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: 8925Y

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2481505.203042
FMO2-HF: Nuclear repulsion 2388788.601431
FMO2-HF: Total energy -92716.601611
FMO2-MP2: Total energy -92984.685487


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.
-8.386-4.9111.919-1.835-3.56-0.013
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 : -0.027 / 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-1-0.935-0.9622.537-7.356-4.6801.902-1.734-2.845-0.013
4B4GLN0-0.038-0.0363.420-0.1380.5920.018-0.100-0.6480.000
5B5ILE00.0130.0185.0300.1900.259-0.001-0.001-0.0670.000
6B6ASN0-0.050-0.0538.2780.1980.1980.0000.0000.0000.000
7B7GLU-1-0.907-0.93810.056-0.703-0.7030.0000.0000.0000.000
8B8ASN0-0.075-0.03913.2690.1520.1520.0000.0000.0000.000
9B9TYR0-0.043-0.01812.1200.0820.0820.0000.0000.0000.000
10B10GLU-1-0.834-0.90911.752-0.562-0.5620.0000.0000.0000.000
11B11ASN0-0.049-0.0138.735-0.040-0.0400.0000.0000.0000.000
12B12LYS10.7740.87310.6050.4880.4880.0000.0000.0000.000
13B13GLN00.0260.03610.932-0.002-0.0020.0000.0000.0000.000
14B14GLN00.0830.03713.3640.0400.0400.0000.0000.0000.000
15B15LEU0-0.016-0.01916.401-0.033-0.0330.0000.0000.0000.000
16B16VAL0-0.0040.00714.0270.0050.0050.0000.0000.0000.000
17B17GLU-1-0.883-0.93017.413-0.017-0.0170.0000.0000.0000.000
18B18GLN0-0.072-0.03920.4290.0040.0040.0000.0000.0000.000
19B19THR0-0.002-0.00622.181-0.002-0.0020.0000.0000.0000.000
20B20GLU-1-0.914-0.95325.9510.0360.0360.0000.0000.0000.000
21B21ILE0-0.127-0.06924.9650.0140.0140.0000.0000.0000.000
22B22THR0-0.015-0.00823.6290.0070.0070.0000.0000.0000.000
23B23THR00.0350.02817.6040.0010.0010.0000.0000.0000.000
24B24PHE0-0.056-0.02620.913-0.004-0.0040.0000.0000.0000.000
25B25GLU-1-0.904-0.96614.243-0.161-0.1610.0000.0000.0000.000
26B26ASN0-0.083-0.03717.755-0.012-0.0120.0000.0000.0000.000
27B27ASP-1-0.791-0.90816.711-0.405-0.4050.0000.0000.0000.000
28B28LEU0-0.084-0.05619.1680.0310.0310.0000.0000.0000.000
29B29ILE0-0.026-0.01321.276-0.006-0.0060.0000.0000.0000.000
30B30VAL00.0130.01922.3180.0050.0050.0000.0000.0000.000
31B31LEU0-0.067-0.03724.797-0.002-0.0020.0000.0000.0000.000
32B32GLU-1-0.929-0.96428.309-0.047-0.0470.0000.0000.0000.000
33B33ASP-1-0.892-0.94230.555-0.057-0.0570.0000.0000.0000.000
34B34GLY0-0.003-0.00134.1800.0030.0030.0000.0000.0000.000
35B35PRO0-0.067-0.03037.438-0.002-0.0020.0000.0000.0000.000
36B36GLN0-0.013-0.02634.8560.0050.0050.0000.0000.0000.000
37B37MET0-0.085-0.04538.7270.0020.0020.0000.0000.0000.000
38B38GLU-1-0.893-0.92537.453-0.020-0.0200.0000.0000.0000.000
39B39GLU-1-0.952-0.97240.800-0.010-0.0100.0000.0000.0000.000
40B40SER0-0.035-0.02342.5770.0010.0010.0000.0000.0000.000
41B41LEU00.0150.00544.5030.0010.0010.0000.0000.0000.000
42B42PRO00.0270.00847.6400.0020.0020.0000.0000.0000.000
43B43PHE00.0320.01647.6490.0000.0000.0000.0000.0000.000
44B44ALA0-0.0040.00049.8240.0000.0000.0000.0000.0000.000
45B45PHE0-0.028-0.01351.802-0.001-0.0010.0000.0000.0000.000
46B46HIS0-0.038-0.02546.7460.0000.0000.0000.0000.0000.000
47B47GLY00.0380.01450.1500.0010.0010.0000.0000.0000.000
48B48GLN0-0.051-0.03051.0940.0010.0010.0000.0000.0000.000
49B49HIS0-0.0180.00347.0490.0000.0000.0000.0000.0000.000
50B50THR0-0.032-0.02048.1490.0010.0010.0000.0000.0000.000
51B51ASP-1-0.823-0.88649.5130.0240.0240.0000.0000.0000.000
52B52ASN0-0.013-0.00849.352-0.001-0.0010.0000.0000.0000.000
53B53ARG10.8380.90645.985-0.032-0.0320.0000.0000.0000.000
54B54GLN00.0260.01242.496-0.002-0.0020.0000.0000.0000.000
55B55HIS0-0.041-0.02943.5920.0050.0050.0000.0000.0000.000
56B56THR00.0360.02838.192-0.001-0.0010.0000.0000.0000.000
57B57VAL00.0440.01136.611-0.002-0.0020.0000.0000.0000.000
58B58VAL00.0320.02638.4120.0010.0010.0000.0000.0000.000
59B59ASN00.015-0.01341.087-0.003-0.0030.0000.0000.0000.000
60B60PHE00.006-0.00243.5460.0000.0000.0000.0000.0000.000
61B61LEU00.0230.00540.905-0.001-0.0010.0000.0000.0000.000
62B62GLN00.0430.02544.738-0.001-0.0010.0000.0000.0000.000
63B63ARG10.8430.93647.371-0.032-0.0320.0000.0000.0000.000
64B64PRO00.0150.01650.2780.0010.0010.0000.0000.0000.000
65B65GLN0-0.028-0.01851.809-0.002-0.0020.0000.0000.0000.000
66B66VAL00.0290.00953.7640.0010.0010.0000.0000.0000.000
67B67ILE0-0.047-0.00853.4250.0000.0000.0000.0000.0000.000
68B68PHE0-0.015-0.02856.815-0.001-0.0010.0000.0000.0000.000
69B69ASP-1-0.893-0.94660.6090.0240.0240.0000.0000.0000.000
70B70SER0-0.0130.00163.865-0.001-0.0010.0000.0000.0000.000
71B71SER00.0100.01566.9000.0000.0000.0000.0000.0000.000
72B72TRP0-0.017-0.00368.1610.0010.0010.0000.0000.0000.000
73B73ALA00.0500.01671.8130.0000.0000.0000.0000.0000.000
74B74SER0-0.058-0.05674.9820.0010.0010.0000.0000.0000.000
75B75ASP-1-0.906-0.93875.6540.0220.0220.0000.0000.0000.000
76B76VAL0-0.0080.00370.6820.0000.0000.0000.0000.0000.000
77B77PRO0-0.020-0.01173.6550.0000.0000.0000.0000.0000.000
78B78ARG10.9700.97371.248-0.027-0.0270.0000.0000.0000.000
79B79ASN0-0.063-0.02068.5810.0000.0000.0000.0000.0000.000
80B80LYS10.9070.95268.295-0.029-0.0290.0000.0000.0000.000
81B81GLN0-0.003-0.00761.2890.0000.0000.0000.0000.0000.000
82B82PHE00.0250.01963.661-0.001-0.0010.0000.0000.0000.000
83B83MET0-0.0190.01559.304-0.001-0.0010.0000.0000.0000.000
84B84ASP-1-0.885-0.93260.7100.0300.0300.0000.0000.0000.000
85B85SER0-0.092-0.07257.2810.0020.0020.0000.0000.0000.000
86B86ILE00.0480.03853.146-0.001-0.0010.0000.0000.0000.000
87B87MET0-0.077-0.05050.4300.0030.0030.0000.0000.0000.000
88B88ILE0-0.0060.02047.720-0.001-0.0010.0000.0000.0000.000
89B89PRO00.0420.00243.9490.0030.0030.0000.0000.0000.000
90B90ASP-1-0.811-0.89146.7240.0510.0510.0000.0000.0000.000
91B91ASP-1-0.838-0.89848.3750.0380.0380.0000.0000.0000.000
92B92ILE0-0.013-0.00148.942-0.001-0.0010.0000.0000.0000.000
93B93ILE0-0.025-0.03643.594-0.002-0.0020.0000.0000.0000.000
94B94SER0-0.044-0.02446.605-0.001-0.0010.0000.0000.0000.000
95B95PHE00.0040.01648.905-0.003-0.0030.0000.0000.0000.000
96B96PRO00.0260.00348.3460.0020.0020.0000.0000.0000.000
97B97MET00.0120.02347.1570.0000.0000.0000.0000.0000.000
98B98PHE00.0050.00545.3670.0010.0010.0000.0000.0000.000
99B99ALA00.0340.02243.7440.0020.0020.0000.0000.0000.000
100B100GLU-1-0.904-0.96042.7180.0270.0270.0000.0000.0000.000
101B101LYS10.7740.87840.835-0.031-0.0310.0000.0000.0000.000
102B102LEU00.0290.00839.1970.0030.0030.0000.0000.0000.000
103B103LYS10.8270.91637.159-0.031-0.0310.0000.0000.0000.000
104B104GLY00.0150.00435.031-0.005-0.0050.0000.0000.0000.000
105B105PHE00.0010.01733.2940.0030.0030.0000.0000.0000.000
106B106SER00.0080.00431.623-0.004-0.0040.0000.0000.0000.000
107B107SER0-0.053-0.03933.7340.0010.0010.0000.0000.0000.000
108B108LEU00.0270.02336.2520.0000.0000.0000.0000.0000.000
109B109ARG10.7890.87535.505-0.104-0.1040.0000.0000.0000.000
110B110ALA00.0410.03638.8780.0010.0010.0000.0000.0000.000
111B111THR0-0.068-0.04641.883-0.001-0.0010.0000.0000.0000.000
112B112ALA00.0100.01645.233-0.002-0.0020.0000.0000.0000.000
113B113VAL0-0.030-0.01247.9030.0010.0010.0000.0000.0000.000
114B114ILE0-0.0090.00151.245-0.001-0.0010.0000.0000.0000.000
115B115THR00.004-0.01354.5910.0010.0010.0000.0000.0000.000
116B116VAL0-0.050-0.02157.722-0.001-0.0010.0000.0000.0000.000
117B117GLN0-0.005-0.00760.9020.0000.0000.0000.0000.0000.000
118B118PHE0-0.041-0.04364.0160.0000.0000.0000.0000.0000.000
119B119GLN0-0.0080.00567.7880.0000.0000.0000.0000.0000.000
120B120THR00.017-0.01270.9520.0000.0000.0000.0000.0000.000
121B121GLN00.001-0.00474.0260.0000.0000.0000.0000.0000.000
122B122PRO00.000-0.02677.4760.0000.0000.0000.0000.0000.000
123B123PHE0-0.044-0.01079.1670.0000.0000.0000.0000.0000.000
124B124GLN0-0.0260.00575.9150.0000.0000.0000.0000.0000.000
125B125ALA00.0150.00276.4400.0000.0000.0000.0000.0000.000
126B126GLY00.0590.02674.6200.0000.0000.0000.0000.0000.000
127B127ARG10.7730.87368.729-0.030-0.0300.0000.0000.0000.000
128B128VAL00.0310.03265.6070.0000.0000.0000.0000.0000.000
129B129MET0-0.064-0.02362.9970.0010.0010.0000.0000.0000.000
130B130LEU00.0600.03258.600-0.001-0.0010.0000.0000.0000.000
131B131GLY00.0500.01657.8180.0010.0010.0000.0000.0000.000
132B132SER0-0.003-0.00152.823-0.001-0.0010.0000.0000.0000.000
133B133PHE0-0.0010.00052.2900.0010.0010.0000.0000.0000.000
134B134PRO00.0630.02648.7080.0000.0000.0000.0000.0000.000
135B135LEU0-0.007-0.00843.9800.0000.0000.0000.0000.0000.000
136B136PRO0-0.012-0.00347.9900.0000.0000.0000.0000.0000.000
137B137THR00.000-0.02146.413-0.001-0.0010.0000.0000.0000.000
138B138LEU0-0.0280.00343.3280.0000.0000.0000.0000.0000.000
139B139ASN0-0.0150.00847.7250.0000.0000.0000.0000.0000.000
140B140PRO00.0840.02950.734-0.003-0.0030.0000.0000.0000.000
141B141THR0-0.025-0.02153.940-0.002-0.0020.0000.0000.0000.000
142B142ARG10.9130.95654.745-0.052-0.0520.0000.0000.0000.000
143B143VAL00.0320.04653.969-0.002-0.0020.0000.0000.0000.000
144B144LYS10.9880.97956.566-0.037-0.0370.0000.0000.0000.000
145B145PHE0-0.027-0.01659.886-0.001-0.0010.0000.0000.0000.000
146B146ALA00.0110.01658.048-0.001-0.0010.0000.0000.0000.000
147B147THR00.0440.01759.6360.0000.0000.0000.0000.0000.000
148B148ASN0-0.0220.01061.533-0.001-0.0010.0000.0000.0000.000
149B149HIS0-0.036-0.03764.673-0.002-0.0020.0000.0000.0000.000
150B150VAL00.1230.06864.9500.0020.0020.0000.0000.0000.000
151B151SER0-0.074-0.04665.8730.0000.0000.0000.0000.0000.000
152B152ARG10.8460.90662.246-0.037-0.0370.0000.0000.0000.000
153B153LEU00.0410.02859.1670.0020.0020.0000.0000.0000.000
154B154MET00.000-0.00260.1040.0010.0010.0000.0000.0000.000
155B155LEU0-0.064-0.00958.8760.0000.0000.0000.0000.0000.000
156B156LEU0-0.026-0.00253.7480.0020.0020.0000.0000.0000.000
157B157ASN0-0.008-0.01153.120-0.001-0.0010.0000.0000.0000.000
158B158HIS00.006-0.00655.668-0.002-0.0020.0000.0000.0000.000
159B159VAL00.0330.03458.2120.0010.0010.0000.0000.0000.000
160B160GLN0-0.053-0.04560.889-0.002-0.0020.0000.0000.0000.000
161B161CYS00.0390.03864.6500.0000.0000.0000.0000.0000.000
162B162ASP-1-0.816-0.89066.9610.0270.0270.0000.0000.0000.000
163B163ILE00.0430.01369.9110.0000.0000.0000.0000.0000.000
164B164ALA00.0090.01971.933-0.001-0.0010.0000.0000.0000.000
165B165LYS10.7580.87170.554-0.026-0.0260.0000.0000.0000.000
166B166GLU-1-0.834-0.91565.8670.0310.0310.0000.0000.0000.000
167B167THR00.0320.01566.8580.0000.0000.0000.0000.0000.000
168B168GLU-1-0.866-0.91060.6060.0320.0320.0000.0000.0000.000
169B169VAL0-0.036-0.01660.7820.0010.0010.0000.0000.0000.000
170B170SER00.0070.00556.2660.0000.0000.0000.0000.0000.000
171B171LEU0-0.023-0.00754.2120.0010.0010.0000.0000.0000.000
172B172ARG10.8080.88146.489-0.059-0.0590.0000.0000.0000.000
173B173ILE0-0.014-0.02048.8990.0000.0000.0000.0000.0000.000
174B174PRO00.022-0.00245.4120.0010.0010.0000.0000.0000.000
175B175PHE0-0.0100.01139.025-0.001-0.0010.0000.0000.0000.000
176B176VAL0-0.007-0.01142.9330.0030.0030.0000.0000.0000.000
177B177SER00.0330.00240.057-0.003-0.0030.0000.0000.0000.000
178B178PRO0-0.036-0.00439.1220.0030.0030.0000.0000.0000.000
179B179TYR0-0.010-0.00735.9600.0080.0080.0000.0000.0000.000
180B180ASN00.0620.02131.795-0.007-0.0070.0000.0000.0000.000
181B181SER00.003-0.00434.643-0.002-0.0020.0000.0000.0000.000
182B182TYR0-0.031-0.04736.9440.0000.0000.0000.0000.0000.000
183B183ASP-1-0.780-0.85537.3100.0750.0750.0000.0000.0000.000
184B184LEU00.0290.01237.238-0.005-0.0050.0000.0000.0000.000
185B185VAL0-0.046-0.01334.920-0.007-0.0070.0000.0000.0000.000
186B186SER0-0.080-0.07938.213-0.005-0.0050.0000.0000.0000.000
187B187LYS10.8730.94640.248-0.051-0.0510.0000.0000.0000.000
188B188ARG10.8930.94440.484-0.060-0.0600.0000.0000.0000.000
189B189PHE00.001-0.01040.1160.0020.0020.0000.0000.0000.000
190B190PRO00.0510.03543.3360.0020.0020.0000.0000.0000.000
191B191TRP00.0410.02142.7520.0010.0010.0000.0000.0000.000
192B192ALA0-0.022-0.01545.9630.0000.0000.0000.0000.0000.000
193B193LYS10.9080.96849.804-0.042-0.0420.0000.0000.0000.000
194B194VAL00.0080.01153.1640.0000.0000.0000.0000.0000.000
195B195VAL0-0.050-0.02855.654-0.001-0.0010.0000.0000.0000.000
196B196GLY00.0860.03959.3470.0010.0010.0000.0000.0000.000
197B197LEU0-0.078-0.03962.554-0.001-0.0010.0000.0000.0000.000
198B198VAL00.0510.04265.7460.0000.0000.0000.0000.0000.000
199B199TYR0-0.026-0.04067.6930.0000.0000.0000.0000.0000.000
200B200SER0-0.065-0.05370.1590.0000.0000.0000.0000.0000.000
201B201PRO00.0140.00773.5620.0000.0000.0000.0000.0000.000
202B202LEU00.0270.03173.2740.0000.0000.0000.0000.0000.000
203B203THR0-0.003-0.00976.8960.0000.0000.0000.0000.0000.000
204B204THR0-0.008-0.00379.896-0.001-0.0010.0000.0000.0000.000
205B205THR00.0220.01680.1000.0000.0000.0000.0000.0000.000
206B206ILE0-0.0220.00577.8970.0000.0000.0000.0000.0000.000
207B207PRO00.0280.02274.3500.0010.0010.0000.0000.0000.000
208B208VAL0-0.0080.00070.0670.0000.0000.0000.0000.0000.000
209B209ASP-1-0.849-0.94069.7110.0210.0210.0000.0000.0000.000
210B210PHE0-0.054-0.04063.4500.0010.0010.0000.0000.0000.000
211B211ILE00.0410.02961.2440.0000.0000.0000.0000.0000.000
212B212VAL0-0.033-0.00857.5770.0010.0010.0000.0000.0000.000
213B213TYR00.028-0.00256.097-0.001-0.0010.0000.0000.0000.000
214B214GLY00.013-0.00752.9890.0010.0010.0000.0000.0000.000
215B215HIS0-0.071-0.04049.027-0.003-0.0030.0000.0000.0000.000
216B216PHE0-0.044-0.02044.5780.0020.0020.0000.0000.0000.000
217B217GLU-1-0.758-0.86845.3400.0500.0500.0000.0000.0000.000
218B218ASP-1-0.817-0.88742.1300.0690.0690.0000.0000.0000.000
219B219VAL0-0.031-0.01239.3360.0040.0040.0000.0000.0000.000
220B220GLU-1-0.812-0.88034.8040.1110.1110.0000.0000.0000.000
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