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: 2LL2R

Calculation Name: 3K5R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K5R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WTR5

Base Structure: X-ray

Registration Date: 2023-09-27

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2375188.28626
FMO2-HF: Nuclear repulsion 2291443.641909
FMO2-HF: Total energy -83744.644352
FMO2-MP2: Total energy -83989.802295


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-36.743-29.8647.38-7.206-7.053-0.016
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.081 / q_NPA : -0.064
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].
3A2ILE0-0.018-0.0023.495-2.503-0.753-0.010-1.039-0.7020.000
4A3VAL0-0.055-0.0284.6470.9060.986-0.001-0.009-0.0690.000
5A4VAL00.004-0.0017.364-0.104-0.1040.0000.0000.0000.000
6A5SER00.000-0.01311.0310.2150.2150.0000.0000.0000.000
7A6PRO0-0.0110.00314.196-0.071-0.0710.0000.0000.0000.000
8A7ILE00.0180.02016.2630.0220.0220.0000.0000.0000.000
9A8LEU00.0070.00719.387-0.017-0.0170.0000.0000.0000.000
10A9ILE0-0.036-0.02922.782-0.001-0.0010.0000.0000.0000.000
11A10PRO00.0180.02025.311-0.005-0.0050.0000.0000.0000.000
12A11GLU-1-0.786-0.89128.8280.0280.0280.0000.0000.0000.000
13A12ASN0-0.047-0.04031.444-0.002-0.0020.0000.0000.0000.000
14A13GLN00.0000.01325.978-0.010-0.0100.0000.0000.0000.000
15A14ARG10.9730.98731.736-0.040-0.0400.0000.0000.0000.000
16A15GLN00.0420.03432.2800.0010.0010.0000.0000.0000.000
17A16PRO0-0.062-0.03831.1000.0070.0070.0000.0000.0000.000
18A17PHE0-0.0160.00828.1590.0050.0050.0000.0000.0000.000
19A18PRO00.007-0.02024.884-0.003-0.0030.0000.0000.0000.000
20A19ARG10.8630.94225.057-0.005-0.0050.0000.0000.0000.000
21A20ASP-1-0.802-0.88319.556-0.063-0.0630.0000.0000.0000.000
22A21VAL0-0.087-0.05819.9830.0190.0190.0000.0000.0000.000
23A22GLY00.0700.03216.9720.0340.0340.0000.0000.0000.000
24A23LYS10.7930.91811.968-0.431-0.4310.0000.0000.0000.000
25A24VAL0-0.015-0.0018.9720.0830.0830.0000.0000.0000.000
26A25VAL0-0.024-0.0124.747-0.0250.046-0.001-0.002-0.0680.000
27A26ASP-1-0.800-0.9283.713-6.232-6.1640.000-0.039-0.0290.000
28A27SER0-0.090-0.0402.055-5.736-4.9073.900-2.274-2.4550.026
29A28ASP-1-0.890-0.9492.488-22.044-18.0543.493-3.833-3.650-0.042
30A29ARG10.8570.9294.3011.6351.726-0.001-0.010-0.0800.000
31A30PRO0-0.047-0.0116.8950.6460.6460.0000.0000.0000.000
32A31GLU-1-0.934-0.9799.894-0.582-0.5820.0000.0000.0000.000
33A32GLY0-0.004-0.00113.248-0.015-0.0150.0000.0000.0000.000
34A33SER0-0.027-0.00810.1160.1950.1950.0000.0000.0000.000
35A34LYS10.8110.92012.8010.6740.6740.0000.0000.0000.000
36A35PHE00.0090.0028.112-0.062-0.0620.0000.0000.0000.000
37A36ARG10.7750.86813.2750.6560.6560.0000.0000.0000.000
38A37LEU00.0180.01615.501-0.029-0.0290.0000.0000.0000.000
39A38THR0-0.025-0.02017.5530.0190.0190.0000.0000.0000.000
40A39GLY00.0590.02720.2290.0130.0130.0000.0000.0000.000
41A40LYS10.9420.98122.9100.0320.0320.0000.0000.0000.000
42A41GLY00.0230.00624.8180.0070.0070.0000.0000.0000.000
43A42VAL0-0.031-0.00820.963-0.001-0.0010.0000.0000.0000.000
44A43ASP-1-0.802-0.90323.781-0.208-0.2080.0000.0000.0000.000
45A44GLN0-0.034-0.02425.6850.0140.0140.0000.0000.0000.000
46A45ASP-1-0.859-0.91128.074-0.085-0.0850.0000.0000.0000.000
47A46PRO0-0.0170.00229.0880.0040.0040.0000.0000.0000.000
48A47LYS10.8740.91628.2110.1030.1030.0000.0000.0000.000
49A48GLY0-0.0070.00126.3130.0070.0070.0000.0000.0000.000
50A49THR0-0.0190.02226.4000.0110.0110.0000.0000.0000.000
51A50PHE00.0390.01521.5010.0140.0140.0000.0000.0000.000
52A51ARG10.9070.96121.2560.1760.1760.0000.0000.0000.000
53A52ILE00.0520.03213.3410.0260.0260.0000.0000.0000.000
54A53ASN0-0.050-0.01316.387-0.063-0.0630.0000.0000.0000.000
55A54GLU-1-0.791-0.89715.101-0.525-0.5250.0000.0000.0000.000
56A55ASN00.0400.02514.085-0.204-0.2040.0000.0000.0000.000
57A56THR0-0.014-0.01912.524-0.102-0.1020.0000.0000.0000.000
58A57GLY00.0680.05011.6140.0270.0270.0000.0000.0000.000
59A58SER0-0.046-0.03412.6840.0790.0790.0000.0000.0000.000
60A59VAL00.007-0.00815.170-0.056-0.0560.0000.0000.0000.000
61A60SER00.0120.00717.6660.0410.0410.0000.0000.0000.000
62A61VAL0-0.004-0.00221.383-0.017-0.0170.0000.0000.0000.000
63A62THR0-0.051-0.06624.5890.0100.0100.0000.0000.0000.000
64A63ARG10.8390.92127.5760.0430.0430.0000.0000.0000.000
65A64THR00.013-0.01529.4420.0050.0050.0000.0000.0000.000
66A65LEU0-0.052-0.02626.634-0.008-0.0080.0000.0000.0000.000
67A66ASP-1-0.772-0.86131.3790.0170.0170.0000.0000.0000.000
68A67ARG10.9030.94129.935-0.068-0.0680.0000.0000.0000.000
69A68GLU-1-0.917-0.96132.8360.0360.0360.0000.0000.0000.000
70A69THR0-0.137-0.06833.837-0.006-0.0060.0000.0000.0000.000
71A70ILE0-0.107-0.06528.962-0.006-0.0060.0000.0000.0000.000
72A71ALA00.0680.04730.1960.0010.0010.0000.0000.0000.000
73A72THR0-0.075-0.04025.1340.0050.0050.0000.0000.0000.000
74A73TYR00.012-0.02223.834-0.020-0.0200.0000.0000.0000.000
75A74GLN0-0.013-0.00819.733-0.001-0.0010.0000.0000.0000.000
76A75LEU0-0.015-0.00418.499-0.021-0.0210.0000.0000.0000.000
77A76TYR0-0.010-0.01016.5440.0390.0390.0000.0000.0000.000
78A77VAL00.0050.00311.592-0.004-0.0040.0000.0000.0000.000
79A78GLU-1-0.766-0.84212.026-0.583-0.5830.0000.0000.0000.000
80A79THR00.0720.0368.7600.1760.1760.0000.0000.0000.000
81A80THR0-0.026-0.01211.7380.1130.1130.0000.0000.0000.000
82A81ASP-1-0.820-0.91214.259-0.981-0.9810.0000.0000.0000.000
83A82ALA00.0590.02716.3460.0500.0500.0000.0000.0000.000
84A83SER0-0.056-0.04218.9500.0430.0430.0000.0000.0000.000
85A84GLY00.0480.03219.1610.0530.0530.0000.0000.0000.000
86A85LYS10.7750.87314.6690.9260.9260.0000.0000.0000.000
87A86THR0-0.017-0.01313.917-0.052-0.0520.0000.0000.0000.000
88A87LEU0-0.100-0.05210.2180.0780.0780.0000.0000.0000.000
89A88GLU-1-0.869-0.9286.439-2.388-2.3880.0000.0000.0000.000
90A89GLY0-0.027-0.0279.8070.1940.1940.0000.0000.0000.000
91A90PRO0-0.036-0.02712.122-0.055-0.0550.0000.0000.0000.000
92A91VAL00.0130.0279.9670.1210.1210.0000.0000.0000.000
93A92PRO0-0.021-0.02013.415-0.022-0.0220.0000.0000.0000.000
94A93LEU00.0260.01414.2020.0310.0310.0000.0000.0000.000
95A94GLU-1-0.898-0.94116.4120.0540.0540.0000.0000.0000.000
96A95VAL0-0.004-0.00119.6230.0200.0200.0000.0000.0000.000
97A96ILE00.0030.00121.793-0.005-0.0050.0000.0000.0000.000
98A97VAL0-0.016-0.00724.6840.0040.0040.0000.0000.0000.000
99A98ILE0-0.034-0.01726.0220.0040.0040.0000.0000.0000.000
100A99ASP-1-0.802-0.90629.0990.0520.0520.0000.0000.0000.000
101A100GLN0-0.002-0.00932.6750.0040.0040.0000.0000.0000.000
102A101ASN0-0.121-0.06734.3500.0000.0000.0000.0000.0000.000
103A102ASP-1-0.856-0.88730.4190.1260.1260.0000.0000.0000.000
104A103ASN0-0.043-0.04031.506-0.001-0.0010.0000.0000.0000.000
105A104ARG10.7930.86328.184-0.137-0.1370.0000.0000.0000.000
106A105PRO00.0080.02126.566-0.001-0.0010.0000.0000.0000.000
107A106ILE0-0.006-0.01522.2000.0110.0110.0000.0000.0000.000
108A107PHE0-0.019-0.00319.130-0.004-0.0040.0000.0000.0000.000
109A108ARG10.8880.92519.528-0.119-0.1190.0000.0000.0000.000
110A109GLU-1-0.866-0.91716.4820.2290.2290.0000.0000.0000.000
111A110GLY00.0020.01613.6270.0780.0780.0000.0000.0000.000
112A111PRO0-0.018-0.0269.219-0.095-0.0950.0000.0000.0000.000
113A112TYR00.0360.02411.0010.0670.0670.0000.0000.0000.000
114A113ILE0-0.005-0.0065.6900.0900.0900.0000.0000.0000.000
115A114GLY00.002-0.0029.396-0.094-0.0940.0000.0000.0000.000
116A115HIS10.8070.8675.458-2.450-2.4500.0000.0000.0000.000
117A116VAL00.0180.01110.646-0.159-0.1590.0000.0000.0000.000
118A117MET0-0.0190.02313.0170.0310.0310.0000.0000.0000.000
119A118GLU-1-0.780-0.88714.8030.3520.3520.0000.0000.0000.000
120A119GLY0-0.031-0.02116.734-0.039-0.0390.0000.0000.0000.000
121A120SER0-0.094-0.07317.508-0.031-0.0310.0000.0000.0000.000
122A121PRO0-0.021-0.01620.193-0.003-0.0030.0000.0000.0000.000
123A122THR0-0.020-0.00922.6580.0190.0190.0000.0000.0000.000
124A123GLY0-0.019-0.00923.779-0.023-0.0230.0000.0000.0000.000
125A124THR0-0.055-0.03618.445-0.015-0.0150.0000.0000.0000.000
126A125THR00.003-0.01019.4290.0170.0170.0000.0000.0000.000
127A126VAL0-0.047-0.02114.0790.0160.0160.0000.0000.0000.000
128A127MET0-0.0140.00412.6370.0780.0780.0000.0000.0000.000
129A128ARG10.8470.89916.352-0.335-0.3350.0000.0000.0000.000
130A129MET0-0.078-0.02016.6870.0590.0590.0000.0000.0000.000
131A130THR00.0350.00419.218-0.013-0.0130.0000.0000.0000.000
132A131ALA0-0.049-0.02221.5670.0110.0110.0000.0000.0000.000
133A132PHE0-0.027-0.02424.013-0.009-0.0090.0000.0000.0000.000
134A133ASP-1-0.899-0.93824.3460.1330.1330.0000.0000.0000.000
135A134ALA0-0.022-0.00725.2610.0170.0170.0000.0000.0000.000
136A135ASP-1-0.930-0.96127.2380.1220.1220.0000.0000.0000.000
137A136ASP-1-0.856-0.90729.3580.1070.1070.0000.0000.0000.000
138A137PRO0-0.091-0.08331.084-0.001-0.0010.0000.0000.0000.000
139A138ALA0-0.0180.00933.4370.0030.0030.0000.0000.0000.000
140A139THR00.0980.02628.3010.0010.0010.0000.0000.0000.000
141A140ASP-1-0.944-0.97531.6400.1240.1240.0000.0000.0000.000
142A141ASN0-0.122-0.07133.958-0.001-0.0010.0000.0000.0000.000
143A142ALA00.0350.03932.032-0.003-0.0030.0000.0000.0000.000
144A143LEU0-0.045-0.01833.6330.0050.0050.0000.0000.0000.000
145A144LEU00.0220.02127.0980.0050.0050.0000.0000.0000.000
146A145ARG10.7910.88329.385-0.176-0.1760.0000.0000.0000.000
147A146TYR00.0010.00724.3920.0080.0080.0000.0000.0000.000
148A147ASN00.026-0.00825.343-0.003-0.0030.0000.0000.0000.000
149A148ILE0-0.0040.01220.4280.0180.0180.0000.0000.0000.000
150A149ARG10.8360.91222.707-0.286-0.2860.0000.0000.0000.000
151A150GLN0-0.028-0.02520.611-0.045-0.0450.0000.0000.0000.000
152A151GLN0-0.0010.00318.3330.0330.0330.0000.0000.0000.000
153A152THR0-0.0300.01216.766-0.077-0.0770.0000.0000.0000.000
154A153PRO00.0310.00615.5650.0900.0900.0000.0000.0000.000
155A154ASP-1-0.893-0.94518.4430.3890.3890.0000.0000.0000.000
156A155LYS10.8670.93920.488-0.433-0.4330.0000.0000.0000.000
157A156PRO00.0520.02219.8130.0510.0510.0000.0000.0000.000
158A157SER00.0180.00022.523-0.040-0.0400.0000.0000.0000.000
159A158PRO00.0300.02022.4380.0370.0370.0000.0000.0000.000
160A159ASN0-0.033-0.01523.1350.0030.0030.0000.0000.0000.000
161A160MET00.001-0.00218.721-0.046-0.0460.0000.0000.0000.000
162A161PHE00.021-0.00415.6050.0000.0000.0000.0000.0000.000
163A162TYR0-0.010-0.00121.166-0.031-0.0310.0000.0000.0000.000
164A163ILE0-0.0040.02120.8890.0210.0210.0000.0000.0000.000
165A164ASP-1-0.838-0.91123.5430.2090.2090.0000.0000.0000.000
166A165PRO00.002-0.00526.0870.0020.0020.0000.0000.0000.000
167A166GLU-1-0.899-0.93328.4470.1620.1620.0000.0000.0000.000
168A167LYS10.8880.92325.798-0.219-0.2190.0000.0000.0000.000
169A168GLY00.0740.03523.0650.0080.0080.0000.0000.0000.000
170A169ASP-1-0.855-0.88821.1250.3640.3640.0000.0000.0000.000
171A170ILE00.0230.00417.071-0.024-0.0240.0000.0000.0000.000
172A171VAL00.0000.00219.4670.0240.0240.0000.0000.0000.000
173A172THR00.0370.02418.5880.0040.0040.0000.0000.0000.000
174A173VAL0-0.017-0.01821.033-0.039-0.0390.0000.0000.0000.000
175A174VAL0-0.0160.00621.385-0.028-0.0280.0000.0000.0000.000
176A175SER00.0200.01724.009-0.002-0.0020.0000.0000.0000.000
177A176PRO00.0460.01822.3150.0210.0210.0000.0000.0000.000
178A177ALA0-0.043-0.03121.9960.0140.0140.0000.0000.0000.000
179A178LEU0-0.034-0.01222.222-0.003-0.0030.0000.0000.0000.000
180A179LEU0-0.054-0.01516.9540.0360.0360.0000.0000.0000.000
181A180ASP-1-0.738-0.86918.0100.3030.3030.0000.0000.0000.000
182A181ARG10.7930.8648.731-0.629-0.6290.0000.0000.0000.000
183A182GLU-1-0.971-0.97515.6330.2520.2520.0000.0000.0000.000
184A183THR0-0.084-0.03817.995-0.026-0.0260.0000.0000.0000.000
185A184LEU0-0.092-0.03915.4410.0010.0010.0000.0000.0000.000
186A185GLU-1-0.935-0.94416.9140.4180.4180.0000.0000.0000.000
187A186ASN0-0.002-0.03012.4720.1370.1370.0000.0000.0000.000
188A187PRO00.0290.03610.8940.0000.0000.0000.0000.0000.000
189A188LYS10.9210.9606.468-2.705-2.7050.0000.0000.0000.000
190A189TYR0-0.006-0.03211.140-0.102-0.1020.0000.0000.0000.000
191A190GLU-1-0.903-0.96112.3440.9800.9800.0000.0000.0000.000
192A191LEU0-0.047-0.03213.969-0.120-0.1200.0000.0000.0000.000
193A192ILE00.0010.00716.5320.0180.0180.0000.0000.0000.000
194A193ILE0-0.004-0.01018.258-0.028-0.0280.0000.0000.0000.000
195A194GLU-1-0.835-0.90320.9530.2300.2300.0000.0000.0000.000
196A195ALA0-0.006-0.00224.3610.0060.0060.0000.0000.0000.000
197A196GLN0-0.018-0.02326.469-0.015-0.0150.0000.0000.0000.000
198A197ASP-1-0.788-0.90430.2210.1530.1530.0000.0000.0000.000
199A198MET0-0.063-0.01432.811-0.003-0.0030.0000.0000.0000.000
200A199ALA0-0.061-0.03335.416-0.009-0.0090.0000.0000.0000.000
201A200GLY00.0590.02536.8070.0020.0020.0000.0000.0000.000
202A201LEU0-0.045-0.04438.9590.0000.0000.0000.0000.0000.000
203A202ASP-1-0.824-0.87934.8830.0950.0950.0000.0000.0000.000
204A203VAL0-0.036-0.01735.3580.0090.0090.0000.0000.0000.000
205A204GLY0-0.031-0.02135.370-0.005-0.0050.0000.0000.0000.000
206A205LEU0-0.058-0.01532.0850.0090.0090.0000.0000.0000.000
207A206THR0-0.043-0.04428.5170.0050.0050.0000.0000.0000.000
208A207GLY00.0380.03125.791-0.013-0.0130.0000.0000.0000.000
209A208THR0-0.040-0.03321.7900.0080.0080.0000.0000.0000.000
210A209ALA0-0.008-0.00117.561-0.018-0.0180.0000.0000.0000.000
211A210THR0-0.017-0.00414.158-0.017-0.0170.0000.0000.0000.000
212A211ALA00.0180.00813.0660.0110.0110.0000.0000.0000.000
213A212THR0-0.025-0.0048.8410.1410.1410.0000.0000.0000.000
214A213ILE0-0.0150.00011.1090.0520.0520.0000.0000.0000.000
215A214VAL0-0.044-0.0146.563-0.003-0.0030.0000.0000.0000.000
216A215ILE00.0210.0219.919-0.102-0.1020.0000.0000.0000.000
217A216ASP-1-0.849-0.9178.0621.4291.4290.0000.0000.0000.000
218A217ASP-1-0.805-0.89210.9400.2660.2660.0000.0000.0000.000