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: MV2LZ

Calculation Name: 4X80-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X80

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2276155.458442
FMO2-HF: Nuclear repulsion 2190814.857953
FMO2-HF: Total energy -85340.600488
FMO2-MP2: Total energy -85586.460188


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(H:1:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-21.602-19.281-0.007-0.918-1.3970.005
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.972 / q_NPA : -0.995
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].
3H3LYS10.8470.9123.450-48.675-46.537-0.004-0.845-1.2900.005
4H4LEU0-0.003-0.0055.392-2.348-2.313-0.001-0.002-0.0320.000
5H5GLU-1-0.812-0.8888.04636.44036.4400.0000.0000.0000.000
6H6GLU-1-0.759-0.87010.68119.94919.9490.0000.0000.0000.000
7H7SER0-0.024-0.02114.4410.0310.0310.0000.0000.0000.000
8H8GLY00.008-0.00617.264-0.384-0.3840.0000.0000.0000.000
9H9GLY00.0030.01820.555-0.660-0.6600.0000.0000.0000.000
10H10GLY00.0320.00422.4900.0750.0750.0000.0000.0000.000
11H11LEU0-0.034-0.00825.765-0.086-0.0860.0000.0000.0000.000
12H12VAL0-0.0160.00029.480-0.115-0.1150.0000.0000.0000.000
13H13GLN00.0200.02231.757-0.080-0.0800.0000.0000.0000.000
14H14PRO00.020-0.01834.5910.1290.1290.0000.0000.0000.000
15H15GLY0-0.042-0.01335.718-0.200-0.2000.0000.0000.0000.000
16H16GLY0-0.0290.00134.083-0.070-0.0700.0000.0000.0000.000
17H17SER0-0.017-0.04630.683-0.046-0.0460.0000.0000.0000.000
18H18MET0-0.022-0.00124.9980.1590.1590.0000.0000.0000.000
19H19LYS10.8960.97121.660-13.690-13.6900.0000.0000.0000.000
20H20LEU00.0100.02119.7800.3080.3080.0000.0000.0000.000
21H21SER0-0.032-0.04417.519-0.601-0.6010.0000.0000.0000.000
22H22CYS0-0.056-0.02713.327-0.135-0.1350.0000.0000.0000.000
23H23ALA00.0050.02011.218-0.959-0.9590.0000.0000.0000.000
24H24ALA00.0370.0169.4171.6651.6650.0000.0000.0000.000
25H25SER0-0.009-0.0155.1890.4930.4930.0000.0000.0000.000
26H26GLY00.0510.0213.9790.9100.952-0.001-0.0590.0180.000
27H27PHE0-0.043-0.0284.691-0.909-0.803-0.001-0.012-0.0930.000
28H28THR00.0040.0087.9820.2810.2810.0000.0000.0000.000
29H29SER00.018-0.01011.623-0.663-0.6630.0000.0000.0000.000
30H30SER0-0.027-0.01813.325-1.119-1.1190.0000.0000.0000.000
31H31ASP-1-0.877-0.91315.18815.43515.4350.0000.0000.0000.000
32H32ALA00.0010.00813.7900.0010.0010.0000.0000.0000.000
33H33TRP0-0.069-0.02915.938-0.763-0.7630.0000.0000.0000.000
34H34MET0-0.0090.00412.8880.9700.9700.0000.0000.0000.000
35H35ASH0-0.001-0.05617.164-1.011-1.0110.0000.0000.0000.000
36H36TRP0-0.0080.01317.2980.8560.8560.0000.0000.0000.000
37H37VAL0-0.009-0.01619.217-0.807-0.8070.0000.0000.0000.000
38H38ARG10.8040.90920.206-10.276-10.2760.0000.0000.0000.000
39H39GLN00.0280.02121.2940.2290.2290.0000.0000.0000.000
40H40SER0-0.003-0.02023.8580.1430.1430.0000.0000.0000.000
41H41PRO0-0.007-0.00627.0620.0280.0280.0000.0000.0000.000
42H42GLU-1-0.875-0.91329.4539.7989.7980.0000.0000.0000.000
43H43LYS10.8480.90529.589-9.757-9.7570.0000.0000.0000.000
44H44GLY00.0210.03227.0370.0420.0420.0000.0000.0000.000
45H45LEU0-0.031-0.02820.9030.2190.2190.0000.0000.0000.000
46H46GLU-1-0.765-0.86124.4939.8409.8400.0000.0000.0000.000
47H47TRP00.0160.01122.1750.1460.1460.0000.0000.0000.000
48H48VAL0-0.0150.00423.622-0.558-0.5580.0000.0000.0000.000
49H49ALA00.019-0.00623.438-0.522-0.5220.0000.0000.0000.000
50H50GLU-1-0.781-0.81621.27313.37713.3770.0000.0000.0000.000
51H51ILE0-0.049-0.02420.219-0.659-0.6590.0000.0000.0000.000
52H52ARG10.8670.92220.531-10.960-10.9600.0000.0000.0000.000
53H53ASN00.0400.00721.4480.2980.2980.0000.0000.0000.000
54H54DLY00.0580.04522.339-0.651-0.6510.0000.0000.0000.000
55H55ALA0-0.024-0.02524.4460.1050.1050.0000.0000.0000.000
56H56ASN00.0140.00525.539-0.011-0.0110.0000.0000.0000.000
57H57ASN0-0.0110.01625.349-0.601-0.6010.0000.0000.0000.000
58H58HIS00.0560.03528.525-0.139-0.1390.0000.0000.0000.000
59H59ALA0-0.021-0.01925.4490.1660.1660.0000.0000.0000.000
60H60ARG10.8790.93025.331-10.559-10.5590.0000.0000.0000.000
61H61HIS0-0.0080.00926.252-0.551-0.5510.0000.0000.0000.000
62H62TYR00.013-0.01226.6990.5310.5310.0000.0000.0000.000
63H63ASN00.0050.00828.131-0.685-0.6850.0000.0000.0000.000
64H64GLU-1-0.778-0.88729.7868.5228.5220.0000.0000.0000.000
65H65SER00.0010.00331.566-0.188-0.1880.0000.0000.0000.000
66H66VAL00.005-0.00628.165-0.107-0.1070.0000.0000.0000.000
67H67LYS10.8470.91231.577-8.624-8.6240.0000.0000.0000.000
68H68GLY0-0.026-0.01033.410-0.205-0.2050.0000.0000.0000.000
69H69ARG10.7240.85031.958-9.468-9.4680.0000.0000.0000.000
70H70PHE00.021-0.00626.5890.1870.1870.0000.0000.0000.000
71H71THR0-0.059-0.02427.129-0.247-0.2470.0000.0000.0000.000
72H72ILE00.0010.02320.7230.2960.2960.0000.0000.0000.000
73H73SER0-0.038-0.04122.465-0.527-0.5270.0000.0000.0000.000
74H74ARG10.8320.88617.577-14.353-14.3530.0000.0000.0000.000
75H75ASP-1-0.833-0.89519.23813.75713.7570.0000.0000.0000.000
76H76ASP-1-0.726-0.86216.90316.69116.6910.0000.0000.0000.000
77H77SER0-0.111-0.05516.6630.6800.6800.0000.0000.0000.000
78H78LYS10.8960.95016.652-14.117-14.1170.0000.0000.0000.000
79H79SER0-0.0060.02111.6241.0321.0320.0000.0000.0000.000
80H80SER0-0.0070.00613.0861.0271.0270.0000.0000.0000.000
81H81VAL0-0.003-0.00315.321-1.132-1.1320.0000.0000.0000.000
82H82TYR0-0.051-0.05717.5820.0230.0230.0000.0000.0000.000
83H83LEU00.0090.00420.343-0.380-0.3800.0000.0000.0000.000
84H84GLN0-0.006-0.00522.9660.1070.1070.0000.0000.0000.000
85H85MET0-0.0080.01324.635-0.151-0.1510.0000.0000.0000.000
86H86ASN00.0670.04128.3110.0050.0050.0000.0000.0000.000
87H87SER00.003-0.00732.0570.0070.0070.0000.0000.0000.000
88H88LEU0-0.0050.01828.689-0.072-0.0720.0000.0000.0000.000
89H89ARG10.9250.94632.637-9.026-9.0260.0000.0000.0000.000
90H90ALA00.0580.02732.4780.2780.2780.0000.0000.0000.000
91H91GLU-1-0.851-0.91532.1039.0939.0930.0000.0000.0000.000
92H92ASP-1-0.781-0.84928.89810.06610.0660.0000.0000.0000.000
93H93SER0-0.007-0.00427.5610.5040.5040.0000.0000.0000.000
94H94GLY00.0290.01525.426-0.180-0.1800.0000.0000.0000.000
95H95ILE0-0.051-0.01218.9920.0990.0990.0000.0000.0000.000
96H96TYR0-0.044-0.05720.214-0.209-0.2090.0000.0000.0000.000
97H97TYR00.001-0.01915.3130.6840.6840.0000.0000.0000.000
98H99THR0-0.001-0.03313.6690.9540.9540.0000.0000.0000.000
99H100ARG10.8250.8908.982-23.723-23.7230.0000.0000.0000.000
100H101THR0-0.020-0.01414.3610.2190.2190.0000.0000.0000.000
101H102TYR00.004-0.01916.431-0.600-0.6000.0000.0000.0000.000
102H103TYR0-0.0230.0119.9191.4091.4090.0000.0000.0000.000
103H104TYR00.017-0.02212.786-0.185-0.1850.0000.0000.0000.000
104H105GLY00.0170.01916.9970.0390.0390.0000.0000.0000.000
105H106SER00.005-0.00419.786-0.113-0.1130.0000.0000.0000.000
106H107SER0-0.035-0.01020.766-0.554-0.5540.0000.0000.0000.000
107H108TYR00.022-0.00319.8580.3950.3950.0000.0000.0000.000
108H109GLY0-0.0050.00020.148-0.504-0.5040.0000.0000.0000.000
109H110TYR0-0.0170.00216.433-0.525-0.5250.0000.0000.0000.000
110H111CYS0-0.019-0.00315.6090.1120.1120.0000.0000.0000.000
111H112ASP-1-0.784-0.86211.74121.13521.1350.0000.0000.0000.000
112H113VAL0-0.028-0.0028.1801.5591.5590.0000.0000.0000.000
113H114TRP0-0.014-0.03010.454-2.081-2.0810.0000.0000.0000.000
114H115GLY00.0450.03310.3172.1932.1930.0000.0000.0000.000
115H116THR0-0.052-0.02610.701-0.215-0.2150.0000.0000.0000.000
116H117GLY0-0.001-0.00612.894-1.330-1.3300.0000.0000.0000.000
117H118THR0-0.055-0.02916.0940.0390.0390.0000.0000.0000.000
118H119THR00.003-0.00718.623-0.226-0.2260.0000.0000.0000.000
119H120VAL0-0.0090.00522.239-0.151-0.1510.0000.0000.0000.000
120H121THR0-0.008-0.00825.237-0.187-0.1870.0000.0000.0000.000
121H122VAL0-0.0020.00328.744-0.104-0.1040.0000.0000.0000.000
122H123SER00.019-0.00931.831-0.317-0.3170.0000.0000.0000.000
123H124SER00.0220.01034.9710.0900.0900.0000.0000.0000.000
124H125DAL00.0230.01237.167-0.207-0.2070.0000.0000.0000.000
125H126LYS10.8980.95636.324-7.612-7.6120.0000.0000.0000.000
126H127THR00.004-0.00832.4860.0170.0170.0000.0000.0000.000
127H128THR0-0.043-0.01934.721-0.314-0.3140.0000.0000.0000.000
128H129PRO00.0190.01134.2260.2450.2450.0000.0000.0000.000
129H130PRO00.0110.01532.601-0.220-0.2200.0000.0000.0000.000
130H131SER0-0.032-0.00435.786-0.156-0.1560.0000.0000.0000.000
131H132VAL0-0.001-0.01134.3690.1060.1060.0000.0000.0000.000
132H133TYR0-0.012-0.02037.383-0.157-0.1570.0000.0000.0000.000
133H134PRO0-0.0070.00139.0370.1730.1730.0000.0000.0000.000
134H135LEU0-0.029-0.01538.785-0.203-0.2030.0000.0000.0000.000
135H136ALA00.0070.00641.0920.1410.1410.0000.0000.0000.000
136H137PRO00.007-0.00242.869-0.108-0.1080.0000.0000.0000.000
137H138GLY00.0220.02145.786-0.074-0.0740.0000.0000.0000.000
138H139SER00.000-0.01949.5840.0130.0130.0000.0000.0000.000
139H140ALA00.0110.00552.249-0.016-0.0160.0000.0000.0000.000
140H141ALA0-0.032-0.00249.180-0.053-0.0530.0000.0000.0000.000
141H142GLN00.015-0.00651.288-0.059-0.0590.0000.0000.0000.000
142H143THR0-0.056-0.01045.9030.0700.0700.0000.0000.0000.000
143H144ASN00.0250.02445.263-0.190-0.1900.0000.0000.0000.000
144H145SER00.0590.02843.7680.0240.0240.0000.0000.0000.000
145H146MET0-0.043-0.00637.7860.2010.2010.0000.0000.0000.000
146H147VAL00.0160.00240.434-0.200-0.2000.0000.0000.0000.000
147H148THR00.0140.01437.4540.2780.2780.0000.0000.0000.000
148H149LEU0-0.0050.01437.492-0.225-0.2250.0000.0000.0000.000
149H150GLY00.044-0.00236.2650.1860.1860.0000.0000.0000.000
150H151CYS0-0.0760.00631.7230.0880.0880.0000.0000.0000.000
151H152LEU0-0.0010.00335.9450.1050.1050.0000.0000.0000.000
152H153VAL00.0140.00832.302-0.133-0.1330.0000.0000.0000.000
153H154LYS10.8750.91035.512-7.714-7.7140.0000.0000.0000.000
154H155GLY00.0150.01637.997-0.016-0.0160.0000.0000.0000.000
155H156TYR00.005-0.02430.337-0.155-0.1550.0000.0000.0000.000
156H157PHE00.0510.03633.0490.0350.0350.0000.0000.0000.000
157H158PRO0-0.0120.01229.006-0.166-0.1660.0000.0000.0000.000
158H159GLU-1-0.767-0.86026.87410.95210.9520.0000.0000.0000.000
159H160PRO0-0.033-0.01523.1750.1400.1400.0000.0000.0000.000
160H161VAL00.007-0.00826.413-0.094-0.0940.0000.0000.0000.000
161H162THR0-0.045-0.02422.2150.3470.3470.0000.0000.0000.000
162H163VAL00.015-0.00925.378-0.310-0.3100.0000.0000.0000.000
163H164THR0-0.034-0.01523.7300.3780.3780.0000.0000.0000.000
164H165TRP00.0370.01827.005-0.592-0.5920.0000.0000.0000.000
165H166ASN00.002-0.02328.5650.1550.1550.0000.0000.0000.000
166H167SER00.002-0.00526.9530.1030.1030.0000.0000.0000.000
167H168GLY00.0140.01724.1610.4700.4700.0000.0000.0000.000
168H169SER0-0.061-0.03224.8420.3680.3680.0000.0000.0000.000
169H170LEU0-0.033-0.01326.796-0.297-0.2970.0000.0000.0000.000
170H171SER00.0300.01024.3790.0560.0560.0000.0000.0000.000
171H172SER00.005-0.00326.3740.1600.1600.0000.0000.0000.000
172H173GLY00.0240.01228.803-0.248-0.2480.0000.0000.0000.000
173H174VAL0-0.028-0.00927.487-0.370-0.3700.0000.0000.0000.000
174H175HIS0-0.007-0.00129.6760.3340.3340.0000.0000.0000.000
175H176THR00.0020.00027.646-0.453-0.4530.0000.0000.0000.000
176H177PHE0-0.028-0.00529.2580.2280.2280.0000.0000.0000.000
177H178PRO00.020-0.00129.4620.1050.1050.0000.0000.0000.000
178H179ALA00.0080.02230.610-0.358-0.3580.0000.0000.0000.000
179H180VAL0-0.015-0.00832.6180.0040.0040.0000.0000.0000.000
180H181LEU0-0.015-0.00835.281-0.054-0.0540.0000.0000.0000.000
181H182GLN00.0150.00537.269-0.146-0.1460.0000.0000.0000.000
182H183SER0-0.024-0.02140.7810.0270.0270.0000.0000.0000.000
183H184ASP-1-0.911-0.95738.6747.9607.9600.0000.0000.0000.000
184H185LEU0-0.0220.00037.3070.1170.1170.0000.0000.0000.000
185H186TYR00.0250.01531.797-0.090-0.0900.0000.0000.0000.000
186H187THR0-0.047-0.02635.600-0.231-0.2310.0000.0000.0000.000
187H188LEU00.0440.03629.6340.0310.0310.0000.0000.0000.000
188H189SER00.0100.00934.284-0.083-0.0830.0000.0000.0000.000
189H190SER00.018-0.00130.4570.2420.2420.0000.0000.0000.000
190H191SER00.0420.01833.244-0.338-0.3380.0000.0000.0000.000
191H192VAL00.0000.00432.3710.3380.3380.0000.0000.0000.000
192H193THR0-0.032-0.02534.081-0.259-0.2590.0000.0000.0000.000
193H194VAL0-0.016-0.01234.7360.2750.2750.0000.0000.0000.000
194H195PRO00.0500.01636.746-0.230-0.2300.0000.0000.0000.000
195H196SER00.019-0.00839.9480.1110.1110.0000.0000.0000.000
196H197SER0-0.0150.00542.162-0.051-0.0510.0000.0000.0000.000
197H198THR0-0.040-0.03136.6860.0360.0360.0000.0000.0000.000
198H199TRP0-0.0380.00039.7330.0480.0480.0000.0000.0000.000
199H200PRO0-0.028-0.03641.509-0.107-0.1070.0000.0000.0000.000
200H201SER0-0.096-0.09941.4710.0020.0020.0000.0000.0000.000
201H202GLN00.2550.18837.225-0.049-0.0490.0000.0000.0000.000
202H203THR0-0.037-0.03636.812-0.233-0.2330.0000.0000.0000.000
203H204VAL00.0070.02634.5410.2350.2350.0000.0000.0000.000
204H205THR0-0.025-0.03333.220-0.318-0.3180.0000.0000.0000.000
205H207ASN00.003-0.01627.9930.0660.0660.0000.0000.0000.000
206H208VAL00.0160.00929.0060.2540.2540.0000.0000.0000.000
207H209ALA0-0.024-0.00626.015-0.196-0.1960.0000.0000.0000.000
208H210HIS00.0250.02127.5950.0730.0730.0000.0000.0000.000
209H211PRO00.028-0.00123.828-0.246-0.2460.0000.0000.0000.000
210H212ALA00.0040.00926.415-0.099-0.0990.0000.0000.0000.000
211H213SER0-0.005-0.02628.688-0.274-0.2740.0000.0000.0000.000
212H214SER0-0.040-0.01128.953-0.147-0.1470.0000.0000.0000.000
213H215THR0-0.0030.00529.984-0.274-0.2740.0000.0000.0000.000
214H216LYS10.9670.96425.477-11.542-11.5420.0000.0000.0000.000
215H217VAL0-0.034-0.00630.713-0.269-0.2690.0000.0000.0000.000
216H218ASP-1-0.820-0.89331.27810.53910.5390.0000.0000.0000.000
217H219LYS10.9010.95134.092-8.284-8.2840.0000.0000.0000.000
218H220LYS10.9280.96436.651-7.722-7.7220.0000.0000.0000.000
219H221ILE0-0.014-0.00837.114-0.196-0.1960.0000.0000.0000.000
220H222VAL0-0.037-0.02040.238-0.017-0.0170.0000.0000.0000.000
221H223PRO00.0270.02343.884-0.058-0.0580.0000.0000.0000.000