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: G5N61

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2480375.50581
FMO2-HF: Nuclear repulsion 2387659.662345
FMO2-HF: Total energy -92715.843465
FMO2-MP2: Total energy -92983.925714


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.
-8.242-4.951.967-1.918-3.341-0.014
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 : -0.031 / q_NPA : -0.029
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-1-0.938-0.9592.466-7.783-4.9831.965-1.870-2.895-0.014
4B4GLN0-0.042-0.0334.0020.3870.8790.002-0.048-0.4460.000
5B5ILE00.0160.0125.4710.1520.1520.0000.0000.0000.000
6B6ASN0-0.078-0.0608.5940.2740.2740.0000.0000.0000.000
7B7GLU-1-0.873-0.93810.025-0.654-0.6540.0000.0000.0000.000
8B8ASN0-0.079-0.02913.4990.1430.1430.0000.0000.0000.000
9B9TYR0-0.047-0.02312.4530.0780.0780.0000.0000.0000.000
10B10GLU-1-0.841-0.90812.105-0.579-0.5790.0000.0000.0000.000
11B11ASN0-0.0130.0018.841-0.008-0.0080.0000.0000.0000.000
12B12LYS10.8300.90510.6930.5370.5370.0000.0000.0000.000
13B13GLN0-0.0100.01510.338-0.019-0.0190.0000.0000.0000.000
14B14GLN00.0510.01212.9640.0410.0410.0000.0000.0000.000
15B15LEU0-0.030-0.02116.219-0.027-0.0270.0000.0000.0000.000
16B16VAL00.0130.01914.045-0.008-0.0080.0000.0000.0000.000
17B17GLU-1-0.937-0.95817.467-0.026-0.0260.0000.0000.0000.000
18B18GLN0-0.043-0.01919.7100.0050.0050.0000.0000.0000.000
19B19THR00.008-0.00121.4180.0020.0020.0000.0000.0000.000
20B20GLU-1-0.935-0.95825.1710.0320.0320.0000.0000.0000.000
21B21ILE0-0.100-0.06224.6140.0140.0140.0000.0000.0000.000
22B22THR0-0.030-0.01523.1900.0070.0070.0000.0000.0000.000
23B23THR00.0490.02417.1190.0060.0060.0000.0000.0000.000
24B24PHE0-0.062-0.01620.235-0.008-0.0080.0000.0000.0000.000
25B25GLU-1-0.891-0.95314.115-0.211-0.2110.0000.0000.0000.000
26B26ASN0-0.095-0.05317.4960.0000.0000.0000.0000.0000.000
27B27ASP-1-0.847-0.92916.837-0.430-0.4300.0000.0000.0000.000
28B28LEU0-0.068-0.05819.0030.0260.0260.0000.0000.0000.000
29B29ILE00.0050.00421.478-0.007-0.0070.0000.0000.0000.000
30B30VAL00.0220.02122.0880.0050.0050.0000.0000.0000.000
31B31LEU0-0.071-0.03324.6840.0010.0010.0000.0000.0000.000
32B32GLU-1-0.927-0.96928.273-0.056-0.0560.0000.0000.0000.000
33B33ASP-1-0.915-0.95830.448-0.061-0.0610.0000.0000.0000.000
34B34GLY0-0.013-0.00734.0850.0030.0030.0000.0000.0000.000
35B35PRO0-0.071-0.02537.340-0.002-0.0020.0000.0000.0000.000
36B36GLN00.0290.00435.1030.0040.0040.0000.0000.0000.000
37B37MET0-0.093-0.05338.6030.0030.0030.0000.0000.0000.000
38B38GLU-1-0.893-0.92637.423-0.023-0.0230.0000.0000.0000.000
39B39GLU-1-0.959-0.97540.386-0.011-0.0110.0000.0000.0000.000
40B40SER0-0.025-0.01742.3750.0000.0000.0000.0000.0000.000
41B41LEU00.002-0.00344.2510.0010.0010.0000.0000.0000.000
42B42PRO00.020-0.00247.1760.0020.0020.0000.0000.0000.000
43B43PHE00.0370.00847.2320.0000.0000.0000.0000.0000.000
44B44ALA0-0.0180.00249.5710.0000.0000.0000.0000.0000.000
45B45PHE0-0.018-0.01451.3600.0000.0000.0000.0000.0000.000
46B46HIS0-0.020-0.00846.2380.0000.0000.0000.0000.0000.000
47B47GLY00.0410.01849.9180.0010.0010.0000.0000.0000.000
48B48GLN0-0.058-0.02850.6910.0010.0010.0000.0000.0000.000
49B49HIS0-0.0160.00146.8000.0000.0000.0000.0000.0000.000
50B50THR0-0.041-0.01747.7530.0010.0010.0000.0000.0000.000
51B51ASP-1-0.819-0.89148.9710.0210.0210.0000.0000.0000.000
52B52ASN0-0.010-0.00448.7730.0000.0000.0000.0000.0000.000
53B53ARG10.8630.92045.805-0.030-0.0300.0000.0000.0000.000
54B54GLN00.0280.01741.767-0.002-0.0020.0000.0000.0000.000
55B55HIS0-0.052-0.03543.2630.0050.0050.0000.0000.0000.000
56B56THR00.0100.01937.615-0.001-0.0010.0000.0000.0000.000
57B57VAL00.0490.02036.508-0.002-0.0020.0000.0000.0000.000
58B58VAL00.0300.02337.8970.0010.0010.0000.0000.0000.000
59B59ASN00.037-0.00540.564-0.003-0.0030.0000.0000.0000.000
60B60PHE0-0.005-0.01542.914-0.001-0.0010.0000.0000.0000.000
61B61LEU00.0140.00340.789-0.001-0.0010.0000.0000.0000.000
62B62GLN00.0260.00744.0010.0000.0000.0000.0000.0000.000
63B63ARG10.8340.93646.857-0.030-0.0300.0000.0000.0000.000
64B64PRO00.0350.02849.6490.0010.0010.0000.0000.0000.000
65B65GLN0-0.039-0.02551.312-0.002-0.0020.0000.0000.0000.000
66B66VAL00.0210.00753.3130.0010.0010.0000.0000.0000.000
67B67ILE0-0.037-0.00553.0310.0000.0000.0000.0000.0000.000
68B68PHE0-0.016-0.03256.613-0.001-0.0010.0000.0000.0000.000
69B69ASP-1-0.881-0.95060.3210.0230.0230.0000.0000.0000.000
70B70SER0-0.0170.00363.535-0.001-0.0010.0000.0000.0000.000
71B71SER0-0.0020.00966.5780.0000.0000.0000.0000.0000.000
72B72TRP0-0.009-0.01267.7460.0010.0010.0000.0000.0000.000
73B73ALA00.0280.01871.2470.0000.0000.0000.0000.0000.000
74B74SER0-0.016-0.03174.6250.0010.0010.0000.0000.0000.000
75B75ASP-1-0.933-0.95375.3060.0210.0210.0000.0000.0000.000
76B76VAL0-0.0090.01370.5890.0000.0000.0000.0000.0000.000
77B77PRO0-0.033-0.01773.4390.0000.0000.0000.0000.0000.000
78B78ARG10.9970.97571.411-0.027-0.0270.0000.0000.0000.000
79B79ASN0-0.073-0.03468.7160.0010.0010.0000.0000.0000.000
80B80LYS10.9220.96468.684-0.027-0.0270.0000.0000.0000.000
81B81GLN0-0.016-0.01961.7130.0000.0000.0000.0000.0000.000
82B82PHE00.0420.02463.766-0.001-0.0010.0000.0000.0000.000
83B83MET0-0.0230.01559.013-0.001-0.0010.0000.0000.0000.000
84B84ASP-1-0.879-0.92960.2230.0280.0280.0000.0000.0000.000
85B85SER0-0.109-0.08357.5490.0020.0020.0000.0000.0000.000
86B86ILE00.0320.03053.047-0.001-0.0010.0000.0000.0000.000
87B87MET0-0.082-0.04850.3670.0030.0030.0000.0000.0000.000
88B88ILE0-0.0090.02447.634-0.001-0.0010.0000.0000.0000.000
89B89PRO00.046-0.00643.9790.0020.0020.0000.0000.0000.000
90B90ASP-1-0.811-0.87846.5040.0480.0480.0000.0000.0000.000
91B91ASP-1-0.828-0.89948.0310.0350.0350.0000.0000.0000.000
92B92ILE0-0.026-0.00948.546-0.001-0.0010.0000.0000.0000.000
93B93ILE0-0.024-0.03443.017-0.002-0.0020.0000.0000.0000.000
94B94SER0-0.047-0.02746.174-0.001-0.0010.0000.0000.0000.000
95B95PHE00.0000.01548.493-0.003-0.0030.0000.0000.0000.000
96B96PRO00.0350.00548.1140.0020.0020.0000.0000.0000.000
97B97MET00.0010.02347.0450.0000.0000.0000.0000.0000.000
98B98PHE00.031-0.00345.1480.0010.0010.0000.0000.0000.000
99B99ALA00.0290.02843.5010.0020.0020.0000.0000.0000.000
100B100GLU-1-0.948-0.98042.4590.0220.0220.0000.0000.0000.000
101B101LYS10.7890.89740.753-0.027-0.0270.0000.0000.0000.000
102B102LEU00.0270.00639.0310.0020.0020.0000.0000.0000.000
103B103LYS10.9120.96536.936-0.023-0.0230.0000.0000.0000.000
104B104GLY00.0300.01834.327-0.001-0.0010.0000.0000.0000.000
105B105PHE00.0170.00833.1280.0040.0040.0000.0000.0000.000
106B106SER0-0.0110.01031.236-0.002-0.0020.0000.0000.0000.000
107B107SER0-0.043-0.04133.3110.0000.0000.0000.0000.0000.000
108B108LEU00.0310.00835.764-0.001-0.0010.0000.0000.0000.000
109B109ARG10.8580.93536.233-0.104-0.1040.0000.0000.0000.000
110B110ALA00.0390.02538.9020.0010.0010.0000.0000.0000.000
111B111THR0-0.090-0.04341.934-0.001-0.0010.0000.0000.0000.000
112B112ALA00.0060.01045.432-0.002-0.0020.0000.0000.0000.000
113B113VAL0-0.038-0.02348.0980.0010.0010.0000.0000.0000.000
114B114ILE00.0070.01151.406-0.002-0.0020.0000.0000.0000.000
115B115THR00.003-0.01654.4770.0010.0010.0000.0000.0000.000
116B116VAL0-0.050-0.02157.399-0.001-0.0010.0000.0000.0000.000
117B117GLN0-0.029-0.03060.3290.0000.0000.0000.0000.0000.000
118B118PHE0-0.022-0.03263.8230.0000.0000.0000.0000.0000.000
119B119GLN0-0.0010.01967.4510.0000.0000.0000.0000.0000.000
120B120THR00.022-0.01670.6000.0000.0000.0000.0000.0000.000
121B121GLN00.0120.00973.8680.0000.0000.0000.0000.0000.000
122B122PRO00.013-0.01677.1400.0000.0000.0000.0000.0000.000
123B123PHE0-0.083-0.03678.6500.0000.0000.0000.0000.0000.000
124B124GLN0-0.0010.02175.7410.0000.0000.0000.0000.0000.000
125B125ALA00.010-0.00376.8450.0010.0010.0000.0000.0000.000
126B126GLY00.0440.02374.4850.0000.0000.0000.0000.0000.000
127B127ARG10.7970.88568.740-0.031-0.0310.0000.0000.0000.000
128B128VAL0-0.0030.00966.0170.0000.0000.0000.0000.0000.000
129B129MET0-0.069-0.01763.3460.0010.0010.0000.0000.0000.000
130B130LEU00.0650.03358.647-0.001-0.0010.0000.0000.0000.000
131B131GLY00.0410.00958.4650.0010.0010.0000.0000.0000.000
132B132SER00.0210.00653.442-0.001-0.0010.0000.0000.0000.000
133B133PHE0-0.014-0.00952.6780.0010.0010.0000.0000.0000.000
134B134PRO00.0320.01649.1330.0000.0000.0000.0000.0000.000
135B135LEU0-0.012-0.00244.5620.0000.0000.0000.0000.0000.000
136B136PRO0-0.024-0.01048.602-0.001-0.0010.0000.0000.0000.000
137B137THR00.036-0.00946.638-0.001-0.0010.0000.0000.0000.000
138B138LEU0-0.0220.01243.4520.0000.0000.0000.0000.0000.000
139B139ASN0-0.0220.00047.8180.0010.0010.0000.0000.0000.000
140B140PRO00.0770.02450.553-0.002-0.0020.0000.0000.0000.000
141B141THR0-0.024-0.01553.703-0.002-0.0020.0000.0000.0000.000
142B142ARG10.9440.96454.953-0.052-0.0520.0000.0000.0000.000
143B143VAL00.0400.05154.475-0.001-0.0010.0000.0000.0000.000
144B144LYS10.9800.97957.019-0.035-0.0350.0000.0000.0000.000
145B145PHE0-0.024-0.01660.167-0.001-0.0010.0000.0000.0000.000
146B146ALA0-0.0060.00458.348-0.001-0.0010.0000.0000.0000.000
147B147THR00.0410.00859.6040.0000.0000.0000.0000.0000.000
148B148ASN0-0.0190.02061.6450.0000.0000.0000.0000.0000.000
149B149HIS0-0.017-0.00964.817-0.002-0.0020.0000.0000.0000.000
150B150VAL00.1200.05765.1090.0020.0020.0000.0000.0000.000
151B151SER0-0.073-0.06365.7590.0000.0000.0000.0000.0000.000
152B152ARG10.8340.89862.562-0.037-0.0370.0000.0000.0000.000
153B153LEU00.0160.03159.2250.0020.0020.0000.0000.0000.000
154B154MET00.010-0.00160.2970.0010.0010.0000.0000.0000.000
155B155LEU0-0.065-0.01459.4990.0000.0000.0000.0000.0000.000
156B156LEU0-0.0280.00054.3120.0020.0020.0000.0000.0000.000
157B157ASN00.0010.00853.503-0.001-0.0010.0000.0000.0000.000
158B158HIS0-0.002-0.01056.208-0.002-0.0020.0000.0000.0000.000
159B159VAL00.0530.02658.2090.0010.0010.0000.0000.0000.000
160B160GLN0-0.069-0.03660.930-0.002-0.0020.0000.0000.0000.000
161B161CYS00.0340.03864.6820.0000.0000.0000.0000.0000.000
162B162ASP-1-0.824-0.90866.9860.0270.0270.0000.0000.0000.000
163B163ILE00.0690.03569.7220.0000.0000.0000.0000.0000.000
164B164ALA0-0.0170.00371.883-0.001-0.0010.0000.0000.0000.000
165B165LYS10.7720.88070.912-0.026-0.0260.0000.0000.0000.000
166B166GLU-1-0.843-0.92266.0130.0310.0310.0000.0000.0000.000
167B167THR00.0160.00366.437-0.001-0.0010.0000.0000.0000.000
168B168GLU-1-0.881-0.92660.0740.0320.0320.0000.0000.0000.000
169B169VAL0-0.018-0.01160.9950.0010.0010.0000.0000.0000.000
170B170SER00.0200.01756.2410.0000.0000.0000.0000.0000.000
171B171LEU0-0.049-0.00254.4410.0010.0010.0000.0000.0000.000
172B172ARG10.8370.89846.928-0.058-0.0580.0000.0000.0000.000
173B173ILE0-0.014-0.00948.9040.0010.0010.0000.0000.0000.000
174B174PRO00.019-0.00845.5880.0010.0010.0000.0000.0000.000
175B175PHE0-0.0070.00639.416-0.001-0.0010.0000.0000.0000.000
176B176VAL0-0.020-0.02043.0540.0030.0030.0000.0000.0000.000
177B177SER00.0310.00540.440-0.003-0.0030.0000.0000.0000.000
178B178PRO0-0.035-0.00239.7940.0030.0030.0000.0000.0000.000
179B179TYR0-0.004-0.01236.6540.0080.0080.0000.0000.0000.000
180B180ASN00.0570.03331.670-0.009-0.0090.0000.0000.0000.000
181B181SER00.003-0.00234.898-0.004-0.0040.0000.0000.0000.000
182B182TYR0-0.044-0.06037.283-0.001-0.0010.0000.0000.0000.000
183B183ASP-1-0.807-0.87836.8260.0700.0700.0000.0000.0000.000
184B184LEU00.0510.03036.861-0.005-0.0050.0000.0000.0000.000
185B185VAL0-0.048-0.01634.454-0.007-0.0070.0000.0000.0000.000
186B186SER0-0.076-0.07137.807-0.005-0.0050.0000.0000.0000.000
187B187LYS10.8950.95239.966-0.045-0.0450.0000.0000.0000.000
188B188ARG10.8880.96240.117-0.055-0.0550.0000.0000.0000.000
189B189PHE0-0.018-0.02040.3240.0030.0030.0000.0000.0000.000
190B190PRO00.0610.03643.6010.0030.0030.0000.0000.0000.000
191B191TRP00.0690.02142.9370.0010.0010.0000.0000.0000.000
192B192ALA0-0.022-0.02546.6330.0000.0000.0000.0000.0000.000
193B193LYS10.9180.97950.411-0.041-0.0410.0000.0000.0000.000
194B194VAL00.0120.01053.5790.0000.0000.0000.0000.0000.000
195B195VAL0-0.052-0.02055.967-0.002-0.0020.0000.0000.0000.000
196B196GLY00.1010.03959.5830.0010.0010.0000.0000.0000.000
197B197LEU0-0.081-0.03262.746-0.001-0.0010.0000.0000.0000.000
198B198VAL00.0820.05565.9980.0000.0000.0000.0000.0000.000
199B199TYR0-0.018-0.02868.2210.0000.0000.0000.0000.0000.000
200B200SER0-0.044-0.03870.3050.0000.0000.0000.0000.0000.000
201B201PRO0-0.0130.00173.6970.0000.0000.0000.0000.0000.000
202B202LEU00.0290.03173.4180.0000.0000.0000.0000.0000.000
203B203THR0-0.005-0.01077.1200.0000.0000.0000.0000.0000.000
204B204THR0-0.012-0.00479.905-0.001-0.0010.0000.0000.0000.000
205B205THR00.0230.00080.0710.0000.0000.0000.0000.0000.000
206B206ILE0-0.035-0.00377.3160.0000.0000.0000.0000.0000.000
207B207PRO00.0320.02473.8440.0010.0010.0000.0000.0000.000
208B208VAL00.0000.00569.9920.0000.0000.0000.0000.0000.000
209B209ASP-1-0.848-0.93369.0070.0200.0200.0000.0000.0000.000
210B210PHE0-0.052-0.04262.7960.0010.0010.0000.0000.0000.000
211B211ILE00.0430.03260.4340.0000.0000.0000.0000.0000.000
212B212VAL0-0.0270.00156.9770.0010.0010.0000.0000.0000.000
213B213TYR00.018-0.00955.545-0.001-0.0010.0000.0000.0000.000
214B214GLY00.023-0.00152.5220.0010.0010.0000.0000.0000.000
215B215HIS0-0.062-0.03348.713-0.003-0.0030.0000.0000.0000.000
216B216PHE0-0.035-0.01244.5170.0020.0020.0000.0000.0000.000
217B217GLU-1-0.776-0.88145.0100.0500.0500.0000.0000.0000.000
218B218ASP-1-0.843-0.91041.9160.0710.0710.0000.0000.0000.000
219B219VAL0-0.013-0.00938.8070.0030.0030.0000.0000.0000.000
220B220GLU-1-0.884-0.93934.7730.1110.1110.0000.0000.0000.000
221B221LEU0-0.034-0.02434.9920.0000.0000.0000.0000.0000.000
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