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: ZN6MN

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2016486.571834
FMO2-HF: Nuclear repulsion 1939402.926107
FMO2-HF: Total energy -77083.645727
FMO2-MP2: Total energy -77307.750992


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.
-15.684-7.5043.714-4.131-7.763-0.011
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 : -0.017 / 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].
3A7LYS10.8650.9493.806-2.079-0.458-0.018-0.864-0.7380.002
4A8PRO0-0.040-0.0186.8150.7350.7350.0000.0000.0000.000
5A9SER0-0.030-0.0229.490-0.093-0.0930.0000.0000.0000.000
6A10LEU00.009-0.00112.989-0.106-0.1060.0000.0000.0000.000
7A11LEU0-0.0120.00115.9310.0290.0290.0000.0000.0000.000
8A12ALA00.034-0.00219.308-0.064-0.0640.0000.0000.0000.000
9A13HIS0-0.0580.00921.7290.0480.0480.0000.0000.0000.000
10A14PRO00.044-0.00524.993-0.026-0.0260.0000.0000.0000.000
11A15GLY00.0620.01826.2580.0300.0300.0000.0000.0000.000
12A16PRO00.004-0.00524.339-0.022-0.0220.0000.0000.0000.000
13A17LEU0-0.0190.01326.471-0.028-0.0280.0000.0000.0000.000
14A18VAL0-0.047-0.02027.7820.0120.0120.0000.0000.0000.000
15A19LYS10.8260.89831.0340.0160.0160.0000.0000.0000.000
16A20SER00.1110.01233.335-0.010-0.0100.0000.0000.0000.000
17A21GLU-1-0.897-0.89334.379-0.086-0.0860.0000.0000.0000.000
18A22GLU-1-0.895-0.94031.805-0.032-0.0320.0000.0000.0000.000
19A23THR0-0.070-0.04527.851-0.013-0.0130.0000.0000.0000.000
20A24VAL00.0060.00924.7700.0210.0210.0000.0000.0000.000
21A25ILE0-0.013-0.01421.267-0.032-0.0320.0000.0000.0000.000
22A26LEU00.017-0.00518.5390.0290.0290.0000.0000.0000.000
23A27GLN0-0.019-0.00716.972-0.046-0.0460.0000.0000.0000.000
24A28CYS0-0.0150.00311.878-0.070-0.0700.0000.0000.0000.000
25A29TRP0-0.0070.00111.8570.0140.0140.0000.0000.0000.000
26A30SER00.012-0.0087.7840.4080.4080.0000.0000.0000.000
27A31ASP-1-0.765-0.8458.6363.0963.0960.0000.0000.0000.000
28A32VAL0-0.0160.0064.942-0.012-0.0120.0000.0000.0000.000
29A33ARG10.9460.9747.446-1.380-1.3800.0000.0000.0000.000
30A34PHE0-0.027-0.0072.338-1.321-0.5620.949-0.495-1.2130.004
31A35GLN0-0.002-0.0136.5870.2290.2290.0000.0000.0000.000
32A36HIS00.0310.0007.9580.4770.4770.0000.0000.0000.000
33A37PHE0-0.033-0.0118.138-0.555-0.5550.0000.0000.0000.000
34A38LEU0-0.014-0.0089.3910.0640.0640.0000.0000.0000.000
35A39LEU0-0.0070.00211.7170.0280.0280.0000.0000.0000.000
36A40HIS0-0.0050.00914.1840.0670.0670.0000.0000.0000.000
37A41ARG10.8660.93515.6710.4710.4710.0000.0000.0000.000
38A42GLU-1-0.868-0.94518.761-0.654-0.6540.0000.0000.0000.000
39A43GLY00.014-0.00120.4350.0590.0590.0000.0000.0000.000
40A44LYS10.7950.90024.1450.2100.2100.0000.0000.0000.000
41A45PHE00.0410.04225.107-0.021-0.0210.0000.0000.0000.000
42A46LYS10.7710.88418.9060.6690.6690.0000.0000.0000.000
43A47ASP-1-0.842-0.90520.565-0.573-0.5730.0000.0000.0000.000
44A48THR0-0.092-0.07114.266-0.099-0.0990.0000.0000.0000.000
45A49LEU00.0280.03015.9490.0450.0450.0000.0000.0000.000
46A50HIS0-0.011-0.02612.072-0.065-0.0650.0000.0000.0000.000
47A51LEU00.0050.01113.3700.1410.1410.0000.0000.0000.000
48A52ILE0-0.0190.00112.574-0.108-0.1080.0000.0000.0000.000
49A53GLY00.001-0.00711.6810.0910.0910.0000.0000.0000.000
50A54GLU-1-0.817-0.88812.6940.1050.1050.0000.0000.0000.000
51A55HIS0-0.055-0.06010.8940.2380.2380.0000.0000.0000.000
52A56HIS0-0.047-0.01315.2290.0480.0480.0000.0000.0000.000
53A57ASP-1-0.882-0.96116.6880.7780.7780.0000.0000.0000.000
54A58GLY0-0.0030.00414.7280.0100.0100.0000.0000.0000.000
55A59VAL0-0.045-0.01712.8880.2310.2310.0000.0000.0000.000
56A60SER0-0.0230.0059.556-0.234-0.2340.0000.0000.0000.000
57A61LYS10.7860.85512.006-0.088-0.0880.0000.0000.0000.000
58A62ALA00.0330.03813.091-0.092-0.0920.0000.0000.0000.000
59A63ASN00.005-0.00414.7310.0420.0420.0000.0000.0000.000
60A64PHE00.0430.02313.522-0.026-0.0260.0000.0000.0000.000
61A65SER00.0100.00419.2260.0480.0480.0000.0000.0000.000
62A66ILE0-0.025-0.00520.944-0.036-0.0360.0000.0000.0000.000
63A67GLY00.0360.02124.5800.0300.0300.0000.0000.0000.000
64A68PRO0-0.003-0.01227.8730.0040.0040.0000.0000.0000.000
65A69MET0-0.0340.01426.530-0.014-0.0140.0000.0000.0000.000
66A70MET00.0430.01430.1770.0130.0130.0000.0000.0000.000
67A71GLN00.0690.00530.205-0.014-0.0140.0000.0000.0000.000
68A72ASP-1-0.910-0.96229.065-0.254-0.2540.0000.0000.0000.000
69A73LEU00.0210.00125.452-0.038-0.0380.0000.0000.0000.000
70A74ALA0-0.0110.02524.981-0.014-0.0140.0000.0000.0000.000
71A75GLY00.018-0.01624.139-0.019-0.0190.0000.0000.0000.000
72A76THR0-0.050-0.03718.9700.0180.0180.0000.0000.0000.000
73A77TYR00.0040.00117.632-0.089-0.0890.0000.0000.0000.000
74A78ARG10.9450.97313.1430.6390.6390.0000.0000.0000.000
75A80TYR00.003-0.0057.0710.1690.1690.0000.0000.0000.000
76A81GLY00.0670.0346.0010.6100.6100.0000.0000.0000.000
77A82SER0-0.006-0.0053.541-2.527-2.1830.007-0.116-0.2360.000
78A83VAL00.013-0.0023.2521.6392.0110.014-0.063-0.323-0.001
79A84THR00.0460.0065.382-0.224-0.206-0.0010.000-0.0170.000
80A85HIS0-0.0290.0156.525-0.615-0.6150.0000.0000.0000.000
81A86SER00.017-0.0086.356-0.290-0.2900.0000.0000.0000.000
82A87PRO00.0040.0136.053-1.328-1.3280.0000.0000.0000.000
83A88TYR00.0240.0067.6230.0710.0710.0000.0000.0000.000
84A89GLN0-0.0330.0072.863-0.5650.2230.058-0.193-0.6530.001
85A90LEU0-0.021-0.0252.880-7.498-5.2990.114-1.379-0.933-0.015
86A91SER00.0190.0282.640-7.306-4.6392.513-2.167-3.014-0.003
87A92ALA0-0.032-0.0143.3720.6490.0610.0781.146-0.6360.001
88A93PRO00.015-0.0025.7420.5000.5000.0000.0000.0000.000
89A94SER00.0420.0239.3030.2620.2620.0000.0000.0000.000
90A95ASP-1-0.880-0.92911.6630.2220.2220.0000.0000.0000.000
91A96PRO0-0.045-0.02914.618-0.028-0.0280.0000.0000.0000.000
92A97LEU00.0180.01717.2600.0720.0720.0000.0000.0000.000
93A98ASP-1-0.859-0.91319.969-0.239-0.2390.0000.0000.0000.000
94A99ILE0-0.045-0.01022.3150.0360.0360.0000.0000.0000.000
95A100VAL00.003-0.00825.015-0.029-0.0290.0000.0000.0000.000
96A101ILE00.0640.05428.6640.0090.0090.0000.0000.0000.000
97A102THR0-0.071-0.04731.8190.0090.0090.0000.0000.0000.000
98A103GLY0-0.005-0.02035.104-0.003-0.0030.0000.0000.0000.000
99A104LEU0-0.0130.02534.587-0.002-0.0020.0000.0000.0000.000
100A105TYR0-0.005-0.03136.196-0.001-0.0010.0000.0000.0000.000
101A106GLU-1-0.865-0.91241.837-0.031-0.0310.0000.0000.0000.000
102A107LYS10.8320.92042.9740.0090.0090.0000.0000.0000.000
103A108PRO0-0.017-0.00441.5720.0000.0000.0000.0000.0000.000
104A109SER0-0.034-0.02544.8690.0040.0040.0000.0000.0000.000
105A110LEU0-0.006-0.01141.606-0.001-0.0010.0000.0000.0000.000
106A111SER0-0.0310.00845.3470.0040.0040.0000.0000.0000.000
107A112ALA00.0500.00146.1700.0020.0020.0000.0000.0000.000
108A113GLN0-0.008-0.02047.187-0.003-0.0030.0000.0000.0000.000
109A114PRO00.0620.02847.2160.0030.0030.0000.0000.0000.000
110A115GLY00.0280.04250.261-0.005-0.0050.0000.0000.0000.000
111A116PRO0-0.026-0.01948.1110.0030.0030.0000.0000.0000.000
112A117THR0-0.052-0.03348.8190.0020.0020.0000.0000.0000.000
113A118VAL00.0080.02746.9980.0010.0010.0000.0000.0000.000
114A119LEU00.001-0.01049.6000.0030.0030.0000.0000.0000.000
115A120ALA00.0310.00146.7620.0010.0010.0000.0000.0000.000
116A121GLY0-0.047-0.01545.701-0.001-0.0010.0000.0000.0000.000
117A122GLU-1-0.851-0.92546.2590.0600.0600.0000.0000.0000.000
118A123SER0-0.050-0.01744.1860.0050.0050.0000.0000.0000.000
119A124VAL0-0.020-0.01343.392-0.006-0.0060.0000.0000.0000.000
120A125THR0-0.051-0.03942.9180.0040.0040.0000.0000.0000.000
121A126LEU0-0.0200.02440.627-0.005-0.0050.0000.0000.0000.000
122A127SER00.010-0.01142.541-0.002-0.0020.0000.0000.0000.000
123A128CYS0-0.036-0.00738.3090.0000.0000.0000.0000.0000.000
124A129SER0-0.004-0.00244.165-0.004-0.0040.0000.0000.0000.000
125A130SER00.0810.03745.1890.0010.0010.0000.0000.0000.000
126A131ARG10.9620.98847.0390.0290.0290.0000.0000.0000.000
127A132SER00.0040.00344.784-0.002-0.0020.0000.0000.0000.000
128A133SER00.009-0.02443.1700.0040.0040.0000.0000.0000.000
129A134TYR0-0.060-0.03140.132-0.007-0.0070.0000.0000.0000.000
130A135ASP-1-0.780-0.89437.316-0.080-0.0800.0000.0000.0000.000
131A136MET0-0.091-0.04032.7300.0080.0080.0000.0000.0000.000
132A137TYR00.011-0.02836.669-0.002-0.0020.0000.0000.0000.000
133A138HIS0-0.052-0.02531.160-0.002-0.0020.0000.0000.0000.000
134A139LEU0-0.014-0.00934.7100.0000.0000.0000.0000.0000.000
135A140SER00.024-0.03032.7430.0030.0030.0000.0000.0000.000
136A141ARG10.7800.87534.189-0.126-0.1260.0000.0000.0000.000
137A142GLU-1-0.768-0.87234.4540.0650.0650.0000.0000.0000.000
138A143GLY0-0.038-0.00532.3710.0090.0090.0000.0000.0000.000
139A144GLU-1-0.935-0.95330.9900.1590.1590.0000.0000.0000.000
140A145ALA0-0.030-0.01927.131-0.006-0.0060.0000.0000.0000.000
141A146HIS00.0030.01023.218-0.027-0.0270.0000.0000.0000.000
142A147GLU-1-0.819-0.86228.4150.0480.0480.0000.0000.0000.000
143A148ARG10.9220.96529.642-0.079-0.0790.0000.0000.0000.000
144A149ARG10.9580.99127.2430.0410.0410.0000.0000.0000.000
145A150PHE00.022-0.01032.9940.0090.0090.0000.0000.0000.000
146A151SER00.0030.00135.765-0.008-0.0080.0000.0000.0000.000
147A152ALA0-0.0210.00837.6180.0070.0070.0000.0000.0000.000
148A153GLY00.0280.02041.093-0.003-0.0030.0000.0000.0000.000
149A154PRO0-0.082-0.07842.9310.0020.0020.0000.0000.0000.000
150A155LYS10.9010.97245.7750.0560.0560.0000.0000.0000.000
151A156VAL00.0610.04049.5180.0020.0020.0000.0000.0000.000
152A157ASN00.0160.00852.0260.0020.0020.0000.0000.0000.000
153A158GLY0-0.053-0.02852.3600.0000.0000.0000.0000.0000.000
154A159THR0-0.009-0.02349.184-0.004-0.0040.0000.0000.0000.000
155A160PHE0-0.0030.03444.190-0.004-0.0040.0000.0000.0000.000
156A161GLN0-0.002-0.00844.463-0.004-0.0040.0000.0000.0000.000
157A162ALA00.0220.01139.908-0.004-0.0040.0000.0000.0000.000
158A163ASP-1-0.809-0.87542.0510.0150.0150.0000.0000.0000.000
159A164PHE0-0.043-0.04635.9570.0020.0020.0000.0000.0000.000
160A165PRO00.001-0.01738.7410.0040.0040.0000.0000.0000.000
161A166LEU0-0.051-0.01737.9070.0060.0060.0000.0000.0000.000
162A167GLY00.0220.02738.8940.0100.0100.0000.0000.0000.000
163A168PRO0-0.014-0.00840.174-0.006-0.0060.0000.0000.0000.000
164A169ALA0-0.003-0.02841.3520.0070.0070.0000.0000.0000.000
165A170THR00.0020.00737.8480.0020.0020.0000.0000.0000.000
166A171HIS00.0130.01138.605-0.006-0.0060.0000.0000.0000.000
167A172GLY00.022-0.00141.626-0.005-0.0050.0000.0000.0000.000
168A173GLY0-0.006-0.01140.3580.0100.0100.0000.0000.0000.000
169A174THR00.0060.01640.047-0.007-0.0070.0000.0000.0000.000
170A175TYR00.0230.00837.8110.0070.0070.0000.0000.0000.000
171A176ARG10.8320.88038.112-0.042-0.0420.0000.0000.0000.000
172A178PHE00.0170.02135.303-0.006-0.0060.0000.0000.0000.000
173A179GLY00.0620.02738.0920.0050.0050.0000.0000.0000.000
174A180SER0-0.008-0.00534.141-0.005-0.0050.0000.0000.0000.000
175A181PHE00.0240.00236.2780.0100.0100.0000.0000.0000.000
176A182ARG10.8020.90034.0610.0850.0850.0000.0000.0000.000
177A183ASP-1-0.904-0.95732.962-0.143-0.1430.0000.0000.0000.000
178A184SER00.007-0.01131.573-0.014-0.0140.0000.0000.0000.000
179A185PRO0-0.0010.00628.7580.0120.0120.0000.0000.0000.000
180A186TYR0-0.056-0.03123.8760.0080.0080.0000.0000.0000.000
181A187GLU-1-0.828-0.89929.663-0.173-0.1730.0000.0000.0000.000
182A188TRP0-0.033-0.02530.1440.0140.0140.0000.0000.0000.000
183A189SER0-0.0080.00735.386-0.003-0.0030.0000.0000.0000.000
184A190ASN0-0.046-0.03938.1080.0070.0070.0000.0000.0000.000
185A191SER00.0450.01039.2190.0030.0030.0000.0000.0000.000
186A192SER0-0.030-0.00140.6090.0010.0010.0000.0000.0000.000
187A193ASP-1-0.824-0.89842.8590.0010.0010.0000.0000.0000.000
188A194PRO0-0.052-0.03042.7020.0020.0020.0000.0000.0000.000
189A195LEU00.0090.01443.2400.0000.0000.0000.0000.0000.000
190A196LEU00.001-0.00643.5230.0060.0060.0000.0000.0000.000
191A197VAL0-0.006-0.00343.209-0.003-0.0030.0000.0000.0000.000
192A198SER0-0.050-0.02244.7400.0060.0060.0000.0000.0000.000
193A199VAL00.0330.02143.935-0.004-0.0040.0000.0000.0000.000
194A200THR0-0.0060.01447.1080.0040.0040.0000.0000.0000.000
195A201GLY00.0400.02148.8820.0020.0020.0000.0000.0000.000
196A202ASN0-0.024-0.01048.009-0.004-0.0040.0000.0000.0000.000
197A203PRO00.0180.01150.5470.0050.0050.0000.0000.0000.000