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

tag_button

FMODB ID: 5333Z

Calculation Name: 5RT0-A-Xray89

Preferred Name:

Target Type:

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

ligand 3-letter code: 4BL

PDB ID: 5RT0

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 206
LigandResidueName 4BL
LigandFragmentNumber 206
LigandCharge 4BL=-1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1788646.556952
FMO2-HF: Nuclear repulsion 1722642.806854
FMO2-HF: Total energy -66003.750098
FMO2-MP2: Total energy -66197.229764


3D Structure
Snapshot
 
Ligand structure

4BL

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.
-78.848-82.34723.313-4.542-15.274-0.101


Interactive mode: IFIE and PIEDA for fragment #206(A:201:4BL )


Summations of interaction energy for fragment #206(A:201:4BL )
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.
-78.848-82.34723.313-4.542-15.2740.101
Interaction energy analysis for fragmet #206(A:201:4BL )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.900 / q_NPA : -0.942
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 00.012-0.00712.407-0.069-0.0690.0000.0000.0000.000
2A4ASN 0-0.023-0.02211.1010.8850.8850.0000.0000.0000.000
3A5SER 00.0260.0049.1140.7000.7000.0000.0000.0000.000
4A6PHE 0-0.068-0.0087.6913.6063.6060.0000.0000.0000.000
5A7SER 00.022-0.0011.727-22.740-26.19910.993-4.585-2.9490.057
6A8GLY 00.0380.0092.4061.8782.7149.555-5.838-4.5540.040
7A9TYR 0-0.116-0.0633.024-7.370-15.5550.2378.999-1.0510.007
8A10LEU 0-0.0030.0096.1530.6600.6600.0000.0000.0000.000
9A11LYS 10.8000.8898.079-21.995-21.9950.0000.0000.0000.000
10A12LEU 0-0.044-0.01111.629-0.673-0.6730.0000.0000.0000.000
11A13THR 00.0310.00714.319-0.922-0.9220.0000.0000.0000.000
12A14ASP -1-0.865-0.89616.27417.25917.2590.0000.0000.0000.000
13A15ASN 00.002-0.00317.5000.5350.5350.0000.0000.0000.000
14A16VAL 00.0070.01414.6080.5650.5650.0000.0000.0000.000
15A17TYR 00.0390.02610.2381.0831.0830.0000.0000.0000.000
16A18ILE 00.0120.0058.827-0.995-0.9950.0000.0000.0000.000
17A19LYS 10.8470.9233.054-70.822-67.3520.573-1.129-2.9150.013
18A20ASN 0-0.053-0.0272.378-4.863-3.3540.979-0.767-1.721-0.004
19A21ALA 00.009-0.0102.6632.8134.0690.872-0.750-1.378-0.009
20A22ASP -1-0.832-0.9154.90118.10018.161-0.001-0.004-0.0550.000
21A23ILE 00.012-0.0027.9341.3681.3680.0000.0000.0000.000
22A24VAL 00.0240.01710.762-0.055-0.0550.0000.0000.0000.000
23A25GLU -1-0.821-0.8977.93221.39421.3940.0000.0000.0000.000
24A26GLU -1-0.769-0.8776.73147.11847.1180.0000.0000.0000.000
25A27ALA 0-0.016-0.0179.1750.1900.1900.0000.0000.0000.000
26A28LYS 10.8190.89911.824-20.474-20.4740.0000.0000.0000.000
27A29LYS 10.8170.9195.219-44.785-44.7850.0000.0000.0000.000
28A30VAL 0-0.035-0.0279.0210.0740.0740.0000.0000.0000.000
29A31LYS 10.8620.95611.503-19.162-19.1620.0000.0000.0000.000
30A32PRO 00.0120.02513.717-0.571-0.5710.0000.0000.0000.000
31A33THR 00.032-0.00715.549-0.971-0.9710.0000.0000.0000.000
32A34VAL 0-0.022-0.01918.071-0.948-0.9480.0000.0000.0000.000
33A35VAL 00.0080.01015.6451.2731.2730.0000.0000.0000.000
34A36VAL 00.0070.00017.476-1.068-1.0680.0000.0000.0000.000
35A37ASN 0-0.007-0.02717.5320.9190.9190.0000.0000.0000.000
36A38ALA 0-0.0040.02118.311-0.367-0.3670.0000.0000.0000.000
37A39ALA 00.0390.03520.172-0.305-0.3050.0000.0000.0000.000
38A40ASN 0-0.004-0.02023.693-0.424-0.4240.0000.0000.0000.000
39A41VAL 00.0460.02226.7720.0740.0740.0000.0000.0000.000
40A42TYR 0-0.0010.00030.035-0.136-0.1360.0000.0000.0000.000
41A43LEU 00.0020.01426.734-0.007-0.0070.0000.0000.0000.000
42A44LYS 10.9761.00427.912-9.063-9.0630.0000.0000.0000.000
43A45HIS 00.0240.01722.8380.4090.4090.0000.0000.0000.000
44A46GLY 00.0380.03323.6930.1310.1310.0000.0000.0000.000
45A47GLY 00.0530.01820.759-0.017-0.0170.0000.0000.0000.000
46A48GLY 00.0260.02317.3890.0250.0250.0000.0000.0000.000
47A49VAL 00.0350.00613.9880.2310.2310.0000.0000.0000.000
48A50ALA 00.0180.02216.4260.2570.2570.0000.0000.0000.000
49A51GLY 0-0.0140.00719.895-0.113-0.1130.0000.0000.0000.000
50A52ALA 0-0.012-0.00615.055-0.155-0.1550.0000.0000.0000.000
51A53LEU 00.020-0.00115.5040.2030.2030.0000.0000.0000.000
52A54ASN 00.0630.00618.005-0.129-0.1290.0000.0000.0000.000
53A55LYS 10.9560.98718.201-13.571-13.5710.0000.0000.0000.000
54A56ALA 0-0.0220.00116.608-0.225-0.2250.0000.0000.0000.000
55A57THR 0-0.046-0.01318.566-0.065-0.0650.0000.0000.0000.000
56A58ASN 0-0.036-0.02521.717-0.499-0.4990.0000.0000.0000.000
57A59ASN 0-0.003-0.00123.820-0.354-0.3540.0000.0000.0000.000
58A60ALA 00.0350.02825.434-0.374-0.3740.0000.0000.0000.000
59A61MET 00.0140.01820.792-0.215-0.2150.0000.0000.0000.000
60A62GLN 0-0.048-0.03025.6720.0650.0650.0000.0000.0000.000
61A63VAL 00.0160.01627.767-0.296-0.2960.0000.0000.0000.000
62A64GLU -1-0.724-0.83827.44811.16511.1650.0000.0000.0000.000
63A65SER 00.004-0.00427.542-0.097-0.0970.0000.0000.0000.000
64A66ASP -1-0.864-0.92430.0499.1219.1210.0000.0000.0000.000
65A67ASP -1-0.887-0.91433.0388.4528.4520.0000.0000.0000.000
66A68TYR 00.0410.01131.982-0.150-0.1500.0000.0000.0000.000
67A69ILE 0-0.040-0.02431.722-0.210-0.2100.0000.0000.0000.000
68A70ALA 0-0.031-0.00434.959-0.233-0.2330.0000.0000.0000.000
69A71THR 0-0.038-0.00637.589-0.299-0.2990.0000.0000.0000.000
70A72ASN 0-0.092-0.05635.799-0.268-0.2680.0000.0000.0000.000
71A73GLY 00.0160.02437.515-0.091-0.0910.0000.0000.0000.000
72A74PRO 0-0.072-0.04333.8630.2550.2550.0000.0000.0000.000
73A75LEU 0-0.0050.00228.491-0.098-0.0980.0000.0000.0000.000
74A76LYS 10.9800.98332.491-8.592-8.5920.0000.0000.0000.000
75A77VAL 00.0270.00428.7760.3170.3170.0000.0000.0000.000
76A78GLY 00.0060.01428.178-0.225-0.2250.0000.0000.0000.000
77A79GLY 0-0.020-0.00129.0450.1280.1280.0000.0000.0000.000
78A80SER 0-0.017-0.03926.5640.3800.3800.0000.0000.0000.000
79A81CYS 0-0.0460.00227.466-0.323-0.3230.0000.0000.0000.000
80A82VAL 00.0150.01426.1990.5120.5120.0000.0000.0000.000
81A83LEU 0-0.0030.00526.489-0.462-0.4620.0000.0000.0000.000
82A84SER 00.0320.01425.9280.7520.7520.0000.0000.0000.000
83A85GLY 0-0.0070.01021.7120.1130.1130.0000.0000.0000.000
84A86HIS 0-0.030-0.03120.8950.6660.6660.0000.0000.0000.000
85A87ASN 0-0.024-0.02719.1520.0370.0370.0000.0000.0000.000
86A88LEU 0-0.022-0.02115.8270.9560.9560.0000.0000.0000.000
87A89ALA 00.000-0.00116.5131.3581.3580.0000.0000.0000.000
88A90LYS 10.8520.94718.928-13.552-13.5520.0000.0000.0000.000
89A91HIS 00.0240.00821.504-0.793-0.7930.0000.0000.0000.000
90A92CYS 0-0.0070.00321.3421.0511.0510.0000.0000.0000.000
91A93LEU 0-0.0360.00321.942-0.720-0.7200.0000.0000.0000.000
92A94HIS 00.0480.00022.2020.5720.5720.0000.0000.0000.000
93A95VAL 00.0130.00022.442-0.538-0.5380.0000.0000.0000.000
94A96VAL 0-0.0310.01323.4090.2460.2460.0000.0000.0000.000
95A97GLY 00.0500.02923.764-0.197-0.1970.0000.0000.0000.000
96A98PRO 0-0.0100.00724.748-0.178-0.1780.0000.0000.0000.000
97A99ASN 0-0.0020.01024.9570.2330.2330.0000.0000.0000.000
98A100VAL 00.0740.03025.218-0.401-0.4010.0000.0000.0000.000
99A101ASN 0-0.057-0.02724.049-0.504-0.5040.0000.0000.0000.000
100A102LYS 10.8000.89828.039-9.687-9.6870.0000.0000.0000.000
101A103GLY 0-0.0080.00230.448-0.240-0.2400.0000.0000.0000.000
102A104GLU -1-0.794-0.84429.1109.4879.4870.0000.0000.0000.000
103A105ASP -1-0.812-0.91030.2489.0839.0830.0000.0000.0000.000
104A106ILE 00.0470.01024.6200.2540.2540.0000.0000.0000.000
105A107GLN 00.0120.00827.7610.5400.5400.0000.0000.0000.000
106A108LEU 0-0.043-0.02529.5150.1840.1840.0000.0000.0000.000
107A109LEU 0-0.024-0.01921.9910.2510.2510.0000.0000.0000.000
108A110LYS 10.8930.93625.297-10.689-10.6890.0000.0000.0000.000
109A111SER 00.0250.00527.0660.1690.1690.0000.0000.0000.000
110A112ALA 00.0230.01024.8100.1100.1100.0000.0000.0000.000
111A113TYR 00.030-0.00318.5530.5690.5690.0000.0000.0000.000
112A114GLU -1-0.812-0.86124.08110.73110.7310.0000.0000.0000.000
113A115ASN 0-0.070-0.02425.542-0.223-0.2230.0000.0000.0000.000
114A116PHE 00.040-0.00818.3920.1400.1400.0000.0000.0000.000
115A117ASN 0-0.0150.00023.3170.6650.6650.0000.0000.0000.000
116A118GLN 0-0.0450.00325.456-0.296-0.2960.0000.0000.0000.000
117A119HIS 0-0.041-0.02921.9360.2330.2330.0000.0000.0000.000
118A120GLU -1-0.874-0.93221.31314.23814.2380.0000.0000.0000.000
119A121VAL 00.011-0.00815.0700.7780.7780.0000.0000.0000.000
120A122LEU 0-0.0450.02016.793-0.635-0.6350.0000.0000.0000.000
121A123LEU 0-0.0100.01911.3141.0561.0560.0000.0000.0000.000
122A124ALA 00.028-0.00514.123-1.531-1.5310.0000.0000.0000.000
123A125PRO 0-0.0360.00213.1991.3831.3830.0000.0000.0000.000
124A126LEU 00.0370.01413.589-0.519-0.5190.0000.0000.0000.000
125A127LEU 00.0030.02015.873-0.512-0.5120.0000.0000.0000.000
126A128SER 00.035-0.00819.427-0.048-0.0480.0000.0000.0000.000
127A129ALA 0-0.0110.01216.220-0.375-0.3750.0000.0000.0000.000
128A130GLY 00.0340.02816.923-0.150-0.1500.0000.0000.0000.000
129A131ILE 00.013-0.01617.409-0.469-0.4690.0000.0000.0000.000
130A132PHE 0-0.088-0.03420.383-0.537-0.5370.0000.0000.0000.000
131A133GLY 00.0180.01721.294-0.373-0.3730.0000.0000.0000.000
132A134ALA 00.0010.00221.657-0.315-0.3150.0000.0000.0000.000
133A135ASP -1-0.795-0.89619.62313.10313.1030.0000.0000.0000.000
134A136PRO 0-0.014-0.01915.1330.1160.1160.0000.0000.0000.000
135A137ILE 00.0220.00916.5820.5900.5900.0000.0000.0000.000
136A138HIS 00.0410.02617.9440.2500.2500.0000.0000.0000.000
137A139SER 0-0.018-0.02917.9980.1650.1650.0000.0000.0000.000
138A140LEU 0-0.0070.00013.7870.1970.1970.0000.0000.0000.000
139A141ARG 10.8450.91817.461-13.319-13.3190.0000.0000.0000.000
140A142VAL 0-0.0020.00720.636-0.165-0.1650.0000.0000.0000.000
141A143CYS 0-0.0190.00917.180-0.103-0.1030.0000.0000.0000.000
142A144VAL 00.0210.01917.861-0.007-0.0070.0000.0000.0000.000
143A145ASP -1-0.804-0.89420.43712.39112.3910.0000.0000.0000.000
144A146THR 0-0.132-0.07523.350-0.913-0.9130.0000.0000.0000.000
145A147VAL 0-0.044-0.00620.442-0.379-0.3790.0000.0000.0000.000
146A148ARG 10.9120.96122.266-11.437-11.4370.0000.0000.0000.000
147A149THR 0-0.0300.01021.1860.2050.2050.0000.0000.0000.000
148A150ASN 0-0.0210.00115.9430.7790.7790.0000.0000.0000.000
149A151VAL 00.010-0.00315.8040.1260.1260.0000.0000.0000.000
150A152TYR 00.0330.0329.792-0.001-0.0010.0000.0000.0000.000
151A153LEU 00.013-0.01211.896-0.763-0.7630.0000.0000.0000.000
152A154ALA 00.0260.0158.4452.5482.5480.0000.0000.0000.000
153A155VAL 0-0.019-0.0107.628-2.869-2.8690.0000.0000.0000.000
154A156PHE 00.003-0.0046.5251.4411.4410.0000.0000.0000.000
155A157ASP -1-0.795-0.9036.80018.02918.0290.0000.0000.0000.000
156A158LYS 10.8640.9194.073-25.595-25.4490.000-0.018-0.1280.000
157A159ASN 0-0.028-0.0196.758-0.189-0.1890.0000.0000.0000.000
158A160LEU 00.0090.00110.172-0.289-0.2890.0000.0000.0000.000
159A161TYR 0-0.021-0.0095.6650.3290.3290.0000.0000.0000.000
160A162ASP -1-0.766-0.8577.22923.29223.2920.0000.0000.0000.000
161A163LYS 10.9410.9859.363-14.263-14.2630.0000.0000.0000.000
162A164LEU 0-0.041-0.01311.011-0.716-0.7160.0000.0000.0000.000
163A165VAL 00.0180.0158.894-0.318-0.3180.0000.0000.0000.000
164A166SER 0-0.047-0.03312.006-0.627-0.6270.0000.0000.0000.000
165A167SER 0-0.111-0.07614.356-0.818-0.8180.0000.0000.0000.000
166A168PHE 0-0.014-0.00215.193-0.580-0.5800.0000.0000.0000.000
167A169LEU -1-0.885-0.92817.11114.40714.4070.0000.0000.0000.000
168A314HOH 0-0.008-0.02129.9960.1750.1750.0000.0000.0000.000
169A326HOH 0-0.078-0.06532.7120.0900.0900.0000.0000.0000.000
170A330HOH 0-0.049-0.03625.484-0.141-0.1410.0000.0000.0000.000
171A336HOH 00.007-0.00520.3770.1480.1480.0000.0000.0000.000
172A337HOH 0-0.023-0.02329.786-0.099-0.0990.0000.0000.0000.000
173A339HOH 0-0.007-0.01115.181-0.249-0.2490.0000.0000.0000.000
174A342HOH 0-0.046-0.03830.463-0.126-0.1260.0000.0000.0000.000
175A347HOH 0-0.013-0.03524.9420.0520.0520.0000.0000.0000.000
176A352HOH 0-0.008-0.01122.7210.1130.1130.0000.0000.0000.000
177A353HOH 00.008-0.00618.075-0.201-0.2010.0000.0000.0000.000
178A362HOH 0-0.059-0.03936.837-0.091-0.0910.0000.0000.0000.000
179A368HOH 0-0.061-0.04722.682-0.133-0.1330.0000.0000.0000.000
180A370HOH 00.0150.00328.7240.0850.0850.0000.0000.0000.000
181A380HOH 0-0.016-0.01023.0420.1530.1530.0000.0000.0000.000
182A381HOH 0-0.027-0.01720.3250.2700.2700.0000.0000.0000.000
183A383HOH 0-0.064-0.06026.765-0.028-0.0280.0000.0000.0000.000
184A388HOH 0-0.008-0.01519.980-0.086-0.0860.0000.0000.0000.000
185A390HOH 0-0.028-0.02218.7670.2580.2580.0000.0000.0000.000
186A393HOH 0-0.039-0.03221.648-0.092-0.0920.0000.0000.0000.000
187A394HOH 0-0.020-0.02011.741-0.475-0.4750.0000.0000.0000.000
188A397HOH 0-0.016-0.02516.7300.1580.1580.0000.0000.0000.000
189A399HOH 00.0280.0132.949-1.985-1.1180.105-0.450-0.523-0.003
190A402HOH 0-0.020-0.02123.447-0.301-0.3010.0000.0000.0000.000
191A407HOH 00.004-0.00228.2000.2130.2130.0000.0000.0000.000
192A409HOH 00.0270.02019.9520.2320.2320.0000.0000.0000.000
193A411HOH 00.007-0.00517.637-0.149-0.1490.0000.0000.0000.000
194A413HOH 0-0.022-0.04017.7780.4980.4980.0000.0000.0000.000
195A414HOH 00.014-0.01024.5450.0380.0380.0000.0000.0000.000
196A421HOH 0-0.036-0.02515.092-0.150-0.1500.0000.0000.0000.000
197A423HOH 0-0.018-0.01917.9850.0930.0930.0000.0000.0000.000
198A428HOH 0-0.041-0.04328.654-0.034-0.0340.0000.0000.0000.000
199A429HOH 0-0.028-0.01828.194-0.037-0.0370.0000.0000.0000.000
200A433HOH 00.0290.01131.655-0.030-0.0300.0000.0000.0000.000
201A436HOH 0-0.009-0.01219.7590.1770.1770.0000.0000.0000.000
202A451HOH 0-0.002-0.00916.240-0.213-0.2130.0000.0000.0000.000
203A456HOH 0-0.012-0.01918.1260.1500.1500.0000.0000.0000.000
204A459HOH 0-0.004-0.00525.931-0.175-0.1750.0000.0000.0000.000
205A469HOH 00.0040.00810.692-0.245-0.2450.0000.0000.0000.000