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: 173GZ

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 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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2396211.567944
FMO2-HF: Nuclear repulsion 2307347.994591
FMO2-HF: Total energy -88863.573353
FMO2-MP2: Total energy -89122.637345


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.
-58.108-56.142-0.015-0.679-1.2730.002
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 : -0.937 / q_NPA : -0.975
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].
3H3GLN0-0.050-0.0163.825-4.886-3.220-0.012-0.607-1.0470.002
4H4LEU00.0200.0025.775-1.784-1.7840.0000.0000.0000.000
5H5VAL0-0.010-0.0058.854-0.239-0.2390.0000.0000.0000.000
6H6GLU-1-0.741-0.86511.33518.40918.4090.0000.0000.0000.000
7H7SER0-0.045-0.04215.0410.1830.1830.0000.0000.0000.000
8H8GLY00.0300.00817.791-0.311-0.3110.0000.0000.0000.000
9H9GLY0-0.0070.01320.870-0.586-0.5860.0000.0000.0000.000
10H10GLY00.023-0.00122.7190.1140.1140.0000.0000.0000.000
11H11LEU0-0.063-0.01725.831-0.166-0.1660.0000.0000.0000.000
12H12VAL00.0200.01029.596-0.054-0.0540.0000.0000.0000.000
13H13LYS10.9100.96631.794-8.171-8.1710.0000.0000.0000.000
14H14PRO00.020-0.00634.8760.1370.1370.0000.0000.0000.000
15H15GLY0-0.008-0.00136.192-0.181-0.1810.0000.0000.0000.000
16H16GLY0-0.0150.00334.522-0.051-0.0510.0000.0000.0000.000
17H17SER0-0.017-0.02331.407-0.025-0.0250.0000.0000.0000.000
18H18LEU0-0.024-0.02325.552-0.037-0.0370.0000.0000.0000.000
19H19ARG10.8900.94623.281-11.197-11.1970.0000.0000.0000.000
20H20LEU0-0.0070.01520.3110.1920.1920.0000.0000.0000.000
21H21SER0-0.006-0.01917.725-0.435-0.4350.0000.0000.0000.000
22H22CYS0-0.038-0.00313.3800.5990.5990.0000.0000.0000.000
23H23ALA00.0130.03611.112-0.667-0.6670.0000.0000.0000.000
24H24ALA00.0260.0039.3691.0871.0870.0000.0000.0000.000
25H25SER00.0320.0064.025-0.789-0.614-0.001-0.028-0.1460.000
26H26GLY00.0370.0164.6721.4471.456-0.001-0.0350.0260.000
27H27PHE0-0.001-0.0055.325-0.805-0.689-0.001-0.009-0.1060.000
28H28THR00.0190.0148.840-0.139-0.1390.0000.0000.0000.000
29H29PHE00.0520.04612.114-1.295-1.2950.0000.0000.0000.000
30H30SER00.0350.01813.559-0.787-0.7870.0000.0000.0000.000
31H31ASN0-0.057-0.02716.079-1.809-1.8090.0000.0000.0000.000
32H32THR00.0470.01313.8830.0760.0760.0000.0000.0000.000
33H33TRP0-0.041-0.01416.683-0.602-0.6020.0000.0000.0000.000
34H34MET0-0.0100.02813.5710.9980.9980.0000.0000.0000.000
35H35SER00.024-0.01017.965-1.209-1.2090.0000.0000.0000.000
36H36TRP0-0.010-0.01218.1540.8360.8360.0000.0000.0000.000
37H37VAL00.0220.00719.486-0.728-0.7280.0000.0000.0000.000
38H38ARG10.7560.86320.323-9.878-9.8780.0000.0000.0000.000
39H39GLN00.000-0.00921.6280.3040.3040.0000.0000.0000.000
40H40ALA00.0290.02723.9480.1020.1020.0000.0000.0000.000
41H41PRO00.019-0.00326.4950.1450.1450.0000.0000.0000.000
42H42GLY00.003-0.00427.115-0.362-0.3620.0000.0000.0000.000
43H43LYS10.9110.96927.836-9.387-9.3870.0000.0000.0000.000
44H44GLY00.0490.02726.0670.3570.3570.0000.0000.0000.000
45H45LEU0-0.005-0.00120.591-0.041-0.0410.0000.0000.0000.000
46H46GLU-1-0.803-0.87124.2329.7519.7510.0000.0000.0000.000
47H47TRP00.0030.00022.8510.0020.0020.0000.0000.0000.000
48H48VAL0-0.024-0.00623.774-0.476-0.4760.0000.0000.0000.000
49H49GLY00.045-0.00623.946-0.592-0.5920.0000.0000.0000.000
50H50ARG10.7680.91722.472-10.868-10.8680.0000.0000.0000.000
51H51ILE0-0.040-0.02020.862-0.584-0.5840.0000.0000.0000.000
52H52SER00.0300.03021.6790.4000.4000.0000.0000.0000.000
53H52ARG10.8190.89519.590-13.377-13.3770.0000.0000.0000.000
54H52ASN00.037-0.00921.080-0.961-0.9610.0000.0000.0000.000
55H52LYS10.9220.97523.292-11.862-11.8620.0000.0000.0000.000
56H53ASP-1-0.799-0.90524.13111.83811.8380.0000.0000.0000.000
57H54GLY0-0.015-0.00326.719-0.406-0.4060.0000.0000.0000.000
58H55ALA0-0.035-0.00424.851-0.174-0.1740.0000.0000.0000.000
59H56LYS10.9400.97725.866-9.587-9.5870.0000.0000.0000.000
60H57THR00.0290.00825.6230.2590.2590.0000.0000.0000.000
61H58GLU-1-0.873-0.90227.1559.9579.9570.0000.0000.0000.000
62H59TYR00.0260.00527.2710.4360.4360.0000.0000.0000.000
63H60ALA00.0700.03828.451-0.341-0.3410.0000.0000.0000.000
64H61ALA0-0.004-0.01830.232-0.110-0.1100.0000.0000.0000.000
65H62PRO00.0090.01031.050-0.150-0.1500.0000.0000.0000.000
66H63VAL00.0180.00328.264-0.112-0.1120.0000.0000.0000.000
67H64ARG10.8700.94531.603-8.977-8.9770.0000.0000.0000.000
68H65GLY00.0060.00633.230-0.240-0.2400.0000.0000.0000.000
69H66ARG10.7440.85832.139-9.139-9.1390.0000.0000.0000.000
70H67PHE0-0.004-0.01027.0520.1350.1350.0000.0000.0000.000
71H68THR0-0.007-0.00427.657-0.258-0.2580.0000.0000.0000.000
72H69ILE0-0.0100.01222.2910.2440.2440.0000.0000.0000.000
73H70SER00.003-0.00523.008-0.221-0.2210.0000.0000.0000.000
74H71ARG10.7780.86917.170-14.666-14.6660.0000.0000.0000.000
75H72ASP-1-0.831-0.93418.59113.28713.2870.0000.0000.0000.000
76H73ASP-1-0.766-0.89516.69415.61215.6120.0000.0000.0000.000
77H74SER0-0.0200.01716.4130.3300.3300.0000.0000.0000.000
78H75ARG10.8530.92114.895-15.449-15.4490.0000.0000.0000.000
79H76ASP-1-0.854-0.91911.52021.35621.3560.0000.0000.0000.000
80H77THR0-0.057-0.02612.8380.8090.8090.0000.0000.0000.000
81H78LEU0-0.0030.00715.498-0.945-0.9450.0000.0000.0000.000
82H79TYR0-0.019-0.02217.7470.3280.3280.0000.0000.0000.000
83H80LEU00.0160.00820.870-0.237-0.2370.0000.0000.0000.000
84H81GLN00.0070.00923.5650.0960.0960.0000.0000.0000.000
85H82MET0-0.0110.00126.025-0.241-0.2410.0000.0000.0000.000
86H82THR0-0.001-0.01428.855-0.180-0.1800.0000.0000.0000.000
87H82SER00.0260.01232.596-0.086-0.0860.0000.0000.0000.000
88H82LEU0-0.0300.00129.285-0.022-0.0220.0000.0000.0000.000
89H83LYS10.9830.99433.181-8.469-8.4690.0000.0000.0000.000
90H84ILE00.0480.01832.9440.2580.2580.0000.0000.0000.000
91H85GLU-1-0.891-0.96632.6698.5628.5620.0000.0000.0000.000
92H86ASP-1-0.771-0.82929.1879.6619.6610.0000.0000.0000.000
93H87SER0-0.0110.01427.8020.4570.4570.0000.0000.0000.000
94H88GLY00.013-0.00325.518-0.167-0.1670.0000.0000.0000.000
95H89ARG10.8000.90116.017-15.588-15.5880.0000.0000.0000.000
96H90TYR0-0.003-0.03320.540-0.177-0.1770.0000.0000.0000.000
97H91PHE0-0.020-0.02415.5510.4440.4440.0000.0000.0000.000
98H92CYS0-0.065-0.04114.277-0.770-0.7700.0000.0000.0000.000
99H93THR0-0.016-0.01714.3200.4700.4700.0000.0000.0000.000
100H94ALA00.0430.02512.595-0.696-0.6960.0000.0000.0000.000
101H95ASP-1-0.782-0.88814.55115.26615.2660.0000.0000.0000.000
102H96LEU0-0.030-0.00714.2820.3860.3860.0000.0000.0000.000
103H97GLY0-0.037-0.02018.217-0.608-0.6080.0000.0000.0000.000
104H98GLU-1-0.911-0.94621.22713.44513.4450.0000.0000.0000.000
105H99PRO0-0.011-0.02123.337-0.526-0.5260.0000.0000.0000.000
106H100VAL00.0280.03026.6870.0650.0650.0000.0000.0000.000
107H100VAL0-0.004-0.00328.413-0.160-0.1600.0000.0000.0000.000
108H100SER0-0.014-0.00331.183-0.308-0.3080.0000.0000.0000.000
109H100ARG10.9590.98633.448-8.499-8.4990.0000.0000.0000.000
110H100PHE00.0570.02735.2700.1040.1040.0000.0000.0000.000
111H100PHE0-0.020-0.02437.1190.0720.0720.0000.0000.0000.000
112H100GLU-1-0.907-0.94834.0828.6028.6020.0000.0000.0000.000
113H100TRP0-0.041-0.02533.0320.2470.2470.0000.0000.0000.000
114H100GLY00.0060.00931.848-0.230-0.2300.0000.0000.0000.000
115H100SER0-0.088-0.03930.6410.2770.2770.0000.0000.0000.000
116H100TYR00.006-0.01225.5660.2060.2060.0000.0000.0000.000
117H100TYR0-0.001-0.00124.450-0.289-0.2890.0000.0000.0000.000
118H100TYR0-0.063-0.08421.0020.2800.2800.0000.0000.0000.000
119H100TYR0-0.070-0.03715.800-0.819-0.8190.0000.0000.0000.000
120H100MET0-0.019-0.00617.2570.2600.2600.0000.0000.0000.000
121H101ASP-1-0.836-0.90612.28220.59320.5930.0000.0000.0000.000
122H102LEU00.0170.0197.6271.0091.0090.0000.0000.0000.000
123H103TRP0-0.013-0.02611.075-1.785-1.7850.0000.0000.0000.000
124H104GLY00.0610.04510.2232.0312.0310.0000.0000.0000.000
125H105LYS10.9490.9679.091-26.337-26.3370.0000.0000.0000.000
126H106GLY00.0170.02012.833-1.329-1.3290.0000.0000.0000.000
127H107THR0-0.056-0.02915.992-0.079-0.0790.0000.0000.0000.000
128H108THR0-0.027-0.01418.756-0.264-0.2640.0000.0000.0000.000
129H109VAL00.0030.00422.306-0.056-0.0560.0000.0000.0000.000
130H110THR0-0.057-0.03725.383-0.117-0.1170.0000.0000.0000.000
131H111VAL00.0440.02228.871-0.086-0.0860.0000.0000.0000.000
132H112SER00.0320.00932.063-0.262-0.2620.0000.0000.0000.000
133H113SER00.025-0.00335.1280.1230.1230.0000.0000.0000.000
134H114ALA0-0.0250.00636.822-0.194-0.1940.0000.0000.0000.000
135H115SER0-0.003-0.01137.3310.1770.1770.0000.0000.0000.000
136H116THR0-0.033-0.02135.790-0.010-0.0100.0000.0000.0000.000
137H117LYS10.8430.92237.743-7.347-7.3470.0000.0000.0000.000
138H118GLY00.0550.03538.9840.1720.1720.0000.0000.0000.000
139H119PRO0-0.042-0.01038.831-0.134-0.1340.0000.0000.0000.000
140H120SER0-0.018-0.01441.292-0.117-0.1170.0000.0000.0000.000
141H121VAL0-0.024-0.00543.2580.0090.0090.0000.0000.0000.000
142H122PHE00.006-0.00244.746-0.197-0.1970.0000.0000.0000.000
143H123PRO0-0.001-0.01646.4310.1250.1250.0000.0000.0000.000
144H124LEU0-0.0430.00144.298-0.047-0.0470.0000.0000.0000.000
145H125ALA0-0.005-0.00348.4690.0290.0290.0000.0000.0000.000
146H126PRO00.0270.03650.762-0.017-0.0170.0000.0000.0000.000
147H127SER00.0400.00352.419-0.129-0.1290.0000.0000.0000.000
148H128SER00.0520.01855.2080.0770.0770.0000.0000.0000.000
149H129LYS10.9090.95355.109-5.338-5.3380.0000.0000.0000.000
150H130SER0-0.013-0.00350.1920.1130.1130.0000.0000.0000.000
151H131THR0-0.015-0.01551.3990.1100.1100.0000.0000.0000.000
152H132SER0-0.019-0.00550.930-0.061-0.0610.0000.0000.0000.000
153H133GLY00.0220.01052.8310.0640.0640.0000.0000.0000.000
154H134GLY00.0330.01854.214-0.077-0.0770.0000.0000.0000.000
155H135THR0-0.061-0.04248.0820.1290.1290.0000.0000.0000.000
156H136ALA0-0.0170.00850.945-0.056-0.0560.0000.0000.0000.000
157H137ALA00.0180.01846.8280.1520.1520.0000.0000.0000.000
158H138LEU00.0100.01446.094-0.168-0.1680.0000.0000.0000.000
159H139GLY00.0670.01544.2800.1880.1880.0000.0000.0000.000
160H140CYS0-0.107-0.01041.929-0.084-0.0840.0000.0000.0000.000
161H141LEU00.0250.01742.2860.1790.1790.0000.0000.0000.000
162H142VAL0-0.0030.00438.269-0.139-0.1390.0000.0000.0000.000
163H143LYS10.9260.92540.069-6.754-6.7540.0000.0000.0000.000
164H144ASP-1-0.810-0.88241.1896.9546.9540.0000.0000.0000.000
165H145TYR00.0280.03234.263-0.208-0.2080.0000.0000.0000.000
166H146PHE00.0690.03133.5290.1330.1330.0000.0000.0000.000
167H147PRO0-0.010-0.00830.932-0.141-0.1410.0000.0000.0000.000
168H148GLU-1-0.822-0.92828.6239.5529.5520.0000.0000.0000.000
169H149PRO0-0.025-0.01028.311-0.137-0.1370.0000.0000.0000.000
170H150VAL00.009-0.00430.337-0.239-0.2390.0000.0000.0000.000
171H151THR0-0.047-0.01130.8750.2120.2120.0000.0000.0000.000
172H152VAL00.005-0.02133.550-0.249-0.2490.0000.0000.0000.000
173H153SER0-0.013-0.00235.7530.2250.2250.0000.0000.0000.000
174H154TRP00.0330.00037.882-0.288-0.2880.0000.0000.0000.000
175H155ASN0-0.001-0.00941.3220.0720.0720.0000.0000.0000.000
176H156SER0-0.038-0.03840.790-0.010-0.0100.0000.0000.0000.000
177H157GLY00.0040.00538.2480.1580.1580.0000.0000.0000.000
178H158ALA0-0.0260.00538.8550.0880.0880.0000.0000.0000.000
179H159LEU0-0.034-0.01141.309-0.007-0.0070.0000.0000.0000.000
180H160THR00.026-0.00236.3600.0760.0760.0000.0000.0000.000
181H161SER0-0.0020.00337.6500.1630.1630.0000.0000.0000.000
182H162GLY00.0410.01539.464-0.169-0.1690.0000.0000.0000.000
183H163VAL0-0.034-0.01336.791-0.140-0.1400.0000.0000.0000.000
184H164HIS00.0150.00836.4610.3510.3510.0000.0000.0000.000
185H165THR00.002-0.00734.279-0.321-0.3210.0000.0000.0000.000
186H166PHE0-0.0160.00733.9280.2500.2500.0000.0000.0000.000
187H167PRO00.029-0.00230.8220.0300.0300.0000.0000.0000.000
188H168ALA0-0.0140.01332.176-0.308-0.3080.0000.0000.0000.000
189H169VAL0-0.010-0.00333.3020.1500.1500.0000.0000.0000.000
190H170LEU0-0.037-0.01333.429-0.099-0.0990.0000.0000.0000.000
191H171GLN0-0.019-0.02136.120-0.280-0.2800.0000.0000.0000.000
192H172SER00.0390.01239.4410.0530.0530.0000.0000.0000.000
193H173SER0-0.022-0.00941.7410.0300.0300.0000.0000.0000.000
194H174GLY00.0070.00437.875-0.009-0.0090.0000.0000.0000.000
195H175LEU0-0.060-0.02037.1320.2050.2050.0000.0000.0000.000
196H176TYR00.0150.00131.007-0.037-0.0370.0000.0000.0000.000
197H177SER00.002-0.01636.980-0.281-0.2810.0000.0000.0000.000
198H178LEU00.0220.03634.4510.0890.0890.0000.0000.0000.000
199H179SER0-0.008-0.01837.958-0.297-0.2970.0000.0000.0000.000
200H180SER0-0.026-0.01038.0230.1350.1350.0000.0000.0000.000
201H181VAL00.0470.01539.776-0.235-0.2350.0000.0000.0000.000
202H182VAL00.0010.00140.8150.2000.2000.0000.0000.0000.000
203H183THR0-0.0160.00043.075-0.140-0.1400.0000.0000.0000.000
204H184VAL00.0110.00245.3060.0960.0960.0000.0000.0000.000
205H185PRO00.1020.04948.078-0.086-0.0860.0000.0000.0000.000
206H186SER00.0030.00751.409-0.012-0.0120.0000.0000.0000.000
207H187SER00.0100.00654.383-0.046-0.0460.0000.0000.0000.000
208H188SER0-0.022-0.01251.936-0.021-0.0210.0000.0000.0000.000
209H189LEU00.018-0.00352.3140.0500.0500.0000.0000.0000.000
210H190GLY0-0.009-0.00155.151-0.094-0.0940.0000.0000.0000.000
211H191THR0-0.0190.00155.448-0.072-0.0720.0000.0000.0000.000
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