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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 9GYJ2

Calculation Name: 5RSG-B-Xray89

Preferred Name:

Target Type:

Ligand Name: n-methyl-n-7h-pyrrolo[2,3-d]pyrimidin-4-yl-beta-alanine

ligand 3-letter code: W5J

PDB ID: 5RSG

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 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1786674.056645
FMO2-HF: Nuclear repulsion 1720291.813796
FMO2-HF: Total energy -66382.242849
FMO2-MP2: Total energy -66575.821543


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.
-1.7340.816-0.007-1.165-1.3780.006
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 : 0.004 / q_NPA : 0.004
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 00.0400.0163.676-0.7311.819-0.007-1.165-1.3780.006
4B4ASN 0-0.004-0.0105.941-0.586-0.5860.0000.0000.0000.000
5B5SER 00.0250.0228.173-0.239-0.2390.0000.0000.0000.000
6B6PHE 0-0.019-0.01510.1300.1200.1200.0000.0000.0000.000
7B7SER 00.014-0.00213.880-0.046-0.0460.0000.0000.0000.000
8B8GLY 00.0190.00515.8360.0490.0490.0000.0000.0000.000
9B9TYR 0-0.078-0.05816.5790.0300.0300.0000.0000.0000.000
10B10LEU 00.0160.02120.945-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8560.92022.9800.1950.1950.0000.0000.0000.000
12B12LEU 0-0.043-0.00824.9550.0070.0070.0000.0000.0000.000
13B13THR 00.039-0.00426.5440.0010.0010.0000.0000.0000.000
14B14ASP -1-0.873-0.94325.355-0.162-0.1620.0000.0000.0000.000
15B15ASN 0-0.046-0.02122.429-0.021-0.0210.0000.0000.0000.000
16B16VAL 00.0160.01822.2990.0100.0100.0000.0000.0000.000
17B17TYR 00.0060.00620.643-0.022-0.0220.0000.0000.0000.000
18B18ILE 00.0150.01122.7030.0200.0200.0000.0000.0000.000
19B19LYS 10.8380.89917.8580.0970.0970.0000.0000.0000.000
20B20ASN 0-0.044-0.01222.8010.0120.0120.0000.0000.0000.000
21B21ALA 00.005-0.01519.956-0.008-0.0080.0000.0000.0000.000
22B22ASP -1-0.811-0.88921.0030.0870.0870.0000.0000.0000.000
23B23ILE 00.0350.00718.6920.0020.0020.0000.0000.0000.000
24B24VAL 00.0160.01417.4290.0250.0250.0000.0000.0000.000
25B25GLU -1-0.813-0.89416.1470.1720.1720.0000.0000.0000.000
26B26GLU -1-0.767-0.85415.133-0.086-0.0860.0000.0000.0000.000
27B27ALA 0-0.0020.00113.356-0.012-0.0120.0000.0000.0000.000
28B28LYS 10.8440.90811.433-0.133-0.1330.0000.0000.0000.000
29B29LYS 10.7740.88510.4410.1450.1450.0000.0000.0000.000
30B30VAL 0-0.071-0.0339.589-0.072-0.0720.0000.0000.0000.000
31B31LYS 10.9530.9945.245-0.376-0.3760.0000.0000.0000.000
32B32PRO 00.0250.0307.9220.1450.1450.0000.0000.0000.000
33B33THR 00.007-0.00110.2080.2430.2430.0000.0000.0000.000
34B34VAL 0-0.006-0.00810.9270.0320.0320.0000.0000.0000.000
35B35VAL 0-0.0120.00314.615-0.051-0.0510.0000.0000.0000.000
36B36VAL 0-0.007-0.00316.5980.0120.0120.0000.0000.0000.000
37B37ASN 00.003-0.02920.353-0.015-0.0150.0000.0000.0000.000
38B38ALA 0-0.0170.01422.781-0.009-0.0090.0000.0000.0000.000
39B39ALA 00.0410.03826.0500.0000.0000.0000.0000.0000.000
40B40ASN 00.015-0.00727.808-0.010-0.0100.0000.0000.0000.000
41B41VAL 00.0410.01430.4910.0080.0080.0000.0000.0000.000
42B42TYR 00.0360.01432.4290.0030.0030.0000.0000.0000.000
43B43LEU 0-0.030-0.00326.3740.0060.0060.0000.0000.0000.000
44B44LYS 10.8600.93828.904-0.100-0.1000.0000.0000.0000.000
45B45HIS 00.0050.00125.586-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0290.02428.3730.0030.0030.0000.0000.0000.000
47B47GLY 00.0250.00030.3350.0010.0010.0000.0000.0000.000
48B48GLY 00.0060.00228.9500.0040.0040.0000.0000.0000.000
49B49VAL 00.0630.02523.0030.0070.0070.0000.0000.0000.000
50B50ALA 00.0090.01824.1330.0140.0140.0000.0000.0000.000
51B51GLY 0-0.0040.01224.9640.0140.0140.0000.0000.0000.000
52B52ALA 0-0.037-0.02923.5080.0090.0090.0000.0000.0000.000
53B53LEU 00.013-0.00318.7410.0150.0150.0000.0000.0000.000
54B54ASN 00.0690.02320.7300.0370.0370.0000.0000.0000.000
55B55LYS 10.9290.97022.766-0.103-0.1030.0000.0000.0000.000
56B56ALA 00.0140.02218.4700.0070.0070.0000.0000.0000.000
57B57THR 0-0.041-0.01117.8390.0250.0250.0000.0000.0000.000
58B58ASN 0-0.024-0.01819.681-0.007-0.0070.0000.0000.0000.000
59B59ASN 0-0.019-0.00922.755-0.011-0.0110.0000.0000.0000.000
60B60ALA 00.0510.03920.367-0.009-0.0090.0000.0000.0000.000
61B61MET 00.0400.03819.670-0.012-0.0120.0000.0000.0000.000
62B62GLN 0-0.041-0.03322.351-0.014-0.0140.0000.0000.0000.000
63B63VAL 0-0.0050.00525.346-0.010-0.0100.0000.0000.0000.000
64B64GLU -1-0.720-0.83820.4540.2830.2830.0000.0000.0000.000
65B65SER 00.000-0.00524.681-0.010-0.0100.0000.0000.0000.000
66B66ASP -1-0.815-0.88726.4870.1100.1100.0000.0000.0000.000
67B67ASP -1-0.868-0.90727.2850.1570.1570.0000.0000.0000.000
68B68TYR 00.0600.01726.007-0.008-0.0080.0000.0000.0000.000
69B69ILE 0-0.050-0.02328.281-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.036-0.00631.610-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.033-0.00330.136-0.007-0.0070.0000.0000.0000.000
72B72ASN 0-0.088-0.05528.602-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.0210.00232.379-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.059-0.03332.5940.0060.0060.0000.0000.0000.000
75B75LEU 0-0.023-0.01027.657-0.003-0.0030.0000.0000.0000.000
76B76LYS 10.9930.99032.184-0.053-0.0530.0000.0000.0000.000
77B77VAL 00.0300.00332.6370.0040.0040.0000.0000.0000.000
78B78GLY 00.0020.01132.033-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0010.01729.989-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.040-0.04824.7760.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0180.02124.686-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0180.01718.2210.0030.0030.0000.0000.0000.000
83B83LEU 00.0030.01120.006-0.004-0.0040.0000.0000.0000.000
84B84SER 00.0430.02116.3210.0570.0570.0000.0000.0000.000
85B85GLY 00.0180.02114.484-0.054-0.0540.0000.0000.0000.000
86B86HIS 0-0.045-0.03714.7670.0150.0150.0000.0000.0000.000
87B87ASN 0-0.039-0.02912.5460.0940.0940.0000.0000.0000.000
88B88LEU 0-0.025-0.00512.618-0.016-0.0160.0000.0000.0000.000
89B89ALA 00.0310.01710.909-0.029-0.0290.0000.0000.0000.000
90B90LYS 10.9140.9909.531-0.756-0.7560.0000.0000.0000.000
91B91HIS 00.015-0.00811.394-0.025-0.0250.0000.0000.0000.000
92B92CYS 0-0.027-0.01015.038-0.020-0.0200.0000.0000.0000.000
93B93LEU 0-0.0300.00418.020-0.010-0.0100.0000.0000.0000.000
94B94HIS 00.0490.00520.573-0.036-0.0360.0000.0000.0000.000
95B95VAL 0-0.001-0.00523.739-0.007-0.0070.0000.0000.0000.000
96B96VAL 0-0.0300.01226.324-0.001-0.0010.0000.0000.0000.000
97B97GLY 00.0220.00829.993-0.006-0.0060.0000.0000.0000.000
98B98PRO 0-0.0130.00531.6780.0040.0040.0000.0000.0000.000
99B99ASN 0-0.0020.00034.585-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0800.03836.4370.0000.0000.0000.0000.0000.000
101B101ASN 0-0.038-0.01537.398-0.004-0.0040.0000.0000.0000.000
102B102LYS 10.7630.87836.482-0.049-0.0490.0000.0000.0000.000
103B103GLY 00.0020.00941.0810.0000.0000.0000.0000.0000.000
104B104GLU -1-0.820-0.87636.8420.0450.0450.0000.0000.0000.000
105B105ASP -1-0.829-0.91640.5440.0120.0120.0000.0000.0000.000
106B106ILE 00.0360.00236.4500.0020.0020.0000.0000.0000.000
107B107GLN 0-0.023-0.01237.3810.0010.0010.0000.0000.0000.000
108B108LEU 00.014-0.00335.719-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.031-0.01631.3950.0040.0040.0000.0000.0000.000
110B110LYS 10.8730.93031.8250.0150.0150.0000.0000.0000.000
111B111SER 00.0300.01631.400-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0240.00829.7360.0040.0040.0000.0000.0000.000
113B113TYR 00.027-0.01326.3100.0080.0080.0000.0000.0000.000
114B114GLU -1-0.874-0.91826.5850.0040.0040.0000.0000.0000.000
115B115ASN 0-0.023-0.00324.9560.0060.0060.0000.0000.0000.000
116B116PHE 00.023-0.01422.2520.0130.0130.0000.0000.0000.000
117B117ASN 0-0.044-0.01921.635-0.014-0.0140.0000.0000.0000.000
118B118GLN 0-0.0300.01122.102-0.009-0.0090.0000.0000.0000.000
119B119HIS 00.0050.00217.1900.0320.0320.0000.0000.0000.000
120B120GLU -1-0.840-0.90315.531-0.105-0.1050.0000.0000.0000.000
121B121VAL 0-0.016-0.01312.775-0.042-0.0420.0000.0000.0000.000
122B122LEU 0-0.0090.02715.1840.0720.0720.0000.0000.0000.000
123B123LEU 0-0.0050.01514.751-0.044-0.0440.0000.0000.0000.000
124B124ALA 00.003-0.01017.1050.0350.0350.0000.0000.0000.000
125B125PRO 0-0.0030.01220.704-0.018-0.0180.0000.0000.0000.000
126B126LEU 00.0060.00323.863-0.002-0.0020.0000.0000.0000.000
127B127LEU 00.0220.02225.8330.0070.0070.0000.0000.0000.000
128B128SER 00.009-0.02528.756-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0160.02629.998-0.003-0.0030.0000.0000.0000.000
130B130GLY 00.0360.01731.7210.0070.0070.0000.0000.0000.000
131B131ILE 0-0.005-0.00831.377-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.059-0.01930.7820.0010.0010.0000.0000.0000.000
133B133GLY 00.0250.01334.546-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.0130.00234.754-0.003-0.0030.0000.0000.0000.000
135B135ASP -1-0.821-0.91535.798-0.006-0.0060.0000.0000.0000.000
136B136PRO 0-0.027-0.02132.263-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.008-0.00432.656-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0590.03234.583-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.026-0.02930.650-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.018-0.01028.3190.0000.0000.0000.0000.0000.000
141B141ARG 10.8190.87630.8210.0340.0340.0000.0000.0000.000
142B142VAL 00.0270.01831.824-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0130.00526.4880.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0140.00128.394-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.762-0.83229.608-0.043-0.0430.0000.0000.0000.000
146B146THR 0-0.114-0.06129.1820.0030.0030.0000.0000.0000.000
147B147VAL 0-0.058-0.01823.4300.0030.0030.0000.0000.0000.000
148B148ARG 10.9230.97225.4030.0270.0270.0000.0000.0000.000
149B149THR 0-0.0160.01819.866-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.033-0.00817.552-0.010-0.0100.0000.0000.0000.000
151B151VAL 00.0400.01718.3850.0230.0230.0000.0000.0000.000
152B152TYR 0-0.020-0.00916.555-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.020-0.00119.4490.0310.0310.0000.0000.0000.000
154B154ALA 00.0030.00019.891-0.016-0.0160.0000.0000.0000.000
155B155VAL 0-0.030-0.01821.9780.0130.0130.0000.0000.0000.000
156B156PHE 00.0250.01424.599-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.790-0.89226.123-0.006-0.0060.0000.0000.0000.000
158B158LYS 10.8650.91429.0390.0440.0440.0000.0000.0000.000
159B159ASN 0-0.012-0.02830.077-0.009-0.0090.0000.0000.0000.000
160B160LEU 0-0.0010.00830.528-0.002-0.0020.0000.0000.0000.000
161B161TYR 0-0.021-0.01925.488-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.762-0.85429.873-0.050-0.0500.0000.0000.0000.000
163B163LYS 10.9481.01432.7250.0120.0120.0000.0000.0000.000
164B164LEU 0-0.0310.00329.460-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0320.00528.929-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.076-0.04731.792-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.013-0.02435.369-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.0080.00731.2640.0020.0020.0000.0000.0000.000
169B169LEU -1-0.914-0.93234.127-0.056-0.0560.0000.0000.0000.000
170B212HOH 0-0.066-0.04511.8590.0410.0410.0000.0000.0000.000
171B216HOH 0-0.038-0.03238.8130.0020.0020.0000.0000.0000.000
172B218HOH 0-0.005-0.01233.7190.0010.0010.0000.0000.0000.000
173B230HOH 0-0.035-0.03011.484-0.024-0.0240.0000.0000.0000.000
174B234HOH 0-0.043-0.03427.7130.0000.0000.0000.0000.0000.000
175B249HOH 0-0.081-0.06625.3370.0050.0050.0000.0000.0000.000
176B251HOH 0-0.037-0.02931.1040.0020.0020.0000.0000.0000.000
177B254HOH 0-0.041-0.03034.8450.0010.0010.0000.0000.0000.000
178B255HOH 0-0.011-0.03519.454-0.014-0.0140.0000.0000.0000.000
179B256HOH 00.0240.00029.553-0.002-0.0020.0000.0000.0000.000
180B257HOH 0-0.026-0.03513.7530.0000.0000.0000.0000.0000.000
181B258HOH 0-0.021-0.02322.8840.0040.0040.0000.0000.0000.000
182B260HOH 0-0.010-0.01328.458-0.004-0.0040.0000.0000.0000.000
183B268HOH 00.0150.00324.0560.0060.0060.0000.0000.0000.000
184B269HOH 00.000-0.00322.1890.0030.0030.0000.0000.0000.000
185B270HOH 0-0.067-0.05029.104-0.003-0.0030.0000.0000.0000.000
186B272HOH 0-0.025-0.02428.3940.0010.0010.0000.0000.0000.000
187B276HOH 0-0.086-0.06337.036-0.001-0.0010.0000.0000.0000.000
188B277HOH 0-0.022-0.00827.476-0.002-0.0020.0000.0000.0000.000
189B278HOH 0-0.033-0.03022.9090.0000.0000.0000.0000.0000.000
190B280HOH 0-0.030-0.03023.0720.0060.0060.0000.0000.0000.000
191B281HOH 0-0.018-0.03112.5230.0320.0320.0000.0000.0000.000
192B289HOH 00.0210.01428.062-0.002-0.0020.0000.0000.0000.000
193B296HOH 00.007-0.01527.948-0.003-0.0030.0000.0000.0000.000
194B299HOH 0-0.015-0.00915.3630.0140.0140.0000.0000.0000.000
195B311HOH 0-0.040-0.03134.011-0.002-0.0020.0000.0000.0000.000
196B320HOH 00.0020.00331.6690.0030.0030.0000.0000.0000.000
197B322HOH 0-0.030-0.03234.8210.0020.0020.0000.0000.0000.000
198B324HOH 0-0.019-0.00229.5740.0030.0030.0000.0000.0000.000
199B325HOH 00.000-0.01815.7950.0190.0190.0000.0000.0000.000
200B328HOH 00.0140.00528.357-0.003-0.0030.0000.0000.0000.000
201B332HOH 00.0360.02433.7100.0020.0020.0000.0000.0000.000
202B334HOH 00.0270.01831.6710.0010.0010.0000.0000.0000.000
203B335HOH 00.0170.00730.0760.0020.0020.0000.0000.0000.000
204B338HOH 00.006-0.00530.584-0.002-0.0020.0000.0000.0000.000
205B350HOH 0-0.016-0.02828.658-0.001-0.0010.0000.0000.0000.000
206B355HOH 0-0.029-0.02028.9090.0000.0000.0000.0000.0000.000