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: 53Z9Z

Calculation Name: 3KF8-A-Xray317

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: 2021-09-07

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:


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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 209
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2527358.802901
FMO2-HF: Nuclear repulsion 2443206.876454
FMO2-HF: Total energy -84151.926447
FMO2-MP2: Total energy -84404.537306


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:6:ACE )


Summations of interaction energy for fragment #1(A:6:ACE )
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.
1.9222.642-0.004-0.289-0.4270
Interaction energy analysis for fragmet #1(A:6:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.005
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].
3A8TYR 00.0310.0273.8811.1111.831-0.004-0.289-0.4270.000
4A9PRO 0-0.005-0.0126.911-0.052-0.0520.0000.0000.0000.000
5A10LYS 10.9720.9948.7940.9840.9840.0000.0000.0000.000
6A11THR 00.0300.01312.6320.0340.0340.0000.0000.0000.000
7A12LYS 10.9340.96916.2260.1860.1860.0000.0000.0000.000
8A13ILE 00.0360.02018.7190.0160.0160.0000.0000.0000.000
9A14ASP -1-0.967-0.98022.522-0.114-0.1140.0000.0000.0000.000
10A15TRP 00.0080.00823.1180.0110.0110.0000.0000.0000.000
11A16GLY 00.0250.01927.8620.0070.0070.0000.0000.0000.000
12A17PRO 0-0.035-0.02928.481-0.008-0.0080.0000.0000.0000.000
13A18GLY 00.037-0.00130.1870.0020.0020.0000.0000.0000.000
14A19GLU -1-0.923-0.94930.054-0.113-0.1130.0000.0000.0000.000
15A20ASN 0-0.063-0.03431.5140.0080.0080.0000.0000.0000.000
16A21HIS 00.0750.04027.8140.0040.0040.0000.0000.0000.000
17A22ILE 0-0.020-0.00929.9750.0010.0010.0000.0000.0000.000
18A23CYS 0-0.035-0.00432.7980.0050.0050.0000.0000.0000.000
19A24LEU 0-0.006-0.01036.3180.0040.0040.0000.0000.0000.000
20A25LYS 10.9540.98435.0080.0720.0720.0000.0000.0000.000
21A26THR 00.005-0.00136.4060.0060.0060.0000.0000.0000.000
22A27PRO 0-0.034-0.01336.697-0.004-0.0040.0000.0000.0000.000
23A28PHE 0-0.040-0.01736.2660.0000.0000.0000.0000.0000.000
24A29LYS 10.9280.97133.2490.0670.0670.0000.0000.0000.000
25A30ASN 00.0480.01630.5780.0100.0100.0000.0000.0000.000
26A31PHE 00.0080.01132.876-0.003-0.0030.0000.0000.0000.000
27A32TYR 00.0410.03128.2450.0010.0010.0000.0000.0000.000
28A33VAL 00.0600.04131.5860.0060.0060.0000.0000.0000.000
29A34ILE 00.0670.02032.395-0.004-0.0040.0000.0000.0000.000
30A35GLU -1-0.903-0.95130.642-0.081-0.0810.0000.0000.0000.000
31A36LEU 0-0.015-0.02226.408-0.006-0.0060.0000.0000.0000.000
32A37PHE 0-0.022-0.00328.319-0.006-0.0060.0000.0000.0000.000
33A38HIS 00.0030.01125.796-0.009-0.0090.0000.0000.0000.000
34A39GLN 0-0.049-0.03422.635-0.019-0.0190.0000.0000.0000.000
35A40ALA 0-0.0170.01424.764-0.011-0.0110.0000.0000.0000.000
36A41PRO 0-0.018-0.00624.4490.0050.0050.0000.0000.0000.000
37A42THR 0-0.060-0.05126.1120.0080.0080.0000.0000.0000.000
38A43PHE 0-0.041-0.02129.2830.0090.0090.0000.0000.0000.000
39A44ASP -1-0.877-0.93629.325-0.071-0.0710.0000.0000.0000.000
40A45LYS 10.9350.97927.1920.0910.0910.0000.0000.0000.000
41A46THR 00.001-0.00731.2600.0000.0000.0000.0000.0000.000
42A47ILE 0-0.0290.00131.590-0.001-0.0010.0000.0000.0000.000
43A48PRO 0-0.051-0.02233.8190.0030.0030.0000.0000.0000.000
44A49LEU 00.0120.00436.412-0.002-0.0020.0000.0000.0000.000
45A50PHE 0-0.0040.00239.0070.0030.0030.0000.0000.0000.000
46A51ILE 00.008-0.00642.186-0.001-0.0010.0000.0000.0000.000
47A52SER 0-0.0280.00244.917-0.001-0.0010.0000.0000.0000.000
48A53ASP -1-0.803-0.89640.005-0.054-0.0540.0000.0000.0000.000
49A54ILE 0-0.0220.00541.365-0.002-0.0020.0000.0000.0000.000
50A55ASN 0-0.005-0.02643.064-0.001-0.0010.0000.0000.0000.000
51A56ASN 0-0.054-0.02544.3610.0020.0020.0000.0000.0000.000
52A57SER 0-0.048-0.01840.988-0.002-0.0020.0000.0000.0000.000
53A58PRO 0-0.035-0.01741.1680.0030.0030.0000.0000.0000.000
54A59ASN 00.0060.01843.790-0.002-0.0020.0000.0000.0000.000
55A60LEU 00.0550.01240.341-0.001-0.0010.0000.0000.0000.000
56A61TYR 0-0.018-0.06743.412-0.002-0.0020.0000.0000.0000.000
57A62GLY 0-0.032-0.04445.8710.0000.0000.0000.0000.0000.000
58A63ILE 0-0.103-0.04839.347-0.001-0.0010.0000.0000.0000.000
59A64TYR 0-0.031-0.04035.329-0.002-0.0020.0000.0000.0000.000
60A65ASN 00.0120.01441.6230.0030.0030.0000.0000.0000.000
61A66TYR 00.0570.00241.5460.0000.0000.0000.0000.0000.000
62A67ILE 00.0160.02338.9380.0010.0010.0000.0000.0000.000
63A68ALA 00.016-0.01042.2170.0000.0000.0000.0000.0000.000
64A69ASP -1-0.858-0.84343.605-0.036-0.0360.0000.0000.0000.000
65A70HIS 0-0.036-0.01541.1660.0020.0020.0000.0000.0000.000
66A71LEU 0-0.048-0.03438.090-0.002-0.0020.0000.0000.0000.000
67A72ARG 10.9040.95741.5480.0360.0360.0000.0000.0000.000
68A73HIS 00.0340.02637.9140.0030.0030.0000.0000.0000.000
69A74VAL 0-0.0110.01037.109-0.002-0.0020.0000.0000.0000.000
70A75VAL 0-0.0040.02438.7620.0020.0020.0000.0000.0000.000
71A76LEU 00.0080.00635.707-0.003-0.0030.0000.0000.0000.000
72A77VAL 00.0480.02736.1450.0040.0040.0000.0000.0000.000
73A78ASN 0-0.029-0.02334.541-0.003-0.0030.0000.0000.0000.000
74A79ASN 0-0.062-0.05631.2610.0040.0040.0000.0000.0000.000
75A80TYR 00.018-0.00228.309-0.006-0.0060.0000.0000.0000.000
76A81PRO 0-0.0250.00931.3690.0060.0060.0000.0000.0000.000
77A82VAL 00.014-0.01133.112-0.003-0.0030.0000.0000.0000.000
78A83ASN 0-0.020-0.00134.1530.0040.0040.0000.0000.0000.000
79A84GLN 00.0690.03933.2760.0030.0030.0000.0000.0000.000
80A85ILE 00.012-0.00136.224-0.003-0.0030.0000.0000.0000.000
81A86ASN 00.0660.04637.6770.0030.0030.0000.0000.0000.000
82A87ILE 0-0.035-0.02139.591-0.002-0.0020.0000.0000.0000.000
83A88PHE 00.0520.00442.5900.0020.0020.0000.0000.0000.000
84A89GLY 00.0300.00345.037-0.001-0.0010.0000.0000.0000.000
85A90LYS 10.9150.96448.5450.0240.0240.0000.0000.0000.000
86A91ILE 00.0110.01852.224-0.001-0.0010.0000.0000.0000.000
87A92VAL 0-0.011-0.01854.3940.0010.0010.0000.0000.0000.000
88A93TYR 0-0.026-0.01856.6040.0010.0010.0000.0000.0000.000
89A94GLU -1-0.729-0.82057.053-0.018-0.0180.0000.0000.0000.000
90A95GLN 0-0.030-0.02358.7730.0010.0010.0000.0000.0000.000
91A96TYR 00.005-0.02959.1710.0000.0000.0000.0000.0000.000
92A97LYS 10.8790.93758.8030.0200.0200.0000.0000.0000.000
93A98GLU -1-0.904-0.96160.781-0.014-0.0140.0000.0000.0000.000
94A99LYS 10.9160.97657.8510.0190.0190.0000.0000.0000.000
95A100GLU -1-0.858-0.91762.662-0.013-0.0130.0000.0000.0000.000
96A101PHE 0-0.026-0.02959.107-0.001-0.0010.0000.0000.0000.000
97A102ASN 0-0.031-0.01563.0260.0010.0010.0000.0000.0000.000
98A103GLY 00.0030.00463.2970.0000.0000.0000.0000.0000.000
99A104VAL 0-0.076-0.02358.7920.0000.0000.0000.0000.0000.000
100A105GLU -1-0.813-0.89261.894-0.013-0.0130.0000.0000.0000.000
101A106GLU -1-0.927-0.96356.855-0.018-0.0180.0000.0000.0000.000
102A107SER 0-0.019-0.00858.4910.0000.0000.0000.0000.0000.000
103A108TYR 0-0.128-0.08453.114-0.001-0.0010.0000.0000.0000.000
104A109VAL 0-0.020-0.01254.9830.0010.0010.0000.0000.0000.000
105A110ILE 0-0.046-0.02054.611-0.001-0.0010.0000.0000.0000.000
106A111LEU 00.000-0.00952.2240.0010.0010.0000.0000.0000.000
107A112VAL 0-0.0080.00753.276-0.001-0.0010.0000.0000.0000.000
108A113ILE 0-0.0030.01248.2370.0010.0010.0000.0000.0000.000
109A114SER 00.014-0.01650.564-0.001-0.0010.0000.0000.0000.000
110A115ASP -1-0.769-0.88245.167-0.036-0.0360.0000.0000.0000.000
111A116PHE 0-0.130-0.09348.2440.0000.0000.0000.0000.0000.000
112A117ILE 00.0480.04643.8760.0010.0010.0000.0000.0000.000
113A118GLY 00.0210.01946.821-0.002-0.0020.0000.0000.0000.000
114A119ILE 0-0.030-0.03048.1510.0020.0020.0000.0000.0000.000
115A120ASP -1-0.882-0.93849.201-0.034-0.0340.0000.0000.0000.000
116A121SER 0-0.0140.02848.425-0.001-0.0010.0000.0000.0000.000
117A122LYS 10.9470.95049.4280.0280.0280.0000.0000.0000.000
118A123ILE 00.0540.03946.286-0.001-0.0010.0000.0000.0000.000
119A124ARG 10.7950.89250.3100.0290.0290.0000.0000.0000.000
120A125VAL 00.0100.00747.958-0.002-0.0020.0000.0000.0000.000
121A126ARG 10.8280.88149.8950.0270.0270.0000.0000.0000.000
122A127LEU 0-0.015-0.00149.030-0.001-0.0010.0000.0000.0000.000
123A128SER 00.0990.04051.4110.0010.0010.0000.0000.0000.000
124A129GLN 00.048-0.01953.5190.0000.0000.0000.0000.0000.000
125A130GLU -1-0.948-0.95353.097-0.016-0.0160.0000.0000.0000.000
126A131GLN 00.0860.04347.4930.0010.0010.0000.0000.0000.000
127A132PHE 0-0.021-0.01051.2840.0000.0000.0000.0000.0000.000
128A133LYS 10.9690.96253.6600.0140.0140.0000.0000.0000.000
129A134GLU -1-0.967-0.96150.891-0.015-0.0150.0000.0000.0000.000
130A135VAL 0-0.037-0.00349.0890.0000.0000.0000.0000.0000.000
131A136GLY 0-0.022-0.02851.7140.0000.0000.0000.0000.0000.000
132A137LEU 0-0.090-0.02852.6810.0000.0000.0000.0000.0000.000
133A138THR 0-0.022-0.05056.4310.0000.0000.0000.0000.0000.000
134A139LEU 00.0050.01259.388-0.001-0.0010.0000.0000.0000.000
135A140ASP -1-0.808-0.88961.956-0.014-0.0140.0000.0000.0000.000
136A141LYS 10.8430.92662.2310.0170.0170.0000.0000.0000.000
137A142LYS 10.9020.97762.4090.0120.0120.0000.0000.0000.000
138A143ASN 0-0.003-0.04356.8700.0000.0000.0000.0000.0000.000
139A144TYR 00.0200.01457.162-0.001-0.0010.0000.0000.0000.000
140A145GLY 0-0.039-0.02156.4760.0010.0010.0000.0000.0000.000
141A146LYS 10.8500.94253.8010.0160.0160.0000.0000.0000.000
142A147ILE 00.0070.01747.996-0.001-0.0010.0000.0000.0000.000
143A148VAL 0-0.011-0.00548.2740.0010.0010.0000.0000.0000.000
144A149GLU -1-0.833-0.93740.410-0.037-0.0370.0000.0000.0000.000
145A150LEU 0-0.047-0.03843.8030.0020.0020.0000.0000.0000.000
146A151GLU -1-0.853-0.93937.802-0.042-0.0420.0000.0000.0000.000
147A152GLY 0-0.022-0.01740.7130.0030.0030.0000.0000.0000.000
148A153GLU -1-0.881-0.91040.088-0.042-0.0420.0000.0000.0000.000
149A154ILE 0-0.018-0.00741.5320.0020.0020.0000.0000.0000.000
150A155TYR 00.0150.01243.704-0.001-0.0010.0000.0000.0000.000
151A156ASN 0-0.008-0.00943.3480.0020.0020.0000.0000.0000.000
152A157TRP 00.001-0.01247.192-0.001-0.0010.0000.0000.0000.000
153A158TYR 0-0.086-0.07942.4700.0010.0010.0000.0000.0000.000
154A159ASP -1-0.820-0.89948.935-0.030-0.0300.0000.0000.0000.000
155A160SER 00.037-0.00150.080-0.001-0.0010.0000.0000.0000.000
156A161ILE 00.0280.01851.069-0.001-0.0010.0000.0000.0000.000
157A162ASN 0-0.111-0.06154.0030.0000.0000.0000.0000.0000.000
158A163VAL 00.0410.05048.193-0.001-0.0010.0000.0000.0000.000
159A164SER 0-0.0040.00348.882-0.001-0.0010.0000.0000.0000.000
160A165LYS 10.9100.96050.3420.0280.0280.0000.0000.0000.000
161A166LYS 10.9210.95746.3790.0410.0410.0000.0000.0000.000
162A167PRO 0-0.032-0.00547.5990.0020.0020.0000.0000.0000.000
163A168ASP -1-0.770-0.85050.720-0.029-0.0290.0000.0000.0000.000
164A169ARG 10.8430.90044.5360.0410.0410.0000.0000.0000.000
165A170GLU -1-0.822-0.90948.279-0.025-0.0250.0000.0000.0000.000
166A171LEU 0-0.0070.01143.221-0.001-0.0010.0000.0000.0000.000
167A172LYN 0-0.018-0.00145.5950.0030.0030.0000.0000.0000.000
168A173VAL 0-0.021-0.01745.000-0.002-0.0020.0000.0000.0000.000
169A174SER 00.0130.00941.7010.0010.0010.0000.0000.0000.000
170A175LYS 10.9690.97739.4050.0310.0310.0000.0000.0000.000
171A176ILE 00.0140.00543.932-0.002-0.0020.0000.0000.0000.000
172A177THR 00.0070.00943.7430.0020.0020.0000.0000.0000.000
173A178VAL 0-0.031-0.01646.288-0.001-0.0010.0000.0000.0000.000
174A179LEU 0-0.029-0.01244.0050.0010.0010.0000.0000.0000.000
175A180SER 00.0090.00647.9700.0010.0010.0000.0000.0000.000
176A181HIS 00.0420.01151.5390.0000.0000.0000.0000.0000.000
177A182ARG 10.8900.94254.7710.0150.0150.0000.0000.0000.000
178A183PRO 00.0260.01655.289-0.001-0.0010.0000.0000.0000.000
179A184ASP -1-0.896-0.95554.404-0.020-0.0200.0000.0000.0000.000
180A185GLY 00.0420.01551.7640.0000.0000.0000.0000.0000.000
181A186LEU 00.0320.02849.969-0.001-0.0010.0000.0000.0000.000
182A187HIS 00.0190.00547.570-0.002-0.0020.0000.0000.0000.000
183A188PHE 00.0550.01645.795-0.001-0.0010.0000.0000.0000.000
184A189GLU -1-0.903-0.95645.207-0.028-0.0280.0000.0000.0000.000
185A190PHE 0-0.007-0.00845.094-0.002-0.0020.0000.0000.0000.000
186A191GLU -1-0.987-0.97341.121-0.031-0.0310.0000.0000.0000.000
187A192GLN 00.0300.01340.735-0.005-0.0050.0000.0000.0000.000
188A193TRP 0-0.014-0.02140.739-0.003-0.0030.0000.0000.0000.000
189A194LYS 10.9390.97938.2340.0330.0330.0000.0000.0000.000
190A195LYS 10.9220.97735.6030.0380.0380.0000.0000.0000.000
191A196ARG 10.7660.87436.0010.0380.0380.0000.0000.0000.000
192A197MET 0-0.013-0.00937.306-0.004-0.0040.0000.0000.0000.000
193A198GLU -1-0.951-0.97533.455-0.056-0.0560.0000.0000.0000.000
194A199PHE 00.0200.00930.253-0.006-0.0060.0000.0000.0000.000
195A200ARG 10.8860.92032.5750.0510.0510.0000.0000.0000.000
196A201LYS 10.8790.93533.5280.0540.0540.0000.0000.0000.000
197A202ASN 00.006-0.00228.481-0.004-0.0040.0000.0000.0000.000
198A203ASN 0-0.065-0.02928.023-0.014-0.0140.0000.0000.0000.000
199A204LEU 0-0.0020.01529.902-0.001-0.0010.0000.0000.0000.000
200A205VAL 0-0.041-0.00533.0210.0010.0010.0000.0000.0000.000
201A206GLU -1-0.922-0.95428.490-0.112-0.1120.0000.0000.0000.000
202A207PRO 0-0.044-0.01130.626-0.002-0.0020.0000.0000.0000.000
203A208TRP 00.0230.00725.465-0.003-0.0030.0000.0000.0000.000
204A209VAL 00.0220.00525.2020.0060.0060.0000.0000.0000.000
205A210PHE 0-0.030-0.01222.805-0.015-0.0150.0000.0000.0000.000
206A211ILE 00.0350.00220.0190.0070.0070.0000.0000.0000.000
207A212PRO 0-0.048-0.03320.296-0.022-0.0220.0000.0000.0000.000
208A213THR 0-0.017-0.00115.149-0.001-0.0010.0000.0000.0000.000
209A214NME 00.0100.01915.831-0.042-0.0420.0000.0000.0000.000