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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: M333Z

Calculation Name: 5RSH-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 4-(5-azaspiro[2.5]octan-5-yl)-7h-pyrrolo[2,3-d]pyrimidine

ligand 3-letter code: W5G

PDB ID: 5RSH

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 214
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1831572.545976
FMO2-HF: Nuclear repulsion 1764828.858624
FMO2-HF: Total energy -66743.687352
FMO2-MP2: Total energy -66939.349999


3D Structure
Snapshot
 
Ligand structure

W5G

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.
-81.192-57.15163.217-26.141-61.1200.079


Interactive mode: IFIE and PIEDA for fragment #214(A:201:W5G )


Summations of interaction energy for fragment #214(A:201:W5G )
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.
-81.192-57.15163.217-26.141-61.12-0.079
Interaction energy analysis for fragmet #214(A:201:W5G )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.078 / q_NPA : -0.022
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 00.017-0.00321.8410.0060.0060.0000.0000.0000.000
2A4ASN 0-0.007-0.00716.7210.0090.0090.0000.0000.0000.000
3A5SER 00.0360.00916.477-0.018-0.0180.0000.0000.0000.000
4A6PHE 0-0.0480.00710.433-0.006-0.0060.0000.0000.0000.000
5A7SER 00.0350.00913.589-0.036-0.0360.0000.0000.0000.000
6A8GLY 00.006-0.00813.1930.0880.0880.0000.0000.0000.000
7A9TYR 0-0.051-0.0338.3350.1370.1370.0000.0000.0000.000
8A10LEU 0-0.0060.00712.699-0.127-0.1270.0000.0000.0000.000
9A11LYS 10.8060.89413.724-0.383-0.3830.0000.0000.0000.000
10A12LEU 0-0.046-0.01111.103-0.025-0.0250.0000.0000.0000.000
11A13THR 00.0380.00915.737-0.053-0.0530.0000.0000.0000.000
12A14ASP -1-0.868-0.90018.1270.4000.4000.0000.0000.0000.000
13A15ASN 00.002-0.00216.615-0.025-0.0250.0000.0000.0000.000
14A16VAL 00.0030.01311.9450.0800.0800.0000.0000.0000.000
15A17TYR 00.0450.02812.260-0.099-0.0990.0000.0000.0000.000
16A18ILE 00.0240.0127.2900.2270.2270.0000.0000.0000.000
17A19LYS 10.8210.8917.798-1.273-1.2730.0000.0000.0000.000
18A20ASN 00.0150.0116.7180.7260.7260.0000.0000.0000.000
19A21ALA 0-0.029-0.0265.729-0.697-0.6970.0000.0000.0000.000
20A22ASP -1-0.796-0.8851.763-22.211-23.58012.186-5.336-5.481-0.061
21A23ILE 00.014-0.0122.222-9.579-7.6216.298-2.747-5.5090.024
22A24VAL 00.0150.0073.018-1.246-0.2800.049-0.254-0.7620.001
23A25GLU -1-0.813-0.8865.295-0.561-0.465-0.001-0.002-0.0930.000
24A26GLU -1-0.752-0.8336.8611.0041.0040.0000.0000.0000.000
25A27ALA 0-0.028-0.0217.686-0.081-0.0810.0000.0000.0000.000
26A28LYS 10.8210.8948.7380.8240.8240.0000.0000.0000.000
27A29LYS 10.8190.90611.161-0.512-0.5120.0000.0000.0000.000
28A30VAL 0-0.049-0.03112.198-0.018-0.0180.0000.0000.0000.000
29A31LYS 10.8710.96113.237-0.174-0.1740.0000.0000.0000.000
30A32PRO 00.0030.01910.933-0.013-0.0130.0000.0000.0000.000
31A33THR 00.031-0.00614.256-0.058-0.0580.0000.0000.0000.000
32A34VAL 0-0.010-0.01312.643-0.052-0.0520.0000.0000.0000.000
33A35VAL 00.0000.0068.0290.1150.1150.0000.0000.0000.000
34A36VAL 00.0090.0028.182-0.189-0.1890.0000.0000.0000.000
35A37ASN 00.007-0.0237.4430.9200.9200.0000.0000.0000.000
36A38ALA 0-0.0010.0185.761-0.189-0.1890.0000.0000.0000.000
37A39ALA 00.0360.0397.740-0.297-0.2970.0000.0000.0000.000
38A40ASN 00.004-0.01010.897-0.047-0.0470.0000.0000.0000.000
39A41VAL 00.0440.02013.0320.0180.0180.0000.0000.0000.000
40A42TYR 00.0030.00216.482-0.006-0.0060.0000.0000.0000.000
41A43LEU 0-0.0010.01214.689-0.015-0.0150.0000.0000.0000.000
42A44LYS 10.9791.00914.5840.1240.1240.0000.0000.0000.000
43A45HIS 00.0230.0159.8350.0820.0820.0000.0000.0000.000
44A46GLY 00.0490.04310.220-0.132-0.1320.0000.0000.0000.000
45A47GLY 00.0420.0127.258-0.220-0.2200.0000.0000.0000.000
46A48GLY 00.0080.0143.3270.0750.3360.021-0.103-0.1790.000
47A49VAL 00.0280.0122.625-5.527-2.4227.559-2.637-8.0270.015
48A50ALA 00.0180.0173.738-1.402-2.1350.0761.191-0.5350.003
49A51GLY 0-0.0190.0066.435-0.308-0.3080.0000.0000.0000.000
50A52ALA 00.0080.0042.714-1.012-0.4130.446-0.299-0.7460.000
51A53LEU 00.0420.0154.595-0.224-0.046-0.001-0.017-0.1600.000
52A54ASN 00.0560.0066.8850.1310.1310.0000.0000.0000.000
53A55LYS 10.9701.0017.7111.6451.6450.0000.0000.0000.000
54A56ALA 0-0.038-0.0097.8180.1480.1480.0000.0000.0000.000
55A57THR 0-0.054-0.0179.8310.2160.2160.0000.0000.0000.000
56A58ASN 0-0.038-0.02612.5850.0640.0640.0000.0000.0000.000
57A59ASN 0-0.0010.00513.1390.0160.0160.0000.0000.0000.000
58A60ALA 00.0310.02314.5970.0550.0550.0000.0000.0000.000
59A61MET 00.0100.01610.3430.0500.0500.0000.0000.0000.000
60A62GLN 0-0.053-0.03213.9930.0320.0320.0000.0000.0000.000
61A63VAL 00.0240.02215.4790.0290.0290.0000.0000.0000.000
62A64GLU -1-0.729-0.84117.2780.1480.1480.0000.0000.0000.000
63A65SER 00.001-0.00915.9170.0540.0540.0000.0000.0000.000
64A66ASP -1-0.808-0.89418.243-0.097-0.0970.0000.0000.0000.000
65A67ASP -1-0.850-0.88220.5740.0300.0300.0000.0000.0000.000
66A68TYR 00.017-0.00920.5630.0200.0200.0000.0000.0000.000
67A69ILE 0-0.042-0.02619.5030.0090.0090.0000.0000.0000.000
68A70ALA 0-0.030-0.00322.847-0.001-0.0010.0000.0000.0000.000
69A71THR 0-0.037-0.00525.796-0.003-0.0030.0000.0000.0000.000
70A72ASN 0-0.083-0.04624.5170.0050.0050.0000.0000.0000.000
71A73GLY 00.0320.02924.9900.0060.0060.0000.0000.0000.000
72A74PRO 0-0.051-0.02820.7050.0170.0170.0000.0000.0000.000
73A75LEU 0-0.0100.00316.1560.0100.0100.0000.0000.0000.000
74A76LYS 10.9740.98119.601-0.183-0.1830.0000.0000.0000.000
75A77VAL 00.0260.00214.5490.0410.0410.0000.0000.0000.000
76A78GLY 00.0120.01915.058-0.020-0.0200.0000.0000.0000.000
77A79GLY 0-0.022-0.00516.2700.0270.0270.0000.0000.0000.000
78A80SER 0-0.013-0.03715.6570.0560.0560.0000.0000.0000.000
79A81CYS 0-0.0380.00616.936-0.050-0.0500.0000.0000.0000.000
80A82VAL 00.0110.01016.8760.0730.0730.0000.0000.0000.000
81A83LEU 00.0020.00716.687-0.055-0.0550.0000.0000.0000.000
82A84SER 00.0320.01417.3850.0610.0610.0000.0000.0000.000
83A85GLY 0-0.0090.01013.8540.0340.0340.0000.0000.0000.000
84A86HIS 0-0.029-0.03213.564-0.092-0.0920.0000.0000.0000.000
85A87ASN 0-0.023-0.02512.7310.0700.0700.0000.0000.0000.000
86A88LEU 0-0.018-0.0218.292-0.038-0.0380.0000.0000.0000.000
87A89ALA 0-0.006-0.00311.9740.1070.1070.0000.0000.0000.000
88A90LYS 10.8470.94414.122-0.304-0.3040.0000.0000.0000.000
89A91HIS 00.0320.01316.279-0.076-0.0760.0000.0000.0000.000
90A92CYS 0-0.014-0.00312.0050.1460.1460.0000.0000.0000.000
91A93LEU 0-0.0280.00712.758-0.102-0.1020.0000.0000.0000.000
92A94HIS 00.046-0.00112.0530.3040.3040.0000.0000.0000.000
93A95VAL 00.0190.00511.107-0.139-0.1390.0000.0000.0000.000
94A96VAL 0-0.0320.01410.9470.1040.1040.0000.0000.0000.000
95A97GLY 00.0570.03210.075-0.029-0.0290.0000.0000.0000.000
96A98PRO 0-0.0110.00311.038-0.068-0.0680.0000.0000.0000.000
97A99ASN 0-0.038-0.02210.447-0.056-0.0560.0000.0000.0000.000
98A100VAL 00.0630.01910.9210.0090.0090.0000.0000.0000.000
99A101ASN 0-0.075-0.0469.2970.0500.0500.0000.0000.0000.000
100A102LYS 10.8150.90912.9430.0540.0540.0000.0000.0000.000
101A103GLY 00.0010.00815.5320.0210.0210.0000.0000.0000.000
102A104GLU -1-0.790-0.84314.3160.0830.0830.0000.0000.0000.000
103A105ASP -1-0.816-0.91215.9600.1150.1150.0000.0000.0000.000
104A106ILE 00.0490.00811.2940.0280.0280.0000.0000.0000.000
105A107GLN 00.0140.01014.6500.0700.0700.0000.0000.0000.000
106A108LEU 0-0.050-0.03115.9020.0350.0350.0000.0000.0000.000
107A109LEU 0-0.023-0.0169.2070.0470.0470.0000.0000.0000.000
108A110LYS 10.8740.93113.303-0.285-0.2850.0000.0000.0000.000
109A111SER 00.0280.00715.5320.0250.0250.0000.0000.0000.000
110A112ALA 00.0240.01112.6590.0190.0190.0000.0000.0000.000
111A113TYR 00.016-0.0077.3370.1760.1760.0000.0000.0000.000
112A114GLU -1-0.847-0.91113.6590.3530.3530.0000.0000.0000.000
113A115ASN 0-0.061-0.02315.298-0.055-0.0550.0000.0000.0000.000
114A116PHE 00.041-0.0059.3810.0120.0120.0000.0000.0000.000
115A117ASN 0-0.028-0.00615.260-0.006-0.0060.0000.0000.0000.000
116A118GLN 0-0.0420.00418.512-0.059-0.0590.0000.0000.0000.000
117A119HIS 0-0.032-0.02416.078-0.018-0.0180.0000.0000.0000.000
118A120GLU -1-0.825-0.88517.4280.3830.3830.0000.0000.0000.000
119A121VAL 0-0.008-0.01614.3400.0180.0180.0000.0000.0000.000
120A122LEU 0-0.0430.01611.388-0.017-0.0170.0000.0000.0000.000
121A123LEU 0-0.0270.0096.5790.0070.0070.0000.0000.0000.000
122A124ALA 00.035-0.0016.537-0.032-0.0320.0000.0000.0000.000
123A125PRO 0-0.0440.0002.951-1.0410.3690.366-0.488-1.2880.002
124A126LEU 00.0420.0152.476-2.781-1.2970.420-0.372-1.531-0.001
125A127LEU 0-0.0180.0064.192-0.781-0.4630.001-0.066-0.2530.000
126A128SER 00.040-0.0166.357-0.140-0.1400.0000.0000.0000.000
127A129ALA 00.0150.0352.539-0.864-0.4092.082-0.618-1.9190.000
128A130GLY 00.0220.0202.523-3.116-1.1901.577-1.291-2.213-0.003
129A131ILE 00.030-0.0092.7682.1830.6530.2551.858-0.5830.000
130A132PHE 0-0.0430.0185.9610.2870.2870.0000.0000.0000.000
131A133GLY 00.0160.0156.6750.1620.1620.0000.0000.0000.000
132A134ALA 00.0300.0227.4440.0770.0770.0000.0000.0000.000
133A135ASP -1-0.808-0.9096.5130.0140.0140.0000.0000.0000.000
134A136PRO 0-0.016-0.0153.089-0.3270.1430.047-0.098-0.4190.000
135A137ILE 00.0270.0115.2320.2070.242-0.001-0.001-0.0340.000
136A138HIS 00.0350.0218.4960.0690.0690.0000.0000.0000.000
137A139SER 0-0.011-0.0215.9880.1120.1120.0000.0000.0000.000
138A140LEU 0-0.0080.0037.4090.1010.1010.0000.0000.0000.000
139A141ARG 10.8430.9148.708-0.445-0.4450.0000.0000.0000.000
140A142VAL 00.0040.01011.420-0.019-0.0190.0000.0000.0000.000
141A143CYS 0-0.0230.0059.532-0.028-0.0280.0000.0000.0000.000
142A144VAL 00.0230.01911.682-0.033-0.0330.0000.0000.0000.000
143A145ASP -1-0.809-0.89414.1610.3600.3600.0000.0000.0000.000
144A146THR 0-0.126-0.07214.811-0.082-0.0820.0000.0000.0000.000
145A147VAL 0-0.056-0.01613.036-0.032-0.0320.0000.0000.0000.000
146A148ARG 10.9330.97416.190-0.386-0.3860.0000.0000.0000.000
147A149THR 0-0.0320.00916.825-0.015-0.0150.0000.0000.0000.000
148A150ASN 0-0.035-0.00415.9550.0330.0330.0000.0000.0000.000
149A151VAL 00.0160.0029.8050.0370.0370.0000.0000.0000.000
150A152TYR 00.0120.0139.892-0.062-0.0620.0000.0000.0000.000
151A153LEU 00.014-0.0096.3640.2400.2400.0000.0000.0000.000
152A154ALA 0-0.010-0.0023.221-0.785-0.1470.016-0.129-0.5250.000
153A155VAL 0-0.004-0.0052.307-4.208-1.2523.073-2.042-3.987-0.026
154A156PHE 00.002-0.0102.115-12.406-5.43312.695-4.334-15.334-0.001
155A157ASP -1-0.794-0.9023.901-3.205-1.9700.022-0.220-1.0350.000
156A158LYS 10.8550.9105.222-0.296-0.231-0.001-0.001-0.0640.000
157A159ASN 0-0.037-0.0218.2200.0530.0530.0000.0000.0000.000
158A160LEU 00.0260.0062.257-0.633-0.4692.238-0.381-2.021-0.001
159A161TYR 0-0.012-0.0015.8630.0540.0540.0000.0000.0000.000
160A162ASP -1-0.757-0.8497.0730.4490.4490.0000.0000.0000.000
161A163LYS 10.9380.9868.552-0.146-0.1460.0000.0000.0000.000
162A164LEU 0-0.043-0.0134.660-0.1030.000-0.001-0.004-0.0980.000
163A165VAL 00.0220.0169.206-0.052-0.0520.0000.0000.0000.000
164A166SER 0-0.047-0.03112.428-0.084-0.0840.0000.0000.0000.000
165A167SER 0-0.113-0.07811.459-0.051-0.0510.0000.0000.0000.000
166A168PHE 0-0.013-0.00112.288-0.001-0.0010.0000.0000.0000.000
167A169LEU -1-0.881-0.92614.3760.3620.3620.0000.0000.0000.000
168A301HOH 0-0.051-0.03925.820-0.003-0.0030.0000.0000.0000.000
169A304HOH 00.008-0.0066.3580.0580.0580.0000.0000.0000.000
170A312HOH 0-0.014-0.0159.7300.0500.0500.0000.0000.0000.000
171A321HOH 0-0.006-0.00516.7050.0100.0100.0000.0000.0000.000
172A322HOH 0-0.074-0.06021.8570.0110.0110.0000.0000.0000.000
173A333HOH 0-0.050-0.03712.048-0.003-0.0030.0000.0000.0000.000
174A338HOH 0-0.004-0.0092.496-2.671-1.9561.676-0.938-1.453-0.010
175A341HOH 0-0.022-0.02322.816-0.006-0.0060.0000.0000.0000.000
176A343HOH 0-0.055-0.04419.491-0.012-0.0120.0000.0000.0000.000
177A350HOH 0-0.014-0.0189.1500.0190.0190.0000.0000.0000.000
178A351HOH 0-0.060-0.03824.004-0.005-0.0050.0000.0000.0000.000
179A354HOH 0-0.033-0.0276.1190.2030.2030.0000.0000.0000.000
180A359HOH 0-0.013-0.03515.0300.0200.0200.0000.0000.0000.000
181A360HOH 00.008-0.00518.826-0.010-0.0100.0000.0000.0000.000
182A368HOH 0-0.028-0.00910.902-0.036-0.0360.0000.0000.0000.000
183A369HOH 00.0140.00118.7220.0000.0000.0000.0000.0000.000
184A374HOH 0-0.026-0.01616.8650.0110.0110.0000.0000.0000.000
185A381HOH 0-0.067-0.0509.425-0.090-0.0900.0000.0000.0000.000
186A382HOH 0-0.001-0.00717.7450.0130.0130.0000.0000.0000.000
187A385HOH 0-0.015-0.0099.704-0.022-0.0220.0000.0000.0000.000
188A389HOH 00.0230.01311.5260.0640.0640.0000.0000.0000.000
189A390HOH 0-0.031-0.03712.137-0.017-0.0170.0000.0000.0000.000
190A392HOH 0-0.002-0.0281.983-9.997-11.7889.788-4.008-3.990-0.003
191A396HOH 0-0.017-0.02413.204-0.034-0.0340.0000.0000.0000.000
192A397HOH 0-0.009-0.0118.7520.0810.0810.0000.0000.0000.000
193A400HOH 0-0.016-0.0164.863-0.176-0.1300.000-0.002-0.0440.000
194A401HOH 0-0.004-0.00522.6970.0120.0120.0000.0000.0000.000
195A404HOH 0-0.021-0.02117.811-0.022-0.0220.0000.0000.0000.000
196A406HOH 00.0280.0206.6250.1680.1680.0000.0000.0000.000
197A409HOH 0-0.020-0.03822.0340.0090.0090.0000.0000.0000.000
198A413HOH 0-0.018-0.01810.9970.0120.0120.0000.0000.0000.000
199A417HOH 00.013-0.01011.8470.0480.0480.0000.0000.0000.000
200A419HOH 0-0.001-0.0093.3450.0630.3120.007-0.097-0.1580.000
201A420HOH 0-0.014-0.03120.6090.0210.0210.0000.0000.0000.000
202A421HOH 00.0250.01119.996-0.002-0.0020.0000.0000.0000.000
203A422HOH 0-0.009-0.01220.2950.0100.0100.0000.0000.0000.000
204A428HOH 0-0.060-0.05714.136-0.011-0.0110.0000.0000.0000.000
205A429HOH 00.0010.00319.9370.0020.0020.0000.0000.0000.000
206A430HOH 0-0.025-0.0202.106-1.2890.3561.664-1.795-1.514-0.013
207A431HOH 00.004-0.00119.2140.0190.0190.0000.0000.0000.000
208A453HOH 0-0.016-0.0214.105-0.1250.0430.001-0.028-0.1420.000
209A458HOH 00.0190.01019.377-0.008-0.0080.0000.0000.0000.000
210A463HOH 0-0.035-0.02518.368-0.015-0.0150.0000.0000.0000.000
211A481HOH 0-0.001-0.0102.253-1.649-0.4030.659-0.882-1.023-0.005
212A502HOH 0-0.034-0.02810.603-0.041-0.0410.0000.0000.0000.000
213A523HOH 00.0100.00412.4440.0220.0220.0000.0000.0000.000