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: V5611

Calculation Name: 5U3J-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U3J

Chain ID: H

ChEMBL ID:

UniProt ID: V9QIE5

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2395464.645813
FMO2-HF: Nuclear repulsion 2306601.69315
FMO2-HF: Total energy -88862.952662
FMO2-MP2: Total energy -89121.953947


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.
-51.408-49.717-0.009-0.578-1.1040.002
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 : -0.943 / q_NPA : -0.977
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].
3H3GLN0-0.045-0.0133.825-2.940-1.368-0.007-0.537-1.0280.002
4H4LEU00.012-0.0105.607-1.872-1.8720.0000.0000.0000.000
5H5VAL0-0.007-0.0048.745-0.123-0.1230.0000.0000.0000.000
6H6GLU-1-0.753-0.87311.18818.40118.4010.0000.0000.0000.000
7H7SER0-0.042-0.03914.8900.2420.2420.0000.0000.0000.000
8H8GLY00.0240.00517.655-0.329-0.3290.0000.0000.0000.000
9H9GLY0-0.032-0.00320.739-0.567-0.5670.0000.0000.0000.000
10H10GLY00.0320.00522.5790.1180.1180.0000.0000.0000.000
11H11LEU0-0.051-0.01325.698-0.157-0.1570.0000.0000.0000.000
12H12VAL00.0150.00829.463-0.061-0.0610.0000.0000.0000.000
13H13LYS10.9720.98731.652-8.121-8.1210.0000.0000.0000.000
14H14PRO00.022-0.00434.7270.1430.1430.0000.0000.0000.000
15H15GLY0-0.008-0.00136.033-0.183-0.1830.0000.0000.0000.000
16H16GLY0-0.0200.00034.372-0.052-0.0520.0000.0000.0000.000
17H17SER0-0.044-0.03831.3520.1020.1020.0000.0000.0000.000
18H18LEU00.005-0.00925.465-0.032-0.0320.0000.0000.0000.000
19H19ARG10.9150.96923.331-11.235-11.2350.0000.0000.0000.000
20H20LEU0-0.0130.00920.1460.1930.1930.0000.0000.0000.000
21H21SER0-0.032-0.02518.049-0.167-0.1670.0000.0000.0000.000
22H22CYS00.0600.05212.9030.4180.4180.0000.0000.0000.000
23H23ALA0-0.0090.02611.070-0.639-0.6390.0000.0000.0000.000
24H24ALA00.011-0.0079.3361.0851.0850.0000.0000.0000.000
25H25SER0-0.004-0.0064.9581.6821.6820.0000.0000.0000.000
26H26GLY00.0830.0314.7001.3381.348-0.001-0.0330.0230.000
27H27PHE00.004-0.0055.357-0.676-0.567-0.001-0.008-0.0990.000
28H28THR00.0160.0108.862-0.183-0.1830.0000.0000.0000.000
29H29PHE00.0590.05312.090-1.261-1.2610.0000.0000.0000.000
30H30SER00.0350.01013.544-0.739-0.7390.0000.0000.0000.000
31H31ASN0-0.106-0.06016.105-1.762-1.7620.0000.0000.0000.000
32H32THR00.0460.01813.9050.1130.1130.0000.0000.0000.000
33H33TRP0-0.050-0.02016.683-0.569-0.5690.0000.0000.0000.000
34H34MET0-0.0090.03413.5820.9140.9140.0000.0000.0000.000
35H35SER00.034-0.01517.801-1.284-1.2840.0000.0000.0000.000
36H36TRP0-0.005-0.00617.9380.8100.8100.0000.0000.0000.000
37H37VAL00.0150.00019.331-0.708-0.7080.0000.0000.0000.000
38H38ARG10.7870.91020.159-9.897-9.8970.0000.0000.0000.000
39H39GLN00.0120.00321.2520.3790.3790.0000.0000.0000.000
40H40ALA00.0320.02723.7950.0980.0980.0000.0000.0000.000
41H41PRO00.010-0.00626.3640.1620.1620.0000.0000.0000.000
42H42GLY00.004-0.00426.984-0.360-0.3600.0000.0000.0000.000
43H43LYS10.9140.97027.695-9.409-9.4090.0000.0000.0000.000
44H44GLY00.0410.01525.9280.3600.3600.0000.0000.0000.000
45H45LEU0-0.009-0.00520.727-0.045-0.0450.0000.0000.0000.000
46H46GLU-1-0.826-0.90824.0959.6989.6980.0000.0000.0000.000
47H47TRP0-0.022-0.01822.4700.0020.0020.0000.0000.0000.000
48H48VAL0-0.028-0.00823.562-0.497-0.4970.0000.0000.0000.000
49H49GLY00.053-0.00623.780-0.601-0.6010.0000.0000.0000.000
50H50ARG10.8070.96722.303-10.837-10.8370.0000.0000.0000.000
51H51ILE0-0.047-0.02320.863-0.598-0.5980.0000.0000.0000.000
52H52SER00.0240.02921.6790.4370.4370.0000.0000.0000.000
53H52ARG10.9170.96519.694-13.262-13.2620.0000.0000.0000.000
54H52ASN00.0760.02421.715-0.784-0.7840.0000.0000.0000.000
55H52LYS10.9060.96223.280-12.085-12.0850.0000.0000.0000.000
56H53ASP-1-0.793-0.91724.37611.75411.7540.0000.0000.0000.000
57H54GLY0-0.025-0.01026.712-0.401-0.4010.0000.0000.0000.000
58H55ALA0-0.029-0.00124.901-0.162-0.1620.0000.0000.0000.000
59H56LYS10.9400.97325.848-9.539-9.5390.0000.0000.0000.000
60H57THR00.0120.00825.7620.3340.3340.0000.0000.0000.000
61H58GLU-1-0.884-0.92727.0499.8949.8940.0000.0000.0000.000
62H59TYR00.0300.00827.0170.4400.4400.0000.0000.0000.000
63H60ALA00.0550.03028.329-0.317-0.3170.0000.0000.0000.000
64H61ALA0-0.011-0.02030.065-0.115-0.1150.0000.0000.0000.000
65H62PRO00.0120.01330.858-0.153-0.1530.0000.0000.0000.000
66H63VAL00.0130.00028.165-0.122-0.1220.0000.0000.0000.000
67H64ARG10.9150.96731.434-8.936-8.9360.0000.0000.0000.000
68H65GLY00.0040.00733.061-0.240-0.2400.0000.0000.0000.000
69H66ARG10.7320.84931.910-9.182-9.1820.0000.0000.0000.000
70H67PHE0-0.012-0.00826.9590.1230.1230.0000.0000.0000.000
71H68THR0-0.009-0.00627.613-0.270-0.2700.0000.0000.0000.000
72H69ILE0-0.0070.01222.2470.2310.2310.0000.0000.0000.000
73H70SER0-0.007-0.00322.982-0.221-0.2210.0000.0000.0000.000
74H71ARG10.7980.89217.181-14.662-14.6620.0000.0000.0000.000
75H72ASP-1-0.870-0.94418.56912.98612.9860.0000.0000.0000.000
76H73ASP-1-0.817-0.94016.68315.50915.5090.0000.0000.0000.000
77H74SER0-0.0480.00216.3990.6770.6770.0000.0000.0000.000
78H75ARG10.8980.94614.896-15.260-15.2600.0000.0000.0000.000
79H76ASP-1-0.864-0.92011.33021.28921.2890.0000.0000.0000.000
80H77THR0-0.063-0.03412.8170.7980.7980.0000.0000.0000.000
81H78LEU0-0.008-0.00115.476-0.921-0.9210.0000.0000.0000.000
82H79TYR0-0.002-0.01417.7240.2480.2480.0000.0000.0000.000
83H80LEU00.0100.00320.846-0.224-0.2240.0000.0000.0000.000
84H81GLN00.0130.00523.4030.2100.2100.0000.0000.0000.000
85H82MET0-0.011-0.00125.978-0.236-0.2360.0000.0000.0000.000
86H82THR0-0.005-0.01828.694-0.194-0.1940.0000.0000.0000.000
87H82SER00.0240.01132.435-0.087-0.0870.0000.0000.0000.000
88H82LEU0-0.029-0.00429.141-0.029-0.0290.0000.0000.0000.000
89H83LYS11.0001.00233.014-8.537-8.5370.0000.0000.0000.000
90H84ILE00.0590.02132.7860.2640.2640.0000.0000.0000.000
91H85GLU-1-0.919-0.97432.5168.5198.5190.0000.0000.0000.000
92H86ASP-1-0.777-0.83129.0299.6649.6640.0000.0000.0000.000
93H87SER0-0.0060.02927.6430.4650.4650.0000.0000.0000.000
94H88GLY00.0200.00025.367-0.163-0.1630.0000.0000.0000.000
95H89ARG10.8340.92916.226-15.427-15.4270.0000.0000.0000.000
96H90TYR0-0.021-0.05420.379-0.188-0.1880.0000.0000.0000.000
97H91PHE0-0.019-0.02115.1420.3810.3810.0000.0000.0000.000
98H92CYS0-0.085-0.06614.160-0.868-0.8680.0000.0000.0000.000
99H93THR00.011-0.00214.1380.9070.9070.0000.0000.0000.000
100H94ALA00.0340.01712.455-0.709-0.7090.0000.0000.0000.000
101H95ASP-1-0.776-0.87214.39615.40615.4060.0000.0000.0000.000
102H96LEU0-0.0160.00214.0710.3470.3470.0000.0000.0000.000
103H97GLY0-0.038-0.02118.099-0.617-0.6170.0000.0000.0000.000
104H98GLU-1-0.912-0.94521.12813.73213.7320.0000.0000.0000.000
105H99PRO0-0.009-0.02323.236-0.535-0.5350.0000.0000.0000.000
106H100VAL00.0280.03026.5930.0930.0930.0000.0000.0000.000
107H100VAL0-0.010-0.00428.312-0.171-0.1710.0000.0000.0000.000
108H100SER0-0.010-0.01131.099-0.344-0.3440.0000.0000.0000.000
109H100ARG10.9870.99133.364-8.468-8.4680.0000.0000.0000.000
110H100PHE00.0610.03535.1760.0980.0980.0000.0000.0000.000
111H100PHE0-0.021-0.02637.0270.0720.0720.0000.0000.0000.000
112H100GLU-1-0.931-0.95034.0148.6908.6900.0000.0000.0000.000
113H100TRP0-0.035-0.01832.9390.2470.2470.0000.0000.0000.000
114H100GLY0-0.0010.00631.752-0.231-0.2310.0000.0000.0000.000
115H100SER0-0.077-0.03430.5350.2740.2740.0000.0000.0000.000
116H100TYR0-0.017-0.02825.2140.2170.2170.0000.0000.0000.000
117H100TYR0-0.0040.00224.298-0.307-0.3070.0000.0000.0000.000
118H100TYR0-0.088-0.11120.5850.3260.3260.0000.0000.0000.000
119H100TYR0-0.023-0.00716.281-0.712-0.7120.0000.0000.0000.000
120H100MET0-0.034-0.01817.1270.3170.3170.0000.0000.0000.000
121H101ASP-1-0.890-0.93912.12021.22521.2250.0000.0000.0000.000
122H102LEU00.0120.0217.4861.0261.0260.0000.0000.0000.000
123H103TRP00.006-0.01710.921-1.847-1.8470.0000.0000.0000.000
124H104GLY00.0590.04210.0632.0542.0540.0000.0000.0000.000
125H105LYS10.9290.9549.293-25.399-25.3990.0000.0000.0000.000
126H106GLY00.0190.02112.693-1.276-1.2760.0000.0000.0000.000
127H107THR0-0.032-0.01715.8420.1410.1410.0000.0000.0000.000
128H108THR0-0.057-0.03018.612-0.262-0.2620.0000.0000.0000.000
129H109VAL0-0.0030.00422.165-0.051-0.0510.0000.0000.0000.000
130H110THR0-0.058-0.03925.237-0.109-0.1090.0000.0000.0000.000
131H111VAL00.0460.02328.728-0.087-0.0870.0000.0000.0000.000
132H112SER00.0200.00131.915-0.253-0.2530.0000.0000.0000.000
133H113SER00.002-0.01434.9860.1230.1230.0000.0000.0000.000
134H114ALA0-0.0320.00936.672-0.192-0.1920.0000.0000.0000.000
135H115SER0-0.013-0.01237.2030.1360.1360.0000.0000.0000.000
136H116THR0-0.039-0.02635.852-0.008-0.0080.0000.0000.0000.000
137H117LYS10.9030.96537.632-7.320-7.3200.0000.0000.0000.000
138H118GLY00.0390.02738.8810.1760.1760.0000.0000.0000.000
139H119PRO0-0.040-0.01738.735-0.130-0.1300.0000.0000.0000.000
140H120SER0-0.020-0.01341.197-0.127-0.1270.0000.0000.0000.000
141H121VAL0-0.026-0.00343.2810.0110.0110.0000.0000.0000.000
142H122PHE00.007-0.00444.660-0.193-0.1930.0000.0000.0000.000
143H123PRO0-0.002-0.01946.3470.1290.1290.0000.0000.0000.000
144H124LEU0-0.0490.00344.153-0.040-0.0400.0000.0000.0000.000
145H125ALA00.002-0.00148.3880.0320.0320.0000.0000.0000.000
146H126PRO00.0330.03850.636-0.020-0.0200.0000.0000.0000.000
147H127SER00.0520.00452.350-0.130-0.1300.0000.0000.0000.000
148H128SER00.0500.01955.1400.0770.0770.0000.0000.0000.000
149H129LYS10.9160.95854.973-5.349-5.3490.0000.0000.0000.000
150H130SER0-0.033-0.02050.4860.1240.1240.0000.0000.0000.000
151H131THR0-0.0120.00751.3330.1230.1230.0000.0000.0000.000
152H132SER0-0.020-0.00750.914-0.059-0.0590.0000.0000.0000.000
153H133GLY00.0270.01352.7000.0640.0640.0000.0000.0000.000
154H134GLY00.0290.01953.958-0.079-0.0790.0000.0000.0000.000
155H135THR0-0.059-0.04047.9490.1130.1130.0000.0000.0000.000
156H136ALA0-0.0140.00850.855-0.056-0.0560.0000.0000.0000.000
157H137ALA00.0190.00746.7510.1500.1500.0000.0000.0000.000
158H138LEU00.0170.01545.988-0.152-0.1520.0000.0000.0000.000
159H139GLY00.0540.00044.2000.1940.1940.0000.0000.0000.000
160H140CYS0-0.105-0.01341.798-0.079-0.0790.0000.0000.0000.000
161H141LEU00.0170.01242.0920.1730.1730.0000.0000.0000.000
162H142VAL00.0020.00638.280-0.135-0.1350.0000.0000.0000.000
163H143LYS10.9610.97039.969-6.752-6.7520.0000.0000.0000.000
164H144ASP-1-0.844-0.92941.1546.9426.9420.0000.0000.0000.000
165H145TYR00.0020.00734.066-0.058-0.0580.0000.0000.0000.000
166H146PHE00.0590.02733.4010.1400.1400.0000.0000.0000.000
167H147PRO0-0.005-0.00430.807-0.140-0.1400.0000.0000.0000.000
168H148GLU-1-0.816-0.92728.5759.5329.5320.0000.0000.0000.000
169H149PRO0-0.027-0.00428.257-0.106-0.1060.0000.0000.0000.000
170H150VAL00.0310.00030.244-0.243-0.2430.0000.0000.0000.000
171H151THR0-0.079-0.02130.8320.2000.2000.0000.0000.0000.000
172H152VAL00.021-0.01333.482-0.241-0.2410.0000.0000.0000.000
173H153SER0-0.0180.00435.6980.1580.1580.0000.0000.0000.000
174H154TRP00.0580.01137.834-0.279-0.2790.0000.0000.0000.000
175H155ASN00.0330.02141.2790.0170.0170.0000.0000.0000.000
176H156SER0-0.023-0.03040.7080.0090.0090.0000.0000.0000.000
177H157GLY0-0.037-0.02138.1370.1710.1710.0000.0000.0000.000
178H158ALA0-0.0160.01038.6980.0950.0950.0000.0000.0000.000
179H159LEU0-0.031-0.01041.121-0.008-0.0080.0000.0000.0000.000
180H160THR00.022-0.00736.0980.0780.0780.0000.0000.0000.000
181H161SER0-0.0040.00337.4350.1680.1680.0000.0000.0000.000
182H162GLY00.0450.02339.242-0.167-0.1670.0000.0000.0000.000
183H163VAL0-0.028-0.01536.768-0.147-0.1470.0000.0000.0000.000
184H164HIS00.0160.00836.3940.3520.3520.0000.0000.0000.000
185H165THR0-0.005-0.01734.079-0.327-0.3270.0000.0000.0000.000
186H166PHE0-0.0220.00033.8500.2620.2620.0000.0000.0000.000
187H167PRO00.018-0.00530.7320.0270.0270.0000.0000.0000.000
188H168ALA0-0.0050.02132.070-0.318-0.3180.0000.0000.0000.000
189H169VAL0-0.012-0.00533.1880.1480.1480.0000.0000.0000.000
190H170LEU0-0.033-0.00833.478-0.100-0.1000.0000.0000.0000.000
191H171GLN0-0.022-0.01735.991-0.236-0.2360.0000.0000.0000.000
192H172SER00.0340.00939.3060.0390.0390.0000.0000.0000.000
193H173SER0-0.024-0.01141.6020.0350.0350.0000.0000.0000.000
194H174GLY00.0170.01037.740-0.011-0.0110.0000.0000.0000.000
195H175LEU0-0.066-0.02337.0020.2020.2020.0000.0000.0000.000
196H176TYR00.0290.00531.223-0.031-0.0310.0000.0000.0000.000
197H177SER0-0.021-0.02136.863-0.268-0.2680.0000.0000.0000.000
198H178LEU00.0160.02734.3300.1050.1050.0000.0000.0000.000
199H179SER00.002-0.01037.859-0.293-0.2930.0000.0000.0000.000
200H180SER0-0.0250.00438.0530.1430.1430.0000.0000.0000.000
201H181VAL00.0500.01939.701-0.232-0.2320.0000.0000.0000.000
202H182VAL00.0160.00440.7530.2060.2060.0000.0000.0000.000
203H183THR0-0.053-0.01743.019-0.174-0.1740.0000.0000.0000.000
204H184VAL00.0230.01045.1540.0890.0890.0000.0000.0000.000
205H185PRO00.0840.05047.920-0.084-0.0840.0000.0000.0000.000
206H186SER00.0060.00351.183-0.021-0.0210.0000.0000.0000.000
207H187SER00.0340.01254.251-0.044-0.0440.0000.0000.0000.000
208H188SER0-0.019-0.01851.750-0.018-0.0180.0000.0000.0000.000
209H189LEU00.001-0.00752.4000.0520.0520.0000.0000.0000.000
210H190GLY0-0.0090.00055.094-0.094-0.0940.0000.0000.0000.000
211H191THR0-0.0180.00155.182-0.074-0.0740.0000.0000.0000.000
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