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: M34QZ

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2520803.799218
FMO2-HF: Nuclear repulsion 2436822.57834
FMO2-HF: Total energy -83981.220878
FMO2-MP2: Total energy -84233.29492


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.
-2.625-0.0280.085-1.043-1.6390.003
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 : -0.021 / q_NPA : -0.028
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].
3A9PRO0-0.005-0.0133.790-0.6691.041-0.017-0.817-0.8760.001
4A10LYS10.9680.9912.888-2.052-1.1650.102-0.226-0.7630.002
5A11THR00.0310.0147.396-0.053-0.0530.0000.0000.0000.000
6A12LYS10.9320.96711.1500.0640.0640.0000.0000.0000.000
7A13ILE00.0390.02213.405-0.028-0.0280.0000.0000.0000.000
8A14ASP-1-0.967-0.98017.222-0.048-0.0480.0000.0000.0000.000
9A15TRP00.0080.00917.4340.0000.0000.0000.0000.0000.000
10A16GLY00.0250.01922.0630.0060.0060.0000.0000.0000.000
11A17PRO0-0.036-0.02922.2630.0040.0040.0000.0000.0000.000
12A18GLY00.036-0.00123.6870.0040.0040.0000.0000.0000.000
13A19GLU-1-0.924-0.94923.6080.0530.0530.0000.0000.0000.000
14A20ASN0-0.061-0.03425.1430.0040.0040.0000.0000.0000.000
15A21HIS00.0750.04121.5110.0010.0010.0000.0000.0000.000
16A22ILE0-0.019-0.00923.9020.0050.0050.0000.0000.0000.000
17A23CYS0-0.034-0.00326.836-0.006-0.0060.0000.0000.0000.000
18A24LEU0-0.008-0.01130.469-0.003-0.0030.0000.0000.0000.000
19A25LYS10.9570.98628.818-0.028-0.0280.0000.0000.0000.000
20A26THR00.0040.00030.672-0.004-0.0040.0000.0000.0000.000
21A27PRO0-0.036-0.01430.9560.0040.0040.0000.0000.0000.000
22A28PHE0-0.040-0.01730.6590.0020.0020.0000.0000.0000.000
23A29LYS10.9240.97027.681-0.060-0.0600.0000.0000.0000.000
24A30ASN00.0510.01724.850-0.012-0.0120.0000.0000.0000.000
25A31PHE00.0050.01127.3640.0050.0050.0000.0000.0000.000
26A32TYR00.0410.03122.587-0.001-0.0010.0000.0000.0000.000
27A33VAL00.0600.04125.9950.0000.0000.0000.0000.0000.000
28A34ILE00.0710.02127.0910.0030.0030.0000.0000.0000.000
29A35GLU-1-0.905-0.95225.2720.0040.0040.0000.0000.0000.000
30A36LEU0-0.018-0.02321.071-0.003-0.0030.0000.0000.0000.000
31A37PHE0-0.019-0.00123.2590.0090.0090.0000.0000.0000.000
32A38HIS00.0010.01021.1700.0030.0030.0000.0000.0000.000
33A39GLN0-0.049-0.03317.6230.0160.0160.0000.0000.0000.000
34A40ALA0-0.0160.01520.1830.0190.0190.0000.0000.0000.000
35A41PRO0-0.016-0.00620.346-0.006-0.0060.0000.0000.0000.000
36A42THR0-0.056-0.05122.0770.0000.0000.0000.0000.0000.000
37A43PHE0-0.046-0.02325.193-0.005-0.0050.0000.0000.0000.000
38A44ASP-1-0.875-0.93425.5810.0280.0280.0000.0000.0000.000
39A45LYS10.9340.97823.885-0.106-0.1060.0000.0000.0000.000
40A46THR00.000-0.00727.8690.0000.0000.0000.0000.0000.000
41A47ILE0-0.0240.00228.0210.0070.0070.0000.0000.0000.000
42A48PRO0-0.054-0.02330.552-0.006-0.0060.0000.0000.0000.000
43A49LEU00.0130.00432.3820.0050.0050.0000.0000.0000.000
44A50PHE0-0.0080.00235.364-0.002-0.0020.0000.0000.0000.000
45A51ILE00.013-0.00438.3870.0000.0000.0000.0000.0000.000
46A52SER0-0.0270.00240.667-0.001-0.0010.0000.0000.0000.000
47A53ASP-1-0.807-0.89835.7290.0660.0660.0000.0000.0000.000
48A54ILE0-0.0210.00637.264-0.001-0.0010.0000.0000.0000.000
49A55ASN0-0.002-0.02538.718-0.003-0.0030.0000.0000.0000.000
50A56ASN0-0.056-0.02539.585-0.005-0.0050.0000.0000.0000.000
51A57SER0-0.046-0.01736.1690.0000.0000.0000.0000.0000.000
52A58PRO0-0.036-0.01735.935-0.003-0.0030.0000.0000.0000.000
53A59ASN00.0110.01938.725-0.001-0.0010.0000.0000.0000.000
54A60LEU00.0530.01235.3680.0000.0000.0000.0000.0000.000
55A61TYR0-0.018-0.06738.2250.0000.0000.0000.0000.0000.000
56A62GLY0-0.038-0.04540.533-0.002-0.0020.0000.0000.0000.000
57A63ILE0-0.100-0.04833.9520.0020.0020.0000.0000.0000.000
58A64TYR0-0.029-0.03830.1110.0010.0010.0000.0000.0000.000
59A65ASN00.0070.01336.190-0.003-0.0030.0000.0000.0000.000
60A66TYR00.0590.00335.9310.0010.0010.0000.0000.0000.000
61A67ILE00.0170.02333.607-0.001-0.0010.0000.0000.0000.000
62A68ALA00.017-0.01036.9970.0000.0000.0000.0000.0000.000
63A69ASP-1-0.858-0.84538.4260.0090.0090.0000.0000.0000.000
64A70HIS0-0.036-0.01536.047-0.001-0.0010.0000.0000.0000.000
65A71LEU0-0.050-0.03433.0240.0010.0010.0000.0000.0000.000
66A72ARG10.9050.95836.655-0.011-0.0110.0000.0000.0000.000
67A73HIS00.0360.02533.4490.0020.0020.0000.0000.0000.000
68A74VAL0-0.0150.00832.3860.0030.0030.0000.0000.0000.000
69A75VAL00.0010.02634.384-0.001-0.0010.0000.0000.0000.000
70A76LEU00.0050.00530.5950.0030.0030.0000.0000.0000.000
71A77VAL00.0480.02831.600-0.002-0.0020.0000.0000.0000.000
72A78ASN0-0.026-0.02229.5340.0000.0000.0000.0000.0000.000
73A79ASN0-0.063-0.05825.862-0.002-0.0020.0000.0000.0000.000
74A80TYR00.0180.00023.5750.0000.0000.0000.0000.0000.000
75A81PRO0-0.0280.00826.573-0.003-0.0030.0000.0000.0000.000
76A82VAL00.013-0.01228.7800.0040.0040.0000.0000.0000.000
77A83ASN0-0.0150.00030.061-0.005-0.0050.0000.0000.0000.000
78A84GLN00.0670.03830.060-0.007-0.0070.0000.0000.0000.000
79A85ILE00.014-0.00132.6630.0060.0060.0000.0000.0000.000
80A86ASN00.0610.04634.428-0.002-0.0020.0000.0000.0000.000
81A87ILE0-0.029-0.02036.2930.0040.0040.0000.0000.0000.000
82A88PHE00.0460.00139.268-0.001-0.0010.0000.0000.0000.000
83A89GLY00.0350.00541.8940.0000.0000.0000.0000.0000.000
84A90LYS10.9140.96545.381-0.039-0.0390.0000.0000.0000.000
85A91ILE00.0100.01749.1080.0000.0000.0000.0000.0000.000
86A92VAL0-0.011-0.01851.2150.0000.0000.0000.0000.0000.000
87A93TYR0-0.026-0.01953.262-0.001-0.0010.0000.0000.0000.000
88A94GLU-1-0.729-0.82053.7020.0230.0230.0000.0000.0000.000
89A95GLN0-0.032-0.02455.439-0.002-0.0020.0000.0000.0000.000
90A96TYR00.004-0.03055.8500.0000.0000.0000.0000.0000.000
91A97LYS10.8800.93755.110-0.015-0.0150.0000.0000.0000.000
92A98GLU-1-0.901-0.95957.5600.0120.0120.0000.0000.0000.000
93A99LYS10.9140.97554.252-0.011-0.0110.0000.0000.0000.000
94A100GLU-1-0.855-0.91559.2680.0060.0060.0000.0000.0000.000
95A101PHE0-0.054-0.03155.5640.0000.0000.0000.0000.0000.000
96A102ASN0-0.027-0.01759.7120.0000.0000.0000.0000.0000.000
97A103GLY00.0020.00460.2170.0000.0000.0000.0000.0000.000
98A104VAL0-0.053-0.02355.9260.0000.0000.0000.0000.0000.000
99A105GLU-1-0.822-0.89358.9900.0070.0070.0000.0000.0000.000
100A106GLU-1-0.921-0.96053.5770.0080.0080.0000.0000.0000.000
101A107SER0-0.021-0.00955.4870.0000.0000.0000.0000.0000.000
102A108TYR0-0.127-0.08349.9140.0010.0010.0000.0000.0000.000
103A109VAL0-0.019-0.01251.8380.0000.0000.0000.0000.0000.000
104A110ILE0-0.049-0.02151.3030.0000.0000.0000.0000.0000.000
105A111LEU00.004-0.00749.0260.0000.0000.0000.0000.0000.000
106A112VAL0-0.0120.00649.7390.0000.0000.0000.0000.0000.000
107A113ILE0-0.0030.01244.9400.0000.0000.0000.0000.0000.000
108A114SER00.016-0.01546.9760.0000.0000.0000.0000.0000.000
109A115ASP-1-0.764-0.88041.5590.0490.0490.0000.0000.0000.000
110A116PHE0-0.133-0.09544.8400.0010.0010.0000.0000.0000.000
111A117ILE00.0450.04540.1370.0000.0000.0000.0000.0000.000
112A118GLY00.0240.02142.7890.0020.0020.0000.0000.0000.000
113A119ILE0-0.032-0.03043.878-0.002-0.0020.0000.0000.0000.000
114A120ASP-1-0.883-0.93844.7110.0350.0350.0000.0000.0000.000
115A121SER0-0.0130.02744.3630.0010.0010.0000.0000.0000.000
116A122LYS10.9520.95145.392-0.034-0.0340.0000.0000.0000.000
117A123ILE00.0520.03842.4520.0000.0000.0000.0000.0000.000
118A124ARG10.7910.89146.467-0.022-0.0220.0000.0000.0000.000
119A125VAL00.0100.00644.5090.0010.0010.0000.0000.0000.000
120A126ARG10.8300.88146.433-0.017-0.0170.0000.0000.0000.000
121A127LEU0-0.017-0.00145.9660.0010.0010.0000.0000.0000.000
122A128SER00.0980.04048.374-0.001-0.0010.0000.0000.0000.000
123A129GLN00.051-0.01850.4760.0010.0010.0000.0000.0000.000
124A130GLU-1-0.948-0.95350.3700.0130.0130.0000.0000.0000.000
125A131GLN00.0860.04344.6120.0000.0000.0000.0000.0000.000
126A132PHE0-0.022-0.00948.5780.0020.0020.0000.0000.0000.000
127A133LYS10.9690.96150.845-0.014-0.0140.0000.0000.0000.000
128A134GLU-1-0.967-0.96048.4990.0190.0190.0000.0000.0000.000
129A135VAL0-0.038-0.00346.6000.0010.0010.0000.0000.0000.000
130A136GLY0-0.021-0.02849.2370.0020.0020.0000.0000.0000.000
131A137LEU0-0.089-0.02749.8290.0000.0000.0000.0000.0000.000
132A138THR0-0.026-0.05053.748-0.001-0.0010.0000.0000.0000.000
133A139LEU00.0090.01356.4480.0000.0000.0000.0000.0000.000
134A140ASP-1-0.809-0.89059.0860.0190.0190.0000.0000.0000.000
135A141LYS10.8420.92659.151-0.018-0.0180.0000.0000.0000.000
136A142LYS10.9030.97759.487-0.019-0.0190.0000.0000.0000.000
137A143ASN0-0.007-0.04353.9620.0020.0020.0000.0000.0000.000
138A144TYR00.0230.01554.2110.0020.0020.0000.0000.0000.000
139A145GLY0-0.038-0.02053.4700.0000.0000.0000.0000.0000.000
140A146LYS10.8500.94151.042-0.025-0.0250.0000.0000.0000.000
141A147ILE00.0070.01745.1810.0000.0000.0000.0000.0000.000
142A148VAL0-0.014-0.00645.1950.0000.0000.0000.0000.0000.000
143A149GLU-1-0.830-0.93637.5890.0600.0600.0000.0000.0000.000
144A150LEU0-0.047-0.03840.713-0.003-0.0030.0000.0000.0000.000
145A151GLU-1-0.857-0.93934.9260.0520.0520.0000.0000.0000.000
146A152GLY0-0.022-0.01937.379-0.004-0.0040.0000.0000.0000.000
147A153GLU-1-0.880-0.90836.4870.0220.0220.0000.0000.0000.000
148A154ILE0-0.023-0.00937.5440.0000.0000.0000.0000.0000.000
149A155TYR00.0190.01339.592-0.001-0.0010.0000.0000.0000.000
150A156ASN0-0.009-0.00939.0180.0030.0030.0000.0000.0000.000
151A157TRP00.001-0.01142.724-0.001-0.0010.0000.0000.0000.000
152A158TYR0-0.081-0.07837.8150.0010.0010.0000.0000.0000.000
153A159ASP-1-0.822-0.90044.0400.0140.0140.0000.0000.0000.000
154A160SER00.035-0.00244.8630.0010.0010.0000.0000.0000.000
155A161ILE00.0300.01945.8530.0000.0000.0000.0000.0000.000
156A162ASN0-0.112-0.06148.8210.0010.0010.0000.0000.0000.000
157A163VAL00.0430.04942.8310.0020.0020.0000.0000.0000.000
158A164SER0-0.0050.00343.5780.0010.0010.0000.0000.0000.000
159A165LYS10.9110.96144.983-0.017-0.0170.0000.0000.0000.000
160A166LYS10.9200.95741.326-0.036-0.0360.0000.0000.0000.000
161A167PRO0-0.029-0.00342.841-0.001-0.0010.0000.0000.0000.000
162A168ASP-1-0.771-0.85146.0460.0230.0230.0000.0000.0000.000
163A169ARG10.8440.89939.854-0.035-0.0350.0000.0000.0000.000
164A170GLU-1-0.821-0.90944.2440.0180.0180.0000.0000.0000.000
165A171LEU0-0.0080.01139.7220.0000.0000.0000.0000.0000.000
166A172LYN0-0.018-0.00242.093-0.002-0.0020.0000.0000.0000.000
167A173VAL0-0.020-0.01741.6180.0010.0010.0000.0000.0000.000
168A174SER00.0140.00938.621-0.002-0.0020.0000.0000.0000.000
169A175LYS10.9700.97836.950-0.044-0.0440.0000.0000.0000.000
170A176ILE00.0120.00541.0620.0020.0020.0000.0000.0000.000
171A177THR00.0070.00941.096-0.001-0.0010.0000.0000.0000.000
172A178VAL0-0.030-0.01643.6730.0010.0010.0000.0000.0000.000
173A179LEU0-0.030-0.01341.4400.0010.0010.0000.0000.0000.000
174A180SER00.0110.00745.4670.0000.0000.0000.0000.0000.000
175A181HIS00.0420.01249.069-0.001-0.0010.0000.0000.0000.000
176A182ARG10.8890.94152.338-0.031-0.0310.0000.0000.0000.000
177A183PRO00.0250.01552.7090.0010.0010.0000.0000.0000.000
178A184ASP-1-0.896-0.95551.9700.0410.0410.0000.0000.0000.000
179A185GLY00.0420.01649.1860.0000.0000.0000.0000.0000.000
180A186LEU00.0340.02947.3820.0020.0020.0000.0000.0000.000
181A187HIS00.0170.00345.3640.0030.0030.0000.0000.0000.000
182A188PHE00.0540.01743.4310.0030.0030.0000.0000.0000.000
183A189GLU-1-0.903-0.95542.5620.0460.0460.0000.0000.0000.000
184A190PHE0-0.007-0.00842.2740.0030.0030.0000.0000.0000.000
185A191GLU-1-0.988-0.97338.6930.0670.0670.0000.0000.0000.000
186A192GLN00.0300.01338.0830.0060.0060.0000.0000.0000.000
187A193TRP0-0.013-0.02037.7970.0040.0040.0000.0000.0000.000
188A194LYS10.9370.97935.651-0.076-0.0760.0000.0000.0000.000
189A195LYS10.9220.97732.831-0.065-0.0650.0000.0000.0000.000
190A196ARG10.7640.87332.993-0.056-0.0560.0000.0000.0000.000
191A197MET0-0.012-0.00833.7560.0020.0020.0000.0000.0000.000
192A198GLU-1-0.953-0.97630.5620.1140.1140.0000.0000.0000.000
193A199PHE00.0240.00926.9590.0100.0100.0000.0000.0000.000
194A200ARG10.8830.91928.809-0.069-0.0690.0000.0000.0000.000
195A201LYS10.8880.93729.670-0.100-0.1000.0000.0000.0000.000
196A202ASN0-0.001-0.00524.9830.0050.0050.0000.0000.0000.000
197A203ASN0-0.064-0.03024.2890.0210.0210.0000.0000.0000.000
198A204LEU0-0.0030.01625.749-0.004-0.0040.0000.0000.0000.000
199A205VAL0-0.041-0.00428.493-0.006-0.0060.0000.0000.0000.000
200A206GLU-1-0.923-0.95423.8030.1600.1600.0000.0000.0000.000
201A207PRO0-0.044-0.01125.6220.0000.0000.0000.0000.0000.000
202A208TRP00.0250.00820.3740.0060.0060.0000.0000.0000.000
203A209VAL00.0210.00319.546-0.012-0.0120.0000.0000.0000.000
204A210PHE0-0.032-0.01317.5300.0200.0200.0000.0000.0000.000
205A211ILE00.0300.00114.190-0.013-0.0130.0000.0000.0000.000
206A212PRO0-0.050-0.02114.5500.0130.0130.0000.0000.0000.000
207A213THR00.0030.0109.0300.0370.0370.0000.0000.0000.000