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: YZ7Y2

Calculation Name: 1OSP-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OSP

Chain ID: H

ChEMBL ID:

UniProt ID: P01867

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2207115.127416
FMO2-HF: Nuclear repulsion 2124484.993059
FMO2-HF: Total energy -82630.134357
FMO2-MP2: Total energy -82870.211655


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.
-9.998-3.8260.928-2.974-4.1250.014
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 : -0.916 / q_NPA : -0.964
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].
3H3GLN0-0.0080.0022.994-1.3711.7800.183-1.475-1.858-0.001
4H4LEU00.008-0.0125.838-3.164-3.1640.0000.0000.0000.000
5H5GLN0-0.025-0.0228.7960.1030.1030.0000.0000.0000.000
6H6GLU-1-0.742-0.84912.31920.16820.1680.0000.0000.0000.000
7H7SER00.004-0.00215.666-0.569-0.5690.0000.0000.0000.000
8H8GLY00.0200.00019.062-0.176-0.1760.0000.0000.0000.000
9H9PRO0-0.010-0.00322.7200.0790.0790.0000.0000.0000.000
10H10SER00.0740.04225.179-0.012-0.0120.0000.0000.0000.000
11H11LEU0-0.075-0.03326.281-0.160-0.1600.0000.0000.0000.000
12H12VAL00.0010.01729.134-0.072-0.0720.0000.0000.0000.000
13H13LYS10.8990.94231.297-8.245-8.2450.0000.0000.0000.000
14H14PRO00.0470.01234.3500.0820.0820.0000.0000.0000.000
15H15SER0-0.048-0.01435.902-0.261-0.2610.0000.0000.0000.000
16H16GLN0-0.0270.00033.808-0.013-0.0130.0000.0000.0000.000
17H17THR00.012-0.01429.3680.0280.0280.0000.0000.0000.000
18H18LEU0-0.0120.02124.649-0.005-0.0050.0000.0000.0000.000
19H19SER0-0.006-0.01625.022-0.035-0.0350.0000.0000.0000.000
20H20LEU0-0.020-0.00120.028-0.080-0.0800.0000.0000.0000.000
21H21THR0-0.012-0.01017.575-0.295-0.2950.0000.0000.0000.000
22H22CYS0-0.0110.01212.2770.6170.6170.0000.0000.0000.000
23H23SER00.001-0.00713.816-0.611-0.6110.0000.0000.0000.000
24H24VAL00.007-0.0058.1681.1241.1240.0000.0000.0000.000
25H25THR0-0.0220.0017.627-1.072-1.0720.0000.0000.0000.000
26H26GLY00.0520.0233.7912.1792.2880.001-0.079-0.0320.000
27H27GLU-1-0.795-0.8673.92236.46036.8700.000-0.095-0.3150.000
28H28PRO0-0.0080.0166.538-1.337-1.3370.0000.0000.0000.000
29H29ILE00.019-0.00510.3420.1580.1580.0000.0000.0000.000
30H30THR0-0.070-0.03612.425-1.070-1.0700.0000.0000.0000.000
31H31SER0-0.017-0.01911.462-1.574-1.5740.0000.0000.0000.000
32H32GLY00.0310.03412.0151.2651.2650.0000.0000.0000.000
33H33PHE0-0.078-0.04212.439-1.954-1.9540.0000.0000.0000.000
34H34TRP00.0340.0167.8921.7721.7720.0000.0000.0000.000
35H35ASP-1-0.767-0.89713.40418.79318.7930.0000.0000.0000.000
36H36TRP00.0220.01414.7960.7540.7540.0000.0000.0000.000
37H37ILE0-0.033-0.01114.926-0.850-0.8500.0000.0000.0000.000
38H38ARG10.8070.88018.496-11.896-11.8960.0000.0000.0000.000
39H39LYS10.9060.93819.519-14.921-14.9210.0000.0000.0000.000
40H40PHE00.0160.01022.111-0.202-0.2020.0000.0000.0000.000
41H41PRO00.0420.00825.6240.2250.2250.0000.0000.0000.000
42H42GLY00.0030.01827.823-0.041-0.0410.0000.0000.0000.000
43H43ASN00.0200.01223.2170.4910.4910.0000.0000.0000.000
44H44LYS10.8520.93323.437-10.817-10.8170.0000.0000.0000.000
45H45LEU00.0380.02218.4760.0630.0630.0000.0000.0000.000
46H46GLU-1-0.818-0.91321.60311.15811.1580.0000.0000.0000.000
47H47PHE0-0.0100.02617.9760.1480.1480.0000.0000.0000.000
48H48MET0-0.0160.00320.441-0.717-0.7170.0000.0000.0000.000
49H49GLY00.0560.00520.292-0.806-0.8060.0000.0000.0000.000
50H50TYR0-0.0180.00017.0760.5870.5870.0000.0000.0000.000
51H51ILE0-0.040-0.01017.063-1.004-1.0040.0000.0000.0000.000
52H52ARG10.9790.99516.459-13.933-13.9330.0000.0000.0000.000
53H53TYR00.0370.02417.044-0.826-0.8260.0000.0000.0000.000
54H54GLY00.0150.01418.136-0.646-0.6460.0000.0000.0000.000
55H55GLY0-0.037-0.04520.577-0.335-0.3350.0000.0000.0000.000
56H56GLY00.0020.02321.444-0.315-0.3150.0000.0000.0000.000
57H57THR0-0.027-0.02421.1360.6580.6580.0000.0000.0000.000
58H58TYR0-0.0020.00321.860-0.288-0.2880.0000.0000.0000.000
59H59TYR00.0510.01422.5920.5840.5840.0000.0000.0000.000
60H60ASN00.0160.01524.269-0.688-0.6880.0000.0000.0000.000
61H61PRO00.006-0.00325.934-0.205-0.2050.0000.0000.0000.000
62H62SER0-0.038-0.02828.627-0.455-0.4550.0000.0000.0000.000
63H63LEU0-0.074-0.02225.280-0.049-0.0490.0000.0000.0000.000
64H64LYS10.9160.96729.503-9.169-9.1690.0000.0000.0000.000
65H65SER0-0.001-0.00330.361-0.438-0.4380.0000.0000.0000.000
66H66PRO00.0120.01529.6250.3790.3790.0000.0000.0000.000
67H67ILE0-0.010-0.01823.5670.0410.0410.0000.0000.0000.000
68H68SER0-0.054-0.01725.899-0.238-0.2380.0000.0000.0000.000
69H69ILE00.0220.01719.3080.2670.2670.0000.0000.0000.000
70H70THR0-0.0040.00221.329-0.173-0.1730.0000.0000.0000.000
71H71ARG10.9040.95016.978-14.114-14.1140.0000.0000.0000.000
72H72ASP-1-0.797-0.87718.32812.77312.7730.0000.0000.0000.000
73H73THR00.023-0.00616.0010.5410.5410.0000.0000.0000.000
74H74SER0-0.039-0.00316.0970.1580.1580.0000.0000.0000.000
75H75LYS10.8600.91416.770-13.067-13.0670.0000.0000.0000.000
76H76ASN0-0.034-0.0109.9000.0400.0400.0000.0000.0000.000
77H77HIS00.0080.01713.2220.4440.4440.0000.0000.0000.000
78H78TYR0-0.028-0.04012.158-0.382-0.3820.0000.0000.0000.000
79H79TYR00.0130.00117.0920.2640.2640.0000.0000.0000.000
80H80LEU00.0000.01219.816-0.016-0.0160.0000.0000.0000.000
81H81GLN0-0.023-0.02021.768-0.430-0.4300.0000.0000.0000.000
82H82LEU00.0090.00425.534-0.016-0.0160.0000.0000.0000.000
83H83ASN00.0020.00227.876-0.253-0.2530.0000.0000.0000.000
84H84SER0-0.048-0.02931.547-0.049-0.0490.0000.0000.0000.000
85H85VAL0-0.0040.02829.382-0.083-0.0830.0000.0000.0000.000
86H86VAL0-0.007-0.02032.435-0.419-0.4190.0000.0000.0000.000
87H87THR00.034-0.01432.4910.2190.2190.0000.0000.0000.000
88H88GLU-1-0.898-0.93532.1209.2699.2690.0000.0000.0000.000
89H89ASP-1-0.784-0.87028.53310.62810.6280.0000.0000.0000.000
90H90THR0-0.031-0.00627.3740.4280.4280.0000.0000.0000.000
91H91ALA0-0.016-0.01123.801-0.019-0.0190.0000.0000.0000.000
92H92THR0-0.0110.00419.062-0.115-0.1150.0000.0000.0000.000
93H93TYR0-0.020-0.03619.7650.2070.2070.0000.0000.0000.000
94H94TYR00.0010.00214.061-0.357-0.3570.0000.0000.0000.000
95H95CYS0-0.110-0.04812.580-0.567-0.5670.0000.0000.0000.000
96H96ALA00.032-0.00410.4891.4231.4230.0000.0000.0000.000
97H97ARG10.8290.9046.473-35.591-35.5910.0000.0000.0000.000
98H98SER0-0.030-0.0359.4331.9811.9810.0000.0000.0000.000
99H99ARG10.8110.8759.054-24.231-24.2310.0000.0000.0000.000
100H100ASP-1-0.814-0.8739.34726.00126.0010.0000.0000.0000.000
101H101TYR0-0.042-0.0587.183-1.367-1.3670.0000.0000.0000.000
102H102TYR0-0.022-0.02213.113-1.170-1.1700.0000.0000.0000.000
103H103GLY0-0.0070.00616.4890.5110.5110.0000.0000.0000.000
104H104SER00.016-0.00518.048-0.090-0.0900.0000.0000.0000.000
105H105SER00.0010.01713.7550.5100.5100.0000.0000.0000.000
106H106GLY00.0360.02114.481-0.598-0.5980.0000.0000.0000.000
107H107PHE0-0.005-0.01312.2721.2661.2660.0000.0000.0000.000
108H108ALA0-0.0010.0197.742-0.528-0.5280.0000.0000.0000.000
109H109PHE0-0.0040.0092.770-5.119-2.6170.744-1.325-1.9200.015
110H110TRP0-0.041-0.0427.066-5.824-5.8240.0000.0000.0000.000
111H111GLY00.0730.0408.5302.6312.6310.0000.0000.0000.000
112H112GLU-1-0.919-0.94910.90319.74919.7490.0000.0000.0000.000
113H113GLY0-0.020-0.01813.497-0.912-0.9120.0000.0000.0000.000
114H114THR0-0.014-0.02516.358-0.685-0.6850.0000.0000.0000.000
115H115LEU0-0.033-0.00219.689-0.267-0.2670.0000.0000.0000.000
116H116VAL0-0.018-0.00622.945-0.309-0.3090.0000.0000.0000.000
117H117THR0-0.016-0.02025.473-0.188-0.1880.0000.0000.0000.000
118H118VAL00.0200.00629.106-0.101-0.1010.0000.0000.0000.000
119H119SER00.022-0.00631.603-0.329-0.3290.0000.0000.0000.000
120H120ALA00.0330.00735.0930.0370.0370.0000.0000.0000.000
121H121ALA0-0.0090.01637.185-0.190-0.1900.0000.0000.0000.000
122H122LYS10.9600.98037.613-7.312-7.3120.0000.0000.0000.000
123H123THR00.0430.01533.9250.0240.0240.0000.0000.0000.000
124H124THR0-0.041-0.01636.189-0.302-0.3020.0000.0000.0000.000
125H125PRO00.0420.02435.6190.2340.2340.0000.0000.0000.000
126H126PRO0-0.0170.00034.045-0.192-0.1920.0000.0000.0000.000
127H127SER0-0.0040.00637.069-0.158-0.1580.0000.0000.0000.000
128H128VAL0-0.002-0.00536.3960.0360.0360.0000.0000.0000.000
129H129TYR0-0.025-0.02138.987-0.177-0.1770.0000.0000.0000.000
130H130PRO00.0500.02040.0400.1920.1920.0000.0000.0000.000
131H131LEU0-0.067-0.02838.879-0.167-0.1670.0000.0000.0000.000
132H132ALA00.0370.01441.3570.1890.1890.0000.0000.0000.000
133H133PRO0-0.007-0.01043.889-0.058-0.0580.0000.0000.0000.000
134H134GLY00.0340.03046.425-0.091-0.0910.0000.0000.0000.000
135H135CYS0-0.109-0.05249.4670.0430.0430.0000.0000.0000.000
136H136GLY00.0050.01251.743-0.049-0.0490.0000.0000.0000.000
137H137ASP-1-0.893-0.94751.7145.9055.9050.0000.0000.0000.000
138H138THR0-0.014-0.00950.8330.0740.0740.0000.0000.0000.000
139H139THR0-0.015-0.01545.468-0.051-0.0510.0000.0000.0000.000
140H140GLY00.0490.03546.892-0.082-0.0820.0000.0000.0000.000
141H141SER0-0.003-0.00743.155-0.010-0.0100.0000.0000.0000.000
142H142SER0-0.054-0.00439.3750.0980.0980.0000.0000.0000.000
143H143VAL00.0270.02440.376-0.195-0.1950.0000.0000.0000.000
144H144THR00.013-0.00437.4740.2800.2800.0000.0000.0000.000
145H145LEU00.0140.03138.149-0.223-0.2230.0000.0000.0000.000
146H146GLY00.041-0.00236.5570.2750.2750.0000.0000.0000.000
147H147CYS0-0.0670.00333.7020.0080.0080.0000.0000.0000.000
148H148LEU00.0080.02436.1490.2130.2130.0000.0000.0000.000
149H149VAL00.015-0.00533.268-0.115-0.1150.0000.0000.0000.000
150H150LYS10.9830.97836.187-7.322-7.3220.0000.0000.0000.000
151H151GLY00.0040.00638.677-0.101-0.1010.0000.0000.0000.000
152H152TYR00.004-0.00731.196-0.243-0.2430.0000.0000.0000.000
153H153PHE00.003-0.01534.323-0.041-0.0410.0000.0000.0000.000
154H154PRO0-0.021-0.00830.6990.0970.0970.0000.0000.0000.000
155H155GLU-1-0.740-0.85828.29010.81910.8190.0000.0000.0000.000
156H156SER0-0.045-0.01925.2670.5210.5210.0000.0000.0000.000
157H157VAL0-0.021-0.00527.153-0.094-0.0940.0000.0000.0000.000
158H158THR0-0.040-0.03124.8120.5940.5940.0000.0000.0000.000
159H159VAL0-0.029-0.00727.525-0.286-0.2860.0000.0000.0000.000
160H160THR00.0240.02427.4760.4270.4270.0000.0000.0000.000
161H161TRP0-0.004-0.01628.884-0.554-0.5540.0000.0000.0000.000
162H162ASN0-0.036-0.01830.4000.0860.0860.0000.0000.0000.000
163H163SER00.015-0.00533.062-0.197-0.1970.0000.0000.0000.000
164H164GLY00.0400.03234.8950.1430.1430.0000.0000.0000.000
165H165SER0-0.049-0.03235.1800.0460.0460.0000.0000.0000.000
166H166LEU00.0130.00831.5050.1820.1820.0000.0000.0000.000
167H167SER0-0.035-0.00930.7660.3000.3000.0000.0000.0000.000
168H168SER00.0310.01531.065-0.260-0.2600.0000.0000.0000.000
169H169SER00.0100.01030.5640.3490.3490.0000.0000.0000.000
170H170VAL0-0.0030.00028.214-0.361-0.3610.0000.0000.0000.000
171H171HIS00.0020.01829.0290.3690.3690.0000.0000.0000.000
172H172THR00.018-0.00326.937-0.415-0.4150.0000.0000.0000.000
173H173PHE0-0.0090.00528.6730.3080.3080.0000.0000.0000.000
174H174PRO00.022-0.00528.5070.0110.0110.0000.0000.0000.000
175H175ALA00.0020.02529.867-0.398-0.3980.0000.0000.0000.000
176H176LEU0-0.020-0.02031.8260.0870.0870.0000.0000.0000.000
177H177LEU0-0.0240.00334.646-0.184-0.1840.0000.0000.0000.000
178H178GLN0-0.011-0.02136.594-0.213-0.2130.0000.0000.0000.000
179H179SER0-0.021-0.01940.426-0.004-0.0040.0000.0000.0000.000
180H180GLY00.0150.02039.796-0.116-0.1160.0000.0000.0000.000
181H181LEU0-0.046-0.02438.1190.1380.1380.0000.0000.0000.000
182H182TYR00.0290.01631.484-0.066-0.0660.0000.0000.0000.000
183H183THR0-0.056-0.03636.064-0.283-0.2830.0000.0000.0000.000
184H184MET00.0190.03729.4750.0360.0360.0000.0000.0000.000
185H185SER00.008-0.00533.303-0.327-0.3270.0000.0000.0000.000
186H186SER0-0.007-0.00331.0830.3230.3230.0000.0000.0000.000
187H187SER00.0400.00732.951-0.356-0.3560.0000.0000.0000.000
188H188VAL0-0.017-0.01032.1950.3510.3510.0000.0000.0000.000
189H189THR0-0.015-0.00734.365-0.233-0.2330.0000.0000.0000.000
190H190VAL00.026-0.00434.9650.3250.3250.0000.0000.0000.000
191H191PRO00.0500.01636.968-0.224-0.2240.0000.0000.0000.000
192H192SER00.0650.02240.1880.0390.0390.0000.0000.0000.000
193H193SER0-0.018-0.00942.902-0.060-0.0600.0000.0000.0000.000
194H194THR0-0.102-0.06739.1520.0630.0630.0000.0000.0000.000
195H195TRP00.0690.03540.1680.1900.1900.0000.0000.0000.000
196H196PRO00.0020.00142.154-0.022-0.0220.0000.0000.0000.000
197H197SER0-0.050-0.02644.351-0.066-0.0660.0000.0000.0000.000
198H198GLN0-0.027-0.02040.1410.1410.1410.0000.0000.0000.000
199H199THR00.0070.00739.1430.0320.0320.0000.0000.0000.000
200H200VAL00.0190.01236.2450.2010.2010.0000.0000.0000.000
201H201THR0-0.017-0.01335.679-0.335-0.3350.0000.0000.0000.000
202H203SER0-0.008-0.03531.467-0.163-0.1630.0000.0000.0000.000
203H204VAL0-0.016-0.01831.0390.3680.3680.0000.0000.0000.000
204H205ALA00.0440.03328.274-0.273-0.2730.0000.0000.0000.000
205H206HIS00.010-0.00829.797-0.083-0.0830.0000.0000.0000.000
206H207PRO00.0760.03025.584-0.304-0.3040.0000.0000.0000.000
207H208ALA0-0.0060.00928.421-0.152-0.1520.0000.0000.0000.000
208H209SER0-0.047-0.04729.892-0.311-0.3110.0000.0000.0000.000
209H210SER0-0.038-0.01531.191-0.216-0.2160.0000.0000.0000.000
210H211THR0-0.015-0.00432.216-0.205-0.2050.0000.0000.0000.000
211H212THR00.011-0.02031.4840.4850.4850.0000.0000.0000.000
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