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: 942R2

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2274868.016382
FMO2-HF: Nuclear repulsion 2189528.180484
FMO2-HF: Total energy -85339.835898
FMO2-MP2: Total energy -85585.646626


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.
-31.87-29.659-0.007-0.902-1.3030.005
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 : -0.974 / q_NPA : -0.998
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].
3H3LYS10.9380.9683.543-53.082-50.988-0.005-0.828-1.2610.005
4H4LEU0-0.002-0.0095.493-2.006-2.0060.0000.0000.0000.000
5H5GLU-1-0.916-0.9518.28531.88631.8860.0000.0000.0000.000
6H6GLU-1-0.762-0.86910.77319.34319.3430.0000.0000.0000.000
7H7SER0-0.022-0.01914.5270.0110.0110.0000.0000.0000.000
8H8GLY00.006-0.00717.352-0.370-0.3700.0000.0000.0000.000
9H9GLY0-0.0050.01720.624-0.638-0.6380.0000.0000.0000.000
10H10GLY00.0290.00222.5540.0740.0740.0000.0000.0000.000
11H11LEU0-0.032-0.00725.817-0.077-0.0770.0000.0000.0000.000
12H12VAL0-0.021-0.00329.529-0.103-0.1030.0000.0000.0000.000
13H13GLN00.0280.02431.824-0.087-0.0870.0000.0000.0000.000
14H14PRO00.010-0.01934.6660.1250.1250.0000.0000.0000.000
15H15GLY0-0.031-0.00335.809-0.191-0.1910.0000.0000.0000.000
16H16GLY0-0.030-0.00334.174-0.063-0.0630.0000.0000.0000.000
17H17SER0-0.017-0.02730.9490.0060.0060.0000.0000.0000.000
18H18MET0-0.0050.00425.1110.1410.1410.0000.0000.0000.000
19H19LYS10.9230.97522.592-13.087-13.0870.0000.0000.0000.000
20H20LEU00.0110.01919.8950.2830.2830.0000.0000.0000.000
21H21SER0-0.031-0.03917.564-0.537-0.5370.0000.0000.0000.000
22H22CYS0-0.060-0.03613.361-0.074-0.0740.0000.0000.0000.000
23H23ALA00.0110.02411.329-0.912-0.9120.0000.0000.0000.000
24H24ALA00.0280.0109.5791.5371.5370.0000.0000.0000.000
25H25SER00.005-0.0095.0040.7020.7020.0000.0000.0000.000
26H26GLY00.0350.0153.9630.8430.870-0.001-0.0610.0340.000
27H27PHE0-0.066-0.0334.675-0.838-0.748-0.001-0.013-0.0760.000
28H28THR00.0350.0207.9620.2380.2380.0000.0000.0000.000
29H29SER00.0600.01111.605-0.762-0.7620.0000.0000.0000.000
30H30SER0-0.006-0.00213.308-1.001-1.0010.0000.0000.0000.000
31H31ASP-1-0.900-0.92915.07914.87514.8750.0000.0000.0000.000
32H32ALA0-0.0040.00213.7780.0280.0280.0000.0000.0000.000
33H33TRP0-0.059-0.01615.916-0.751-0.7510.0000.0000.0000.000
34H34MET0-0.0030.00613.1980.9970.9970.0000.0000.0000.000
35H35ASH0-0.016-0.04817.161-0.808-0.8080.0000.0000.0000.000
36H36TRP0-0.0040.02017.3700.8250.8250.0000.0000.0000.000
37H37VAL0-0.003-0.01519.173-0.785-0.7850.0000.0000.0000.000
38H38ARG10.8180.92520.250-10.163-10.1630.0000.0000.0000.000
39H39GLN00.0370.02821.3010.2960.2960.0000.0000.0000.000
40H40SER00.0270.01523.8620.1230.1230.0000.0000.0000.000
41H41PRO0-0.009-0.00927.0570.0290.0290.0000.0000.0000.000
42H42GLU-1-0.913-0.95229.4269.5069.5060.0000.0000.0000.000
43H43LYS10.9050.95029.804-9.522-9.5220.0000.0000.0000.000
44H44GLY00.0200.03327.0220.0410.0410.0000.0000.0000.000
45H45LEU0-0.032-0.02821.0310.2150.2150.0000.0000.0000.000
46H46GLU-1-0.847-0.92724.4919.8179.8170.0000.0000.0000.000
47H47TRP00.0200.01122.1430.1490.1490.0000.0000.0000.000
48H48VAL0-0.0250.00223.588-0.556-0.5560.0000.0000.0000.000
49H49ALA00.020-0.00923.503-0.515-0.5150.0000.0000.0000.000
50H50GLU-1-0.792-0.83621.20113.15813.1580.0000.0000.0000.000
51H51ILE0-0.049-0.02020.207-0.668-0.6680.0000.0000.0000.000
52H52ARG10.8670.93220.531-10.853-10.8530.0000.0000.0000.000
53H53ASN00.0300.00121.4440.2440.2440.0000.0000.0000.000
54H54DLY00.0550.04022.319-0.630-0.6300.0000.0000.0000.000
55H55ALA0-0.018-0.01824.4170.0980.0980.0000.0000.0000.000
56H56ASN00.0060.00025.5840.0080.0080.0000.0000.0000.000
57H57ASN00.0200.03825.560-0.605-0.6050.0000.0000.0000.000
58H58HIS00.0420.02128.504-0.193-0.1930.0000.0000.0000.000
59H59ALA0-0.039-0.03025.3970.1550.1550.0000.0000.0000.000
60H60ARG10.9200.95425.331-10.388-10.3880.0000.0000.0000.000
61H61HIS00.0070.01926.251-0.567-0.5670.0000.0000.0000.000
62H62TYR00.007-0.00526.6990.4710.4710.0000.0000.0000.000
63H63ASN00.0070.00628.136-0.670-0.6700.0000.0000.0000.000
64H64GLU-1-0.870-0.95329.7678.3158.3150.0000.0000.0000.000
65H65SER0-0.009-0.00331.642-0.159-0.1590.0000.0000.0000.000
66H66VAL00.0080.00828.362-0.112-0.1120.0000.0000.0000.000
67H67LYS10.9470.97931.670-8.683-8.6830.0000.0000.0000.000
68H68GLY0-0.031-0.01033.528-0.202-0.2020.0000.0000.0000.000
69H69ARG10.7260.86232.165-9.334-9.3340.0000.0000.0000.000
70H70PHE00.0260.00326.7410.1830.1830.0000.0000.0000.000
71H71THR0-0.058-0.02727.311-0.269-0.2690.0000.0000.0000.000
72H72ILE0-0.0100.00720.9390.2830.2830.0000.0000.0000.000
73H73SER0-0.056-0.04722.628-0.490-0.4900.0000.0000.0000.000
74H74ARG10.8070.87717.385-14.265-14.2650.0000.0000.0000.000
75H75ASP-1-0.853-0.92119.26213.51813.5180.0000.0000.0000.000
76H76ASP-1-0.780-0.90117.10315.84015.8400.0000.0000.0000.000
77H77SER0-0.092-0.03916.6370.7720.7720.0000.0000.0000.000
78H78LYS10.9230.96316.607-14.372-14.3720.0000.0000.0000.000
79H79SER0-0.0130.00611.7471.1321.1320.0000.0000.0000.000
80H80SER0-0.023-0.01313.0391.0691.0690.0000.0000.0000.000
81H81VAL0-0.0060.00315.446-1.073-1.0730.0000.0000.0000.000
82H82TYR0-0.041-0.03317.7320.1990.1990.0000.0000.0000.000
83H83LEU00.0040.00220.490-0.369-0.3690.0000.0000.0000.000
84H84GLN0-0.025-0.01423.094-0.015-0.0150.0000.0000.0000.000
85H85MET0-0.0040.01724.543-0.179-0.1790.0000.0000.0000.000
86H86ASN00.0910.03028.4220.0970.0970.0000.0000.0000.000
87H87SER0-0.023-0.01832.169-0.099-0.0990.0000.0000.0000.000
88H88LEU0-0.0090.01128.739-0.076-0.0760.0000.0000.0000.000
89H89ARG10.9860.98532.709-8.801-8.8010.0000.0000.0000.000
90H90ALA00.0700.03632.5340.2770.2770.0000.0000.0000.000
91H91GLU-1-0.907-0.95232.1388.8508.8500.0000.0000.0000.000
92H92ASP-1-0.790-0.87928.9899.9739.9730.0000.0000.0000.000
93H93SER0-0.014-0.00827.6120.5020.5020.0000.0000.0000.000
94H94GLY00.0270.01225.447-0.175-0.1750.0000.0000.0000.000
95H95ILE0-0.042-0.00718.9810.0970.0970.0000.0000.0000.000
96H96TYR0-0.049-0.05620.276-0.219-0.2190.0000.0000.0000.000
97H97TYR00.006-0.02015.3250.6640.6640.0000.0000.0000.000
98H99THR0-0.007-0.03613.6570.9050.9050.0000.0000.0000.000
99H100ARG10.8400.9059.436-22.946-22.9460.0000.0000.0000.000
100H101THR0-0.005-0.02414.3420.0820.0820.0000.0000.0000.000
101H102TYR0-0.010-0.03516.412-0.606-0.6060.0000.0000.0000.000
102H103TYR0-0.0100.01910.1510.8450.8450.0000.0000.0000.000
103H104TYR00.011-0.00812.985-0.185-0.1850.0000.0000.0000.000
104H105GLY00.0150.01716.9740.0380.0380.0000.0000.0000.000
105H106SER00.0030.00219.786-0.116-0.1160.0000.0000.0000.000
106H107SER0-0.0240.00020.765-0.554-0.5540.0000.0000.0000.000
107H108TYR00.004-0.01219.8440.3840.3840.0000.0000.0000.000
108H109GLY0-0.0010.00520.133-0.488-0.4880.0000.0000.0000.000
109H110TYR0-0.0070.00616.569-0.512-0.5120.0000.0000.0000.000
110H111CYS0-0.045-0.01415.5600.1550.1550.0000.0000.0000.000
111H112ASP-1-0.780-0.87312.03020.54020.5400.0000.0000.0000.000
112H113VAL0-0.030-0.0048.2321.5711.5710.0000.0000.0000.000
113H114TRP0-0.004-0.02310.430-1.956-1.9560.0000.0000.0000.000
114H115GLY00.0410.03210.3002.1032.1030.0000.0000.0000.000
115H116THR0-0.063-0.02710.677-0.316-0.3160.0000.0000.0000.000
116H117GLY00.002-0.00212.886-1.237-1.2370.0000.0000.0000.000
117H118THR0-0.050-0.02516.1150.0420.0420.0000.0000.0000.000
118H119THR00.008-0.00818.661-0.218-0.2180.0000.0000.0000.000
119H120VAL0-0.0050.00722.266-0.140-0.1400.0000.0000.0000.000
120H121THR0-0.013-0.01125.283-0.165-0.1650.0000.0000.0000.000
121H122VAL0-0.0030.00328.779-0.098-0.0980.0000.0000.0000.000
122H123SER00.006-0.01931.880-0.313-0.3130.0000.0000.0000.000
123H124SER00.0120.00135.0110.0990.0990.0000.0000.0000.000
124H125DAL00.0010.00937.259-0.171-0.1710.0000.0000.0000.000
125H126LYS10.9630.98336.356-7.320-7.3200.0000.0000.0000.000
126H127THR0-0.003-0.01232.7820.0100.0100.0000.0000.0000.000
127H128THR0-0.041-0.01935.145-0.309-0.3090.0000.0000.0000.000
128H129PRO00.0110.00934.6000.2480.2480.0000.0000.0000.000
129H130PRO00.0090.01332.951-0.222-0.2220.0000.0000.0000.000
130H131SER0-0.038-0.00836.148-0.165-0.1650.0000.0000.0000.000
131H132VAL00.009-0.00434.7000.1040.1040.0000.0000.0000.000
132H133TYR0-0.016-0.02237.689-0.203-0.2030.0000.0000.0000.000
133H134PRO0-0.0120.00039.3170.1790.1790.0000.0000.0000.000
134H135LEU0-0.022-0.01438.925-0.200-0.2000.0000.0000.0000.000
135H136ALA00.0080.00441.3200.1420.1420.0000.0000.0000.000
136H137PRO00.006-0.00243.027-0.108-0.1080.0000.0000.0000.000
137H138GLY00.0220.02245.995-0.074-0.0740.0000.0000.0000.000
138H139SER0-0.002-0.01849.7970.0150.0150.0000.0000.0000.000
139H140ALA00.0130.00652.440-0.015-0.0150.0000.0000.0000.000
140H141ALA0-0.031-0.00349.373-0.052-0.0520.0000.0000.0000.000
141H142GLN00.015-0.00351.467-0.062-0.0620.0000.0000.0000.000
142H143THR0-0.055-0.01046.1930.0670.0670.0000.0000.0000.000
143H144ASN00.0240.02345.340-0.193-0.1930.0000.0000.0000.000
144H145SER00.0550.02743.9260.0310.0310.0000.0000.0000.000
145H146MET0-0.0380.00138.0700.2130.2130.0000.0000.0000.000
146H147VAL00.0150.00440.522-0.204-0.2040.0000.0000.0000.000
147H148THR0-0.009-0.01637.7300.1820.1820.0000.0000.0000.000
148H149LEU0-0.024-0.00537.679-0.223-0.2230.0000.0000.0000.000
149H150GLY00.039-0.00536.5040.1840.1840.0000.0000.0000.000
150H151CYS0-0.0680.00631.9280.1080.1080.0000.0000.0000.000
151H152LEU0-0.012-0.00336.2400.0960.0960.0000.0000.0000.000
152H153VAL00.0150.00932.674-0.131-0.1310.0000.0000.0000.000
153H154LYS10.9530.96035.849-7.557-7.5570.0000.0000.0000.000
154H155GLY00.0180.01638.367-0.015-0.0150.0000.0000.0000.000
155H156TYR00.0170.00230.910-0.129-0.1290.0000.0000.0000.000
156H157PHE00.0420.03333.4400.0380.0380.0000.0000.0000.000
157H158PRO00.0000.01829.400-0.162-0.1620.0000.0000.0000.000
158H159GLU-1-0.782-0.87927.23510.78210.7820.0000.0000.0000.000
159H160PRO0-0.025-0.01423.7150.1430.1430.0000.0000.0000.000
160H161VAL00.003-0.00826.825-0.093-0.0930.0000.0000.0000.000
161H162THR0-0.043-0.02422.5470.3330.3330.0000.0000.0000.000
162H163VAL00.012-0.00925.703-0.295-0.2950.0000.0000.0000.000
163H164THR0-0.040-0.03223.9840.3430.3430.0000.0000.0000.000
164H165TRP00.0480.01527.230-0.592-0.5920.0000.0000.0000.000
165H166ASN0-0.042-0.04028.7100.1480.1480.0000.0000.0000.000
166H167SER00.017-0.00227.0540.0870.0870.0000.0000.0000.000
167H168GLY00.0060.01224.2990.4750.4750.0000.0000.0000.000
168H169SER0-0.066-0.02824.9530.3580.3580.0000.0000.0000.000
169H170LEU0-0.018-0.00826.874-0.274-0.2740.0000.0000.0000.000
170H171SER00.0400.01324.384-0.037-0.0370.0000.0000.0000.000
171H172SER0-0.011-0.00526.5000.0510.0510.0000.0000.0000.000
172H173GLY00.0210.00928.920-0.244-0.2440.0000.0000.0000.000
173H174VAL0-0.034-0.01427.761-0.369-0.3690.0000.0000.0000.000
174H175HIS00.0100.00729.8890.3720.3720.0000.0000.0000.000
175H176THR0-0.024-0.01827.799-0.429-0.4290.0000.0000.0000.000
176H177PHE0-0.029-0.01229.5700.2080.2080.0000.0000.0000.000
177H178PRO00.020-0.00129.7880.0950.0950.0000.0000.0000.000
178H179ALA00.0090.02431.002-0.342-0.3420.0000.0000.0000.000
179H180VAL0-0.009-0.00333.0110.0050.0050.0000.0000.0000.000
180H181LEU0-0.015-0.00735.597-0.052-0.0520.0000.0000.0000.000
181H182GLN0-0.042-0.03137.413-0.096-0.0960.0000.0000.0000.000
182H183SER0-0.032-0.02241.041-0.032-0.0320.0000.0000.0000.000
183H184ASP-1-0.907-0.95638.7607.7957.7950.0000.0000.0000.000
184H185LEU0-0.026-0.00537.6580.1160.1160.0000.0000.0000.000
185H186TYR00.0290.01532.383-0.063-0.0630.0000.0000.0000.000
186H187THR0-0.038-0.02536.015-0.166-0.1660.0000.0000.0000.000
187H188LEU00.0210.02729.9740.0330.0330.0000.0000.0000.000
188H189SER00.0030.00334.643-0.081-0.0810.0000.0000.0000.000
189H190SER00.0200.01631.2350.2630.2630.0000.0000.0000.000
190H191SER00.0180.00833.500-0.207-0.2070.0000.0000.0000.000
191H192VAL00.0400.02432.3230.3300.3300.0000.0000.0000.000
192H193THR00.0030.01434.271-0.421-0.4210.0000.0000.0000.000
193H194VAL0-0.013-0.00534.8620.2740.2740.0000.0000.0000.000
194H195PRO00.0440.00536.820-0.231-0.2310.0000.0000.0000.000
195H196SER00.015-0.02440.0250.0970.0970.0000.0000.0000.000
196H197SER0-0.0200.00341.993-0.058-0.0580.0000.0000.0000.000
197H198THR0-0.037-0.01236.7940.0310.0310.0000.0000.0000.000
198H199TRP0-0.0280.00539.8930.0490.0490.0000.0000.0000.000
199H200PRO0-0.046-0.04941.609-0.110-0.1100.0000.0000.0000.000
200H201SER0-0.050-0.10441.5950.0460.0460.0000.0000.0000.000
201H202GLN00.3160.14737.226-0.031-0.0310.0000.0000.0000.000
202H203THR0-0.214-0.03637.696-0.279-0.2790.0000.0000.0000.000
203H204VAL00.0750.06234.7380.2290.2290.0000.0000.0000.000
204H205THR0-0.030-0.03533.454-0.305-0.3050.0000.0000.0000.000
205H207ASN00.0120.00428.2100.1110.1110.0000.0000.0000.000
206H208VAL00.0220.01429.2700.2460.2460.0000.0000.0000.000
207H209ALA0-0.012-0.00226.416-0.192-0.1920.0000.0000.0000.000
208H210HIS00.0070.00127.9360.0730.0730.0000.0000.0000.000
209H211PRO00.019-0.00424.329-0.237-0.2370.0000.0000.0000.000
210H212ALA00.0090.01026.785-0.097-0.0970.0000.0000.0000.000
211H213SER0-0.008-0.02529.093-0.265-0.2650.0000.0000.0000.000
212H214SER0-0.040-0.00929.283-0.145-0.1450.0000.0000.0000.000
213H215THR0-0.0050.00730.326-0.262-0.2620.0000.0000.0000.000
214H216LYS10.9610.95825.171-11.673-11.6730.0000.0000.0000.000
215H217VAL0-0.0190.00430.994-0.259-0.2590.0000.0000.0000.000
216H218ASP-1-0.815-0.88231.60910.44310.4430.0000.0000.0000.000
217H219LYS10.9070.95034.318-8.165-8.1650.0000.0000.0000.000
218H220LYS10.9640.99036.861-7.646-7.6460.0000.0000.0000.000
219H221ILE0-0.012-0.00837.513-0.197-0.1970.0000.0000.0000.000
220H222VAL0-0.043-0.02440.431-0.010-0.0100.0000.0000.0000.000
221H223PRO00.0320.02544.065-0.068-0.0680.0000.0000.0000.000