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: 6GNJZ

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2017812.53081
FMO2-HF: Nuclear repulsion 1940730.580725
FMO2-HF: Total energy -77081.950084
FMO2-MP2: Total energy -77306.263681


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.
-14.241-8.5177.024-3.957-8.791-0.005
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 : -0.007 / q_NPA : -0.015
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].
3A7LYS10.9651.0093.806-2.238-0.585-0.018-0.870-0.7660.003
4A8PRO0-0.043-0.0146.8150.6890.6890.0000.0000.0000.000
5A9SER0-0.018-0.0189.117-0.077-0.0770.0000.0000.0000.000
6A10LEU00.0170.00312.918-0.127-0.1270.0000.0000.0000.000
7A11LEU0-0.0130.00115.4060.0280.0280.0000.0000.0000.000
8A12ALA00.046-0.00118.772-0.065-0.0650.0000.0000.0000.000
9A13HIS0-0.085-0.00520.5280.0490.0490.0000.0000.0000.000
10A14PRO00.0580.00824.490-0.026-0.0260.0000.0000.0000.000
11A15GLY00.0690.01425.7370.0310.0310.0000.0000.0000.000
12A16PRO00.003-0.00423.898-0.025-0.0250.0000.0000.0000.000
13A17LEU0-0.0330.00125.980-0.027-0.0270.0000.0000.0000.000
14A18VAL0-0.0130.00527.5410.0100.0100.0000.0000.0000.000
15A19LYS10.8520.92130.6070.0000.0000.0000.0000.0000.000
16A20SER00.087-0.00432.970-0.009-0.0090.0000.0000.0000.000
17A21GLU-1-0.881-0.88034.155-0.076-0.0760.0000.0000.0000.000
18A22GLU-1-0.949-0.99031.880-0.017-0.0170.0000.0000.0000.000
19A23THR0-0.061-0.03227.487-0.012-0.0120.0000.0000.0000.000
20A24VAL00.0140.01124.2610.0200.0200.0000.0000.0000.000
21A25ILE0-0.027-0.01420.840-0.034-0.0340.0000.0000.0000.000
22A26LEU0-0.003-0.01118.2120.0340.0340.0000.0000.0000.000
23A27GLN00.0280.02216.305-0.020-0.0200.0000.0000.0000.000
24A28CYS0-0.031-0.00111.273-0.071-0.0710.0000.0000.0000.000
25A29TRP0-0.012-0.00311.337-0.014-0.0140.0000.0000.0000.000
26A30SER00.009-0.0067.7680.4230.4230.0000.0000.0000.000
27A31ASP-1-0.809-0.9028.8442.9002.9000.0000.0000.0000.000
28A32VAL0-0.037-0.0044.8260.0160.0160.0000.0000.0000.000
29A33ARG10.9420.9617.207-1.103-1.1030.0000.0000.0000.000
30A34PHE0-0.080-0.0272.010-1.142-1.3222.871-0.953-1.7370.003
31A35GLN00.0390.0146.3590.3200.3200.0000.0000.0000.000
32A36HIS00.010-0.0187.9060.4730.4730.0000.0000.0000.000
33A37PHE0-0.0390.0098.036-0.638-0.6380.0000.0000.0000.000
34A38LEU0-0.009-0.0049.1890.0720.0720.0000.0000.0000.000
35A39LEU0-0.0020.00511.5550.0440.0440.0000.0000.0000.000
36A40HIS0-0.033-0.01314.0670.0430.0430.0000.0000.0000.000
37A41ARG10.8750.94515.5640.4380.4380.0000.0000.0000.000
38A42GLU-1-0.882-0.97118.796-0.558-0.5580.0000.0000.0000.000
39A43GLY0-0.016-0.01920.3700.0580.0580.0000.0000.0000.000
40A44LYS10.8730.94024.0870.1870.1870.0000.0000.0000.000
41A45PHE00.0280.03725.182-0.020-0.0200.0000.0000.0000.000
42A46LYS10.8880.95618.8650.6550.6550.0000.0000.0000.000
43A47ASP-1-0.851-0.90620.497-0.561-0.5610.0000.0000.0000.000
44A48THR0-0.084-0.06414.165-0.084-0.0840.0000.0000.0000.000
45A49LEU00.0130.02715.8420.0370.0370.0000.0000.0000.000
46A50HIS0-0.029-0.03612.098-0.051-0.0510.0000.0000.0000.000
47A51LEU00.0150.01013.2420.1380.1380.0000.0000.0000.000
48A52ILE0-0.030-0.00612.418-0.135-0.1350.0000.0000.0000.000
49A53GLY0-0.022-0.04011.4950.0990.0990.0000.0000.0000.000
50A54GLU-1-0.890-0.93212.4710.0440.0440.0000.0000.0000.000
51A55HIS0-0.037-0.04710.7550.1790.1790.0000.0000.0000.000
52A56HIS0-0.059-0.01714.9530.0500.0500.0000.0000.0000.000
53A57ASP-1-0.899-0.96716.3130.7260.7260.0000.0000.0000.000
54A58GLY00.0040.00514.7400.0160.0160.0000.0000.0000.000
55A59VAL0-0.038-0.01312.4520.2300.2300.0000.0000.0000.000
56A60SER00.0080.0208.669-0.096-0.0960.0000.0000.0000.000
57A61LYS10.8410.88611.628-0.109-0.1090.0000.0000.0000.000
58A62ALA00.0540.04212.726-0.101-0.1010.0000.0000.0000.000
59A63ASN00.0230.01214.3860.0570.0570.0000.0000.0000.000
60A64PHE00.0440.02013.120-0.031-0.0310.0000.0000.0000.000
61A65SER00.0140.00518.8940.0510.0510.0000.0000.0000.000
62A66ILE0-0.036-0.01120.783-0.038-0.0380.0000.0000.0000.000
63A67GLY00.0320.01024.2550.0290.0290.0000.0000.0000.000
64A68PRO0-0.008-0.00627.5710.0070.0070.0000.0000.0000.000
65A69MET0-0.0460.00827.215-0.015-0.0150.0000.0000.0000.000
66A70MET00.0270.00629.9940.0110.0110.0000.0000.0000.000
67A71GLN00.0720.01430.049-0.013-0.0130.0000.0000.0000.000
68A72ASP-1-0.961-0.98628.898-0.229-0.2290.0000.0000.0000.000
69A73LEU00.0410.01125.301-0.036-0.0360.0000.0000.0000.000
70A74ALA0-0.0200.02324.827-0.011-0.0110.0000.0000.0000.000
71A75GLY00.013-0.01924.027-0.021-0.0210.0000.0000.0000.000
72A76THR0-0.031-0.00918.7350.0220.0220.0000.0000.0000.000
73A77TYR0-0.010-0.01517.395-0.089-0.0890.0000.0000.0000.000
74A78ARG10.9500.97413.0190.5520.5520.0000.0000.0000.000
75A80TYR00.004-0.0016.8920.2280.2280.0000.0000.0000.000
76A81GLY00.0640.0245.6330.6310.6310.0000.0000.0000.000
77A82SER00.0160.0123.689-3.190-2.7140.011-0.198-0.289-0.001
78A83VAL00.0250.0033.7091.7902.0240.001-0.032-0.2020.000
79A84THR00.028-0.0025.609-0.158-0.1580.0000.0000.0000.000
80A85HIS0-0.0210.0147.335-0.483-0.4830.0000.0000.0000.000
81A86SER0-0.009-0.0176.347-0.374-0.3740.0000.0000.0000.000
82A87PRO00.0100.0036.131-1.234-1.2340.0000.0000.0000.000
83A88TYR00.0270.0197.7040.1020.1020.0000.0000.0000.000
84A89GLN0-0.054-0.0033.153-0.801-0.1400.019-0.125-0.5560.000
85A90LEU0-0.020-0.0242.975-7.017-5.0310.070-1.241-0.816-0.013
86A91SER00.0290.0332.530-6.949-4.5113.923-2.735-3.6260.001
87A92ALA0-0.026-0.0103.2411.427-0.1170.1472.197-0.7990.002
88A93PRO0-0.004-0.0135.8550.4550.4550.0000.0000.0000.000
89A94SER00.0200.0059.3860.2770.2770.0000.0000.0000.000
90A95ASP-1-0.960-0.97511.5760.3640.3640.0000.0000.0000.000
91A96PRO0-0.075-0.03814.618-0.045-0.0450.0000.0000.0000.000
92A97LEU00.0310.01917.3420.0680.0680.0000.0000.0000.000
93A98ASP-1-0.863-0.94019.784-0.170-0.1700.0000.0000.0000.000
94A99ILE0-0.042-0.00921.8110.0340.0340.0000.0000.0000.000
95A100VAL00.0150.00524.825-0.029-0.0290.0000.0000.0000.000
96A101ILE00.0800.06028.4840.0080.0080.0000.0000.0000.000
97A102THR0-0.090-0.05831.6360.0130.0130.0000.0000.0000.000
98A103GLY0-0.009-0.01934.911-0.004-0.0040.0000.0000.0000.000
99A104LEU0-0.0120.03434.641-0.002-0.0020.0000.0000.0000.000
100A105TYR00.0390.00036.272-0.002-0.0020.0000.0000.0000.000
101A106GLU-1-0.905-0.93041.678-0.020-0.0200.0000.0000.0000.000
102A107LYS10.8620.93342.788-0.002-0.0020.0000.0000.0000.000
103A108PRO0-0.019-0.00541.5850.0000.0000.0000.0000.0000.000
104A109SER0-0.023-0.02144.7460.0040.0040.0000.0000.0000.000
105A110LEU00.001-0.00441.9100.0000.0000.0000.0000.0000.000
106A111SER0-0.0040.01945.3470.0020.0020.0000.0000.0000.000
107A112ALA00.0370.00046.1700.0030.0030.0000.0000.0000.000
108A113GLN0-0.027-0.03047.174-0.004-0.0040.0000.0000.0000.000
109A114PRO00.0780.04347.2340.0040.0040.0000.0000.0000.000
110A115GLY00.0330.04050.254-0.005-0.0050.0000.0000.0000.000
111A116PRO0-0.028-0.02348.1220.0040.0040.0000.0000.0000.000
112A117THR0-0.010-0.01248.8190.0010.0010.0000.0000.0000.000
113A118VAL0-0.0110.02546.7520.0000.0000.0000.0000.0000.000
114A119LEU00.0310.00149.6000.0030.0030.0000.0000.0000.000
115A120ALA00.017-0.00246.7720.0020.0020.0000.0000.0000.000
116A121GLY0-0.045-0.01545.719-0.002-0.0020.0000.0000.0000.000
117A122GLU-1-0.878-0.94446.2780.0730.0730.0000.0000.0000.000
118A123SER0-0.061-0.01844.2250.0060.0060.0000.0000.0000.000
119A124VAL0-0.012-0.01043.470-0.007-0.0070.0000.0000.0000.000
120A125THR0-0.054-0.03742.9390.0050.0050.0000.0000.0000.000
121A126LEU0-0.0180.02440.403-0.006-0.0060.0000.0000.0000.000
122A127SER0-0.009-0.00642.556-0.001-0.0010.0000.0000.0000.000
123A128CYS0-0.031-0.00738.3090.0010.0010.0000.0000.0000.000
124A129SER00.0180.00644.165-0.003-0.0030.0000.0000.0000.000
125A130SER00.0640.02645.173-0.002-0.0020.0000.0000.0000.000
126A131ARG10.9790.99347.0530.0170.0170.0000.0000.0000.000
127A132SER00.0200.00744.730-0.003-0.0030.0000.0000.0000.000
128A133SER00.008-0.01943.5240.0040.0040.0000.0000.0000.000
129A134TYR0-0.053-0.02039.842-0.006-0.0060.0000.0000.0000.000
130A135ASP-1-0.816-0.90637.287-0.059-0.0590.0000.0000.0000.000
131A136MET0-0.110-0.05332.3640.0080.0080.0000.0000.0000.000
132A137TYR00.016-0.04036.615-0.003-0.0030.0000.0000.0000.000
133A138HIS0-0.053-0.02931.7160.0020.0020.0000.0000.0000.000
134A139LEU0-0.012-0.00534.720-0.002-0.0020.0000.0000.0000.000
135A140SER00.0540.01732.6240.0040.0040.0000.0000.0000.000
136A141ARG10.8470.94534.169-0.153-0.1530.0000.0000.0000.000
137A142GLU-1-0.897-0.97434.4540.0860.0860.0000.0000.0000.000
138A143GLY0-0.036-0.00632.3840.0080.0080.0000.0000.0000.000
139A144GLU-1-0.986-1.00630.9980.1940.1940.0000.0000.0000.000
140A145ALA0-0.024-0.01227.077-0.004-0.0040.0000.0000.0000.000
141A146HIS0-0.0100.00823.324-0.024-0.0240.0000.0000.0000.000
142A147GLU-1-0.848-0.91728.4150.0920.0920.0000.0000.0000.000
143A148ARG10.9280.97129.642-0.101-0.1010.0000.0000.0000.000
144A149ARG10.9500.99127.658-0.012-0.0120.0000.0000.0000.000
145A150PHE00.017-0.01732.9940.0080.0080.0000.0000.0000.000
146A151SER00.0060.00235.464-0.012-0.0120.0000.0000.0000.000
147A152ALA0-0.0220.01137.5210.0070.0070.0000.0000.0000.000
148A153GLY00.0320.02240.998-0.003-0.0030.0000.0000.0000.000
149A154PRO0-0.092-0.08842.8390.0010.0010.0000.0000.0000.000
150A155LYS10.8460.95045.7810.0390.0390.0000.0000.0000.000
151A156VAL00.0390.03449.1810.0020.0020.0000.0000.0000.000
152A157ASN00.0410.01451.9310.0010.0010.0000.0000.0000.000
153A158GLY0-0.063-0.02552.4590.0000.0000.0000.0000.0000.000
154A159THR00.014-0.00949.157-0.004-0.0040.0000.0000.0000.000
155A160PHE00.0320.04744.466-0.003-0.0030.0000.0000.0000.000
156A161GLN00.0090.01544.345-0.004-0.0040.0000.0000.0000.000
157A162ALA00.0140.01339.945-0.004-0.0040.0000.0000.0000.000
158A163ASP-1-0.825-0.91242.0670.0330.0330.0000.0000.0000.000
159A164PHE0-0.068-0.05335.6360.0040.0040.0000.0000.0000.000
160A165PRO0-0.005-0.01938.9210.0040.0040.0000.0000.0000.000
161A166LEU0-0.043-0.02037.9990.0080.0080.0000.0000.0000.000
162A167GLY00.0260.03238.9120.0100.0100.0000.0000.0000.000
163A168PRO0-0.025-0.01140.218-0.006-0.0060.0000.0000.0000.000
164A169ALA00.020-0.02541.3710.0080.0080.0000.0000.0000.000
165A170THR00.0030.01737.7500.0010.0010.0000.0000.0000.000
166A171HIS00.0180.00338.922-0.007-0.0070.0000.0000.0000.000
167A172GLY00.008-0.00741.626-0.004-0.0040.0000.0000.0000.000
168A173GLY0-0.011-0.01940.3570.0100.0100.0000.0000.0000.000
169A174THR00.0160.01840.074-0.007-0.0070.0000.0000.0000.000
170A175TYR00.0260.01537.7450.0080.0080.0000.0000.0000.000
171A176ARG10.9500.97738.004-0.054-0.0540.0000.0000.0000.000
172A178PHE00.0210.01435.093-0.006-0.0060.0000.0000.0000.000
173A179GLY00.0610.03038.0920.0050.0050.0000.0000.0000.000
174A180SER0-0.036-0.01834.522-0.008-0.0080.0000.0000.0000.000
175A181PHE00.0240.00636.1490.0100.0100.0000.0000.0000.000
176A182ARG10.8700.93034.1540.0590.0590.0000.0000.0000.000
177A183ASP-1-0.875-0.95133.042-0.114-0.1140.0000.0000.0000.000
178A184SER00.0010.00031.485-0.013-0.0130.0000.0000.0000.000
179A185PRO0-0.0080.00028.7930.0100.0100.0000.0000.0000.000
180A186TYR0-0.058-0.03524.503-0.002-0.0020.0000.0000.0000.000
181A187GLU-1-0.876-0.94829.526-0.133-0.1330.0000.0000.0000.000
182A188TRP0-0.009-0.01230.5180.0140.0140.0000.0000.0000.000
183A189SER00.0020.00135.225-0.004-0.0040.0000.0000.0000.000
184A190ASN0-0.048-0.04437.9230.0070.0070.0000.0000.0000.000
185A191SER0-0.014-0.01438.7020.0050.0050.0000.0000.0000.000
186A192SER00.0040.00740.2690.0010.0010.0000.0000.0000.000
187A193ASP-1-0.856-0.90642.7330.0150.0150.0000.0000.0000.000
188A194PRO0-0.052-0.03042.7740.0030.0030.0000.0000.0000.000
189A195LEU00.0250.01743.244-0.001-0.0010.0000.0000.0000.000
190A196LEU00.007-0.00743.5230.0060.0060.0000.0000.0000.000
191A197VAL0-0.018-0.00943.297-0.003-0.0030.0000.0000.0000.000
192A198SER0-0.052-0.02744.7400.0060.0060.0000.0000.0000.000
193A199VAL00.0180.01643.995-0.004-0.0040.0000.0000.0000.000
194A200THR0-0.0030.01947.1080.0030.0030.0000.0000.0000.000
195A201GLY00.0320.01448.8820.0030.0030.0000.0000.0000.000
196A202ASN0-0.0140.00048.328-0.003-0.0030.0000.0000.0000.000
197A203PRO00.0060.00250.5470.0050.0050.0000.0000.0000.000