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: 49K6N

Calculation Name: 4RIS-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RIS

Chain ID: H

ChEMBL ID:

UniProt ID: Q70966

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2304074.108735
FMO2-HF: Nuclear repulsion 2217617.458544
FMO2-HF: Total energy -86456.650192
FMO2-MP2: Total energy -86708.524426


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:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-74.564-71.5020.435-1.298-2.1970.002
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.919 / q_NPA : -0.966
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].
3H3GLN0-0.055-0.0282.616-10.621-8.4140.402-0.944-1.6650.000
4H4LEU0-0.031-0.0145.984-1.016-1.0160.0000.0000.0000.000
5H5VAL00.0060.0028.713-0.643-0.6430.0000.0000.0000.000
6H6GLN00.003-0.02711.449-0.205-0.2050.0000.0000.0000.000
7H7SER00.0090.02415.2510.1270.1270.0000.0000.0000.000
8H8GLY00.0200.00817.987-0.007-0.0070.0000.0000.0000.000
9H9ALA0-0.037-0.01619.626-0.214-0.2140.0000.0000.0000.000
10H10GLU-1-0.859-0.94122.86511.07211.0720.0000.0000.0000.000
11H11VAL0-0.065-0.04426.088-0.192-0.1920.0000.0000.0000.000
12H12LYS10.8440.93229.081-9.954-9.9540.0000.0000.0000.000
13H13LYS10.8800.92732.306-8.174-8.1740.0000.0000.0000.000
14H14PRO0-0.049-0.03735.4640.1260.1260.0000.0000.0000.000
15H15GLY00.0270.02137.126-0.200-0.2000.0000.0000.0000.000
16H16GLU-1-0.819-0.88533.1579.1239.1230.0000.0000.0000.000
17H17SER00.0140.02231.7760.1290.1290.0000.0000.0000.000
18H18LEU0-0.014-0.01025.5280.0440.0440.0000.0000.0000.000
19H19LYS10.8530.92222.994-12.328-12.3280.0000.0000.0000.000
20H20ILE00.0290.04721.2200.2230.2230.0000.0000.0000.000
21H21SER0-0.006-0.02717.6800.1890.1890.0000.0000.0000.000
22H22CYS0-0.014-0.00414.7600.0860.0860.0000.0000.0000.000
23H23LYS10.8790.95310.350-24.023-24.0230.0000.0000.0000.000
24H24GLY00.0350.0159.5740.7900.7900.0000.0000.0000.000
25H25SER0-0.059-0.0365.314-0.634-0.6340.0000.0000.0000.000
26H26GLY00.1250.0503.5740.2890.8030.033-0.312-0.2340.002
27H27TYR0-0.014-0.0084.0741.0231.3640.000-0.042-0.2980.000
28H28SER00.0260.0207.296-2.484-2.4840.0000.0000.0000.000
29H29PHE00.0650.01510.943-1.320-1.3200.0000.0000.0000.000
30H30THR0-0.019-0.02112.565-0.866-0.8660.0000.0000.0000.000
31H31SER0-0.055-0.01913.638-1.426-1.4260.0000.0000.0000.000
32H32TYR0-0.023-0.00911.4210.9590.9590.0000.0000.0000.000
33H33TRP0-0.007-0.00315.747-0.147-0.1470.0000.0000.0000.000
34H34ILE0-0.023-0.00614.0551.1121.1120.0000.0000.0000.000
35H35GLY0-0.012-0.00317.522-1.100-1.1000.0000.0000.0000.000
36H36TRP00.001-0.00818.6540.7480.7480.0000.0000.0000.000
37H37VAL0-0.008-0.01020.803-0.618-0.6180.0000.0000.0000.000
38H38ARG10.8380.88822.310-9.741-9.7410.0000.0000.0000.000
39H39GLN00.0180.01423.3900.4560.4560.0000.0000.0000.000
40H40MET00.0770.07125.830-0.185-0.1850.0000.0000.0000.000
41H41PRO00.011-0.00528.7770.1010.1010.0000.0000.0000.000
42H42GLY00.0080.01029.225-0.304-0.3040.0000.0000.0000.000
43H43LYS10.8200.89329.379-9.137-9.1370.0000.0000.0000.000
44H44GLY00.0480.02627.5550.3140.3140.0000.0000.0000.000
45H45LEU0-0.0020.00121.705-0.016-0.0160.0000.0000.0000.000
46H46GLU-1-0.761-0.85425.6749.6949.6940.0000.0000.0000.000
47H47TRP00.0160.00923.3580.0920.0920.0000.0000.0000.000
48H48MET0-0.028-0.00424.864-0.343-0.3430.0000.0000.0000.000
49H49GLY00.0540.00724.716-0.505-0.5050.0000.0000.0000.000
50H50ILE0-0.086-0.02720.5640.5440.5440.0000.0000.0000.000
51H51ILE00.0290.02120.015-0.616-0.6160.0000.0000.0000.000
52H52TYR00.0790.04818.3401.2931.2930.0000.0000.0000.000
53H52PRO00.008-0.00416.072-0.683-0.6830.0000.0000.0000.000
54H53GLY00.0080.01418.9010.0190.0190.0000.0000.0000.000
55H54ASP-1-0.893-0.95020.16312.98112.9810.0000.0000.0000.000
56H55SER0-0.051-0.01922.621-0.404-0.4040.0000.0000.0000.000
57H56ASP-1-0.742-0.82323.91610.96310.9630.0000.0000.0000.000
58H57THR0-0.035-0.04024.4440.7130.7130.0000.0000.0000.000
59H58ARG10.7470.84526.276-11.947-11.9470.0000.0000.0000.000
60H59TYR00.0510.02726.9010.4890.4890.0000.0000.0000.000
61H60SER0-0.0230.00328.597-0.362-0.3620.0000.0000.0000.000
62H61PRO00.032-0.00530.284-0.096-0.0960.0000.0000.0000.000
63H62SER0-0.010-0.00432.263-0.216-0.2160.0000.0000.0000.000
64H63PHE00.003-0.01329.570-0.033-0.0330.0000.0000.0000.000
65H64GLN00.0140.01931.8900.2590.2590.0000.0000.0000.000
66H65GLY00.0200.01333.142-0.297-0.2970.0000.0000.0000.000
67H66GLN0-0.077-0.02932.729-0.217-0.2170.0000.0000.0000.000
68H67VAL0-0.049-0.02027.6160.0880.0880.0000.0000.0000.000
69H68THR0-0.048-0.02527.664-0.232-0.2320.0000.0000.0000.000
70H69ILE00.0280.02422.5610.2850.2850.0000.0000.0000.000
71H70SER0-0.012-0.00523.030-0.339-0.3390.0000.0000.0000.000
72H71ALA00.007-0.01218.7670.5930.5930.0000.0000.0000.000
73H72ASP-1-0.817-0.88018.53114.33914.3390.0000.0000.0000.000
74H73LYS10.9210.94516.573-13.808-13.8080.0000.0000.0000.000
75H74SER0-0.076-0.04415.8360.9650.9650.0000.0000.0000.000
76H75ILE00.0340.02115.3590.9130.9130.0000.0000.0000.000
77H76SER0-0.036-0.00711.5911.8451.8450.0000.0000.0000.000
78H77THR0-0.004-0.00712.5511.5541.5540.0000.0000.0000.000
79H78ALA00.0150.01515.195-0.870-0.8700.0000.0000.0000.000
80H79TYR0-0.015-0.03717.8040.2900.2900.0000.0000.0000.000
81H80LEU00.0020.01320.778-0.194-0.1940.0000.0000.0000.000
82H81GLN00.0240.01523.8170.3150.3150.0000.0000.0000.000
83H82TRP00.0600.02125.687-0.114-0.1140.0000.0000.0000.000
84H82SER00.006-0.00730.6360.0610.0610.0000.0000.0000.000
85H82SER0-0.009-0.01833.735-0.203-0.2030.0000.0000.0000.000
86H82LEU00.0040.02029.8490.0050.0050.0000.0000.0000.000
87H83LYS10.8550.91134.022-9.153-9.1530.0000.0000.0000.000
88H84ALA00.0690.02434.3350.2190.2190.0000.0000.0000.000
89H85SER0-0.045-0.03334.4280.0680.0680.0000.0000.0000.000
90H86ASP-1-0.808-0.88430.7699.2759.2750.0000.0000.0000.000
91H87THR0-0.0080.01829.4960.4420.4420.0000.0000.0000.000
92H88ALA0-0.036-0.02626.858-0.189-0.1890.0000.0000.0000.000
93H89MET00.0100.04221.0020.2690.2690.0000.0000.0000.000
94H90TYR0-0.021-0.04722.003-0.294-0.2940.0000.0000.0000.000
95H91TYR00.023-0.00217.4260.5630.5630.0000.0000.0000.000
96H93ALA00.0360.01314.1220.8240.8240.0000.0000.0000.000
97H94ARG10.8090.8947.817-31.990-31.9900.0000.0000.0000.000
98H95LEU0-0.0080.00713.976-0.017-0.0170.0000.0000.0000.000
99H96GLY00.0530.04413.2470.2640.2640.0000.0000.0000.000
100H97GLY00.0180.00113.788-1.474-1.4740.0000.0000.0000.000
101H98ARG10.8240.92915.273-14.157-14.1570.0000.0000.0000.000
102H99TYR00.034-0.01416.813-1.287-1.2870.0000.0000.0000.000
103H100TYR00.0290.01118.4850.0560.0560.0000.0000.0000.000
104H100TYR0-0.0040.00022.328-0.068-0.0680.0000.0000.0000.000
105H100ASP-1-0.802-0.88524.31912.39812.3980.0000.0000.0000.000
106H100SER00.0160.01325.7770.0280.0280.0000.0000.0000.000
107H100SER0-0.082-0.06222.9890.3060.3060.0000.0000.0000.000
108H100GLY0-0.019-0.00521.3140.8490.8490.0000.0000.0000.000
109H100TYR0-0.028-0.02216.2080.0520.0520.0000.0000.0000.000
110H100TYR0-0.017-0.00818.5870.8860.8860.0000.0000.0000.000
111H100TYR00.0050.00013.644-1.036-1.0360.0000.0000.0000.000
112H100PHE0-0.020-0.01915.9910.6810.6810.0000.0000.0000.000
113H101ASP-1-0.772-0.85711.13026.05426.0540.0000.0000.0000.000
114H102TYR00.0070.0135.1980.7770.7770.0000.0000.0000.000
115H103TRP0-0.007-0.02310.585-2.096-2.0960.0000.0000.0000.000
116H104GLY00.0230.01810.8611.5391.5390.0000.0000.0000.000
117H105GLN0-0.028-0.01612.5820.2840.2840.0000.0000.0000.000
118H106GLY00.0000.00514.006-0.942-0.9420.0000.0000.0000.000
119H107THR0-0.065-0.04517.5090.3780.3780.0000.0000.0000.000
120H108LEU00.0020.00320.327-0.336-0.3360.0000.0000.0000.000
121H109VAL00.0120.00923.6450.0260.0260.0000.0000.0000.000
122H110THR0-0.008-0.01126.634-0.210-0.2100.0000.0000.0000.000
123H111VAL0-0.015-0.00229.988-0.099-0.0990.0000.0000.0000.000
124H112SER0-0.003-0.01333.159-0.287-0.2870.0000.0000.0000.000
125H113SER00.0440.01136.4090.0560.0560.0000.0000.0000.000
126H114ALA0-0.0320.00537.599-0.143-0.1430.0000.0000.0000.000
127H115SER00.0210.00437.4710.2250.2250.0000.0000.0000.000
128H116THR0-0.022-0.00734.954-0.048-0.0480.0000.0000.0000.000
129H117LYS10.8350.91637.202-7.215-7.2150.0000.0000.0000.000
130H118GLY00.0810.04739.0400.1470.1470.0000.0000.0000.000
131H119PRO0-0.059-0.02339.315-0.128-0.1280.0000.0000.0000.000
132H120SER0-0.0110.01042.009-0.174-0.1740.0000.0000.0000.000
133H121VAL00.022-0.01443.7120.1300.1300.0000.0000.0000.000
134H122PHE00.0090.01246.305-0.176-0.1760.0000.0000.0000.000
135H123PRO0-0.037-0.01648.0220.1040.1040.0000.0000.0000.000
136H124LEU0-0.020-0.00745.944-0.101-0.1010.0000.0000.0000.000
137H125ALA0-0.006-0.00849.9840.0400.0400.0000.0000.0000.000
138H126PRO00.0690.06052.426-0.023-0.0230.0000.0000.0000.000
139H127SER00.010-0.00954.318-0.075-0.0750.0000.0000.0000.000
140H128SER0-0.035-0.05758.055-0.014-0.0140.0000.0000.0000.000
141H129LYS10.9000.93860.464-4.881-4.8810.0000.0000.0000.000
142H130SER0-0.0120.02657.166-0.012-0.0120.0000.0000.0000.000
143H131THR00.0500.02058.808-0.015-0.0150.0000.0000.0000.000
144H132SER00.0150.00258.9420.0690.0690.0000.0000.0000.000
145H133GLY00.0070.00458.676-0.073-0.0730.0000.0000.0000.000
146H134GLY00.0160.02455.9230.0570.0570.0000.0000.0000.000
147H135THR0-0.040-0.01951.0090.0260.0260.0000.0000.0000.000
148H136ALA0-0.018-0.00652.583-0.054-0.0540.0000.0000.0000.000
149H137ALA00.0170.01747.8900.0920.0920.0000.0000.0000.000
150H138LEU0-0.027-0.01247.908-0.147-0.1470.0000.0000.0000.000
151H139GLY00.0670.00745.8830.1610.1610.0000.0000.0000.000
152H140CYS0-0.088-0.00343.355-0.090-0.0900.0000.0000.0000.000
153H141LEU00.0400.03743.5270.1680.1680.0000.0000.0000.000
154H142VAL0-0.015-0.00639.903-0.126-0.1260.0000.0000.0000.000
155H143LYS10.8820.91241.675-6.517-6.5170.0000.0000.0000.000
156H144ASP-1-0.793-0.87742.2036.7326.7320.0000.0000.0000.000
157H145TYR00.0500.03735.088-0.137-0.1370.0000.0000.0000.000
158H146PHE00.0560.02633.7480.0860.0860.0000.0000.0000.000
159H147PRO00.0320.02531.298-0.164-0.1640.0000.0000.0000.000
160H148GLU-1-0.834-0.90730.6549.2559.2550.0000.0000.0000.000
161H149PRO0-0.010-0.00728.7280.1400.1400.0000.0000.0000.000
162H150VAL00.006-0.01131.456-0.173-0.1730.0000.0000.0000.000
163H151THR0-0.058-0.03132.5630.2500.2500.0000.0000.0000.000
164H152VAL0-0.016-0.01434.874-0.202-0.2020.0000.0000.0000.000
165H153SER0-0.0120.00337.3800.1950.1950.0000.0000.0000.000
166H154TRP00.0140.00139.603-0.241-0.2410.0000.0000.0000.000
167H155ASN00.030-0.00343.0340.0940.0940.0000.0000.0000.000
168H156SER0-0.012-0.00742.474-0.026-0.0260.0000.0000.0000.000
169H157GLY00.0130.01840.3090.1030.1030.0000.0000.0000.000
170H158ALA0-0.043-0.01341.1410.0590.0590.0000.0000.0000.000
171H159LEU0-0.027-0.01243.204-0.134-0.1340.0000.0000.0000.000
172H160THR00.0220.00338.7750.0710.0710.0000.0000.0000.000
173H161SER00.0370.00640.4120.1530.1530.0000.0000.0000.000
174H162GLY00.0370.02141.473-0.137-0.1370.0000.0000.0000.000
175H163VAL0-0.057-0.01738.967-0.098-0.0980.0000.0000.0000.000
176H164HIS0-0.017-0.00635.7590.3440.3440.0000.0000.0000.000
177H165THR0-0.011-0.00835.841-0.304-0.3040.0000.0000.0000.000
178H166PHE00.0010.01535.3560.2150.2150.0000.0000.0000.000
179H167PRO00.0400.01232.2860.0320.0320.0000.0000.0000.000
180H168ALA0-0.018-0.00633.627-0.256-0.2560.0000.0000.0000.000
181H169VAL00.0020.00535.3240.0950.0950.0000.0000.0000.000
182H170LEU0-0.020-0.00434.685-0.110-0.1100.0000.0000.0000.000
183H171GLN0-0.014-0.00737.566-0.232-0.2320.0000.0000.0000.000
184H172SER00.0280.00340.5220.1220.1220.0000.0000.0000.000
185H173SER00.0010.00242.7420.0520.0520.0000.0000.0000.000
186H174GLY00.0270.01638.6490.0270.0270.0000.0000.0000.000
187H175LEU0-0.052-0.01737.8880.1970.1970.0000.0000.0000.000
188H176TYR0-0.025-0.03531.598-0.104-0.1040.0000.0000.0000.000
189H177SER0-0.034-0.03338.396-0.178-0.1780.0000.0000.0000.000
190H178LEU00.0050.02135.7490.1250.1250.0000.0000.0000.000
191H179SER00.006-0.01739.496-0.295-0.2950.0000.0000.0000.000
192H180SER0-0.0070.00239.5190.1370.1370.0000.0000.0000.000
193H181VAL0-0.004-0.01041.141-0.210-0.2100.0000.0000.0000.000
194H182VAL00.0400.02542.3890.1670.1670.0000.0000.0000.000
195H183THR00.0060.00044.824-0.157-0.1570.0000.0000.0000.000
196H184VAL00.0130.01547.4740.0660.0660.0000.0000.0000.000
197H185PRO00.0550.02850.254-0.072-0.0720.0000.0000.0000.000
198H186SER00.0470.00553.6150.0110.0110.0000.0000.0000.000
199H187SER0-0.009-0.01256.371-0.032-0.0320.0000.0000.0000.000
200H188SER0-0.044-0.02454.142-0.029-0.0290.0000.0000.0000.000
201H189LEU0-0.012-0.00853.8510.0120.0120.0000.0000.0000.000
202H190GLY0-0.0070.00356.793-0.007-0.0070.0000.0000.0000.000
203H191THR0-0.041-0.02258.114-0.043-0.0430.0000.0000.0000.000
204H192GLN0-0.0040.00552.9420.0790.0790.0000.0000.0000.000
205H193THR0-0.0050.01451.633-0.059-0.0590.0000.0000.0000.000
206H194TYR00.0280.00948.8840.1340.1340.0000.0000.0000.000
207H195ILE00.011-0.00946.556-0.100-0.1000.0000.0000.0000.000
208H197ASN00.010-0.01540.954-0.060-0.0600.0000.0000.0000.000
209H198VAL00.004-0.00539.6710.1690.1690.0000.0000.0000.000
210H199ASN00.008-0.00334.060-0.148-0.1480.0000.0000.0000.000
211H200HIS00.0420.02934.893-0.021-0.0210.0000.0000.0000.000
212H201LYS11.0291.01328.975-9.865-9.8650.0000.0000.0000.000
213H202PRO0-0.022-0.00631.336-0.022-0.0220.0000.0000.0000.000
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