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: 2N5LR

Calculation Name: 1QDL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QDL

Chain ID: B

ChEMBL ID:

UniProt ID: Q06128

Base Structure: X-ray

Registration Date: 2023-09-23

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2309270.272267
FMO2-HF: Nuclear repulsion 2233765.42433
FMO2-HF: Total energy -75504.847936
FMO2-MP2: Total energy -75729.882126


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:1:MET)


Summations of interaction energy for fragment #1(B:1: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.
-8.66-3.3773.45-2.604-6.128-0.01
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.016
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].
3B3LEU0-0.002-0.0022.957-1.9361.3650.232-1.530-2.003-0.003
4B4THR0-0.014-0.0214.5050.8640.995-0.001-0.023-0.1070.000
5B5LEU00.0100.0078.1090.2380.2380.0000.0000.0000.000
6B6ILE0-0.037-0.0379.7720.1790.1790.0000.0000.0000.000
7B7ILE00.0250.00912.6580.0610.0610.0000.0000.0000.000
8B8ASP-1-0.767-0.86815.764-0.350-0.3500.0000.0000.0000.000
9B9ASN0-0.032-0.02117.7150.0110.0110.0000.0000.0000.000
10B10TYR0-0.053-0.07020.9690.0490.0490.0000.0000.0000.000
11B11ASP-1-0.746-0.88820.333-0.297-0.2970.0000.0000.0000.000
12B12SER0-0.085-0.05121.6660.0180.0180.0000.0000.0000.000
13B13PHE0-0.042-0.02221.1290.0270.0270.0000.0000.0000.000
14B14VAL00.001-0.00715.337-0.007-0.0070.0000.0000.0000.000
15B15TYR00.0490.01813.975-0.056-0.0560.0000.0000.0000.000
16B16ASN0-0.032-0.01315.5660.0280.0280.0000.0000.0000.000
17B17ILE0-0.019-0.00914.0650.0150.0150.0000.0000.0000.000
18B18ALA00.0240.01211.405-0.044-0.0440.0000.0000.0000.000
19B19GLN0-0.028-0.00611.4290.0580.0580.0000.0000.0000.000
20B20ILE00.0040.00913.3080.0490.0490.0000.0000.0000.000
21B21VAL0-0.037-0.0248.8290.0110.0110.0000.0000.0000.000
22B22GLY00.0400.0258.874-0.079-0.0790.0000.0000.0000.000
23B23GLU-1-0.908-0.9199.7580.2160.2160.0000.0000.0000.000
24B24LEU0-0.095-0.05011.6830.0600.0600.0000.0000.0000.000
25B25GLY0-0.023-0.0018.010-0.105-0.1050.0000.0000.0000.000
26B26SER0-0.060-0.0255.6650.0820.0820.0000.0000.0000.000
27B27TYR00.029-0.0082.592-2.176-0.4703.221-1.028-3.898-0.007
28B28PRO0-0.032-0.0064.443-1.043-0.991-0.001-0.020-0.0310.000
29B29ILE0-0.008-0.0114.6400.0080.101-0.001-0.003-0.0890.000
30B30VAL0-0.021-0.0117.9890.0280.0280.0000.0000.0000.000
31B31ILE0-0.0090.00311.7670.0130.0130.0000.0000.0000.000
32B32ARG10.8440.91213.9250.3460.3460.0000.0000.0000.000
33B33ASN0-0.082-0.04717.652-0.023-0.0230.0000.0000.0000.000
34B34ASP-1-0.793-0.88619.701-0.378-0.3780.0000.0000.0000.000
35B35GLU-1-0.856-0.91416.737-0.458-0.4580.0000.0000.0000.000
36B36ILE0-0.027-0.00513.283-0.023-0.0230.0000.0000.0000.000
37B37SER0-0.0020.00517.318-0.003-0.0030.0000.0000.0000.000
38B38ILE00.0760.03117.310-0.068-0.0680.0000.0000.0000.000
39B39LYS10.8060.87717.2870.5140.5140.0000.0000.0000.000
40B40GLY0-0.0140.00215.2990.0130.0130.0000.0000.0000.000
41B41ILE00.0430.01012.940-0.125-0.1250.0000.0000.0000.000
42B42GLU-1-0.778-0.89412.551-0.869-0.8690.0000.0000.0000.000
43B43ARG10.8130.91312.8490.6760.6760.0000.0000.0000.000
44B44ILE0-0.030-0.0127.2870.0540.0540.0000.0000.0000.000
45B45ASP-1-0.978-0.9728.248-2.405-2.4050.0000.0000.0000.000
46B46PRO0-0.0150.0107.561-0.463-0.4630.0000.0000.0000.000
47B47ASP-1-0.809-0.9006.033-5.441-5.4410.0000.0000.0000.000
48B48ARG10.7460.8347.8842.9172.9170.0000.0000.0000.000
49B49LEU0-0.0050.00010.588-0.182-0.1820.0000.0000.0000.000
50B50ILE0-0.017-0.01613.2100.1590.1590.0000.0000.0000.000
51B51ILE0-0.0260.00415.198-0.003-0.0030.0000.0000.0000.000
52B52SER00.032-0.00617.8480.0380.0380.0000.0000.0000.000
53B53PRO0-0.045-0.01119.3740.0150.0150.0000.0000.0000.000
54B54GLY00.0950.06122.208-0.027-0.0270.0000.0000.0000.000
55B55PRO0-0.060-0.01524.8190.0140.0140.0000.0000.0000.000
56B56GLY00.0470.01427.998-0.009-0.0090.0000.0000.0000.000
57B57THR0-0.089-0.10030.228-0.005-0.0050.0000.0000.0000.000
58B58PRO00.012-0.00427.450-0.002-0.0020.0000.0000.0000.000
59B59GLU-1-0.905-0.92229.061-0.219-0.2190.0000.0000.0000.000
60B60LYS10.7690.87331.4070.2290.2290.0000.0000.0000.000
61B61ARG10.8610.88924.4950.3740.3740.0000.0000.0000.000
62B62GLU-1-0.872-0.92826.991-0.237-0.2370.0000.0000.0000.000
63B63ASP-1-0.752-0.85326.917-0.247-0.2470.0000.0000.0000.000
64B64ILE0-0.063-0.02423.946-0.017-0.0170.0000.0000.0000.000
65B65GLY00.0410.03722.813-0.045-0.0450.0000.0000.0000.000
66B66VAL0-0.047-0.03618.4410.0150.0150.0000.0000.0000.000
67B67SER00.005-0.00820.186-0.049-0.0490.0000.0000.0000.000
68B68LEU0-0.037-0.02421.235-0.023-0.0230.0000.0000.0000.000
69B69ASP-1-0.818-0.87422.267-0.429-0.4290.0000.0000.0000.000
70B70VAL00.0200.00516.978-0.015-0.0150.0000.0000.0000.000
71B71ILE0-0.002-0.00719.920-0.032-0.0320.0000.0000.0000.000
72B72LYS10.8890.96221.9220.3700.3700.0000.0000.0000.000
73B73TYR0-0.048-0.02221.9560.0310.0310.0000.0000.0000.000
74B74LEU00.0240.01415.3670.0080.0080.0000.0000.0000.000
75B75GLY00.0620.03018.356-0.048-0.0480.0000.0000.0000.000
76B76LYS10.7540.86519.8640.4350.4350.0000.0000.0000.000
77B77ARG10.8900.92816.4280.6660.6660.0000.0000.0000.000
78B78THR00.0660.05212.7290.0000.0000.0000.0000.0000.000
79B79PRO0-0.022-0.01613.5580.1470.1470.0000.0000.0000.000
80B80ILE0-0.0210.00214.936-0.090-0.0900.0000.0000.0000.000
81B81LEU0-0.0140.00416.9450.0920.0920.0000.0000.0000.000
82B82GLY00.0180.00918.250-0.031-0.0310.0000.0000.0000.000
83B83VAL00.028-0.00619.7270.0370.0370.0000.0000.0000.000
84B84CYS0-0.020-0.00722.4190.0080.0080.0000.0000.0000.000
85B85LEU00.0160.02924.473-0.004-0.0040.0000.0000.0000.000
86B86GLY00.0830.03421.788-0.004-0.0040.0000.0000.0000.000
87B87HIS0-0.060-0.01922.791-0.035-0.0350.0000.0000.0000.000
88B88GLN00.0280.00524.9740.0120.0120.0000.0000.0000.000
89B89ALA0-0.001-0.00123.8960.0130.0130.0000.0000.0000.000
90B90ILE00.004-0.00121.3600.0050.0050.0000.0000.0000.000
91B91GLY00.0290.00025.5730.0110.0110.0000.0000.0000.000
92B92TYR00.0010.00229.1460.0090.0090.0000.0000.0000.000
93B93ALA0-0.049-0.02126.2230.0110.0110.0000.0000.0000.000
94B94PHE00.002-0.01224.9630.0010.0010.0000.0000.0000.000
95B95GLY00.0080.00530.4620.0180.0180.0000.0000.0000.000
96B96ALA0-0.0450.00332.4040.0180.0180.0000.0000.0000.000
97B97LYS10.8310.87934.0030.1770.1770.0000.0000.0000.000
98B98ILE0-0.0020.00630.923-0.010-0.0100.0000.0000.0000.000
99B99ARG10.7110.80734.8900.1810.1810.0000.0000.0000.000
100B100ARG10.9810.98536.3700.1370.1370.0000.0000.0000.000
101B101ALA0-0.0030.01536.2000.0030.0030.0000.0000.0000.000
102B102ARG10.8550.91938.1880.1570.1570.0000.0000.0000.000
103B103LYS10.8790.93939.7090.1250.1250.0000.0000.0000.000
104B104VAL00.0360.02936.476-0.009-0.0090.0000.0000.0000.000
105B105PHE0-0.039-0.02434.1990.0110.0110.0000.0000.0000.000
106B106HIS00.0350.02432.701-0.019-0.0190.0000.0000.0000.000
107B107GLY00.0660.03131.2540.0110.0110.0000.0000.0000.000
108B108LYS10.8460.93232.3050.1250.1250.0000.0000.0000.000
109B109ILE00.0100.00431.512-0.012-0.0120.0000.0000.0000.000
110B110SER0-0.088-0.06433.1180.0020.0020.0000.0000.0000.000
111B111ASN0-0.004-0.02833.401-0.002-0.0020.0000.0000.0000.000
112B112ILE00.0060.01429.775-0.001-0.0010.0000.0000.0000.000
113B113ILE00.0360.00533.0100.0040.0040.0000.0000.0000.000
114B114LEU0-0.020-0.01028.795-0.011-0.0110.0000.0000.0000.000
115B115VAL0-0.033-0.02932.7710.0140.0140.0000.0000.0000.000
116B116ASN0-0.007-0.00629.9240.0050.0050.0000.0000.0000.000
117B117ASN0-0.005-0.00332.5450.0140.0140.0000.0000.0000.000
118B118SER0-0.012-0.01131.1780.0090.0090.0000.0000.0000.000
119B119PRO0-0.0060.01427.731-0.011-0.0110.0000.0000.0000.000
120B120LEU00.0400.01425.572-0.012-0.0120.0000.0000.0000.000
121B121SER0-0.0040.00219.9940.0360.0360.0000.0000.0000.000
122B122LEU00.0080.01619.4560.0080.0080.0000.0000.0000.000
123B123TYR00.021-0.00821.8140.0110.0110.0000.0000.0000.000
124B124TYR00.0210.02322.1180.0390.0390.0000.0000.0000.000
125B125GLY00.0270.00823.8860.0030.0030.0000.0000.0000.000
126B126ILE0-0.0440.00223.8090.0170.0170.0000.0000.0000.000
127B127ALA00.0140.00927.4700.0070.0070.0000.0000.0000.000
128B128LYS10.9230.93431.2270.1080.1080.0000.0000.0000.000
129B129GLU-1-0.870-0.91233.599-0.123-0.1230.0000.0000.0000.000
130B130PHE0-0.025-0.01127.7140.0090.0090.0000.0000.0000.000
131B131LYS10.9050.95131.3280.1110.1110.0000.0000.0000.000
132B132ALA00.0510.02128.039-0.006-0.0060.0000.0000.0000.000
133B133THR0-0.0320.01127.8670.0140.0140.0000.0000.0000.000
134B134ARG10.8240.89328.5470.1520.1520.0000.0000.0000.000
135B135TYR00.0260.00427.0270.0240.0240.0000.0000.0000.000
136B136HIS00.0390.01629.553-0.008-0.0080.0000.0000.0000.000
137B137SER00.023-0.01431.7810.0110.0110.0000.0000.0000.000
138B138LEU0-0.0450.00432.2000.0110.0110.0000.0000.0000.000
139B139VAL0-0.0130.00032.620-0.004-0.0040.0000.0000.0000.000
140B140VAL00.0330.02529.8670.0020.0020.0000.0000.0000.000
141B141ASP-1-0.806-0.88733.186-0.167-0.1670.0000.0000.0000.000
142B142GLU-1-0.833-0.90636.063-0.185-0.1850.0000.0000.0000.000
143B143VAL0-0.017-0.00732.493-0.007-0.0070.0000.0000.0000.000
144B144HIS10.8070.90334.6530.2490.2490.0000.0000.0000.000
145B145ARG10.9340.95633.4610.2130.2130.0000.0000.0000.000
146B146PRO0-0.0020.01529.8580.0130.0130.0000.0000.0000.000
147B147LEU0-0.030-0.00927.432-0.021-0.0210.0000.0000.0000.000
148B148ILE0-0.023-0.01529.9820.0260.0260.0000.0000.0000.000
149B149VAL00.0070.00430.208-0.017-0.0170.0000.0000.0000.000
150B150ASP-1-0.827-0.90228.020-0.303-0.3030.0000.0000.0000.000
151B151ALA00.008-0.00530.1480.0100.0100.0000.0000.0000.000
152B152ILE0-0.0200.00831.966-0.006-0.0060.0000.0000.0000.000
153B153SER0-0.011-0.02334.8590.0050.0050.0000.0000.0000.000
154B154ALA00.024-0.00536.1700.0050.0050.0000.0000.0000.000
155B155GLU-1-0.781-0.83237.260-0.132-0.1320.0000.0000.0000.000
156B156ASP-1-0.819-0.90938.026-0.143-0.1430.0000.0000.0000.000
157B157ASN0-0.0120.00939.3020.0040.0040.0000.0000.0000.000
158B158GLU-1-0.703-0.82335.750-0.167-0.1670.0000.0000.0000.000
159B159ILE00.0190.00431.8220.0000.0000.0000.0000.0000.000
160B160MET0-0.039-0.01830.466-0.005-0.0050.0000.0000.0000.000
161B161ALA0-0.030-0.01327.060-0.016-0.0160.0000.0000.0000.000
162B162ILE0-0.0240.00026.6670.0260.0260.0000.0000.0000.000
163B163HIS10.8970.93624.7260.3130.3130.0000.0000.0000.000
164B164HIS00.0470.04225.0440.0300.0300.0000.0000.0000.000
165B165GLU-1-0.856-0.92526.819-0.262-0.2620.0000.0000.0000.000
166B166GLU-1-0.821-0.90225.762-0.376-0.3760.0000.0000.0000.000
167B167TYR0-0.041-0.01522.408-0.030-0.0300.0000.0000.0000.000
168B168PRO00.0300.03518.0130.0420.0420.0000.0000.0000.000
169B169ILE0-0.026-0.00819.009-0.063-0.0630.0000.0000.0000.000
170B170TYR00.008-0.02420.5660.0870.0870.0000.0000.0000.000
171B171GLY00.0110.01321.775-0.042-0.0420.0000.0000.0000.000
172B172VAL0-0.016-0.00622.7680.0310.0310.0000.0000.0000.000
173B173GLN00.014-0.01425.275-0.011-0.0110.0000.0000.0000.000
174B174PHE0-0.007-0.01725.1430.0120.0120.0000.0000.0000.000
175B175HIS00.024-0.00823.943-0.021-0.0210.0000.0000.0000.000
176B176PRO0-0.064-0.01920.5390.0340.0340.0000.0000.0000.000
177B177GLU-1-0.748-0.87319.163-0.292-0.2920.0000.0000.0000.000
178B178SER00.003-0.00520.9390.0310.0310.0000.0000.0000.000
179B179VAL00.0580.00924.4610.0010.0010.0000.0000.0000.000
180B180GLY0-0.032-0.00426.2040.0130.0130.0000.0000.0000.000
181B181THR0-0.047-0.04525.2570.0050.0050.0000.0000.0000.000
182B182SER00.0330.02325.469-0.014-0.0140.0000.0000.0000.000
183B183LEU0-0.007-0.00124.9650.0060.0060.0000.0000.0000.000
184B184GLY0-0.004-0.00122.965-0.023-0.0230.0000.0000.0000.000
185B185TYR00.022-0.02816.137-0.075-0.0750.0000.0000.0000.000
186B186LYS10.8780.94218.6520.1470.1470.0000.0000.0000.000
187B187ILE0-0.016-0.00419.973-0.029-0.0290.0000.0000.0000.000
188B188LEU00.0340.01016.085-0.056-0.0560.0000.0000.0000.000
189B189TYR00.0330.01914.997-0.092-0.0920.0000.0000.0000.000
190B190ASN0-0.049-0.03515.617-0.057-0.0570.0000.0000.0000.000
191B191PHE0-0.009-0.01613.737-0.020-0.0200.0000.0000.0000.000
192B192LEU00.0100.0069.938-0.107-0.1070.0000.0000.0000.000
193B193ASN0-0.044-0.01911.885-0.122-0.1220.0000.0000.0000.000
194B194ARG10.8560.93213.8860.3930.3930.0000.0000.0000.000
195B195VAL0-0.0100.01914.7370.0260.0260.0000.0000.0000.000