FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LJL89

Calculation Name: 5RT0-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 6-methyl-1h-indole-2-carboxylic acid

ligand 3-letter code: 4BL

PDB ID: 5RT0

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1777535.78794
FMO2-HF: Nuclear repulsion 1711381.668786
FMO2-HF: Total energy -66154.119154
FMO2-MP2: Total energy -66347.123853


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.
-1.9280.606-0.016-1.111-1.4080.006
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 : -0.001 / q_NPA : 0.002
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 00.0370.0133.769-0.6841.850-0.016-1.111-1.4080.006
4B4ASN 0-0.003-0.0106.022-0.581-0.5810.0000.0000.0000.000
5B5SER 00.0170.0167.976-0.155-0.1550.0000.0000.0000.000
6B6PHE 0-0.023-0.01310.0120.0900.0900.0000.0000.0000.000
7B7SER 00.0310.00713.787-0.050-0.0500.0000.0000.0000.000
8B8GLY 00.0250.00715.6900.0500.0500.0000.0000.0000.000
9B9TYR 0-0.083-0.05716.5820.0290.0290.0000.0000.0000.000
10B10LEU 00.0280.02720.803-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8420.91522.8340.1920.1920.0000.0000.0000.000
12B12LEU 0-0.035-0.00424.8570.0060.0060.0000.0000.0000.000
13B13THR 00.032-0.00926.5480.0010.0010.0000.0000.0000.000
14B14ASP -1-0.868-0.94625.443-0.160-0.1600.0000.0000.0000.000
15B15ASN 0-0.049-0.02122.451-0.021-0.0210.0000.0000.0000.000
16B16VAL 00.0230.02322.3120.0100.0100.0000.0000.0000.000
17B17TYR 0-0.0060.00020.603-0.022-0.0220.0000.0000.0000.000
18B18ILE 00.0130.01322.7030.0210.0210.0000.0000.0000.000
19B19LYS 10.8510.90517.7690.0780.0780.0000.0000.0000.000
20B20ASN 0-0.053-0.01522.8110.0120.0120.0000.0000.0000.000
21B21ALA 00.022-0.00819.953-0.007-0.0070.0000.0000.0000.000
22B22ASP -1-0.780-0.87120.9150.1010.1010.0000.0000.0000.000
23B23ILE 00.0370.00518.6980.0050.0050.0000.0000.0000.000
24B24VAL 00.0010.00417.4120.0290.0290.0000.0000.0000.000
25B25GLU -1-0.949-0.97416.1460.1050.1050.0000.0000.0000.000
26B26GLU -1-0.777-0.86515.055-0.056-0.0560.0000.0000.0000.000
27B27ALA 0-0.0030.00013.348-0.006-0.0060.0000.0000.0000.000
28B28LYS 10.9270.96911.424-0.189-0.1890.0000.0000.0000.000
29B29LYS 10.7930.89610.3990.1300.1300.0000.0000.0000.000
30B30VAL 0-0.082-0.0389.522-0.065-0.0650.0000.0000.0000.000
31B31LYS 10.9751.0065.103-0.521-0.5210.0000.0000.0000.000
32B32PRO 00.0130.0237.9870.1470.1470.0000.0000.0000.000
33B33THR 00.0160.00310.2720.2380.2380.0000.0000.0000.000
34B34VAL 0-0.016-0.01510.9860.0290.0290.0000.0000.0000.000
35B35VAL 0-0.0070.00614.675-0.048-0.0480.0000.0000.0000.000
36B36VAL 0-0.009-0.00316.6050.0100.0100.0000.0000.0000.000
37B37ASN 00.005-0.02720.389-0.014-0.0140.0000.0000.0000.000
38B38ALA 0-0.0070.02022.796-0.009-0.0090.0000.0000.0000.000
39B39ALA 00.0280.03026.0450.0000.0000.0000.0000.0000.000
40B40ASN 00.019-0.00427.810-0.010-0.0100.0000.0000.0000.000
41B41VAL 00.0240.00730.5190.0080.0080.0000.0000.0000.000
42B42TYR 00.0410.02032.4730.0020.0020.0000.0000.0000.000
43B43LEU 0-0.039-0.00926.4300.0060.0060.0000.0000.0000.000
44B44LYS 10.8640.94128.955-0.102-0.1020.0000.0000.0000.000
45B45HIS 0-0.001-0.00425.612-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0300.02328.3700.0030.0030.0000.0000.0000.000
47B47GLY 00.0260.00330.3410.0010.0010.0000.0000.0000.000
48B48GLY 00.0090.00128.9540.0050.0050.0000.0000.0000.000
49B49VAL 00.0650.02823.0110.0080.0080.0000.0000.0000.000
50B50ALA 00.0150.01924.1270.0150.0150.0000.0000.0000.000
51B51GLY 0-0.0140.00724.9580.0150.0150.0000.0000.0000.000
52B52ALA 0-0.039-0.03223.4820.0100.0100.0000.0000.0000.000
53B53LEU 00.0200.00418.7440.0160.0160.0000.0000.0000.000
54B54ASN 00.0610.01720.7310.0370.0370.0000.0000.0000.000
55B55LYS 10.9300.97122.752-0.110-0.1100.0000.0000.0000.000
56B56ALA 0-0.0030.01618.4610.0080.0080.0000.0000.0000.000
57B57THR 0-0.039-0.01417.7950.0260.0260.0000.0000.0000.000
58B58ASN 0-0.022-0.01619.651-0.005-0.0050.0000.0000.0000.000
59B59ASN 0-0.015-0.00922.755-0.011-0.0110.0000.0000.0000.000
60B60ALA 00.0430.03220.387-0.009-0.0090.0000.0000.0000.000
61B61MET 00.0130.02019.663-0.013-0.0130.0000.0000.0000.000
62B62GLN 0-0.039-0.03322.369-0.015-0.0150.0000.0000.0000.000
63B63VAL 0-0.010-0.00125.321-0.010-0.0100.0000.0000.0000.000
64B64GLU -1-0.711-0.83220.5330.2820.2820.0000.0000.0000.000
65B65SER 0-0.023-0.02224.709-0.011-0.0110.0000.0000.0000.000
66B66ASP -1-0.822-0.89326.5440.1110.1110.0000.0000.0000.000
67B67ASP -1-0.908-0.94227.3640.1490.1490.0000.0000.0000.000
68B68TYR 00.0440.00826.131-0.008-0.0080.0000.0000.0000.000
69B69ILE 0-0.033-0.01628.406-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.0260.00031.675-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.037-0.00730.250-0.007-0.0070.0000.0000.0000.000
72B72ASN 0-0.096-0.06128.706-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.0170.00732.452-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.054-0.03332.6600.0060.0060.0000.0000.0000.000
75B75LEU 0-0.032-0.01627.737-0.003-0.0030.0000.0000.0000.000
76B76LYS 11.0020.99532.274-0.052-0.0520.0000.0000.0000.000
77B77VAL 00.019-0.00232.6810.0040.0040.0000.0000.0000.000
78B78GLY 00.0120.01632.105-0.005-0.0050.0000.0000.0000.000
79B79GLY 0-0.0050.01630.019-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.044-0.05324.8510.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0150.02324.768-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0130.01418.3050.0040.0040.0000.0000.0000.000
83B83LEU 0-0.0050.00820.078-0.005-0.0050.0000.0000.0000.000
84B84SER 00.0360.01516.3750.0570.0570.0000.0000.0000.000
85B85GLY 00.0090.01614.437-0.052-0.0520.0000.0000.0000.000
86B86HIS 0-0.040-0.03314.7430.0170.0170.0000.0000.0000.000
87B87ASN 0-0.059-0.04212.5210.0810.0810.0000.0000.0000.000
88B88LEU 0-0.033-0.01612.612-0.014-0.0140.0000.0000.0000.000
89B89ALA 00.0280.01710.926-0.027-0.0270.0000.0000.0000.000
90B90LYS 10.9090.9789.586-0.739-0.7390.0000.0000.0000.000
91B91HIS 00.011-0.00611.446-0.030-0.0300.0000.0000.0000.000
92B92CYS 0-0.031-0.01615.101-0.019-0.0190.0000.0000.0000.000
93B93LEU 0-0.0310.00618.034-0.011-0.0110.0000.0000.0000.000
94B94HIS 00.0510.00720.640-0.035-0.0350.0000.0000.0000.000
95B95VAL 00.007-0.00123.792-0.007-0.0070.0000.0000.0000.000
96B96VAL 0-0.0320.01026.3730.0000.0000.0000.0000.0000.000
97B97GLY 00.0350.01930.000-0.007-0.0070.0000.0000.0000.000
98B98PRO 0-0.0010.01331.6940.0050.0050.0000.0000.0000.000
99B99ASN 00.0100.01034.678-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0840.03836.4900.0000.0000.0000.0000.0000.000
101B101ASN 0-0.042-0.01937.417-0.005-0.0050.0000.0000.0000.000
102B102LYS 10.7610.88036.402-0.052-0.0520.0000.0000.0000.000
103B103GLY 00.0050.01041.0970.0000.0000.0000.0000.0000.000
104B104GLU -1-0.832-0.87236.8400.0460.0460.0000.0000.0000.000
105B105ASP -1-0.810-0.91240.5290.0140.0140.0000.0000.0000.000
106B106ILE 00.0270.00136.5230.0020.0020.0000.0000.0000.000
107B107GLN 0-0.033-0.02037.4400.0010.0010.0000.0000.0000.000
108B108LEU 00.0190.00235.749-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.030-0.01231.4030.0040.0040.0000.0000.0000.000
110B110LYS 10.8800.93031.8780.0140.0140.0000.0000.0000.000
111B111SER 00.0220.00331.440-0.001-0.0010.0000.0000.0000.000
112B112ALA 0-0.009-0.00329.7770.0040.0040.0000.0000.0000.000
113B113TYR 00.023-0.01326.3320.0080.0080.0000.0000.0000.000
114B114GLU -1-0.870-0.91726.6080.0030.0030.0000.0000.0000.000
115B115ASN 0-0.052-0.01624.9740.0050.0050.0000.0000.0000.000
116B116PHE 00.045-0.00122.2900.0130.0130.0000.0000.0000.000
117B117ASN 0-0.035-0.01521.660-0.013-0.0130.0000.0000.0000.000
118B118GLN 0-0.0410.00522.154-0.009-0.0090.0000.0000.0000.000
119B119HIS 00.0030.00217.2650.0300.0300.0000.0000.0000.000
120B120GLU -1-0.838-0.90515.591-0.108-0.1080.0000.0000.0000.000
121B121VAL 0-0.018-0.01112.817-0.042-0.0420.0000.0000.0000.000
122B122LEU 0-0.0100.02715.2370.0720.0720.0000.0000.0000.000
123B123LEU 0-0.0040.01514.776-0.043-0.0430.0000.0000.0000.000
124B124ALA 00.006-0.00717.1220.0340.0340.0000.0000.0000.000
125B125PRO 00.0000.01520.722-0.017-0.0170.0000.0000.0000.000
126B126LEU 00.0140.00423.873-0.002-0.0020.0000.0000.0000.000
127B127LEU 00.0140.01925.8520.0070.0070.0000.0000.0000.000
128B128SER 00.015-0.02328.753-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0160.02529.975-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0320.01431.7360.0070.0070.0000.0000.0000.000
131B131ILE 00.001-0.00531.348-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.073-0.02630.6820.0000.0000.0000.0000.0000.000
133B133GLY 00.0310.01334.527-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.024-0.00434.729-0.004-0.0040.0000.0000.0000.000
135B135ASP -1-0.812-0.90935.852-0.003-0.0030.0000.0000.0000.000
136B136PRO 0-0.029-0.02132.306-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.017-0.00132.688-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0610.03534.597-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.030-0.03330.687-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.020-0.01028.3250.0000.0000.0000.0000.0000.000
141B141ARG 10.8570.90330.8460.0320.0320.0000.0000.0000.000
142B142VAL 00.0180.01331.866-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0100.00926.4870.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0080.00328.402-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.763-0.83229.606-0.042-0.0420.0000.0000.0000.000
146B146THR 0-0.112-0.06429.1940.0020.0020.0000.0000.0000.000
147B147VAL 0-0.061-0.01723.4680.0020.0020.0000.0000.0000.000
148B148ARG 10.9240.96925.4550.0260.0260.0000.0000.0000.000
149B149THR 0-0.0250.01419.893-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.030-0.00517.622-0.009-0.0090.0000.0000.0000.000
151B151VAL 00.0350.01118.4570.0240.0240.0000.0000.0000.000
152B152TYR 0-0.022-0.00816.607-0.027-0.0270.0000.0000.0000.000
153B153LEU 00.0270.00119.4600.0310.0310.0000.0000.0000.000
154B154ALA 0-0.002-0.00219.933-0.015-0.0150.0000.0000.0000.000
155B155VAL 0-0.022-0.01722.0140.0130.0130.0000.0000.0000.000
156B156PHE 00.0190.01224.635-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.793-0.89326.1560.0000.0000.0000.0000.0000.000
158B158LYS 10.8750.92028.9560.0370.0370.0000.0000.0000.000
159B159ASN 0-0.014-0.02730.094-0.009-0.0090.0000.0000.0000.000
160B160LEU 0-0.0120.00130.553-0.003-0.0030.0000.0000.0000.000
161B161TYR 0-0.018-0.01925.498-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.762-0.85629.892-0.044-0.0440.0000.0000.0000.000
163B163LYS 10.9461.00932.7170.0090.0090.0000.0000.0000.000
164B164LEU 0-0.0300.00829.479-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0380.00728.896-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.059-0.03131.803-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.035-0.02935.367-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.015-0.00231.3460.0020.0020.0000.0000.0000.000
169B169LEU -1-0.865-0.89734.140-0.053-0.0530.0000.0000.0000.000
170B217HOH 0-0.042-0.03327.6410.0000.0000.0000.0000.0000.000
171B224HOH 0-0.005-0.01033.7060.0010.0010.0000.0000.0000.000
172B232HOH 0-0.033-0.02911.769-0.031-0.0310.0000.0000.0000.000
173B236HOH 0-0.060-0.04438.9340.0020.0020.0000.0000.0000.000
174B241HOH 0-0.020-0.02322.7610.0040.0040.0000.0000.0000.000
175B243HOH 0-0.025-0.03513.7830.0010.0010.0000.0000.0000.000
176B249HOH 0-0.041-0.03034.6210.0010.0010.0000.0000.0000.000
177B251HOH 0-0.011-0.01228.468-0.004-0.0040.0000.0000.0000.000
178B255HOH 0-0.050-0.05133.9280.0020.0020.0000.0000.0000.000
179B256HOH 0-0.020-0.02331.6420.0010.0010.0000.0000.0000.000
180B258HOH 00.0160.00424.1220.0060.0060.0000.0000.0000.000
181B259HOH 0-0.011-0.03419.445-0.014-0.0140.0000.0000.0000.000
182B260HOH 0-0.032-0.03023.0840.0060.0060.0000.0000.0000.000
183B265HOH 0-0.022-0.00927.479-0.002-0.0020.0000.0000.0000.000
184B266HOH 0-0.068-0.05129.065-0.003-0.0030.0000.0000.0000.000
185B270HOH 00.0230.00029.529-0.002-0.0020.0000.0000.0000.000
186B271HOH 0-0.035-0.03838.5280.0020.0020.0000.0000.0000.000
187B275HOH 0-0.016-0.01015.3990.0150.0150.0000.0000.0000.000
188B279HOH 0-0.001-0.00322.2270.0030.0030.0000.0000.0000.000
189B286HOH 0-0.075-0.05436.782-0.001-0.0010.0000.0000.0000.000
190B288HOH 0-0.023-0.02328.4110.0010.0010.0000.0000.0000.000
191B290HOH 0-0.019-0.03212.5810.0310.0310.0000.0000.0000.000
192B298HOH 00.0220.01428.066-0.002-0.0020.0000.0000.0000.000
193B309HOH 0-0.020-0.00329.4980.0030.0030.0000.0000.0000.000
194B310HOH 00.008-0.01427.964-0.003-0.0030.0000.0000.0000.000
195B313HOH 0-0.041-0.03234.079-0.002-0.0020.0000.0000.0000.000
196B319HOH 00.0040.00431.7140.0030.0030.0000.0000.0000.000
197B320HOH 00.002-0.01615.8500.0190.0190.0000.0000.0000.000
198B323HOH 00.007-0.00934.7390.0020.0020.0000.0000.0000.000
199B337HOH 00.0280.01831.7540.0010.0010.0000.0000.0000.000
200B339HOH 00.0170.00730.1090.0020.0020.0000.0000.0000.000
201B346HOH 00.0160.00628.443-0.003-0.0030.0000.0000.0000.000
202B347HOH 00.006-0.00430.652-0.002-0.0020.0000.0000.0000.000
203B351HOH 0-0.014-0.02728.6570.0000.0000.0000.0000.0000.000