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: R1JM8

Calculation Name: 1HF2-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HF2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0D7

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None


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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2054690.347063
FMO2-HF: Nuclear repulsion 1980975.87873
FMO2-HF: Total energy -73714.468333
FMO2-MP2: Total energy -73932.307894


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:1:MET )


Summations of interaction energy for fragment #1(A:1:MET )
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.
-26.862-24.9521.376-9.479-13.8080.004
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.001
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].
3A3ASP -1-0.904-0.9433.7971.4473.612-0.018-1.077-1.0700.000
4A4PHE 00.0380.0336.444-0.301-0.3010.0000.0000.0000.000
5A5LYS 10.9410.9688.008-2.270-2.2700.0000.0000.0000.000
6A6MET 00.0430.04012.297-0.130-0.1300.0000.0000.0000.000
7A7THR 0-0.018-0.00314.9330.0380.0380.0000.0000.0000.000
8A8LYS 10.9590.96217.566-0.350-0.3500.0000.0000.0000.000
9A9GLU -1-0.912-0.95217.9340.1850.1850.0000.0000.0000.000
10A10GLY 0-0.0140.00319.524-0.046-0.0460.0000.0000.0000.000
11A11LEU 00.019-0.00214.8630.0740.0740.0000.0000.0000.000
12A12VAL 0-0.018-0.00811.923-0.082-0.0820.0000.0000.0000.000
13A13LEU 0-0.0120.0097.8680.1810.1810.0000.0000.0000.000
14A14LEU 0-0.025-0.0296.352-0.056-0.0560.0000.0000.0000.000
15A15ILE 0-0.011-0.0094.2330.1370.2210.000-0.036-0.0490.000
16A16LYS 10.8900.9491.891-14.067-16.41711.588-4.668-4.5690.027
17A17ASP -1-0.855-0.9563.296-2.896-2.0300.063-0.385-0.544-0.003
18A18TYR 0-0.095-0.0653.288-2.238-0.6660.095-0.541-1.125-0.003
19A19GLN 00.006-0.0134.707-0.383-0.3580.000-0.015-0.0100.000
20A20ASN 00.0440.0125.780-0.070-0.0700.0000.0000.0000.000
21A21LEU 00.0390.0294.687-0.720-0.6230.000-0.004-0.0920.000
22A22GLU -1-0.799-0.8795.492-1.691-1.6910.0000.0000.0000.000
23A23GLU -1-0.927-0.9632.853-7.490-5.5410.368-0.896-1.421-0.009
24A24VAL 00.0040.0012.043-4.650-2.9853.890-2.722-2.833-0.006
25A25LEU 0-0.022-0.0132.8522.6400.4380.0302.395-0.223-0.002
26A26ASN 00.0360.0194.9100.6920.6920.0000.0000.0000.000
27A27ALA 00.0040.0012.1021.500-0.6755.358-1.458-1.7260.000
28A28ILE 0-0.053-0.0254.0260.9361.1520.002-0.072-0.1460.000
29A29SER 00.0140.0076.7050.5060.5060.0000.0000.0000.000
30A30ALA 00.0250.0246.8310.3170.3170.0000.0000.0000.000
31A31ARG 10.8280.8966.069-0.485-0.4850.0000.0000.0000.000
32A32ILE 0-0.033-0.0258.7180.2660.2660.0000.0000.0000.000
33A33THR 0-0.013-0.00611.4440.1390.1390.0000.0000.0000.000
34A34GLN 0-0.008-0.0128.136-0.117-0.1170.0000.0000.0000.000
35A35MET 0-0.080-0.02610.3580.1460.1460.0000.0000.0000.000
36A36GLY 00.0610.04314.0760.0290.0290.0000.0000.0000.000
37A37GLY 0-0.044-0.02617.407-0.027-0.0270.0000.0000.0000.000
38A38PHE 0-0.077-0.03216.7590.0310.0310.0000.0000.0000.000
39A39PHE 0-0.003-0.01813.5970.0190.0190.0000.0000.0000.000
40A40ALA 0-0.001-0.00819.077-0.023-0.0230.0000.0000.0000.000
41A41LYS 10.9300.94920.7520.1580.1580.0000.0000.0000.000
42A42GLY 0-0.018-0.00421.499-0.013-0.0130.0000.0000.0000.000
43A43ASP -1-0.805-0.87119.513-0.018-0.0180.0000.0000.0000.000
44A44ARG 10.9620.97819.7290.0060.0060.0000.0000.0000.000
45A45ILE 0-0.008-0.00513.1840.0450.0450.0000.0000.0000.000
46A46SER 0-0.0100.00116.016-0.059-0.0590.0000.0000.0000.000
47A47LEU 00.0050.0079.8500.0230.0230.0000.0000.0000.000
48A48MET 0-0.0140.01110.8070.0880.0880.0000.0000.0000.000
49A49ILE 00.0200.0067.6860.0260.0260.0000.0000.0000.000
50A50GLU -1-0.812-0.9116.0301.2111.2110.0000.0000.0000.000
51A51ASN 00.0000.0358.974-0.011-0.0110.0000.0000.0000.000
52A52HIS 00.043-0.00310.898-0.079-0.0790.0000.0000.0000.000
53A53ASN 0-0.030-0.02412.549-0.066-0.0660.0000.0000.0000.000
54A54LYS 10.9130.97510.1100.1140.1140.0000.0000.0000.000
55A55HIS 10.8400.9257.7920.4620.4620.0000.0000.0000.000
56A56SER 00.0230.02411.902-0.056-0.0560.0000.0000.0000.000
57A57GLN 00.0490.00614.3500.0340.0340.0000.0000.0000.000
58A58ASP -1-0.759-0.8649.918-0.761-0.7610.0000.0000.0000.000
59A59ILE 0-0.047-0.01712.013-0.081-0.0810.0000.0000.0000.000
60A60PRO 00.018-0.00213.767-0.025-0.0250.0000.0000.0000.000
61A61ARG 10.8980.92011.3430.8810.8810.0000.0000.0000.000
62A62ILE 00.0190.0308.421-0.060-0.0600.0000.0000.0000.000
63A63VAL 0-0.008-0.01411.0520.0260.0260.0000.0000.0000.000
64A64SER 0-0.074-0.03214.4260.0380.0380.0000.0000.0000.000
65A65HIS 00.0140.0029.7540.1060.1060.0000.0000.0000.000
66A66LEU 00.002-0.00910.6870.0050.0050.0000.0000.0000.000
67A67ARG 10.8650.93613.6360.3460.3460.0000.0000.0000.000
68A68ASN 0-0.073-0.04215.9640.1000.1000.0000.0000.0000.000
69A69LEU 0-0.040-0.01311.4750.0100.0100.0000.0000.0000.000
70A70GLY 0-0.063-0.02315.8860.0410.0410.0000.0000.0000.000
71A71LEU 00.0090.01013.7840.0430.0430.0000.0000.0000.000
72A72GLU -1-0.794-0.88416.974-0.256-0.2560.0000.0000.0000.000
73A73VAL 00.004-0.00114.5310.0400.0400.0000.0000.0000.000
74A74SER 0-0.053-0.02617.3910.0140.0140.0000.0000.0000.000
75A75GLN 00.0370.00518.402-0.014-0.0140.0000.0000.0000.000
76A76ILE 00.0200.02014.521-0.002-0.0020.0000.0000.0000.000
77A77LEU 0-0.035-0.03314.8040.0230.0230.0000.0000.0000.000
78A78VAL 0-0.003-0.00414.503-0.013-0.0130.0000.0000.0000.000
79A79GLY 00.0150.00414.0700.0200.0200.0000.0000.0000.000
80A80NME 00.0270.02110.1130.0920.0920.0000.0000.0000.000
81A89ACE 00.009-0.00918.812-0.013-0.0130.0000.0000.0000.000
82A90LYS 10.9120.95015.918-0.290-0.2900.0000.0000.0000.000
83A91VAL 00.0460.02115.6800.0170.0170.0000.0000.0000.000
84A92GLN 0-0.045-0.00417.710-0.032-0.0320.0000.0000.0000.000
85A93SER 00.0450.00318.962-0.013-0.0130.0000.0000.0000.000
86A94ARG 10.9300.96319.049-0.077-0.0770.0000.0000.0000.000
87A95THR 0-0.0160.00320.083-0.016-0.0160.0000.0000.0000.000
88A96THR 0-0.009-0.00220.7830.0020.0020.0000.0000.0000.000
89A97VAL 0-0.0090.00118.293-0.008-0.0080.0000.0000.0000.000
90A98GLU -1-0.813-0.89421.724-0.050-0.0500.0000.0000.0000.000
91A99SER 0-0.028-0.01521.870-0.007-0.0070.0000.0000.0000.000
92A100THR 0-0.069-0.03524.0680.0150.0150.0000.0000.0000.000
93A101GLY 00.011-0.00525.448-0.017-0.0170.0000.0000.0000.000
94A102LYS 10.9770.98623.8810.2320.2320.0000.0000.0000.000
95A103VAL 00.0020.02027.8520.0050.0050.0000.0000.0000.000
96A104ILE 0-0.018-0.00227.7380.0060.0060.0000.0000.0000.000
97A105LYS 10.9670.97731.6660.0840.0840.0000.0000.0000.000
98A106ARG 10.8750.91028.7190.0720.0720.0000.0000.0000.000
99A107ASN 00.0120.00933.875-0.008-0.0080.0000.0000.0000.000
100A108ILE 00.0030.01227.7980.0020.0020.0000.0000.0000.000
101A109ARG 10.9840.98030.4740.0250.0250.0000.0000.0000.000
102A110SER 0-0.001-0.00828.948-0.006-0.0060.0000.0000.0000.000
103A111GLY 00.0240.01625.8970.0070.0070.0000.0000.0000.000
104A112GLN 0-0.0170.00624.861-0.003-0.0030.0000.0000.0000.000
105A113THR 00.0520.01120.2520.0010.0010.0000.0000.0000.000
106A114VAL 0-0.0040.01222.734-0.007-0.0070.0000.0000.0000.000
107A115VAL 00.0130.01817.311-0.011-0.0110.0000.0000.0000.000
108A116HIS 0-0.012-0.01920.744-0.017-0.0170.0000.0000.0000.000
109A117SER 00.004-0.00818.010-0.012-0.0120.0000.0000.0000.000
110A118GLY 00.0460.02620.084-0.010-0.0100.0000.0000.0000.000
111A119ASP -1-0.841-0.90523.558-0.179-0.1790.0000.0000.0000.000
112A120VAL 0-0.061-0.03524.972-0.001-0.0010.0000.0000.0000.000
113A121ILE 00.0100.01227.7920.0090.0090.0000.0000.0000.000
114A122VAL 0-0.016-0.01530.2910.0010.0010.0000.0000.0000.000
115A123PHE 0-0.014-0.00432.7870.0040.0040.0000.0000.0000.000
116A124GLY 00.0270.00236.1500.0050.0050.0000.0000.0000.000
117A125ASN 0-0.0130.00835.478-0.002-0.0020.0000.0000.0000.000
118A126VAL 00.0440.03729.3710.0000.0000.0000.0000.0000.000
119A127ASN 0-0.039-0.03432.2130.0060.0060.0000.0000.0000.000
120A128LYS 11.0370.99530.9700.0090.0090.0000.0000.0000.000
121A129GLY 00.0380.03728.675-0.001-0.0010.0000.0000.0000.000
122A130ALA 0-0.042-0.00426.9540.0010.0010.0000.0000.0000.000
123A131GLU -1-0.860-0.91821.572-0.115-0.1150.0000.0000.0000.000
124A132ILE 0-0.005-0.00524.182-0.002-0.0020.0000.0000.0000.000
125A133LEU 0-0.0190.00017.624-0.006-0.0060.0000.0000.0000.000
126A134ALA 00.030-0.00421.090-0.013-0.0130.0000.0000.0000.000
127A135GLY 0-0.018-0.01919.906-0.007-0.0070.0000.0000.0000.000
128A136GLY 00.0480.03420.601-0.004-0.0040.0000.0000.0000.000
129A137SER 00.0750.03624.2450.0100.0100.0000.0000.0000.000
130A138VAL 0-0.045-0.02326.438-0.005-0.0050.0000.0000.0000.000
131A139VAL 00.0150.01828.9800.0090.0090.0000.0000.0000.000
132A140VAL 0-0.033-0.02931.623-0.001-0.0010.0000.0000.0000.000
133A141PHE 00.003-0.00733.9390.0050.0050.0000.0000.0000.000
134A142GLY 00.041-0.00737.4580.0040.0040.0000.0000.0000.000
135A143LYS 10.9300.97237.4840.0300.0300.0000.0000.0000.000
136A144ALA 0-0.001-0.00932.698-0.001-0.0010.0000.0000.0000.000
137A145GLN 0-0.040-0.06033.2120.0060.0060.0000.0000.0000.000
138A146GLY 0-0.0020.01929.1950.0030.0030.0000.0000.0000.000
139A147ASN 0-0.001-0.00225.1340.0020.0020.0000.0000.0000.000
140A148ILE 00.0180.00225.928-0.008-0.0080.0000.0000.0000.000
141A149ARG 10.8620.91320.4100.1410.1410.0000.0000.0000.000
142A150ALA 00.0410.02222.640-0.015-0.0150.0000.0000.0000.000
143A151GLY 00.0310.00022.834-0.001-0.0010.0000.0000.0000.000
144A152LEU 0-0.114-0.04117.503-0.017-0.0170.0000.0000.0000.000
145A153ASN 0-0.077-0.02616.528-0.076-0.0760.0000.0000.0000.000
146A154GLU -1-0.929-0.96618.795-0.218-0.2180.0000.0000.0000.000
147A155GLY 00.0030.00822.0120.0090.0090.0000.0000.0000.000
148A156GLY 0-0.019-0.04322.9890.0120.0120.0000.0000.0000.000
149A157GLN 0-0.022-0.00526.1560.0230.0230.0000.0000.0000.000
150A158ALA 00.0180.04325.4270.0070.0070.0000.0000.0000.000
151A159VAL 00.010-0.00727.4950.0110.0110.0000.0000.0000.000
152A160VAL 0-0.020-0.00828.112-0.007-0.0070.0000.0000.0000.000
153A161ALA 00.0170.01430.7350.0080.0080.0000.0000.0000.000
154A162ALA 0-0.027-0.01233.810-0.003-0.0030.0000.0000.0000.000
155A163LEU 0-0.0100.01536.1340.0020.0020.0000.0000.0000.000
156A164ASP -1-0.803-0.89838.472-0.038-0.0380.0000.0000.0000.000
157A165LEU 00.0110.01232.903-0.001-0.0010.0000.0000.0000.000
158A166GLN 0-0.033-0.03636.4290.0040.0040.0000.0000.0000.000
159A167THR 0-0.001-0.01130.8190.0030.0030.0000.0000.0000.000
160A168SER 0-0.087-0.02529.6000.0060.0060.0000.0000.0000.000
161A169LEU 0-0.027-0.01524.7290.0030.0030.0000.0000.0000.000
162A170ILE 00.0210.01327.596-0.005-0.0050.0000.0000.0000.000
163A171GLN 0-0.014-0.00919.5700.0110.0110.0000.0000.0000.000
164A172ILE 00.0180.01124.599-0.005-0.0050.0000.0000.0000.000
165A173ALA 00.0050.02121.2160.0050.0050.0000.0000.0000.000
166A174GLY 00.003-0.00821.114-0.002-0.0020.0000.0000.0000.000
167A175PHE 0-0.040-0.00822.0330.0170.0170.0000.0000.0000.000
168A176ILE 00.031-0.00922.592-0.007-0.0070.0000.0000.0000.000
169A177THR 0-0.0020.00726.7020.0110.0110.0000.0000.0000.000
170A178HIS 00.008-0.00627.522-0.002-0.0020.0000.0000.0000.000
171A179SER 0-0.048-0.01331.9310.0040.0040.0000.0000.0000.000
172A180LYS 10.8910.95934.3210.0320.0320.0000.0000.0000.000
173A181GLY 00.0300.01736.6470.0000.0000.0000.0000.0000.000
174A182GLU -1-0.927-0.95639.096-0.040-0.0400.0000.0000.0000.000
175A183GLU -1-0.965-0.99042.332-0.029-0.0290.0000.0000.0000.000
176A184ASN 0-0.073-0.03742.937-0.001-0.0010.0000.0000.0000.000
177A185VAL 00.0510.04242.8730.0000.0000.0000.0000.0000.000
178A186PRO 0-0.037-0.00740.546-0.004-0.0040.0000.0000.0000.000
179A187SER 0-0.016-0.00538.3570.0010.0010.0000.0000.0000.000
180A188ILE 0-0.023-0.02234.680-0.005-0.0050.0000.0000.0000.000
181A189ALA 00.004-0.00531.7930.0030.0030.0000.0000.0000.000
182A190HIS 0-0.018-0.02731.251-0.016-0.0160.0000.0000.0000.000
183A191VAL 00.0080.01627.7490.0070.0070.0000.0000.0000.000
184A192LYS 10.9520.98931.1870.0750.0750.0000.0000.0000.000
185A193GLY 0-0.001-0.00634.0380.0030.0030.0000.0000.0000.000
186A194ASN 0-0.041-0.02729.365-0.010-0.0100.0000.0000.0000.000
187A195ARG 10.9440.97030.5850.0670.0670.0000.0000.0000.000
188A196ILE 00.0050.01527.357-0.003-0.0030.0000.0000.0000.000
189A197VAL 0-0.047-0.02531.7280.0090.0090.0000.0000.0000.000
190A198ILE 00.0120.00033.980-0.006-0.0060.0000.0000.0000.000
191A199GLU -1-0.823-0.89736.854-0.070-0.0700.0000.0000.0000.000
192A200PRO 00.0400.02439.604-0.004-0.0040.0000.0000.0000.000
193A201PHE 00.039-0.02841.010-0.003-0.0030.0000.0000.0000.000
194A202ASP -1-0.939-0.96041.970-0.056-0.0560.0000.0000.0000.000
195A203LYS 10.8930.94143.7640.0490.0490.0000.0000.0000.000
196A204VAL 0-0.0410.01338.025-0.001-0.0010.0000.0000.0000.000
197A205SER 0-0.035-0.01540.0000.0010.0010.0000.0000.0000.000
198A206PHE 00.014-0.00534.873-0.001-0.0010.0000.0000.0000.000
199A207NME 00.0040.01336.1090.0010.0010.0000.0000.0000.000