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

tag_button

FMODB ID: 2222R

Calculation Name: 5RUL-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 4,6-dimethylpyrimidin-2-amine

ligand 3-letter code: 5ZE

PDB ID: 5RUL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-10-07

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1801203.293251
FMO2-HF: Nuclear repulsion 1734935.165816
FMO2-HF: Total energy -66268.127434
FMO2-MP2: Total energy -66462.250574


3D Structure
Snapshot
 
Ligand structure

5ZE

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.
-32.969-17.31911.818-7.659-19.8100.033


Interactive mode: IFIE and PIEDA for fragment #212(A:201:5ZE )


Summations of interaction energy for fragment #212(A:201:5ZE )
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.
-32.969-17.31911.818-7.659-19.81-0.033
Interaction energy analysis for fragmet #212(A:201:5ZE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.011
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].
1A3VAL 00.012-0.00623.9480.0030.0030.0000.0000.0000.000
2A4ASN 0-0.015-0.01718.981-0.026-0.0260.0000.0000.0000.000
3A5SER 00.0290.00617.795-0.002-0.0020.0000.0000.0000.000
4A6PHE 0-0.0390.00612.240-0.064-0.0640.0000.0000.0000.000
5A7SER 00.0250.00815.2160.0420.0420.0000.0000.0000.000
6A8GLY 00.007-0.00814.835-0.088-0.0880.0000.0000.0000.000
7A9TYR 0-0.053-0.03711.078-0.048-0.0480.0000.0000.0000.000
8A10LEU 0-0.0010.01115.6080.0370.0370.0000.0000.0000.000
9A11LYS 10.8090.89616.9270.1420.1420.0000.0000.0000.000
10A12LEU 0-0.052-0.01515.3110.0050.0050.0000.0000.0000.000
11A13THR 00.0330.00519.5110.0130.0130.0000.0000.0000.000
12A14ASP -1-0.854-0.88721.796-0.100-0.1000.0000.0000.0000.000
13A15ASN 0-0.006-0.00919.823-0.014-0.0140.0000.0000.0000.000
14A16VAL 00.0060.01615.288-0.011-0.0110.0000.0000.0000.000
15A17TYR 00.0370.02415.629-0.014-0.0140.0000.0000.0000.000
16A18ILE 00.0200.01011.119-0.011-0.0110.0000.0000.0000.000
17A19LYS 10.8350.90310.4770.9610.9610.0000.0000.0000.000
18A20ASN 0-0.059-0.0298.282-0.006-0.0060.0000.0000.0000.000
19A21ALA 00.001-0.0127.0950.0680.0680.0000.0000.0000.000
20A22ASP -1-0.799-0.9032.551-21.633-15.9362.349-3.459-4.587-0.049
21A23ILE 00.013-0.0082.3600.6270.9071.664-0.452-1.491-0.001
22A24VAL 00.0090.0043.7801.0831.5190.004-0.067-0.3730.000
23A25GLU -1-0.820-0.9005.845-1.435-1.4350.0000.0000.0000.000
24A26GLU -1-0.762-0.8417.191-0.549-0.5490.0000.0000.0000.000
25A27ALA 0-0.014-0.0118.1930.3280.3280.0000.0000.0000.000
26A28LYS 10.8280.9068.4811.9041.9040.0000.0000.0000.000
27A29LYS 10.8250.91311.7261.1191.1190.0000.0000.0000.000
28A30VAL 0-0.046-0.03212.8780.0980.0980.0000.0000.0000.000
29A31LYS 10.8760.96413.7610.5180.5180.0000.0000.0000.000
30A32PRO 00.0040.01811.9680.0690.0690.0000.0000.0000.000
31A33THR 00.031-0.00615.2470.0130.0130.0000.0000.0000.000
32A34VAL 0-0.016-0.01413.5810.0340.0340.0000.0000.0000.000
33A35VAL 00.0090.0108.083-0.076-0.0760.0000.0000.0000.000
34A36VAL 00.004-0.0019.4990.1000.1000.0000.0000.0000.000
35A37ASN 0-0.003-0.0217.2700.3050.3050.0000.0000.0000.000
36A38ALA 0-0.0070.0146.729-0.135-0.1350.0000.0000.0000.000
37A39ALA 00.0510.0508.2560.4890.4890.0000.0000.0000.000
38A40ASN 0-0.005-0.02311.176-0.204-0.2040.0000.0000.0000.000
39A41VAL 00.0440.02013.761-0.045-0.0450.0000.0000.0000.000
40A42TYR 00.0000.00016.653-0.061-0.0610.0000.0000.0000.000
41A43LEU 00.0010.01214.274-0.018-0.0180.0000.0000.0000.000
42A44LYS 10.9821.01114.171-0.779-0.7790.0000.0000.0000.000
43A45HIS 00.0300.01610.0650.4830.4830.0000.0000.0000.000
44A46GLY 00.0260.02110.1210.0130.0130.0000.0000.0000.000
45A47GLY 00.0390.0176.670-0.304-0.3040.0000.0000.0000.000
46A48GLY 00.0000.0042.737-2.667-1.8851.426-1.016-1.1910.010
47A49VAL 00.0260.0102.454-2.516-0.3921.759-0.324-3.5590.005
48A50ALA 00.0210.0213.660-2.523-2.2690.0140.091-0.3600.001
49A51GLY 00.0010.0146.565-0.873-0.8730.0000.0000.0000.000
50A52ALA 00.0050.0122.813-3.270-1.7241.486-0.893-2.1390.006
51A53LEU 00.0400.0094.379-1.612-1.3150.000-0.033-0.2640.000
52A54ASN 00.053-0.0016.830-0.397-0.3970.0000.0000.0000.000
53A55LYS 10.9640.9975.419-0.011-0.0110.0000.0000.0000.000
54A56ALA 0-0.039-0.0077.415-0.133-0.1330.0000.0000.0000.000
55A57THR 0-0.053-0.0149.2020.0090.0090.0000.0000.0000.000
56A58ASN 0-0.038-0.02711.5780.0530.0530.0000.0000.0000.000
57A59ASN 0-0.0010.00512.2850.1280.1280.0000.0000.0000.000
58A60ALA 00.0330.02713.8060.0440.0440.0000.0000.0000.000
59A61MET 00.0070.0129.8700.1000.1000.0000.0000.0000.000
60A62GLN 0-0.056-0.03113.8530.2120.2120.0000.0000.0000.000
61A63VAL 00.0260.02315.604-0.006-0.0060.0000.0000.0000.000
62A64GLU -1-0.725-0.83816.7950.1540.1540.0000.0000.0000.000
63A65SER 00.007-0.00515.4290.0200.0200.0000.0000.0000.000
64A66ASP -1-0.814-0.89617.8080.4910.4910.0000.0000.0000.000
65A67ASP -1-0.821-0.86220.4960.1700.1700.0000.0000.0000.000
66A68TYR 00.005-0.01619.844-0.016-0.0160.0000.0000.0000.000
67A69ILE 0-0.039-0.02519.008-0.011-0.0110.0000.0000.0000.000
68A70ALA 0-0.027-0.00122.323-0.014-0.0140.0000.0000.0000.000
69A71THR 0-0.037-0.00525.246-0.024-0.0240.0000.0000.0000.000
70A72ASN 0-0.085-0.04823.738-0.031-0.0310.0000.0000.0000.000
71A73GLY 00.0280.02724.897-0.003-0.0030.0000.0000.0000.000
72A74PRO 0-0.048-0.02621.2050.0150.0150.0000.0000.0000.000
73A75LEU 0-0.0070.00316.391-0.033-0.0330.0000.0000.0000.000
74A76LYS 10.9760.98320.449-0.238-0.2380.0000.0000.0000.000
75A77VAL 00.0240.00217.1660.0290.0290.0000.0000.0000.000
76A78GLY 00.0210.02317.744-0.050-0.0500.0000.0000.0000.000
77A79GLY 0-0.026-0.00718.912-0.048-0.0480.0000.0000.0000.000
78A80SER 0-0.014-0.04016.3820.0470.0470.0000.0000.0000.000
79A81CYS 0-0.0340.00816.593-0.019-0.0190.0000.0000.0000.000
80A82VAL 00.0100.00916.3780.0230.0230.0000.0000.0000.000
81A83LEU 00.0060.01115.913-0.001-0.0010.0000.0000.0000.000
82A84SER 00.0300.01316.807-0.061-0.0610.0000.0000.0000.000
83A85GLY 0-0.0120.00813.6550.0460.0460.0000.0000.0000.000
84A86HIS 0-0.024-0.02913.686-0.123-0.1230.0000.0000.0000.000
85A87ASN 0-0.028-0.02812.7260.0280.0280.0000.0000.0000.000
86A88LEU 0-0.014-0.0178.659-0.120-0.1200.0000.0000.0000.000
87A89ALA 0-0.013-0.00812.476-0.084-0.0840.0000.0000.0000.000
88A90LYS 10.8530.94614.3410.1100.1100.0000.0000.0000.000
89A91HIS 00.0290.01216.2640.0140.0140.0000.0000.0000.000
90A92CYS 0-0.013-0.00211.241-0.044-0.0440.0000.0000.0000.000
91A93LEU 0-0.0300.00512.7510.0420.0420.0000.0000.0000.000
92A94HIS 00.0530.00511.9090.2070.2070.0000.0000.0000.000
93A95VAL 00.011-0.00111.806-0.067-0.0670.0000.0000.0000.000
94A96VAL 0-0.0380.00612.1070.1860.1860.0000.0000.0000.000
95A97GLY 00.0480.02912.964-0.123-0.1230.0000.0000.0000.000
96A98PRO 0-0.0060.00514.0610.0980.0980.0000.0000.0000.000
97A99ASN 0-0.043-0.02511.2480.0040.0040.0000.0000.0000.000
98A100VAL 00.0710.02913.365-0.076-0.0760.0000.0000.0000.000
99A101ASN 0-0.059-0.03210.676-0.175-0.1750.0000.0000.0000.000
100A102LYS 10.8170.90913.943-0.931-0.9310.0000.0000.0000.000
101A103GLY 00.0020.01016.902-0.042-0.0420.0000.0000.0000.000
102A104GLU -1-0.789-0.84316.3910.6560.6560.0000.0000.0000.000
103A105ASP -1-0.817-0.91118.8800.2810.2810.0000.0000.0000.000
104A106ILE 00.0500.01116.2630.0270.0270.0000.0000.0000.000
105A107GLN 00.0070.00519.255-0.003-0.0030.0000.0000.0000.000
106A108LEU 0-0.051-0.02819.433-0.011-0.0110.0000.0000.0000.000
107A109LEU 0-0.032-0.02213.8210.0210.0210.0000.0000.0000.000
108A110LYS 10.9010.94217.455-0.136-0.1360.0000.0000.0000.000
109A111SER 00.0320.00619.942-0.015-0.0150.0000.0000.0000.000
110A112ALA 00.0100.01115.425-0.006-0.0060.0000.0000.0000.000
111A113TYR 00.023-0.00512.201-0.005-0.0050.0000.0000.0000.000
112A114GLU -1-0.802-0.85516.9030.1160.1160.0000.0000.0000.000
113A115ASN 0-0.069-0.02616.887-0.043-0.0430.0000.0000.0000.000
114A116PHE 00.040-0.00611.584-0.020-0.0200.0000.0000.0000.000
115A117ASN 0-0.0140.00217.329-0.052-0.0520.0000.0000.0000.000
116A118GLN 0-0.0430.00420.346-0.024-0.0240.0000.0000.0000.000
117A119HIS 0-0.037-0.02517.930-0.035-0.0350.0000.0000.0000.000
118A120GLU -1-0.871-0.93219.723-0.065-0.0650.0000.0000.0000.000
119A121VAL 00.006-0.01016.768-0.016-0.0160.0000.0000.0000.000
120A122LEU 0-0.0370.02313.3360.0090.0090.0000.0000.0000.000
121A123LEU 0-0.0160.0158.515-0.027-0.0270.0000.0000.0000.000
122A124ALA 00.024-0.0058.5970.0620.0620.0000.0000.0000.000
123A125PRO 0-0.0310.0064.700-0.264-0.198-0.001-0.006-0.0600.000
124A126LEU 00.0390.0136.5560.0040.0040.0000.0000.0000.000
125A127LEU 0-0.0020.0098.1600.3770.3770.0000.0000.0000.000
126A128SER 00.025-0.01210.457-0.137-0.1370.0000.0000.0000.000
127A129ALA 00.0010.0227.659-0.090-0.0900.0000.0000.0000.000
128A130GLY 00.0510.0274.7700.3780.421-0.001-0.005-0.0370.000
129A131ILE 00.0360.0034.289-0.384-0.217-0.001-0.008-0.1590.000
130A132PHE 0-0.062-0.0046.636-0.163-0.1630.0000.0000.0000.000
131A133GLY 00.0260.0219.062-0.166-0.1660.0000.0000.0000.000
132A134ALA 00.0060.00711.148-0.127-0.1270.0000.0000.0000.000
133A135ASP -1-0.793-0.89811.7150.2020.2020.0000.0000.0000.000
134A136PRO 0-0.019-0.02210.2210.0100.0100.0000.0000.0000.000
135A137ILE 00.0290.01312.231-0.037-0.0370.0000.0000.0000.000
136A138HIS 00.0350.02315.425-0.038-0.0380.0000.0000.0000.000
137A139SER 0-0.007-0.02211.849-0.042-0.0420.0000.0000.0000.000
138A140LEU 0-0.015-0.00413.256-0.016-0.0160.0000.0000.0000.000
139A141ARG 10.8490.92114.528-0.052-0.0520.0000.0000.0000.000
140A142VAL 00.0080.01016.900-0.012-0.0120.0000.0000.0000.000
141A143CYS 0-0.0290.00313.452-0.020-0.0200.0000.0000.0000.000
142A144VAL 00.0150.01716.398-0.021-0.0210.0000.0000.0000.000
143A145ASP -1-0.800-0.89418.9720.0460.0460.0000.0000.0000.000
144A146THR 0-0.122-0.06619.1430.0080.0080.0000.0000.0000.000
145A147VAL 0-0.052-0.01316.1770.0020.0020.0000.0000.0000.000
146A148ARG 10.9190.96519.624-0.079-0.0790.0000.0000.0000.000
147A149THR 0-0.0380.00419.367-0.013-0.0130.0000.0000.0000.000
148A150ASN 0-0.0190.00219.170-0.005-0.0050.0000.0000.0000.000
149A151VAL 00.0160.00213.067-0.010-0.0100.0000.0000.0000.000
150A152TYR 00.0290.02712.7960.0030.0030.0000.0000.0000.000
151A153LEU 00.017-0.0089.741-0.044-0.0440.0000.0000.0000.000
152A154ALA 00.0060.0025.870-0.088-0.0880.0000.0000.0000.000
153A155VAL 0-0.0020.0075.5760.2400.2400.0000.0000.0000.000
154A156PHE 00.0180.0032.575-3.1680.0463.016-1.156-5.073-0.004
155A157ASP -1-0.853-0.9234.805-0.753-0.632-0.001-0.010-0.1100.000
156A158LYS 10.8700.9188.0370.6410.6410.0000.0000.0000.000
157A159ASN 0-0.0020.00111.2200.1260.1260.0000.0000.0000.000
158A160LEU 0-0.007-0.0118.2230.0800.0800.0000.0000.0000.000
159A161TYR 0-0.014-0.01410.1560.0480.0480.0000.0000.0000.000
160A162ASP -1-0.766-0.86011.633-0.372-0.3720.0000.0000.0000.000
161A163LYS 10.9490.99014.5890.0240.0240.0000.0000.0000.000
162A164LEU 0-0.042-0.01610.5410.0400.0400.0000.0000.0000.000
163A165VAL 00.0140.01214.7920.0200.0200.0000.0000.0000.000
164A166SER 0-0.048-0.03417.0240.0200.0200.0000.0000.0000.000
165A167SER 0-0.099-0.06817.7410.0240.0240.0000.0000.0000.000
166A168PHE 0-0.015-0.00317.8220.0240.0240.0000.0000.0000.000
167A169LEU -1-0.885-0.92819.939-0.043-0.0430.0000.0000.0000.000
168A301HOH 0-0.011-0.0068.920-0.063-0.0630.0000.0000.0000.000
169A304HOH 0-0.065-0.05126.3750.0010.0010.0000.0000.0000.000
170A307HOH 0-0.031-0.0284.5020.2680.3000.000-0.003-0.0290.000
171A310HOH 0-0.032-0.02724.0240.0050.0050.0000.0000.0000.000
172A322HOH 0-0.007-0.02024.569-0.006-0.0060.0000.0000.0000.000
173A328HOH 0-0.075-0.06121.207-0.004-0.0040.0000.0000.0000.000
174A339HOH 0-0.021-0.02323.8080.0050.0050.0000.0000.0000.000
175A346HOH 0-0.044-0.03411.774-0.023-0.0230.0000.0000.0000.000
176A351HOH 0-0.052-0.0395.8100.1550.1550.0000.0000.0000.000
177A352HOH 00.0280.0039.6760.0440.0440.0000.0000.0000.000
178A353HOH 0-0.012-0.01422.7330.0050.0050.0000.0000.0000.000
179A356HOH 0-0.014-0.03614.4700.0360.0360.0000.0000.0000.000
180A357HOH 0-0.059-0.03724.611-0.005-0.0050.0000.0000.0000.000
181A359HOH 00.007-0.00723.1500.0030.0030.0000.0000.0000.000
182A361HOH 0-0.011-0.0147.895-0.169-0.1690.0000.0000.0000.000
183A362HOH 0-0.006-0.01011.1880.0410.0410.0000.0000.0000.000
184A364HOH 0-0.065-0.0529.5900.0600.0600.0000.0000.0000.000
185A372HOH 0-0.022-0.00611.843-0.017-0.0170.0000.0000.0000.000
186A374HOH 0-0.027-0.01721.095-0.007-0.0070.0000.0000.0000.000
187A377HOH 00.0140.00119.037-0.013-0.0130.0000.0000.0000.000
188A379HOH 0-0.030-0.03814.2400.0460.0460.0000.0000.0000.000
189A383HOH 0-0.029-0.0229.071-0.015-0.0150.0000.0000.0000.000
190A390HOH 0-0.018-0.0245.1160.0810.0810.0000.0000.0000.000
191A392HOH 0-0.007-0.01518.170-0.001-0.0010.0000.0000.0000.000
192A398HOH 0-0.0090.0006.7940.3910.3910.0000.0000.0000.000
193A399HOH 0-0.018-0.02614.757-0.012-0.0120.0000.0000.0000.000
194A400HOH 00.0260.01513.389-0.045-0.0450.0000.0000.0000.000
195A404HOH 0-0.020-0.02121.9130.0040.0040.0000.0000.0000.000
196A405HOH 0-0.004-0.00522.6110.0010.0010.0000.0000.0000.000
197A406HOH 0-0.015-0.0129.6220.0020.0020.0000.0000.0000.000
198A408HOH 00.0190.0086.8560.5690.5690.0000.0000.0000.000
199A410HOH 00.004-0.00119.780-0.007-0.0070.0000.0000.0000.000
200A414HOH 0-0.022-0.04025.509-0.006-0.0060.0000.0000.0000.000
201A419HOH 0-0.028-0.01824.4390.0050.0050.0000.0000.0000.000
202A422HOH 0-0.019-0.01917.249-0.006-0.0060.0000.0000.0000.000
203A423HOH 00.0250.01120.7430.0070.0070.0000.0000.0000.000
204A428HOH 00.012-0.01011.5290.0390.0390.0000.0000.0000.000
205A430HOH 0-0.060-0.05715.5010.0180.0180.0000.0000.0000.000
206A435HOH 0-0.008-0.01124.553-0.002-0.0020.0000.0000.0000.000
207A457HOH 0-0.035-0.02517.7980.0050.0050.0000.0000.0000.000
208A461HOH 0-0.021-0.0234.9060.8380.8710.000-0.001-0.0320.000
209A463HOH 0-0.004-0.00523.6030.0030.0030.0000.0000.0000.000
210A466HOH 00.0240.0192.682-0.742-0.1840.104-0.317-0.346-0.001
211A498HOH 0-0.034-0.0279.223-0.064-0.0640.0000.0000.0000.000