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: 9GKY2

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2044577.840333
FMO2-HF: Nuclear repulsion 1971052.015271
FMO2-HF: Total energy -73525.825062
FMO2-MP2: Total energy -73742.870656


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.
-46.151-39.85419.285-11.618-13.9620.032
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 : 0.043 / q_NPA : 0.035
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-1-0.886-0.9373.7971.7263.869-0.027-1.045-1.0700.000
4A4PHE00.0600.0376.424-0.275-0.2750.0000.0000.0000.000
5A5LYS10.9340.9688.042-2.253-2.2530.0000.0000.0000.000
6A6MET00.0450.03912.297-0.120-0.1200.0000.0000.0000.000
7A7THR0-0.027-0.01414.7850.0360.0360.0000.0000.0000.000
8A8LYS10.9720.97317.566-0.330-0.3300.0000.0000.0000.000
9A9GLU-1-0.795-0.86318.0170.1530.1530.0000.0000.0000.000
10A10GLY00.0170.02519.520-0.042-0.0420.0000.0000.0000.000
11A11LEU00.021-0.00415.3830.0730.0730.0000.0000.0000.000
12A12VAL0-0.020-0.01012.134-0.078-0.0780.0000.0000.0000.000
13A13LEU0-0.0130.0058.1090.1740.1740.0000.0000.0000.000
14A14LEU0-0.026-0.0245.966-0.096-0.0960.0000.0000.0000.000
15A15ILE0-0.006-0.0094.1000.0700.178-0.001-0.039-0.0680.000
16A16LYS10.8770.9161.970-29.699-32.60415.758-6.957-5.8960.058
17A17ASP-1-0.783-0.8873.060-3.096-1.9510.151-0.539-0.757-0.005
18A18TYR0-0.062-0.0523.045-3.013-0.9430.364-0.803-1.631-0.005
19A19GLN00.0180.0064.640-0.755-0.7160.001-0.021-0.0180.000
20A20ASN00.0490.0145.831-0.177-0.192-0.001-0.0060.0230.000
21A21LEU00.0200.0215.377-0.227-0.2270.0000.0000.0000.000
22A22GLU-1-0.759-0.8436.123-1.308-1.3080.0000.0000.0000.000
23A23GLU-1-0.890-0.9422.424-7.883-5.8330.570-1.237-1.383-0.011
24A24VAL00.0230.0102.335-3.295-1.6531.204-0.913-1.933-0.002
25A25LEU0-0.002-0.0013.3010.3200.0300.0020.407-0.119-0.001
26A26ASN00.0060.0155.2290.6530.6530.0000.0000.0000.000
27A27ALA00.003-0.0032.5630.0450.2391.265-0.444-1.016-0.002
28A28ILE0-0.043-0.0224.5230.8280.944-0.001-0.021-0.0940.000
29A29SER00.0070.0057.0980.5240.5240.0000.0000.0000.000
30A30ALA00.0160.0216.9990.2910.2910.0000.0000.0000.000
31A31ARG10.8150.8806.024-0.447-0.4470.0000.0000.0000.000
32A32ILE0-0.017-0.0199.0110.2610.2610.0000.0000.0000.000
33A33THR0-0.019-0.01611.9650.1330.1330.0000.0000.0000.000
34A34GLN00.0010.0098.5030.1240.1240.0000.0000.0000.000
35A35MET0-0.078-0.02310.2550.1590.1590.0000.0000.0000.000
36A36GLY00.0620.04114.0590.0350.0350.0000.0000.0000.000
37A37GLY0-0.044-0.02617.390-0.022-0.0220.0000.0000.0000.000
38A38PHE0-0.078-0.03416.4350.0320.0320.0000.0000.0000.000
39A39PHE0-0.004-0.00613.5840.0190.0190.0000.0000.0000.000
40A40ALA00.0000.00419.153-0.024-0.0240.0000.0000.0000.000
41A41LYS10.9320.94721.2120.1510.1510.0000.0000.0000.000
42A42GLY0-0.016-0.00321.810-0.011-0.0110.0000.0000.0000.000
43A43ASP-1-0.801-0.88919.883-0.004-0.0040.0000.0000.0000.000
44A44ARG10.9170.96019.7860.0100.0100.0000.0000.0000.000
45A45ILE0-0.023-0.00513.3060.0390.0390.0000.0000.0000.000
46A46SER00.0060.01015.961-0.052-0.0520.0000.0000.0000.000
47A47LEU00.0040.0049.8660.0190.0190.0000.0000.0000.000
48A48MET0-0.0080.02510.5700.1070.1070.0000.0000.0000.000
49A49ILE00.0270.0107.4520.0080.0080.0000.0000.0000.000
50A50GLU-1-0.815-0.9246.0931.2051.2050.0000.0000.0000.000
51A51ASN0-0.0230.0208.6980.0040.0040.0000.0000.0000.000
52A52HIS00.037-0.00910.639-0.082-0.0820.0000.0000.0000.000
53A53ASN0-0.009-0.01212.350-0.047-0.0470.0000.0000.0000.000
54A54LYS10.7990.8868.629-0.128-0.1280.0000.0000.0000.000
55A55HIS10.8130.9117.7670.1640.1640.0000.0000.0000.000
56A56SER00.0190.02111.759-0.056-0.0560.0000.0000.0000.000
57A57GLN00.000-0.01914.1110.0180.0180.0000.0000.0000.000
58A58ASP-1-0.737-0.84710.720-0.413-0.4130.0000.0000.0000.000
59A59ILE0-0.025-0.01112.542-0.076-0.0760.0000.0000.0000.000
60A60PRO00.0220.00714.045-0.028-0.0280.0000.0000.0000.000
61A61ARG10.8700.88911.6850.6660.6660.0000.0000.0000.000
62A62ILE00.0170.0278.641-0.064-0.0640.0000.0000.0000.000
63A63VAL0-0.003-0.01411.4010.0030.0030.0000.0000.0000.000
64A64SER0-0.054-0.02514.6800.0420.0420.0000.0000.0000.000
65A65HIS0-0.036-0.02010.1630.0920.0920.0000.0000.0000.000
66A66LEU00.003-0.00510.466-0.013-0.0130.0000.0000.0000.000
67A67ARG10.8750.94513.6770.2730.2730.0000.0000.0000.000
68A68ASN0-0.080-0.04816.0590.0730.0730.0000.0000.0000.000
69A69LEU0-0.027-0.01011.7900.0010.0010.0000.0000.0000.000
70A70GLY0-0.065-0.02216.0880.0300.0300.0000.0000.0000.000
71A71LEU00.0250.01914.0740.0370.0370.0000.0000.0000.000
72A72GLU-1-0.801-0.87217.098-0.194-0.1940.0000.0000.0000.000
73A73VAL00.009-0.00214.4510.0340.0340.0000.0000.0000.000
74A74SER00.0100.00217.4290.0010.0010.0000.0000.0000.000
75A75GLN0-0.027-0.01418.376-0.005-0.0050.0000.0000.0000.000
76A76ILE00.0200.02214.514-0.003-0.0030.0000.0000.0000.000
77A77LEU0-0.046-0.03314.7560.0230.0230.0000.0000.0000.000
78A78VAL00.0080.00314.432-0.011-0.0110.0000.0000.0000.000
79A79GLY00.0290.00611.6840.0440.0440.0000.0000.0000.000
80A90LYS10.9240.94515.812-0.361-0.3610.0000.0000.0000.000
81A91VAL00.0320.00615.5790.0230.0230.0000.0000.0000.000
82A92GLN0-0.0270.01017.621-0.019-0.0190.0000.0000.0000.000
83A93SER00.018-0.00918.885-0.020-0.0200.0000.0000.0000.000
84A94ARG10.7880.85018.971-0.119-0.1190.0000.0000.0000.000
85A95THR0-0.0050.00120.233-0.002-0.0020.0000.0000.0000.000
86A96THR0-0.018-0.00120.7030.0020.0020.0000.0000.0000.000
87A97VAL00.005-0.00518.251-0.008-0.0080.0000.0000.0000.000
88A98GLU-1-0.797-0.88521.692-0.028-0.0280.0000.0000.0000.000
89A99SER0-0.033-0.03521.984-0.005-0.0050.0000.0000.0000.000
90A100THR0-0.068-0.04624.0980.0110.0110.0000.0000.0000.000
91A101GLY00.0180.00625.698-0.015-0.0150.0000.0000.0000.000
92A102LYS10.9160.95023.3880.1950.1950.0000.0000.0000.000
93A103VAL00.0010.01528.2410.0050.0050.0000.0000.0000.000
94A104ILE0-0.018-0.00327.8760.0040.0040.0000.0000.0000.000
95A105LYS10.9630.97732.0120.0650.0650.0000.0000.0000.000
96A106ARG10.8780.91128.6820.0470.0470.0000.0000.0000.000
97A107ASN00.0120.01933.839-0.006-0.0060.0000.0000.0000.000
98A108ILE00.0040.00927.5700.0020.0020.0000.0000.0000.000
99A109ARG10.9830.98130.4710.0080.0080.0000.0000.0000.000
100A110SER00.009-0.00628.854-0.005-0.0050.0000.0000.0000.000
101A111GLY00.0260.02025.7720.0050.0050.0000.0000.0000.000
102A112GLN0-0.0420.00024.762-0.001-0.0010.0000.0000.0000.000
103A113THR00.0490.01320.1770.0040.0040.0000.0000.0000.000
104A114VAL0-0.0030.01122.687-0.006-0.0060.0000.0000.0000.000
105A115VAL00.0160.01717.581-0.006-0.0060.0000.0000.0000.000
106A116HIS00.024-0.00121.027-0.022-0.0220.0000.0000.0000.000
107A117SER00.0340.00718.9000.0050.0050.0000.0000.0000.000
108A118GLY00.0360.02520.568-0.008-0.0080.0000.0000.0000.000
109A119ASP-1-0.848-0.91024.077-0.139-0.1390.0000.0000.0000.000
110A120VAL0-0.063-0.03825.332-0.002-0.0020.0000.0000.0000.000
111A121ILE00.0080.01028.2760.0070.0070.0000.0000.0000.000
112A122VAL0-0.011-0.01230.4500.0000.0000.0000.0000.0000.000
113A123PHE0-0.009-0.00133.1760.0030.0030.0000.0000.0000.000
114A124GLY00.0290.00336.1610.0030.0030.0000.0000.0000.000
115A125ASN0-0.035-0.01235.401-0.001-0.0010.0000.0000.0000.000
116A126VAL00.0420.03829.3100.0000.0000.0000.0000.0000.000
117A127ASN0-0.024-0.02732.0180.0060.0060.0000.0000.0000.000
118A128LYS11.0320.99830.846-0.007-0.0070.0000.0000.0000.000
119A129GLY00.0410.03928.522-0.001-0.0010.0000.0000.0000.000
120A130ALA0-0.044-0.00626.8210.0020.0020.0000.0000.0000.000
121A131GLU-1-0.840-0.91221.154-0.058-0.0580.0000.0000.0000.000
122A132ILE0-0.009-0.00724.176-0.002-0.0020.0000.0000.0000.000
123A133LEU0-0.0170.00217.709-0.001-0.0010.0000.0000.0000.000
124A134ALA00.032-0.00321.458-0.012-0.0120.0000.0000.0000.000
125A135GLY0-0.016-0.02020.504-0.002-0.0020.0000.0000.0000.000
126A136GLY00.0410.02721.191-0.004-0.0040.0000.0000.0000.000
127A137SER00.0830.04324.8500.0100.0100.0000.0000.0000.000
128A138VAL0-0.056-0.03126.909-0.004-0.0040.0000.0000.0000.000
129A139VAL00.0110.01629.5420.0070.0070.0000.0000.0000.000
130A140VAL0-0.025-0.02631.829-0.001-0.0010.0000.0000.0000.000
131A141PHE00.003-0.00534.3340.0040.0040.0000.0000.0000.000
132A142GLY00.0370.00037.7700.0030.0030.0000.0000.0000.000
133A143LYS10.8580.92337.5300.0150.0150.0000.0000.0000.000
134A144ALA0-0.009-0.01432.721-0.001-0.0010.0000.0000.0000.000
135A145GLN0-0.018-0.04933.0960.0060.0060.0000.0000.0000.000
136A146GLY0-0.0050.01929.0660.0030.0030.0000.0000.0000.000
137A147ASN0-0.006-0.00424.2900.0030.0030.0000.0000.0000.000
138A148ILE00.011-0.00725.808-0.006-0.0060.0000.0000.0000.000
139A149ARG10.8310.91420.3660.0760.0760.0000.0000.0000.000
140A150ALA00.0350.02223.159-0.012-0.0120.0000.0000.0000.000
141A151GLY00.0370.00323.5030.0020.0020.0000.0000.0000.000
142A152LEU0-0.113-0.04618.180-0.011-0.0110.0000.0000.0000.000
143A153ASN0-0.086-0.02917.256-0.053-0.0530.0000.0000.0000.000
144A154GLU-1-0.909-0.95619.453-0.164-0.1640.0000.0000.0000.000
145A155GLY00.0120.01122.7290.0050.0050.0000.0000.0000.000
146A156GLY0-0.011-0.04023.7080.0080.0080.0000.0000.0000.000
147A157GLN0-0.024-0.00426.8890.0150.0150.0000.0000.0000.000
148A158ALA00.0240.04626.0820.0050.0050.0000.0000.0000.000
149A159VAL0-0.013-0.01528.1720.0090.0090.0000.0000.0000.000
150A160VAL0-0.003-0.00528.566-0.005-0.0050.0000.0000.0000.000
151A161ALA00.0100.01331.3560.0060.0060.0000.0000.0000.000
152A162ALA0-0.018-0.00934.349-0.002-0.0020.0000.0000.0000.000
153A163LEU00.0030.01336.5430.0010.0010.0000.0000.0000.000
154A164ASP-1-0.733-0.85538.643-0.020-0.0200.0000.0000.0000.000
155A165LEU00.0070.01333.0410.0000.0000.0000.0000.0000.000
156A166GLN00.010-0.01436.3540.0040.0040.0000.0000.0000.000
157A167THR00.0320.00630.7560.0030.0030.0000.0000.0000.000
158A168SER0-0.092-0.01929.4890.0040.0040.0000.0000.0000.000
159A169LEU0-0.021-0.00524.5750.0030.0030.0000.0000.0000.000
160A170ILE00.0250.01327.737-0.004-0.0040.0000.0000.0000.000
161A171GLN0-0.013-0.00719.9130.0120.0120.0000.0000.0000.000
162A172ILE00.0180.00725.268-0.005-0.0050.0000.0000.0000.000
163A173ALA00.0010.01521.9080.0050.0050.0000.0000.0000.000
164A174GLY00.006-0.00421.8420.0010.0010.0000.0000.0000.000
165A175PHE0-0.037-0.00322.7660.0130.0130.0000.0000.0000.000
166A176ILE00.026-0.01322.520-0.005-0.0050.0000.0000.0000.000
167A177THR00.0130.00726.9420.0060.0060.0000.0000.0000.000
168A178HIS0-0.002-0.01727.607-0.001-0.0010.0000.0000.0000.000
169A179SER0-0.054-0.00231.8040.0030.0030.0000.0000.0000.000
170A180LYS10.8180.91134.3700.0140.0140.0000.0000.0000.000
171A181GLY00.0340.01936.6510.0000.0000.0000.0000.0000.000
172A182GLU-1-0.919-0.95539.276-0.024-0.0240.0000.0000.0000.000
173A183GLU-1-0.941-0.98842.461-0.014-0.0140.0000.0000.0000.000
174A184ASN0-0.114-0.05742.902-0.001-0.0010.0000.0000.0000.000
175A185VAL00.0500.04243.047-0.001-0.0010.0000.0000.0000.000
176A186PRO0-0.0240.00040.996-0.002-0.0020.0000.0000.0000.000
177A187SER0-0.027-0.00738.6270.0010.0010.0000.0000.0000.000
178A188ILE0-0.035-0.03235.513-0.003-0.0030.0000.0000.0000.000
179A189ALA00.005-0.00132.4910.0030.0030.0000.0000.0000.000
180A190HIS0-0.027-0.03931.945-0.012-0.0120.0000.0000.0000.000
181A191VAL00.0270.02228.4420.0060.0060.0000.0000.0000.000
182A192LYS10.8500.93831.9170.0510.0510.0000.0000.0000.000
183A193GLY00.010-0.00434.7840.0030.0030.0000.0000.0000.000
184A194ASN0-0.045-0.03229.970-0.008-0.0080.0000.0000.0000.000
185A195ARG10.9510.97931.2510.0420.0420.0000.0000.0000.000
186A196ILE00.0050.01427.919-0.003-0.0030.0000.0000.0000.000
187A197VAL0-0.057-0.02932.4170.0070.0070.0000.0000.0000.000
188A198ILE00.012-0.00334.063-0.004-0.0040.0000.0000.0000.000
189A199GLU-1-0.752-0.84737.421-0.048-0.0480.0000.0000.0000.000
190A200PRO00.0610.03040.263-0.003-0.0030.0000.0000.0000.000
191A201PHE00.031-0.02641.652-0.002-0.0020.0000.0000.0000.000
192A202ASP-1-0.902-0.93542.611-0.037-0.0370.0000.0000.0000.000
193A203LYS10.8460.91644.4210.0350.0350.0000.0000.0000.000
194A204VAL0-0.0400.00638.6200.0000.0000.0000.0000.0000.000
195A205SER0-0.008-0.00640.7070.0000.0000.0000.0000.0000.000
196A206PHE00.0100.00835.5660.0010.0010.0000.0000.0000.000