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: 17VKZ

Calculation Name: 3LRS-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LRS

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptAll
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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2247581.961042
FMO2-HF: Nuclear repulsion 2162532.169159
FMO2-HF: Total energy -85049.791883
FMO2-MP2: Total energy -85295.550391


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(H:1:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
1.8023.9710.001-0.9-1.270.003
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.006
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].
3H3GLN00.001-0.0013.8810.8492.557-0.010-0.748-0.9500.003
4H4LEU0-0.016-0.0156.204-0.006-0.0060.0000.0000.0000.000
5H5VAL00.0100.0079.4480.2020.2020.0000.0000.0000.000
6H6GLU-1-0.764-0.88712.0350.0120.0120.0000.0000.0000.000
7H7SER0-0.047-0.03215.8530.0150.0150.0000.0000.0000.000
8H8GLY00.0360.00518.6280.0010.0010.0000.0000.0000.000
9H9GLY00.0150.01721.7950.0100.0100.0000.0000.0000.000
10H10GLY0-0.001-0.00723.649-0.009-0.0090.0000.0000.0000.000
11H11VAL0-0.015-0.00726.6900.0090.0090.0000.0000.0000.000
12H12VAL0-0.007-0.00229.387-0.009-0.0090.0000.0000.0000.000
13H13GLN00.0280.01032.1830.0070.0070.0000.0000.0000.000
14H14PRO00.0240.00735.331-0.003-0.0030.0000.0000.0000.000
15H15GLY0-0.038-0.00737.094-0.003-0.0030.0000.0000.0000.000
16H16GLY0-0.002-0.00135.431-0.004-0.0040.0000.0000.0000.000
17H17SER0-0.034-0.02732.0120.0030.0030.0000.0000.0000.000
18H18LEU00.0100.00726.1150.0010.0010.0000.0000.0000.000
19H19ARG10.9170.95922.1960.1410.1410.0000.0000.0000.000
20H20LEU00.0090.02921.291-0.011-0.0110.0000.0000.0000.000
21H21SER0-0.003-0.02018.872-0.013-0.0130.0000.0000.0000.000
22H22CYS0-0.071-0.02114.283-0.037-0.0370.0000.0000.0000.000
23H23LEU00.0120.03310.400-0.005-0.0050.0000.0000.0000.000
24H24ALA00.0400.0109.795-0.043-0.0430.0000.0000.0000.000
25H25SER0-0.040-0.0255.650-0.165-0.1650.0000.0000.0000.000
26H26GLY00.0570.0213.485-0.858-0.6200.012-0.132-0.1180.000
27H27PHE00.0240.0244.0780.8461.069-0.001-0.020-0.2020.000
28H28THR0-0.024-0.0177.1770.0900.0900.0000.0000.0000.000
29H29PHE00.0580.02110.9650.1360.1360.0000.0000.0000.000
30H30HIS00.0240.00312.3990.0490.0490.0000.0000.0000.000
31H31LYS10.8690.95312.8490.3840.3840.0000.0000.0000.000
32H32TYR00.0280.02210.556-0.024-0.0240.0000.0000.0000.000
33H33GLY00.0380.02915.478-0.028-0.0280.0000.0000.0000.000
34H34MET0-0.057-0.01313.169-0.039-0.0390.0000.0000.0000.000
35H35HIS00.045-0.01216.8360.0020.0020.0000.0000.0000.000
36H36TRP0-0.040-0.02117.744-0.016-0.0160.0000.0000.0000.000
37H37VAL0-0.001-0.00419.1070.0090.0090.0000.0000.0000.000
38H38ARG10.7810.86520.871-0.078-0.0780.0000.0000.0000.000
39H39GLN00.006-0.00121.6270.0320.0320.0000.0000.0000.000
40H40ALA00.0540.03624.241-0.005-0.0050.0000.0000.0000.000
41H41PRO00.011-0.01127.1410.0180.0180.0000.0000.0000.000
42H42GLY00.0230.03227.070-0.009-0.0090.0000.0000.0000.000
43H43LYS10.8470.91927.272-0.142-0.1420.0000.0000.0000.000
44H44GLY00.0580.03125.7470.0210.0210.0000.0000.0000.000
45H45LEU0-0.011-0.00419.539-0.014-0.0140.0000.0000.0000.000
46H46GLU-1-0.789-0.87123.5930.0810.0810.0000.0000.0000.000
47H47TRP00.001-0.00221.743-0.002-0.0020.0000.0000.0000.000
48H48VAL0-0.023-0.01323.363-0.010-0.0100.0000.0000.0000.000
49H49ALA00.009-0.00823.242-0.012-0.0120.0000.0000.0000.000
50H50LEU0-0.0040.01920.0890.0060.0060.0000.0000.0000.000
51H51ILE0-0.064-0.02219.981-0.004-0.0040.0000.0000.0000.000
52H52SER00.001-0.01820.389-0.001-0.0010.0000.0000.0000.000
53H52ASP-1-0.778-0.87018.103-0.141-0.1410.0000.0000.0000.000
54H53ASP-1-0.736-0.84819.148-0.146-0.1460.0000.0000.0000.000
55H54GLY0-0.042-0.01821.922-0.006-0.0060.0000.0000.0000.000
56H55MET0-0.071-0.04123.1400.0140.0140.0000.0000.0000.000
57H56ARG10.8060.88723.1590.0990.0990.0000.0000.0000.000
58H57LYS10.8760.92724.9580.0750.0750.0000.0000.0000.000
59H58TYR00.0200.01425.0480.0050.0050.0000.0000.0000.000
60H59HIS00.0470.01026.143-0.013-0.0130.0000.0000.0000.000
61H60SER00.0230.01727.8840.0030.0030.0000.0000.0000.000
62H61ASP-1-0.855-0.93229.4360.0300.0300.0000.0000.0000.000
63H62SER0-0.037-0.00130.742-0.005-0.0050.0000.0000.0000.000
64H63MET0-0.045-0.02027.759-0.003-0.0030.0000.0000.0000.000
65H64TRP0-0.031-0.02532.304-0.007-0.0070.0000.0000.0000.000
66H65GLY00.0170.01133.764-0.003-0.0030.0000.0000.0000.000
67H66ARG10.7100.82932.801-0.027-0.0270.0000.0000.0000.000
68H67VAL00.0050.00628.111-0.004-0.0040.0000.0000.0000.000
69H68THR0-0.035-0.02028.029-0.002-0.0020.0000.0000.0000.000
70H69ILE00.0170.03020.661-0.011-0.0110.0000.0000.0000.000
71H70SER0-0.043-0.03622.996-0.002-0.0020.0000.0000.0000.000
72H71ARG10.8240.89615.6190.2690.2690.0000.0000.0000.000
73H72ASP-1-0.745-0.83118.794-0.241-0.2410.0000.0000.0000.000
74H73ASN00.0360.00216.788-0.075-0.0750.0000.0000.0000.000
75H74SER0-0.074-0.04916.913-0.027-0.0270.0000.0000.0000.000
76H75LYS10.8370.89516.1910.2520.2520.0000.0000.0000.000
77H76ASN0-0.0050.01811.4210.0130.0130.0000.0000.0000.000
78H77THR00.0240.00313.006-0.071-0.0710.0000.0000.0000.000
79H78LEU0-0.0130.00015.6930.0390.0390.0000.0000.0000.000
80H79TYR0-0.027-0.03917.919-0.008-0.0080.0000.0000.0000.000
81H80LEU00.0030.00721.2240.0120.0120.0000.0000.0000.000
82H81GLN0-0.041-0.01623.955-0.007-0.0070.0000.0000.0000.000
83H82PHE00.0250.00725.4980.0110.0110.0000.0000.0000.000
84H82SER0-0.019-0.01730.223-0.006-0.0060.0000.0000.0000.000
85H82SER00.0270.01534.0220.0050.0050.0000.0000.0000.000
86H82LEU0-0.0070.02030.2600.0060.0060.0000.0000.0000.000
87H83LYS10.9770.98733.907-0.027-0.0270.0000.0000.0000.000
88H84VAL00.0380.03533.7390.0020.0020.0000.0000.0000.000
89H85GLU-1-0.856-0.92133.3020.0510.0510.0000.0000.0000.000
90H86ASP-1-0.789-0.85430.1040.0380.0380.0000.0000.0000.000
91H87THR0-0.064-0.03028.7840.0000.0000.0000.0000.0000.000
92H88ALA0-0.007-0.01125.2600.0120.0120.0000.0000.0000.000
93H89MET0-0.0460.02019.5400.0000.0000.0000.0000.0000.000
94H90PHE00.025-0.00921.0690.0130.0130.0000.0000.0000.000
95H91PHE00.006-0.00815.554-0.020-0.0200.0000.0000.0000.000
96H93ALA00.0420.00713.2010.0460.0460.0000.0000.0000.000
97H94ARG10.7230.8007.9310.0070.0070.0000.0000.0000.000
98H95GLU-1-0.860-0.91113.3280.1970.1970.0000.0000.0000.000
99H96ALA00.0250.01613.440-0.056-0.0560.0000.0000.0000.000
100H97GLY00.034-0.00513.990-0.023-0.0230.0000.0000.0000.000
101H98GLY00.0110.00514.226-0.007-0.0070.0000.0000.0000.000
102H99PRO0-0.035-0.00216.1820.0120.0120.0000.0000.0000.000
103H100TYR00.001-0.00213.054-0.027-0.0270.0000.0000.0000.000
104H100TYR0-0.040-0.01719.0780.0010.0010.0000.0000.0000.000
105H100ASN00.0220.00218.658-0.017-0.0170.0000.0000.0000.000
106H100TYR0-0.042-0.03116.157-0.002-0.0020.0000.0000.0000.000
107H100HIS0-0.0110.00419.3430.0240.0240.0000.0000.0000.000
108H100TYR00.002-0.00213.6410.0050.0050.0000.0000.0000.000
109H100MET0-0.0110.00315.041-0.021-0.0210.0000.0000.0000.000
110H101ASP-1-0.803-0.87510.8980.3450.3450.0000.0000.0000.000
111H102VAL0-0.0110.0126.9710.2740.2740.0000.0000.0000.000
112H103TRP0-0.006-0.0279.361-0.280-0.2800.0000.0000.0000.000
113H104GLY00.0350.0359.7450.0630.0630.0000.0000.0000.000
114H105LYS10.8080.88911.720-0.093-0.0930.0000.0000.0000.000
115H106GLY00.0280.01113.896-0.048-0.0480.0000.0000.0000.000
116H107THR0-0.0060.01017.1640.0170.0170.0000.0000.0000.000
117H108THR0-0.002-0.00719.6580.0150.0150.0000.0000.0000.000
118H109VAL00.0030.00223.165-0.020-0.0200.0000.0000.0000.000
119H110THR0-0.012-0.01726.3700.0140.0140.0000.0000.0000.000
120H111VAL0-0.0040.00429.664-0.009-0.0090.0000.0000.0000.000
121H112SER00.013-0.03232.6180.0040.0040.0000.0000.0000.000
122H113SER00.0410.01335.921-0.003-0.0030.0000.0000.0000.000
123H114ALA0-0.058-0.00538.359-0.003-0.0030.0000.0000.0000.000
124H115SER00.0260.01437.961-0.001-0.0010.0000.0000.0000.000
125H116THR0-0.027-0.03238.1060.0010.0010.0000.0000.0000.000
126H117LYS10.8280.93240.456-0.035-0.0350.0000.0000.0000.000
127H118GLY00.0990.04641.7690.0040.0040.0000.0000.0000.000
128H119PRO0-0.065-0.03842.186-0.001-0.0010.0000.0000.0000.000
129H120SER00.0000.01744.590-0.003-0.0030.0000.0000.0000.000
130H121VAL0-0.012-0.01546.3660.0040.0040.0000.0000.0000.000
131H122PHE00.0140.00148.138-0.003-0.0030.0000.0000.0000.000
132H123PRO0-0.018-0.00749.8140.0030.0030.0000.0000.0000.000
133H124LEU0-0.014-0.00846.869-0.001-0.0010.0000.0000.0000.000
134H125ALA00.0420.01051.5150.0010.0010.0000.0000.0000.000
135H126PRO0-0.0070.01254.7490.0010.0010.0000.0000.0000.000
136H127SER00.0240.01355.756-0.001-0.0010.0000.0000.0000.000
137H128SER00.024-0.00757.7460.0010.0010.0000.0000.0000.000
138H129LYN00.004-0.00753.8870.0010.0010.0000.0000.0000.000
139H130SER00.0610.03956.048-0.002-0.0020.0000.0000.0000.000
140H131THR00.0040.01357.1190.0020.0020.0000.0000.0000.000
141H132SER0-0.039-0.01458.905-0.001-0.0010.0000.0000.0000.000
142H133GLY0-0.036-0.03260.798-0.001-0.0010.0000.0000.0000.000
143H134GLY00.0150.01658.461-0.001-0.0010.0000.0000.0000.000
144H135THR0-0.070-0.03252.121-0.001-0.0010.0000.0000.0000.000
145H136ALA00.0360.03754.8680.0000.0000.0000.0000.0000.000
146H137ALA0-0.014-0.01349.9170.0030.0030.0000.0000.0000.000
147H138LEU00.0130.01750.790-0.003-0.0030.0000.0000.0000.000
148H139GLY00.033-0.01048.3070.0040.0040.0000.0000.0000.000
149H140CYS0-0.0810.00047.176-0.003-0.0030.0000.0000.0000.000
150H141LEU00.0280.03844.0880.0040.0040.0000.0000.0000.000
151H142VAL0-0.008-0.00942.410-0.004-0.0040.0000.0000.0000.000
152H143LYS10.8640.90242.128-0.044-0.0440.0000.0000.0000.000
153H144ASP-1-0.806-0.87442.3890.0410.0410.0000.0000.0000.000
154H145TYR0-0.033-0.03136.607-0.005-0.0050.0000.0000.0000.000
155H146PHE00.0380.01633.5430.0040.0040.0000.0000.0000.000
156H147PRO00.0120.02033.515-0.004-0.0040.0000.0000.0000.000
157H148GLU-1-0.776-0.87832.3120.0850.0850.0000.0000.0000.000
158H149PRO0-0.034-0.00832.850-0.004-0.0040.0000.0000.0000.000
159H150VAL0-0.008-0.01334.930-0.007-0.0070.0000.0000.0000.000
160H151THR0-0.061-0.03737.5030.0060.0060.0000.0000.0000.000
161H152VAL00.017-0.00939.660-0.005-0.0050.0000.0000.0000.000
162H153SER0-0.035-0.00742.3030.0040.0040.0000.0000.0000.000
163H154TRP00.0270.01045.035-0.004-0.0040.0000.0000.0000.000
164H155ASN00.007-0.01648.4740.0010.0010.0000.0000.0000.000
165H156SER0-0.009-0.01249.393-0.001-0.0010.0000.0000.0000.000
166H157GLY00.0010.00647.097-0.001-0.0010.0000.0000.0000.000
167H158ALA0-0.044-0.01348.0580.0020.0020.0000.0000.0000.000
168H159LEU0-0.029-0.00849.1610.0000.0000.0000.0000.0000.000
169H160THR00.0130.00044.6190.0010.0010.0000.0000.0000.000
170H161SER00.0280.00644.9770.0050.0050.0000.0000.0000.000
171H162GLY00.0500.02345.894-0.003-0.0030.0000.0000.0000.000
172H163VAL0-0.032-0.00843.107-0.001-0.0010.0000.0000.0000.000
173H164HIS0-0.0090.00541.2150.0090.0090.0000.0000.0000.000
174H165THR00.007-0.00138.833-0.007-0.0070.0000.0000.0000.000
175H166PHE0-0.0160.00737.3720.0070.0070.0000.0000.0000.000
176H167PRO00.020-0.00832.549-0.004-0.0040.0000.0000.0000.000
177H168ALA0-0.0130.01134.022-0.005-0.0050.0000.0000.0000.000
178H169VAL0-0.022-0.01433.8170.0080.0080.0000.0000.0000.000
179H170LEU0-0.033-0.01032.539-0.006-0.0060.0000.0000.0000.000
180H171GLN0-0.028-0.02635.4650.0020.0020.0000.0000.0000.000
181H172SER00.023-0.01637.803-0.003-0.0030.0000.0000.0000.000
182H173SER00.009-0.00439.159-0.002-0.0020.0000.0000.0000.000
183H174GLY00.0510.03036.823-0.004-0.0040.0000.0000.0000.000
184H175LEU0-0.076-0.01237.384-0.001-0.0010.0000.0000.0000.000
185H176TYR00.005-0.00431.1700.0010.0010.0000.0000.0000.000
186H177SER00.013-0.00937.885-0.007-0.0070.0000.0000.0000.000
187H178LEU00.0340.03937.2760.0060.0060.0000.0000.0000.000
188H179SER0-0.010-0.02539.817-0.007-0.0070.0000.0000.0000.000
189H180SER0-0.0110.00241.3590.0040.0040.0000.0000.0000.000
190H181VAL00.0320.00343.740-0.004-0.0040.0000.0000.0000.000
191H182VAL0-0.0010.00145.6410.0030.0030.0000.0000.0000.000
192H183THR0-0.021-0.00347.594-0.001-0.0010.0000.0000.0000.000
193H184VAL00.0050.00249.8820.0000.0000.0000.0000.0000.000
194H185PRO00.0620.02353.3070.0000.0000.0000.0000.0000.000
195H186SER00.0290.01456.712-0.001-0.0010.0000.0000.0000.000
196H187SER0-0.010-0.00459.122-0.001-0.0010.0000.0000.0000.000
197H188SER0-0.030-0.01257.548-0.001-0.0010.0000.0000.0000.000
198H189LEU00.0120.00356.6810.0000.0000.0000.0000.0000.000
199H190GLY00.0170.01560.315-0.001-0.0010.0000.0000.0000.000
200H191THR0-0.065-0.02661.961-0.001-0.0010.0000.0000.0000.000
201H192GLN00.0090.01956.537-0.002-0.0020.0000.0000.0000.000
202H193THR0-0.033-0.01757.684-0.001-0.0010.0000.0000.0000.000
203H194TYR00.011-0.01153.1940.0020.0020.0000.0000.0000.000
204H195ILE00.006-0.01052.294-0.001-0.0010.0000.0000.0000.000
205H197ASN00.0520.01347.087-0.001-0.0010.0000.0000.0000.000
206H198VAL0-0.008-0.00143.6160.0040.0040.0000.0000.0000.000
207H199ASN0-0.001-0.01942.084-0.006-0.0060.0000.0000.0000.000
208H200HIS00.0210.02238.0880.0020.0020.0000.0000.0000.000
209H201LYS10.9650.97136.672-0.065-0.0650.0000.0000.0000.000
210H202PRO00.0040.01736.108-0.004-0.0040.0000.0000.0000.000
211H203SER00.022-0.01138.624-0.004-0.0040.0000.0000.0000.000
212H204ASN0-0.074-0.03941.825-0.001-0.0010.0000.0000.0000.000
213H205THR00.0250.02543.924-0.001-0.0010.0000.0000.0000.000
214H206LYS10.9200.95244.842-0.032-0.0320.0000.0000.0000.000
215H207VAL00.0030.00047.353-0.002-0.0020.0000.0000.0000.000
216H208ASP-1-0.839-0.89848.8910.0420.0420.0000.0000.0000.000
217H209LYS10.8810.92951.244-0.040-0.0400.0000.0000.0000.000
218H210ARG10.8810.92852.716-0.031-0.0310.0000.0000.0000.000
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