FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 2NKLR

Calculation Name: 3HNR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HNR

Chain ID: A

ChEMBL ID:

UniProt ID: Q6HDF0

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2246580.494477
FMO2-HF: Nuclear repulsion 2169668.33203
FMO2-HF: Total energy -76912.162446
FMO2-MP2: Total energy -77139.555564


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:24:ASP)


Summations of interaction energy for fragment #1(A:24:ASP)
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.
19.52523.1240.069-1.451-2.2170.006
Interaction energy analysis for fragmet #1(A:24:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.890 / q_NPA : -0.957
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].
3A26GLN0-0.037-0.0323.748-14.699-12.4360.017-1.062-1.2180.005
4A27TYR0-0.008-0.0423.268-5.482-4.4640.054-0.361-0.7120.001
5A28LYS10.8440.9294.969-35.218-34.986-0.001-0.024-0.2060.000
6A29GLU-1-0.848-0.9366.12524.16224.1620.0000.0000.0000.000
7A30VAL0-0.0140.0237.512-2.705-2.7050.0000.0000.0000.000
8A31PHE00.0300.0174.571-2.476-2.390-0.001-0.004-0.0810.000
9A32ALA0-0.026-0.0058.1700.0420.0420.0000.0000.0000.000
10A33HIS0-0.038-0.03110.372-1.401-1.4010.0000.0000.0000.000
11A34TYR00.0200.0349.799-1.311-1.3110.0000.0000.0000.000
12A35GLU-1-0.819-0.92011.89619.06119.0610.0000.0000.0000.000
13A36ASP-1-0.823-0.91014.46117.59317.5930.0000.0000.0000.000
14A37ILE0-0.027-0.02113.356-1.260-1.2600.0000.0000.0000.000
15A38LEU0-0.042-0.01514.244-0.970-0.9700.0000.0000.0000.000
16A39GLU-1-0.807-0.91117.42914.09514.0950.0000.0000.0000.000
17A40ASP-1-0.850-0.90319.93012.38812.3880.0000.0000.0000.000
18A41VAL00.014-0.00319.625-0.719-0.7190.0000.0000.0000.000
19A42VAL0-0.003-0.00121.121-0.692-0.6920.0000.0000.0000.000
20A43ASN0-0.073-0.03723.442-1.040-1.0400.0000.0000.0000.000
21A44LYS10.7970.91523.817-12.912-12.9120.0000.0000.0000.000
22A45SER0-0.010-0.00325.710-0.509-0.5090.0000.0000.0000.000
23A46PHE0-0.016-0.02827.685-0.145-0.1450.0000.0000.0000.000
24A47GLY00.0140.01031.0390.0190.0190.0000.0000.0000.000
25A48ASN0-0.059-0.02531.4900.3020.3020.0000.0000.0000.000
26A49VAL00.0360.01025.603-0.050-0.0500.0000.0000.0000.000
27A50LEU0-0.018-0.00727.591-0.030-0.0300.0000.0000.0000.000
28A51GLU-1-0.780-0.88420.04914.30514.3050.0000.0000.0000.000
29A52PHE0-0.001-0.01522.660-0.114-0.1140.0000.0000.0000.000
30A53GLY0-0.011-0.00218.8920.4220.4220.0000.0000.0000.000
31A54VAL0-0.026-0.00217.5590.7050.7050.0000.0000.0000.000
32A55GLY00.0670.03415.0810.8470.8470.0000.0000.0000.000
33A56THR0-0.029-0.03212.618-0.724-0.7240.0000.0000.0000.000
34A57GLY00.0600.02515.491-0.073-0.0730.0000.0000.0000.000
35A58ASN0-0.026-0.01511.611-1.242-1.2420.0000.0000.0000.000
36A59LEU00.0620.03215.971-0.319-0.3190.0000.0000.0000.000
37A60THR00.017-0.03118.335-0.394-0.3940.0000.0000.0000.000
38A61ASN0-0.032-0.01118.204-1.180-1.1800.0000.0000.0000.000
39A62LYS10.7950.89616.880-17.394-17.3940.0000.0000.0000.000
40A63LEU00.0110.00921.136-0.616-0.6160.0000.0000.0000.000
41A64LEU0-0.017-0.01123.941-0.557-0.5570.0000.0000.0000.000
42A65LEU0-0.045-0.01621.526-0.458-0.4580.0000.0000.0000.000
43A66ALA0-0.0290.00025.243-0.365-0.3650.0000.0000.0000.000
44A67GLY0-0.028-0.01326.945-0.369-0.3690.0000.0000.0000.000
45A68ARG10.7960.90327.039-11.190-11.1900.0000.0000.0000.000
46A69THR00.0060.00829.1680.1230.1230.0000.0000.0000.000
47A70VAL0-0.011-0.00524.5190.0460.0460.0000.0000.0000.000
48A71TYR0-0.037-0.03027.760-0.207-0.2070.0000.0000.0000.000
49A72GLY00.0110.01224.3790.2030.2030.0000.0000.0000.000
50A73ILE0-0.042-0.00924.004-0.387-0.3870.0000.0000.0000.000
51A74GLU-1-0.805-0.91718.71815.86315.8630.0000.0000.0000.000
52A75PRO00.0630.04821.136-0.251-0.2510.0000.0000.0000.000
53A76SER00.0240.00617.551-0.420-0.4200.0000.0000.0000.000
54A77ARG10.8410.86520.506-10.873-10.8730.0000.0000.0000.000
55A78GLU-1-0.946-0.96915.17517.80817.8080.0000.0000.0000.000
56A79MET0-0.0080.00213.3570.5860.5860.0000.0000.0000.000
57A80ARG10.8310.89217.719-12.099-12.0990.0000.0000.0000.000
58A81MET0-0.050-0.00920.516-0.516-0.5160.0000.0000.0000.000
59A82ILE00.0150.00614.332-0.002-0.0020.0000.0000.0000.000
60A83ALA00.0040.00918.1730.0940.0940.0000.0000.0000.000
61A84LYS10.8310.91819.455-11.828-11.8280.0000.0000.0000.000
62A85GLU-1-0.883-0.93020.06812.27412.2740.0000.0000.0000.000
63A86LYS10.8010.88714.021-19.691-19.6910.0000.0000.0000.000
64A87LEU0-0.0310.00520.302-0.200-0.2000.0000.0000.0000.000
65A88PRO00.004-0.00122.775-0.274-0.2740.0000.0000.0000.000
66A89LYS10.8460.89824.591-12.213-12.2130.0000.0000.0000.000
67A90GLU-1-0.939-0.96628.6709.1219.1210.0000.0000.0000.000
68A91PHE0-0.016-0.00623.279-0.106-0.1060.0000.0000.0000.000
69A92SER00.0080.00827.9800.0900.0900.0000.0000.0000.000
70A93ILE00.0070.00521.7910.1860.1860.0000.0000.0000.000
71A94THR0-0.051-0.03826.4500.0520.0520.0000.0000.0000.000
72A95GLU-1-0.782-0.84125.66411.68511.6850.0000.0000.0000.000
73A96GLY00.0570.03226.803-0.047-0.0470.0000.0000.0000.000
74A97ASP-1-0.778-0.88724.70511.35111.3510.0000.0000.0000.000
75A98PHE00.035-0.00320.325-0.323-0.3230.0000.0000.0000.000
76A99LEU0-0.0170.01025.969-0.375-0.3750.0000.0000.0000.000
77A100SER0-0.061-0.05028.831-0.619-0.6190.0000.0000.0000.000
78A101PHE0-0.031-0.00328.7160.2270.2270.0000.0000.0000.000
79A102GLU-1-0.859-0.91430.6619.1159.1150.0000.0000.0000.000
80A103VAL0-0.002-0.01131.9130.2590.2590.0000.0000.0000.000
81A104PRO0-0.025-0.00631.272-0.242-0.2420.0000.0000.0000.000
82A105THR00.003-0.00534.295-0.216-0.2160.0000.0000.0000.000
83A106SER0-0.042-0.01436.331-0.246-0.2460.0000.0000.0000.000
84A107ILE0-0.030-0.01631.0830.1540.1540.0000.0000.0000.000
85A108ASP-1-0.819-0.88533.1038.5008.5000.0000.0000.0000.000
86A109THR0-0.100-0.06428.0410.1650.1650.0000.0000.0000.000
87A110ILE00.0130.01726.7840.0730.0730.0000.0000.0000.000
88A111VAL00.022-0.00422.6910.0950.0950.0000.0000.0000.000
89A112SER00.0250.00819.9200.1240.1240.0000.0000.0000.000
90A113THR00.010-0.00315.347-0.059-0.0590.0000.0000.0000.000
91A114TYR0-0.058-0.05210.8500.4690.4690.0000.0000.0000.000
92A115ALA00.0340.02314.2820.4940.4940.0000.0000.0000.000
93A116PHE00.0420.01817.045-0.571-0.5710.0000.0000.0000.000
94A117HIS10.7930.86713.560-18.905-18.9050.0000.0000.0000.000
95A118HIS0-0.037-0.00914.5220.4720.4720.0000.0000.0000.000
96A119LEU0-0.0310.00619.178-0.485-0.4850.0000.0000.0000.000
97A120THR00.016-0.02422.7420.1080.1080.0000.0000.0000.000
98A121ASP-1-0.752-0.85824.59711.74411.7440.0000.0000.0000.000
99A122ASP-1-0.915-0.95226.7059.4409.4400.0000.0000.0000.000
100A123GLU-1-0.832-0.88525.86111.02311.0230.0000.0000.0000.000
101A124LYS10.7530.85721.734-12.938-12.9380.0000.0000.0000.000
102A125ASN00.0280.00527.016-0.162-0.1620.0000.0000.0000.000
103A126VAL0-0.016-0.00630.712-0.245-0.2450.0000.0000.0000.000
104A127ALA0-0.0100.00227.727-0.195-0.1950.0000.0000.0000.000
105A128ILE00.007-0.00227.037-0.179-0.1790.0000.0000.0000.000
106A129ALA00.0250.02030.805-0.248-0.2480.0000.0000.0000.000
107A130LYS10.8440.91432.327-9.326-9.3260.0000.0000.0000.000
108A131TYR0-0.008-0.03426.953-0.023-0.0230.0000.0000.0000.000
109A132SER00.009-0.01132.646-0.189-0.1890.0000.0000.0000.000
110A133GLN0-0.095-0.04435.689-0.202-0.2020.0000.0000.0000.000
111A134LEU0-0.047-0.02433.507-0.233-0.2330.0000.0000.0000.000
112A135LEU0-0.0070.02531.420-0.072-0.0720.0000.0000.0000.000
113A136ASN00.018-0.00335.848-0.370-0.3700.0000.0000.0000.000
114A137LYS10.8580.90937.553-7.005-7.0050.0000.0000.0000.000
115A138GLY0-0.043-0.01837.225-0.049-0.0490.0000.0000.0000.000
116A139GLY00.0220.02234.5630.1900.1900.0000.0000.0000.000
117A140LYS10.7790.85629.615-10.249-10.2490.0000.0000.0000.000
118A141ILE0-0.0080.02326.2960.0640.0640.0000.0000.0000.000
119A142VAL0-0.0030.00423.425-0.040-0.0400.0000.0000.0000.000
120A143PHE00.0070.01921.6230.3540.3540.0000.0000.0000.000
121A144ALA00.0340.02117.505-0.104-0.1040.0000.0000.0000.000
122A145ASP-1-0.745-0.86415.55918.22918.2290.0000.0000.0000.000
123A146THR0-0.026-0.01212.671-0.103-0.1030.0000.0000.0000.000
124A147ILE0-0.047-0.00715.750-0.711-0.7110.0000.0000.0000.000
125A148PHE00.0240.01515.4910.2910.2910.0000.0000.0000.000
126A149ALA00.0260.01121.011-0.503-0.5030.0000.0000.0000.000
127A150ASP-1-0.833-0.93524.07811.31611.3160.0000.0000.0000.000
128A151GLN0-0.005-0.01923.7010.2580.2580.0000.0000.0000.000
129A152ASP-1-0.803-0.86023.66412.47012.4700.0000.0000.0000.000
130A153ALA0-0.007-0.01121.6360.5930.5930.0000.0000.0000.000
131A154TYR0-0.050-0.01718.0440.6490.6490.0000.0000.0000.000
132A155ASP-1-0.778-0.89918.84713.59313.5930.0000.0000.0000.000
133A156LYS10.7730.86620.048-12.036-12.0360.0000.0000.0000.000
134A157THR0-0.036-0.02014.4690.8040.8040.0000.0000.0000.000
135A158VAL00.0300.01215.1991.2391.2390.0000.0000.0000.000
136A159GLU-1-0.888-0.92616.04115.83715.8370.0000.0000.0000.000
137A160ALA0-0.027-0.01815.5350.5290.5290.0000.0000.0000.000
138A161ALA0-0.031-0.01011.7271.2641.2640.0000.0000.0000.000
139A162LYS10.9110.93512.929-14.412-14.4120.0000.0000.0000.000
140A163GLN0-0.101-0.04115.447-0.553-0.5530.0000.0000.0000.000
141A164ARG10.8790.95411.262-23.480-23.4800.0000.0000.0000.000
142A165GLY00.0220.01010.886-0.656-0.6560.0000.0000.0000.000
143A166PHE0-0.049-0.0198.5662.6112.6110.0000.0000.0000.000
144A167HIS00.0870.0299.591-1.176-1.1760.0000.0000.0000.000
145A168GLN00.0290.0287.2980.1100.1100.0000.0000.0000.000
146A169LEU00.0400.0277.642-1.486-1.4860.0000.0000.0000.000
147A170ALA00.007-0.0039.202-1.749-1.7490.0000.0000.0000.000
148A171ASN0-0.009-0.00112.221-1.936-1.9360.0000.0000.0000.000
149A172ASP-1-0.808-0.8459.60022.57122.5710.0000.0000.0000.000
150A173LEU00.001-0.01112.265-1.228-1.2280.0000.0000.0000.000
151A174GLN0-0.044-0.00914.475-0.871-0.8710.0000.0000.0000.000
152A175THR0-0.057-0.02915.302-0.875-0.8750.0000.0000.0000.000
153A176GLU-1-0.807-0.90513.93916.09516.0950.0000.0000.0000.000
154A177TYR00.0060.01916.861-0.337-0.3370.0000.0000.0000.000
155A178TYR0-0.097-0.07312.274-0.519-0.5190.0000.0000.0000.000
156A179THR0-0.030-0.05018.859-0.594-0.5940.0000.0000.0000.000
157A180ARG10.8620.91721.526-11.165-11.1650.0000.0000.0000.000
158A181ILE00.0520.02722.908-0.389-0.3890.0000.0000.0000.000
159A182PRO00.0150.00525.761-0.264-0.2640.0000.0000.0000.000
160A183VAL0-0.0180.01526.940-0.365-0.3650.0000.0000.0000.000
161A184MET00.0280.01722.969-0.311-0.3110.0000.0000.0000.000
162A185GLN0-0.067-0.04727.4530.1370.1370.0000.0000.0000.000
163A186THR0-0.001-0.01230.324-0.361-0.3610.0000.0000.0000.000
164A187ILE0-0.0050.01127.952-0.288-0.2880.0000.0000.0000.000
165A188PHE00.005-0.00826.351-0.181-0.1810.0000.0000.0000.000
166A189GLU-1-0.847-0.91431.9128.6988.6980.0000.0000.0000.000
167A190ASN0-0.082-0.04635.218-0.459-0.4590.0000.0000.0000.000
168A191ASN0-0.037-0.01433.194-0.391-0.3910.0000.0000.0000.000
169A192GLY0-0.0100.01536.163-0.047-0.0470.0000.0000.0000.000
170A193PHE0-0.045-0.03132.899-0.053-0.0530.0000.0000.0000.000
171A194HIS0-0.010-0.00234.303-0.007-0.0070.0000.0000.0000.000
172A195VAL0-0.012-0.01428.2980.1120.1120.0000.0000.0000.000
173A196THR0-0.0160.00728.162-0.249-0.2490.0000.0000.0000.000
174A197PHE00.023-0.00123.8660.3680.3680.0000.0000.0000.000
175A198THR0-0.004-0.00922.767-0.355-0.3550.0000.0000.0000.000
176A199ARG10.8220.91818.404-15.166-15.1660.0000.0000.0000.000
177A200LEU00.0310.01617.166-0.321-0.3210.0000.0000.0000.000
178A201ASN0-0.0030.00511.9190.5070.5070.0000.0000.0000.000
179A202HIS0-0.039-0.02314.283-1.293-1.2930.0000.0000.0000.000
180A203PHE00.0500.01611.346-0.946-0.9460.0000.0000.0000.000
181A204VAL0-0.0100.00212.884-1.050-1.0500.0000.0000.0000.000
182A205TRP0-0.010-0.01815.773-0.781-0.7810.0000.0000.0000.000
183A206VAL00.0150.01319.1420.3030.3030.0000.0000.0000.000
184A207MET0-0.061-0.02120.914-0.555-0.5550.0000.0000.0000.000
185A208GLU-1-0.794-0.89524.29410.93510.9350.0000.0000.0000.000
186A209ALA00.0290.00927.142-0.334-0.3340.0000.0000.0000.000
187A210THR0-0.008-0.00830.2120.0480.0480.0000.0000.0000.000
188A211LYS10.8460.96833.514-8.156-8.1560.0000.0000.0000.000
189A212GLN0-0.016-0.02136.175-0.309-0.3090.0000.0000.0000.000
190A213LEU0-0.014-0.00839.300-0.228-0.2280.0000.0000.0000.000
191A214GLU-1-0.803-0.91040.5027.2757.2750.0000.0000.0000.000
192A215HIS00.0140.02040.091-0.127-0.1270.0000.0000.0000.000
193A216HIS10.9150.96642.132-6.836-6.8360.0000.0000.0000.000