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: YMYR2

Calculation Name: 5B5H-A-Xray549

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5B5H

Chain ID: A

ChEMBL ID:

UniProt ID: Q76CE8

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2281176.321174
FMO2-HF: Nuclear repulsion 2204965.515619
FMO2-HF: Total energy -76210.805555
FMO2-MP2: Total energy -76437.964183


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-33.312-34.97818.365-9.44-7.259-0.097
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.886
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].
3A3PRO0-0.0310.0013.665-3.114-1.9590.004-0.564-0.5950.000
117A117PRO00.0000.0082.6031.2721.9680.497-0.317-0.876-0.002
118A118GLY0-0.009-0.0034.785-0.1120.055-0.001-0.012-0.1540.000
137A137THR00.0210.0004.2975.5325.609-0.001-0.005-0.0710.000
139A139THR0-0.037-0.0294.7291.7711.858-0.001-0.008-0.0780.000
140A140ASP-1-0.798-0.8501.674-125.751-130.04017.862-8.383-5.190-0.094
141A141THR0-0.014-0.0373.48211.42311.8640.005-0.151-0.295-0.001
4A4THR00.0460.0286.286-3.965-3.9650.0000.0000.0000.000
5A5ALA00.0750.0428.0442.0972.0970.0000.0000.0000.000
6A6VAL00.0160.0119.5511.4661.4660.0000.0000.0000.000
7A7PRO0-0.034-0.00213.2990.1480.1480.0000.0000.0000.000
8A8LEU00.0460.00016.0430.8310.8310.0000.0000.0000.000
9A9GLY00.0160.01618.4780.8090.8090.0000.0000.0000.000
10A10THR0-0.038-0.05421.099-0.111-0.1110.0000.0000.0000.000
11A11ALA00.0450.01622.0730.3580.3580.0000.0000.0000.000
12A12GLY0-0.021-0.00720.229-0.161-0.1610.0000.0000.0000.000
13A13ASN0-0.067-0.02620.858-0.375-0.3750.0000.0000.0000.000
14A14TYR0-0.045-0.00523.5730.4020.4020.0000.0000.0000.000
15A15ALA00.0030.01422.913-0.819-0.8190.0000.0000.0000.000
16A16ILE0-0.030-0.02124.305-0.280-0.2800.0000.0000.0000.000
17A17LEU0-0.0090.00025.2550.2870.2870.0000.0000.0000.000
18A18ALA00.0020.01127.299-0.264-0.2640.0000.0000.0000.000
19A19SER00.035-0.00730.0200.0100.0100.0000.0000.0000.000
20A20ALA0-0.055-0.03932.5350.2940.2940.0000.0000.0000.000
21A21GLY00.0260.00134.0040.3180.3180.0000.0000.0000.000
22A22VAL0-0.025-0.00431.648-0.374-0.3740.0000.0000.0000.000
23A23SER00.0030.00934.0780.2200.2200.0000.0000.0000.000
24A24THR0-0.011-0.00534.484-0.333-0.3330.0000.0000.0000.000
25A25VAL0-0.0050.00136.3850.3000.3000.0000.0000.0000.000
26A26PRO00.0190.02937.829-0.146-0.1460.0000.0000.0000.000
27A27GLN0-0.028-0.00436.3640.3360.3360.0000.0000.0000.000
28A28SER00.0230.00932.814-0.132-0.1320.0000.0000.0000.000
29A29VAL0-0.021-0.01630.4370.2170.2170.0000.0000.0000.000
30A30ILE00.0020.00728.032-0.403-0.4030.0000.0000.0000.000
31A31THR0-0.027-0.00926.3240.3650.3650.0000.0000.0000.000
32A32GLY00.0500.01925.901-0.663-0.6630.0000.0000.0000.000
33A33ALA0-0.021-0.00126.8790.4150.4150.0000.0000.0000.000
34A34VAL00.019-0.00227.710-0.398-0.3980.0000.0000.0000.000
35A35GLY00.0140.00529.6040.3290.3290.0000.0000.0000.000
36A36LEU0-0.040-0.00730.786-0.237-0.2370.0000.0000.0000.000
37A37SER00.0210.01532.5690.3330.3330.0000.0000.0000.000
38A38PRO00.0370.01732.674-0.347-0.3470.0000.0000.0000.000
39A39ALA0-0.016-0.00936.0400.2690.2690.0000.0000.0000.000
40A40ALA00.0320.01937.676-0.124-0.1240.0000.0000.0000.000
41A41ALA00.0630.00139.465-0.119-0.1190.0000.0000.0000.000
42A42THR0-0.021-0.00340.517-0.022-0.0220.0000.0000.0000.000
43A43PHE0-0.040-0.02038.1330.0630.0630.0000.0000.0000.000
44A44LEU0-0.0200.00634.748-0.323-0.3230.0000.0000.0000.000
45A45THR00.004-0.00737.9320.2160.2160.0000.0000.0000.000
46A46GLY00.0410.01038.441-0.200-0.2000.0000.0000.0000.000
47A47PHE00.017-0.01833.4000.0410.0410.0000.0000.0000.000
48A48SER0-0.0470.00339.1510.0570.0570.0000.0000.0000.000
49A49LEU00.0050.01238.192-0.006-0.0060.0000.0000.0000.000
50A50THR00.0220.02041.6200.2780.2780.0000.0000.0000.000
51A51MET00.0020.00241.580-0.273-0.2730.0000.0000.0000.000
52A52SER0-0.0100.01740.4660.1760.1760.0000.0000.0000.000
53A53SER00.0230.00242.5520.0210.0210.0000.0000.0000.000
54A54THR0-0.003-0.00241.6100.0580.0580.0000.0000.0000.000
55A55GLY00.0320.01843.6630.0290.0290.0000.0000.0000.000
56A56THR0-0.033-0.01338.628-0.163-0.1630.0000.0000.0000.000
57A57PHE00.0400.02736.376-0.224-0.2240.0000.0000.0000.000
58A58SER0-0.0040.00237.3690.2860.2860.0000.0000.0000.000
59A59THR00.005-0.00136.982-0.265-0.2650.0000.0000.0000.000
60A60SER00.050-0.01336.6420.1320.1320.0000.0000.0000.000
61A61THR00.0240.01137.240-0.211-0.2110.0000.0000.0000.000
62A62GLN00.0180.01935.277-0.207-0.2070.0000.0000.0000.000
63A63VAL0-0.012-0.00831.381-0.329-0.3290.0000.0000.0000.000
64A64THR00.0120.02130.4370.2700.2700.0000.0000.0000.000
65A65GLY00.010-0.01330.136-0.525-0.5250.0000.0000.0000.000
66A66GLN0-0.0220.00131.6770.2520.2520.0000.0000.0000.000
67A67LEU00.0110.00932.152-0.343-0.3430.0000.0000.0000.000
68A68THR0-0.012-0.01732.6230.2340.2340.0000.0000.0000.000
69A69ALA00.0340.01834.433-0.223-0.2230.0000.0000.0000.000
70A70ALA00.0330.00236.4770.0490.0490.0000.0000.0000.000
71A71ASP-1-0.848-0.91337.715-7.758-7.7580.0000.0000.0000.000
72A72TYR0-0.070-0.03738.0080.2010.2010.0000.0000.0000.000
73A73GLY00.0370.01540.8430.0100.0100.0000.0000.0000.000
74A74THR00.010-0.00139.880-0.271-0.2710.0000.0000.0000.000
75A75PRO00.0430.01336.2850.1240.1240.0000.0000.0000.000
76A76THR00.000-0.01134.974-0.235-0.2350.0000.0000.0000.000
77A77PRO00.0510.03434.784-0.331-0.3310.0000.0000.0000.000
78A78SER0-0.047-0.01535.103-0.213-0.2130.0000.0000.0000.000
79A79ILE00.0260.01930.312-0.296-0.2960.0000.0000.0000.000
80A80LEU0-0.023-0.00130.247-0.428-0.4280.0000.0000.0000.000
81A81THR0-0.022-0.02930.445-0.259-0.2590.0000.0000.0000.000
82A82THR0-0.042-0.02227.414-0.159-0.1590.0000.0000.0000.000
83A83ALA00.0310.02526.135-0.425-0.4250.0000.0000.0000.000
84A84ILE0-0.012-0.01325.878-0.564-0.5640.0000.0000.0000.000
85A85GLY00.0290.02226.932-0.249-0.2490.0000.0000.0000.000
86A86ASP-1-0.794-0.86522.666-13.476-13.4760.0000.0000.0000.000
87A87MET0-0.0280.00322.126-0.900-0.9000.0000.0000.0000.000
88A88GLY0-0.007-0.00422.664-0.460-0.4600.0000.0000.0000.000
89A89THR0-0.015-0.02220.741-0.284-0.2840.0000.0000.0000.000
90A90ALA0-0.013-0.00318.391-0.738-0.7380.0000.0000.0000.000
91A91TYR0-0.021-0.02018.258-0.805-0.8050.0000.0000.0000.000
92A92VAL00.0350.01419.844-0.508-0.5080.0000.0000.0000.000
93A93ASN00.0180.02814.985-1.736-1.7360.0000.0000.0000.000
94A94ALA00.0430.02115.122-1.181-1.1810.0000.0000.0000.000
95A95ALA0-0.005-0.01015.981-0.676-0.6760.0000.0000.0000.000
96A96THR0-0.070-0.05318.5780.1420.1420.0000.0000.0000.000
97A97ARG10.7140.86610.34725.48625.4860.0000.0000.0000.000
98A98SER00.0500.02115.1320.0350.0350.0000.0000.0000.000
99A99GLY00.0200.00913.251-1.195-1.1950.0000.0000.0000.000
100A100PRO0-0.029-0.01811.678-1.771-1.7710.0000.0000.0000.000
101A101ASN00.0010.0027.504-1.480-1.4800.0000.0000.0000.000
102A102PHE00.0030.0047.8481.1941.1940.0000.0000.0000.000
103A103LEU00.0240.00512.770-0.166-0.1660.0000.0000.0000.000
104A104GLU-1-0.765-0.86016.456-13.860-13.8600.0000.0000.0000.000
105A105ILE00.0270.02813.9130.5640.5640.0000.0000.0000.000
106A106TYR00.022-0.01314.6010.3790.3790.0000.0000.0000.000
107A107THR00.0120.01620.0910.5900.5900.0000.0000.0000.000
108A108GLY00.0370.02920.2830.4640.4640.0000.0000.0000.000
109A109ALA00.0070.00821.253-0.041-0.0410.0000.0000.0000.000
110A110LEU00.008-0.00116.654-0.278-0.2780.0000.0000.0000.000
111A111GLY0-0.010-0.00318.984-0.401-0.4010.0000.0000.0000.000
112A112GLY0-0.001-0.00420.7980.2440.2440.0000.0000.0000.000
113A113LYS10.7820.91116.22114.42414.4240.0000.0000.0000.000
114A114ILE00.0390.00911.581-0.168-0.1680.0000.0000.0000.000
115A115LEU0-0.020-0.00910.9580.2100.2100.0000.0000.0000.000
116A116PRO00.0580.0416.324-1.603-1.6030.0000.0000.0000.000
119A119LEU0-0.061-0.0196.5611.1791.1790.0000.0000.0000.000
120A120TYR0-0.019-0.0408.8212.4022.4020.0000.0000.0000.000
121A121LYS10.9120.95912.61716.81216.8120.0000.0000.0000.000
122A122TRP0-0.024-0.02114.880-0.284-0.2840.0000.0000.0000.000
123A123THR0-0.055-0.07419.6870.2940.2940.0000.0000.0000.000
124A124SER00.0070.00122.8660.4150.4150.0000.0000.0000.000
125A125PRO0-0.021-0.01823.587-0.394-0.3940.0000.0000.0000.000
126A126VAL0-0.0010.02119.195-0.227-0.2270.0000.0000.0000.000
127A127GLY00.0410.00722.2850.3280.3280.0000.0000.0000.000
128A128ALA0-0.069-0.01621.043-0.227-0.2270.0000.0000.0000.000
129A129SER00.0590.02023.1450.1000.1000.0000.0000.0000.000
130A130ALA0-0.022-0.02224.0440.4710.4710.0000.0000.0000.000
131A131ASP-1-0.782-0.89621.006-13.615-13.6150.0000.0000.0000.000
132A132PHE0-0.021-0.00715.4810.0990.0990.0000.0000.0000.000
133A133THR0-0.0110.00013.5220.0990.0990.0000.0000.0000.000
134A134ILE00.0120.0139.792-0.508-0.5080.0000.0000.0000.000
135A135ILE0-0.018-0.0138.9990.7630.7630.0000.0000.0000.000
136A136GLY00.033-0.0015.853-3.352-3.3520.0000.0000.0000.000
138A138SER0-0.0020.0046.602-2.721-2.7210.0000.0000.0000.000
142A142TRP0-0.032-0.0246.043-4.466-4.4660.0000.0000.0000.000
143A143ILE0-0.0300.0008.9102.3272.3270.0000.0000.0000.000
144A144PHE00.0060.00411.598-0.330-0.3300.0000.0000.0000.000
145A145GLN0-0.010-0.02014.6171.7371.7370.0000.0000.0000.000
146A146ILE0-0.019-0.00917.2500.1660.1660.0000.0000.0000.000
147A147ALA00.0070.00820.5290.3310.3310.0000.0000.0000.000
148A148GLY00.0350.02423.8660.5650.5650.0000.0000.0000.000
149A149THR0-0.014-0.01725.279-0.264-0.2640.0000.0000.0000.000
150A150LEU00.0050.00920.098-0.358-0.3580.0000.0000.0000.000
151A151GLY00.0090.00423.9380.4110.4110.0000.0000.0000.000
152A152LEU0-0.060-0.02021.716-0.453-0.4530.0000.0000.0000.000
153A153ALA00.0460.02224.6740.3780.3780.0000.0000.0000.000
154A154ALA00.025-0.00127.342-0.270-0.2700.0000.0000.0000.000
155A155GLY0-0.055-0.02528.7790.0300.0300.0000.0000.0000.000
156A156LYS10.8340.94324.23410.88910.8890.0000.0000.0000.000
157A157LYS10.9290.95221.68812.16212.1620.0000.0000.0000.000
158A158ILE00.0050.03215.878-0.200-0.2000.0000.0000.0000.000
159A159ILE0-0.025-0.02416.4420.1270.1270.0000.0000.0000.000
160A160LEU0-0.0040.01112.746-1.122-1.1220.0000.0000.0000.000
161A161ALA00.0240.00312.1831.3661.3660.0000.0000.0000.000
162A162GLY00.0170.00010.155-2.236-2.2360.0000.0000.0000.000
163A163GLY00.0170.00310.418-0.874-0.8740.0000.0000.0000.000
164A164ALA0-0.0370.0058.636-0.205-0.2050.0000.0000.0000.000
165A165GLN0-0.004-0.0329.5895.4205.4200.0000.0000.0000.000
166A166ALA00.0490.01511.159-1.522-1.5220.0000.0000.0000.000
167A167LYS10.9610.98811.83123.80523.8050.0000.0000.0000.000
168A168ASN0-0.080-0.0317.0413.5523.5520.0000.0000.0000.000
169A169ILE0-0.0120.0059.294-3.005-3.0050.0000.0000.0000.000
170A170VAL0-0.013-0.00111.7302.2882.2880.0000.0000.0000.000
171A171TRP0-0.001-0.00714.161-0.530-0.5300.0000.0000.0000.000
172A172VAL0-0.0090.00516.6260.9090.9090.0000.0000.0000.000
173A173VAL00.0130.00518.794-0.009-0.0090.0000.0000.0000.000
174A174ALA0-0.020-0.00122.0820.3780.3780.0000.0000.0000.000
175A175GLY00.0490.02725.2530.5420.5420.0000.0000.0000.000
176A176ALA0-0.0030.00226.368-0.309-0.3090.0000.0000.0000.000
177A177VAL00.009-0.00623.323-0.257-0.2570.0000.0000.0000.000
178A178SER0-0.025-0.01926.2530.5790.5790.0000.0000.0000.000
179A179ILE0-0.0090.00123.597-0.355-0.3550.0000.0000.0000.000
180A180GLU-1-0.841-0.93327.151-9.915-9.9150.0000.0000.0000.000
181A181ALA00.002-0.00829.344-0.212-0.2120.0000.0000.0000.000
182A182GLY00.0180.00530.273-0.053-0.0530.0000.0000.0000.000
183A183ALA0-0.0300.01025.414-0.230-0.2300.0000.0000.0000.000
184A184LYS10.8020.88519.19716.13216.1320.0000.0000.0000.000
185A185PHE00.0600.00518.900-0.486-0.4860.0000.0000.0000.000
186A186GLU-1-0.797-0.88915.833-17.340-17.3400.0000.0000.0000.000
187A187GLY00.0180.01215.246-0.877-0.8770.0000.0000.0000.000
188A188VAL0-0.026-0.02015.6201.4541.4540.0000.0000.0000.000
189A189ILE0-0.006-0.00117.335-0.590-0.5900.0000.0000.0000.000
190A190LEU0-0.014-0.00217.2290.4540.4540.0000.0000.0000.000
191A191ALA00.0260.01020.746-0.156-0.1560.0000.0000.0000.000
192A192LYS10.8860.94124.03011.85911.8590.0000.0000.0000.000
193A193THR0-0.023-0.02526.5210.5650.5650.0000.0000.0000.000
194A194ALA00.0080.02328.086-0.275-0.2750.0000.0000.0000.000
195A195VAL00.0120.00525.433-0.331-0.3310.0000.0000.0000.000
196A196THR0-0.046-0.01828.4140.4130.4130.0000.0000.0000.000
197A197LEU00.0660.04026.203-0.324-0.3240.0000.0000.0000.000
198A198LYS10.8810.94729.8769.6659.6650.0000.0000.0000.000
199A199THR00.0610.03031.905-0.220-0.2200.0000.0000.0000.000
200A200GLY00.0300.01532.562-0.043-0.0430.0000.0000.0000.000
201A201SER0-0.087-0.02927.918-0.335-0.3350.0000.0000.0000.000
202A202SER0-0.008-0.02025.2880.0240.0240.0000.0000.0000.000
203A203LEU0-0.0140.00321.155-0.292-0.2920.0000.0000.0000.000
204A204ASN0-0.040-0.02018.8560.8450.8450.0000.0000.0000.000
205A205GLY00.035-0.00118.274-1.111-1.1110.0000.0000.0000.000
206A206ARG10.7500.85418.27316.95716.9570.0000.0000.0000.000
207A207ILE0-0.0020.00221.143-0.371-0.3710.0000.0000.0000.000
208A208LEU0-0.0020.00220.0720.5320.5320.0000.0000.0000.000
209A209SER00.011-0.00623.757-0.171-0.1710.0000.0000.0000.000
210A210GLN00.0350.01524.6950.6800.6800.0000.0000.0000.000
211A211THR00.0130.00528.5880.3220.3220.0000.0000.0000.000
212A212ALA00.0260.02231.4230.1510.1510.0000.0000.0000.000
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