FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: N8K1Q

Calculation Name: 5H4U-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5H4U

Chain ID: A

ChEMBL ID:

UniProt ID: D3GDK4

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2308956.590479
FMO2-HF: Nuclear repulsion 2227374.831108
FMO2-HF: Total energy -81581.759372
FMO2-MP2: Total energy -81806.471294


3D Structure Molmil
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(A:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
42.71849.8232.513-3.695-5.922-0.034
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.825 / q_NPA : 0.916
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].
3A3SER0-0.023-0.0113.3451.1883.2330.046-0.877-1.214-0.003
4A4GLY00.0610.0405.0890.8890.916-0.001-0.004-0.0220.000
184A189THR0-0.024-0.0323.135-3.322-2.8250.150-0.109-0.5380.000
185A190GLN00.0170.0272.260-11.237-8.6871.382-1.557-2.375-0.014
186A191VAL0-0.016-0.0132.525-8.311-6.3680.937-1.146-1.734-0.017
187A192ARG10.8430.8995.11829.21629.259-0.001-0.002-0.0390.000
5A5SER0-0.007-0.0068.8221.2371.2370.0000.0000.0000.000
6A6GLY00.0250.00612.344-0.836-0.8360.0000.0000.0000.000
7A7VAL00.0090.02014.4700.7270.7270.0000.0000.0000.000
8A8THR0-0.054-0.05416.234-0.702-0.7020.0000.0000.0000.000
9A9THR0-0.003-0.02018.7380.8770.8770.0000.0000.0000.000
10A10ARG10.7400.86121.16710.66610.6660.0000.0000.0000.000
11A11TYR00.0020.01020.7260.4760.4760.0000.0000.0000.000
12A12TRP00.011-0.02123.776-0.367-0.3670.0000.0000.0000.000
13A13ASP-1-0.772-0.89226.135-11.414-11.4140.0000.0000.0000.000
14A14CYS0-0.098-0.03527.5890.6020.6020.0000.0000.0000.000
15A15CYS0-0.087-0.03426.2430.5660.5660.0000.0000.0000.000
16A16LYS10.8260.92624.84711.42711.4270.0000.0000.0000.000
17A17PRO0-0.0040.00820.4240.0330.0330.0000.0000.0000.000
18A18SER00.002-0.04117.9870.0450.0450.0000.0000.0000.000
19A19CYS00.0140.0119.9330.3860.3860.0000.0000.0000.000
20A20SER0-0.041-0.02418.266-0.228-0.2280.0000.0000.0000.000
21A21TRP0-0.006-0.00320.9890.8530.8530.0000.0000.0000.000
22A22GLY00.0130.00020.679-0.639-0.6390.0000.0000.0000.000
23A23GLY00.002-0.00919.9210.0610.0610.0000.0000.0000.000
24A24LYS10.8070.89916.81614.78814.7880.0000.0000.0000.000
25A25ALA00.011-0.00112.622-1.132-1.1320.0000.0000.0000.000
26A26SER0-0.0060.01213.1221.3311.3310.0000.0000.0000.000
27A27VAL00.010-0.01713.313-1.663-1.6630.0000.0000.0000.000
28A28THR00.0100.00515.6270.6550.6550.0000.0000.0000.000
29A29LYS10.8930.94118.47313.86913.8690.0000.0000.0000.000
30A30PRO00.0320.01218.610-0.789-0.7890.0000.0000.0000.000
31A31VAL0-0.030-0.01317.4960.1880.1880.0000.0000.0000.000
32A32ARG10.8300.90119.98611.99711.9970.0000.0000.0000.000
33A33THR00.0390.02523.426-0.060-0.0600.0000.0000.0000.000
34A34CYS0-0.122-0.04325.3750.6220.6220.0000.0000.0000.000
35A35LYS11.0281.01529.6048.4148.4140.0000.0000.0000.000
36A36ALA00.0670.03532.527-0.144-0.1440.0000.0000.0000.000
37A37ASN00.0440.01834.033-0.324-0.3240.0000.0000.0000.000
38A38GLY00.0610.04130.424-0.004-0.0040.0000.0000.0000.000
39A39ASN00.0170.01129.683-0.572-0.5720.0000.0000.0000.000
40A40THR00.003-0.00230.986-0.064-0.0640.0000.0000.0000.000
41A41THR00.0420.01127.710-0.088-0.0880.0000.0000.0000.000
42A42ILE0-0.054-0.00428.9090.3850.3850.0000.0000.0000.000
43A43ASP-1-0.766-0.87628.602-10.788-10.7880.0000.0000.0000.000
44A44SER0-0.0020.00224.458-0.075-0.0750.0000.0000.0000.000
45A45ASN0-0.021-0.01926.010-0.588-0.5880.0000.0000.0000.000
46A46THR0-0.058-0.02928.4180.3040.3040.0000.0000.0000.000
47A47GLN00.0900.04829.305-0.622-0.6220.0000.0000.0000.000
48A48SER00.0630.01428.2210.1920.1920.0000.0000.0000.000
49A49GLY00.0300.02230.0040.2550.2550.0000.0000.0000.000
50A51ASN0-0.049-0.02128.6070.0940.0940.0000.0000.0000.000
51A52GLY00.0220.01632.9020.1180.1180.0000.0000.0000.000
52A53GLY0-0.030-0.00733.6350.1820.1820.0000.0000.0000.000
53A54SER0-0.026-0.02533.4540.1380.1380.0000.0000.0000.000
54A55SER0-0.039-0.01228.369-0.119-0.1190.0000.0000.0000.000
55A56TYR00.025-0.00828.8840.0720.0720.0000.0000.0000.000
56A57VAL00.0320.03323.795-0.220-0.2200.0000.0000.0000.000
57A59ASN00.003-0.04125.947-0.342-0.3420.0000.0000.0000.000
58A60ASP-1-0.862-0.93224.928-12.190-12.1900.0000.0000.0000.000
59A61GLN0-0.094-0.04920.931-0.414-0.4140.0000.0000.0000.000
60A62GLN00.013-0.00322.307-0.063-0.0630.0000.0000.0000.000
61A63PRO0-0.0180.00220.916-0.399-0.3990.0000.0000.0000.000
62A64PHE0-0.020-0.02518.8660.6190.6190.0000.0000.0000.000
63A65THR00.0100.00720.523-0.373-0.3730.0000.0000.0000.000
64A66GLN0-0.008-0.00718.1130.7660.7660.0000.0000.0000.000
65A67GLY00.0280.02019.700-0.483-0.4830.0000.0000.0000.000
66A68ASN00.014-0.00620.5500.4770.4770.0000.0000.0000.000
67A69VAL0-0.0190.01314.765-0.156-0.1560.0000.0000.0000.000
68A70GLY00.0560.03217.5420.5430.5430.0000.0000.0000.000
69A71TYR0-0.026-0.02614.373-1.030-1.0300.0000.0000.0000.000
70A72GLY00.0590.02116.4360.9700.9700.0000.0000.0000.000
71A73PHE0-0.027-0.00116.241-1.017-1.0170.0000.0000.0000.000
72A74ALA00.0190.01014.8950.5800.5800.0000.0000.0000.000
73A75ALA00.0050.01416.474-0.373-0.3730.0000.0000.0000.000
74A76ALA0-0.007-0.01213.036-0.407-0.4070.0000.0000.0000.000
75A77SER00.0350.03114.7560.1320.1320.0000.0000.0000.000
76A78ILE0-0.007-0.0058.632-0.290-0.2900.0000.0000.0000.000
77A79SER0-0.013-0.04311.300-0.950-0.9500.0000.0000.0000.000
78A80GLY00.0420.03512.524-0.702-0.7020.0000.0000.0000.000
79A81GLN0-0.036-0.0235.830-0.120-0.1200.0000.0000.0000.000
80A82PRO00.0270.02310.6191.6371.6370.0000.0000.0000.000
81A83GLU-1-0.674-0.79011.580-18.345-18.3450.0000.0000.0000.000
82A84SER00.0340.02012.342-1.123-1.1230.0000.0000.0000.000
83A85GLN0-0.048-0.0225.9861.0101.0100.0000.0000.0000.000
84A86THR00.0360.0227.763-2.275-2.2750.0000.0000.0000.000
85A88CYS0-0.0550.00811.498-0.944-0.9440.0000.0000.0000.000
86A89ALA00.0270.0317.191-0.822-0.8220.0000.0000.0000.000
87A90CYS0-0.064-0.0237.7874.5964.5960.0000.0000.0000.000
88A91TYR00.0650.0186.229-4.425-4.4250.0000.0000.0000.000
89A92GLU-1-0.867-0.8927.260-20.189-20.1890.0000.0000.0000.000
90A93MET00.0190.0008.643-2.221-2.2210.0000.0000.0000.000
91A94THR0-0.042-0.01011.3841.1541.1540.0000.0000.0000.000
92A95PHE00.0520.01814.043-0.415-0.4150.0000.0000.0000.000
93A96THR0-0.025-0.02516.458-0.095-0.0950.0000.0000.0000.000
94A97ASN00.0610.03218.8470.0320.0320.0000.0000.0000.000
95A98THR00.0500.03922.3780.4370.4370.0000.0000.0000.000
96A99ALA00.0610.02224.280-0.128-0.1280.0000.0000.0000.000
97A100ILE0-0.039-0.00520.7040.1760.1760.0000.0000.0000.000
98A101SER0-0.039-0.01120.212-0.937-0.9370.0000.0000.0000.000
99A102GLY00.0120.00618.1090.4390.4390.0000.0000.0000.000
100A103GLN0-0.026-0.01417.7830.0800.0800.0000.0000.0000.000
101A104LYS10.8570.90710.97819.99219.9920.0000.0000.0000.000
102A105MET0-0.017-0.00214.1471.0771.0770.0000.0000.0000.000
103A106ILE0-0.015-0.01110.340-1.527-1.5270.0000.0000.0000.000
104A107VAL00.0220.00811.8131.3641.3640.0000.0000.0000.000
105A108GLN0-0.002-0.00311.364-0.849-0.8490.0000.0000.0000.000
106A109VAL0-0.0060.00211.4731.3281.3280.0000.0000.0000.000
107A110THR0-0.009-0.01913.560-0.397-0.3970.0000.0000.0000.000
108A111ASN00.0450.01616.6590.7930.7930.0000.0000.0000.000
109A112THR0-0.003-0.01816.242-1.548-1.5480.0000.0000.0000.000
110A113GLY00.0100.00617.3430.8990.8990.0000.0000.0000.000
111A114SER0-0.031-0.02419.3570.4590.4590.0000.0000.0000.000
112A115ASP-1-0.958-0.97618.704-16.906-16.9060.0000.0000.0000.000
113A116LEU00.0040.00819.3400.8350.8350.0000.0000.0000.000
114A117ASN00.0310.01118.361-1.704-1.7040.0000.0000.0000.000
115A118GLY00.0360.04115.6390.5710.5710.0000.0000.0000.000
116A119ASN0-0.059-0.02411.209-1.816-1.8160.0000.0000.0000.000
117A120HIS00.0290.00614.0841.1351.1350.0000.0000.0000.000
118A121PHE0-0.013-0.0179.831-1.069-1.0690.0000.0000.0000.000
119A122ASP-1-0.816-0.87716.125-14.509-14.5090.0000.0000.0000.000
120A123LEU0-0.001-0.01817.281-0.292-0.2920.0000.0000.0000.000
121A124MET0-0.034-0.01219.5850.5230.5230.0000.0000.0000.000
122A125ILE0-0.007-0.01321.7950.0380.0380.0000.0000.0000.000
123A126PRO0-0.029-0.00224.6460.2570.2570.0000.0000.0000.000
124A127GLY00.0530.02028.2070.1200.1200.0000.0000.0000.000
125A128GLY0-0.023-0.01327.1630.2090.2090.0000.0000.0000.000
126A129GLY00.0560.04228.250-0.068-0.0680.0000.0000.0000.000
127A130VAL0-0.075-0.03228.374-0.316-0.3160.0000.0000.0000.000
128A131GLY00.0400.01827.868-0.338-0.3380.0000.0000.0000.000
129A132ILE00.0230.01526.1590.4080.4080.0000.0000.0000.000
130A133PHE00.0320.02425.4170.4710.4710.0000.0000.0000.000
131A134ASN0-0.026-0.04630.130-0.089-0.0890.0000.0000.0000.000
132A135GLY00.0860.04031.1160.2480.2480.0000.0000.0000.000
133A137GLN0-0.042-0.01333.7140.2230.2230.0000.0000.0000.000
134A138SER0-0.024-0.01235.0230.1310.1310.0000.0000.0000.000
135A139GLN0-0.054-0.02030.540-0.057-0.0570.0000.0000.0000.000
136A140TRP0-0.052-0.04931.8200.1870.1870.0000.0000.0000.000
137A141GLY00.0320.03337.3170.1540.1540.0000.0000.0000.000
138A142ALA0-0.039-0.00636.2380.1230.1230.0000.0000.0000.000
139A143PRO00.0680.02837.8050.0830.0830.0000.0000.0000.000
140A144SER00.0780.04037.574-0.240-0.2400.0000.0000.0000.000
141A145ASN0-0.047-0.02836.531-0.059-0.0590.0000.0000.0000.000
142A146GLY00.0440.02133.980-0.280-0.2800.0000.0000.0000.000
143A147TRP0-0.019-0.03231.1400.1510.1510.0000.0000.0000.000
144A148GLY00.0260.01234.108-0.235-0.2350.0000.0000.0000.000
145A149GLN00.0130.00733.8690.1140.1140.0000.0000.0000.000
146A150ARG10.8670.92932.4549.1569.1560.0000.0000.0000.000
147A151TYR00.0210.00728.180-0.242-0.2420.0000.0000.0000.000
148A152GLY00.0460.02628.8350.2550.2550.0000.0000.0000.000
149A153GLY00.0340.01829.840-0.081-0.0810.0000.0000.0000.000
150A154ILE0-0.041-0.01332.0430.2480.2480.0000.0000.0000.000
151A155SER00.0120.01033.225-0.311-0.3110.0000.0000.0000.000
152A156SER0-0.045-0.03534.568-0.110-0.1100.0000.0000.0000.000
153A157GLN0-0.008-0.01234.0500.1270.1270.0000.0000.0000.000
154A158SER00.0350.01635.145-0.061-0.0610.0000.0000.0000.000
155A159GLU-1-0.734-0.87136.753-8.171-8.1710.0000.0000.0000.000
156A160CYS0-0.069-0.01227.027-0.235-0.2350.0000.0000.0000.000
157A161ASN0-0.082-0.04935.548-0.039-0.0390.0000.0000.0000.000
158A162GLN00.0070.00038.2100.2110.2110.0000.0000.0000.000
159A163LEU0-0.0050.01031.847-0.074-0.0740.0000.0000.0000.000
160A164PRO00.0410.02534.2260.2200.2200.0000.0000.0000.000
161A165THR00.0350.01034.715-0.260-0.2600.0000.0000.0000.000
162A166SER0-0.011-0.00432.314-0.069-0.0690.0000.0000.0000.000
163A167LEU00.0040.01128.949-0.328-0.3280.0000.0000.0000.000
164A168ARG10.8950.94630.6377.9397.9390.0000.0000.0000.000
165A169ALA00.0150.03028.4720.0180.0180.0000.0000.0000.000
166A170GLY00.0610.00926.187-0.144-0.1440.0000.0000.0000.000
167A172ASN00.021-0.01329.8170.1630.1630.0000.0000.0000.000
168A173TRP0-0.027-0.01020.0540.0570.0570.0000.0000.0000.000
169A174ARG10.8160.90025.8539.9029.9020.0000.0000.0000.000
170A175PHE00.021-0.00326.867-0.072-0.0720.0000.0000.0000.000
171A176GLY00.0230.02228.7020.1490.1490.0000.0000.0000.000
172A177TRP0-0.032-0.02318.182-0.125-0.1250.0000.0000.0000.000
173A178PHE0-0.002-0.00820.538-0.320-0.3200.0000.0000.0000.000
174A179LYS10.8780.94124.20811.20211.2020.0000.0000.0000.000
175A180ASN00.0060.01227.568-0.004-0.0040.0000.0000.0000.000
176A181ALA0-0.0240.00623.7690.1270.1270.0000.0000.0000.000
177A182ASP-1-0.830-0.91425.487-11.073-11.0730.0000.0000.0000.000
178A183ASN0-0.005-0.00522.784-0.285-0.2850.0000.0000.0000.000
179A184PRO0-0.0270.01420.164-0.149-0.1490.0000.0000.0000.000
180A185SER00.0300.01818.154-0.702-0.7020.0000.0000.0000.000
181A186MET0-0.069-0.02812.342-0.100-0.1000.0000.0000.0000.000
182A187LYS10.9751.00011.27219.71219.7120.0000.0000.0000.000
183A188PHE00.009-0.0127.4270.1920.1920.0000.0000.0000.000
188A194PRO00.0440.03210.6910.9750.9750.0000.0000.0000.000
189A195THR00.0720.01313.2680.3770.3770.0000.0000.0000.000
190A196ILE0-0.0210.00516.4470.4690.4690.0000.0000.0000.000
191A197LEU00.0130.01613.3720.6280.6280.0000.0000.0000.000
192A198THR00.0470.01514.0240.8220.8220.0000.0000.0000.000
193A199GLN0-0.0040.01116.9630.6370.6370.0000.0000.0000.000
194A200LYS10.8700.95419.95013.80413.8040.0000.0000.0000.000
195A201SER0-0.002-0.03516.4620.6210.6210.0000.0000.0000.000
196A202GLN0-0.046-0.02019.6470.4380.4380.0000.0000.0000.000
197A204VAL00.018-0.00313.555-0.948-0.9480.0000.0000.0000.000
198A205ARG10.8470.9097.95930.44030.4400.0000.0000.0000.000
199A206THR00.003-0.01212.062-0.124-0.1240.0000.0000.0000.000
200A207PRO0-0.056-0.02110.9370.7400.7400.0000.0000.0000.000
201A208GLY-1-0.817-0.8628.032-33.443-33.4430.0000.0000.0000.000