Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 1N47Z

Calculation Name: 5MQC-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MQC

Chain ID: B

ChEMBL ID:

UniProt ID: Q9J7C2

Base Structure: X-ray

Registration Date: 2023-09-20

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2480767.233804
FMO2-HF: Nuclear repulsion 2388052.67941
FMO2-HF: Total energy -92714.554393
FMO2-MP2: Total energy -92982.690924


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.
-8.991-5.5751.892-2.054-3.255-0.017
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 : -0.024 / q_NPA : -0.028
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].
3B3GLU-1-0.938-0.9572.437-7.806-4.9701.883-1.918-2.801-0.016
4B4GLN0-0.028-0.0283.668-0.3540.2260.009-0.136-0.454-0.001
5B5ILE00.0120.0105.8170.2230.2230.0000.0000.0000.000
6B6ASN0-0.069-0.0548.9250.2320.2320.0000.0000.0000.000
7B7GLU-1-0.875-0.94010.269-0.592-0.5920.0000.0000.0000.000
8B8ASN0-0.072-0.02413.7030.1420.1420.0000.0000.0000.000
9B9TYR0-0.075-0.03712.4930.0690.0690.0000.0000.0000.000
10B10GLU-1-0.849-0.91712.305-0.567-0.5670.0000.0000.0000.000
11B11ASN00.0000.0128.5650.0310.0310.0000.0000.0000.000
12B12LYS10.8740.93510.7640.5560.5560.0000.0000.0000.000
13B13GLN00.0200.02810.308-0.070-0.0700.0000.0000.0000.000
14B14GLN00.0300.00612.8640.0510.0510.0000.0000.0000.000
15B15LEU0-0.061-0.03316.109-0.029-0.0290.0000.0000.0000.000
16B16VAL00.0110.01413.899-0.008-0.0080.0000.0000.0000.000
17B17GLU-1-0.938-0.95717.256-0.035-0.0350.0000.0000.0000.000
18B18GLN0-0.061-0.03519.3650.0080.0080.0000.0000.0000.000
19B19THR00.0210.00621.1060.0030.0030.0000.0000.0000.000
20B20GLU-1-0.956-0.96824.8130.0290.0290.0000.0000.0000.000
21B21ILE0-0.069-0.04324.2160.0140.0140.0000.0000.0000.000
22B22THR0-0.036-0.02222.8040.0050.0050.0000.0000.0000.000
23B23THR00.0470.02216.8190.0090.0090.0000.0000.0000.000
24B24PHE0-0.074-0.02219.917-0.008-0.0080.0000.0000.0000.000
25B25GLU-1-0.890-0.95513.828-0.272-0.2720.0000.0000.0000.000
26B26ASN0-0.062-0.02317.267-0.007-0.0070.0000.0000.0000.000
27B27ASP-1-0.858-0.94516.726-0.446-0.4460.0000.0000.0000.000
28B28LEU0-0.090-0.06818.9370.0280.0280.0000.0000.0000.000
29B29ILE00.0130.00021.471-0.006-0.0060.0000.0000.0000.000
30B30VAL00.0170.01821.7370.0040.0040.0000.0000.0000.000
31B31LEU0-0.067-0.02824.5900.0020.0020.0000.0000.0000.000
32B32GLU-1-0.928-0.97328.181-0.062-0.0620.0000.0000.0000.000
33B33ASP-1-0.922-0.96530.324-0.064-0.0640.0000.0000.0000.000
34B34GLY0-0.016-0.00533.9680.0030.0030.0000.0000.0000.000
35B35PRO0-0.069-0.02637.203-0.001-0.0010.0000.0000.0000.000
36B36GLN00.0390.01135.2060.0030.0030.0000.0000.0000.000
37B37MET0-0.090-0.05238.4960.0030.0030.0000.0000.0000.000
38B38GLU-1-0.906-0.93037.441-0.026-0.0260.0000.0000.0000.000
39B39GLU-1-0.952-0.97540.229-0.011-0.0110.0000.0000.0000.000
40B40SER0-0.047-0.02742.1740.0010.0010.0000.0000.0000.000
41B41LEU00.0120.00344.0450.0010.0010.0000.0000.0000.000
42B42PRO00.023-0.00446.9450.0020.0020.0000.0000.0000.000
43B43PHE00.0280.00647.1820.0000.0000.0000.0000.0000.000
44B44ALA0-0.0130.00449.3150.0000.0000.0000.0000.0000.000
45B45PHE0-0.029-0.01851.1000.0000.0000.0000.0000.0000.000
46B46HIS00.0150.00945.9620.0000.0000.0000.0000.0000.000
47B47GLY00.0230.01049.6190.0010.0010.0000.0000.0000.000
48B48GLN0-0.054-0.02450.3990.0010.0010.0000.0000.0000.000
49B49HIS0-0.023-0.00746.4590.0000.0000.0000.0000.0000.000
50B50THR0-0.041-0.02247.5670.0010.0010.0000.0000.0000.000
51B51ASP-1-0.838-0.90548.4470.0210.0210.0000.0000.0000.000
52B52ASN0-0.0090.00348.4410.0000.0000.0000.0000.0000.000
53B53ARG10.8700.92445.558-0.031-0.0310.0000.0000.0000.000
54B54GLN00.0650.04041.196-0.001-0.0010.0000.0000.0000.000
55B55HIS0-0.112-0.06542.8890.0050.0050.0000.0000.0000.000
56B56THR0-0.0130.01137.194-0.002-0.0020.0000.0000.0000.000
57B57VAL00.0590.01636.224-0.003-0.0030.0000.0000.0000.000
58B58VAL00.0540.03237.5420.0010.0010.0000.0000.0000.000
59B59ASN00.0610.02040.146-0.001-0.0010.0000.0000.0000.000
60B60PHE00.003-0.03142.500-0.002-0.0020.0000.0000.0000.000
61B61LEU00.0260.01340.196-0.001-0.0010.0000.0000.0000.000
62B62GLN0-0.015-0.01343.1730.0040.0040.0000.0000.0000.000
63B63ARG10.8530.95546.424-0.031-0.0310.0000.0000.0000.000
64B64PRO00.0360.03149.2270.0010.0010.0000.0000.0000.000
65B65GLN0-0.0010.00050.811-0.002-0.0020.0000.0000.0000.000
66B66VAL0-0.002-0.00652.7920.0010.0010.0000.0000.0000.000
67B67ILE0-0.029-0.00952.6740.0000.0000.0000.0000.0000.000
68B68PHE0-0.026-0.03556.081-0.001-0.0010.0000.0000.0000.000
69B69ASP-1-0.879-0.95359.7860.0230.0230.0000.0000.0000.000
70B70SER0-0.027-0.00163.006-0.001-0.0010.0000.0000.0000.000
71B71SER00.0080.01866.0430.0000.0000.0000.0000.0000.000
72B72TRP0-0.031-0.01967.2090.0010.0010.0000.0000.0000.000
73B73ALA00.0360.01970.6950.0000.0000.0000.0000.0000.000
74B74SER0-0.018-0.02074.0650.0010.0010.0000.0000.0000.000
75B75ASP-1-0.908-0.94874.7550.0210.0210.0000.0000.0000.000
76B76VAL0-0.0030.01670.0820.0000.0000.0000.0000.0000.000
77B77PRO0-0.034-0.01772.6720.0000.0000.0000.0000.0000.000
78B78ARG10.9850.96871.249-0.028-0.0280.0000.0000.0000.000
79B79ASN0-0.069-0.03768.2950.0010.0010.0000.0000.0000.000
80B80LYS10.9350.97268.109-0.028-0.0280.0000.0000.0000.000
81B81GLN0-0.014-0.02161.4150.0000.0000.0000.0000.0000.000
82B82PHE00.0330.02363.253-0.001-0.0010.0000.0000.0000.000
83B83MET0-0.0270.01358.774-0.001-0.0010.0000.0000.0000.000
84B84ASP-1-0.864-0.92059.6510.0280.0280.0000.0000.0000.000
85B85SER0-0.129-0.09157.0870.0020.0020.0000.0000.0000.000
86B86ILE00.0500.03952.477-0.001-0.0010.0000.0000.0000.000
87B87MET0-0.082-0.04849.8310.0030.0030.0000.0000.0000.000
88B88ILE0-0.0010.03047.076-0.001-0.0010.0000.0000.0000.000
89B89PRO00.048-0.00543.5360.0030.0030.0000.0000.0000.000
90B90ASP-1-0.750-0.81145.4880.0480.0480.0000.0000.0000.000
91B91ASP-1-0.849-0.92747.4860.0350.0350.0000.0000.0000.000
92B92ILE0-0.027-0.01447.866-0.001-0.0010.0000.0000.0000.000
93B93ILE0-0.021-0.03942.566-0.002-0.0020.0000.0000.0000.000
94B94SER0-0.044-0.00645.657-0.002-0.0020.0000.0000.0000.000
95B95PHE00.0020.01547.978-0.003-0.0030.0000.0000.0000.000
96B96PRO00.026-0.00147.6120.0020.0020.0000.0000.0000.000
97B97MET00.0050.03046.565-0.001-0.0010.0000.0000.0000.000
98B98PHE0-0.003-0.01444.6240.0010.0010.0000.0000.0000.000
99B99ALA00.0240.02042.9980.0020.0020.0000.0000.0000.000
100B100GLU-1-0.988-1.00141.9710.0200.0200.0000.0000.0000.000
101B101LYS10.8690.94140.244-0.027-0.0270.0000.0000.0000.000
102B102LEU00.0320.00738.5400.0020.0020.0000.0000.0000.000
103B103LYS10.9290.97236.768-0.020-0.0200.0000.0000.0000.000
104B104GLY00.0240.01533.853-0.001-0.0010.0000.0000.0000.000
105B105PHE00.0090.00632.6370.0030.0030.0000.0000.0000.000
106B106SER0-0.016-0.00430.705-0.001-0.0010.0000.0000.0000.000
107B107SER0-0.031-0.02132.859-0.003-0.0030.0000.0000.0000.000
108B108LEU00.0280.01435.212-0.001-0.0010.0000.0000.0000.000
109B109ARG10.9040.93336.367-0.107-0.1070.0000.0000.0000.000
110B110ALA00.0350.02738.3290.0010.0010.0000.0000.0000.000
111B111THR0-0.065-0.01041.366-0.002-0.0020.0000.0000.0000.000
112B112ALA00.0110.01344.912-0.002-0.0020.0000.0000.0000.000
113B113VAL0-0.033-0.02247.5320.0010.0010.0000.0000.0000.000
114B114ILE00.0000.00950.845-0.002-0.0020.0000.0000.0000.000
115B115THR00.009-0.01753.9160.0010.0010.0000.0000.0000.000
116B116VAL0-0.040-0.01656.844-0.001-0.0010.0000.0000.0000.000
117B117GLN00.0090.00659.9240.0000.0000.0000.0000.0000.000
118B118PHE00.006-0.01363.2770.0000.0000.0000.0000.0000.000
119B119GLN00.0110.02366.9010.0000.0000.0000.0000.0000.000
120B120THR00.029-0.00470.0570.0000.0000.0000.0000.0000.000
121B121GLN0-0.0100.01873.3200.0000.0000.0000.0000.0000.000
122B122PRO00.011-0.02576.5960.0000.0000.0000.0000.0000.000
123B123PHE0-0.059-0.02778.1000.0000.0000.0000.0000.0000.000
124B124GLN00.0140.01874.9730.0000.0000.0000.0000.0000.000
125B125ALA00.0200.00576.2980.0010.0010.0000.0000.0000.000
126B126GLY00.0430.02273.9150.0000.0000.0000.0000.0000.000
127B127ARG10.8830.95268.394-0.032-0.0320.0000.0000.0000.000
128B128VAL00.0100.01065.4340.0000.0000.0000.0000.0000.000
129B129MET0-0.048-0.00562.9390.0010.0010.0000.0000.0000.000
130B130LEU00.0510.02858.051-0.001-0.0010.0000.0000.0000.000
131B131GLY00.0340.00558.1450.0010.0010.0000.0000.0000.000
132B132SER00.015-0.02053.1330.0000.0000.0000.0000.0000.000
133B133PHE0-0.0200.00853.1380.0020.0020.0000.0000.0000.000
134B134PRO00.0280.01649.1750.0000.0000.0000.0000.0000.000
135B135LEU0-0.0050.00644.5260.0000.0000.0000.0000.0000.000
136B136PRO0-0.023-0.01048.273-0.001-0.0010.0000.0000.0000.000
137B137THR00.037-0.00646.299-0.002-0.0020.0000.0000.0000.000
138B138LEU0-0.0170.00843.3810.0000.0000.0000.0000.0000.000
139B139ASN0-0.0070.01047.8040.0010.0010.0000.0000.0000.000
140B140PRO00.0740.01950.618-0.002-0.0020.0000.0000.0000.000
141B141THR0-0.024-0.01553.642-0.002-0.0020.0000.0000.0000.000
142B142ARG10.9410.96355.016-0.054-0.0540.0000.0000.0000.000
143B143VAL00.0310.04554.153-0.001-0.0010.0000.0000.0000.000
144B144LYS10.9840.97256.842-0.036-0.0360.0000.0000.0000.000
145B145PHE0-0.021-0.01660.122-0.001-0.0010.0000.0000.0000.000
146B146ALA0-0.0060.00658.235-0.001-0.0010.0000.0000.0000.000
147B147THR00.0230.00559.0820.0000.0000.0000.0000.0000.000
148B148ASN0-0.0120.02361.309-0.001-0.0010.0000.0000.0000.000
149B149HIS0-0.017-0.00464.590-0.002-0.0020.0000.0000.0000.000
150B150VAL00.1220.05764.9770.0020.0020.0000.0000.0000.000
151B151SER0-0.076-0.07365.744-0.001-0.0010.0000.0000.0000.000
152B152ARG10.8290.89962.599-0.038-0.0380.0000.0000.0000.000
153B153LEU00.0140.03259.0230.0020.0020.0000.0000.0000.000
154B154MET00.0000.00060.2810.0010.0010.0000.0000.0000.000
155B155LEU0-0.045-0.00259.5430.0010.0010.0000.0000.0000.000
156B156LEU0-0.046-0.00454.2950.0020.0020.0000.0000.0000.000
157B157ASN00.0180.00852.834-0.002-0.0020.0000.0000.0000.000
158B158HIS0-0.031-0.02656.256-0.002-0.0020.0000.0000.0000.000
159B159VAL00.0500.02457.9150.0010.0010.0000.0000.0000.000
160B160GLN0-0.061-0.03960.676-0.002-0.0020.0000.0000.0000.000
161B161CYS00.0440.03464.3320.0000.0000.0000.0000.0000.000
162B162ASP-1-0.979-0.98066.5260.0270.0270.0000.0000.0000.000
163B163ILE00.0670.03469.2850.0000.0000.0000.0000.0000.000
164B164ALA0-0.0190.00271.319-0.001-0.0010.0000.0000.0000.000
165B165LYS10.8020.89670.826-0.027-0.0270.0000.0000.0000.000
166B166GLU-1-0.814-0.92265.6170.0320.0320.0000.0000.0000.000
167B167THR00.012-0.01166.196-0.001-0.0010.0000.0000.0000.000
168B168GLU-1-0.940-0.95759.1910.0330.0330.0000.0000.0000.000
169B169VAL00.000-0.00260.3880.0010.0010.0000.0000.0000.000
170B170SER00.0160.01655.662-0.001-0.0010.0000.0000.0000.000
171B171LEU0-0.060-0.01354.0390.0010.0010.0000.0000.0000.000
172B172ARG10.9670.98047.653-0.060-0.0600.0000.0000.0000.000
173B173ILE0-0.006-0.00648.4400.0010.0010.0000.0000.0000.000
174B174PRO00.013-0.00845.6370.0010.0010.0000.0000.0000.000
175B175PHE0-0.0140.00039.3240.0000.0000.0000.0000.0000.000
176B176VAL0-0.018-0.01643.0670.0040.0040.0000.0000.0000.000
177B177SER00.0480.01140.293-0.003-0.0030.0000.0000.0000.000
178B178PRO0-0.0290.00239.8240.0040.0040.0000.0000.0000.000
179B179TYR00.002-0.00836.3820.0090.0090.0000.0000.0000.000
180B180ASN00.0510.04131.499-0.010-0.0100.0000.0000.0000.000
181B181SER0-0.004-0.00134.355-0.004-0.0040.0000.0000.0000.000
182B182TYR0-0.117-0.13136.704-0.001-0.0010.0000.0000.0000.000
183B183ASP-1-0.796-0.86335.7870.0720.0720.0000.0000.0000.000
184B184LEU00.0410.02036.558-0.005-0.0050.0000.0000.0000.000
185B185VAL0-0.058-0.01833.988-0.006-0.0060.0000.0000.0000.000
186B186SER0-0.092-0.09137.291-0.005-0.0050.0000.0000.0000.000
187B187LYS10.9300.96939.442-0.043-0.0430.0000.0000.0000.000
188B188ARG10.9040.97239.535-0.056-0.0560.0000.0000.0000.000
189B189PHE0-0.025-0.02039.9110.0030.0030.0000.0000.0000.000
190B190PRO00.0500.02743.0290.0030.0030.0000.0000.0000.000
191B191TRP00.0780.02342.3400.0010.0010.0000.0000.0000.000
192B192ALA0-0.025-0.02546.1220.0010.0010.0000.0000.0000.000
193B193LYS10.9160.97849.877-0.043-0.0430.0000.0000.0000.000
194B194VAL00.0130.01153.0060.0000.0000.0000.0000.0000.000
195B195VAL0-0.039-0.01655.394-0.002-0.0020.0000.0000.0000.000
196B196GLY00.0960.03559.0100.0010.0010.0000.0000.0000.000
197B197LEU0-0.078-0.02762.174-0.001-0.0010.0000.0000.0000.000
198B198VAL00.0790.05465.4230.0000.0000.0000.0000.0000.000
199B199TYR0-0.021-0.03168.2830.0000.0000.0000.0000.0000.000
200B200SER0-0.037-0.03969.9390.0000.0000.0000.0000.0000.000
201B201PRO0-0.0120.00073.1240.0000.0000.0000.0000.0000.000
202B202LEU00.0380.03773.0000.0000.0000.0000.0000.0000.000
203B203THR0-0.011-0.01576.5530.0000.0000.0000.0000.0000.000
204B204THR0-0.020-0.00679.342-0.001-0.0010.0000.0000.0000.000
205B205THR00.004-0.01679.5120.0000.0000.0000.0000.0000.000
206B206ILE0-0.051-0.01076.7400.0000.0000.0000.0000.0000.000
207B207PRO00.0090.01473.3280.0010.0010.0000.0000.0000.000
208B208VAL0-0.0020.00469.5590.0000.0000.0000.0000.0000.000
209B209ASP-1-0.831-0.92868.4120.0210.0210.0000.0000.0000.000
210B210PHE0-0.056-0.04562.1690.0010.0010.0000.0000.0000.000
211B211ILE00.0480.03559.8580.0000.0000.0000.0000.0000.000
212B212VAL0-0.031-0.00456.4440.0010.0010.0000.0000.0000.000
213B213TYR00.009-0.00954.990-0.001-0.0010.0000.0000.0000.000
214B214GLY00.023-0.00351.9740.0020.0020.0000.0000.0000.000
215B215HIS0-0.058-0.01848.257-0.003-0.0030.0000.0000.0000.000
216B216PHE0-0.045-0.01843.9690.0020.0020.0000.0000.0000.000
217B217GLU-1-0.845-0.94244.4590.0520.0520.0000.0000.0000.000
218B218ASP-1-0.921-0.96241.4030.0760.0760.0000.0000.0000.000
219B219VAL0-0.027-0.02838.2760.0030.0030.0000.0000.0000.000
220B220GLU-1-0.926-0.95534.4300.1160.1160.0000.0000.0000.000
221B221LEU0-0.046-0.03234.3100.0000.0000.0000.0000.0000.000
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