-0.005-0.0050.0000.0000.0000.000
194A200THR0-0.0110.00447.2570.0040.0040.0000.0000.0000.000
195A201GLY00.0130.00448.8740.0020.0020.0000.0000.0000.000
196A202ASN0-0.015-0.00948.247-0.005-0.0050.0000.0000.0000.000
197A203PRO00.0120.01150.8510.0060.0060.0000.0000.0000.000