Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LJ9L9

Calculation Name: 1HF2-A-Xray372

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: 2023-06-19

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 OptH
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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2044077.591205
FMO2-HF: Nuclear repulsion 1970553.244793
FMO2-HF: Total energy -73524.346412
FMO2-MP2: Total energy -73741.515365


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.
-27.115-25.07821.357-9.523-13.8680.006
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 : 0.015 / 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-1-0.906-0.9443.7971.3653.578-0.027-1.100-1.0850.000
4A4PHE00.0400.0346.442-0.281-0.2810.0000.0000.0000.000
5A5LYS10.9360.9668.008-2.267-2.2670.0000.0000.0000.000
6A6MET00.0450.04112.297-0.123-0.1230.0000.0000.0000.000
7A7THR0-0.021-0.00414.9330.0390.0390.0000.0000.0000.000
8A8LYS10.9600.96217.566-0.345-0.3450.0000.0000.0000.000
9A9GLU-1-0.912-0.95217.9340.1830.1830.0000.0000.0000.000
10A10GLY0-0.0130.00419.524-0.045-0.0450.0000.0000.0000.000
11A11LEU00.020-0.00214.8600.0720.0720.0000.0000.0000.000
12A12VAL0-0.022-0.01011.924-0.081-0.0810.0000.0000.0000.000
13A13LEU0-0.0080.0117.8690.1800.1800.0000.0000.0000.000
14A14LEU0-0.033-0.0336.353-0.058-0.0580.0000.0000.0000.000
15A15ILE0-0.005-0.0064.2330.1430.226-0.001-0.037-0.0460.000
16A16LYS10.8830.9471.892-14.224-16.46311.652-4.790-4.6230.028
17A17ASP-1-0.852-0.9553.296-2.861-2.0040.062-0.377-0.542-0.003
18A18TYR0-0.096-0.0663.288-2.241-0.6750.094-0.534-1.126-0.003
19A19GLN00.007-0.0134.707-0.374-0.352-0.001-0.016-0.0040.000
20A20ASN00.0420.0115.780-0.058-0.0580.0000.0000.0000.000
21A21LEU00.0400.0304.687-0.695-0.603-0.001-0.003-0.0880.000
22A22GLU-1-0.799-0.8805.492-1.672-1.6720.0000.0000.0000.000
23A23GLU-1-0.928-0.9642.853-7.427-5.4730.365-0.895-1.424-0.009
24A24VAL00.0040.0022.043-4.579-2.9203.837-2.665-2.830-0.006
25A25LEU0-0.016-0.0112.8522.5920.3850.0212.411-0.225-0.001
26A26ASN00.0300.0174.9100.6870.6870.0000.0000.0000.000
27A27ALA00.0040.0012.1021.507-0.6765.355-1.444-1.7270.000
28A28ILE0-0.051-0.0244.0260.8781.0980.001-0.073-0.1480.000
29A29SER00.0120.0076.7050.4890.4890.0000.0000.0000.000
30A30ALA00.0260.0256.8300.3100.3100.0000.0000.0000.000
31A31ARG10.8280.8976.068-0.499-0.4990.0000.0000.0000.000
32A32ILE0-0.032-0.0258.7180.2590.2590.0000.0000.0000.000
33A33THR0-0.014-0.00711.4440.1360.1360.0000.0000.0000.000
34A34GLN0-0.007-0.0118.136-0.121-0.1210.0000.0000.0000.000
35A35MET0-0.077-0.02410.3570.1420.1420.0000.0000.0000.000
36A36GLY00.0570.04114.0740.0300.0300.0000.0000.0000.000
37A37GLY0-0.046-0.02617.405-0.027-0.0270.0000.0000.0000.000
38A38PHE0-0.076-0.03316.7570.0290.0290.0000.0000.0000.000
39A39PHE0-0.003-0.01813.5950.0190.0190.0000.0000.0000.000
40A40ALA0-0.001-0.00719.077-0.022-0.0220.0000.0000.0000.000
41A41LYS10.9300.94820.7520.1580.1580.0000.0000.0000.000
42A42GLY0-0.018-0.00521.499-0.014-0.0140.0000.0000.0000.000
43A43ASP-1-0.805-0.87119.513-0.019-0.0190.0000.0000.0000.000
44A44ARG10.9630.97919.7290.0070.0070.0000.0000.0000.000
45A45ILE0-0.008-0.00513.1840.0430.0430.0000.0000.0000.000
46A46SER0-0.0090.00116.016-0.058-0.0580.0000.0000.0000.000
47A47LEU00.0080.0089.8490.0230.0230.0000.0000.0000.000
48A48MET0-0.0260.01010.8120.1000.1000.0000.0000.0000.000
49A49ILE00.0260.0117.6860.0260.0260.0000.0000.0000.000
50A50GLU-1-0.815-0.9086.0311.1901.1900.0000.0000.0000.000
51A51ASN0-0.0080.0278.975-0.003-0.0030.0000.0000.0000.000
52A52HIS00.022-0.01310.898-0.124-0.1240.0000.0000.0000.000
53A53ASN00.006-0.00512.549-0.065-0.0650.0000.0000.0000.000
54A54LYS10.9060.97110.1120.1210.1210.0000.0000.0000.000
55A55HIS10.8370.9227.7900.4720.4720.0000.0000.0000.000
56A56SER00.0290.02811.902-0.059-0.0590.0000.0000.0000.000
57A57GLN00.0410.00314.3510.0350.0350.0000.0000.0000.000
58A58ASP-1-0.760-0.8649.918-0.759-0.7590.0000.0000.0000.000
59A59ILE0-0.046-0.01612.013-0.082-0.0820.0000.0000.0000.000
60A60PRO00.015-0.00413.767-0.025-0.0250.0000.0000.0000.000
61A61ARG10.9020.92111.3430.8800.8800.0000.0000.0000.000
62A62ILE00.0210.0318.420-0.057-0.0570.0000.0000.0000.000
63A63VAL0-0.010-0.01511.0520.0220.0220.0000.0000.0000.000
64A64SER0-0.072-0.03214.4260.0380.0380.0000.0000.0000.000
65A65HIS00.0130.0029.7540.1070.1070.0000.0000.0000.000
66A66LEU00.000-0.01010.6870.0040.0040.0000.0000.0000.000
67A67ARG10.8650.93513.6360.3440.3440.0000.0000.0000.000
68A68ASN0-0.071-0.04115.9640.0990.0990.0000.0000.0000.000
69A69LEU0-0.039-0.01311.4750.0100.0100.0000.0000.0000.000
70A70GLY0-0.063-0.02215.8860.0390.0390.0000.0000.0000.000
71A71LEU00.0100.01013.7840.0420.0420.0000.0000.0000.000
72A72GLU-1-0.798-0.88416.974-0.257-0.2570.0000.0000.0000.000
73A73VAL00.005-0.00114.5300.0390.0390.0000.0000.0000.000
74A74SER0-0.050-0.02617.3910.0130.0130.0000.0000.0000.000
75A75GLN00.0350.00418.402-0.013-0.0130.0000.0000.0000.000
76A76ILE00.0260.02214.521-0.002-0.0020.0000.0000.0000.000
77A77LEU0-0.042-0.03614.8050.0230.0230.0000.0000.0000.000
78A78VAL00.0070.00614.503-0.014-0.0140.0000.0000.0000.000
79A79GLY00.0390.01211.5790.0480.0480.0000.0000.0000.000
80A90LYS10.9470.96015.909-0.338-0.3380.0000.0000.0000.000
81A91VAL00.017-0.00215.6810.0210.0210.0000.0000.0000.000
82A92GLN0-0.0390.00117.712-0.030-0.0300.0000.0000.0000.000
83A93SER00.0480.00518.959-0.011-0.0110.0000.0000.0000.000
84A94ARG10.9280.96119.049-0.074-0.0740.0000.0000.0000.000
85A95THR0-0.0140.00520.085-0.015-0.0150.0000.0000.0000.000
86A96THR0-0.008-0.00120.7830.0020.0020.0000.0000.0000.000
87A97VAL0-0.0070.00118.293-0.007-0.0070.0000.0000.0000.000
88A98GLU-1-0.814-0.89321.724-0.051-0.0510.0000.0000.0000.000
89A99SER0-0.028-0.01621.870-0.007-0.0070.0000.0000.0000.000
90A100THR0-0.069-0.03524.0680.0150.0150.0000.0000.0000.000
91A101GLY00.011-0.00525.448-0.017-0.0170.0000.0000.0000.000
92A102LYS10.9790.98623.8810.2320.2320.0000.0000.0000.000
93A103VAL00.0010.01827.8520.0050.0050.0000.0000.0000.000
94A104ILE0-0.016-0.00127.7380.0060.0060.0000.0000.0000.000
95A105LYS10.9660.97631.6660.0840.0840.0000.0000.0000.000
96A106ARG10.8730.91128.7190.0720.0720.0000.0000.0000.000
97A107ASN00.0140.01033.875-0.008-0.0080.0000.0000.0000.000
98A108ILE00.0050.01327.7980.0020.0020.0000.0000.0000.000
99A109ARG10.9790.98030.4740.0250.0250.0000.0000.0000.000
100A110SER00.002-0.00728.948-0.007-0.0070.0000.0000.0000.000
101A111GLY00.0220.01525.8970.0070.0070.0000.0000.0000.000
102A112GLN0-0.0190.00224.861-0.003-0.0030.0000.0000.0000.000
103A113THR00.0530.01220.2530.0020.0020.0000.0000.0000.000
104A114VAL0-0.0070.01122.734-0.006-0.0060.0000.0000.0000.000
105A115VAL00.0130.01717.311-0.010-0.0100.0000.0000.0000.000
106A116HIS0-0.012-0.01820.744-0.016-0.0160.0000.0000.0000.000
107A117SER00.005-0.00818.048-0.012-0.0120.0000.0000.0000.000
108A118GLY00.0460.02620.084-0.011-0.0110.0000.0000.0000.000
109A119ASP-1-0.843-0.90623.558-0.180-0.1800.0000.0000.0000.000
110A120VAL0-0.059-0.03324.972-0.002-0.0020.0000.0000.0000.000
111A121ILE00.0090.01127.7920.0080.0080.0000.0000.0000.000
112A122VAL0-0.012-0.01330.2910.0010.0010.0000.0000.0000.000
113A123PHE0-0.017-0.00532.7870.0040.0040.0000.0000.0000.000
114A124GLY00.0290.00236.1500.0040.0040.0000.0000.0000.000
115A125ASN0-0.0140.00835.478-0.002-0.0020.0000.0000.0000.000
116A126VAL00.0470.03929.3710.0000.0000.0000.0000.0000.000
117A127ASN0-0.041-0.03532.2130.0060.0060.0000.0000.0000.000
118A128LYS11.0350.99330.9700.0100.0100.0000.0000.0000.000
119A129GLY00.0370.03828.675-0.002-0.0020.0000.0000.0000.000
120A130ALA0-0.041-0.00526.9540.0010.0010.0000.0000.0000.000
121A131GLU-1-0.859-0.91821.572-0.117-0.1170.0000.0000.0000.000
122A132ILE0-0.009-0.00624.182-0.001-0.0010.0000.0000.0000.000
123A133LEU0-0.0160.00117.624-0.005-0.0050.0000.0000.0000.000
124A134ALA00.034-0.00221.090-0.012-0.0120.0000.0000.0000.000
125A135GLY0-0.021-0.02019.906-0.006-0.0060.0000.0000.0000.000
126A136GLY00.0500.03420.601-0.005-0.0050.0000.0000.0000.000
127A137SER00.0820.03924.2450.0090.0090.0000.0000.0000.000
128A138VAL0-0.053-0.02626.438-0.005-0.0050.0000.0000.0000.000
129A139VAL00.0140.01728.9800.0090.0090.0000.0000.0000.000
130A140VAL0-0.031-0.02831.623-0.001-0.0010.0000.0000.0000.000
131A141PHE00.000-0.00833.9390.0050.0050.0000.0000.0000.000
132A142GLY00.041-0.00737.4580.0040.0040.0000.0000.0000.000
133A143LYS10.9310.97337.4840.0300.0300.0000.0000.0000.000
134A144ALA0-0.003-0.01032.698-0.001-0.0010.0000.0000.0000.000
135A145GLN0-0.038-0.05933.2120.0060.0060.0000.0000.0000.000
136A146GLY0-0.0020.01929.1950.0030.0030.0000.0000.0000.000
137A147ASN00.001-0.00125.1340.0030.0030.0000.0000.0000.000
138A148ILE00.0190.00225.928-0.007-0.0070.0000.0000.0000.000
139A149ARG10.8610.91320.4100.1440.1440.0000.0000.0000.000
140A150ALA00.0450.02422.640-0.015-0.0150.0000.0000.0000.000
141A151GLY00.020-0.00322.8340.0000.0000.0000.0000.0000.000
142A152LEU0-0.103-0.03817.503-0.015-0.0150.0000.0000.0000.000
143A153ASN0-0.081-0.02716.528-0.074-0.0740.0000.0000.0000.000
144A154GLU-1-0.932-0.96718.795-0.218-0.2180.0000.0000.0000.000
145A155GLY00.0020.00722.0120.0080.0080.0000.0000.0000.000
146A156GLY0-0.018-0.04222.9890.0110.0110.0000.0000.0000.000
147A157GLN0-0.024-0.00726.1560.0230.0230.0000.0000.0000.000
148A158ALA00.0190.04325.4270.0070.0070.0000.0000.0000.000
149A159VAL00.009-0.00727.4950.0100.0100.0000.0000.0000.000
150A160VAL0-0.015-0.00628.112-0.007-0.0070.0000.0000.0000.000
151A161ALA00.0130.01330.7350.0080.0080.0000.0000.0000.000
152A162ALA0-0.027-0.01333.810-0.003-0.0030.0000.0000.0000.000
153A163LEU0-0.0090.01536.1340.0020.0020.0000.0000.0000.000
154A164ASP-1-0.803-0.89938.472-0.039-0.0390.0000.0000.0000.000
155A165LEU00.0060.01032.903-0.001-0.0010.0000.0000.0000.000
156A166GLN0-0.027-0.03436.4290.0040.0040.0000.0000.0000.000
157A167THR0-0.001-0.01230.8190.0030.0030.0000.0000.0000.000
158A168SER0-0.087-0.02629.6000.0060.0060.0000.0000.0000.000
159A169LEU0-0.028-0.01524.7290.0030.0030.0000.0000.0000.000
160A170ILE00.0210.01427.596-0.005-0.0050.0000.0000.0000.000
161A171GLN0-0.015-0.00819.5700.0110.0110.0000.0000.0000.000
162A172ILE00.0190.01124.599-0.004-0.0040.0000.0000.0000.000
163A173ALA00.0060.02121.2160.0060.0060.0000.0000.0000.000
164A174GLY00.003-0.00921.114-0.002-0.0020.0000.0000.0000.000
165A175PHE0-0.039-0.00822.0330.0160.0160.0000.0000.0000.000
166A176ILE00.030-0.01022.592-0.008-0.0080.0000.0000.0000.000
167A177THR0-0.0040.00626.7020.0100.0100.0000.0000.0000.000
168A178HIS00.009-0.00527.522-0.003-0.0030.0000.0000.0000.000
169A179SER0-0.047-0.01331.9310.0040.0040.0000.0000.0000.000
170A180LYS10.8910.95934.3210.0330.0330.0000.0000.0000.000
171A181GLY00.0290.01836.6470.0000.0000.0000.0000.0000.000
172A182GLU-1-0.926-0.95639.096-0.040-0.0400.0000.0000.0000.000
173A183GLU-1-0.964-0.99042.332-0.029-0.0290.0000.0000.0000.000
174A184ASN0-0.072-0.03742.937-0.001-0.0010.0000.0000.0000.000
175A185VAL00.0480.04142.8730.0000.0000.0000.0000.0000.000
176A186PRO0-0.037-0.00740.546-0.003-0.0030.0000.0000.0000.000
177A187SER0-0.014-0.00438.3570.0010.0010.0000.0000.0000.000
178A188ILE0-0.027-0.02334.680-0.005-0.0050.0000.0000.0000.000
179A189ALA00.001-0.00531.7920.0030.0030.0000.0000.0000.000
180A190HIS0-0.016-0.02731.251-0.015-0.0150.0000.0000.0000.000
181A191VAL00.0160.01827.7490.0070.0070.0000.0000.0000.000
182A192LYS10.9540.99131.1870.0750.0750.0000.0000.0000.000
183A193GLY0-0.007-0.01034.0380.0030.0030.0000.0000.0000.000
184A194ASN0-0.041-0.02729.365-0.009-0.0090.0000.0000.0000.000
185A195ARG10.9450.97030.5850.0680.0680.0000.0000.0000.000
186A196ILE00.0030.01527.357-0.003-0.0030.0000.0000.0000.000
187A197VAL0-0.047-0.02531.7280.0080.0080.0000.0000.0000.000
188A198ILE00.0150.00033.980-0.006-0.0060.0000.0000.0000.000
189A199GLU-1-0.824-0.89736.854-0.070-0.0700.0000.0000.0000.000
190A200PRO00.0370.02339.604-0.004-0.0040.0000.0000.0000.000
191A201PHE00.044-0.02741.010-0.003-0.0030.0000.0000.0000.000
192A202ASP-1-0.942-0.96241.970-0.056-0.0560.0000.0000.0000.000
193A203LYS10.8930.94143.7640.0500.0500.0000.0000.0000.000
194A204VAL0-0.0400.01338.025-0.001-0.0010.0000.0000.0000.000
195A205SER0-0.042-0.01339.9900.0010.0010.0000.0000.0000.000
196A206PHE00.0270.01034.8760.0000.0000.0000.0000.0000.000