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: QYNLY

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 OptHSide
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 -2227771.830649
FMO2-HF: Nuclear repulsion 2140359.115137
FMO2-HF: Total energy -87412.715512
FMO2-MP2: Total energy -87671.599817


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.
-0.1921.843-0.018-0.948-1.0680.001
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 : -0.015 / q_NPA : -0.022
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].
3B832HIS0-0.055-0.0163.8481.5983.491-0.018-0.885-0.9890.001
4B833ILE00.0370.0156.091-0.399-0.3990.0000.0000.0000.000
5B834GLN0-0.012-0.0029.0550.0520.0520.0000.0000.0000.000
6B835GLU-1-0.773-0.84910.619-0.062-0.0620.0000.0000.0000.000
7B836LEU0-0.029-0.00913.386-0.018-0.0180.0000.0000.0000.000
8B837ALA00.0060.00516.5980.0250.0250.0000.0000.0000.000
9B838CYS0-0.0290.00320.302-0.013-0.0130.0000.0000.0000.000
10B839VAL0-0.027-0.01923.4750.0150.0150.0000.0000.0000.000
11B840SER00.0630.03726.597-0.007-0.0070.0000.0000.0000.000
12B841ARG10.9070.94426.5660.1060.1060.0000.0000.0000.000
13B842ASP-1-0.824-0.90132.814-0.054-0.0540.0000.0000.0000.000
14B843THR0-0.076-0.03935.837-0.004-0.0040.0000.0000.0000.000
15B844LYS10.9270.94237.3620.0620.0620.0000.0000.0000.000
16B845LEU0-0.042-0.02538.7450.0030.0030.0000.0000.0000.000
17B846GLY00.0570.04040.3890.0000.0000.0000.0000.0000.000
18B847PRO00.0050.00137.136-0.004-0.0040.0000.0000.0000.000
19B848GLU-1-0.799-0.87731.202-0.108-0.1080.0000.0000.0000.000
20B849GLU-1-0.922-0.95533.551-0.071-0.0710.0000.0000.0000.000
21B850ILE0-0.053-0.04327.288-0.009-0.0090.0000.0000.0000.000
22B851THR00.0400.02130.4110.0070.0070.0000.0000.0000.000
23B852ALA00.0700.01830.521-0.011-0.0110.0000.0000.0000.000
24B853ASP-1-0.990-0.97931.745-0.087-0.0870.0000.0000.0000.000
25B854ILE0-0.0270.00129.2820.0000.0000.0000.0000.0000.000
26B855PRO00.0120.02133.263-0.002-0.0020.0000.0000.0000.000
27B856ASN0-0.053-0.05633.409-0.004-0.0040.0000.0000.0000.000
28B857VAL00.0080.00329.220-0.012-0.0120.0000.0000.0000.000
29B858GLY00.0090.00831.3160.0080.0080.0000.0000.0000.000
30B859GLU-1-0.855-0.94231.400-0.108-0.1080.0000.0000.0000.000
31B860ALA0-0.053-0.02928.507-0.003-0.0030.0000.0000.0000.000
32B861ALA0-0.010-0.01126.523-0.007-0.0070.0000.0000.0000.000
33B862LEU00.0600.02727.059-0.007-0.0070.0000.0000.0000.000
34B863SER0-0.0180.01229.1190.0020.0020.0000.0000.0000.000
35B864LYS10.8230.89723.5340.1760.1760.0000.0000.0000.000
36B865LEU0-0.0130.01624.785-0.008-0.0080.0000.0000.0000.000
37B866ASP-1-0.726-0.84627.245-0.093-0.0930.0000.0000.0000.000
38B867GLU-1-0.859-0.92629.301-0.062-0.0620.0000.0000.0000.000
39B868SER0-0.065-0.03529.7980.0020.0020.0000.0000.0000.000
40B869GLY0-0.0120.00229.096-0.001-0.0010.0000.0000.0000.000
41B870ILE0-0.077-0.03323.774-0.016-0.0160.0000.0000.0000.000
42B871VAL00.0240.02120.0030.0030.0030.0000.0000.0000.000
43B872TYR00.0080.00623.2730.0180.0180.0000.0000.0000.000
44B873ILE0-0.008-0.01819.546-0.029-0.0290.0000.0000.0000.000
45B874GLY0-0.014-0.00918.4560.0190.0190.0000.0000.0000.000
46B875ALA0-0.048-0.00419.382-0.009-0.0090.0000.0000.0000.000
47B876GLU-1-0.889-0.96313.685-0.596-0.5960.0000.0000.0000.000
48B877VAL0-0.034-0.00115.2050.0130.0130.0000.0000.0000.000
49B878THR0-0.025-0.03315.139-0.092-0.0920.0000.0000.0000.000
50B879GLY00.0120.00415.5330.0380.0380.0000.0000.0000.000
51B880GLY0-0.039-0.03016.6380.0360.0360.0000.0000.0000.000
52B881ASP-1-0.838-0.91319.239-0.303-0.3030.0000.0000.0000.000
53B882ILE0-0.024-0.02420.350-0.014-0.0140.0000.0000.0000.000
54B883LEU0-0.019-0.00216.6620.0000.0000.0000.0000.0000.000
55B884VAL00.007-0.01421.1620.0220.0220.0000.0000.0000.000
56B885GLY00.0410.01024.109-0.008-0.0080.0000.0000.0000.000
57B886LYS10.7570.87427.0490.1400.1400.0000.0000.0000.000
58B887VAL00.0430.03029.153-0.007-0.0070.0000.0000.0000.000
59B888THR0-0.025-0.01032.1980.0020.0020.0000.0000.0000.000
60B889PRO00.0670.06334.327-0.003-0.0030.0000.0000.0000.000
61B890LYS10.7970.88337.6600.0880.0880.0000.0000.0000.000
62B891GLY00.0230.01239.3000.0000.0000.0000.0000.0000.000
63B892GLU-1-0.726-0.86042.673-0.061-0.0610.0000.0000.0000.000
64B893THR0-0.058-0.03943.500-0.001-0.0010.0000.0000.0000.000
65B894GLN0-0.043-0.01839.542-0.004-0.0040.0000.0000.0000.000
66B895LEU0-0.075-0.00341.709-0.003-0.0030.0000.0000.0000.000
67B896THR00.002-0.02942.3220.0030.0030.0000.0000.0000.000
68B897PRO00.0170.00245.0620.0020.0020.0000.0000.0000.000
69B898GLU-1-0.843-0.90345.450-0.070-0.0700.0000.0000.0000.000
70B899GLU-1-0.792-0.90241.317-0.087-0.0870.0000.0000.0000.000
71B900LYS10.8250.90045.5340.0640.0640.0000.0000.0000.000
72B901LEU00.0000.01248.3690.0030.0030.0000.0000.0000.000
73B902LEU00.0260.00144.1300.0020.0020.0000.0000.0000.000
74B903ARG10.8690.92645.8160.0600.0600.0000.0000.0000.000
75B904ALA0-0.033-0.01647.8200.0020.0020.0000.0000.0000.000
76B905ILE0-0.077-0.02850.2970.0020.0020.0000.0000.0000.000
77B906PHE0-0.025-0.01746.9700.0010.0010.0000.0000.0000.000
78B907GLY00.0180.02748.9130.0010.0010.0000.0000.0000.000
79B908GLU-1-0.897-0.95646.369-0.054-0.0540.0000.0000.0000.000
80B909LYS10.7830.86843.1120.0560.0560.0000.0000.0000.000
81B910ALA00.0300.04142.858-0.003-0.0030.0000.0000.0000.000
82B911SER0-0.021-0.02140.990-0.006-0.0060.0000.0000.0000.000
83B912ASP-1-0.838-0.90441.123-0.067-0.0670.0000.0000.0000.000
84B913VAL00.0290.00536.0970.0000.0000.0000.0000.0000.000
85B914LYS10.9090.94333.6410.1060.1060.0000.0000.0000.000
86B915ASP-1-0.712-0.81728.799-0.165-0.1650.0000.0000.0000.000
87B916SER0-0.082-0.05428.407-0.006-0.0060.0000.0000.0000.000
88B917SER0-0.043-0.05325.791-0.007-0.0070.0000.0000.0000.000
89B918LEU0-0.037-0.00919.107-0.009-0.0090.0000.0000.0000.000
90B919ARG10.8570.91620.7100.2140.2140.0000.0000.0000.000
91B920VAL0-0.0050.01414.572-0.013-0.0130.0000.0000.0000.000
92B921PRO00.0000.00114.2270.0140.0140.0000.0000.0000.000
93B922ASN00.0430.00915.495-0.027-0.0270.0000.0000.0000.000
94B923GLY0-0.029-0.00713.304-0.042-0.0420.0000.0000.0000.000
95B924VAL0-0.010-0.0039.356-0.123-0.1230.0000.0000.0000.000
96B925SER00.025-0.00810.2260.1890.1890.0000.0000.0000.000
97B926GLY0-0.024-0.0139.932-0.300-0.3000.0000.0000.0000.000
98B927THR00.0120.02311.7040.0830.0830.0000.0000.0000.000
99B928VAL0-0.019-0.00513.867-0.004-0.0040.0000.0000.0000.000
100B929ILE0-0.022-0.01412.5180.0300.0300.0000.0000.0000.000
101B930ASP-1-0.827-0.92316.5590.0010.0010.0000.0000.0000.000
102B931VAL0-0.061-0.01918.510-0.037-0.0370.0000.0000.0000.000
103B932GLN0-0.025-0.01121.2060.0260.0260.0000.0000.0000.000
104B933VAL0-0.011-0.00523.328-0.011-0.0110.0000.0000.0000.000
105B934PHE0-0.0070.01023.2750.0100.0100.0000.0000.0000.000
106B935THR0-0.019-0.02828.425-0.012-0.0120.0000.0000.0000.000
107B936ARG10.8920.96031.9890.0400.0400.0000.0000.0000.000
108B937ASP-1-0.908-0.95834.388-0.014-0.0140.0000.0000.0000.000
109B938GLY00.0180.00237.750-0.001-0.0010.0000.0000.0000.000
110B939VAL0-0.089-0.04035.264-0.001-0.0010.0000.0000.0000.000
111B940GLU-1-0.938-0.95938.135-0.038-0.0380.0000.0000.0000.000
112B941LYS10.8060.88934.7630.0140.0140.0000.0000.0000.000
113B942ASP-1-0.792-0.90832.908-0.059-0.0590.0000.0000.0000.000
114B943LYS10.9020.92835.9630.0540.0540.0000.0000.0000.000
115B944ARG10.8730.92125.0370.0930.0930.0000.0000.0000.000
116B945ALA0-0.021-0.01031.9900.0050.0050.0000.0000.0000.000
117B946LEU00.0360.03032.9600.0070.0070.0000.0000.0000.000
118B947GLU-1-0.850-0.92634.167-0.035-0.0350.0000.0000.0000.000
119B948ILE0-0.014-0.00828.6890.0060.0060.0000.0000.0000.000
120B949GLU-1-0.816-0.91532.698-0.006-0.0060.0000.0000.0000.000
121B950GLU-1-0.906-0.94635.199-0.003-0.0030.0000.0000.0000.000
122B951MET0-0.065-0.04831.7360.0070.0070.0000.0000.0000.000
123B952GLN00.014-0.00729.8170.0070.0070.0000.0000.0000.000
124B953LEU0-0.0020.00534.2950.0060.0060.0000.0000.0000.000
125B954LYS10.8220.90437.3670.0030.0030.0000.0000.0000.000
126B955GLN0-0.0050.00131.2460.0020.0020.0000.0000.0000.000
127B956ALA00.0370.03236.3150.0030.0030.0000.0000.0000.000
128B957LYS10.9570.98337.535-0.014-0.0140.0000.0000.0000.000
129B958LYS10.8780.93436.754-0.040-0.0400.0000.0000.0000.000
130B959ASP-1-0.813-0.92235.5800.0470.0470.0000.0000.0000.000
131B960LEU00.0280.02038.4480.0020.0020.0000.0000.0000.000
132B961SER0-0.085-0.04241.9380.0000.0000.0000.0000.0000.000
133B962GLU-1-0.851-0.91337.2680.0510.0510.0000.0000.0000.000
134B963GLU-1-0.798-0.89739.2850.0540.0540.0000.0000.0000.000
135B964LEU00.004-0.00742.2430.0010.0010.0000.0000.0000.000
136B965GLN0-0.045-0.02044.8360.0000.0000.0000.0000.0000.000
137B966ILE0-0.029-0.02140.8390.0000.0000.0000.0000.0000.000
138B967LEU0-0.0100.00345.3210.0000.0000.0000.0000.0000.000
139B968GLU-1-0.877-0.93547.4410.0310.0310.0000.0000.0000.000
140B969ALA0-0.032-0.02047.9730.0000.0000.0000.0000.0000.000
141B970GLY00.0140.02348.8650.0010.0010.0000.0000.0000.000
142B971LEU00.0500.03449.667-0.001-0.0010.0000.0000.0000.000
143B972PHE00.012-0.00852.339-0.001-0.0010.0000.0000.0000.000
144B973SER0-0.108-0.05752.172-0.001-0.0010.0000.0000.0000.000
145B974ARG10.9180.95154.224-0.041-0.0410.0000.0000.0000.000
146B975ILE00.0400.03255.848-0.001-0.0010.0000.0000.0000.000
147B976ARG10.8720.93458.168-0.031-0.0310.0000.0000.0000.000
148B977ALA0-0.034-0.00257.994-0.001-0.0010.0000.0000.0000.000
149B978VAL0-0.031-0.03859.122-0.001-0.0010.0000.0000.0000.000
150B979LEU00.0230.03261.610-0.001-0.0010.0000.0000.0000.000
151B980VAL0-0.057-0.06463.191-0.001-0.0010.0000.0000.0000.000
152B981ALA0-0.047-0.03463.876-0.001-0.0010.0000.0000.0000.000
153B982GLY00.0340.01465.6610.0000.0000.0000.0000.0000.000
154B983GLY00.0220.02267.886-0.001-0.0010.0000.0000.0000.000
155B984VAL0-0.065-0.00667.1200.0000.0000.0000.0000.0000.000
156B985GLU-1-0.876-0.94767.3100.0210.0210.0000.0000.0000.000
157B986ALA0-0.024-0.02865.6930.0000.0000.0000.0000.0000.000
158B987GLU-1-0.860-0.91065.0620.0230.0230.0000.0000.0000.000
159B988LYS10.9260.96166.122-0.019-0.0190.0000.0000.0000.000
160B989LEU00.0650.02462.4180.0000.0000.0000.0000.0000.000
161B990ASP-1-0.930-0.95060.9470.0270.0270.0000.0000.0000.000
162B991LYS10.8210.91061.573-0.021-0.0210.0000.0000.0000.000
163B992LEU0-0.0110.00862.8850.0000.0000.0000.0000.0000.000
164B993PRO00.0370.01960.3600.0010.0010.0000.0000.0000.000
165B994ARG10.8990.94053.836-0.032-0.0320.0000.0000.0000.000
166B995ASP-1-0.860-0.91958.5840.0210.0210.0000.0000.0000.000
167B996ARG10.7770.86559.694-0.019-0.0190.0000.0000.0000.000
168B997TRP0-0.021-0.03058.0750.0010.0010.0000.0000.0000.000
169B998LEU00.0130.00057.6170.0000.0000.0000.0000.0000.000
170B999GLU-1-0.900-0.92261.8820.0180.0180.0000.0000.0000.000
171B1000LEU0-0.041-0.00865.4870.0000.0000.0000.0000.0000.000
172B1001GLY00.0560.03466.2710.0010.0010.0000.0000.0000.000
173B1002LEU0-0.060-0.03366.0000.0000.0000.0000.0000.0000.000
174B1003THR0-0.041-0.03069.4690.0000.0000.0000.0000.0000.000
175B1004ASP-1-0.939-0.95071.0460.0230.0230.0000.0000.0000.000
176B1005GLU-1-0.727-0.85468.7640.0280.0280.0000.0000.0000.000
177B1006GLU-1-0.944-0.97065.4960.0300.0300.0000.0000.0000.000
178B1007LYS10.7740.85164.374-0.028-0.0280.0000.0000.0000.000
179B1008GLN0-0.014-0.01964.6170.0000.0000.0000.0000.0000.000
180B1009ASN00.0440.01263.649-0.001-0.0010.0000.0000.0000.000
181B1010GLN0-0.051-0.02560.2880.0020.0020.0000.0000.0000.000
182B1011LEU0-0.019-0.01059.6660.0010.0010.0000.0000.0000.000
183B1012GLU-1-0.861-0.91160.9490.0250.0250.0000.0000.0000.000
184B1013GLN0-0.047-0.03256.9010.0010.0010.0000.0000.0000.000
185B1014LEU0-0.043-0.01354.7970.0010.0010.0000.0000.0000.000
186B1015ALA00.0200.02055.5210.0010.0010.0000.0000.0000.000
187B1016GLU-1-0.875-0.93356.2830.0300.0300.0000.0000.0000.000
188B1017GLN0-0.009-0.01552.0540.0010.0010.0000.0000.0000.000
189B1018TYR00.004-0.00251.2230.0000.0000.0000.0000.0000.000
190B1019ASP-1-0.895-0.94151.5120.0270.0270.0000.0000.0000.000
191B1020GLU-1-0.969-0.97450.6960.0370.0370.0000.0000.0000.000
192B1021LEU0-0.017-0.02146.5790.0010.0010.0000.0000.0000.000
193B1022LYS10.9450.96847.506-0.025-0.0250.0000.0000.0000.000
194B1023HIS0-0.011-0.00548.032-0.001-0.0010.0000.0000.0000.000
195B1024GLU-1-0.825-0.90345.6060.0340.0340.0000.0000.0000.000
196B1025PHE0-0.052-0.03041.3150.0010.0010.0000.0000.0000.000
197B1026GLU-1-0.890-0.95243.5570.0250.0250.0000.0000.0000.000
198B1027LYS10.7480.87344.880-0.032-0.0320.0000.0000.0000.000
199B1028LYS10.8380.89937.722-0.052-0.0520.0000.0000.0000.000
200B1029LEU0-0.022-0.00940.4460.0000.0000.0000.0000.0000.000
201B1030GLU-1-0.810-0.87541.1400.0140.0140.0000.0000.0000.000
202B1031ALA0-0.039-0.01739.988-0.002-0.0020.0000.0000.0000.000
203B1032LYS10.8770.93934.662-0.045-0.0450.0000.0000.0000.000
204B1033ARG10.8770.90837.497-0.017-0.0170.0000.0000.0000.000
205B1034ARG10.8660.93338.996-0.015-0.0150.0000.0000.0000.000
206B1035LYS10.9170.94533.294-0.040-0.0400.0000.0000.0000.000
207B1036ILE0-0.0210.01034.308-0.002-0.0020.0000.0000.0000.000
208B1037THR0-0.028-0.00535.258-0.004-0.0040.0000.0000.0000.000
209B1038GLN0-0.0190.01935.305-0.002-0.0020.0000.0000.0000.000
210B1039GLY00.0270.01235.247-0.001-0.0010.0000.0000.0000.000
211B1040ASP-1-0.879-0.95030.611-0.012-0.0120.0000.0000.0000.000
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