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: 53Z2Z

Calculation Name: 3MKQ-B-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 177
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1600495.836583
FMO2-HF: Nuclear repulsion 1531496.342959
FMO2-HF: Total energy -68999.493623
FMO2-MP2: Total energy -69201.999746


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.
-127.77-126.22813.805-9.013-6.332-0.073
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 : 1 / q_Mulliken : 0.819 / q_NPA : 0.883
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].
3B644GLN 00.0810.0221.918-29.439-26.9617.957-5.876-4.559-0.070
4B645PHE 0-0.050-0.0181.8522.1231.0805.848-3.125-1.679-0.003
5B646VAL 00.0040.0215.1625.6895.7960.000-0.012-0.0940.000
6B647GLN 0-0.009-0.0187.4262.4072.4070.0000.0000.0000.000
7B648ASP -1-0.808-0.90910.924-18.875-18.8750.0000.0000.0000.000
8B649PRO 0-0.028-0.00812.131-1.824-1.8240.0000.0000.0000.000
9B650HIS 10.9340.97513.13517.31417.3140.0000.0000.0000.000
10B651ILE 00.0840.04111.121-0.087-0.0870.0000.0000.0000.000
11B652ARG 10.8550.9438.06729.62629.6260.0000.0000.0000.000
12B653PHE 00.0000.00910.373-1.065-1.0650.0000.0000.0000.000
13B654ASP -1-0.816-0.91913.147-19.286-19.2860.0000.0000.0000.000
14B655LEU 0-0.0040.0037.814-0.347-0.3470.0000.0000.0000.000
15B656ALA 0-0.050-0.0169.649-0.602-0.6020.0000.0000.0000.000
16B657LEU 00.005-0.01210.5551.0341.0340.0000.0000.0000.000
17B658GLU -1-0.966-0.96211.780-21.201-21.2010.0000.0000.0000.000
18B659TYR 0-0.130-0.0716.460-1.858-1.8580.0000.0000.0000.000
19B660GLY 00.0610.04710.953-0.285-0.2850.0000.0000.0000.000
20B661ASN 0-0.057-0.0297.6101.2661.2660.0000.0000.0000.000
21B662LEU 00.062-0.00211.159-0.466-0.4660.0000.0000.0000.000
22B663ASP -1-0.936-0.95010.625-23.099-23.0990.0000.0000.0000.000
23B664ALA 0-0.001-0.0127.909-0.288-0.2880.0000.0000.0000.000
24B665ALA 00.0280.0139.8120.5730.5730.0000.0000.0000.000
25B666LEU 00.0230.00212.9561.4671.4670.0000.0000.0000.000
26B667ASP -1-0.939-0.96310.713-25.513-25.5130.0000.0000.0000.000
27B668GLU -1-0.902-0.9759.963-28.126-28.1260.0000.0000.0000.000
28B669ALA 0-0.004-0.00713.3781.5491.5490.0000.0000.0000.000
29B670LYS 10.9210.96716.36919.36919.3690.0000.0000.0000.000
30B671LYS 10.8350.92810.68427.43327.4330.0000.0000.0000.000
31B672LEU 0-0.061-0.03115.3500.7860.7860.0000.0000.0000.000
32B673ASN 0-0.0050.00618.8260.9250.9250.0000.0000.0000.000
33B674ASP -1-0.836-0.91621.320-13.941-13.9410.0000.0000.0000.000
34B675SER 00.014-0.02323.110-0.138-0.1380.0000.0000.0000.000
35B676ILE 0-0.0120.00222.987-0.040-0.0400.0000.0000.0000.000
36B677THR 0-0.030-0.01918.200-0.426-0.4260.0000.0000.0000.000
37B678TRP 00.0270.01119.957-0.780-0.7800.0000.0000.0000.000
38B679GLU -1-0.869-0.95522.338-12.104-12.1040.0000.0000.0000.000
39B680ARG 10.8500.93817.36617.07017.0700.0000.0000.0000.000
40B681LEU 0-0.0170.00816.578-0.394-0.3940.0000.0000.0000.000
41B682ILE 0-0.008-0.00219.605-0.014-0.0140.0000.0000.0000.000
42B683GLN 0-0.043-0.02622.7100.4640.4640.0000.0000.0000.000
43B684GLU -1-0.837-0.91316.634-17.568-17.5680.0000.0000.0000.000
44B685ALA 0-0.041-0.02320.101-0.120-0.1200.0000.0000.0000.000
45B686LEU 0-0.009-0.01820.9370.2760.2760.0000.0000.0000.000
46B687ALA 0-0.0320.00821.1120.4360.4360.0000.0000.0000.000
47B688GLN 0-0.067-0.03215.8960.1510.1510.0000.0000.0000.000
48B689GLY 00.0120.00921.5990.1640.1640.0000.0000.0000.000
49B690ASN 0-0.004-0.00419.2090.9000.9000.0000.0000.0000.000
50B691ALA 00.0860.02922.842-0.096-0.0960.0000.0000.0000.000
51B692SER 0-0.028-0.00822.968-0.228-0.2280.0000.0000.0000.000
52B693LEU 0-0.002-0.01018.0270.0740.0740.0000.0000.0000.000
53B694ALA 00.0570.02722.0290.0310.0310.0000.0000.0000.000
54B695GLU -1-0.790-0.83824.669-10.534-10.5340.0000.0000.0000.000
55B696MET 0-0.0140.00220.1630.2740.2740.0000.0000.0000.000
56B697ILE 00.011-0.00320.5900.1370.1370.0000.0000.0000.000
57B698TYR 00.012-0.01424.5070.4030.4030.0000.0000.0000.000
58B699GLN 0-0.035-0.01827.7140.0920.0920.0000.0000.0000.000
59B700THR 0-0.074-0.02624.3410.1670.1670.0000.0000.0000.000
60B701GLN 0-0.022-0.01726.2930.1870.1870.0000.0000.0000.000
61B702HIS 0-0.0040.00628.9210.4560.4560.0000.0000.0000.000
62B703SER 0-0.053-0.02031.0780.2200.2200.0000.0000.0000.000
63B704PHE 00.0770.00732.942-0.091-0.0910.0000.0000.0000.000
64B705ASP -1-0.765-0.85435.501-8.270-8.2700.0000.0000.0000.000
65B706LYS 10.9010.95429.39810.76710.7670.0000.0000.0000.000
66B707LEU 0-0.020-0.00129.927-0.124-0.1240.0000.0000.0000.000
67B708SER 00.0160.01433.1230.1370.1370.0000.0000.0000.000
68B709PHE 00.0010.00333.4540.1100.1100.0000.0000.0000.000
69B710LEU 0-0.009-0.00328.7380.0140.0140.0000.0000.0000.000
70B711TYR 0-0.059-0.11731.3540.0340.0340.0000.0000.0000.000
71B712LEU 0-0.0130.01435.0460.1480.1480.0000.0000.0000.000
72B713VAL 0-0.046-0.02632.8480.1120.1120.0000.0000.0000.000
73B714THR 0-0.039-0.00731.488-0.168-0.1680.0000.0000.0000.000
74B715GLY 00.0080.00633.897-0.001-0.0010.0000.0000.0000.000
75B716ASP -1-0.866-0.95033.710-9.188-9.1880.0000.0000.0000.000
76B717VAL 00.0310.00136.3940.0530.0530.0000.0000.0000.000
77B718ASN 0-0.020-0.01137.5270.2980.2980.0000.0000.0000.000
78B719LYS 10.8310.91430.30910.49210.4920.0000.0000.0000.000
79B720LEU 00.0100.00936.758-0.004-0.0040.0000.0000.0000.000
80B721SER 00.0240.00938.9180.1670.1670.0000.0000.0000.000
81B722LYS 10.9380.97035.4598.9608.9600.0000.0000.0000.000
82B723MET 0-0.044-0.01034.409-0.026-0.0260.0000.0000.0000.000
83B724GLN 00.0480.03539.138-0.011-0.0110.0000.0000.0000.000
84B725ASN 0-0.010-0.01442.241-0.019-0.0190.0000.0000.0000.000
85B726ILE 0-0.0490.00037.7410.0670.0670.0000.0000.0000.000
86B727ALA 00.0200.00341.0480.0680.0680.0000.0000.0000.000
87B728GLN 00.0430.01242.9240.0390.0390.0000.0000.0000.000
88B729THR 0-0.092-0.04742.9030.1250.1250.0000.0000.0000.000
89B730ARG 10.8220.90939.1648.0638.0630.0000.0000.0000.000
90B731GLU -1-0.921-0.95243.798-6.598-6.5980.0000.0000.0000.000
91B732ASP -1-0.867-0.91042.696-7.476-7.4760.0000.0000.0000.000
92B733PHE 00.0780.00445.256-0.072-0.0720.0000.0000.0000.000
93B734GLY 0-0.0200.00445.1710.0680.0680.0000.0000.0000.000
94B735SER 0-0.053-0.06240.599-0.042-0.0420.0000.0000.0000.000
95B736MET 0-0.030-0.00343.101-0.005-0.0050.0000.0000.0000.000
96B737LEU 00.0090.00745.7710.0420.0420.0000.0000.0000.000
97B738LEU 00.0040.01139.5240.0090.0090.0000.0000.0000.000
98B739ASN 0-0.030-0.04040.120-0.047-0.0470.0000.0000.0000.000
99B740THR 00.1030.06043.1700.0970.0970.0000.0000.0000.000
100B741PHE 0-0.066-0.03944.7220.1480.1480.0000.0000.0000.000
101B742TYR 0-0.041-0.02138.826-0.081-0.0810.0000.0000.0000.000
102B743ASN 0-0.032-0.00843.3100.0700.0700.0000.0000.0000.000
103B744ASN 0-0.0130.01345.1010.1240.1240.0000.0000.0000.000
104B745SER 00.0210.03248.4090.2160.2160.0000.0000.0000.000
105B746THR 00.006-0.01250.406-0.006-0.0060.0000.0000.0000.000
106B747LYS 10.9850.99253.4215.6605.6600.0000.0000.0000.000
107B748GLU -1-0.845-0.92347.659-6.800-6.8000.0000.0000.0000.000
108B749ARG 10.8600.93649.2196.4496.4490.0000.0000.0000.000
109B750SER 0-0.035-0.01752.0760.0570.0570.0000.0000.0000.000
110B751SER 00.0400.02154.0110.1080.1080.0000.0000.0000.000
111B752ILE 0-0.016-0.00749.1440.0070.0070.0000.0000.0000.000
112B753PHE 0-0.014-0.02152.637-0.021-0.0210.0000.0000.0000.000
113B754ALA 00.0060.01254.9650.0520.0520.0000.0000.0000.000
114B755GLU -1-0.960-0.97954.216-5.959-5.9590.0000.0000.0000.000
115B756GLY 0-0.0260.00753.878-0.036-0.0360.0000.0000.0000.000
116B757GLY 0-0.030-0.01554.5010.0060.0060.0000.0000.0000.000
117B758SER 0-0.068-0.04057.0380.1420.1420.0000.0000.0000.000
118B759LEU 00.1160.04058.785-0.059-0.0590.0000.0000.0000.000
119B760PRO 0-0.0020.00661.1060.0110.0110.0000.0000.0000.000
120B761LEU 00.0040.00255.9580.0080.0080.0000.0000.0000.000
121B762ALA 0-0.0070.01057.827-0.039-0.0390.0000.0000.0000.000
122B763TYR 00.0700.02558.800-0.001-0.0010.0000.0000.0000.000
123B764ALA 00.0040.00659.3670.0060.0060.0000.0000.0000.000
124B765VAL 0-0.046-0.01955.166-0.027-0.0270.0000.0000.0000.000
125B766ALA 00.0230.01858.195-0.018-0.0180.0000.0000.0000.000
126B767LYS 10.9320.96160.4884.8484.8480.0000.0000.0000.000
127B768ALA 0-0.035-0.00359.0540.0390.0390.0000.0000.0000.000
128B769ASN 0-0.105-0.07356.175-0.078-0.0780.0000.0000.0000.000
129B770GLY 00.0240.02859.663-0.014-0.0140.0000.0000.0000.000
130B771ASP -1-0.945-0.96960.264-5.309-5.3090.0000.0000.0000.000
131B772GLU -1-0.804-0.94062.574-4.876-4.8760.0000.0000.0000.000
132B773ALA 0-0.043-0.00764.6590.0510.0510.0000.0000.0000.000
133B774ALA 00.0050.00261.3320.0270.0270.0000.0000.0000.000
134B775ALA 0-0.024-0.01363.3690.0120.0120.0000.0000.0000.000
135B776SER 00.005-0.01264.7360.0360.0360.0000.0000.0000.000
136B777ALA 00.0760.04864.6930.0360.0360.0000.0000.0000.000
137B778PHE 0-0.002-0.01059.082-0.015-0.0150.0000.0000.0000.000
138B779LEU 0-0.054-0.02364.7140.0020.0020.0000.0000.0000.000
139B780GLU -1-0.993-0.99367.897-4.594-4.5940.0000.0000.0000.000
140B781GLN 0-0.096-0.04762.773-0.015-0.0150.0000.0000.0000.000
141B782ALA 0-0.074-0.01866.117-0.015-0.0150.0000.0000.0000.000
142B783GLU -1-0.943-0.98567.729-4.470-4.4700.0000.0000.0000.000
143B784VAL 0-0.067-0.03268.9210.0420.0420.0000.0000.0000.000
144B785ASP -1-0.825-0.89171.704-4.290-4.2900.0000.0000.0000.000
145B786GLU -1-0.971-1.01770.885-4.561-4.5610.0000.0000.0000.000
146B787GLN 0-0.078-0.02972.7450.0430.0430.0000.0000.0000.000
147B788ASP -1-0.962-0.99273.879-4.273-4.2730.0000.0000.0000.000
148B789VAL 0-0.032-0.00368.110-0.078-0.0780.0000.0000.0000.000
149B790THR 0-0.065-0.04269.1420.0620.0620.0000.0000.0000.000
150B791LEU 0-0.035-0.01365.840-0.081-0.0810.0000.0000.0000.000
151B792PRO 0-0.018-0.01062.5710.0390.0390.0000.0000.0000.000
152B793ASP -1-0.908-0.94665.709-4.704-4.7040.0000.0000.0000.000
153B794GLN 0-0.064-0.04364.365-0.016-0.0160.0000.0000.0000.000
154B795MET 0-0.027-0.00462.005-0.092-0.0920.0000.0000.0000.000
155B796ASP -1-0.887-0.95858.521-5.381-5.3810.0000.0000.0000.000
156B797ALA 00.0130.03357.943-0.050-0.0500.0000.0000.0000.000
157B798SER 0-0.079-0.06951.584-0.062-0.0620.0000.0000.0000.000
158B799ASN 0-0.032-0.03053.227-0.126-0.1260.0000.0000.0000.000
159B800PHE 0-0.004-0.00552.141-0.061-0.0610.0000.0000.0000.000
160B801VAL 0-0.0370.00547.025-0.109-0.1090.0000.0000.0000.000
161B802GLN 00.0220.00544.5730.0450.0450.0000.0000.0000.000
162B803ARG 10.9550.96845.3866.5376.5370.0000.0000.0000.000
163B804PRO 0-0.0020.01341.081-0.057-0.0570.0000.0000.0000.000
164B805VAL 00.0490.01240.6320.1550.1550.0000.0000.0000.000
165B806ILE 0-0.026-0.01336.1470.0350.0350.0000.0000.0000.000
166B807SER 0-0.047-0.01138.743-0.026-0.0260.0000.0000.0000.000
167B808LYS 10.9620.97432.0349.7939.7930.0000.0000.0000.000
168B809PRO 00.0180.02533.024-0.038-0.0380.0000.0000.0000.000
169B810LEU 0-0.020-0.00729.514-0.183-0.1830.0000.0000.0000.000
170B811GLU -1-0.917-0.96826.229-11.788-11.7880.0000.0000.0000.000
171B812LYS 10.9030.93820.11614.26814.2680.0000.0000.0000.000
172B813TRP 00.0050.02125.0450.6340.6340.0000.0000.0000.000
173B814PRO 0-0.041-0.02324.322-0.524-0.5240.0000.0000.0000.000
174B815LEU 0-0.0010.00019.6650.1750.1750.0000.0000.0000.000
175B816LYS 10.9130.95521.30012.73712.7370.0000.0000.0000.000
176B817GLU -1-0.922-0.96618.183-16.364-16.3640.0000.0000.0000.000
177B818ALA -1-0.984-0.97415.709-17.200-17.2000.0000.0000.0000.000