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

tag_button

FMODB ID: R9YL8

Calculation Name: 3TBI-B-Xray372

Preferred Name: DNA-directed RNA polymerase beta chain

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3TBI

Chain ID: B

ChEMBL ID: CHEMBL1852

UniProt ID: P0A8V2

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2226360.10185
FMO2-HF: Nuclear repulsion 2138949.998063
FMO2-HF: Total energy -87410.103787
FMO2-MP2: Total energy -87669.147177


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:830:MET)


Summations of interaction energy for fragment #1(B:830:MET)
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.
-0.4761.927-0.015-1.112-1.2770.001
Interaction energy analysis for fragmet #1(B:830:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.020
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].
3B832HIS0-0.056-0.0143.5071.1203.307-0.016-1.012-1.1590.001
4B833ILE00.0460.0246.135-0.445-0.4450.0000.0000.0000.000
5B834GLN0-0.0120.0018.9760.0100.0100.0000.0000.0000.000
6B835GLU-1-0.888-0.95110.518-0.017-0.0170.0000.0000.0000.000
7B836LEU0-0.043-0.01913.364-0.019-0.0190.0000.0000.0000.000
8B837ALA00.0100.00616.4470.0210.0210.0000.0000.0000.000
9B838CYS0-0.0340.00220.167-0.014-0.0140.0000.0000.0000.000
10B839VAL0-0.035-0.02323.3040.0140.0140.0000.0000.0000.000
11B840SER00.0140.02526.450-0.006-0.0060.0000.0000.0000.000
12B841ARG10.9390.94026.6860.0770.0770.0000.0000.0000.000
13B842ASP-1-0.818-0.90132.670-0.041-0.0410.0000.0000.0000.000
14B843THR0-0.081-0.03535.642-0.003-0.0030.0000.0000.0000.000
15B844LYS10.9210.93737.1910.0500.0500.0000.0000.0000.000
16B845LEU0-0.050-0.03038.4220.0030.0030.0000.0000.0000.000
17B846GLY00.0580.04140.199-0.001-0.0010.0000.0000.0000.000
18B847PRO00.0180.01236.973-0.003-0.0030.0000.0000.0000.000
19B848GLU-1-0.830-0.90731.046-0.088-0.0880.0000.0000.0000.000
20B849GLU-1-0.933-0.95733.347-0.059-0.0590.0000.0000.0000.000
21B850ILE0-0.045-0.04227.015-0.008-0.0080.0000.0000.0000.000
22B851THR00.0100.01230.1860.0060.0060.0000.0000.0000.000
23B852ALA00.1080.02530.267-0.010-0.0100.0000.0000.0000.000
24B853ASP-1-0.999-0.98531.481-0.080-0.0800.0000.0000.0000.000
25B854ILE0-0.0360.01128.8120.0000.0000.0000.0000.0000.000
26B855PRO00.0240.02632.969-0.002-0.0020.0000.0000.0000.000
27B856ASN0-0.056-0.05933.089-0.004-0.0040.0000.0000.0000.000
28B857VAL00.0050.00929.333-0.011-0.0110.0000.0000.0000.000
29B858GLY0-0.0010.00330.9680.0070.0070.0000.0000.0000.000
30B859GLU-1-0.854-0.94531.060-0.105-0.1050.0000.0000.0000.000
31B860ALA0-0.046-0.02228.099-0.003-0.0030.0000.0000.0000.000
32B861ALA0-0.012-0.01226.188-0.007-0.0070.0000.0000.0000.000
33B862LEU00.0540.01926.741-0.006-0.0060.0000.0000.0000.000
34B863SER0-0.0290.00528.6200.0020.0020.0000.0000.0000.000
35B864LYS10.8250.90023.6090.1690.1690.0000.0000.0000.000
36B865LEU0-0.0140.01624.490-0.007-0.0070.0000.0000.0000.000
37B866ASP-1-0.733-0.84626.982-0.081-0.0810.0000.0000.0000.000
38B867GLU-1-0.910-0.97029.073-0.055-0.0550.0000.0000.0000.000
39B868SER0-0.079-0.06729.5400.0020.0020.0000.0000.0000.000
40B869GLY0-0.029-0.00528.8590.0000.0000.0000.0000.0000.000
41B870ILE0-0.085-0.04223.537-0.014-0.0140.0000.0000.0000.000
42B871VAL00.0230.02219.7170.0020.0020.0000.0000.0000.000
43B872TYR00.006-0.00123.0540.0180.0180.0000.0000.0000.000
44B873ILE00.004-0.01119.633-0.028-0.0280.0000.0000.0000.000
45B874GLY0-0.021-0.01518.3960.0170.0170.0000.0000.0000.000
46B875ALA0-0.054-0.00919.292-0.012-0.0120.0000.0000.0000.000
47B876GLU-1-0.894-0.96815.313-0.444-0.4440.0000.0000.0000.000
48B877VAL0-0.063-0.01115.0280.0110.0110.0000.0000.0000.000
49B878THR0-0.001-0.01814.805-0.131-0.1310.0000.0000.0000.000
50B879GLY0-0.019-0.01215.1150.0410.0410.0000.0000.0000.000
51B880GLY0-0.044-0.02916.2680.0320.0320.0000.0000.0000.000
52B881ASP-1-0.824-0.91918.983-0.299-0.2990.0000.0000.0000.000
53B882ILE0-0.011-0.01720.030-0.011-0.0110.0000.0000.0000.000
54B883LEU0-0.025-0.00716.399-0.001-0.0010.0000.0000.0000.000
55B884VAL00.019-0.00420.9010.0220.0220.0000.0000.0000.000
56B885GLY00.039-0.00223.873-0.008-0.0080.0000.0000.0000.000
57B886LYS10.7720.89826.8740.1220.1220.0000.0000.0000.000
58B887VAL00.0490.02628.913-0.007-0.0070.0000.0000.0000.000
59B888THR0-0.049-0.02632.0320.0020.0020.0000.0000.0000.000
60B889PRO00.0870.06634.087-0.004-0.0040.0000.0000.0000.000
61B890LYS10.8500.92437.2320.0810.0810.0000.0000.0000.000
62B891GLY00.0220.01239.0410.0000.0000.0000.0000.0000.000
63B892GLU-1-0.837-0.93942.424-0.053-0.0530.0000.0000.0000.000
64B893THR0-0.057-0.03843.196-0.001-0.0010.0000.0000.0000.000
65B894GLN0-0.042-0.01839.466-0.003-0.0030.0000.0000.0000.000
66B895LEU0-0.080-0.01041.418-0.003-0.0030.0000.0000.0000.000
67B896THR00.0130.02342.1110.0040.0040.0000.0000.0000.000
68B897PRO00.013-0.00844.7500.0020.0020.0000.0000.0000.000
69B898GLU-1-0.877-0.95245.214-0.066-0.0660.0000.0000.0000.000
70B899GLU-1-0.801-0.92141.270-0.079-0.0790.0000.0000.0000.000
71B900LYS10.8880.93545.2160.0560.0560.0000.0000.0000.000
72B901LEU00.0070.01848.0640.0030.0030.0000.0000.0000.000
73B902LEU00.0250.00443.9100.0020.0020.0000.0000.0000.000
74B903ARG10.9430.98046.0400.0530.0530.0000.0000.0000.000
75B904ALA0-0.040-0.02247.5190.0020.0020.0000.0000.0000.000
76B905ILE0-0.079-0.02549.8830.0020.0020.0000.0000.0000.000
77B906PHE0-0.033-0.02346.9850.0010.0010.0000.0000.0000.000
78B907GLY00.0150.02548.6210.0010.0010.0000.0000.0000.000
79B908GLU-1-0.963-1.00146.207-0.047-0.0470.0000.0000.0000.000
80B909LYS10.9010.95842.8220.0480.0480.0000.0000.0000.000
81B910ALA00.0220.03942.581-0.002-0.0020.0000.0000.0000.000
82B911SER0-0.034-0.03040.694-0.005-0.0050.0000.0000.0000.000
83B912ASP-1-0.902-0.95440.654-0.059-0.0590.0000.0000.0000.000
84B913VAL00.0520.02435.8530.0000.0000.0000.0000.0000.000
85B914LYS10.8900.93532.9710.0960.0960.0000.0000.0000.000
86B915ASP-1-0.755-0.84628.355-0.151-0.1510.0000.0000.0000.000
87B916SER0-0.087-0.04728.121-0.005-0.0050.0000.0000.0000.000
88B917SER00.026-0.01525.520-0.003-0.0030.0000.0000.0000.000
89B918LEU0-0.048-0.01018.713-0.008-0.0080.0000.0000.0000.000
90B919ARG10.8750.92920.4120.1960.1960.0000.0000.0000.000
91B920VAL00.0030.01814.178-0.007-0.0070.0000.0000.0000.000
92B921PRO0-0.0120.00213.6790.0150.0150.0000.0000.0000.000
93B922ASN00.0570.00615.144-0.032-0.0320.0000.0000.0000.000
94B923GLY0-0.037-0.01212.927-0.037-0.0370.0000.0000.0000.000
95B924VAL0-0.0120.0079.337-0.129-0.1290.0000.0000.0000.000
96B925SER00.001-0.0249.8560.1550.1550.0000.0000.0000.000
97B926GLY0-0.019-0.0099.594-0.294-0.2940.0000.0000.0000.000
98B927THR00.0190.02011.4110.0870.0870.0000.0000.0000.000
99B928VAL0-0.044-0.00813.6880.0060.0060.0000.0000.0000.000
100B929ILE0-0.019-0.01312.5310.0240.0240.0000.0000.0000.000
101B930ASP-1-0.852-0.93816.5280.0370.0370.0000.0000.0000.000
102B931VAL0-0.052-0.01418.399-0.033-0.0330.0000.0000.0000.000
103B932GLN00.0090.00521.1000.0200.0200.0000.0000.0000.000
104B933VAL0-0.013-0.00723.261-0.010-0.0100.0000.0000.0000.000
105B934PHE0-0.0010.00623.5140.0110.0110.0000.0000.0000.000
106B935THR0-0.054-0.04528.365-0.012-0.0120.0000.0000.0000.000
107B936ARG10.9110.96831.9140.0230.0230.0000.0000.0000.000
108B937ASP-1-0.934-0.96734.326-0.002-0.0020.0000.0000.0000.000
109B938GLY00.0240.00637.704-0.002-0.0020.0000.0000.0000.000
110B939VAL0-0.093-0.04335.331-0.002-0.0020.0000.0000.0000.000
111B940GLU-1-0.948-0.96538.035-0.029-0.0290.0000.0000.0000.000
112B941LYS10.8930.94834.0100.0080.0080.0000.0000.0000.000
113B942ASP-1-0.763-0.86232.700-0.047-0.0470.0000.0000.0000.000
114B943LYS10.9610.97135.7330.0440.0440.0000.0000.0000.000
115B944ARG10.9010.93924.9610.0730.0730.0000.0000.0000.000
116B945ALA0-0.023-0.01431.8890.0050.0050.0000.0000.0000.000
117B946LEU00.0220.02432.8530.0070.0070.0000.0000.0000.000
118B947GLU-1-0.847-0.92033.997-0.025-0.0250.0000.0000.0000.000
119B948ILE0-0.022-0.00928.5410.0060.0060.0000.0000.0000.000
120B949GLU-1-0.858-0.94832.6660.0060.0060.0000.0000.0000.000
121B950GLU-1-0.980-0.99135.1520.0000.0000.0000.0000.0000.000
122B951MET0-0.084-0.06031.7450.0060.0060.0000.0000.0000.000
123B952GLN00.008-0.00829.6090.0050.0050.0000.0000.0000.000
124B953LEU0-0.0060.00734.3330.0060.0060.0000.0000.0000.000
125B954LYS10.9240.96937.459-0.008-0.0080.0000.0000.0000.000
126B955GLN00.0110.00231.8920.0020.0020.0000.0000.0000.000
127B956ALA00.0590.03636.3610.0030.0030.0000.0000.0000.000
128B957LYS10.9460.98137.576-0.020-0.0200.0000.0000.0000.000
129B958LYS10.9310.96737.358-0.042-0.0420.0000.0000.0000.000
130B959ASP-1-0.870-0.94235.2800.0570.0570.0000.0000.0000.000
131B960LEU00.0200.01538.5390.0020.0020.0000.0000.0000.000
132B961SER0-0.118-0.05242.0090.0000.0000.0000.0000.0000.000
133B962GLU-1-0.902-0.95337.3510.0570.0570.0000.0000.0000.000
134B963GLU-1-0.865-0.94539.2940.0590.0590.0000.0000.0000.000
135B964LEU0-0.003-0.01342.3390.0000.0000.0000.0000.0000.000
136B965GLN0-0.047-0.01944.8280.0000.0000.0000.0000.0000.000
137B966ILE0-0.029-0.01840.9270.0000.0000.0000.0000.0000.000
138B967LEU0-0.017-0.00145.4560.0000.0000.0000.0000.0000.000
139B968GLU-1-0.903-0.95947.5410.0340.0340.0000.0000.0000.000
140B969ALA0-0.043-0.02248.1360.0000.0000.0000.0000.0000.000
141B970GLY00.0120.01948.9940.0000.0000.0000.0000.0000.000
142B971LEU00.0480.02849.803-0.001-0.0010.0000.0000.0000.000
143B972PHE00.017-0.00752.447-0.001-0.0010.0000.0000.0000.000
144B973SER0-0.085-0.04652.416-0.001-0.0010.0000.0000.0000.000
145B974ARG10.9390.96554.352-0.044-0.0440.0000.0000.0000.000
146B975ILE00.0420.04355.981-0.001-0.0010.0000.0000.0000.000
147B976ARG11.0061.01058.307-0.034-0.0340.0000.0000.0000.000
148B977ALA0-0.064-0.01258.143-0.001-0.0010.0000.0000.0000.000
149B978VAL0-0.018-0.02859.607-0.001-0.0010.0000.0000.0000.000
150B979LEU00.0250.02761.737-0.001-0.0010.0000.0000.0000.000
151B980VAL0-0.053-0.05763.406-0.001-0.0010.0000.0000.0000.000
152B981ALA0-0.038-0.03064.070-0.001-0.0010.0000.0000.0000.000
153B982GLY00.0260.00865.8110.0000.0000.0000.0000.0000.000
154B983GLY00.0330.03168.024-0.001-0.0010.0000.0000.0000.000
155B984VAL0-0.065-0.00467.1660.0000.0000.0000.0000.0000.000
156B985GLU-1-0.862-0.94767.4780.0220.0220.0000.0000.0000.000
157B986ALA0-0.043-0.04365.8960.0000.0000.0000.0000.0000.000
158B987GLU-1-0.968-0.97065.2610.0240.0240.0000.0000.0000.000
159B988LYS10.8940.95766.326-0.020-0.0200.0000.0000.0000.000
160B989LEU00.0470.01062.4950.0000.0000.0000.0000.0000.000
161B990ASP-1-0.982-0.99061.2880.0270.0270.0000.0000.0000.000
162B991LYS10.9480.98061.766-0.021-0.0210.0000.0000.0000.000
163B992LEU0-0.036-0.00163.065-0.001-0.0010.0000.0000.0000.000
164B993PRO00.0420.02860.6160.0010.0010.0000.0000.0000.000
165B994ARG10.9780.98054.583-0.033-0.0330.0000.0000.0000.000
166B995ASP-1-0.878-0.94058.5880.0240.0240.0000.0000.0000.000
167B996ARG10.8790.93559.801-0.022-0.0220.0000.0000.0000.000
168B997TRP0-0.059-0.06258.7910.0010.0010.0000.0000.0000.000
169B998LEU00.001-0.00957.8070.0000.0000.0000.0000.0000.000
170B999GLU-1-0.954-0.94661.9670.0210.0210.0000.0000.0000.000
171B1000LEU0-0.060-0.01465.5700.0000.0000.0000.0000.0000.000
172B1001GLY00.0490.02966.3600.0010.0010.0000.0000.0000.000
173B1002LEU0-0.055-0.03166.5010.0000.0000.0000.0000.0000.000
174B1003THR0-0.056-0.03669.5630.0000.0000.0000.0000.0000.000
175B1004ASP-1-0.965-0.96371.1260.0250.0250.0000.0000.0000.000
176B1005GLU-1-0.811-0.92768.8350.0300.0300.0000.0000.0000.000
177B1006GLU-1-0.944-0.96765.7790.0320.0320.0000.0000.0000.000
178B1007LYS10.8600.92364.536-0.030-0.0300.0000.0000.0000.000
179B1008GLN00.0370.01464.6970.0010.0010.0000.0000.0000.000
180B1009ASN00.0400.01163.6620.0000.0000.0000.0000.0000.000
181B1010GLN0-0.092-0.04760.4240.0010.0010.0000.0000.0000.000
182B1011LEU0-0.008-0.01159.7260.0010.0010.0000.0000.0000.000
183B1012GLU-1-0.921-0.94561.0070.0290.0290.0000.0000.0000.000
184B1013GLN00.0150.00156.8810.0020.0020.0000.0000.0000.000
185B1014LEU0-0.045-0.01255.1240.0010.0010.0000.0000.0000.000
186B1015ALA00.0040.01355.5730.0010.0010.0000.0000.0000.000
187B1016GLU-1-0.896-0.94956.3160.0340.0340.0000.0000.0000.000
188B1017GLN0-0.019-0.02252.1010.0000.0000.0000.0000.0000.000
189B1018TYR00.000-0.00751.6810.0010.0010.0000.0000.0000.000
190B1019ASP-1-0.906-0.94351.5450.0310.0310.0000.0000.0000.000
191B1020GLU-1-0.968-0.97450.7300.0420.0420.0000.0000.0000.000
192B1021LEU0-0.016-0.02246.6840.0020.0020.0000.0000.0000.000
193B1022LYS10.9500.97047.514-0.029-0.0290.0000.0000.0000.000
194B1023HIS0-0.031-0.01648.0460.0000.0000.0000.0000.0000.000
195B1024GLU-1-0.921-0.97045.5930.0450.0450.0000.0000.0000.000
196B1025PHE0-0.054-0.02741.1550.0020.0020.0000.0000.0000.000
197B1026GLU-1-0.898-0.95643.5580.0310.0310.0000.0000.0000.000
198B1027LYS10.8850.95244.793-0.039-0.0390.0000.0000.0000.000
199B1028LYS10.9130.95836.685-0.061-0.0610.0000.0000.0000.000
200B1029LEU0-0.025-0.01540.4060.0000.0000.0000.0000.0000.000
201B1030GLU-1-0.846-0.89841.1100.0230.0230.0000.0000.0000.000
202B1031ALA0-0.031-0.01439.835-0.001-0.0010.0000.0000.0000.000
203B1032LYS10.9250.96234.974-0.055-0.0550.0000.0000.0000.000
204B1033ARG10.9040.93437.434-0.024-0.0240.0000.0000.0000.000
205B1034ARG10.9380.97538.737-0.029-0.0290.0000.0000.0000.000
206B1035LYS10.8900.92832.906-0.055-0.0550.0000.0000.0000.000
207B1036ILE0-0.0280.00634.472-0.001-0.0010.0000.0000.0000.000
208B1037THR00.0060.00435.247-0.003-0.0030.0000.0000.0000.000
209B1038GLN0-0.111-0.02835.682-0.004-0.0040.0000.0000.0000.000
210B1039GLY00.0200.01235.2090.0000.0000.0000.0000.0000.000
211B1040ASP-1-0.849-0.93330.3270.0070.0070.0000.0000.0000.000
212B1041ASP-1-0.964-0.99432.6510.0070.0070.0000.0000.0000.000
213B1042LEU0-0.049-0.01328.5830.0000.0000.0000.0000.0000.000
214B1043ALA00.0320.00030.1700.0010.0010.0000.0000.0000.000
215B1044PRO0-0.0040.00932.137-0.002-0.0020.0000.0000.0000.000
216B1045GLY00.010-0.00434.153-0.003-0.0030.0000.0000.0000.000
217B1046VAL0-0.020-0.00929.307-0.006-0.0060.0000.0000.0000.000
218B1047LEU0-0.024-0.00332.1620.0070.0070.0000.0000.0000.000
219B1048LYS10.9940.98729.7720.0540.0540.0000.0000.0000.000
220B1049ILE0-0.051-0.02523.876-0.009-0.0090.0000.0000.0000.000
221B1050VAL00.0370.02722.6860.0090.0090.0000.0000.0000.000
222B1051LYS10.9060.95519.444-0.015-0.0150.0000.0000.0000.000
223B1052VAL00.0550.02516.3380.0130.0130.0000.0000.0000.000
224B1053TYR0-0.055-0.02514.743-0.013-0.0130.0000.0000.0000.000
225B1054LEU00.0280.01811.5820.0000.0000.0000.0000.0000.000
226B1055ALA0-0.0110.0029.4540.0000.0000.0000.0000.0000.000
227B1056VAL00.0100.0136.213-0.142-0.1420.0000.0000.0000.000
228B1057LYS10.9670.9774.127-0.1260.0900.001-0.100-0.1180.000