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: 661LZ

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1601078.944803
FMO2-HF: Nuclear repulsion 1532077.863034
FMO2-HF: Total energy -69001.081769
FMO2-MP2: Total energy -69203.491304


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.
-5.057-4.6149.521-4.905-5.059-0.028
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 : 0.040 / q_NPA : 0.003
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].
3B644GLN00.037-0.0052.002-5.263-5.5206.753-3.386-3.110-0.027
4B645PHE0-0.030-0.0102.1920.4171.0212.769-1.510-1.863-0.001
5B646VAL0-0.0010.0215.1410.5810.677-0.001-0.009-0.0860.000
6B647GLN0-0.005-0.0137.4150.1430.1430.0000.0000.0000.000
7B648ASP-1-0.812-0.91110.910-0.452-0.4520.0000.0000.0000.000
8B649PRO00.0270.01912.031-0.119-0.1190.0000.0000.0000.000
9B650HIS10.9020.94713.0830.3880.3880.0000.0000.0000.000
10B651ILE00.0610.02911.245-0.010-0.0100.0000.0000.0000.000
11B652ARG10.7500.8837.5961.0531.0530.0000.0000.0000.000
12B653PHE00.0020.00510.373-0.081-0.0810.0000.0000.0000.000
13B654ASP-1-0.795-0.89113.052-0.515-0.5150.0000.0000.0000.000
14B655LEU0-0.0110.0037.871-0.009-0.0090.0000.0000.0000.000
15B656ALA0-0.031-0.0119.696-0.003-0.0030.0000.0000.0000.000
16B657LEU00.007-0.00810.6000.1030.1030.0000.0000.0000.000
17B658GLU-1-0.947-0.94812.030-0.569-0.5690.0000.0000.0000.000
18B659TYR0-0.139-0.0827.370-0.022-0.0220.0000.0000.0000.000
19B660GLY00.0390.03511.0000.0320.0320.0000.0000.0000.000
20B661ASN0-0.052-0.0337.8970.0840.0840.0000.0000.0000.000
21B662LEU00.0800.01011.251-0.068-0.0680.0000.0000.0000.000
22B663ASP-1-0.930-0.94810.832-0.402-0.4020.0000.0000.0000.000
23B664ALA0-0.010-0.0188.009-0.021-0.0210.0000.0000.0000.000
24B665ALA00.0260.0139.931-0.007-0.0070.0000.0000.0000.000
25B666LEU00.0190.00413.0630.0580.0580.0000.0000.0000.000
26B667ASP-1-0.871-0.93011.006-0.446-0.4460.0000.0000.0000.000
27B668GLU-1-0.797-0.88610.323-0.887-0.8870.0000.0000.0000.000
28B669ALA00.0080.00113.2930.0740.0740.0000.0000.0000.000
29B670LYS10.8500.92714.9880.3960.3960.0000.0000.0000.000
30B671LYS10.8070.89410.6130.7480.7480.0000.0000.0000.000
31B672LEU0-0.054-0.02715.5430.0300.0300.0000.0000.0000.000
32B673ASN0-0.0010.01618.7570.0340.0340.0000.0000.0000.000
33B674ASP-1-0.807-0.87121.274-0.276-0.2760.0000.0000.0000.000
34B675SER00.023-0.02223.020-0.013-0.0130.0000.0000.0000.000
35B676ILE0-0.019-0.00323.167-0.001-0.0010.0000.0000.0000.000
36B677THR0-0.057-0.05618.134-0.019-0.0190.0000.0000.0000.000
37B678TRP00.0310.00319.674-0.029-0.0290.0000.0000.0000.000
38B679GLU-1-0.823-0.92122.241-0.190-0.1900.0000.0000.0000.000
39B680ARG10.8170.90317.6100.4280.4280.0000.0000.0000.000
40B681LEU0-0.0070.00916.699-0.012-0.0120.0000.0000.0000.000
41B682ILE0-0.007-0.00719.7480.0080.0080.0000.0000.0000.000
42B683GLN0-0.055-0.03522.9710.0250.0250.0000.0000.0000.000
43B684GLU-1-0.841-0.91016.714-0.365-0.3650.0000.0000.0000.000
44B685ALA0-0.037-0.01920.2070.0080.0080.0000.0000.0000.000
45B686LEU00.004-0.01421.0470.0190.0190.0000.0000.0000.000
46B687ALA0-0.0430.00421.1740.0190.0190.0000.0000.0000.000
47B688GLN0-0.089-0.04315.7730.0330.0330.0000.0000.0000.000
48B689GLY00.0080.00321.6390.0160.0160.0000.0000.0000.000
49B690ASN0-0.008-0.01519.0000.0380.0380.0000.0000.0000.000
50B691ALA00.0820.03222.930-0.010-0.0100.0000.0000.0000.000
51B692SER0-0.009-0.00723.246-0.006-0.0060.0000.0000.0000.000
52B693LEU00.006-0.00218.0830.0020.0020.0000.0000.0000.000
53B694ALA00.0620.03022.142-0.005-0.0050.0000.0000.0000.000
54B695GLU-1-0.780-0.85024.791-0.102-0.1020.0000.0000.0000.000
55B696MET0-0.026-0.00420.3980.0060.0060.0000.0000.0000.000
56B697ILE00.014-0.00120.6490.0030.0030.0000.0000.0000.000
57B698TYR00.018-0.01324.5150.0100.0100.0000.0000.0000.000
58B699GLN0-0.035-0.01427.6940.0060.0060.0000.0000.0000.000
59B700THR0-0.065-0.02024.1520.0030.0030.0000.0000.0000.000
60B701GLN0-0.033-0.02525.9920.0080.0080.0000.0000.0000.000
61B702HIS0-0.0060.00228.8220.0100.0100.0000.0000.0000.000
62B703SER0-0.033-0.00831.0640.0030.0030.0000.0000.0000.000
63B704PHE00.0690.00532.915-0.002-0.0020.0000.0000.0000.000
64B705ASP-1-0.770-0.85935.530-0.084-0.0840.0000.0000.0000.000
65B706LYS10.8530.93729.1680.1620.1620.0000.0000.0000.000
66B707LEU0-0.028-0.00830.047-0.002-0.0020.0000.0000.0000.000
67B708SER00.006-0.00633.2500.0050.0050.0000.0000.0000.000
68B709PHE00.0050.00433.4510.0040.0040.0000.0000.0000.000
69B710LEU0-0.0030.00128.6490.0020.0020.0000.0000.0000.000
70B711TYR0-0.038-0.06731.6040.0030.0030.0000.0000.0000.000
71B712LEU0-0.0030.01835.1520.0050.0050.0000.0000.0000.000
72B713VAL0-0.048-0.02732.9980.0040.0040.0000.0000.0000.000
73B714THR0-0.060-0.02431.444-0.001-0.0010.0000.0000.0000.000
74B715GLY00.0040.00433.9850.0040.0040.0000.0000.0000.000
75B716ASP-1-0.868-0.94133.934-0.067-0.0670.0000.0000.0000.000
76B717VAL00.0520.00536.485-0.001-0.0010.0000.0000.0000.000
77B718ASN0-0.038-0.01237.762-0.001-0.0010.0000.0000.0000.000
78B719LYS10.8380.89230.3160.0940.0940.0000.0000.0000.000
79B720LEU00.0040.00936.864-0.002-0.0020.0000.0000.0000.000
80B721SER00.0040.00539.0290.0010.0010.0000.0000.0000.000
81B722LYS10.9090.95236.1050.0610.0610.0000.0000.0000.000
82B723MET0-0.027-0.00535.156-0.003-0.0030.0000.0000.0000.000
83B724GLN00.0190.02139.235-0.002-0.0020.0000.0000.0000.000
84B725ASN00.006-0.00342.2950.0010.0010.0000.0000.0000.000
85B726ILE0-0.0280.01237.6420.0010.0010.0000.0000.0000.000
86B727ALA00.0110.00140.9590.0000.0000.0000.0000.0000.000
87B728GLN00.0450.01142.8780.0010.0010.0000.0000.0000.000
88B729THR0-0.097-0.05642.8110.0020.0020.0000.0000.0000.000
89B730ARG10.7380.86338.9450.0770.0770.0000.0000.0000.000
90B731GLU-1-0.930-0.96243.701-0.051-0.0510.0000.0000.0000.000
91B732ASP-1-0.810-0.87942.232-0.074-0.0740.0000.0000.0000.000
92B733PHE00.0890.01745.166-0.001-0.0010.0000.0000.0000.000
93B734GLY0-0.0220.00545.2230.0010.0010.0000.0000.0000.000
94B735SER0-0.023-0.04140.7040.0000.0000.0000.0000.0000.000
95B736MET0-0.0170.00143.1830.0000.0000.0000.0000.0000.000
96B737LEU00.0070.00845.8680.0010.0010.0000.0000.0000.000
97B738LEU0-0.0160.00439.7020.0010.0010.0000.0000.0000.000
98B739ASN0-0.029-0.03640.3790.0000.0000.0000.0000.0000.000
99B740THR00.0420.03143.2930.0030.0030.0000.0000.0000.000
100B741PHE0-0.056-0.02744.9090.0030.0030.0000.0000.0000.000
101B742TYR0-0.049-0.02838.818-0.001-0.0010.0000.0000.0000.000
102B743ASN0-0.031-0.02143.4210.0010.0010.0000.0000.0000.000
103B744ASN0-0.036-0.00445.2080.0020.0020.0000.0000.0000.000
104B745SER00.0000.01548.5160.0030.0030.0000.0000.0000.000
105B746THR00.002-0.01150.516-0.001-0.0010.0000.0000.0000.000
106B747LYS10.9290.94553.5350.0310.0310.0000.0000.0000.000
107B748GLU-1-0.793-0.87547.782-0.048-0.0480.0000.0000.0000.000
108B749ARG10.8890.94449.5020.0480.0480.0000.0000.0000.000
109B750SER0-0.056-0.03052.2010.0000.0000.0000.0000.0000.000
110B751SER00.0430.02254.1100.0010.0010.0000.0000.0000.000
111B752ILE0-0.008-0.00149.5690.0000.0000.0000.0000.0000.000
112B753PHE0-0.016-0.02252.725-0.001-0.0010.0000.0000.0000.000
113B754ALA00.0100.01455.0760.0000.0000.0000.0000.0000.000
114B755GLU-1-0.953-0.97754.024-0.040-0.0400.0000.0000.0000.000
115B756GLY0-0.0210.00253.832-0.001-0.0010.0000.0000.0000.000
116B757GLY0-0.036-0.01754.479-0.001-0.0010.0000.0000.0000.000
117B758SER0-0.070-0.04257.1970.0020.0020.0000.0000.0000.000
118B759LEU00.1010.03758.8900.0000.0000.0000.0000.0000.000
119B760PRO00.0130.01061.4790.0000.0000.0000.0000.0000.000
120B761LEU0-0.0050.00256.0950.0000.0000.0000.0000.0000.000
121B762ALA0-0.0050.01357.9580.0000.0000.0000.0000.0000.000
122B763TYR00.002-0.02758.9300.0000.0000.0000.0000.0000.000
123B764ALA00.0140.01159.5560.0000.0000.0000.0000.0000.000
124B765VAL0-0.036-0.01455.3260.0000.0000.0000.0000.0000.000
125B766ALA00.0170.02058.3160.0000.0000.0000.0000.0000.000
126B767LYS10.8430.90260.6060.0270.0270.0000.0000.0000.000
127B768ALA0-0.059-0.01259.1960.0010.0010.0000.0000.0000.000
128B769ASN0-0.094-0.07756.4950.0000.0000.0000.0000.0000.000
129B770GLY00.0210.02559.7710.0000.0000.0000.0000.0000.000
130B771ASP-1-0.906-0.93660.434-0.029-0.0290.0000.0000.0000.000
131B772GLU-1-0.767-0.90862.685-0.027-0.0270.0000.0000.0000.000
132B773ALA0-0.0460.00164.8280.0000.0000.0000.0000.0000.000
133B774ALA00.0070.00261.4090.0000.0000.0000.0000.0000.000
134B775ALA0-0.002-0.00463.4890.0000.0000.0000.0000.0000.000
135B776SER00.007-0.01564.8580.0000.0000.0000.0000.0000.000
136B777ALA00.0530.03964.8440.0000.0000.0000.0000.0000.000
137B778PHE00.001-0.01159.3470.0000.0000.0000.0000.0000.000
138B779LEU0-0.043-0.02064.8460.0000.0000.0000.0000.0000.000
139B780GLU-1-0.999-0.99568.028-0.023-0.0230.0000.0000.0000.000
140B781GLN0-0.090-0.04162.791-0.001-0.0010.0000.0000.0000.000
141B782ALA0-0.075-0.02066.0990.0000.0000.0000.0000.0000.000
142B783GLU-1-0.941-0.98467.773-0.025-0.0250.0000.0000.0000.000
143B784VAL0-0.064-0.03169.1380.0000.0000.0000.0000.0000.000
144B785ASP-1-0.818-0.90171.838-0.022-0.0220.0000.0000.0000.000
145B786GLU-1-0.786-0.89570.262-0.027-0.0270.0000.0000.0000.000
146B787GLN0-0.168-0.08172.8720.0000.0000.0000.0000.0000.000
147B788ASP-1-0.927-0.96974.349-0.023-0.0230.0000.0000.0000.000
148B789VAL0-0.0230.00768.138-0.001-0.0010.0000.0000.0000.000
149B790THR0-0.075-0.04869.2620.0010.0010.0000.0000.0000.000
150B791LEU0-0.0020.00465.845-0.001-0.0010.0000.0000.0000.000
151B792PRO0-0.020-0.01262.7140.0000.0000.0000.0000.0000.000
152B793ASP-1-0.907-0.94365.828-0.029-0.0290.0000.0000.0000.000
153B794GLN0-0.099-0.06264.5340.0010.0010.0000.0000.0000.000
154B795MET0-0.014-0.00162.115-0.001-0.0010.0000.0000.0000.000
155B796ASP-1-0.857-0.94558.614-0.033-0.0330.0000.0000.0000.000
156B797ALA00.0090.02958.127-0.001-0.0010.0000.0000.0000.000
157B798SER0-0.069-0.05851.681-0.001-0.0010.0000.0000.0000.000
158B799ASN0-0.038-0.03253.3250.0000.0000.0000.0000.0000.000
159B800PHE0-0.0060.00152.1970.0000.0000.0000.0000.0000.000
160B801VAL0-0.030-0.00147.080-0.001-0.0010.0000.0000.0000.000
161B802GLN0-0.014-0.00644.7010.0020.0020.0000.0000.0000.000
162B803ARG10.9620.97245.4200.0380.0380.0000.0000.0000.000
163B804PRO00.0160.01740.9740.0000.0000.0000.0000.0000.000
164B805VAL00.0380.00640.9390.0030.0030.0000.0000.0000.000
165B806ILE0-0.047-0.01936.1830.0030.0030.0000.0000.0000.000
166B807SER0-0.017-0.00139.033-0.001-0.0010.0000.0000.0000.000
167B808LYS10.9570.97531.7040.0490.0490.0000.0000.0000.000
168B809PRO00.0360.03732.9790.0000.0000.0000.0000.0000.000
169B810LEU0-0.037-0.01829.4490.0020.0020.0000.0000.0000.000
170B811GLU-1-0.871-0.95025.634-0.103-0.1030.0000.0000.0000.000
171B812LYS10.8530.92320.9920.1240.1240.0000.0000.0000.000
172B813TRP00.0070.02425.1070.0180.0180.0000.0000.0000.000
173B814PRO0-0.025-0.01624.369-0.007-0.0070.0000.0000.0000.000
174B815LEU00.0020.00719.7900.0000.0000.0000.0000.0000.000
175B816LYS10.8980.94421.3580.0920.0920.0000.0000.0000.000
176B817GLU-1-0.877-0.93418.141-0.075-0.0750.0000.0000.0000.000
177B818ALA0-0.042-0.01315.718-0.011-0.0110.0000.0000.0000.000