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: 7GJLK

Calculation Name: 5RSH-B-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: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-27

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 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1787514.273091
FMO2-HF: Nuclear repulsion 1721056.022993
FMO2-HF: Total energy -66458.250098
FMO2-MP2: Total energy -66652.01753


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(B:1:SER )


Summations of interaction energy for fragment #1(B:1:SER )
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.
-2.0420.489-0.008-1.144-1.3790.006
Interaction energy analysis for fragmet #1(B:1:SER )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : 0.005
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].
3B3VAL 00.0330.0123.668-0.5361.995-0.008-1.144-1.3790.006
4B4ASN 0-0.008-0.0135.986-0.632-0.6320.0000.0000.0000.000
5B5SER 00.0290.0278.105-0.262-0.2620.0000.0000.0000.000
6B6PHE 0-0.016-0.01510.1000.1320.1320.0000.0000.0000.000
7B7SER 00.0240.00413.874-0.049-0.0490.0000.0000.0000.000
8B8GLY 00.0250.00615.7350.0520.0520.0000.0000.0000.000
9B9TYR 0-0.076-0.05416.6640.0280.0280.0000.0000.0000.000
10B10LEU 00.0200.02220.842-0.024-0.0240.0000.0000.0000.000
11B11LYS 10.8490.92023.5910.1960.1960.0000.0000.0000.000
12B12LEU 0-0.035-0.00324.8610.0060.0060.0000.0000.0000.000
13B13THR 00.030-0.01226.4690.0010.0010.0000.0000.0000.000
14B14ASP -1-0.864-0.94425.398-0.168-0.1680.0000.0000.0000.000
15B15ASN 0-0.038-0.01222.408-0.022-0.0220.0000.0000.0000.000
16B16VAL 00.0230.02522.2550.0100.0100.0000.0000.0000.000
17B17TYR 0-0.010-0.00320.670-0.021-0.0210.0000.0000.0000.000
18B18ILE 00.0110.00922.8140.0220.0220.0000.0000.0000.000
19B19LYS 10.8470.90317.8360.0590.0590.0000.0000.0000.000
20B20ASN 0-0.049-0.01322.9000.0120.0120.0000.0000.0000.000
21B21ALA 00.015-0.01120.030-0.006-0.0060.0000.0000.0000.000
22B22ASP -1-0.771-0.86620.9750.1170.1170.0000.0000.0000.000
23B23ILE 00.0340.00518.7790.0080.0080.0000.0000.0000.000
24B24VAL 0-0.0010.00217.4910.0320.0320.0000.0000.0000.000
25B25GLU -1-0.947-0.97316.1900.1320.1320.0000.0000.0000.000
26B26GLU -1-0.778-0.86415.109-0.024-0.0240.0000.0000.0000.000
27B27ALA 0-0.0010.00113.4350.0000.0000.0000.0000.0000.000
28B28LYS 10.9150.96511.489-0.216-0.2160.0000.0000.0000.000
29B29LYS 10.7910.89510.4130.1120.1120.0000.0000.0000.000
30B30VAL 0-0.068-0.0329.586-0.046-0.0460.0000.0000.0000.000
31B31LYS 10.9560.9975.199-0.736-0.7360.0000.0000.0000.000
32B32PRO 00.0200.0268.0890.1530.1530.0000.0000.0000.000
33B33THR 00.0150.00310.2100.2440.2440.0000.0000.0000.000
34B34VAL 0-0.016-0.01610.9160.0290.0290.0000.0000.0000.000
35B35VAL 0-0.0050.00614.613-0.045-0.0450.0000.0000.0000.000
36B36VAL 0-0.014-0.00616.7290.0080.0080.0000.0000.0000.000
37B37ASN 00.006-0.02620.516-0.011-0.0110.0000.0000.0000.000
38B38ALA 0-0.0080.02022.917-0.011-0.0110.0000.0000.0000.000
39B39ALA 00.0280.03026.1940.0000.0000.0000.0000.0000.000
40B40ASN 00.021-0.00327.948-0.010-0.0100.0000.0000.0000.000
41B41VAL 00.0380.01330.6520.0080.0080.0000.0000.0000.000
42B42TYR 00.0390.01832.5290.0020.0020.0000.0000.0000.000
43B43LEU 0-0.036-0.00726.5470.0060.0060.0000.0000.0000.000
44B44LYS 10.8640.93929.083-0.104-0.1040.0000.0000.0000.000
45B45HIS 0-0.003-0.00225.735-0.018-0.0180.0000.0000.0000.000
46B46GLY 00.0310.02128.4720.0040.0040.0000.0000.0000.000
47B47GLY 00.0230.00330.4570.0020.0020.0000.0000.0000.000
48B48GLY 00.0140.00329.0550.0050.0050.0000.0000.0000.000
49B49VAL 00.0610.02623.0940.0090.0090.0000.0000.0000.000
50B50ALA 00.0160.02124.2290.0160.0160.0000.0000.0000.000
51B51GLY 0-0.0130.00625.0560.0150.0150.0000.0000.0000.000
52B52ALA 0-0.036-0.02923.5360.0110.0110.0000.0000.0000.000
53B53LEU 00.013-0.00118.8450.0190.0190.0000.0000.0000.000
54B54ASN 00.0650.02020.8190.0390.0390.0000.0000.0000.000
55B55LYS 10.9290.97122.830-0.120-0.1200.0000.0000.0000.000
56B56ALA 0-0.0010.01618.5080.0090.0090.0000.0000.0000.000
57B57THR 0-0.040-0.01417.8910.0280.0280.0000.0000.0000.000
58B58ASN 0-0.021-0.01519.727-0.006-0.0060.0000.0000.0000.000
59B59ASN 0-0.010-0.00622.819-0.012-0.0120.0000.0000.0000.000
60B60ALA 00.0380.02920.494-0.010-0.0100.0000.0000.0000.000
61B61MET 00.0150.02119.782-0.014-0.0140.0000.0000.0000.000
62B62GLN 0-0.043-0.03622.475-0.016-0.0160.0000.0000.0000.000
63B63VAL 0-0.0090.00125.433-0.011-0.0110.0000.0000.0000.000
64B64GLU -1-0.714-0.83520.6560.2850.2850.0000.0000.0000.000
65B65SER 0-0.019-0.01824.837-0.012-0.0120.0000.0000.0000.000
66B66ASP -1-0.823-0.89526.6630.1140.1140.0000.0000.0000.000
67B67ASP -1-0.913-0.94527.5200.1480.1480.0000.0000.0000.000
68B68TYR 00.0420.00726.134-0.009-0.0090.0000.0000.0000.000
69B69ILE 0-0.031-0.01428.408-0.012-0.0120.0000.0000.0000.000
70B70ALA 0-0.0220.00231.717-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.043-0.01030.236-0.008-0.0080.0000.0000.0000.000
72B72ASN 0-0.091-0.05628.727-0.010-0.0100.0000.0000.0000.000
73B73GLY 0-0.0210.00232.484-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.052-0.03132.6500.0060.0060.0000.0000.0000.000
75B75LEU 0-0.028-0.01227.705-0.004-0.0040.0000.0000.0000.000
76B76LYS 10.9990.99332.238-0.048-0.0480.0000.0000.0000.000
77B77VAL 00.0300.00232.6430.0040.0040.0000.0000.0000.000
78B78GLY 0-0.0030.00832.057-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0010.01830.005-0.004-0.0040.0000.0000.0000.000
80B80SER 0-0.056-0.05624.8080.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0010.03024.725-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0220.01618.2830.0060.0060.0000.0000.0000.000
83B83LEU 0-0.0070.00720.040-0.005-0.0050.0000.0000.0000.000
84B84SER 00.0390.01816.4960.0570.0570.0000.0000.0000.000
85B85GLY 00.0170.02014.551-0.052-0.0520.0000.0000.0000.000
86B86HIS 0-0.029-0.02614.8480.0270.0270.0000.0000.0000.000
87B87ASN 0-0.059-0.04012.6180.0940.0940.0000.0000.0000.000
88B88LEU 0-0.030-0.01412.698-0.004-0.0040.0000.0000.0000.000
89B89ALA 00.0440.02711.040-0.017-0.0170.0000.0000.0000.000
90B90LYS 10.9200.9899.550-0.747-0.7470.0000.0000.0000.000
91B91HIS 00.012-0.00511.407-0.030-0.0300.0000.0000.0000.000
92B92CYS 0-0.028-0.01415.047-0.013-0.0130.0000.0000.0000.000
93B93LEU 0-0.0300.00518.095-0.013-0.0130.0000.0000.0000.000
94B94HIS 00.0460.00520.583-0.034-0.0340.0000.0000.0000.000
95B95VAL 00.0120.00123.721-0.009-0.0090.0000.0000.0000.000
96B96VAL 0-0.0300.01126.3070.0010.0010.0000.0000.0000.000
97B97GLY 00.0290.01630.012-0.007-0.0070.0000.0000.0000.000
98B98PRO 00.0040.01831.7280.0050.0050.0000.0000.0000.000
99B99ASN 00.0060.00834.789-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0820.03836.618-0.001-0.0010.0000.0000.0000.000
101B101ASN 0-0.044-0.01837.528-0.005-0.0050.0000.0000.0000.000
102B102LYS 10.7510.87136.748-0.052-0.0520.0000.0000.0000.000
103B103GLY 00.0080.01341.2250.0000.0000.0000.0000.0000.000
104B104GLU -1-0.797-0.85236.9460.0470.0470.0000.0000.0000.000
105B105ASP -1-0.806-0.90940.6010.0120.0120.0000.0000.0000.000
106B106ILE 00.026-0.00236.5490.0020.0020.0000.0000.0000.000
107B107GLN 0-0.031-0.01837.3860.0010.0010.0000.0000.0000.000
108B108LEU 00.0220.00435.715-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.031-0.01531.4230.0040.0040.0000.0000.0000.000
110B110LYS 10.8960.93531.8220.0200.0200.0000.0000.0000.000
111B111SER 00.0180.00831.401-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0330.01329.7290.0030.0030.0000.0000.0000.000
113B113TYR 00.025-0.01326.2690.0080.0080.0000.0000.0000.000
114B114GLU -1-0.840-0.87226.567-0.005-0.0050.0000.0000.0000.000
115B115ASN 0-0.033-0.00924.9390.0030.0030.0000.0000.0000.000
116B116PHE 00.028-0.00922.2410.0120.0120.0000.0000.0000.000
117B117ASN 0-0.028-0.01021.616-0.015-0.0150.0000.0000.0000.000
118B118GLN 0-0.0350.00622.133-0.012-0.0120.0000.0000.0000.000
119B119HIS 00.0200.01617.1990.0240.0240.0000.0000.0000.000
120B120GLU -1-0.828-0.89715.594-0.153-0.1530.0000.0000.0000.000
121B121VAL 0-0.013-0.00812.767-0.039-0.0390.0000.0000.0000.000
122B122LEU 0-0.0100.02715.1740.0710.0710.0000.0000.0000.000
123B123LEU 0-0.0040.01514.857-0.042-0.0420.0000.0000.0000.000
124B124ALA 00.004-0.01017.2240.0340.0340.0000.0000.0000.000
125B125PRO 0-0.0020.01420.834-0.017-0.0170.0000.0000.0000.000
126B126LEU 00.0140.00623.984-0.003-0.0030.0000.0000.0000.000
127B127LEU 00.0120.01725.9130.0080.0080.0000.0000.0000.000
128B128SER 00.012-0.02628.895-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0060.01930.045-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0390.01731.8580.0080.0080.0000.0000.0000.000
131B131ILE 0-0.011-0.01331.454-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.073-0.02230.8000.0000.0000.0000.0000.0000.000
133B133GLY 00.0290.01134.644-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.0050.00734.855-0.004-0.0040.0000.0000.0000.000
135B135ASP -1-0.795-0.90335.972-0.001-0.0010.0000.0000.0000.000
136B136PRO 0-0.054-0.02732.371-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.0190.00132.801-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0620.03634.715-0.007-0.0070.0000.0000.0000.000
139B139SER 0-0.030-0.03230.808-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.017-0.00828.4300.0000.0000.0000.0000.0000.000
141B141ARG 10.8530.90030.7680.0340.0340.0000.0000.0000.000
142B142VAL 00.0170.01231.819-0.004-0.0040.0000.0000.0000.000
143B143CYS 0-0.0080.01326.421-0.001-0.0010.0000.0000.0000.000
144B144VAL 0-0.0080.00528.347-0.005-0.0050.0000.0000.0000.000
145B145ASP -1-0.754-0.83129.537-0.046-0.0460.0000.0000.0000.000
146B146THR 0-0.114-0.06129.2370.0020.0020.0000.0000.0000.000
147B147VAL 0-0.052-0.01323.4000.0020.0020.0000.0000.0000.000
148B148ARG 10.9000.95625.4150.0360.0360.0000.0000.0000.000
149B149THR 0-0.0190.01819.857-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.046-0.01417.517-0.007-0.0070.0000.0000.0000.000
151B151VAL 00.0370.01418.3960.0240.0240.0000.0000.0000.000
152B152TYR 0-0.022-0.01016.559-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.022-0.00119.5580.0330.0330.0000.0000.0000.000
154B154ALA 00.000-0.00120.025-0.015-0.0150.0000.0000.0000.000
155B155VAL 0-0.026-0.01822.1040.0120.0120.0000.0000.0000.000
156B156PHE 00.0250.01424.713-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.793-0.89126.2410.0060.0060.0000.0000.0000.000
158B158LYS 10.8670.91229.0070.0310.0310.0000.0000.0000.000
159B159ASN 0-0.014-0.02730.166-0.010-0.0100.0000.0000.0000.000
160B160LEU 0-0.0110.00330.661-0.003-0.0030.0000.0000.0000.000
161B161TYR 0-0.012-0.01425.549-0.004-0.0040.0000.0000.0000.000
162B162ASP -1-0.760-0.85829.972-0.041-0.0410.0000.0000.0000.000
163B163LYS 10.9471.00932.7840.0060.0060.0000.0000.0000.000
164B164LEU 0-0.0370.00429.581-0.002-0.0020.0000.0000.0000.000
165B165VAL 00.0380.00828.961-0.004-0.0040.0000.0000.0000.000
166B166SER 0-0.053-0.02831.878-0.003-0.0030.0000.0000.0000.000
167B167SER 0-0.008-0.02335.420-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.0110.00331.2630.0010.0010.0000.0000.0000.000
169B169LEU -1-0.859-0.88334.217-0.055-0.0550.0000.0000.0000.000
170B215HOH 0-0.007-0.01931.569-0.003-0.0030.0000.0000.0000.000
171B218HOH 0-0.043-0.04838.2750.0010.0010.0000.0000.0000.000
172B222HOH 0-0.042-0.03327.6910.0000.0000.0000.0000.0000.000
173B225HOH 0-0.065-0.04311.9310.0390.0390.0000.0000.0000.000
174B226HOH 0-0.036-0.03038.9520.0020.0020.0000.0000.0000.000
175B229HOH 0-0.025-0.02712.450-0.034-0.0340.0000.0000.0000.000
176B235HOH 0-0.006-0.01133.8140.0010.0010.0000.0000.0000.000
177B251HOH 0-0.024-0.02322.3680.0050.0050.0000.0000.0000.000
178B254HOH 0-0.026-0.03513.732-0.004-0.0040.0000.0000.0000.000
179B256HOH 0-0.060-0.05834.0270.0020.0020.0000.0000.0000.000
180B259HOH 0-0.010-0.01228.610-0.004-0.0040.0000.0000.0000.000
181B263HOH 0-0.030-0.02331.2200.0020.0020.0000.0000.0000.000
182B265HOH 0-0.011-0.03419.584-0.014-0.0140.0000.0000.0000.000
183B266HOH 0-0.005-0.01623.9640.0080.0080.0000.0000.0000.000
184B267HOH 0-0.042-0.03034.8410.0010.0010.0000.0000.0000.000
185B270HOH 0-0.068-0.05129.177-0.003-0.0030.0000.0000.0000.000
186B277HOH 0-0.022-0.01027.397-0.001-0.0010.0000.0000.0000.000
187B280HOH 00.022-0.00129.675-0.002-0.0020.0000.0000.0000.000
188B281HOH 0-0.032-0.03023.1720.0060.0060.0000.0000.0000.000
189B286HOH 0-0.070-0.04636.733-0.001-0.0010.0000.0000.0000.000
190B291HOH 0-0.062-0.03838.7590.0020.0020.0000.0000.0000.000
191B293HOH 0-0.024-0.02428.3670.0010.0010.0000.0000.0000.000
192B297HOH 0-0.016-0.01115.3350.0140.0140.0000.0000.0000.000
193B302HOH 0-0.018-0.03012.4970.0350.0350.0000.0000.0000.000
194B304HOH 00.0220.01428.170-0.002-0.0020.0000.0000.0000.000
195B309HOH 00.008-0.01428.071-0.003-0.0030.0000.0000.0000.000
196B317HOH 0-0.041-0.03134.154-0.002-0.0020.0000.0000.0000.000
197B319HOH 0-0.020-0.00229.6200.0030.0030.0000.0000.0000.000
198B326HOH 0-0.020-0.01331.7650.0020.0020.0000.0000.0000.000
199B332HOH 00.000-0.01815.8790.0210.0210.0000.0000.0000.000
200B337HOH 0-0.025-0.02635.1410.0020.0020.0000.0000.0000.000
201B342HOH 00.0280.01831.9000.0010.0010.0000.0000.0000.000
202B343HOH 00.0140.00328.409-0.002-0.0020.0000.0000.0000.000
203B346HOH 0-0.014-0.01330.1110.0010.0010.0000.0000.0000.000
204B352HOH 00.005-0.00530.621-0.002-0.0020.0000.0000.0000.000
205B357HOH 0-0.015-0.02828.7470.0000.0000.0000.0000.0000.000
206B359HOH 00.0110.00234.5610.0010.0010.0000.0000.0000.000
207B370HOH 0-0.026-0.01829.1090.0000.0000.0000.0000.0000.000