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

tag_button

FMODB ID: 22V7R

Calculation Name: 3MKQ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MKQ

Chain ID: B

ChEMBL ID:

UniProt ID: P53622

Base Structure: X-ray

Registration Date: 2023-06-20

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1600484.721562
FMO2-HF: Nuclear repulsion 1531484.975839
FMO2-HF: Total energy -68999.745723
FMO2-MP2: Total energy -69202.264577


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:642:ALA)


Summations of interaction energy for fragment #1(B:642:ALA)
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.
-6.262-9.81116.975-7.779-5.647-0.035
Interaction energy analysis for fragmet #1(B:642:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : -0.002
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].
3B644GLN00.031-0.0061.839-6.263-9.36511.956-5.095-3.760-0.041
4B645PHE0-0.044-0.0151.9040.542-0.0015.020-2.675-1.8020.006
5B646VAL0-0.0080.0155.1980.5200.616-0.001-0.009-0.0850.000
6B647GLN0-0.014-0.0217.4400.1300.1300.0000.0000.0000.000
7B648ASP-1-0.815-0.91310.944-0.426-0.4260.0000.0000.0000.000
8B649PRO0-0.030-0.00612.087-0.135-0.1350.0000.0000.0000.000
9B650HIS10.9280.96913.0930.3800.3800.0000.0000.0000.000
10B651ILE00.0810.03911.125-0.007-0.0070.0000.0000.0000.000
11B652ARG10.8710.9518.0381.0391.0390.0000.0000.0000.000
12B653PHE0-0.0020.00810.373-0.085-0.0850.0000.0000.0000.000
13B654ASP-1-0.821-0.92313.049-0.527-0.5270.0000.0000.0000.000
14B655LEU0-0.0030.0067.819-0.009-0.0090.0000.0000.0000.000
15B656ALA0-0.038-0.0109.649-0.010-0.0100.0000.0000.0000.000
16B657LEU00.005-0.01410.5550.1020.1020.0000.0000.0000.000
17B658GLU-1-0.976-0.96611.783-0.511-0.5110.0000.0000.0000.000
18B659TYR0-0.124-0.0686.461-0.035-0.0350.0000.0000.0000.000
19B660GLY00.0490.03910.9560.0250.0250.0000.0000.0000.000
20B661ASN0-0.056-0.0297.7030.1080.1080.0000.0000.0000.000
21B662LEU00.056-0.00411.295-0.064-0.0640.0000.0000.0000.000
22B663ASP-1-0.940-0.95310.758-0.456-0.4560.0000.0000.0000.000
23B664ALA00.011-0.0058.093-0.023-0.0230.0000.0000.0000.000
24B665ALA00.0360.0179.9080.0060.0060.0000.0000.0000.000
25B666LEU00.013-0.00313.0450.0710.0710.0000.0000.0000.000
26B667ASP-1-0.940-0.96410.607-0.595-0.5950.0000.0000.0000.000
27B668GLU-1-0.892-0.9709.890-0.950-0.9500.0000.0000.0000.000
28B669ALA0-0.008-0.00913.2850.0840.0840.0000.0000.0000.000
29B670LYS10.9150.96316.2680.3780.3780.0000.0000.0000.000
30B671LYS10.8410.93110.6400.7480.7480.0000.0000.0000.000
31B672LEU0-0.057-0.02915.2830.0350.0350.0000.0000.0000.000
32B673ASN0-0.0060.00518.7560.0370.0370.0000.0000.0000.000
33B674ASP-1-0.838-0.91721.241-0.275-0.2750.0000.0000.0000.000
34B675SER00.013-0.02323.013-0.008-0.0080.0000.0000.0000.000
35B676ILE0-0.0120.00222.893-0.002-0.0020.0000.0000.0000.000
36B677THR0-0.028-0.01818.102-0.020-0.0200.0000.0000.0000.000
37B678TRP00.0270.01219.836-0.032-0.0320.0000.0000.0000.000
38B679GLU-1-0.871-0.95622.229-0.208-0.2080.0000.0000.0000.000
39B680ARG10.8480.93717.3660.4280.4280.0000.0000.0000.000
40B681LEU0-0.0180.00916.770-0.013-0.0130.0000.0000.0000.000
41B682ILE00.0000.00019.8070.0070.0070.0000.0000.0000.000
42B683GLN0-0.048-0.02822.7100.0230.0230.0000.0000.0000.000
43B684GLU-1-0.838-0.91216.670-0.387-0.3870.0000.0000.0000.000
44B685ALA0-0.038-0.02120.1670.0060.0060.0000.0000.0000.000
45B686LEU0-0.006-0.01821.0960.0190.0190.0000.0000.0000.000
46B687ALA0-0.0330.00821.1120.0190.0190.0000.0000.0000.000
47B688GLN0-0.076-0.03615.9080.0290.0290.0000.0000.0000.000
48B689GLY00.0100.00621.6110.0150.0150.0000.0000.0000.000
49B690ASN0-0.005-0.00519.3290.0370.0370.0000.0000.0000.000
50B691ALA00.0870.03122.969-0.010-0.0100.0000.0000.0000.000
51B692SER0-0.028-0.00823.095-0.007-0.0070.0000.0000.0000.000
52B693LEU0-0.002-0.01018.1890.0020.0020.0000.0000.0000.000
53B694ALA00.0630.02922.189-0.004-0.0040.0000.0000.0000.000
54B695GLU-1-0.794-0.84024.842-0.115-0.1150.0000.0000.0000.000
55B696MET0-0.0140.00220.0670.0060.0060.0000.0000.0000.000
56B697ILE00.012-0.00220.7130.0030.0030.0000.0000.0000.000
57B698TYR00.013-0.01324.4940.0100.0100.0000.0000.0000.000
58B699GLN0-0.038-0.02027.6200.0040.0040.0000.0000.0000.000
59B700THR0-0.073-0.02624.2280.0030.0030.0000.0000.0000.000
60B701GLN0-0.021-0.01626.1760.0030.0030.0000.0000.0000.000
61B702HIS0-0.0040.00628.8060.0090.0090.0000.0000.0000.000
62B703SER0-0.053-0.02031.0240.0020.0020.0000.0000.0000.000
63B704PHE00.0780.00832.897-0.002-0.0020.0000.0000.0000.000
64B705ASP-1-0.767-0.85535.509-0.090-0.0900.0000.0000.0000.000
65B706LYS10.9010.95429.5190.1620.1620.0000.0000.0000.000
66B707LEU0-0.018-0.00130.031-0.002-0.0020.0000.0000.0000.000
67B708SER00.0150.01433.3020.0050.0050.0000.0000.0000.000
68B709PHE00.0010.00433.6210.0040.0040.0000.0000.0000.000
69B710LEU0-0.011-0.00428.8950.0020.0020.0000.0000.0000.000
70B711TYR0-0.055-0.11531.5140.0030.0030.0000.0000.0000.000
71B712LEU0-0.0120.01435.1960.0050.0050.0000.0000.0000.000
72B713VAL0-0.046-0.02732.9840.0040.0040.0000.0000.0000.000
73B714THR0-0.043-0.00931.6340.0000.0000.0000.0000.0000.000
74B715GLY00.0070.00634.0240.0030.0030.0000.0000.0000.000
75B716ASP-1-0.866-0.94933.838-0.078-0.0780.0000.0000.0000.000
76B717VAL00.0320.00136.523-0.001-0.0010.0000.0000.0000.000
77B718ASN0-0.020-0.01137.6480.0030.0030.0000.0000.0000.000
78B719LYS10.8300.91430.4470.1050.1050.0000.0000.0000.000
79B720LEU00.0120.00936.906-0.002-0.0020.0000.0000.0000.000
80B721SER00.0260.00939.0730.0010.0010.0000.0000.0000.000
81B722LYS10.9350.97035.5450.0720.0720.0000.0000.0000.000
82B723MET0-0.045-0.01034.483-0.002-0.0020.0000.0000.0000.000
83B724GLN00.0470.03539.210-0.002-0.0020.0000.0000.0000.000
84B725ASN0-0.009-0.01342.1920.0010.0010.0000.0000.0000.000
85B726ILE0-0.050-0.00137.6620.0010.0010.0000.0000.0000.000
86B727ALA00.0210.00240.9370.0010.0010.0000.0000.0000.000
87B728GLN00.0440.01242.8560.0010.0010.0000.0000.0000.000
88B729THR0-0.092-0.04742.7860.0030.0030.0000.0000.0000.000
89B730ARG10.8220.90939.0470.0820.0820.0000.0000.0000.000
90B731GLU-1-0.920-0.95243.683-0.055-0.0550.0000.0000.0000.000
91B732ASP-1-0.867-0.91042.588-0.076-0.0760.0000.0000.0000.000
92B733PHE00.0770.00445.147-0.001-0.0010.0000.0000.0000.000
93B734GLY0-0.0200.00445.2030.0010.0010.0000.0000.0000.000
94B735SER0-0.054-0.06240.635-0.001-0.0010.0000.0000.0000.000
95B736MET0-0.025-0.00143.1620.0000.0000.0000.0000.0000.000
96B737LEU00.0080.00645.8450.0010.0010.0000.0000.0000.000
97B738LEU00.0000.01039.7080.0010.0010.0000.0000.0000.000
98B739ASN0-0.031-0.04040.2940.0000.0000.0000.0000.0000.000
99B740THR00.1050.06043.3430.0030.0030.0000.0000.0000.000
100B741PHE0-0.066-0.04044.8920.0030.0030.0000.0000.0000.000
101B742TYR0-0.041-0.02238.998-0.001-0.0010.0000.0000.0000.000
102B743ASN0-0.033-0.00743.4680.0020.0020.0000.0000.0000.000
103B744ASN0-0.0140.01245.2520.0020.0020.0000.0000.0000.000
104B745SER00.0210.03348.5610.0040.0040.0000.0000.0000.000
105B746THR00.004-0.01150.562-0.001-0.0010.0000.0000.0000.000
106B747LYS10.9850.99253.5830.0340.0340.0000.0000.0000.000
107B748GLU-1-0.847-0.92447.825-0.053-0.0530.0000.0000.0000.000
108B749ARG10.8650.93849.3840.0520.0520.0000.0000.0000.000
109B750SER0-0.037-0.01852.2510.0000.0000.0000.0000.0000.000
110B751SER00.0390.02154.1000.0010.0010.0000.0000.0000.000
111B752ILE0-0.012-0.00649.2290.0000.0000.0000.0000.0000.000
112B753PHE0-0.017-0.02252.703-0.001-0.0010.0000.0000.0000.000
113B754ALA00.0090.01355.0550.0000.0000.0000.0000.0000.000
114B755GLU-1-0.962-0.98054.174-0.043-0.0430.0000.0000.0000.000
115B756GLY0-0.0270.00753.811-0.001-0.0010.0000.0000.0000.000
116B757GLY0-0.029-0.01554.460-0.001-0.0010.0000.0000.0000.000
117B758SER0-0.069-0.03957.1220.0020.0020.0000.0000.0000.000
118B759LEU00.1150.04058.871-0.001-0.0010.0000.0000.0000.000
119B760PRO0-0.0010.00661.2010.0000.0000.0000.0000.0000.000
120B761LEU00.0030.00256.1110.0000.0000.0000.0000.0000.000
121B762ALA0-0.0080.01058.0090.0000.0000.0000.0000.0000.000
122B763TYR00.0680.02458.9750.0000.0000.0000.0000.0000.000
123B764ALA00.0060.00759.5460.0000.0000.0000.0000.0000.000
124B765VAL0-0.041-0.01855.3360.0000.0000.0000.0000.0000.000
125B766ALA00.0210.01858.3660.0000.0000.0000.0000.0000.000
126B767LYS10.9320.96060.6550.0300.0300.0000.0000.0000.000
127B768ALA0-0.038-0.00459.2180.0010.0010.0000.0000.0000.000
128B769ASN0-0.102-0.07256.3310.0000.0000.0000.0000.0000.000
129B770GLY00.0240.02759.8160.0000.0000.0000.0000.0000.000
130B771ASP-1-0.946-0.96860.423-0.032-0.0320.0000.0000.0000.000
131B772GLU-1-0.802-0.93962.731-0.029-0.0290.0000.0000.0000.000
132B773ALA0-0.046-0.00864.8190.0000.0000.0000.0000.0000.000
133B774ALA00.0060.00261.5030.0000.0000.0000.0000.0000.000
134B775ALA0-0.026-0.01463.5380.0000.0000.0000.0000.0000.000
135B776SER00.008-0.01064.9080.0000.0000.0000.0000.0000.000
136B777ALA00.0740.04864.8150.0000.0000.0000.0000.0000.000
137B778PHE0-0.001-0.01159.2150.0000.0000.0000.0000.0000.000
138B779LEU0-0.052-0.02364.8240.0000.0000.0000.0000.0000.000
139B780GLU-1-0.995-0.99468.029-0.025-0.0250.0000.0000.0000.000
140B781GLN0-0.096-0.04662.7560.0000.0000.0000.0000.0000.000
141B782ALA0-0.073-0.01766.1660.0000.0000.0000.0000.0000.000
142B783GLU-1-0.944-0.98767.752-0.026-0.0260.0000.0000.0000.000
143B784VAL0-0.067-0.03169.0400.0000.0000.0000.0000.0000.000
144B785ASP-1-0.824-0.89071.817-0.024-0.0240.0000.0000.0000.000
145B786GLU-1-0.972-1.01871.060-0.027-0.0270.0000.0000.0000.000
146B787GLN0-0.078-0.03172.9240.0000.0000.0000.0000.0000.000
147B788ASP-1-0.961-0.99274.064-0.025-0.0250.0000.0000.0000.000
148B789VAL0-0.029-0.00268.290-0.001-0.0010.0000.0000.0000.000
149B790THR0-0.069-0.04369.3240.0010.0010.0000.0000.0000.000
150B791LEU0-0.032-0.01166.011-0.001-0.0010.0000.0000.0000.000
151B792PRO0-0.019-0.01062.7420.0000.0000.0000.0000.0000.000
152B793ASP-1-0.908-0.94665.879-0.030-0.0300.0000.0000.0000.000
153B794GLN0-0.064-0.04464.5160.0000.0000.0000.0000.0000.000
154B795MET0-0.028-0.00462.164-0.002-0.0020.0000.0000.0000.000
155B796ASP-1-0.887-0.95858.668-0.035-0.0350.0000.0000.0000.000
156B797ALA00.0130.03458.088-0.001-0.0010.0000.0000.0000.000
157B798SER0-0.079-0.06951.735-0.001-0.0010.0000.0000.0000.000
158B799ASN0-0.033-0.03053.368-0.001-0.0010.0000.0000.0000.000
159B800PHE0-0.003-0.00452.2760.0000.0000.0000.0000.0000.000
160B801VAL0-0.0370.00647.164-0.001-0.0010.0000.0000.0000.000
161B802GLN00.0210.00444.6960.0030.0030.0000.0000.0000.000
162B803ARG10.9550.96845.5060.0430.0430.0000.0000.0000.000
163B804PRO0-0.0010.01341.1960.0000.0000.0000.0000.0000.000
164B805VAL00.0490.01240.7210.0030.0030.0000.0000.0000.000
165B806ILE0-0.029-0.01436.2290.0030.0030.0000.0000.0000.000
166B807SER0-0.044-0.00938.812-0.002-0.0020.0000.0000.0000.000
167B808LYS10.9620.97432.0930.0600.0600.0000.0000.0000.000
168B809PRO00.0180.02533.1390.0000.0000.0000.0000.0000.000
169B810LEU0-0.022-0.00929.6020.0010.0010.0000.0000.0000.000
170B811GLU-1-0.913-0.96526.338-0.111-0.1110.0000.0000.0000.000
171B812LYS10.9070.94020.2060.1690.1690.0000.0000.0000.000
172B813TRP00.0040.02225.1420.0180.0180.0000.0000.0000.000
173B814PRO0-0.035-0.02024.394-0.009-0.0090.0000.0000.0000.000
174B815LEU00.0090.00619.7320.0000.0000.0000.0000.0000.000
175B816LYS10.9070.95121.3030.1080.1080.0000.0000.0000.000
176B817GLU-1-0.883-0.94118.143-0.109-0.1090.0000.0000.0000.000
177B818ALA0-0.040-0.00815.716-0.013-0.0130.0000.0000.0000.000