FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 76RJK

Calculation Name: 5HQP-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HQP

Chain ID: D

ChEMBL ID:

UniProt ID: Q9BS26

Base Structure: X-ray

Registration Date: 2023-09-24

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2368042.015528
FMO2-HF: Nuclear repulsion 2283221.839895
FMO2-HF: Total energy -84820.175633
FMO2-MP2: Total energy -85064.36681


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(D:2:ILE)


Summations of interaction energy for fragment #1(D:2:ILE)
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.
-15.654-5.73415.561-9.792-15.684-0.04
Interaction energy analysis for fragmet #1(D:2:ILE)
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].
3D4SER0-0.051-0.0253.779-2.4821.095-0.051-1.909-1.6170.010
4D5LEU00.0210.0277.0520.1290.1290.0000.0000.0000.000
5D6ASP-1-0.826-0.9239.955-0.430-0.4300.0000.0000.0000.000
6D7THR0-0.036-0.04113.5840.0450.0450.0000.0000.0000.000
7D8GLU-1-1.003-0.97516.012-0.081-0.0810.0000.0000.0000.000
8D9ASN0-0.024-0.02712.0000.0020.0020.0000.0000.0000.000
9D10ILE00.003-0.00112.6480.0160.0160.0000.0000.0000.000
10D11ASP-1-0.884-0.95613.414-0.050-0.0500.0000.0000.0000.000
11D12GLU-1-0.952-0.96612.8470.1730.1730.0000.0000.0000.000
12D13ILE0-0.010-0.0177.7630.0460.0460.0000.0000.0000.000
13D14LEU0-0.056-0.00711.2660.0420.0420.0000.0000.0000.000
14D15ASN0-0.062-0.06012.7700.0120.0120.0000.0000.0000.000
15D16ASN0-0.027-0.01312.2780.0500.0500.0000.0000.0000.000
16D17ALA00.0280.03010.1890.0410.0410.0000.0000.0000.000
17D18ASP-1-0.801-0.88712.0190.1950.1950.0000.0000.0000.000
18D19VAL0-0.080-0.04311.039-0.070-0.0700.0000.0000.0000.000
19D20ALA00.0580.0358.8930.0500.0500.0000.0000.0000.000
20D21LEU0-0.053-0.0167.860-0.043-0.0430.0000.0000.0000.000
21D22VAL00.0450.0167.072-0.163-0.1630.0000.0000.0000.000
22D23ASN0-0.033-0.0346.8910.1900.1900.0000.0000.0000.000
23D24PHE00.0160.0039.010-0.094-0.0940.0000.0000.0000.000
24D25TYR0-0.055-0.0308.869-0.025-0.0250.0000.0000.0000.000
25D26ALA00.0650.02112.0620.0230.0230.0000.0000.0000.000
26D27ASP-1-0.802-0.90911.845-0.657-0.6570.0000.0000.0000.000
27D28TRP0-0.096-0.04114.5190.0290.0290.0000.0000.0000.000
28D29CYS0-0.076-0.00716.3690.0390.0390.0000.0000.0000.000
29D30ARG10.9740.98315.7730.2090.2090.0000.0000.0000.000
30D31PHE00.004-0.02915.906-0.011-0.0110.0000.0000.0000.000
31D32SER00.039-0.01312.1450.0130.0130.0000.0000.0000.000
32D33GLN00.0140.02011.136-0.028-0.0280.0000.0000.0000.000
33D34MET0-0.061-0.04211.787-0.018-0.0180.0000.0000.0000.000
34D35LEU0-0.0110.0049.0980.0330.0330.0000.0000.0000.000
35D36HIS00.0350.0316.812-0.073-0.0730.0000.0000.0000.000
36D37PRO00.0210.0096.266-0.102-0.1020.0000.0000.0000.000
37D38ILE00.0210.0237.7420.0570.0570.0000.0000.0000.000
38D39PHE0-0.057-0.0253.668-0.3310.0990.012-0.083-0.3580.000
39D40GLU-1-0.878-0.9582.179-4.530-3.5332.648-1.189-2.455-0.004
40D41GLU-1-0.938-0.9453.5710.2360.3810.0040.073-0.2210.000
41D42ALA0-0.037-0.0547.0200.1650.1650.0000.0000.0000.000
42D43SER-1-0.691-0.8362.669-6.444-2.0712.277-3.115-3.535-0.037
43D44ASP-1-0.988-1.0014.3961.7912.1310.000-0.057-0.2820.000
44D45VAL0-0.062-0.0175.4020.0540.0540.0000.0000.0000.000
45D46ILE00.0320.0116.9600.0330.0330.0000.0000.0000.000
46D47LYS10.7320.8532.036-2.093-5.1238.394-1.703-3.6600.013
47D48GLU-1-1.009-1.0085.7340.7500.7500.0000.0000.0000.000
48D49GLU-1-0.816-0.8718.4580.1340.1340.0000.0000.0000.000
49D50PHE0-0.081-0.0269.582-0.046-0.0460.0000.0000.0000.000
50D51PRO0-0.035-0.0188.583-0.078-0.0780.0000.0000.0000.000
51D52ASN0-0.012-0.0328.5070.2030.2030.0000.0000.0000.000
52D53GLU-1-0.959-0.97310.3950.4880.4880.0000.0000.0000.000
53D54ASN0-0.0160.0018.6300.2500.2500.0000.0000.0000.000
54D55GLN00.002-0.0019.280-0.124-0.1240.0000.0000.0000.000
55D56VAL0-0.0170.0116.681-0.115-0.1150.0000.0000.0000.000
56D57VAL00.0070.0064.6100.1420.274-0.001-0.008-0.1230.000
57D58PHE0-0.039-0.0132.880-1.044-0.0520.118-0.262-0.8480.000
58D59ALA00.0610.0332.354-3.824-2.0452.161-1.528-2.412-0.022
59D60ARG10.8850.9424.5841.4731.658-0.001-0.011-0.1730.000
60D61VAL00.0490.0096.8530.0220.0220.0000.0000.0000.000
61D62ASP-1-0.779-0.87910.331-0.530-0.5300.0000.0000.0000.000
62D63CYS0-0.059-0.03212.5630.0760.0760.0000.0000.0000.000
63D64ASP-1-0.841-0.92015.572-0.295-0.2950.0000.0000.0000.000
64D65GLN0-0.085-0.05514.6290.0420.0420.0000.0000.0000.000
65D66HIS00.0820.04113.0710.0140.0140.0000.0000.0000.000
66D67SER0-0.0240.00717.0000.0230.0230.0000.0000.0000.000
67D68ASP-1-0.855-0.89518.837-0.220-0.2200.0000.0000.0000.000
68D69ILE00.0580.00714.4660.0250.0250.0000.0000.0000.000
69D70ALA0-0.028-0.01517.6080.0090.0090.0000.0000.0000.000
70D71GLN0-0.017-0.00918.5380.0210.0210.0000.0000.0000.000
71D72ARG10.8540.91218.2590.2080.2080.0000.0000.0000.000
72D73TYR00.0460.01816.9050.0220.0220.0000.0000.0000.000
73D74ARG10.7880.89519.7020.1220.1220.0000.0000.0000.000
74D75ILE00.0260.02916.0720.0040.0040.0000.0000.0000.000
75D76SER0-0.051-0.01819.4690.0030.0030.0000.0000.0000.000
76D77LYS10.8640.91518.8330.1590.1590.0000.0000.0000.000
77D78TYR00.0420.03915.505-0.011-0.0110.0000.0000.0000.000
78D79PRO0-0.033-0.03212.3450.0260.0260.0000.0000.0000.000
79D80THR0-0.044-0.03713.6600.0410.0410.0000.0000.0000.000
80D81LEU0-0.0220.0079.426-0.035-0.0350.0000.0000.0000.000
81D82LYN0-0.006-0.02411.6860.0580.0580.0000.0000.0000.000
82D83LEU00.0370.03511.824-0.034-0.0340.0000.0000.0000.000
83D84PHE0-0.034-0.02212.880-0.006-0.0060.0000.0000.0000.000
84D85ARG10.9070.94513.688-0.043-0.0430.0000.0000.0000.000
85D86ASN0-0.044-0.01914.989-0.029-0.0290.0000.0000.0000.000
86D87GLY00.0380.04115.385-0.007-0.0070.0000.0000.0000.000
87D88MET0-0.062-0.03016.804-0.030-0.0300.0000.0000.0000.000
88D89MET0-0.026-0.00117.519-0.002-0.0020.0000.0000.0000.000
89D90MET00.0400.02317.6260.0180.0180.0000.0000.0000.000
90D91LYS10.8650.93119.7250.0440.0440.0000.0000.0000.000
91D92ARG00.0480.04619.619-0.020-0.0200.0000.0000.0000.000
92D93GLU-1-0.791-0.89116.618-0.153-0.1530.0000.0000.0000.000
93D94TYR0-0.022-0.02213.9960.0240.0240.0000.0000.0000.000
94D95ARG10.8080.88416.2260.0830.0830.0000.0000.0000.000
95D96GLY0-0.0130.01318.1240.0080.0080.0000.0000.0000.000
96D97GLN0-0.008-0.00317.032-0.037-0.0370.0000.0000.0000.000
97D98ARG10.9921.00012.6660.2640.2640.0000.0000.0000.000
98D99SER0-0.001-0.02012.8160.0170.0170.0000.0000.0000.000
99D100VAL00.1350.0679.664-0.018-0.0180.0000.0000.0000.000
100D101LYS10.8710.93411.5850.0290.0290.0000.0000.0000.000
101D102ALA0-0.051-0.02314.7790.0160.0160.0000.0000.0000.000
102D103LEU00.0190.0078.7330.0080.0080.0000.0000.0000.000
103D104ALA00.0680.05011.2660.0160.0160.0000.0000.0000.000
104D105ASP-1-0.850-0.93312.1790.0590.0590.0000.0000.0000.000
105D106TYR0-0.016-0.00813.1770.0090.0090.0000.0000.0000.000
106D107ILE00.008-0.0088.866-0.005-0.0050.0000.0000.0000.000
107D108ARG10.8250.89212.702-0.099-0.0990.0000.0000.0000.000
108D109GLN0-0.052-0.02014.5450.0030.0030.0000.0000.0000.000
109D110GLN0-0.048-0.02914.5700.0040.0040.0000.0000.0000.000
110D111LYN00.0030.00513.407-0.003-0.0030.0000.0000.0000.000
111D112SER0-0.061-0.02217.1670.0080.0080.0000.0000.0000.000
112D113ASP-1-0.905-0.94020.8570.0930.0930.0000.0000.0000.000
113D114PRO0-0.019-0.01822.2150.0030.0030.0000.0000.0000.000
114D115ILE0-0.096-0.03024.711-0.009-0.0090.0000.0000.0000.000
115D116GLN00.010-0.00627.9200.0020.0020.0000.0000.0000.000
116D117GLU-1-0.808-0.86030.8670.0620.0620.0000.0000.0000.000
117D118ILE0-0.053-0.02532.7230.0000.0000.0000.0000.0000.000
118D119ARG10.7560.85733.605-0.056-0.0560.0000.0000.0000.000
119D120ASP-1-0.901-0.96539.1860.0310.0310.0000.0000.0000.000
120D121LEU00.0010.02240.676-0.001-0.0010.0000.0000.0000.000
121D122ALA0-0.014-0.01142.715-0.002-0.0020.0000.0000.0000.000
122D123GLU-1-0.820-0.92838.0170.0320.0320.0000.0000.0000.000
123D124ILE0-0.0030.00440.925-0.002-0.0020.0000.0000.0000.000
124D125THR0-0.014-0.01542.088-0.002-0.0020.0000.0000.0000.000
125D126THR0-0.092-0.05742.212-0.002-0.0020.0000.0000.0000.000
126D127LEU0-0.0130.00536.8830.0000.0000.0000.0000.0000.000
127D128ASP-1-0.842-0.92038.4500.0070.0070.0000.0000.0000.000
128D129ARG10.8910.92938.147-0.005-0.0050.0000.0000.0000.000
129D130SER0-0.029-0.02537.0060.0010.0010.0000.0000.0000.000
130D131LYS10.9220.98034.554-0.012-0.0120.0000.0000.0000.000
131D132ARG10.8320.90633.272-0.006-0.0060.0000.0000.0000.000
132D133ASN0-0.0100.01533.5000.0000.0000.0000.0000.0000.000
133D134ILE00.0330.02731.873-0.001-0.0010.0000.0000.0000.000
134D135ILE00.0150.00433.2240.0040.0040.0000.0000.0000.000
135D136GLY00.0130.00933.914-0.001-0.0010.0000.0000.0000.000
136D137TYR0-0.028-0.01934.8820.0010.0010.0000.0000.0000.000
137D138PHE00.008-0.02333.0660.0000.0000.0000.0000.0000.000
138D139GLU-1-0.833-0.89136.6430.0480.0480.0000.0000.0000.000
139D140GLN0-0.031-0.02333.1470.0050.0050.0000.0000.0000.000
140D141LYS10.9150.96730.587-0.065-0.0650.0000.0000.0000.000
141D142ASP-1-0.835-0.90228.5320.1180.1180.0000.0000.0000.000
142D143SER0-0.116-0.06729.8250.0050.0050.0000.0000.0000.000
143D144ASP-1-0.806-0.91129.7290.0930.0930.0000.0000.0000.000
144D145ASN0-0.051-0.04729.9730.0020.0020.0000.0000.0000.000
145D146TYR00.0460.03427.472-0.009-0.0090.0000.0000.0000.000
146D147ARG10.9150.94525.073-0.109-0.1090.0000.0000.0000.000
147D148VAL0-0.073-0.02325.2910.0020.0020.0000.0000.0000.000
148D149PHE0-0.053-0.03927.108-0.007-0.0070.0000.0000.0000.000
149D150GLU-1-0.873-0.94323.3920.1080.1080.0000.0000.0000.000
150D151ARG10.9430.99421.590-0.050-0.0500.0000.0000.0000.000
151D152VAL0-0.048-0.05422.583-0.007-0.0070.0000.0000.0000.000
152D153ALA00.0290.01925.071-0.008-0.0080.0000.0000.0000.000
153D154ASN0-0.039-0.02919.501-0.003-0.0030.0000.0000.0000.000
154D155ILE0-0.059-0.01620.936-0.009-0.0090.0000.0000.0000.000
155D156LEU00.024-0.00421.920-0.010-0.0100.0000.0000.0000.000
156D157HIS0-0.047-0.01720.2830.0050.0050.0000.0000.0000.000
157D158ASP-1-0.949-0.96422.218-0.015-0.0150.0000.0000.0000.000
158D159ASP-1-0.958-0.97225.393-0.017-0.0170.0000.0000.0000.000
159D160CYS0-0.117-0.05428.3570.0010.0010.0000.0000.0000.000
160D161ALA0-0.012-0.00128.6940.0030.0030.0000.0000.0000.000
161D162PHE00.0700.02627.2540.0000.0000.0000.0000.0000.000
162D163LEU0-0.034-0.02030.3310.0020.0020.0000.0000.0000.000
163D164SER0-0.027-0.02131.0680.0000.0000.0000.0000.0000.000
164D165ALA00.0970.04133.517-0.001-0.0010.0000.0000.0000.000
165D166PHE0-0.091-0.06436.0940.0040.0040.0000.0000.0000.000
166D167GLY00.0260.02238.715-0.002-0.0020.0000.0000.0000.000
167D168ASP-1-0.916-0.94141.6300.0310.0310.0000.0000.0000.000
168D169VAL0-0.062-0.02141.426-0.002-0.0020.0000.0000.0000.000
169D178ASP-1-0.934-0.96937.5480.0490.0490.0000.0000.0000.000
170D179ASN00.006-0.03538.332-0.001-0.0010.0000.0000.0000.000
171D180ILE00.0220.01033.2560.0010.0010.0000.0000.0000.000
172D181ILE0-0.028-0.02036.952-0.003-0.0030.0000.0000.0000.000
173D182TYR-1-0.802-0.90335.7770.0060.0060.0000.0000.0000.000
174D183LYS10.8610.92738.093-0.016-0.0160.0000.0000.0000.000
175D184PRO00.0780.04138.415-0.001-0.0010.0000.0000.0000.000
176D185PRO0-0.064-0.02138.8910.0010.0010.0000.0000.0000.000
177D186GLY0-0.048-0.04440.441-0.002-0.0020.0000.0000.0000.000
178D187HIS0-0.021-0.01743.4240.0010.0010.0000.0000.0000.000
179D188SER0-0.101-0.02846.2230.0000.0000.0000.0000.0000.000
180D189ALA00.0170.00844.3100.0000.0000.0000.0000.0000.000
181D190PRO00.0220.00045.4350.0010.0010.0000.0000.0000.000
182D191ASP-1-0.730-0.84442.5650.0130.0130.0000.0000.0000.000
183D192MET0-0.079-0.03640.8790.0000.0000.0000.0000.0000.000
184D193VAL00.0580.02040.8080.0010.0010.0000.0000.0000.000
185D194TYR0-0.028-0.01835.280-0.003-0.0030.0000.0000.0000.000
186D195LEU0-0.019-0.01239.4460.0020.0020.0000.0000.0000.000
187D196GLY00.026-0.00438.507-0.003-0.0030.0000.0000.0000.000
188D197ALA0-0.050-0.01236.3980.0020.0020.0000.0000.0000.000
189D198MET00.0280.02333.1050.0010.0010.0000.0000.0000.000
190D199THR00.0360.02131.6730.0000.0000.0000.0000.0000.000
191D200ASN00.0110.00630.5650.0040.0040.0000.0000.0000.000
192D201PHE00.0740.01927.171-0.001-0.0010.0000.0000.0000.000
193D202ASP-1-0.845-0.93827.4940.0200.0200.0000.0000.0000.000
194D203VAL0-0.071-0.02430.007-0.005-0.0050.0000.0000.0000.000
195D204THR00.0140.01930.703-0.002-0.0020.0000.0000.0000.000
196D205TYR0-0.044-0.00926.181-0.001-0.0010.0000.0000.0000.000
197D206ASN00.022-0.01029.483-0.005-0.0050.0000.0000.0000.000
198D207TRP00.0030.01731.856-0.003-0.0030.0000.0000.0000.000
199D208ILE00.0600.02530.237-0.003-0.0030.0000.0000.0000.000
200D209GLN00.0050.00028.713-0.006-0.0060.0000.0000.0000.000
201D210ASP-1-0.879-0.91030.720-0.007-0.0070.0000.0000.0000.000
202D211LYS10.7420.85934.266-0.007-0.0070.0000.0000.0000.000
203D212CYS0-0.033-0.00430.6010.0030.0030.0000.0000.0000.000
204D213VAL0-0.106-0.04030.241-0.005-0.0050.0000.0000.0000.000