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

tag_button

FMODB ID: 76JMK

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 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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2243949.471902
FMO2-HF: Nuclear repulsion 2167037.774059
FMO2-HF: Total energy -76911.697844
FMO2-MP2: Total energy -77139.156879


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.
20.8224.1510.16-1.039-2.4520.005
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 : -0.904 / q_NPA : -0.960
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].
3A26GLN0-0.038-0.0403.069-13.973-11.8660.095-0.801-1.4010.004
4A27TYR0-0.024-0.0453.085-5.141-4.2450.067-0.207-0.7550.001
5A28LYS10.9150.9734.903-35.058-34.811-0.001-0.028-0.2180.000
6A29GLU-1-0.909-0.9785.71823.15423.1540.0000.0000.0000.000
7A30VAL00.0200.0287.467-2.090-2.0900.0000.0000.0000.000
8A31PHE00.0170.0174.686-2.358-2.277-0.001-0.003-0.0780.000
9A32ALA0-0.023-0.0058.2640.1300.1300.0000.0000.0000.000
10A33HIS0-0.032-0.02510.494-1.289-1.2890.0000.0000.0000.000
11A34TYR00.0070.0299.788-1.455-1.4550.0000.0000.0000.000
12A35GLU-1-0.826-0.92511.87420.36820.3680.0000.0000.0000.000
13A36ASP-1-0.834-0.91714.27517.49717.4970.0000.0000.0000.000
14A37ILE0-0.026-0.01913.127-1.367-1.3670.0000.0000.0000.000
15A38LEU0-0.029-0.01314.203-1.022-1.0220.0000.0000.0000.000
16A39GLU-1-0.874-0.94317.65014.04114.0410.0000.0000.0000.000
17A40ASP-1-0.873-0.92619.90912.58412.5840.0000.0000.0000.000
18A41VAL00.003-0.00519.555-0.695-0.6950.0000.0000.0000.000
19A42VAL0-0.0030.00321.251-0.727-0.7270.0000.0000.0000.000
20A43ASN0-0.030-0.01623.669-0.958-0.9580.0000.0000.0000.000
21A44LYS10.7810.91323.725-13.073-13.0730.0000.0000.0000.000
22A45SER0-0.007-0.00526.149-0.356-0.3560.0000.0000.0000.000
23A46PHE0-0.005-0.02428.179-0.052-0.0520.0000.0000.0000.000
24A47GLY00.0210.01331.401-0.014-0.0140.0000.0000.0000.000
25A48ASN0-0.045-0.02231.5420.3440.3440.0000.0000.0000.000
26A49VAL00.0490.00625.758-0.057-0.0570.0000.0000.0000.000
27A50LEU0-0.029-0.01127.350-0.007-0.0070.0000.0000.0000.000
28A51GLU-1-0.786-0.88919.85514.75914.7590.0000.0000.0000.000
29A52PHE0-0.011-0.02122.611-0.148-0.1480.0000.0000.0000.000
30A53GLY0-0.020-0.00418.8380.4580.4580.0000.0000.0000.000
31A54VAL0-0.0200.00117.6940.6870.6870.0000.0000.0000.000
32A55GLY00.0780.05015.3010.8550.8550.0000.0000.0000.000
33A56THR0-0.034-0.03912.800-0.761-0.7610.0000.0000.0000.000
34A57GLY00.0550.02015.670-0.143-0.1430.0000.0000.0000.000
35A58ASN0-0.039-0.01811.418-1.338-1.3380.0000.0000.0000.000
36A59LEU00.0640.03515.862-0.362-0.3620.0000.0000.0000.000
37A60THR00.034-0.01918.290-0.445-0.4450.0000.0000.0000.000
38A61ASN0-0.019-0.00717.523-1.266-1.2660.0000.0000.0000.000
39A62LYS10.8560.92816.303-17.933-17.9330.0000.0000.0000.000
40A63LEU00.0080.01020.915-0.670-0.6700.0000.0000.0000.000
41A64LEU0-0.038-0.02323.534-0.607-0.6070.0000.0000.0000.000
42A65LEU0-0.031-0.00521.028-0.495-0.4950.0000.0000.0000.000
43A66ALA0-0.050-0.01225.001-0.425-0.4250.0000.0000.0000.000
44A67GLY0-0.033-0.02026.788-0.416-0.4160.0000.0000.0000.000
45A68ARG10.8100.91827.172-11.286-11.2860.0000.0000.0000.000
46A69THR00.0030.00529.1010.1380.1380.0000.0000.0000.000
47A70VAL0-0.022-0.00924.6380.0170.0170.0000.0000.0000.000
48A71TYR0-0.020-0.01027.819-0.208-0.2080.0000.0000.0000.000
49A72GLY00.0150.00824.6790.2460.2460.0000.0000.0000.000
50A73ILE0-0.021-0.00623.798-0.463-0.4630.0000.0000.0000.000
51A74GLU-1-0.822-0.92618.67816.30916.3090.0000.0000.0000.000
52A75PRO00.0820.06220.917-0.347-0.3470.0000.0000.0000.000
53A76SER00.0190.01117.696-0.535-0.5350.0000.0000.0000.000
54A77ARG10.8750.89520.610-11.178-11.1780.0000.0000.0000.000
55A78GLU-1-0.949-0.97314.87618.31318.3130.0000.0000.0000.000
56A79MET0-0.018-0.00513.0770.6980.6980.0000.0000.0000.000
57A80ARG10.8000.87617.743-12.315-12.3150.0000.0000.0000.000
58A81MET0-0.068-0.01920.189-0.567-0.5670.0000.0000.0000.000
59A82ILE00.0410.01314.188-0.067-0.0670.0000.0000.0000.000
60A83ALA00.0230.02118.2480.0620.0620.0000.0000.0000.000
61A84LYS10.8400.94019.716-12.133-12.1330.0000.0000.0000.000
62A85GLU-1-0.890-0.93719.80212.67712.6770.0000.0000.0000.000
63A86LYS10.8040.89513.920-20.202-20.2020.0000.0000.0000.000
64A87LEU0-0.047-0.00920.082-0.285-0.2850.0000.0000.0000.000
65A88PRO00.0190.01122.741-0.241-0.2410.0000.0000.0000.000
66A89LYS10.8620.91024.726-12.308-12.3080.0000.0000.0000.000
67A90GLU-1-0.952-0.97628.6739.2759.2750.0000.0000.0000.000
68A91PHE0-0.013-0.00123.564-0.096-0.0960.0000.0000.0000.000
69A92SER00.0020.00028.1450.0140.0140.0000.0000.0000.000
70A93ILE0-0.012-0.01921.9260.2230.2230.0000.0000.0000.000
71A94THR00.0140.01726.6000.0470.0470.0000.0000.0000.000
72A95GLU-1-0.790-0.87725.65811.80911.8090.0000.0000.0000.000
73A96GLY00.0210.02526.5170.0340.0340.0000.0000.0000.000
74A97ASP-1-0.819-0.93424.61911.60211.6020.0000.0000.0000.000
75A98PHE00.038-0.00220.251-0.389-0.3890.0000.0000.0000.000
76A99LEU0-0.0020.02225.812-0.417-0.4170.0000.0000.0000.000
77A100SER0-0.030-0.00828.861-0.648-0.6480.0000.0000.0000.000
78A101PHE0-0.013-0.00228.5530.2860.2860.0000.0000.0000.000
79A102GLU-1-0.915-0.95330.5229.0259.0250.0000.0000.0000.000
80A103VAL0-0.015-0.01431.7930.2550.2550.0000.0000.0000.000
81A104PRO0-0.0080.00131.042-0.230-0.2300.0000.0000.0000.000
82A105THR00.020-0.00534.070-0.265-0.2650.0000.0000.0000.000
83A106SER0-0.064-0.01236.576-0.180-0.1800.0000.0000.0000.000
84A107ILE0-0.025-0.01331.0750.1600.1600.0000.0000.0000.000
85A108ASP-1-0.849-0.90732.8858.5868.5860.0000.0000.0000.000
86A109THR0-0.076-0.04228.0910.1470.1470.0000.0000.0000.000
87A110ILE00.0120.01426.3190.1020.1020.0000.0000.0000.000
88A111VAL00.026-0.00222.5970.1200.1200.0000.0000.0000.000
89A112SER00.0150.00619.7660.1080.1080.0000.0000.0000.000
90A113THR00.001-0.00215.4820.0130.0130.0000.0000.0000.000
91A114TYR0-0.046-0.04110.8380.5870.5870.0000.0000.0000.000
92A115ALA00.0480.02214.3820.4430.4430.0000.0000.0000.000
93A116PHE00.0430.01517.095-0.463-0.4630.0000.0000.0000.000
94A117HIS10.8190.89413.887-19.038-19.0380.0000.0000.0000.000
95A118HIS0-0.064-0.02814.7760.6170.6170.0000.0000.0000.000
96A119LEU0-0.0130.00219.473-0.536-0.5360.0000.0000.0000.000
97A120THR00.004-0.01823.0330.0620.0620.0000.0000.0000.000
98A121ASP-1-0.746-0.86424.86311.78611.7860.0000.0000.0000.000
99A122ASP-1-0.925-0.96026.8779.4909.4900.0000.0000.0000.000
100A123GLU-1-0.837-0.89026.04811.12911.1290.0000.0000.0000.000
101A124LYS10.7550.86621.983-13.084-13.0840.0000.0000.0000.000
102A125ASN00.0350.00727.088-0.141-0.1410.0000.0000.0000.000
103A126VAL0-0.0130.00530.734-0.286-0.2860.0000.0000.0000.000
104A127ALA0-0.006-0.00327.625-0.207-0.2070.0000.0000.0000.000
105A128ILE00.0140.00227.004-0.191-0.1910.0000.0000.0000.000
106A129ALA00.0230.01730.585-0.244-0.2440.0000.0000.0000.000
107A130LYS10.8300.90532.141-9.494-9.4940.0000.0000.0000.000
108A131TYR0-0.021-0.03726.819-0.036-0.0360.0000.0000.0000.000
109A132SER0-0.017-0.02532.453-0.211-0.2110.0000.0000.0000.000
110A133GLN0-0.077-0.03035.171-0.196-0.1960.0000.0000.0000.000
111A134LEU0-0.043-0.02033.182-0.235-0.2350.0000.0000.0000.000
112A135LEU0-0.0030.02831.392-0.115-0.1150.0000.0000.0000.000
113A136ASN00.0160.00135.909-0.335-0.3350.0000.0000.0000.000
114A137LYS10.8860.92537.559-7.041-7.0410.0000.0000.0000.000
115A138GLY0-0.031-0.01337.190-0.065-0.0650.0000.0000.0000.000
116A139GLY00.0080.01234.5400.1840.1840.0000.0000.0000.000
117A140LYS10.7770.84129.704-10.296-10.2960.0000.0000.0000.000
118A141ILE0-0.0190.01226.1210.0580.0580.0000.0000.0000.000
119A142VAL00.0040.00923.145-0.031-0.0310.0000.0000.0000.000
120A143PHE0-0.0100.00921.1640.2840.2840.0000.0000.0000.000
121A144ALA00.0670.03817.261-0.138-0.1380.0000.0000.0000.000
122A145ASP-1-0.774-0.88815.63918.07718.0770.0000.0000.0000.000
123A146THR0-0.022-0.00612.659-0.170-0.1700.0000.0000.0000.000
124A147ILE0-0.042-0.00615.683-0.665-0.6650.0000.0000.0000.000
125A148PHE00.012-0.00215.2920.2910.2910.0000.0000.0000.000
126A149ALA00.0240.02220.948-0.542-0.5420.0000.0000.0000.000
127A150ASP-1-0.832-0.92823.81011.22411.2240.0000.0000.0000.000
128A151GLN0-0.013-0.03223.5240.2510.2510.0000.0000.0000.000
129A152ASP-1-0.798-0.86323.61012.27212.2720.0000.0000.0000.000
130A153ALA0-0.009-0.01521.3490.5020.5020.0000.0000.0000.000
131A154TYR0-0.041-0.01917.8020.6590.6590.0000.0000.0000.000
132A155ASP-1-0.785-0.89318.71413.45313.4530.0000.0000.0000.000
133A156LYS10.7660.86919.888-12.003-12.0030.0000.0000.0000.000
134A157THR0-0.050-0.04114.3550.8150.8150.0000.0000.0000.000
135A158VAL00.0320.01214.9361.2361.2360.0000.0000.0000.000
136A159GLU-1-0.868-0.91215.58815.46015.4600.0000.0000.0000.000
137A160ALA0-0.0010.00915.2770.5610.5610.0000.0000.0000.000
138A161ALA0-0.040-0.02711.3111.0501.0500.0000.0000.0000.000
139A162LYS10.9050.93212.165-14.179-14.1790.0000.0000.0000.000
140A163GLN0-0.121-0.04014.775-0.585-0.5850.0000.0000.0000.000
141A164ARG10.8660.94411.123-23.004-23.0040.0000.0000.0000.000
142A165GLY00.0400.01711.200-0.512-0.5120.0000.0000.0000.000
143A166PHE0-0.057-0.0437.9581.9301.9300.0000.0000.0000.000
144A167HIS00.0990.0509.194-1.605-1.6050.0000.0000.0000.000
145A168GLN00.0210.0206.9230.3000.3000.0000.0000.0000.000
146A169LEU00.0140.0157.347-1.380-1.3800.0000.0000.0000.000
147A170ALA00.0330.0148.849-1.558-1.5580.0000.0000.0000.000
148A171ASN0-0.0070.00811.870-2.012-2.0120.0000.0000.0000.000
149A172ASP-1-0.775-0.8369.99622.47222.4720.0000.0000.0000.000
150A173LEU0-0.001-0.01712.263-1.181-1.1810.0000.0000.0000.000
151A174GLN0-0.045-0.01114.430-0.711-0.7110.0000.0000.0000.000
152A175THR0-0.075-0.02915.448-0.879-0.8790.0000.0000.0000.000
153A176GLU-1-0.845-0.91814.14116.58816.5880.0000.0000.0000.000
154A177TYR00.0150.01317.091-0.566-0.5660.0000.0000.0000.000
155A178TYR0-0.083-0.05412.655-0.450-0.4500.0000.0000.0000.000
156A179THR0-0.021-0.04819.143-0.566-0.5660.0000.0000.0000.000
157A180ARG10.8910.93021.720-11.005-11.0050.0000.0000.0000.000
158A181ILE00.0400.01222.545-0.251-0.2510.0000.0000.0000.000
159A182PRO00.0310.00625.523-0.268-0.2680.0000.0000.0000.000
160A183VAL0-0.0290.00127.049-0.344-0.3440.0000.0000.0000.000
161A184MET00.0250.01322.912-0.334-0.3340.0000.0000.0000.000
162A185GLN0-0.071-0.04627.4360.1160.1160.0000.0000.0000.000
163A186THR0-0.005-0.00430.150-0.348-0.3480.0000.0000.0000.000
164A187ILE0-0.0050.00828.307-0.260-0.2600.0000.0000.0000.000
165A188PHE00.0290.00226.047-0.213-0.2130.0000.0000.0000.000
166A189GLU-1-0.851-0.91031.6238.7758.7750.0000.0000.0000.000
167A190ASN0-0.054-0.02434.841-0.409-0.4090.0000.0000.0000.000
168A191ASN0-0.077-0.03633.294-0.388-0.3880.0000.0000.0000.000
169A192GLY0-0.0020.02335.9340.0270.0270.0000.0000.0000.000
170A193PHE0-0.037-0.02032.637-0.025-0.0250.0000.0000.0000.000
171A194HIS0-0.0020.00434.259-0.124-0.1240.0000.0000.0000.000
172A195VAL0-0.019-0.01827.8110.0950.0950.0000.0000.0000.000
173A196THR0-0.0090.00728.193-0.255-0.2550.0000.0000.0000.000
174A197PHE00.009-0.00123.7960.4090.4090.0000.0000.0000.000
175A198THR00.0100.00622.655-0.366-0.3660.0000.0000.0000.000
176A199ARG10.8090.91318.095-15.197-15.1970.0000.0000.0000.000
177A200LEU00.0370.01716.985-0.247-0.2470.0000.0000.0000.000
178A201ASN00.0270.01812.0200.6610.6610.0000.0000.0000.000
179A202HIS0-0.050-0.02814.166-1.264-1.2640.0000.0000.0000.000
180A203PHE00.0130.00211.399-0.632-0.6320.0000.0000.0000.000
181A204VAL00.0190.02412.882-1.021-1.0210.0000.0000.0000.000
182A205TRP0-0.019-0.01515.665-0.868-0.8680.0000.0000.0000.000
183A206VAL00.000-0.00519.2590.3000.3000.0000.0000.0000.000
184A207MET0-0.049-0.01420.993-0.628-0.6280.0000.0000.0000.000
185A208GLU-1-0.791-0.89024.31410.88710.8870.0000.0000.0000.000
186A209ALA00.0210.01027.137-0.345-0.3450.0000.0000.0000.000
187A210THR00.0090.01129.9500.0400.0400.0000.0000.0000.000
188A211LYS10.8160.93133.328-8.298-8.2980.0000.0000.0000.000
189A212GLN0-0.004-0.02735.955-0.308-0.3080.0000.0000.0000.000
190A213LEU0-0.020-0.00339.098-0.217-0.2170.0000.0000.0000.000
191A214GLU-1-0.830-0.92140.5227.3147.3140.0000.0000.0000.000
192A215HIS00.006-0.00440.129-0.258-0.2580.0000.0000.0000.000
193A216HIS10.9230.98642.385-6.843-6.8430.0000.0000.0000.000