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: K92V3

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 OptAll
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 -2233280.882584
FMO2-HF: Nuclear repulsion 2145866.675588
FMO2-HF: Total energy -87414.206996
FMO2-MP2: Total energy -87672.971721


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.
-0.2021.647-0.016-0.857-0.9780.001
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 : -0.020 / q_NPA : -0.026
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].
3B832HIS0-0.069-0.0273.8091.7623.490-0.016-0.789-0.9240.001
4B833ILE00.0330.0176.218-0.358-0.3580.0000.0000.0000.000
5B834GLN00.0200.0119.1900.0720.0720.0000.0000.0000.000
6B835GLU-1-0.784-0.85110.670-0.044-0.0440.0000.0000.0000.000
7B836LEU0-0.041-0.01313.267-0.027-0.0270.0000.0000.0000.000
8B837ALA00.009-0.00816.6680.0310.0310.0000.0000.0000.000
9B838CYS0-0.0470.00320.461-0.011-0.0110.0000.0000.0000.000
10B839VAL0-0.006-0.01623.7510.0150.0150.0000.0000.0000.000
11B840SER00.0390.03026.979-0.007-0.0070.0000.0000.0000.000
12B841ARG10.9380.94326.7970.1030.1030.0000.0000.0000.000
13B842ASP-1-0.829-0.91633.267-0.051-0.0510.0000.0000.0000.000
14B843THR0-0.044-0.01535.479-0.003-0.0030.0000.0000.0000.000
15B844LYS10.9080.93337.2620.0600.0600.0000.0000.0000.000
16B845LEU0-0.031-0.01339.0380.0020.0020.0000.0000.0000.000
17B846GLY00.0340.02440.3510.0000.0000.0000.0000.0000.000
18B847PRO00.0130.00637.259-0.003-0.0030.0000.0000.0000.000
19B848GLU-1-0.825-0.88831.112-0.106-0.1060.0000.0000.0000.000
20B849GLU-1-0.923-0.95733.747-0.067-0.0670.0000.0000.0000.000
21B850ILE0-0.047-0.03327.317-0.009-0.0090.0000.0000.0000.000
22B851THR00.0380.02030.4370.0080.0080.0000.0000.0000.000
23B852ALA00.0470.00830.627-0.011-0.0110.0000.0000.0000.000
24B853ASP-1-0.991-0.97531.853-0.087-0.0870.0000.0000.0000.000
25B854ILE0-0.0070.00029.549-0.002-0.0020.0000.0000.0000.000
26B855PRO00.0230.02433.589-0.002-0.0020.0000.0000.0000.000
27B856ASN0-0.065-0.06233.453-0.005-0.0050.0000.0000.0000.000
28B857VAL00.0030.01529.268-0.011-0.0110.0000.0000.0000.000
29B858GLY00.0250.01530.8050.0090.0090.0000.0000.0000.000
30B859GLU-1-0.880-0.95630.702-0.112-0.1120.0000.0000.0000.000
31B860ALA0-0.040-0.02228.333-0.002-0.0020.0000.0000.0000.000
32B861ALA00.0020.00026.196-0.010-0.0100.0000.0000.0000.000
33B862LEU00.0710.03126.779-0.006-0.0060.0000.0000.0000.000
34B863SER0-0.0090.01029.1800.0010.0010.0000.0000.0000.000
35B864LYS10.8140.89623.1600.1750.1750.0000.0000.0000.000
36B865LEU0-0.0200.00624.794-0.009-0.0090.0000.0000.0000.000
37B866ASP-1-0.735-0.83927.120-0.088-0.0880.0000.0000.0000.000
38B867GLU-1-0.823-0.92229.390-0.060-0.0600.0000.0000.0000.000
39B868SER0-0.071-0.03829.7940.0020.0020.0000.0000.0000.000
40B869GLY00.0020.01129.023-0.002-0.0020.0000.0000.0000.000
41B870ILE0-0.069-0.03323.873-0.016-0.0160.0000.0000.0000.000
42B871VAL00.0070.01119.9780.0030.0030.0000.0000.0000.000
43B872TYR0-0.023-0.02523.0150.0150.0150.0000.0000.0000.000
44B873ILE0-0.014-0.00719.219-0.028-0.0280.0000.0000.0000.000
45B874GLY0-0.013-0.00818.5110.0210.0210.0000.0000.0000.000
46B875ALA0-0.035-0.00518.890-0.019-0.0190.0000.0000.0000.000
47B876GLU-1-0.825-0.89613.135-0.704-0.7040.0000.0000.0000.000
48B877VAL0-0.027-0.00415.2990.0390.0390.0000.0000.0000.000
49B878THR0-0.024-0.04614.639-0.102-0.1020.0000.0000.0000.000
50B879GLY00.0020.00215.5900.0480.0480.0000.0000.0000.000
51B880GLY0-0.021-0.01516.8360.0330.0330.0000.0000.0000.000
52B881ASP-1-0.840-0.91218.913-0.308-0.3080.0000.0000.0000.000
53B882ILE0-0.040-0.02320.348-0.011-0.0110.0000.0000.0000.000
54B883LEU0-0.022-0.01216.790-0.003-0.0030.0000.0000.0000.000
55B884VAL0-0.007-0.01621.2190.0200.0200.0000.0000.0000.000
56B885GLY00.0310.00924.354-0.006-0.0060.0000.0000.0000.000
57B886LYS10.7850.86827.0970.1360.1360.0000.0000.0000.000
58B887VAL00.0520.04329.330-0.008-0.0080.0000.0000.0000.000
59B888THR0-0.028-0.00932.1810.0020.0020.0000.0000.0000.000
60B889PRO00.0660.03634.395-0.003-0.0030.0000.0000.0000.000
61B890LYS10.7630.87237.3930.0850.0850.0000.0000.0000.000
62B891GLY00.0500.02139.3810.0010.0010.0000.0000.0000.000
63B892GLU-1-0.742-0.87142.864-0.060-0.0600.0000.0000.0000.000
64B893THR0-0.069-0.03643.6770.0000.0000.0000.0000.0000.000
65B894GLN0-0.035-0.01639.469-0.005-0.0050.0000.0000.0000.000
66B895LEU0-0.0410.02041.387-0.003-0.0030.0000.0000.0000.000
67B896THR00.004-0.02242.1920.0030.0030.0000.0000.0000.000
68B897PRO00.009-0.00944.8880.0020.0020.0000.0000.0000.000
69B898GLU-1-0.829-0.89545.579-0.070-0.0700.0000.0000.0000.000
70B899GLU-1-0.799-0.89941.063-0.085-0.0850.0000.0000.0000.000
71B900LYS10.8030.88845.2800.0640.0640.0000.0000.0000.000
72B901LEU0-0.0030.00848.1090.0030.0030.0000.0000.0000.000
73B902LEU00.005-0.01043.9910.0020.0020.0000.0000.0000.000
74B903ARG10.8520.92345.4300.0600.0600.0000.0000.0000.000
75B904ALA0-0.039-0.01747.8130.0020.0020.0000.0000.0000.000
76B905ILE0-0.084-0.03450.4050.0020.0020.0000.0000.0000.000
77B906PHE0-0.026-0.01547.0170.0010.0010.0000.0000.0000.000
78B907GLY00.0320.03248.6310.0010.0010.0000.0000.0000.000
79B908GLU-1-0.878-0.94546.290-0.054-0.0540.0000.0000.0000.000
80B909LYS10.8370.86942.9880.0540.0540.0000.0000.0000.000
81B910ALA00.0000.02742.403-0.004-0.0040.0000.0000.0000.000
82B911SER00.017-0.00741.097-0.006-0.0060.0000.0000.0000.000
83B912ASP-1-0.877-0.91341.571-0.065-0.0650.0000.0000.0000.000
84B913VAL00.0170.01236.379-0.001-0.0010.0000.0000.0000.000
85B914LYS10.9100.95533.7480.1030.1030.0000.0000.0000.000
86B915ASP-1-0.702-0.81928.399-0.164-0.1640.0000.0000.0000.000
87B916SER0-0.069-0.05128.376-0.002-0.0020.0000.0000.0000.000
88B917SER0-0.034-0.04725.407-0.005-0.0050.0000.0000.0000.000
89B918LEU0-0.0260.00419.014-0.013-0.0130.0000.0000.0000.000
90B919ARG10.8580.90820.4330.2220.2220.0000.0000.0000.000
91B920VAL00.0070.01814.324-0.012-0.0120.0000.0000.0000.000
92B921PRO0-0.001-0.00414.0520.0130.0130.0000.0000.0000.000
93B922ASN00.0320.00215.049-0.039-0.0390.0000.0000.0000.000
94B923GLY0-0.026-0.00412.908-0.034-0.0340.0000.0000.0000.000
95B924VAL0-0.0030.0099.028-0.151-0.1510.0000.0000.0000.000
96B925SER00.018-0.0089.8950.2110.2110.0000.0000.0000.000
97B926GLY0-0.017-0.0069.743-0.332-0.3320.0000.0000.0000.000
98B927THR00.0180.02911.5480.1030.1030.0000.0000.0000.000
99B928VAL00.0110.00213.621-0.013-0.0130.0000.0000.0000.000
100B929ILE0-0.046-0.03212.2830.0350.0350.0000.0000.0000.000
101B930ASP-1-0.807-0.90816.2370.0100.0100.0000.0000.0000.000
102B931VAL0-0.055-0.02318.614-0.037-0.0370.0000.0000.0000.000
103B932GLN0-0.058-0.02321.3680.0210.0210.0000.0000.0000.000
104B933VAL0-0.011-0.00923.382-0.012-0.0120.0000.0000.0000.000
105B934PHE00.0050.01523.5430.0100.0100.0000.0000.0000.000
106B935THR0-0.054-0.05428.842-0.012-0.0120.0000.0000.0000.000
107B936ARG10.8540.94232.3380.0360.0360.0000.0000.0000.000
108B937ASP-1-0.857-0.92934.936-0.011-0.0110.0000.0000.0000.000
109B938GLY00.0110.00538.127-0.002-0.0020.0000.0000.0000.000
110B939VAL0-0.081-0.03435.400-0.002-0.0020.0000.0000.0000.000
111B940GLU-1-0.942-0.96638.108-0.037-0.0370.0000.0000.0000.000
112B941LYS10.8120.89834.8400.0080.0080.0000.0000.0000.000
113B942ASP-1-0.766-0.87632.919-0.055-0.0550.0000.0000.0000.000
114B943LYS10.8300.89735.7250.0510.0510.0000.0000.0000.000
115B944ARG10.9050.94325.1410.0860.0860.0000.0000.0000.000
116B945ALA0-0.009-0.00132.2310.0050.0050.0000.0000.0000.000
117B946LEU00.0220.01133.1490.0070.0070.0000.0000.0000.000
118B947GLU-1-0.888-0.95434.226-0.032-0.0320.0000.0000.0000.000
119B948ILE0-0.034-0.01528.7740.0060.0060.0000.0000.0000.000
120B949GLU-1-0.841-0.92432.553-0.002-0.0020.0000.0000.0000.000
121B950GLU-1-0.820-0.89035.2830.0040.0040.0000.0000.0000.000
122B951MET00.0080.00031.3950.0070.0070.0000.0000.0000.000
123B952GLN00.0380.01230.3260.0080.0080.0000.0000.0000.000
124B953LEU0-0.009-0.00534.5250.0060.0060.0000.0000.0000.000
125B954LYS10.7410.85337.3060.0000.0000.0000.0000.0000.000
126B955GLN0-0.020-0.01230.8410.0020.0020.0000.0000.0000.000
127B956ALA00.0180.01636.2340.0030.0030.0000.0000.0000.000
128B957LYS10.9410.96737.807-0.016-0.0160.0000.0000.0000.000
129B958LYS10.8010.88136.405-0.046-0.0460.0000.0000.0000.000
130B959ASP-1-0.828-0.90635.7860.0500.0500.0000.0000.0000.000
131B960LEU00.0230.01938.5460.0020.0020.0000.0000.0000.000
132B961SER0-0.079-0.04541.8480.0000.0000.0000.0000.0000.000
133B962GLU-1-0.753-0.86137.9460.0500.0500.0000.0000.0000.000
134B963GLU-1-0.808-0.89038.9730.0580.0580.0000.0000.0000.000
135B964LEU00.0320.00842.4630.0000.0000.0000.0000.0000.000
136B965GLN0-0.0220.00344.9580.0000.0000.0000.0000.0000.000
137B966ILE0-0.031-0.02041.0350.0000.0000.0000.0000.0000.000
138B967LEU0-0.0110.00445.4610.0000.0000.0000.0000.0000.000
139B968GLU-1-0.877-0.93047.7300.0320.0320.0000.0000.0000.000
140B969ALA0-0.031-0.01947.9010.0000.0000.0000.0000.0000.000
141B970GLY00.0050.00648.8680.0000.0000.0000.0000.0000.000
142B971LEU00.0210.01449.845-0.001-0.0010.0000.0000.0000.000
143B972PHE00.012-0.00752.752-0.001-0.0010.0000.0000.0000.000
144B973SER0-0.085-0.03252.340-0.001-0.0010.0000.0000.0000.000
145B974ARG10.9160.95654.299-0.042-0.0420.0000.0000.0000.000
146B975ILE00.0480.02356.043-0.001-0.0010.0000.0000.0000.000
147B976ARG10.8160.91058.288-0.032-0.0320.0000.0000.0000.000
148B977ALA0-0.020-0.01358.319-0.001-0.0010.0000.0000.0000.000
149B978VAL0-0.022-0.02159.322-0.001-0.0010.0000.0000.0000.000
150B979LEU00.0590.03861.854-0.001-0.0010.0000.0000.0000.000
151B980VAL0-0.004-0.01963.326-0.001-0.0010.0000.0000.0000.000
152B981ALA0-0.048-0.01563.888-0.001-0.0010.0000.0000.0000.000
153B982GLY00.001-0.02465.8010.0000.0000.0000.0000.0000.000
154B983GLY00.0210.03368.046-0.001-0.0010.0000.0000.0000.000
155B984VAL0-0.0190.00267.5650.0000.0000.0000.0000.0000.000
156B985GLU-1-0.803-0.90368.1280.0210.0210.0000.0000.0000.000
157B986ALA0-0.043-0.02566.1990.0000.0000.0000.0000.0000.000
158B987GLU-1-0.855-0.90865.3360.0240.0240.0000.0000.0000.000
159B988LYS10.8550.91067.144-0.021-0.0210.0000.0000.0000.000
160B989LEU00.0390.01462.5050.0000.0000.0000.0000.0000.000
161B990ASP-1-0.835-0.90860.7440.0280.0280.0000.0000.0000.000
162B991LYS10.7450.87261.396-0.023-0.0230.0000.0000.0000.000
163B992LEU0-0.0160.01463.771-0.001-0.0010.0000.0000.0000.000
164B993PRO00.0110.00960.2960.0010.0010.0000.0000.0000.000
165B994ARG10.8700.91953.689-0.033-0.0330.0000.0000.0000.000
166B995ASP-1-0.800-0.89958.6570.0220.0220.0000.0000.0000.000
167B996ARG10.7790.86859.713-0.020-0.0200.0000.0000.0000.000
168B997TRP0-0.025-0.02458.0120.0010.0010.0000.0000.0000.000
169B998LEU00.0140.00557.8840.0000.0000.0000.0000.0000.000
170B999GLU-1-0.868-0.91462.1480.0190.0190.0000.0000.0000.000
171B1000LEU0-0.084-0.02865.508-0.001-0.0010.0000.0000.0000.000
172B1001GLY00.0150.01266.3930.0010.0010.0000.0000.0000.000
173B1002LEU0-0.036-0.02165.8910.0000.0000.0000.0000.0000.000
174B1003THR0-0.038-0.02769.341-0.001-0.0010.0000.0000.0000.000
175B1004ASP-1-0.938-0.95870.6260.0230.0230.0000.0000.0000.000
176B1005GLU-1-0.809-0.89568.7100.0280.0280.0000.0000.0000.000
177B1006GLU-1-0.903-0.96765.2720.0300.0300.0000.0000.0000.000
178B1007LYS10.7600.86364.364-0.028-0.0280.0000.0000.0000.000
179B1008GLN00.0260.00964.1990.0010.0010.0000.0000.0000.000
180B1009ASN00.0310.01063.9950.0000.0000.0000.0000.0000.000
181B1010GLN0-0.036-0.02160.2690.0020.0020.0000.0000.0000.000
182B1011LEU0-0.0190.00159.7510.0010.0010.0000.0000.0000.000
183B1012GLU-1-0.826-0.90560.5680.0260.0260.0000.0000.0000.000
184B1013GLN0-0.071-0.03657.4150.0010.0010.0000.0000.0000.000
185B1014LEU0-0.046-0.02954.8340.0010.0010.0000.0000.0000.000
186B1015ALA00.0150.00955.7480.0010.0010.0000.0000.0000.000
187B1016GLU-1-0.910-0.95256.6720.0300.0300.0000.0000.0000.000
188B1017GLN00.001-0.00952.2460.0010.0010.0000.0000.0000.000
189B1018TYR0-0.032-0.01151.4630.0010.0010.0000.0000.0000.000
190B1019ASP-1-0.818-0.92051.6190.0280.0280.0000.0000.0000.000
191B1020GLU-1-0.962-0.96350.7480.0370.0370.0000.0000.0000.000
192B1021LEU0-0.004-0.01446.7610.0010.0010.0000.0000.0000.000
193B1022LYS10.8570.93047.302-0.026-0.0260.0000.0000.0000.000
194B1023HIS00.0270.02947.9780.0000.0000.0000.0000.0000.000
195B1024GLU-1-0.844-0.91145.3630.0340.0340.0000.0000.0000.000
196B1025PHE0-0.046-0.03241.2270.0010.0010.0000.0000.0000.000
197B1026GLU-1-0.889-0.96243.7450.0260.0260.0000.0000.0000.000
198B1027LYS10.7920.87944.952-0.033-0.0330.0000.0000.0000.000
199B1028LYS10.8010.89138.091-0.056-0.0560.0000.0000.0000.000
200B1029LEU0-0.0110.00640.3700.0000.0000.0000.0000.0000.000
201B1030GLU-1-0.787-0.85641.1400.0160.0160.0000.0000.0000.000
202B1031ALA0-0.053-0.02439.970-0.002-0.0020.0000.0000.0000.000
203B1032LYS10.8660.92934.649-0.049-0.0490.0000.0000.0000.000
204B1033ARG10.8520.88137.771-0.018-0.0180.0000.0000.0000.000
205B1034ARG10.9100.96539.135-0.017-0.0170.0000.0000.0000.000
206B1035LYS10.9150.94533.786-0.042-0.0420.0000.0000.0000.000
207B1036ILE0-0.0340.00234.427-0.002-0.0020.0000.0000.0000.000
208B1037THR0-0.014-0.01835.947-0.004-0.0040.0000.0000.0000.000
209B1038GLN0-0.0400.00936.1590.0000.0000.0000.0000.0000.000
210B1039GLY00.0240.00535.129-0.001-0.0010.0000.0000.0000.000
211B1040ASP-1-0.859-0.93830.646-0.008-0.0080.0000.0000.0000.000
212B1041ASP-1-0.945-0.97733.041-0.010-0.0100.0000.0000.0000.000
213B1042LEU0-0.046-0.01429.172-0.001-0.0010.0000.0000.0000.000
214B1043ALA00.0310.01630.8460.0020.0020.0000.0000.0000.000
215B1044PRO00.011-0.00732.633-0.002-0.0020.0000.0000.0000.000
216B1045GLY00.0160.01134.471-0.004-0.0040.0000.0000.0000.000
217B1046VAL0-0.053-0.01629.526-0.007-0.0070.0000.0000.0000.000
218B1047LEU0-0.0020.00932.7820.0070.0070.0000.0000.0000.000
219B1048LYS10.9140.94730.3980.0610.0610.0000.0000.0000.000
220B1049ILE0-0.042-0.01924.524-0.009-0.0090.0000.0000.0000.000
221B1050VAL00.0260.01923.1240.0090.0090.0000.0000.0000.000
222B1051LYS10.8360.90919.5280.0180.0180.0000.0000.0000.000
223B1052VAL00.0270.00416.8950.0090.0090.0000.0000.0000.000
224B1053TYR0-0.065-0.04314.625-0.019-0.0190.0000.0000.0000.000
225B1054LEU00.0260.01311.4140.0090.0090.0000.0000.0000.000
226B1055ALA0-0.010-0.0079.619-0.040-0.0400.0000.0000.0000.000
227B1056VAL0-0.022-0.0016.160-0.160-0.1600.0000.0000.0000.000
228B1057LYS10.8360.9024.309-0.304-0.1830.000-0.068-0.0540.000