FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: Z73JN

Calculation Name: 2DLI-A-Xray547

Preferred Name: Killer cell immunoglobulin-like receptor 2DL2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DLI

Chain ID: A

ChEMBL ID: CHEMBL3833441

UniProt ID: P43627

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1980335.188056
FMO2-HF: Nuclear repulsion 1903850.658947
FMO2-HF: Total energy -76484.529109
FMO2-MP2: Total energy -76705.53053


3D Structure Molmil
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.
-85.064-78.4322.904-3.566-5.971-0.021
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 : 1 / q_Mulliken : 0.851 / q_NPA : 0.919
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].
3A7LYS10.8850.9433.85822.17423.3300.000-0.558-0.599-0.001
28A32VAL0-0.050-0.0152.943-0.479-0.0090.024-0.174-0.321-0.001
30A34PHE0-0.026-0.0133.016-2.792-2.2520.019-0.164-0.395-0.001
84A89GLN0-0.0090.0042.8340.3620.7910.083-0.109-0.403-0.001
85A90LEU00.0170.0124.0622.5642.771-0.001-0.031-0.1750.000
86A91SER0-0.071-0.0492.198-17.687-15.2272.535-2.300-2.696-0.014
87A92ALA0-0.024-0.0032.8713.7325.0160.242-0.196-1.329-0.003
88A93PRO00.0410.0224.147-0.0240.0620.002-0.034-0.0530.000
4A8PRO0-0.0050.0095.9141.6751.6750.0000.0000.0000.000
5A9SER00.0080.0088.3961.1331.1330.0000.0000.0000.000
6A10LEU0-0.017-0.01112.168-0.173-0.1730.0000.0000.0000.000
7A11LEU0-0.021-0.01414.4730.6580.6580.0000.0000.0000.000
8A12ALA00.0450.01318.234-0.209-0.2090.0000.0000.0000.000
9A13HIS0-0.040-0.01520.1220.3230.3230.0000.0000.0000.000
10A14PRO0-0.0070.00423.7690.2710.2710.0000.0000.0000.000
11A15GLY00.0720.03925.3280.3190.3190.0000.0000.0000.000
12A16ARG10.8580.92022.66112.20712.2070.0000.0000.0000.000
13A17LEU0-0.051-0.01525.097-0.009-0.0090.0000.0000.0000.000
14A18VAL00.0410.02826.9580.0600.0600.0000.0000.0000.000
15A19LYS10.8380.93030.0049.2189.2180.0000.0000.0000.000
16A20SER00.0450.01232.792-0.259-0.2590.0000.0000.0000.000
17A21GLU-1-0.987-0.99333.579-8.279-8.2790.0000.0000.0000.000
18A22GLU-1-0.855-0.90531.897-9.377-9.3770.0000.0000.0000.000
19A23THR0-0.026-0.01928.087-0.235-0.2350.0000.0000.0000.000
20A24VAL00.0100.00223.9320.0760.0760.0000.0000.0000.000
21A25ILE0-0.0240.00020.993-0.302-0.3020.0000.0000.0000.000
22A26LEU0-0.002-0.00518.010-0.031-0.0310.0000.0000.0000.000
23A27GLN0-0.013-0.02216.544-0.771-0.7710.0000.0000.0000.000
24A28CYS0-0.0430.00311.260-0.054-0.0540.0000.0000.0000.000
25A29TRP00.0200.00612.128-0.097-0.0970.0000.0000.0000.000
26A30SER00.010-0.0076.255-0.745-0.7450.0000.0000.0000.000
27A31ASP-1-0.791-0.8548.680-31.791-31.7910.0000.0000.0000.000
29A33ARG10.9230.9616.41522.65122.6510.0000.0000.0000.000
31A35GLU-1-0.797-0.8847.812-22.326-22.3260.0000.0000.0000.000
32A36HIS0-0.0170.0049.8603.4903.4900.0000.0000.0000.000
33A37PHE00.017-0.0149.535-4.039-4.0390.0000.0000.0000.000
34A38LEU0-0.034-0.00610.6631.9661.9660.0000.0000.0000.000
35A39LEU00.009-0.00611.735-1.543-1.5430.0000.0000.0000.000
36A40HIS0-0.054-0.02714.1031.0061.0060.0000.0000.0000.000
37A41ARG10.8630.94415.98513.54713.5470.0000.0000.0000.000
38A42GLU-1-0.806-0.90016.994-17.120-17.1200.0000.0000.0000.000
39A43GLY00.0310.01820.6650.4400.4400.0000.0000.0000.000
40A44LYS10.8650.92124.50010.17110.1710.0000.0000.0000.000
41A45PHE00.0340.01324.139-0.171-0.1710.0000.0000.0000.000
42A46LYS10.8840.94819.82412.42112.4210.0000.0000.0000.000
43A47ASP-1-0.850-0.92119.816-13.977-13.9770.0000.0000.0000.000
44A48THR0-0.053-0.03614.376-0.863-0.8630.0000.0000.0000.000
45A49LEU00.0290.03917.2400.5680.5680.0000.0000.0000.000
46A50HIS00.021-0.01215.084-1.255-1.2550.0000.0000.0000.000
47A51LEU0-0.0120.00215.2341.1611.1610.0000.0000.0000.000
48A52ILE00.0120.00714.446-1.591-1.5910.0000.0000.0000.000
49A53GLY0-0.030-0.02012.3680.4610.4610.0000.0000.0000.000
50A54GLU-1-0.862-0.91013.453-15.929-15.9290.0000.0000.0000.000
51A55HIS0-0.032-0.04112.216-0.275-0.2750.0000.0000.0000.000
52A56HIS0-0.101-0.05515.5891.1281.1280.0000.0000.0000.000
53A57ASP-1-0.856-0.93318.418-14.939-14.9390.0000.0000.0000.000
54A58GLY0-0.0120.00815.810-0.670-0.6700.0000.0000.0000.000
55A59VAL0-0.056-0.03512.230-1.590-1.5900.0000.0000.0000.000
56A60SER0-0.036-0.0059.7650.5900.5900.0000.0000.0000.000
57A61LYS10.9110.93811.67016.17016.1700.0000.0000.0000.000
58A62ALA00.0310.03113.4820.5260.5260.0000.0000.0000.000
59A63ASN00.0120.00015.136-0.349-0.3490.0000.0000.0000.000
60A64PHE00.0650.02814.2000.7500.7500.0000.0000.0000.000
61A65SER0-0.013-0.00619.5960.2690.2690.0000.0000.0000.000
62A66ILE0-0.0180.00320.7390.0140.0140.0000.0000.0000.000
63A67GLY00.0520.00824.4870.3550.3550.0000.0000.0000.000
64A68PRO00.009-0.00228.040-0.071-0.0710.0000.0000.0000.000
65A69MET0-0.0330.01426.141-0.135-0.1350.0000.0000.0000.000
66A70MET00.0560.01329.6870.4090.4090.0000.0000.0000.000
67A71GLN0-0.048-0.05429.539-0.262-0.2620.0000.0000.0000.000
68A72ASP-1-0.931-0.96327.920-10.808-10.8080.0000.0000.0000.000
69A73LEU0-0.020-0.00125.429-0.560-0.5600.0000.0000.0000.000
70A74ALA0-0.0010.01624.575-0.588-0.5880.0000.0000.0000.000
71A75GLY00.002-0.01323.6530.0870.0870.0000.0000.0000.000
72A76THR0-0.064-0.04717.902-0.053-0.0530.0000.0000.0000.000
73A77TYR00.000-0.01417.169-0.393-0.3930.0000.0000.0000.000
74A78ARG10.8380.89512.43918.42418.4240.0000.0000.0000.000
75A80TYR00.001-0.0077.304-2.465-2.4650.0000.0000.0000.000
76A81GLY00.0590.0276.1503.4563.4560.0000.0000.0000.000
77A82SER0-0.042-0.0305.347-7.571-7.5710.0000.0000.0000.000
78A83VAL00.0510.0196.2732.3712.3710.0000.0000.0000.000
79A84THR0-0.013-0.0318.318-0.129-0.1290.0000.0000.0000.000
80A85HIS0-0.047-0.0157.3022.2342.2340.0000.0000.0000.000
81A86SER0-0.030-0.0166.7020.2520.2520.0000.0000.0000.000
82A87PRO00.0230.0117.713-2.850-2.8500.0000.0000.0000.000
83A88TYR0-0.001-0.0048.346-0.133-0.1330.0000.0000.0000.000
89A94SER0-0.004-0.0067.9700.0680.0680.0000.0000.0000.000
90A95ASP-1-0.870-0.9109.998-20.609-20.6090.0000.0000.0000.000
91A96PRO0-0.042-0.01413.459-0.260-0.2600.0000.0000.0000.000
92A97LEU00.0090.01116.2340.6440.6440.0000.0000.0000.000
93A98ASP-1-0.834-0.89718.868-13.977-13.9770.0000.0000.0000.000
94A99ILE0-0.0040.00721.1300.4300.4300.0000.0000.0000.000
95A100VAL0-0.017-0.01524.1180.1510.1510.0000.0000.0000.000
96A101ILE00.0320.03827.8780.0450.0450.0000.0000.0000.000
97A102THR0-0.054-0.05130.9480.2990.2990.0000.0000.0000.000
98A103GLY0-0.006-0.02433.8120.0170.0170.0000.0000.0000.000
99A104LEU00.0290.01334.375-0.020-0.0200.0000.0000.0000.000
100A105TYR0-0.017-0.00436.9900.1110.1110.0000.0000.0000.000
101A106GLU-1-0.878-0.94041.143-6.836-6.8360.0000.0000.0000.000
102A107LYS10.8780.94042.1836.8526.8520.0000.0000.0000.000
103A108PRO0-0.031-0.01040.1930.1620.1620.0000.0000.0000.000
104A109SER0-0.036-0.01943.4890.0780.0780.0000.0000.0000.000
105A110LEU0-0.029-0.00540.816-0.002-0.0020.0000.0000.0000.000
106A111SER0-0.031-0.00744.4870.1730.1730.0000.0000.0000.000
107A112ALA00.0660.01645.617-0.163-0.1630.0000.0000.0000.000
108A113GLN0-0.0020.00847.2320.1840.1840.0000.0000.0000.000
109A114PRO0-0.032-0.00848.2240.1180.1180.0000.0000.0000.000
110A115GLY00.0540.03750.6340.1060.1060.0000.0000.0000.000
111A116PRO0-0.029-0.02647.594-0.116-0.1160.0000.0000.0000.000
112A117THR0-0.060-0.04147.812-0.092-0.0920.0000.0000.0000.000
113A118VAL00.0010.02347.3750.1080.1080.0000.0000.0000.000
114A119LEU00.0340.00849.568-0.057-0.0570.0000.0000.0000.000
115A120ALA00.0480.00947.352-0.131-0.1310.0000.0000.0000.000
116A121GLY0-0.080-0.04046.5680.1170.1170.0000.0000.0000.000
117A122GLU-1-0.888-0.93447.541-6.135-6.1350.0000.0000.0000.000
118A123SER0-0.079-0.03945.773-0.128-0.1280.0000.0000.0000.000
119A124VAL00.0460.02543.2680.1180.1180.0000.0000.0000.000
120A125THR0-0.016-0.01643.351-0.248-0.2480.0000.0000.0000.000
121A126LEU00.0260.00840.3020.1680.1680.0000.0000.0000.000
122A127SER0-0.033-0.02442.700-0.145-0.1450.0000.0000.0000.000
123A128CYS0-0.078-0.02237.274-0.193-0.1930.0000.0000.0000.000
124A129SER00.0530.02443.622-0.057-0.0570.0000.0000.0000.000
125A130SER00.0640.02444.520-0.016-0.0160.0000.0000.0000.000
126A131ARG10.9240.96346.5876.1466.1460.0000.0000.0000.000
127A132SER00.0130.02343.6160.0940.0940.0000.0000.0000.000
128A133SER0-0.006-0.00642.9940.0040.0040.0000.0000.0000.000
129A134TYR0-0.044-0.03639.719-0.171-0.1710.0000.0000.0000.000
130A135ASP-1-0.835-0.90937.121-8.059-8.0590.0000.0000.0000.000
131A136MET0-0.106-0.04832.386-0.038-0.0380.0000.0000.0000.000
132A137TYR00.0150.00237.1920.0180.0180.0000.0000.0000.000
133A138HIS10.8050.88731.3819.4389.4380.0000.0000.0000.000
134A139LEU00.0140.01134.3750.2070.2070.0000.0000.0000.000
135A140SER0-0.027-0.00733.031-0.371-0.3710.0000.0000.0000.000
136A141ARG10.8910.93433.0839.1949.1940.0000.0000.0000.000
137A142GLU-1-0.881-0.92832.596-8.482-8.4820.0000.0000.0000.000
138A143GLY00.0420.02029.5990.1310.1310.0000.0000.0000.000
139A144GLU-1-0.935-0.95628.037-10.305-10.3050.0000.0000.0000.000
140A145ALA0-0.017-0.01122.809-0.097-0.0970.0000.0000.0000.000
141A146HIS0-0.052-0.04120.7380.1320.1320.0000.0000.0000.000
142A147GLU-1-0.793-0.88626.035-9.979-9.9790.0000.0000.0000.000
143A148CYS00.0180.01629.352-0.121-0.1210.0000.0000.0000.000
144A149ARG10.9080.94531.1499.7109.7100.0000.0000.0000.000
145A150PHE00.0020.01533.245-0.150-0.1500.0000.0000.0000.000
146A151SER00.001-0.01935.779-0.072-0.0720.0000.0000.0000.000
147A152ALA0-0.034-0.00937.5820.0950.0950.0000.0000.0000.000
148A153GLY00.0040.00841.2480.0050.0050.0000.0000.0000.000
149A154PRO0-0.030-0.04144.4680.0250.0250.0000.0000.0000.000
150A155LYS10.9020.96346.5746.2666.2660.0000.0000.0000.000
151A156VAL00.0530.03549.5120.1070.1070.0000.0000.0000.000
152A157ASN00.0220.00151.9910.0350.0350.0000.0000.0000.000
153A158GLY0-0.046-0.02853.1870.0620.0620.0000.0000.0000.000
154A159THR00.0050.00348.545-0.081-0.0810.0000.0000.0000.000
155A160PHE00.0450.02544.5050.0850.0850.0000.0000.0000.000
156A161GLN0-0.024-0.02644.2320.0720.0720.0000.0000.0000.000
157A162ALA00.0030.01340.012-0.025-0.0250.0000.0000.0000.000
158A163ASP-1-0.806-0.88142.032-6.975-6.9750.0000.0000.0000.000
159A164PHE0-0.033-0.02835.901-0.230-0.2300.0000.0000.0000.000
160A165PRO00.014-0.00139.9420.0880.0880.0000.0000.0000.000
161A166LEU0-0.016-0.00738.123-0.206-0.2060.0000.0000.0000.000
162A167GLY00.0060.01739.699-0.118-0.1180.0000.0000.0000.000
163A168PRO0-0.024-0.02741.9420.0900.0900.0000.0000.0000.000
164A169ALA00.0250.03042.658-0.198-0.1980.0000.0000.0000.000
165A170THR00.004-0.00840.6920.0260.0260.0000.0000.0000.000
166A171HIS00.0130.00938.0010.1920.1920.0000.0000.0000.000
167A172GLY00.0390.03239.324-0.209-0.2090.0000.0000.0000.000
168A173GLY0-0.010-0.00839.185-0.188-0.1880.0000.0000.0000.000
169A174THR0-0.027-0.01138.9440.2790.2790.0000.0000.0000.000
170A175TYR00.0390.02037.281-0.195-0.1950.0000.0000.0000.000
171A176ARG10.8650.91636.9428.4298.4290.0000.0000.0000.000
172A178PHE00.0400.01834.3570.0750.0750.0000.0000.0000.000
173A179GLY00.0610.02037.297-0.024-0.0240.0000.0000.0000.000
174A180SER0-0.019-0.00834.051-0.218-0.2180.0000.0000.0000.000
175A181PHE00.0260.00735.6310.2070.2070.0000.0000.0000.000
176A182ARG10.9250.94033.6698.0418.0410.0000.0000.0000.000
177A183ASP-1-0.900-0.93432.202-9.002-9.0020.0000.0000.0000.000
178A184SER0-0.017-0.00531.130-0.235-0.2350.0000.0000.0000.000
179A185PRO00.0210.01327.6740.0990.0990.0000.0000.0000.000
180A186TYR0-0.032-0.00722.8920.0700.0700.0000.0000.0000.000
181A187GLU-1-0.793-0.88728.971-9.811-9.8110.0000.0000.0000.000
182A188TRP0-0.026-0.03329.3120.2150.2150.0000.0000.0000.000
183A189SER00.004-0.00434.6170.0440.0440.0000.0000.0000.000
184A190ASN0-0.037-0.01536.981-0.323-0.3230.0000.0000.0000.000
185A191SER00.0050.00936.9700.0460.0460.0000.0000.0000.000
186A192SER0-0.0160.00438.8880.1140.1140.0000.0000.0000.000
187A193ASP-1-0.867-0.92941.395-7.105-7.1050.0000.0000.0000.000
188A194PRO0-0.036-0.01441.093-0.061-0.0610.0000.0000.0000.000
189A195LEU00.0150.00742.1960.2090.2090.0000.0000.0000.000
190A196LEU0-0.0040.00042.601-0.191-0.1910.0000.0000.0000.000
191A197VAL0-0.025-0.01242.7460.1810.1810.0000.0000.0000.000
192A198SER0-0.025-0.02243.800-0.157-0.1570.0000.0000.0000.000
193A199VAL0-0.029-0.02644.2420.0330.0330.0000.0000.0000.000
194A200ILE-1-0.905-0.93347.152-6.415-6.4150.0000.0000.0000.000