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: VYVV1

Calculation Name: 2F1D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | manganese (ii) ion

Ligand 3-letter code: SO4 | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F1D

Chain ID: A

ChEMBL ID:

UniProt ID: P34047

Base Structure: X-ray

Registration Date: 2025-10-05

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 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1950408.685271
FMO2-HF: Nuclear repulsion 1880851.145687
FMO2-HF: Total energy -69557.539584
FMO2-MP2: Total energy -69764.294673


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:10:GLY)


Summations of interaction energy for fragment #1(A:10:GLY)
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.
-215.675-210.39512.866-10.744-7.401-0.119
Interaction energy analysis for fragmet #1(A:10:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.763 / q_NPA : 0.868
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].
3A12ILE00.001-0.0033.081-0.4850.6910.042-0.406-0.812-0.001
20A29ASN0-0.040-0.0231.859-38.992-38.2018.132-5.416-3.506-0.073
21A30LEU00.0270.0014.5835.9266.049-0.001-0.012-0.1100.000
22A31ASP-1-0.812-0.8672.103-70.429-68.2614.672-4.311-2.529-0.040
23A32GLY0-0.015-0.0013.445-15.903-14.8810.021-0.599-0.444-0.005
4A13GLY0-0.0010.0275.4455.0515.0510.0000.0000.0000.000
5A14GLU-1-0.856-0.9309.121-28.278-28.2780.0000.0000.0000.000
6A15VAL0-0.035-0.01911.7281.4101.4100.0000.0000.0000.000
7A16LYS10.8830.95015.43315.36815.3680.0000.0000.0000.000
8A17ARG10.8980.93218.54813.37013.3700.0000.0000.0000.000
9A18VAL0-0.030-0.01721.8040.0010.0010.0000.0000.0000.000
10A19THR0-0.0060.01525.3950.1100.1100.0000.0000.0000.000
11A20LYS10.8010.89828.5759.6659.6650.0000.0000.0000.000
12A21GLU-1-0.895-0.96229.678-9.930-9.9300.0000.0000.0000.000
13A22THR0-0.045-0.04625.628-0.223-0.2230.0000.0000.0000.000
14A23ASN0-0.010-0.00223.721-0.621-0.6210.0000.0000.0000.000
15A24VAL00.0550.02519.171-0.180-0.1800.0000.0000.0000.000
16A25SER0-0.025-0.02516.4390.1290.1290.0000.0000.0000.000
17A26VAL00.0260.02112.8490.1910.1910.0000.0000.0000.000
18A27LYS10.8250.9057.85731.70931.7090.0000.0000.0000.000
19A28ILE00.0340.0207.9950.7510.7510.0000.0000.0000.000
24A33THR0-0.073-0.0515.6054.1944.1940.0000.0000.0000.000
25A34GLY00.0310.0269.0453.0853.0850.0000.0000.0000.000
26A35VAL0-0.073-0.0309.8992.5122.5120.0000.0000.0000.000
27A36ALA00.0360.02211.358-1.374-1.3740.0000.0000.0000.000
28A37ASP-1-0.796-0.87813.952-18.360-18.3600.0000.0000.0000.000
29A38SER0-0.021-0.00115.504-0.467-0.4670.0000.0000.0000.000
30A39SER00.002-0.00317.7290.8630.8630.0000.0000.0000.000
31A40SER0-0.040-0.07021.0470.2550.2550.0000.0000.0000.000
32A41GLY00.0090.00622.5050.3850.3850.0000.0000.0000.000
33A42ILE0-0.043-0.00624.9480.5330.5330.0000.0000.0000.000
34A43PRO00.0290.00224.881-0.403-0.4030.0000.0000.0000.000
35A44PHE00.0140.00524.983-0.298-0.2980.0000.0000.0000.000
36A45LEU00.0150.00621.427-0.322-0.3220.0000.0000.0000.000
37A46ASP-1-0.790-0.86820.320-15.215-15.2150.0000.0000.0000.000
38A47HIS00.0150.00219.907-1.002-1.0020.0000.0000.0000.000
39A48MET0-0.025-0.01320.950-0.351-0.3510.0000.0000.0000.000
40A49LEU0-0.033-0.01516.046-0.835-0.8350.0000.0000.0000.000
41A50ASP-1-0.843-0.92715.897-18.064-18.0640.0000.0000.0000.000
42A51GLN0-0.072-0.02616.933-0.593-0.5930.0000.0000.0000.000
43A52LEU0-0.018-0.01213.705-0.473-0.4730.0000.0000.0000.000
44A53ALA00.0010.00412.122-1.171-1.1710.0000.0000.0000.000
45A54SER0-0.017-0.02812.589-0.973-0.9730.0000.0000.0000.000
46A55HIS0-0.022-0.00815.0800.0840.0840.0000.0000.0000.000
47A56GLY0-0.0050.00912.7910.5010.5010.0000.0000.0000.000
48A57LEU0-0.050-0.02610.036-1.280-1.2800.0000.0000.0000.000
49A58PHE00.0080.0167.679-3.373-3.3730.0000.0000.0000.000
50A59ASP-1-0.801-0.8905.813-43.258-43.2580.0000.0000.0000.000
51A60VAL0-0.005-0.0178.233-1.908-1.9080.0000.0000.0000.000
52A61HIS0-0.067-0.03111.0562.3282.3280.0000.0000.0000.000
53A62VAL00.027-0.00712.896-0.183-0.1830.0000.0000.0000.000
54A63ARG10.7800.87116.25418.37718.3770.0000.0000.0000.000
55A64ALA0-0.019-0.00519.364-0.178-0.1780.0000.0000.0000.000
56A65THR0-0.004-0.00622.4910.3620.3620.0000.0000.0000.000
57A66GLY00.0710.02726.305-0.215-0.2150.0000.0000.0000.000
58A67ASP-1-0.771-0.84528.925-9.707-9.7070.0000.0000.0000.000
59A68VAL00.0300.00929.4090.2110.2110.0000.0000.0000.000
60A69HIS0-0.038-0.01332.1480.0360.0360.0000.0000.0000.000
61A70ILE0-0.096-0.03835.1250.3200.3200.0000.0000.0000.000
62A71ASP-1-0.824-0.94033.729-9.328-9.3280.0000.0000.0000.000
63A72ASP-1-0.839-0.92529.204-10.876-10.8760.0000.0000.0000.000
64A73HIS0-0.043-0.01828.659-0.415-0.4150.0000.0000.0000.000
65A74HIS0-0.048-0.04528.473-0.247-0.2470.0000.0000.0000.000
66A75THR00.0420.01725.023-0.433-0.4330.0000.0000.0000.000
67A76ASN00.0330.01724.262-0.865-0.8650.0000.0000.0000.000
68A77GLU-1-0.843-0.91023.680-11.763-11.7630.0000.0000.0000.000
69A78ASP-1-0.750-0.85623.492-13.012-13.0120.0000.0000.0000.000
70A79ILE0-0.023-0.01118.799-0.890-0.8900.0000.0000.0000.000
71A80ALA00.0030.02418.908-1.047-1.0470.0000.0000.0000.000
72A81LEU0-0.012-0.00219.408-0.747-0.7470.0000.0000.0000.000
73A82ALA0-0.0260.00417.589-0.643-0.6430.0000.0000.0000.000
74A83ILE00.0330.01114.399-1.414-1.4140.0000.0000.0000.000
75A84GLY00.0200.01914.535-1.478-1.4780.0000.0000.0000.000
76A85THR0-0.020-0.02715.869-0.473-0.4730.0000.0000.0000.000
77A86ALA0-0.061-0.03611.684-0.843-0.8430.0000.0000.0000.000
78A87LEU00.0490.02311.126-2.778-2.7780.0000.0000.0000.000
79A88LEU00.0030.00411.665-1.669-1.6690.0000.0000.0000.000
80A89LYS10.8340.89712.03221.75721.7570.0000.0000.0000.000
81A90ALA00.0070.0177.240-1.463-1.4630.0000.0000.0000.000
82A91LEU0-0.013-0.0077.936-2.789-2.7890.0000.0000.0000.000
83A92GLY00.0110.01910.390-0.077-0.0770.0000.0000.0000.000
84A93GLU-1-0.854-0.94111.833-16.409-16.4090.0000.0000.0000.000
85A94ARG10.8880.95712.14519.82819.8280.0000.0000.0000.000
86A95LYS10.7910.88012.53919.66719.6670.0000.0000.0000.000
87A96GLY00.0430.02011.806-1.571-1.5710.0000.0000.0000.000
88A97ILE0-0.039-0.00310.123-0.695-0.6950.0000.0000.0000.000
89A98ASN00.0350.01512.7931.9551.9550.0000.0000.0000.000
90A99ARG10.7890.88514.78516.39616.3960.0000.0000.0000.000
91A100PHE0-0.016-0.02916.4420.3550.3550.0000.0000.0000.000
92A101GLY00.0100.01217.856-0.809-0.8090.0000.0000.0000.000
93A102ASP-1-0.838-0.88318.992-11.990-11.9900.0000.0000.0000.000
94A103PHE00.004-0.00520.709-0.337-0.3370.0000.0000.0000.000
95A104THR00.0170.00122.8540.4040.4040.0000.0000.0000.000
96A105ALA0-0.0140.00523.369-0.135-0.1350.0000.0000.0000.000
97A106PRO00.0020.00225.4860.2640.2640.0000.0000.0000.000
98A107LEU0-0.071-0.04026.641-0.513-0.5130.0000.0000.0000.000
99A108ASP-1-0.878-0.94129.294-9.718-9.7180.0000.0000.0000.000
100A109GLU-1-0.703-0.82332.935-9.361-9.3610.0000.0000.0000.000
101A110ALA0-0.022-0.01230.5850.0980.0980.0000.0000.0000.000
102A111LEU0-0.027-0.01729.478-0.232-0.2320.0000.0000.0000.000
103A112ILE00.0040.00726.5230.2720.2720.0000.0000.0000.000
104A113HIS0-0.015-0.00926.2090.0480.0480.0000.0000.0000.000
105A114VAL0-0.019-0.02121.5290.0970.0970.0000.0000.0000.000
106A115SER0-0.030-0.03123.012-0.274-0.2740.0000.0000.0000.000
107A116LEU0-0.034-0.01717.1420.2610.2610.0000.0000.0000.000
108A117ASP-1-0.785-0.87619.878-14.696-14.6960.0000.0000.0000.000
109A118LEU00.0020.02313.5860.2090.2090.0000.0000.0000.000
110A119SER0-0.071-0.05217.723-0.359-0.3590.0000.0000.0000.000
111A120GLY0-0.032-0.01220.1710.2920.2920.0000.0000.0000.000
112A121ARG10.9090.95221.16313.14713.1470.0000.0000.0000.000
113A122PRO0-0.0010.01923.701-0.143-0.1430.0000.0000.0000.000
114A123TYR0-0.030-0.03124.6170.6280.6280.0000.0000.0000.000
115A124LEU00.0260.01625.050-0.589-0.5890.0000.0000.0000.000
116A125GLY0-0.0190.00727.1660.4940.4940.0000.0000.0000.000
117A126TYR00.0630.01627.574-0.345-0.3450.0000.0000.0000.000
118A127ASN0-0.070-0.04530.0650.2410.2410.0000.0000.0000.000
119A128LEU00.0190.00428.559-0.088-0.0880.0000.0000.0000.000
120A129GLU-1-0.908-0.95632.552-8.345-8.3450.0000.0000.0000.000
121A130ILE0-0.019-0.00430.576-0.159-0.1590.0000.0000.0000.000
122A131PRO00.0410.03434.9830.0960.0960.0000.0000.0000.000
123A132THR0-0.059-0.01835.8770.1850.1850.0000.0000.0000.000
124A133GLN00.0520.01636.073-0.201-0.2010.0000.0000.0000.000
125A134ARG10.8650.92034.4308.8548.8540.0000.0000.0000.000
126A135VAL00.0020.03329.9380.1910.1910.0000.0000.0000.000
127A136GLY00.0090.00431.704-0.287-0.2870.0000.0000.0000.000
128A137THR0-0.005-0.02332.2150.2330.2330.0000.0000.0000.000
129A138TYR0-0.026-0.01125.9300.1360.1360.0000.0000.0000.000
130A139ASP-1-0.802-0.89931.285-9.037-9.0370.0000.0000.0000.000
131A140THR00.024-0.00631.173-0.439-0.4390.0000.0000.0000.000
132A141GLN0-0.022-0.00631.159-0.122-0.1220.0000.0000.0000.000
133A142LEU0-0.049-0.02327.996-0.261-0.2610.0000.0000.0000.000
134A143VAL00.0290.02626.033-0.584-0.5840.0000.0000.0000.000
135A144GLU-1-0.897-0.94126.001-10.648-10.6480.0000.0000.0000.000
136A145HIS10.7920.89626.94110.94810.9480.0000.0000.0000.000
137A146PHE00.0400.02618.449-0.403-0.4030.0000.0000.0000.000
138A147PHE00.0440.00920.360-0.505-0.5050.0000.0000.0000.000
139A148GLN00.0210.01123.016-0.125-0.1250.0000.0000.0000.000
140A149SER0-0.047-0.04423.3660.1270.1270.0000.0000.0000.000
141A150LEU0-0.0030.00716.894-0.388-0.3880.0000.0000.0000.000
142A151VAL0-0.018-0.01219.683-0.687-0.6870.0000.0000.0000.000
143A152ASN0-0.009-0.01921.851-0.179-0.1790.0000.0000.0000.000
144A153THR0-0.053-0.03219.5780.0720.0720.0000.0000.0000.000
145A154SER0-0.020-0.00516.788-1.006-1.0060.0000.0000.0000.000
146A155GLY0-0.0210.00318.088-0.508-0.5080.0000.0000.0000.000
147A156MET0-0.050-0.01416.7280.0980.0980.0000.0000.0000.000
148A157THR00.0120.00920.4770.8180.8180.0000.0000.0000.000
149A158LEU0-0.002-0.00121.029-0.568-0.5680.0000.0000.0000.000
150A159HIS00.0070.01123.6010.2940.2940.0000.0000.0000.000
151A160ILE00.0380.01123.725-0.413-0.4130.0000.0000.0000.000
152A161ARG10.8580.91926.89810.79210.7920.0000.0000.0000.000
153A162GLN00.0330.02829.804-0.417-0.4170.0000.0000.0000.000
154A163LEU0-0.068-0.03731.1270.2940.2940.0000.0000.0000.000
155A164ALA00.0040.00833.2230.3390.3390.0000.0000.0000.000
156A165GLY00.0090.00533.194-0.387-0.3870.0000.0000.0000.000
157A166GLU-1-0.982-0.98134.792-7.895-7.8950.0000.0000.0000.000
158A167ASN0-0.010-0.01833.525-0.193-0.1930.0000.0000.0000.000
159A168SER00.057-0.00633.026-0.271-0.2710.0000.0000.0000.000
160A169HIS0-0.016-0.00327.604-0.066-0.0660.0000.0000.0000.000
161A170HIS10.7830.86528.7979.4089.4080.0000.0000.0000.000
162A171ILE00.0380.03228.693-0.434-0.4340.0000.0000.0000.000
163A172ILE00.0170.01825.703-0.425-0.4250.0000.0000.0000.000
164A173GLU-1-0.776-0.89223.998-13.105-13.1050.0000.0000.0000.000
165A174ALA0-0.019-0.00823.683-0.648-0.6480.0000.0000.0000.000
166A175THR00.020-0.00224.012-0.315-0.3150.0000.0000.0000.000
167A176PHE0-0.003-0.00619.125-0.520-0.5200.0000.0000.0000.000
168A177LYS10.8630.94719.44612.28312.2830.0000.0000.0000.000
169A178ALA0-0.004-0.00619.826-0.698-0.6980.0000.0000.0000.000
170A179PHE00.0280.00416.737-0.588-0.5880.0000.0000.0000.000
171A180ALA0-0.0020.00215.546-0.817-0.8170.0000.0000.0000.000
172A181ARG10.8850.94315.24115.49015.4900.0000.0000.0000.000
173A182ALA00.0140.01216.704-0.557-0.5570.0000.0000.0000.000
174A183LEU00.0170.00112.679-0.446-0.4460.0000.0000.0000.000
175A184ARG10.8500.92111.27922.18922.1890.0000.0000.0000.000
176A185GLN0-0.0030.00212.350-0.524-0.5240.0000.0000.0000.000
177A186ALA00.0320.02514.639-0.072-0.0720.0000.0000.0000.000
178A187THR0-0.050-0.0499.173-1.054-1.0540.0000.0000.0000.000
179A188GLU-1-0.815-0.8799.219-26.908-26.9080.0000.0000.0000.000
180A189THR0-0.050-0.0348.9680.3950.3950.0000.0000.0000.000
181A190ASP-1-0.889-0.94711.692-15.735-15.7350.0000.0000.0000.000
182A191PRO0-0.104-0.05215.458-0.273-0.2730.0000.0000.0000.000
183A192ARG00.0080.02317.0660.7140.7140.0000.0000.0000.000