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: ZY4RN

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1604471.88438
FMO2-HF: Nuclear repulsion 1535470.226371
FMO2-HF: Total energy -69001.658009
FMO2-MP2: Total energy -69203.99614


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.
-2.81-3.4049.109-4.112-4.404-0.034
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 : 0.009 / q_NPA : -0.017
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].
3B644GLN00.0520.0001.930-5.094-6.4957.576-3.165-3.011-0.032
4B645PHE0-0.032-0.0122.2900.4191.1301.534-0.937-1.308-0.002
5B646VAL00.0030.0215.3140.4710.567-0.001-0.010-0.0850.000
6B647GLN0-0.007-0.0057.6540.1220.1220.0000.0000.0000.000
7B648ASP-1-0.809-0.90811.018-0.234-0.2340.0000.0000.0000.000
8B649PRO00.0300.01211.943-0.032-0.0320.0000.0000.0000.000
9B650HIS10.8810.94313.0180.1890.1890.0000.0000.0000.000
10B651ILE00.0710.04310.7590.0300.0300.0000.0000.0000.000
11B652ARG10.7520.8817.4700.8070.8070.0000.0000.0000.000
12B653PHE0-0.005-0.00210.0800.1390.1390.0000.0000.0000.000
13B654ASP-1-0.807-0.89512.7770.0220.0220.0000.0000.0000.000
14B655LEU0-0.010-0.0077.6930.0200.0200.0000.0000.0000.000
15B656ALA0-0.037-0.0139.6460.1610.1610.0000.0000.0000.000
16B657LEU0-0.010-0.01010.4970.0680.0680.0000.0000.0000.000
17B658GLU-1-0.943-0.93911.3880.2020.2020.0000.0000.0000.000
18B659TYR0-0.125-0.0857.1630.0830.0830.0000.0000.0000.000
19B660GLY00.0380.03511.0130.0930.0930.0000.0000.0000.000
20B661ASN0-0.025-0.0188.536-0.122-0.1220.0000.0000.0000.000
21B662LEU00.0730.01611.706-0.068-0.0680.0000.0000.0000.000
22B663ASP-1-0.916-0.94211.0720.2580.2580.0000.0000.0000.000
23B664ALA00.004-0.0087.829-0.108-0.1080.0000.0000.0000.000
24B665ALA00.0230.0149.745-0.141-0.1410.0000.0000.0000.000
25B666LEU00.018-0.00412.780-0.068-0.0680.0000.0000.0000.000
26B667ASP-1-0.852-0.91010.770-0.202-0.2020.0000.0000.0000.000
27B668GLU-1-0.765-0.87910.382-0.505-0.5050.0000.0000.0000.000
28B669ALA00.0160.01113.127-0.012-0.0120.0000.0000.0000.000
29B670LYS10.8220.90014.5390.0280.0280.0000.0000.0000.000
30B671LYS10.7600.87110.8670.3170.3170.0000.0000.0000.000
31B672LEU0-0.049-0.02615.577-0.006-0.0060.0000.0000.0000.000
32B673ASN0-0.0250.00218.7170.0150.0150.0000.0000.0000.000
33B674ASP-1-0.776-0.84521.085-0.050-0.0500.0000.0000.0000.000
34B675SER00.035-0.01422.7520.0070.0070.0000.0000.0000.000
35B676ILE0-0.0220.00323.1810.0100.0100.0000.0000.0000.000
36B677THR0-0.043-0.05617.7080.0120.0120.0000.0000.0000.000
37B678TRP00.011-0.01019.2410.0220.0220.0000.0000.0000.000
38B679GLU-1-0.804-0.91121.8970.0420.0420.0000.0000.0000.000
39B680ARG10.7830.88117.2610.0030.0030.0000.0000.0000.000
40B681LEU00.0020.01416.4190.0170.0170.0000.0000.0000.000
41B682ILE0-0.0130.00019.6170.0170.0170.0000.0000.0000.000
42B683GLN0-0.046-0.03523.1050.0110.0110.0000.0000.0000.000
43B684GLU-1-0.825-0.90416.7990.2320.2320.0000.0000.0000.000
44B685ALA0-0.048-0.02920.2920.0180.0180.0000.0000.0000.000
45B686LEU0-0.024-0.02521.2480.0050.0050.0000.0000.0000.000
46B687ALA0-0.0340.00221.1900.0000.0000.0000.0000.0000.000
47B688GLN0-0.085-0.04115.9310.0090.0090.0000.0000.0000.000
48B689GLY00.0150.00121.7620.0020.0020.0000.0000.0000.000
49B690ASN0-0.001-0.00318.900-0.024-0.0240.0000.0000.0000.000
50B691ALA00.0700.02122.878-0.007-0.0070.0000.0000.0000.000
51B692SER00.0100.00223.722-0.005-0.0050.0000.0000.0000.000
52B693LEU00.0000.00317.980-0.009-0.0090.0000.0000.0000.000
53B694ALA00.0390.01522.001-0.012-0.0120.0000.0000.0000.000
54B695GLU-1-0.765-0.84924.6930.0360.0360.0000.0000.0000.000
55B696MET0-0.0170.00620.224-0.013-0.0130.0000.0000.0000.000
56B697ILE00.0250.01120.389-0.011-0.0110.0000.0000.0000.000
57B698TYR00.010-0.00924.305-0.007-0.0070.0000.0000.0000.000
58B699GLN0-0.038-0.01927.637-0.007-0.0070.0000.0000.0000.000
59B700THR0-0.046-0.02524.166-0.006-0.0060.0000.0000.0000.000
60B701GLN0-0.017-0.01425.584-0.002-0.0020.0000.0000.0000.000
61B702HIS00.0020.00228.7310.0020.0020.0000.0000.0000.000
62B703SER0-0.032-0.01130.6490.0000.0000.0000.0000.0000.000
63B704PHE00.0580.00432.6110.0050.0050.0000.0000.0000.000
64B705ASP-1-0.773-0.83935.2880.0170.0170.0000.0000.0000.000
65B706LYS10.8370.92928.917-0.017-0.0170.0000.0000.0000.000
66B707LEU0-0.025-0.00629.7960.0050.0050.0000.0000.0000.000
67B708SER00.001-0.01433.0710.0020.0020.0000.0000.0000.000
68B709PHE00.002-0.00133.4210.0020.0020.0000.0000.0000.000
69B710LEU00.0010.00728.5190.0030.0030.0000.0000.0000.000
70B711TYR0-0.051-0.06331.1270.0020.0020.0000.0000.0000.000
71B712LEU00.0090.01734.8210.0010.0010.0000.0000.0000.000
72B713VAL0-0.035-0.01732.9630.0010.0010.0000.0000.0000.000
73B714THR0-0.075-0.03831.0870.0050.0050.0000.0000.0000.000
74B715GLY00.0230.00733.7090.0020.0020.0000.0000.0000.000
75B716ASP-1-0.869-0.93533.4090.0390.0390.0000.0000.0000.000
76B717VAL00.0470.00136.196-0.003-0.0030.0000.0000.0000.000
77B718ASN0-0.041-0.01037.229-0.004-0.0040.0000.0000.0000.000
78B719LYS10.8260.89230.402-0.049-0.0490.0000.0000.0000.000
79B720LEU00.0200.01936.540-0.002-0.0020.0000.0000.0000.000
80B721SER00.0150.00838.798-0.002-0.0020.0000.0000.0000.000
81B722LYS10.8850.94436.304-0.024-0.0240.0000.0000.0000.000
82B723MET0-0.0290.00134.901-0.003-0.0030.0000.0000.0000.000
83B724GLN00.0140.00838.782-0.003-0.0030.0000.0000.0000.000
84B725ASN0-0.027-0.01641.777-0.001-0.0010.0000.0000.0000.000
85B726ILE0-0.029-0.00437.196-0.002-0.0020.0000.0000.0000.000
86B727ALA0-0.016-0.00940.491-0.002-0.0020.0000.0000.0000.000
87B728GLN00.0530.00442.347-0.001-0.0010.0000.0000.0000.000
88B729THR0-0.073-0.04442.281-0.001-0.0010.0000.0000.0000.000
89B730ARG10.7320.85638.848-0.006-0.0060.0000.0000.0000.000
90B731GLU-1-0.924-0.95043.550-0.002-0.0020.0000.0000.0000.000
91B732ASP-1-0.780-0.86142.0390.0050.0050.0000.0000.0000.000
92B733PHE00.0720.00145.0270.0020.0020.0000.0000.0000.000
93B734GLY0-0.0220.00944.7200.0010.0010.0000.0000.0000.000
94B735SER0-0.017-0.05340.1460.0010.0010.0000.0000.0000.000
95B736MET0-0.0160.01442.4990.0020.0020.0000.0000.0000.000
96B737LEU00.0160.01745.4090.0010.0010.0000.0000.0000.000
97B738LEU0-0.027-0.00839.3320.0020.0020.0000.0000.0000.000
98B739ASN0-0.044-0.05739.8450.0030.0030.0000.0000.0000.000
99B740THR00.0250.03343.0580.0010.0010.0000.0000.0000.000
100B741PHE0-0.0200.00044.9550.0000.0000.0000.0000.0000.000
101B742TYR0-0.028-0.01638.6810.0020.0020.0000.0000.0000.000
102B743ASN0-0.018-0.02343.2100.0020.0020.0000.0000.0000.000
103B744ASN0-0.052-0.01444.954-0.001-0.0010.0000.0000.0000.000
104B745SER0-0.003-0.00448.227-0.001-0.0010.0000.0000.0000.000
105B746THR0-0.003-0.00850.151-0.001-0.0010.0000.0000.0000.000
106B747LYS10.8660.91053.338-0.012-0.0120.0000.0000.0000.000
107B748GLU-1-0.790-0.85247.5340.0150.0150.0000.0000.0000.000
108B749ARG10.8350.91149.241-0.018-0.0180.0000.0000.0000.000
109B750SER0-0.050-0.03252.104-0.001-0.0010.0000.0000.0000.000
110B751SER00.0380.01053.711-0.001-0.0010.0000.0000.0000.000
111B752ILE0-0.014-0.01349.163-0.001-0.0010.0000.0000.0000.000
112B753PHE0-0.022-0.01852.280-0.001-0.0010.0000.0000.0000.000
113B754ALA00.0000.00854.765-0.001-0.0010.0000.0000.0000.000
114B755GLU-1-0.946-0.98153.3790.0050.0050.0000.0000.0000.000
115B756GLY0-0.0210.00453.648-0.001-0.0010.0000.0000.0000.000
116B757GLY0-0.019-0.00854.2740.0000.0000.0000.0000.0000.000
117B758SER0-0.052-0.03056.6320.0000.0000.0000.0000.0000.000
118B759LEU00.0850.03258.4610.0010.0010.0000.0000.0000.000
119B760PRO00.0190.01061.1470.0010.0010.0000.0000.0000.000
120B761LEU0-0.011-0.00256.0830.0010.0010.0000.0000.0000.000
121B762ALA0-0.0150.01357.8010.0010.0010.0000.0000.0000.000
122B763TYR00.006-0.01758.7580.0010.0010.0000.0000.0000.000
123B764ALA00.0070.01059.6540.0000.0000.0000.0000.0000.000
124B765VAL0-0.036-0.02355.0610.0010.0010.0000.0000.0000.000
125B766ALA00.0020.01458.0890.0010.0010.0000.0000.0000.000
126B767LYS10.7860.86560.501-0.008-0.0080.0000.0000.0000.000
127B768ALA0-0.026-0.00759.0440.0000.0000.0000.0000.0000.000
128B769ASN0-0.069-0.06056.2590.0020.0020.0000.0000.0000.000
129B770GLY00.0230.02459.7560.0000.0000.0000.0000.0000.000
130B771ASP-1-0.837-0.89259.7590.0110.0110.0000.0000.0000.000
131B772GLU-1-0.780-0.90762.4370.0090.0090.0000.0000.0000.000
132B773ALA0-0.0450.00464.590-0.001-0.0010.0000.0000.0000.000
133B774ALA00.0140.01360.951-0.001-0.0010.0000.0000.0000.000
134B775ALA0-0.006-0.00763.0470.0000.0000.0000.0000.0000.000
135B776SER0-0.008-0.02864.482-0.001-0.0010.0000.0000.0000.000
136B777ALA00.0380.02764.5380.0000.0000.0000.0000.0000.000
137B778PHE0-0.024-0.03558.8940.0000.0000.0000.0000.0000.000
138B779LEU0-0.049-0.02364.3100.0000.0000.0000.0000.0000.000
139B780GLU-1-0.973-0.97767.5430.0050.0050.0000.0000.0000.000
140B781GLN0-0.069-0.03662.4650.0000.0000.0000.0000.0000.000
141B782ALA0-0.063-0.02066.1270.0000.0000.0000.0000.0000.000
142B783GLU-1-0.958-0.98267.9070.0020.0020.0000.0000.0000.000
143B784VAL0-0.053-0.02969.0930.0000.0000.0000.0000.0000.000
144B785ASP-1-0.838-0.90771.8700.0050.0050.0000.0000.0000.000
145B786GLU-1-0.758-0.87269.8040.0080.0080.0000.0000.0000.000
146B787GLN0-0.171-0.08972.9160.0000.0000.0000.0000.0000.000
147B788ASP-1-0.893-0.93874.3130.0050.0050.0000.0000.0000.000
148B789VAL0-0.0240.00267.8740.0000.0000.0000.0000.0000.000
149B790THR0-0.076-0.05069.0230.0000.0000.0000.0000.0000.000
150B791LEU00.0000.00465.7070.0000.0000.0000.0000.0000.000
151B792PRO0-0.020-0.01562.5790.0000.0000.0000.0000.0000.000
152B793ASP-1-0.906-0.94365.7600.0110.0110.0000.0000.0000.000
153B794GLN0-0.104-0.06164.6260.0010.0010.0000.0000.0000.000
154B795MET0-0.016-0.00262.0560.0000.0000.0000.0000.0000.000
155B796ASP-1-0.849-0.92858.7530.0180.0180.0000.0000.0000.000
156B797ALA00.0500.04657.8470.0000.0000.0000.0000.0000.000
157B798SER0-0.047-0.04351.5550.0010.0010.0000.0000.0000.000
158B799ASN0-0.059-0.04952.6800.0010.0010.0000.0000.0000.000
159B800PHE0-0.017-0.00252.3040.0010.0010.0000.0000.0000.000
160B801VAL0-0.0340.00147.2700.0020.0020.0000.0000.0000.000
161B802GLN0-0.013-0.00844.9620.0010.0010.0000.0000.0000.000
162B803ARG10.9610.97445.076-0.028-0.0280.0000.0000.0000.000
163B804PRO00.0140.01240.7330.0020.0020.0000.0000.0000.000
164B805VAL00.0240.00341.342-0.002-0.0020.0000.0000.0000.000
165B806ILE0-0.035-0.01036.2690.0010.0010.0000.0000.0000.000
166B807SER0-0.015-0.01039.475-0.001-0.0010.0000.0000.0000.000
167B808LYS10.9370.96731.880-0.069-0.0690.0000.0000.0000.000
168B809PRO00.0500.04132.7250.0020.0020.0000.0000.0000.000
169B810LEU0-0.034-0.02030.0730.0020.0020.0000.0000.0000.000
170B811GLU-1-0.907-0.96225.5190.0850.0850.0000.0000.0000.000
171B812LYS10.8640.93521.138-0.111-0.1110.0000.0000.0000.000
172B813TRP00.0180.02325.519-0.012-0.0120.0000.0000.0000.000
173B814PRO0-0.030-0.00924.8280.0120.0120.0000.0000.0000.000
174B815LEU00.0120.00820.1740.0010.0010.0000.0000.0000.000
175B816LYS10.8940.93021.325-0.182-0.1820.0000.0000.0000.000
176B817GLU-1-0.883-0.93318.2190.2620.2620.0000.0000.0000.000
177B818ALA0-0.043-0.00716.2930.0400.0400.0000.0000.0000.000