Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 7GQ1K

Calculation Name: 3KF8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KF8

Chain ID: A

ChEMBL ID:

UniProt ID: C5M4J8

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2521723.726579
FMO2-HF: Nuclear repulsion 2437740.923808
FMO2-HF: Total energy -83982.802771
FMO2-MP2: Total energy -84234.769208


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:7:LEU)


Summations of interaction energy for fragment #1(A:7:LEU)
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.
-4.946-1.0910.05-1.806-2.10.009
Interaction energy analysis for fragmet #1(A:7:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.004
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].
3A9PRO00.000-0.0143.795-1.1671.700-0.021-1.532-1.3150.007
4A10LYS10.9570.9883.002-3.777-2.7890.071-0.274-0.7850.002
5A11THR00.0260.0117.393-0.016-0.0160.0000.0000.0000.000
6A12LYS10.8920.93611.143-0.143-0.1430.0000.0000.0000.000
7A13ILE00.0300.01713.393-0.047-0.0470.0000.0000.0000.000
8A14ASP-1-0.960-0.96317.2090.0420.0420.0000.0000.0000.000
9A15TRP00.0250.01217.791-0.020-0.0200.0000.0000.0000.000
10A16GLY00.0420.02922.2150.0010.0010.0000.0000.0000.000
11A17PRO0-0.023-0.02122.3820.0150.0150.0000.0000.0000.000
12A18GLY00.0410.00023.791-0.003-0.0030.0000.0000.0000.000
13A19GLU-1-0.895-0.94023.7590.1450.1450.0000.0000.0000.000
14A20ASN0-0.062-0.04025.306-0.010-0.0100.0000.0000.0000.000
15A21HIS00.0630.02821.845-0.014-0.0140.0000.0000.0000.000
16A22ILE0-0.024-0.00423.769-0.005-0.0050.0000.0000.0000.000
17A23CYS0-0.0080.00726.853-0.005-0.0050.0000.0000.0000.000
18A24LEU0-0.015-0.00630.438-0.001-0.0010.0000.0000.0000.000
19A25LYS10.8670.94028.170-0.083-0.0830.0000.0000.0000.000
20A26THR0-0.0070.00130.314-0.010-0.0100.0000.0000.0000.000
21A27PRO0-0.050-0.02030.6160.0070.0070.0000.0000.0000.000
22A28PHE0-0.020-0.01130.3640.0030.0030.0000.0000.0000.000
23A29LYS10.8980.94927.344-0.068-0.0680.0000.0000.0000.000
24A30ASN00.0510.02224.602-0.013-0.0130.0000.0000.0000.000
25A31PHE00.0210.01627.0230.0010.0010.0000.0000.0000.000
26A32TYR00.0290.02421.9110.0010.0010.0000.0000.0000.000
27A33VAL00.0500.03226.133-0.007-0.0070.0000.0000.0000.000
28A34ILE00.0730.02927.0250.0010.0010.0000.0000.0000.000
29A35GLU-1-0.877-0.94125.2800.0200.0200.0000.0000.0000.000
30A36LEU0-0.016-0.01720.853-0.007-0.0070.0000.0000.0000.000
31A37PHE0-0.025-0.00923.2420.0030.0030.0000.0000.0000.000
32A38HIS0-0.0120.00121.253-0.006-0.0060.0000.0000.0000.000
33A39GLN0-0.049-0.03417.5610.0090.0090.0000.0000.0000.000
34A40ALA0-0.0150.01420.0020.0150.0150.0000.0000.0000.000
35A41PRO0-0.0040.00220.145-0.016-0.0160.0000.0000.0000.000
36A42THR0-0.034-0.04521.881-0.009-0.0090.0000.0000.0000.000
37A43PHE0-0.001-0.00125.043-0.004-0.0040.0000.0000.0000.000
38A44ASP-1-0.855-0.91225.608-0.042-0.0420.0000.0000.0000.000
39A45LYS10.9000.96323.571-0.012-0.0120.0000.0000.0000.000
40A46THR00.000-0.00427.8840.0070.0070.0000.0000.0000.000
41A47ILE0-0.0120.01127.9240.0000.0000.0000.0000.0000.000
42A48PRO0-0.043-0.01830.6270.0000.0000.0000.0000.0000.000
43A49LEU00.0100.00332.2980.0070.0070.0000.0000.0000.000
44A50PHE00.0060.01135.227-0.003-0.0030.0000.0000.0000.000
45A51ILE00.009-0.01138.2470.0010.0010.0000.0000.0000.000
46A52SER0-0.016-0.00640.6270.0020.0020.0000.0000.0000.000
47A53ASP-1-0.823-0.91435.5380.0430.0430.0000.0000.0000.000
48A54ILE0-0.0180.00636.9550.0010.0010.0000.0000.0000.000
49A55ASN00.007-0.01438.506-0.001-0.0010.0000.0000.0000.000
50A56ASN0-0.111-0.05839.4830.0010.0010.0000.0000.0000.000
51A57SER0-0.045-0.02035.7940.0030.0030.0000.0000.0000.000
52A58PRO0-0.020-0.01135.684-0.003-0.0030.0000.0000.0000.000
53A59ASN0-0.004-0.00738.424-0.003-0.0030.0000.0000.0000.000
54A60LEU00.0460.01534.9700.0030.0030.0000.0000.0000.000
55A61TYR0-0.004-0.02537.8740.0020.0020.0000.0000.0000.000
56A62GLY0-0.039-0.01540.1790.0000.0000.0000.0000.0000.000
57A63ILE0-0.091-0.04133.5850.0040.0040.0000.0000.0000.000
58A64TYR0-0.016-0.03629.7940.0030.0030.0000.0000.0000.000
59A65ASN0-0.0040.00636.019-0.004-0.0040.0000.0000.0000.000
60A66TYR00.0620.01336.2260.0000.0000.0000.0000.0000.000
61A67ILE00.0240.01933.549-0.003-0.0030.0000.0000.0000.000
62A68ALA00.0210.00137.006-0.003-0.0030.0000.0000.0000.000
63A69ASP-1-0.885-0.88438.3930.0050.0050.0000.0000.0000.000
64A70HIS0-0.039-0.02136.100-0.005-0.0050.0000.0000.0000.000
65A71LEU0-0.041-0.02632.860-0.001-0.0010.0000.0000.0000.000
66A72ARG10.9000.95636.671-0.003-0.0030.0000.0000.0000.000
67A73HIS00.0340.02733.4910.0040.0040.0000.0000.0000.000
68A74VAL0-0.0190.00832.1050.0000.0000.0000.0000.0000.000
69A75VAL00.0090.02434.1320.0020.0020.0000.0000.0000.000
70A76LEU00.0120.01330.3210.0010.0010.0000.0000.0000.000
71A77VAL00.0490.02731.5180.0010.0010.0000.0000.0000.000
72A78ASN00.0250.01529.2170.0040.0040.0000.0000.0000.000
73A79ASN0-0.054-0.06525.638-0.003-0.0030.0000.0000.0000.000
74A80TYR0-0.0100.00023.2480.0010.0010.0000.0000.0000.000
75A81PRO0-0.0260.01126.318-0.004-0.0040.0000.0000.0000.000
76A82VAL0-0.009-0.01828.534-0.003-0.0030.0000.0000.0000.000
77A83ASN0-0.036-0.03329.7620.0020.0020.0000.0000.0000.000
78A84GLN00.0410.02730.171-0.004-0.0040.0000.0000.0000.000
79A85ILE00.006-0.00632.6800.0050.0050.0000.0000.0000.000
80A86ASN00.0550.02634.3720.0000.0000.0000.0000.0000.000
81A87ILE0-0.0040.00236.3060.0050.0050.0000.0000.0000.000
82A88PHE00.0410.00439.281-0.003-0.0030.0000.0000.0000.000
83A89GLY00.0350.00541.9050.0030.0030.0000.0000.0000.000
84A90LYS10.8130.89045.392-0.011-0.0110.0000.0000.0000.000
85A91ILE00.0070.01449.1190.0010.0010.0000.0000.0000.000
86A92VAL0-0.026-0.02651.2260.0000.0000.0000.0000.0000.000
87A93TYR0-0.002-0.00353.2600.0000.0000.0000.0000.0000.000
88A94GLU-1-0.729-0.82953.716-0.005-0.0050.0000.0000.0000.000
89A95GLN0-0.017-0.00555.4590.0000.0000.0000.0000.0000.000
90A96TYR00.015-0.00955.865-0.001-0.0010.0000.0000.0000.000
91A97LYS10.8850.93455.7200.0050.0050.0000.0000.0000.000
92A98GLU-1-0.803-0.89657.575-0.013-0.0130.0000.0000.0000.000
93A99LYS10.8500.96153.6680.0140.0140.0000.0000.0000.000
94A100GLU-1-0.870-0.92359.288-0.011-0.0110.0000.0000.0000.000
95A101PHE0-0.032-0.03455.8570.0010.0010.0000.0000.0000.000
96A102ASN0-0.007-0.00659.7260.0010.0010.0000.0000.0000.000
97A103GLY0-0.0200.00160.228-0.001-0.0010.0000.0000.0000.000
98A104VAL0-0.042-0.02355.815-0.001-0.0010.0000.0000.0000.000
99A105GLU-1-0.829-0.89559.025-0.014-0.0140.0000.0000.0000.000
100A106GLU-1-0.868-0.92953.662-0.019-0.0190.0000.0000.0000.000
101A107SER0-0.067-0.05955.5110.0010.0010.0000.0000.0000.000
102A108TYR0-0.147-0.10049.989-0.001-0.0010.0000.0000.0000.000
103A109VAL0-0.025-0.01851.9480.0010.0010.0000.0000.0000.000
104A110ILE0-0.043-0.01751.3180.0000.0000.0000.0000.0000.000
105A111LEU00.004-0.00449.1140.0010.0010.0000.0000.0000.000
106A112VAL0-0.0070.00649.5710.0000.0000.0000.0000.0000.000
107A113ILE0-0.0050.01044.8960.0000.0000.0000.0000.0000.000
108A114SER00.0440.00646.8420.0020.0020.0000.0000.0000.000
109A115ASP-1-0.758-0.87541.3380.0180.0180.0000.0000.0000.000
110A116PHE0-0.130-0.07944.7300.0010.0010.0000.0000.0000.000
111A117ILE00.0340.03840.3500.0010.0010.0000.0000.0000.000
112A118GLY00.0260.02342.6470.0010.0010.0000.0000.0000.000
113A119ILE0-0.020-0.02443.721-0.002-0.0020.0000.0000.0000.000
114A120ASP-1-0.860-0.92644.5160.0190.0190.0000.0000.0000.000
115A121SER0-0.0050.01444.1650.0000.0000.0000.0000.0000.000
116A122LYS10.9100.93745.226-0.016-0.0160.0000.0000.0000.000
117A123ILE00.0510.03742.2860.0010.0010.0000.0000.0000.000
118A124ARG10.7800.85946.282-0.003-0.0030.0000.0000.0000.000
119A125VAL00.0050.00544.6080.0000.0000.0000.0000.0000.000
120A126ARG10.8450.88146.4490.0110.0110.0000.0000.0000.000
121A127LEU0-0.0190.00646.042-0.001-0.0010.0000.0000.0000.000
122A128SER00.0670.00148.3880.0010.0010.0000.0000.0000.000
123A129GLN00.029-0.02250.4900.0010.0010.0000.0000.0000.000
124A130GLU-1-0.879-0.89650.370-0.022-0.0220.0000.0000.0000.000
125A131GLN00.0480.01444.3360.0010.0010.0000.0000.0000.000
126A132PHE0-0.014-0.00848.5870.0010.0010.0000.0000.0000.000
127A133LYS10.9620.96350.8550.0190.0190.0000.0000.0000.000
128A134GLU-1-0.965-0.96448.727-0.027-0.0270.0000.0000.0000.000
129A135VAL0-0.043-0.01046.354-0.001-0.0010.0000.0000.0000.000
130A136GLY0-0.018-0.02249.2440.0010.0010.0000.0000.0000.000
131A137LEU0-0.087-0.02949.7290.0020.0020.0000.0000.0000.000
132A138THR0-0.013-0.02053.757-0.001-0.0010.0000.0000.0000.000
133A139LEU00.0060.01056.1270.0010.0010.0000.0000.0000.000
134A140ASP-1-0.791-0.88359.097-0.006-0.0060.0000.0000.0000.000
135A141LYS10.8150.89859.1350.0040.0040.0000.0000.0000.000
136A142LYS10.8530.93159.4710.0060.0060.0000.0000.0000.000
137A143ASN0-0.004-0.03453.945-0.001-0.0010.0000.0000.0000.000
138A144TYR00.0140.01154.2210.0010.0010.0000.0000.0000.000
139A145GLY0-0.023-0.01353.4890.0000.0000.0000.0000.0000.000
140A146LYS10.8400.93151.0210.0070.0070.0000.0000.0000.000
141A147ILE0-0.0070.00945.1490.0010.0010.0000.0000.0000.000
142A148VAL0-0.010-0.00645.336-0.002-0.0020.0000.0000.0000.000
143A149GLU-1-0.735-0.85037.312-0.002-0.0020.0000.0000.0000.000
144A150LEU0-0.038-0.02840.721-0.003-0.0030.0000.0000.0000.000
145A151GLU-1-0.810-0.90935.638-0.024-0.0240.0000.0000.0000.000
146A152GLY00.0110.00137.393-0.002-0.0020.0000.0000.0000.000
147A153GLU-1-0.898-0.92036.547-0.025-0.0250.0000.0000.0000.000
148A154ILE0-0.030-0.01437.3750.0010.0010.0000.0000.0000.000
149A155TYR00.0180.01039.6120.0000.0000.0000.0000.0000.000
150A156ASN0-0.016-0.00838.9310.0040.0040.0000.0000.0000.000
151A157TRP00.013-0.00942.556-0.001-0.0010.0000.0000.0000.000
152A158TYR0-0.070-0.06137.6030.0030.0030.0000.0000.0000.000
153A159ASP-1-0.771-0.87243.7880.0130.0130.0000.0000.0000.000
154A160SER00.0520.00944.6110.0020.0020.0000.0000.0000.000
155A161ILE00.0180.01545.6260.0020.0020.0000.0000.0000.000
156A162ASN0-0.101-0.05948.6140.0020.0020.0000.0000.0000.000
157A163VAL00.0380.01342.7510.0010.0010.0000.0000.0000.000
158A164SER00.0090.01243.2390.0010.0010.0000.0000.0000.000
159A165LYS10.8220.91344.652-0.014-0.0140.0000.0000.0000.000
160A166LYS10.9240.96841.255-0.032-0.0320.0000.0000.0000.000
161A167PRO0-0.031-0.00242.491-0.001-0.0010.0000.0000.0000.000
162A168ASP-1-0.788-0.85445.7630.0060.0060.0000.0000.0000.000
163A169ARG10.8340.89039.852-0.020-0.0200.0000.0000.0000.000
164A170GLU-1-0.808-0.87844.055-0.005-0.0050.0000.0000.0000.000
165A171LEU0-0.0130.00239.4130.0000.0000.0000.0000.0000.000
166A172LYN0-0.0060.00642.148-0.001-0.0010.0000.0000.0000.000
167A173VAL0-0.021-0.02041.634-0.001-0.0010.0000.0000.0000.000
168A174SER00.0420.02637.777-0.001-0.0010.0000.0000.0000.000
169A175LYS10.8500.91236.2340.0270.0270.0000.0000.0000.000
170A176ILE00.0360.02041.0730.0030.0030.0000.0000.0000.000
171A177THR0-0.033-0.01541.570-0.003-0.0030.0000.0000.0000.000
172A178VAL0-0.006-0.00443.6800.0030.0030.0000.0000.0000.000
173A179LEU0-0.021-0.00741.477-0.001-0.0010.0000.0000.0000.000
174A180SER00.0100.00645.4720.0000.0000.0000.0000.0000.000
175A181HIS00.0480.01249.0740.0020.0020.0000.0000.0000.000
176A182ARG10.8950.94852.3600.0060.0060.0000.0000.0000.000
177A183PRO00.0340.01352.7150.0000.0000.0000.0000.0000.000
178A184ASP-1-0.891-0.94652.0280.0070.0070.0000.0000.0000.000
179A185GLY00.0370.01149.190-0.001-0.0010.0000.0000.0000.000
180A186LEU00.0300.02647.3870.0010.0010.0000.0000.0000.000
181A187HIS00.004-0.00245.4600.0030.0030.0000.0000.0000.000
182A188PHE00.0600.01743.3550.0010.0010.0000.0000.0000.000
183A189GLU-1-0.816-0.88542.5670.0100.0100.0000.0000.0000.000
184A190PHE0-0.006-0.00642.2810.0030.0030.0000.0000.0000.000
185A191GLU-1-0.979-0.97038.6440.0030.0030.0000.0000.0000.000
186A192GLN0-0.011-0.02738.0880.0030.0030.0000.0000.0000.000
187A193TRP0-0.014-0.02637.8050.0030.0030.0000.0000.0000.000
188A194LYS10.9530.98935.517-0.023-0.0230.0000.0000.0000.000
189A195LYS10.8550.93633.0100.0040.0040.0000.0000.0000.000
190A196ARG10.7560.86332.970-0.006-0.0060.0000.0000.0000.000
191A197MET0-0.0160.00133.6640.0070.0070.0000.0000.0000.000
192A198GLU-1-0.935-0.97830.6120.0440.0440.0000.0000.0000.000
193A199PHE00.0140.00926.7720.0080.0080.0000.0000.0000.000
194A200ARG10.9010.93828.706-0.045-0.0450.0000.0000.0000.000
195A201LYS10.8740.92429.577-0.056-0.0560.0000.0000.0000.000
196A202ASN00.001-0.00825.0010.0150.0150.0000.0000.0000.000
197A203ASN0-0.065-0.02524.1890.0080.0080.0000.0000.0000.000
198A204LEU0-0.0110.01025.6160.0010.0010.0000.0000.0000.000
199A205VAL0-0.042-0.01328.3180.0010.0010.0000.0000.0000.000
200A206GLU-1-0.919-0.95223.9090.1590.1590.0000.0000.0000.000
201A207PRO0-0.034-0.01825.414-0.005-0.0050.0000.0000.0000.000
202A208TRP00.0080.01420.1700.0100.0100.0000.0000.0000.000
203A209VAL00.023-0.00619.680-0.004-0.0040.0000.0000.0000.000
204A210PHE0-0.029-0.00717.6300.0220.0220.0000.0000.0000.000
205A211ILE00.0250.00014.2730.0000.0000.0000.0000.0000.000
206A212PRO0-0.014-0.00214.3480.0190.0190.0000.0000.0000.000
207A213THR00.0210.0259.2850.1140.1140.0000.0000.0000.000