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: QY4MY

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 OptH
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 -2302305.855304
FMO2-HF: Nuclear repulsion 2215850.279365
FMO2-HF: Total energy -86455.575939
FMO2-MP2: Total energy -86707.299516


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.
-64.613-62.1260.07-0.957-1.6020.004
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 : -0.934 / q_NPA : -0.978
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].
3H3GLN0-0.019-0.0143.222-6.744-4.7970.030-0.725-1.2530.003
4H4LEU0-0.0170.0055.971-1.245-1.2450.0000.0000.0000.000
5H5VAL0-0.001-0.0068.338-0.608-0.6080.0000.0000.0000.000
6H6GLN00.001-0.01711.033-0.355-0.3550.0000.0000.0000.000
7H7SER00.0180.02614.8260.1850.1850.0000.0000.0000.000
8H8GLY00.0180.00517.396-0.088-0.0880.0000.0000.0000.000
9H9ALA0-0.018-0.00819.496-0.193-0.1930.0000.0000.0000.000
10H10GLU-1-0.903-0.95722.54611.51211.5120.0000.0000.0000.000
11H11VAL0-0.041-0.02325.653-0.184-0.1840.0000.0000.0000.000
12H12LYS10.9290.96428.664-9.924-9.9240.0000.0000.0000.000
13H13LYS10.9310.97131.774-8.313-8.3130.0000.0000.0000.000
14H14PRO0-0.044-0.03335.0280.1130.1130.0000.0000.0000.000
15H15GLY0-0.0090.01036.471-0.195-0.1950.0000.0000.0000.000
16H16GLU-1-0.889-0.92533.1558.8418.8410.0000.0000.0000.000
17H17SER0-0.0080.00531.7430.1430.1430.0000.0000.0000.000
18H18LEU0-0.010-0.01225.5780.0110.0110.0000.0000.0000.000
19H19LYS10.9120.95723.337-12.213-12.2130.0000.0000.0000.000
20H20ILE00.0210.03420.7990.1490.1490.0000.0000.0000.000
21H21SER0-0.003-0.02617.5710.2190.2190.0000.0000.0000.000
22H22CYS0-0.0320.00614.6220.2210.2210.0000.0000.0000.000
23H23LYS10.9620.9999.649-24.286-24.2860.0000.0000.0000.000
24H24GLY00.0520.0229.3330.9290.9290.0000.0000.0000.000
25H25SER0-0.100-0.0595.525-0.204-0.2040.0000.0000.0000.000
26H26GLY00.1210.0513.2320.7511.0380.041-0.215-0.1130.001
27H27TYR0-0.019-0.0093.9191.7792.032-0.001-0.017-0.2360.000
28H28SER00.0100.0117.400-2.204-2.2040.0000.0000.0000.000
29H29PHE00.0700.02511.052-1.247-1.2470.0000.0000.0000.000
30H30THR0-0.001-0.01612.505-0.887-0.8870.0000.0000.0000.000
31H31SER0-0.045-0.01613.915-0.865-0.8650.0000.0000.0000.000
32H32TYR0-0.028-0.01011.0861.0091.0090.0000.0000.0000.000
33H33TRP0-0.011-0.00115.277-0.139-0.1390.0000.0000.0000.000
34H34ILE00.0000.00213.4541.1071.1070.0000.0000.0000.000
35H35GLY0-0.028-0.01117.160-1.051-1.0510.0000.0000.0000.000
36H36TRP00.0250.00018.2710.7190.7190.0000.0000.0000.000
37H37VAL0-0.011-0.01720.308-0.624-0.6240.0000.0000.0000.000
38H38ARG10.8790.92621.945-9.737-9.7370.0000.0000.0000.000
39H39GLN0-0.005-0.00123.0500.2670.2670.0000.0000.0000.000
40H40MET0-0.027-0.00525.485-0.097-0.0970.0000.0000.0000.000
41H41PRO00.0220.00228.3530.1000.1000.0000.0000.0000.000
42H42GLY00.0060.00928.708-0.328-0.3280.0000.0000.0000.000
43H43LYS10.9140.96429.189-8.982-8.9820.0000.0000.0000.000
44H44GLY00.0400.02127.3740.3080.3080.0000.0000.0000.000
45H45LEU0-0.005-0.00621.863-0.008-0.0080.0000.0000.0000.000
46H46GLU-1-0.803-0.88725.4549.5579.5570.0000.0000.0000.000
47H47TRP00.0130.00622.3900.1560.1560.0000.0000.0000.000
48H48MET0-0.0450.00124.495-0.302-0.3020.0000.0000.0000.000
49H49GLY00.0630.01224.227-0.528-0.5280.0000.0000.0000.000
50H50ILE0-0.095-0.03719.9690.5410.5410.0000.0000.0000.000
51H51ILE00.0060.00419.796-0.529-0.5290.0000.0000.0000.000
52H52TYR00.0530.03718.4771.3121.3120.0000.0000.0000.000
53H52PRO00.008-0.00215.902-0.708-0.7080.0000.0000.0000.000
54H53GLY0-0.021-0.00918.932-0.140-0.1400.0000.0000.0000.000
55H54ASP-1-0.878-0.95720.18012.69512.6950.0000.0000.0000.000
56H55SER0-0.054-0.02122.467-0.488-0.4880.0000.0000.0000.000
57H56ASP-1-0.808-0.87123.87410.94410.9440.0000.0000.0000.000
58H57THR0-0.019-0.03024.2040.6910.6910.0000.0000.0000.000
59H58ARG10.8240.91525.907-11.681-11.6810.0000.0000.0000.000
60H59TYR00.0660.03026.6220.4560.4560.0000.0000.0000.000
61H60SER00.0080.00528.583-0.372-0.3720.0000.0000.0000.000
62H61PRO00.020-0.00230.203-0.058-0.0580.0000.0000.0000.000
63H62SER0-0.0050.00332.050-0.187-0.1870.0000.0000.0000.000
64H63PHE00.008-0.00929.135-0.052-0.0520.0000.0000.0000.000
65H64GLN00.0110.00531.6180.1700.1700.0000.0000.0000.000
66H65GLY00.0060.00632.925-0.276-0.2760.0000.0000.0000.000
67H66GLN0-0.094-0.03632.410-0.238-0.2380.0000.0000.0000.000
68H67VAL0-0.040-0.01327.4080.0540.0540.0000.0000.0000.000
69H68THR0-0.041-0.02227.906-0.183-0.1830.0000.0000.0000.000
70H69ILE00.0030.00522.5820.2980.2980.0000.0000.0000.000
71H70SER0-0.016-0.00323.108-0.161-0.1610.0000.0000.0000.000
72H71ALA00.029-0.00818.8350.6050.6050.0000.0000.0000.000
73H72ASP-1-0.861-0.92318.59513.85513.8550.0000.0000.0000.000
74H73LYS10.9470.97116.659-13.502-13.5020.0000.0000.0000.000
75H74SER0-0.057-0.01815.8450.9310.9310.0000.0000.0000.000
76H75ILE00.0090.00315.3110.8440.8440.0000.0000.0000.000
77H76SER0-0.064-0.03911.3251.6721.6720.0000.0000.0000.000
78H77THR0-0.028-0.00612.7511.1291.1290.0000.0000.0000.000
79H78ALA00.0180.02015.426-0.798-0.7980.0000.0000.0000.000
80H79TYR0-0.041-0.05017.8440.1770.1770.0000.0000.0000.000
81H80LEU00.0150.02720.925-0.210-0.2100.0000.0000.0000.000
82H81GLN00.001-0.00623.7400.1680.1680.0000.0000.0000.000
83H82TRP00.0850.04225.564-0.080-0.0800.0000.0000.0000.000
84H82SER00.007-0.01630.4280.0670.0670.0000.0000.0000.000
85H82SER0-0.017-0.01333.581-0.216-0.2160.0000.0000.0000.000
86H82LEU0-0.0100.01629.598-0.047-0.0470.0000.0000.0000.000
87H83LYS10.9860.99333.775-8.585-8.5850.0000.0000.0000.000
88H84ALA00.0580.01833.9010.2190.2190.0000.0000.0000.000
89H85SER0-0.037-0.02534.1590.0540.0540.0000.0000.0000.000
90H86ASP-1-0.885-0.94530.2939.3959.3950.0000.0000.0000.000
91H87THR0-0.0170.00129.2630.4130.4130.0000.0000.0000.000
92H88ALA0-0.039-0.02626.507-0.173-0.1730.0000.0000.0000.000
93H89MET0-0.0200.01820.8760.2540.2540.0000.0000.0000.000
94H90TYR0-0.017-0.03621.564-0.168-0.1680.0000.0000.0000.000
95H91TYR00.0350.02416.5650.5820.5820.0000.0000.0000.000
96H93ALA00.0460.01213.6960.7610.7610.0000.0000.0000.000
97H94ARG10.8300.9068.294-29.544-29.5440.0000.0000.0000.000
98H95LEU0-0.048-0.01013.662-0.003-0.0030.0000.0000.0000.000
99H96GLY00.0470.03713.0690.3100.3100.0000.0000.0000.000
100H97GLY00.014-0.00113.511-1.547-1.5470.0000.0000.0000.000
101H98ARG10.8850.95214.634-14.227-14.2270.0000.0000.0000.000
102H99TYR00.012-0.01816.586-1.071-1.0710.0000.0000.0000.000
103H100TYR00.0190.00618.2280.2890.2890.0000.0000.0000.000
104H100TYR0-0.0190.00222.337-0.117-0.1170.0000.0000.0000.000
105H100ASP-1-0.858-0.94324.31611.93311.9330.0000.0000.0000.000
106H100SER0-0.037-0.01825.7270.2390.2390.0000.0000.0000.000
107H100SER0-0.022-0.01222.4990.3910.3910.0000.0000.0000.000
108H100GLY0-0.0060.00821.0120.7770.7770.0000.0000.0000.000
109H100TYR0-0.017-0.01516.3200.0880.0880.0000.0000.0000.000
110H100TYR00.006-0.00818.3110.7610.7610.0000.0000.0000.000
111H100TYR0-0.003-0.00114.064-0.661-0.6610.0000.0000.0000.000
112H100PHE0-0.027-0.01415.3470.6790.6790.0000.0000.0000.000
113H101ASP-1-0.753-0.85510.95725.11425.1140.0000.0000.0000.000
114H102TYR0-0.0090.0035.9543.0293.0290.0000.0000.0000.000
115H103TRP00.012-0.00110.285-1.853-1.8530.0000.0000.0000.000
116H104GLY00.0200.00710.6941.4541.4540.0000.0000.0000.000
117H105GLN0-0.014-0.01112.5770.3560.3560.0000.0000.0000.000
118H106GLY00.0080.00913.961-0.889-0.8890.0000.0000.0000.000
119H107THR0-0.057-0.03217.4100.3220.3220.0000.0000.0000.000
120H108LEU00.006-0.00619.985-0.360-0.3600.0000.0000.0000.000
121H109VAL00.0170.01723.368-0.078-0.0780.0000.0000.0000.000
122H110THR0-0.004-0.00326.238-0.255-0.2550.0000.0000.0000.000
123H111VAL0-0.012-0.00729.560-0.077-0.0770.0000.0000.0000.000
124H112SER0-0.002-0.02032.607-0.262-0.2620.0000.0000.0000.000
125H113SER00.0220.00735.8820.0870.0870.0000.0000.0000.000
126H114ALA0-0.0170.00837.465-0.164-0.1640.0000.0000.0000.000
127H115SER00.008-0.00637.1150.1870.1870.0000.0000.0000.000
128H116THR0-0.035-0.02534.6620.0100.0100.0000.0000.0000.000
129H117LYS10.8330.89837.038-7.213-7.2130.0000.0000.0000.000
130H118GLY00.0590.04238.8960.1480.1480.0000.0000.0000.000
131H119PRO0-0.047-0.01239.271-0.140-0.1400.0000.0000.0000.000
132H120SER0-0.0060.01042.062-0.148-0.1480.0000.0000.0000.000
133H121VAL00.023-0.01243.5280.1140.1140.0000.0000.0000.000
134H122PHE0-0.015-0.00946.106-0.183-0.1830.0000.0000.0000.000
135H123PRO0-0.032-0.00847.8720.1080.1080.0000.0000.0000.000
136H124LEU0-0.018-0.00345.775-0.072-0.0720.0000.0000.0000.000
137H125ALA00.0060.00349.8600.0500.0500.0000.0000.0000.000
138H126PRO00.0500.05652.364-0.033-0.0330.0000.0000.0000.000
139H127SER00.001-0.02854.274-0.073-0.0730.0000.0000.0000.000
140H128SER0-0.024-0.05757.9570.0070.0070.0000.0000.0000.000
141H129LYS10.9200.95460.340-4.881-4.8810.0000.0000.0000.000
142H130SER0-0.0350.01157.523-0.020-0.0200.0000.0000.0000.000
143H131THR00.0680.02859.200-0.008-0.0080.0000.0000.0000.000
144H132SER00.0240.00459.0010.0910.0910.0000.0000.0000.000
145H133GLY00.0100.00958.441-0.045-0.0450.0000.0000.0000.000
146H134GLY00.0220.02156.0230.0420.0420.0000.0000.0000.000
147H135THR0-0.064-0.01850.8180.0780.0780.0000.0000.0000.000
148H136ALA00.008-0.00352.200-0.074-0.0740.0000.0000.0000.000
149H137ALA00.0180.02048.1460.1070.1070.0000.0000.0000.000
150H138LEU0-0.020-0.00848.066-0.134-0.1340.0000.0000.0000.000
151H139GLY00.070-0.00345.8560.1610.1610.0000.0000.0000.000
152H140CYS0-0.082-0.00943.328-0.051-0.0510.0000.0000.0000.000
153H141LEU00.0120.00943.5000.1240.1240.0000.0000.0000.000
154H142VAL0-0.016-0.01739.665-0.124-0.1240.0000.0000.0000.000
155H143LYS10.9920.99241.470-6.259-6.2590.0000.0000.0000.000
156H144ASP-1-0.847-0.92441.8616.7716.7710.0000.0000.0000.000
157H145TYR00.0210.02634.793-0.007-0.0070.0000.0000.0000.000
158H146PHE00.0400.02833.5500.1140.1140.0000.0000.0000.000
159H147PRO00.0220.01831.138-0.170-0.1700.0000.0000.0000.000
160H148GLU-1-0.883-0.94730.4419.2389.2380.0000.0000.0000.000
161H149PRO00.005-0.00328.7140.1400.1400.0000.0000.0000.000
162H150VAL0-0.010-0.02631.582-0.142-0.1420.0000.0000.0000.000
163H151THR0-0.036-0.01632.8550.2240.2240.0000.0000.0000.000
164H152VAL0-0.017-0.01434.743-0.211-0.2110.0000.0000.0000.000
165H153SER0-0.017-0.00837.1940.1990.1990.0000.0000.0000.000
166H154TRP0-0.0040.00639.479-0.246-0.2460.0000.0000.0000.000
167H155ASN00.0310.00742.9900.0400.0400.0000.0000.0000.000
168H156SER0-0.018-0.01542.159-0.014-0.0140.0000.0000.0000.000
169H157GLY00.0020.00640.1220.0870.0870.0000.0000.0000.000
170H158ALA0-0.031-0.00540.8940.0640.0640.0000.0000.0000.000
171H159LEU0-0.022-0.00643.096-0.132-0.1320.0000.0000.0000.000
172H160THR00.008-0.00639.0180.0630.0630.0000.0000.0000.000
173H161SER00.015-0.00140.1730.1740.1740.0000.0000.0000.000
174H162GLY00.0330.02041.125-0.137-0.1370.0000.0000.0000.000
175H163VAL0-0.0170.00139.060-0.130-0.1300.0000.0000.0000.000
176H164HIS0-0.0060.00435.0730.3550.3550.0000.0000.0000.000
177H165THR0-0.001-0.01435.680-0.307-0.3070.0000.0000.0000.000
178H166PHE0-0.043-0.01335.2960.2130.2130.0000.0000.0000.000
179H167PRO00.0560.01532.4390.0170.0170.0000.0000.0000.000
180H168ALA0-0.0090.01133.740-0.273-0.2730.0000.0000.0000.000
181H169VAL0-0.0020.01035.2040.1040.1040.0000.0000.0000.000
182H170LEU0-0.0140.00135.240-0.024-0.0240.0000.0000.0000.000
183H171GLN00.0010.04037.556-0.166-0.1660.0000.0000.0000.000
184H172SER00.0320.01040.2600.1210.1210.0000.0000.0000.000
185H173SER00.0080.00042.2350.0380.0380.0000.0000.0000.000
186H174GLY0-0.024-0.01238.3230.0400.0400.0000.0000.0000.000
187H175LEU0-0.046-0.02037.4600.1840.1840.0000.0000.0000.000
188H176TYR00.0310.00932.230-0.026-0.0260.0000.0000.0000.000
189H177SER0-0.017-0.06438.193-0.176-0.1760.0000.0000.0000.000
190H178LEU0-0.0180.00635.4480.1140.1140.0000.0000.0000.000
191H179SER00.0240.00939.417-0.268-0.2680.0000.0000.0000.000
192H180SER0-0.0080.00639.4200.1520.1520.0000.0000.0000.000
193H181VAL0-0.007-0.00941.082-0.199-0.1990.0000.0000.0000.000
194H182VAL00.0350.01642.4100.1610.1610.0000.0000.0000.000
195H183THR0-0.006-0.00144.790-0.182-0.1820.0000.0000.0000.000
196H184VAL00.0020.00647.2620.0670.0670.0000.0000.0000.000
197H185PRO00.0450.02749.948-0.076-0.0760.0000.0000.0000.000
198H186SER00.055-0.00653.2080.0000.0000.0000.0000.0000.000
199H187SER0-0.056-0.02956.133-0.018-0.0180.0000.0000.0000.000
200H188SER00.0180.01754.564-0.034-0.0340.0000.0000.0000.000
201H189LEU00.004-0.00853.7140.0250.0250.0000.0000.0000.000
202H190GLY0-0.029-0.00556.6070.0040.0040.0000.0000.0000.000
203H191THR0-0.057-0.02857.949-0.044-0.0440.0000.0000.0000.000
204H192GLN0-0.014-0.00152.3640.1030.1030.0000.0000.0000.000
205H193THR00.0070.02651.367-0.055-0.0550.0000.0000.0000.000
206H194TYR00.0370.01348.3340.1310.1310.0000.0000.0000.000
207H195ILE00.006-0.00946.521-0.082-0.0820.0000.0000.0000.000
208H197ASN00.012-0.00840.797-0.031-0.0310.0000.0000.0000.000
209H198VAL00.002-0.00139.2950.2000.2000.0000.0000.0000.000
210H199ASN00.008-0.01234.696-0.169-0.1690.0000.0000.0000.000
211H200HIS00.0400.03534.7610.0340.0340.0000.0000.0000.000
212H201LYS11.0151.00027.786-10.180-10.1800.0000.0000.0000.000
213H202PRO0-0.0160.00131.304-0.065-0.0650.0000.0000.0000.000
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