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: J3Y69

Calculation Name: 1TUE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TUE

Chain ID: B

ChEMBL ID:

UniProt ID: P06789

Base Structure: X-ray

Registration Date: 2023-03-13

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2101169.400292
FMO2-HF: Nuclear repulsion 2020569.426408
FMO2-HF: Total energy -80599.973884
FMO2-MP2: Total energy -80832.553461


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:0:HIS)


Summations of interaction energy for fragment #1(B:0:HIS)
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.
-34.021-28.7839.678-6.207-8.711-0.049
Interaction energy analysis for fragmet #1(B:0:HIS)
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 : -0.020
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].
3B2GLN00.0000.0083.072-5.121-0.2981.688-2.284-4.2270.003
4B3THR00.009-0.0033.2343.3493.9490.009-0.164-0.4450.001
5B4PRO00.0600.0115.2340.0450.085-0.001-0.001-0.0390.000
6B5LYS10.9240.9597.7882.8032.8030.0000.0000.0000.000
7B6GLU-1-0.806-0.8962.001-34.773-34.9987.982-3.758-4.000-0.053
8B7THR00.0180.0085.9780.8360.8360.0000.0000.0000.000
9B8LEU0-0.069-0.0468.3070.6170.6170.0000.0000.0000.000
10B9SER0-0.052-0.0378.4150.2270.2270.0000.0000.0000.000
11B10GLU-1-0.825-0.8967.193-2.491-2.4910.0000.0000.0000.000
12B11ARG10.9140.9499.7832.1642.1640.0000.0000.0000.000
13B12LEU0-0.019-0.00513.0110.2120.2120.0000.0000.0000.000
14B13SER00.013-0.00512.7220.1590.1590.0000.0000.0000.000
15B14ALA00.0360.04114.1450.1500.1500.0000.0000.0000.000
16B15LEU0-0.070-0.04015.8000.1390.1390.0000.0000.0000.000
17B16GLN0-0.025-0.04317.9400.0180.0180.0000.0000.0000.000
18B17ASP-1-0.875-0.92216.762-0.779-0.7790.0000.0000.0000.000
19B18LYS10.9390.97019.3930.7270.7270.0000.0000.0000.000
20B19ILE0-0.060-0.03021.9060.0560.0560.0000.0000.0000.000
21B20ILE00.015-0.00222.1990.0460.0460.0000.0000.0000.000
22B21ASP-1-0.818-0.89622.987-0.424-0.4240.0000.0000.0000.000
23B22HIS0-0.100-0.05125.7510.0590.0590.0000.0000.0000.000
24B23TYR0-0.062-0.03627.0870.0110.0110.0000.0000.0000.000
25B24GLU-1-0.965-0.97226.958-0.315-0.3150.0000.0000.0000.000
26B25ASN0-0.117-0.07428.2500.0450.0450.0000.0000.0000.000
27B26ASP-1-0.883-0.93131.598-0.210-0.2100.0000.0000.0000.000
28B27SER0-0.033-0.03233.0870.0270.0270.0000.0000.0000.000
29B28LYS10.8860.94134.9160.1970.1970.0000.0000.0000.000
30B29ASP-1-0.789-0.87334.649-0.229-0.2290.0000.0000.0000.000
31B30ILE00.0540.01735.578-0.018-0.0180.0000.0000.0000.000
32B31ASP-1-0.839-0.91233.718-0.247-0.2470.0000.0000.0000.000
33B32SER0-0.053-0.02831.262-0.024-0.0240.0000.0000.0000.000
34B33GLN00.0450.02730.821-0.046-0.0460.0000.0000.0000.000
35B34ILE0-0.041-0.01431.411-0.027-0.0270.0000.0000.0000.000
36B35GLN0-0.0080.00026.283-0.052-0.0520.0000.0000.0000.000
37B36TYR00.0320.02027.093-0.042-0.0420.0000.0000.0000.000
38B37TRP00.0440.00227.317-0.060-0.0600.0000.0000.0000.000
39B38GLN0-0.046-0.02325.980-0.035-0.0350.0000.0000.0000.000
40B39LEU0-0.0110.00021.907-0.062-0.0620.0000.0000.0000.000
41B40ILE00.0470.04122.953-0.077-0.0770.0000.0000.0000.000
42B41ARG10.8750.93924.7120.4300.4300.0000.0000.0000.000
43B42TRP0-0.032-0.01820.386-0.046-0.0460.0000.0000.0000.000
44B43GLU-1-0.783-0.87919.908-0.837-0.8370.0000.0000.0000.000
45B44ASN0-0.093-0.07420.120-0.077-0.0770.0000.0000.0000.000
46B45ALA00.0040.00721.163-0.013-0.0130.0000.0000.0000.000
47B46ILE0-0.010-0.00215.095-0.059-0.0590.0000.0000.0000.000
48B47PHE00.014-0.00116.985-0.125-0.1250.0000.0000.0000.000
49B48PHE0-0.044-0.01618.9550.0220.0220.0000.0000.0000.000
50B49ALA00.0420.02016.8290.0010.0010.0000.0000.0000.000
51B50ALA0-0.002-0.00114.931-0.080-0.0800.0000.0000.0000.000
52B51ARG10.8400.91215.9040.7890.7890.0000.0000.0000.000
53B52GLU-1-0.932-0.97818.882-0.778-0.7780.0000.0000.0000.000
54B53HIS0-0.092-0.03413.206-0.027-0.0270.0000.0000.0000.000
55B54GLY0-0.0130.00014.785-0.122-0.1220.0000.0000.0000.000
56B55ILE0-0.077-0.02911.557-0.107-0.1070.0000.0000.0000.000
57B56GLN0-0.0040.00014.9120.0780.0780.0000.0000.0000.000
58B57THR00.005-0.01015.1770.0380.0380.0000.0000.0000.000
59B58LEU00.021-0.01011.314-0.316-0.3160.0000.0000.0000.000
60B59ASN00.0260.03911.621-0.163-0.1630.0000.0000.0000.000
61B60HIS0-0.005-0.00613.3990.1730.1730.0000.0000.0000.000
62B61GLN0-0.0070.01316.1000.2180.2180.0000.0000.0000.000
63B62VAL00.0180.00017.435-0.118-0.1180.0000.0000.0000.000
64B63VAL0-0.0100.01016.5010.0410.0410.0000.0000.0000.000
65B64PRO00.0360.03419.5670.0670.0670.0000.0000.0000.000
66B65ALA00.0270.02322.792-0.037-0.0370.0000.0000.0000.000
67B66TYR00.0810.02022.1910.0170.0170.0000.0000.0000.000
68B67ASN0-0.002-0.01525.743-0.019-0.0190.0000.0000.0000.000
69B68ILE00.0160.01926.6030.0240.0240.0000.0000.0000.000
70B69SER00.0400.01923.0800.0040.0040.0000.0000.0000.000
71B70LYS10.9530.97125.5050.4990.4990.0000.0000.0000.000
72B71SER0-0.014-0.00228.1330.0240.0240.0000.0000.0000.000
73B72LYS10.9450.96724.7610.6420.6420.0000.0000.0000.000
74B73ALA0-0.0030.00726.2300.0080.0080.0000.0000.0000.000
75B74HIS0-0.016-0.00828.1420.0030.0030.0000.0000.0000.000
76B75LYS10.8330.89831.7080.3470.3470.0000.0000.0000.000
77B76ALA00.0220.01728.9610.0170.0170.0000.0000.0000.000
78B77ILE0-0.070-0.04429.3060.0120.0120.0000.0000.0000.000
79B78GLU-1-0.831-0.90032.056-0.283-0.2830.0000.0000.0000.000
80B79LEU00.0470.03233.8650.0180.0180.0000.0000.0000.000
81B80GLN0-0.011-0.00729.855-0.015-0.0150.0000.0000.0000.000
82B81MET0-0.055-0.03533.6130.0140.0140.0000.0000.0000.000
83B82ALA00.0120.02436.2390.0170.0170.0000.0000.0000.000
84B83LEU00.0260.01034.7330.0140.0140.0000.0000.0000.000
85B84GLN00.0020.00033.043-0.001-0.0010.0000.0000.0000.000
86B85GLY00.0250.02437.3830.0110.0110.0000.0000.0000.000
87B86LEU0-0.0030.00640.6910.0130.0130.0000.0000.0000.000
88B87ALA0-0.0040.00538.5740.0130.0130.0000.0000.0000.000
89B88GLN0-0.071-0.03740.0090.0080.0080.0000.0000.0000.000
90B89SER0-0.021-0.01643.0420.0120.0120.0000.0000.0000.000
91B90ALA00.003-0.01445.7160.0000.0000.0000.0000.0000.000
92B91TYR0-0.002-0.01046.0740.0060.0060.0000.0000.0000.000
93B92LYS10.8180.92637.7760.1990.1990.0000.0000.0000.000
94B93THR0-0.011-0.02541.923-0.006-0.0060.0000.0000.0000.000
95B94GLU-1-0.817-0.84243.887-0.153-0.1530.0000.0000.0000.000
96B95ASP-1-0.877-0.93941.884-0.174-0.1740.0000.0000.0000.000
97B96TRP0-0.073-0.05539.020-0.003-0.0030.0000.0000.0000.000
98B97THR0-0.002-0.02737.255-0.013-0.0130.0000.0000.0000.000
99B98LEU00.0630.02931.194-0.006-0.0060.0000.0000.0000.000
100B99GLN0-0.0030.00135.285-0.011-0.0110.0000.0000.0000.000
101B100ASP-1-0.812-0.87538.303-0.205-0.2050.0000.0000.0000.000
102B101THR0-0.076-0.05336.114-0.004-0.0040.0000.0000.0000.000
103B102CYS0-0.0260.01635.150-0.019-0.0190.0000.0000.0000.000
104B103GLU-1-0.771-0.89033.642-0.354-0.3540.0000.0000.0000.000
105B104GLU-1-0.960-0.97836.341-0.256-0.2560.0000.0000.0000.000
106B105LEU00.0260.01638.8020.0120.0120.0000.0000.0000.000
107B106TRP0-0.043-0.02538.6070.0150.0150.0000.0000.0000.000
108B107ASN0-0.025-0.04337.3380.0080.0080.0000.0000.0000.000
109B108THR0-0.045-0.01141.4190.0090.0090.0000.0000.0000.000
110B109GLU-1-0.823-0.88344.632-0.195-0.1950.0000.0000.0000.000
111B110PRO0-0.021-0.02747.9260.0050.0050.0000.0000.0000.000
112B111THR00.002-0.00543.494-0.004-0.0040.0000.0000.0000.000
113B112HIS0-0.062-0.04740.0940.0150.0150.0000.0000.0000.000
114B113CYS0-0.053-0.00643.4110.0090.0090.0000.0000.0000.000
115B114PHE00.0080.00838.941-0.009-0.0090.0000.0000.0000.000
116B115LYS10.7960.88743.9940.2260.2260.0000.0000.0000.000
117B116LYS10.8530.93643.7370.1770.1770.0000.0000.0000.000
118B117GLY00.0280.01947.5950.0050.0050.0000.0000.0000.000
119B118GLY00.011-0.00649.5190.0030.0030.0000.0000.0000.000
120B119GLN0-0.049-0.03051.0150.0050.0050.0000.0000.0000.000
121B120THR0-0.031-0.01654.481-0.003-0.0030.0000.0000.0000.000
122B121VAL00.0110.00455.4810.0060.0060.0000.0000.0000.000
123B122GLN00.0220.02657.029-0.001-0.0010.0000.0000.0000.000
124B123VAL00.0280.01159.0700.0050.0050.0000.0000.0000.000
125B124TYR0-0.025-0.00560.438-0.002-0.0020.0000.0000.0000.000
126B125PHE00.0320.00258.3890.0030.0030.0000.0000.0000.000
127B126ASP-1-0.796-0.87163.936-0.107-0.1070.0000.0000.0000.000
128B127GLY0-0.049-0.01367.4190.0030.0030.0000.0000.0000.000
129B128ASN0-0.051-0.04664.3190.0040.0040.0000.0000.0000.000
130B129LYS10.8190.90064.6970.0940.0940.0000.0000.0000.000
131B130ASP-1-0.896-0.93662.163-0.110-0.1100.0000.0000.0000.000
132B131ASN0-0.036-0.01259.990-0.008-0.0080.0000.0000.0000.000
133B132CYS0-0.038-0.03059.2790.0010.0010.0000.0000.0000.000
134B133MET0-0.0140.01452.074-0.005-0.0050.0000.0000.0000.000
135B134THR0-0.033-0.02453.2230.0050.0050.0000.0000.0000.000
136B135TYR0-0.047-0.06752.829-0.005-0.0050.0000.0000.0000.000
137B136VAL0-0.0060.01149.6540.0040.0040.0000.0000.0000.000
138B137ALA00.0000.00452.668-0.002-0.0020.0000.0000.0000.000
139B138TRP0-0.022-0.02046.7280.0020.0020.0000.0000.0000.000
140B139ASP-1-0.797-0.88352.069-0.128-0.1280.0000.0000.0000.000
141B140SER0-0.109-0.05850.0660.0050.0050.0000.0000.0000.000
142B141VAL0-0.007-0.00249.090-0.008-0.0080.0000.0000.0000.000
143B142TYR0-0.055-0.08545.8560.0070.0070.0000.0000.0000.000
144B143TYR00.0560.01646.603-0.007-0.0070.0000.0000.0000.000
145B144MET0-0.0050.00444.095-0.001-0.0010.0000.0000.0000.000
146B145THR0-0.004-0.01547.1080.0010.0010.0000.0000.0000.000
147B146ASP-1-0.886-0.95948.495-0.163-0.1630.0000.0000.0000.000
148B147ALA0-0.079-0.03849.122-0.003-0.0030.0000.0000.0000.000
149B148GLY0-0.025-0.01145.665-0.003-0.0030.0000.0000.0000.000
150B149THR0-0.0200.00745.003-0.006-0.0060.0000.0000.0000.000
151B150TRP0-0.004-0.00642.075-0.001-0.0010.0000.0000.0000.000
152B151ASP-1-0.896-0.94947.093-0.138-0.1380.0000.0000.0000.000
153B152LYS10.8390.91949.7620.1390.1390.0000.0000.0000.000
154B153THR0-0.052-0.02051.3540.0080.0080.0000.0000.0000.000
155B154ALA00.0480.03253.273-0.005-0.0050.0000.0000.0000.000
156B155THR0-0.033-0.01053.806-0.002-0.0020.0000.0000.0000.000
157B156CYS0-0.086-0.03656.2150.0060.0060.0000.0000.0000.000
158B157VAL00.0430.01759.068-0.004-0.0040.0000.0000.0000.000
159B158SER0-0.037-0.02161.1200.0050.0050.0000.0000.0000.000
160B159HIS00.0380.01062.965-0.002-0.0020.0000.0000.0000.000
161B160ARG10.8340.89260.0030.1220.1220.0000.0000.0000.000
162B161GLY00.0430.01259.396-0.003-0.0030.0000.0000.0000.000
163B162LEU0-0.0310.00654.6510.0050.0050.0000.0000.0000.000
164B163TYR00.0130.00256.222-0.003-0.0030.0000.0000.0000.000
165B164TYR00.0580.03450.4170.0020.0020.0000.0000.0000.000
166B165VAL0-0.003-0.00756.1580.0000.0000.0000.0000.0000.000
167B166LYS10.8770.94550.9370.1580.1580.0000.0000.0000.000
168B167GLU-1-0.796-0.90652.948-0.146-0.1460.0000.0000.0000.000
169B168GLY0-0.018-0.00556.6410.0020.0020.0000.0000.0000.000
170B169TYR0-0.019-0.00457.6780.0060.0060.0000.0000.0000.000
171B170ASN0-0.039-0.01757.831-0.005-0.0050.0000.0000.0000.000
172B171THR0-0.0010.00053.233-0.001-0.0010.0000.0000.0000.000
173B172PHE0-0.031-0.02555.5350.0000.0000.0000.0000.0000.000
174B173TYR00.015-0.00751.176-0.004-0.0040.0000.0000.0000.000
175B174ILE0-0.0100.00651.739-0.005-0.0050.0000.0000.0000.000
176B175GLU-1-0.789-0.86854.997-0.124-0.1240.0000.0000.0000.000
177B176PHE00.027-0.00857.426-0.002-0.0020.0000.0000.0000.000
178B177LYS10.8490.92060.0750.1190.1190.0000.0000.0000.000
179B178SER0-0.003-0.01556.7470.0000.0000.0000.0000.0000.000
180B179GLU-1-0.780-0.84454.442-0.159-0.1590.0000.0000.0000.000
181B180CYS00.0320.03157.8590.0010.0010.0000.0000.0000.000
182B181GLU-1-0.902-0.93360.523-0.121-0.1210.0000.0000.0000.000
183B182LYS10.7710.86652.5860.1570.1570.0000.0000.0000.000
184B183TYR0-0.016-0.01152.739-0.006-0.0060.0000.0000.0000.000
185B184GLY00.0350.03859.3070.0020.0020.0000.0000.0000.000
186B185ASN0-0.099-0.04261.7410.0010.0010.0000.0000.0000.000
187B186THR00.024-0.01164.9260.0030.0030.0000.0000.0000.000
188B187GLY0-0.033-0.01666.7010.0030.0030.0000.0000.0000.000
189B188THR0-0.078-0.04267.7230.0010.0010.0000.0000.0000.000
190B189TRP00.013-0.01163.700-0.002-0.0020.0000.0000.0000.000
191B190GLU-1-0.838-0.89165.257-0.092-0.0920.0000.0000.0000.000
192B191VAL00.011-0.00261.587-0.003-0.0030.0000.0000.0000.000
193B192HIS0-0.071-0.04962.6830.0030.0030.0000.0000.0000.000
194B193PHE00.0100.00558.417-0.002-0.0020.0000.0000.0000.000