FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: G59J1

Calculation Name: 4KF7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KF7

Chain ID: A

ChEMBL ID:

UniProt ID: G2QD05

Base Structure: X-ray

Registration Date: 2023-09-24

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 1096
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -34059201.089963
FMO2-HF: Nuclear repulsion 33633525.702906
FMO2-HF: Total energy -425675.387057
FMO2-MP2: Total energy -426916.406329


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.
-3.481-0.663-0.017-1.355-1.4470.004
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 : -0.006 / q_NPA : -0.010
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].
3A3THR0-0.006-0.0073.528-1.6931.048-0.016-1.331-1.3940.004
4A4LEU00.0020.0194.341-0.930-0.853-0.001-0.024-0.0530.000
5A5THR0-0.014-0.0225.9880.6040.6040.0000.0000.0000.000
6A6ASP-1-0.675-0.8297.462-0.421-0.4210.0000.0000.0000.000
7A7ARG10.8840.9437.0090.3500.3500.0000.0000.0000.000
8A8SER0-0.080-0.04311.7360.1250.1250.0000.0000.0000.000
9A9TYR00.1070.07213.5460.0800.0800.0000.0000.0000.000
10A10PHE0-0.017-0.01514.6390.0900.0900.0000.0000.0000.000
11A11PRO00.0270.02415.115-0.001-0.0010.0000.0000.0000.000
12A12PRO00.0190.00114.7590.0150.0150.0000.0000.0000.000
13A13LEU00.1040.04917.0680.0080.0080.0000.0000.0000.000
14A14GLY00.0130.00520.3520.0030.0030.0000.0000.0000.000
15A15GLU-1-0.872-0.92417.937-0.114-0.1140.0000.0000.0000.000
16A16CYS0-0.0290.01320.285-0.019-0.0190.0000.0000.0000.000
17A17LEU0-0.004-0.00823.1610.0020.0020.0000.0000.0000.000
18A18SER00.0000.00925.1010.0000.0000.0000.0000.0000.000
19A19GLY00.0440.02525.9430.0040.0040.0000.0000.0000.000
20A20ASN0-0.090-0.03423.397-0.004-0.0040.0000.0000.0000.000
21A21LYS10.8210.88917.5100.1550.1550.0000.0000.0000.000
22A22ILE00.0170.00922.7360.0060.0060.0000.0000.0000.000
23A23ILE0-0.012-0.01120.679-0.022-0.0220.0000.0000.0000.000
24A24LEU00.0160.00921.1590.0150.0150.0000.0000.0000.000
25A25SER0-0.0180.00322.182-0.029-0.0290.0000.0000.0000.000
26A26TRP00.090-0.00119.815-0.005-0.0050.0000.0000.0000.000
27A27ARG10.8360.90825.2730.1450.1450.0000.0000.0000.000
28A28LEU0-0.046-0.01526.4540.0080.0080.0000.0000.0000.000
29A29VAL00.0200.01322.6050.0040.0040.0000.0000.0000.000
30A30ALA00.0340.02125.9230.0000.0000.0000.0000.0000.000
31A31THR0-0.054-0.03628.8470.0120.0120.0000.0000.0000.000
32A32ALA0-0.074-0.05427.3140.0100.0100.0000.0000.0000.000
33A33LEU0-0.021-0.01525.445-0.004-0.0040.0000.0000.0000.000
34A34GLU-1-0.862-0.90629.866-0.141-0.1410.0000.0000.0000.000
35A35ASP-1-0.829-0.94533.511-0.160-0.1600.0000.0000.0000.000
36A36LEU0-0.055-0.01336.2000.0020.0020.0000.0000.0000.000
37A37ALA0-0.052-0.01332.0900.0020.0020.0000.0000.0000.000
38A38CYS00.0310.02732.332-0.004-0.0040.0000.0000.0000.000
39A39ASP-1-0.816-0.92731.230-0.161-0.1610.0000.0000.0000.000
40A40ARG10.7630.85529.6850.1490.1490.0000.0000.0000.000
41A41LEU00.0250.03025.769-0.012-0.0120.0000.0000.0000.000
42A42ARG10.9340.96726.1710.1650.1650.0000.0000.0000.000
43A43SER0-0.036-0.00625.948-0.012-0.0120.0000.0000.0000.000
44A44ALA00.0480.00621.987-0.020-0.0200.0000.0000.0000.000
45A45ALA00.0180.01820.963-0.034-0.0340.0000.0000.0000.000
46A46VAL00.0670.02620.535-0.036-0.0360.0000.0000.0000.000
47A47SER00.0000.00421.160-0.049-0.0490.0000.0000.0000.000
48A48ALA0-0.024-0.02616.776-0.044-0.0440.0000.0000.0000.000
49A49PHE0-0.0020.00216.358-0.078-0.0780.0000.0000.0000.000
50A50LEU00.0300.00617.254-0.057-0.0570.0000.0000.0000.000
51A51ARG10.8580.94216.2000.4050.4050.0000.0000.0000.000
52A52ASP-1-0.818-0.88211.678-1.126-1.1260.0000.0000.0000.000
53A53GLY00.0610.02210.8060.0320.0320.0000.0000.0000.000
54A54TYR0-0.079-0.06810.4570.0130.0130.0000.0000.0000.000
55A55VAL00.0280.00811.9210.0970.0970.0000.0000.0000.000
56A56HIS00.002-0.00914.328-0.003-0.0030.0000.0000.0000.000
57A57GLN0-0.048-0.02110.5700.1900.1900.0000.0000.0000.000
58A58LEU0-0.026-0.00215.3320.0630.0630.0000.0000.0000.000
59A59LEU0-0.0010.00618.1160.0540.0540.0000.0000.0000.000
60A60ARG10.8950.97614.3910.8420.8420.0000.0000.0000.000
61A61GLU-1-0.856-0.90518.728-0.320-0.3200.0000.0000.0000.000
62A62PRO00.0530.03020.034-0.020-0.0200.0000.0000.0000.000
63A63THR0-0.068-0.06522.4740.0130.0130.0000.0000.0000.000
64A64LYS10.8880.94113.8230.7480.7480.0000.0000.0000.000
65A65THR0-0.036-0.01219.584-0.009-0.0090.0000.0000.0000.000
66A66PHE0-0.030-0.02520.5720.0080.0080.0000.0000.0000.000
67A67ALA00.0320.03820.1510.0270.0270.0000.0000.0000.000
68A68PRO00.0750.03522.2640.0090.0090.0000.0000.0000.000
69A69PRO00.0070.01022.171-0.019-0.0190.0000.0000.0000.000
70A70THR00.0210.01919.0520.0120.0120.0000.0000.0000.000
71A71ASN00.007-0.02420.4790.0150.0150.0000.0000.0000.000
72A72GLU-1-0.933-0.95613.678-0.301-0.3010.0000.0000.0000.000
73A73THR00.022-0.00715.844-0.010-0.0100.0000.0000.0000.000
74A74LYS10.9030.96117.7610.0310.0310.0000.0000.0000.000
75A75LEU0-0.017-0.00914.9030.0220.0220.0000.0000.0000.000
76A76ASP-1-0.877-0.94013.608-0.248-0.2480.0000.0000.0000.000
77A77PHE00.0080.01015.8240.0160.0160.0000.0000.0000.000
78A78GLU-1-0.808-0.88819.2870.0110.0110.0000.0000.0000.000
79A79THR0-0.031-0.01913.8660.0430.0430.0000.0000.0000.000
80A80LYS10.7480.87114.0440.3480.3480.0000.0000.0000.000
81A81THR0-0.082-0.06117.2320.0050.0050.0000.0000.0000.000
82A82GLY00.0270.03019.4530.0070.0070.0000.0000.0000.000
83A83ALA0-0.067-0.02917.6050.0250.0250.0000.0000.0000.000
84A84ILE0-0.0100.00119.5920.0160.0160.0000.0000.0000.000
85A92ASP-1-0.931-0.97232.5990.0040.0040.0000.0000.0000.000
86A93PRO0-0.043-0.02532.339-0.004-0.0040.0000.0000.0000.000
87A94TYR00.0400.01728.114-0.002-0.0020.0000.0000.0000.000
88A95ASN0-0.017-0.01532.091-0.005-0.0050.0000.0000.0000.000
89A96LEU00.0680.03124.913-0.008-0.0080.0000.0000.0000.000
90A97ASP-1-0.871-0.94128.5020.0000.0000.0000.0000.0000.000
91A98THR0-0.017-0.00230.841-0.004-0.0040.0000.0000.0000.000
92A99ILE0-0.0080.00026.380-0.007-0.0070.0000.0000.0000.000
93A100LYS10.8280.90023.0370.0080.0080.0000.0000.0000.000
94A101ASP-1-0.898-0.92727.787-0.042-0.0420.0000.0000.0000.000
95A102ASP-1-0.755-0.84230.290-0.067-0.0670.0000.0000.0000.000
96A103ALA0-0.0300.00225.147-0.007-0.0070.0000.0000.0000.000
97A104ARG10.9050.92425.6460.0150.0150.0000.0000.0000.000
98A105TRP0-0.041-0.02528.288-0.004-0.0040.0000.0000.0000.000
99A106LEU00.0180.00027.575-0.002-0.0020.0000.0000.0000.000
100A107SER0-0.086-0.05825.6660.0000.0000.0000.0000.0000.000
101A108ARG10.9490.98027.6280.0530.0530.0000.0000.0000.000
102A109ASN0-0.006-0.00230.5030.0020.0020.0000.0000.0000.000
103A110VAL0-0.025-0.01329.0910.0010.0010.0000.0000.0000.000
104A111ASN0-0.054-0.02128.568-0.018-0.0180.0000.0000.0000.000
105A112ILE00.0320.03824.589-0.013-0.0130.0000.0000.0000.000
106A113ASN0-0.008-0.00519.7680.0170.0170.0000.0000.0000.000
107A114GLU-1-0.785-0.91021.448-0.142-0.1420.0000.0000.0000.000
108A115VAL00.0020.00716.2150.0170.0170.0000.0000.0000.000
109A116ALA00.0310.01219.619-0.003-0.0030.0000.0000.0000.000
110A117ALA0-0.006-0.00421.3780.0090.0090.0000.0000.0000.000
111A118LEU0-0.011-0.01920.3270.0140.0140.0000.0000.0000.000
112A119ARG10.8260.91718.8300.3400.3400.0000.0000.0000.000
113A120VAL00.0120.00922.2460.0070.0070.0000.0000.0000.000
114A121VAL0-0.009-0.00325.8310.0110.0110.0000.0000.0000.000
115A122ILE0-0.011-0.00422.1350.0130.0130.0000.0000.0000.000
116A123ILE00.0080.01123.4620.0060.0060.0000.0000.0000.000
117A124GLU-1-0.741-0.84126.956-0.076-0.0760.0000.0000.0000.000
118A125TYR0-0.052-0.02228.0140.0110.0110.0000.0000.0000.000
119A126GLN0-0.044-0.03324.656-0.006-0.0060.0000.0000.0000.000
120A127SER0-0.038-0.02529.6190.0010.0010.0000.0000.0000.000
121A128ARG10.8950.92532.3490.0760.0760.0000.0000.0000.000
122A129ALA0-0.017-0.00135.2560.0040.0040.0000.0000.0000.000
123A130HIS00.0510.02334.1390.0000.0000.0000.0000.0000.000
124A131SER00.0080.01635.5240.0020.0020.0000.0000.0000.000
125A132HIS10.8500.93338.1400.0610.0610.0000.0000.0000.000
126A133LEU0-0.037-0.01040.7570.0030.0030.0000.0000.0000.000
127A134THR0-0.010-0.01539.3150.0010.0010.0000.0000.0000.000
128A135GLY0-0.0050.02142.1020.0000.0000.0000.0000.0000.000
129A136PRO00.0310.01844.1300.0000.0000.0000.0000.0000.000
130A137LEU0-0.037-0.02547.9020.0010.0010.0000.0000.0000.000
131A138SER0-0.035-0.03050.3240.0020.0020.0000.0000.0000.000
132A139THR00.026-0.02052.5020.0000.0000.0000.0000.0000.000
133A140GLN00.0100.00555.8680.0000.0000.0000.0000.0000.000
134A141ASP-1-0.833-0.90851.489-0.045-0.0450.0000.0000.0000.000
135A142VAL00.0220.00254.502-0.001-0.0010.0000.0000.0000.000
136A143ALA00.0080.01256.6070.0000.0000.0000.0000.0000.000
137A144ASN00.0120.00056.5060.0020.0020.0000.0000.0000.000
138A145VAL00.0260.01354.6480.0000.0000.0000.0000.0000.000
139A146GLN0-0.009-0.00657.9460.0000.0000.0000.0000.0000.000
140A147GLU-1-0.874-0.91961.167-0.031-0.0310.0000.0000.0000.000
141A148ALA0-0.061-0.03459.4800.0010.0010.0000.0000.0000.000
142A149ALA0-0.063-0.02460.8400.0000.0000.0000.0000.0000.000
143A150GLY00.0210.01862.4810.0010.0010.0000.0000.0000.000
144A151VAL0-0.032-0.01865.6100.0010.0010.0000.0000.0000.000
145A152GLY0-0.012-0.00368.1560.0000.0000.0000.0000.0000.000
146A153ASP-1-0.874-0.92870.071-0.032-0.0320.0000.0000.0000.000
147A154ALA0-0.002-0.02365.663-0.001-0.0010.0000.0000.0000.000
148A155GLN00.025-0.00564.090-0.002-0.0020.0000.0000.0000.000
149A156ALA00.0300.03163.417-0.001-0.0010.0000.0000.0000.000
150A157SER00.0530.01661.227-0.001-0.0010.0000.0000.0000.000
151A158ALA0-0.004-0.00359.640-0.002-0.0020.0000.0000.0000.000
152A159ILE0-0.023-0.01259.049-0.001-0.0010.0000.0000.0000.000
153A160VAL00.004-0.00558.492-0.001-0.0010.0000.0000.0000.000
154A161ALA00.0040.01955.346-0.002-0.0020.0000.0000.0000.000
155A162LEU0-0.002-0.00254.448-0.002-0.0020.0000.0000.0000.000
156A163LEU0-0.040-0.03655.0070.0000.0000.0000.0000.0000.000
157A164ASN0-0.038-0.02852.256-0.002-0.0020.0000.0000.0000.000
158A165VAL0-0.0290.01250.020-0.003-0.0030.0000.0000.0000.000
159A166THR0-0.067-0.03449.129-0.001-0.0010.0000.0000.0000.000
160A167THR00.010-0.01151.0190.0000.0000.0000.0000.0000.000
161A168VAL0-0.037-0.00353.2890.0020.0020.0000.0000.0000.000
162A169ALA00.1050.03150.632-0.001-0.0010.0000.0000.0000.000
163A170ASP-1-0.855-0.87952.723-0.030-0.0300.0000.0000.0000.000
164A171ALA00.008-0.01950.3440.0000.0000.0000.0000.0000.000
165A172ASP-1-0.959-0.97049.316-0.027-0.0270.0000.0000.0000.000
166A173SER0-0.005-0.02849.414-0.001-0.0010.0000.0000.0000.000
167A174ALA00.0310.02247.532-0.001-0.0010.0000.0000.0000.000
168A175TRP0-0.132-0.07641.878-0.002-0.0020.0000.0000.0000.000
169A176ALA00.0250.00644.3280.0000.0000.0000.0000.0000.000
170A177ASP-1-0.880-0.93545.155-0.042-0.0420.0000.0000.0000.000
171A178PHE0-0.103-0.05337.728-0.003-0.0030.0000.0000.0000.000
172A179GLU-1-0.864-0.93239.124-0.051-0.0510.0000.0000.0000.000
173A180SER0-0.0270.00240.4860.0020.0020.0000.0000.0000.000
174A181GLU-1-0.895-0.96137.743-0.044-0.0440.0000.0000.0000.000
175A182THR00.0200.00538.457-0.005-0.0050.0000.0000.0000.000
176A183THR00.002-0.01739.750-0.005-0.0050.0000.0000.0000.000
177A184ARG10.8470.89934.0920.0480.0480.0000.0000.0000.000
178A185ARG10.8000.87233.7450.0440.0440.0000.0000.0000.000
179A186ARG10.9520.97535.4240.0520.0520.0000.0000.0000.000
180A187ARG10.8350.92235.4620.0670.0670.0000.0000.0000.000
181A188LEU0-0.0050.02929.915-0.010-0.0100.0000.0000.0000.000
182A189LEU00.0050.00931.658-0.012-0.0120.0000.0000.0000.000
183A190ALA00.0250.01833.389-0.008-0.0080.0000.0000.0000.000
184A191THR0-0.040-0.04129.047-0.008-0.0080.0000.0000.0000.000
185A192TYR00.0090.00027.030-0.019-0.0190.0000.0000.0000.000
186A193LEU00.0120.01229.566-0.015-0.0150.0000.0000.0000.000
187A194SER00.0410.02031.063-0.004-0.0040.0000.0000.0000.000
188A195GLU-1-0.818-0.90825.008-0.243-0.2430.0000.0000.0000.000
189A196ARG10.7960.87427.2670.1770.1770.0000.0000.0000.000
190A197ARG10.8130.90128.6490.1250.1250.0000.0000.0000.000
191A198SER0-0.037-0.03728.117-0.003-0.0030.0000.0000.0000.000
192A199PHE0-0.0260.00421.816-0.013-0.0130.0000.0000.0000.000
193A200LEU00.0510.02426.034-0.017-0.0170.0000.0000.0000.000
194A201ALA00.0150.01828.149-0.001-0.0010.0000.0000.0000.000
195A202ALA0-0.056-0.02725.283-0.001-0.0010.0000.0000.0000.000
196A203VAL00.0030.00123.492-0.010-0.0100.0000.0000.0000.000
197A204ASP-1-0.763-0.85925.967-0.205-0.2050.0000.0000.0000.000
198A205ALA00.0140.00129.2670.0030.0030.0000.0000.0000.000
199A206LEU0-0.047-0.02022.099-0.001-0.0010.0000.0000.0000.000
200A207LEU00.0130.00025.036-0.008-0.0080.0000.0000.0000.000
201A208ALA00.0330.03827.9540.0060.0060.0000.0000.0000.000
202A209PHE0-0.0080.00025.4730.0080.0080.0000.0000.0000.000
203A210LEU0-0.050-0.03123.4630.0010.0010.0000.0000.0000.000
204A211LEU0-0.012-0.00627.7370.0000.0000.0000.0000.0000.000
205A212HIS0-0.0040.00230.4790.0200.0200.0000.0000.0000.000
206A213SER0-0.035-0.01831.5780.0050.0050.0000.0000.0000.000
207A214ARG10.9350.96132.8840.1720.1720.0000.0000.0000.000
208A215ALA00.1010.06734.2720.0090.0090.0000.0000.0000.000
209A216PRO00.0190.00736.095-0.002-0.0020.0000.0000.0000.000
210A217GLY0-0.0200.00934.9830.0040.0040.0000.0000.0000.000
211A218THR0-0.012-0.03634.9060.0070.0070.0000.0000.0000.000
212A219GLY0-0.015-0.01134.003-0.008-0.0080.0000.0000.0000.000
213A220VAL0-0.0220.01432.852-0.012-0.0120.0000.0000.0000.000
214A221GLU-1-0.928-0.95630.341-0.174-0.1740.0000.0000.0000.000
215A222LEU0-0.026-0.03427.452-0.010-0.0100.0000.0000.0000.000
216A223ASP-1-0.785-0.89126.865-0.250-0.2500.0000.0000.0000.000
217A224PRO0-0.020-0.00424.162-0.025-0.0250.0000.0000.0000.000
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