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

tag_button

FMODB ID: YRYL2

Calculation Name: 1SFS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1SFS

Chain ID: A

ChEMBL ID:

UniProt ID: P84136

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 211
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2623495.878972
FMO2-HF: Nuclear repulsion 2540965.420812
FMO2-HF: Total energy -82530.45816
FMO2-MP2: Total energy -82775.512378


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:4:GLY)


Summations of interaction energy for fragment #1(A:4: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.
14.83319.6543.015-3.748-4.09-0.035
Interaction energy analysis for fragmet #1(A:4:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.918
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].
3A6TRP00.0760.0263.828-0.963-0.175-0.002-0.234-0.5520.000
174A177TYR0-0.077-0.0652.686-1.554-0.4430.174-0.503-0.782-0.005
175A178GLN0-0.041-0.0164.7015.4625.461-0.001-0.0100.0120.000
201A206LEU0-0.035-0.0133.058-6.826-6.2660.115-0.274-0.402-0.002
202A207ALA00.0150.0083.3856.0716.3680.009-0.137-0.169-0.001
203A208ASP-1-0.820-0.8792.528-63.235-61.1862.721-2.578-2.193-0.027
204A209ARG10.9860.9744.35642.27442.291-0.001-0.012-0.0040.000
4A7GLY00.0250.0036.2552.8802.8800.0000.0000.0000.000
5A8VAL00.0110.0199.244-0.501-0.5010.0000.0000.0000.000
6A9ASP-1-0.832-0.88212.248-20.484-20.4840.0000.0000.0000.000
7A10SER00.0550.01815.019-0.010-0.0100.0000.0000.0000.000
8A11ALA00.0540.03518.8000.2530.2530.0000.0000.0000.000
9A12GLN00.0270.01222.0670.3660.3660.0000.0000.0000.000
10A13VAL0-0.010-0.00222.127-0.748-0.7480.0000.0000.0000.000
11A14VAL0-0.0060.00519.0550.0600.0600.0000.0000.0000.000
12A15THR00.0270.01022.2580.2500.2500.0000.0000.0000.000
13A16ASP-1-0.801-0.87423.494-13.343-13.3430.0000.0000.0000.000
14A17GLN00.0320.01023.730-0.729-0.7290.0000.0000.0000.000
15A18LEU00.0270.03020.481-0.289-0.2890.0000.0000.0000.000
16A19PHE00.0300.00316.938-0.927-0.9270.0000.0000.0000.000
17A20GLN00.005-0.01119.460-1.344-1.3440.0000.0000.0000.000
18A21CYS0-0.0100.01618.994-0.009-0.0090.0000.0000.0000.000
19A22VAL00.0380.02014.981-0.568-0.5680.0000.0000.0000.000
20A23ARG10.8280.91316.62314.59814.5980.0000.0000.0000.000
21A24THR0-0.105-0.06017.619-0.151-0.1510.0000.0000.0000.000
22A25GLU-1-0.870-0.93119.146-14.741-14.7410.0000.0000.0000.000
23A26LEU0-0.072-0.03514.056-0.686-0.6860.0000.0000.0000.000
24A27GLY00.019-0.00512.665-1.581-1.5810.0000.0000.0000.000
25A28TYR00.002-0.01712.6451.2511.2510.0000.0000.0000.000
26A29PRO0-0.0140.02411.006-3.168-3.1680.0000.0000.0000.000
27A30LYS10.8150.8708.59133.47633.4760.0000.0000.0000.000
28A31PHE0-0.043-0.0236.3071.4721.4720.0000.0000.0000.000
29A32TRP00.0480.00111.683-1.247-1.2470.0000.0000.0000.000
30A33GLY0-0.029-0.02013.9760.7890.7890.0000.0000.0000.000
31A34ARG10.7610.84815.23214.54414.5440.0000.0000.0000.000
32A35TYR00.0630.03119.074-0.139-0.1390.0000.0000.0000.000
33A36LEU0-0.054-0.04522.0130.4330.4330.0000.0000.0000.000
34A37SER0-0.052-0.03224.2350.4660.4660.0000.0000.0000.000
35A38GLU-1-0.843-0.91426.643-10.860-10.8600.0000.0000.0000.000
36A39VAL0-0.044-0.02027.3110.2710.2710.0000.0000.0000.000
37A40PRO00.0550.01729.082-0.198-0.1980.0000.0000.0000.000
38A41ASN0-0.045-0.02730.688-0.013-0.0130.0000.0000.0000.000
39A42VAL0-0.0170.01225.127-0.175-0.1750.0000.0000.0000.000
40A43SER0-0.005-0.01123.934-0.589-0.5890.0000.0000.0000.000
41A44GLU-1-0.809-0.87725.457-11.134-11.1340.0000.0000.0000.000
42A45GLY0-0.022-0.01024.909-0.602-0.6020.0000.0000.0000.000
43A46LEU0-0.047-0.01920.883-0.004-0.0040.0000.0000.0000.000
44A47THR00.0300.00425.0000.5520.5520.0000.0000.0000.000
45A48ARG10.8880.93125.87210.08310.0830.0000.0000.0000.000
46A49ASP-1-0.844-0.92226.738-10.621-10.6210.0000.0000.0000.000
47A50GLU-1-0.794-0.86822.425-13.832-13.8320.0000.0000.0000.000
48A51ILE0-0.007-0.00421.945-0.603-0.6030.0000.0000.0000.000
49A52VAL0-0.020-0.01622.398-0.539-0.5390.0000.0000.0000.000
50A53ARG10.8790.94423.42912.18712.1870.0000.0000.0000.000
51A54ILE00.003-0.00617.756-0.343-0.3430.0000.0000.0000.000
52A55ARG10.8960.93819.01614.62614.6260.0000.0000.0000.000
53A56ASN0-0.059-0.01520.2500.1070.1070.0000.0000.0000.000
54A57TYR0-0.060-0.04618.6950.1330.1330.0000.0000.0000.000
55A58GLY00.0150.01717.332-0.875-0.8750.0000.0000.0000.000
56A59VAL0-0.081-0.02213.841-1.433-1.4330.0000.0000.0000.000
57A60LYS10.8140.89812.43020.68920.6890.0000.0000.0000.000
58A61VAL00.0380.00814.704-0.513-0.5130.0000.0000.0000.000
59A62LEU0-0.0050.00211.327-0.252-0.2520.0000.0000.0000.000
60A63PRO0-0.0050.00115.2400.4710.4710.0000.0000.0000.000
61A64ILE00.0230.02016.510-0.260-0.2600.0000.0000.0000.000
62A65TYR0-0.015-0.00819.7400.7590.7590.0000.0000.0000.000
63A66ASN00.0760.00022.734-0.144-0.1440.0000.0000.0000.000
64A67ALA00.0340.04324.5250.2920.2920.0000.0000.0000.000
65A68PHE0-0.123-0.07723.5870.3620.3620.0000.0000.0000.000
66A69ARG10.8540.90625.73411.09011.0900.0000.0000.0000.000
67A70GLU-1-0.763-0.86029.031-10.089-10.0890.0000.0000.0000.000
68A71ALA0-0.050-0.02025.988-0.001-0.0010.0000.0000.0000.000
69A72VAL00.0480.03027.999-0.090-0.0900.0000.0000.0000.000
70A73GLY00.0440.01131.2290.2060.2060.0000.0000.0000.000
71A74TYR0-0.048-0.05131.600-0.084-0.0840.0000.0000.0000.000
72A75ALA00.0200.00032.177-0.194-0.1940.0000.0000.0000.000
73A76ASN0-0.010-0.01632.0040.0990.0990.0000.0000.0000.000
74A77GLY00.0620.04328.566-0.221-0.2210.0000.0000.0000.000
75A78GLN0-0.032-0.02628.778-0.028-0.0280.0000.0000.0000.000
76A79VAL0-0.025-0.01031.116-0.063-0.0630.0000.0000.0000.000
77A80ALA00.0230.02426.952-0.092-0.0920.0000.0000.0000.000
78A81ALA00.0270.01626.396-0.264-0.2640.0000.0000.0000.000
79A82ARG10.9150.95227.4499.0499.0490.0000.0000.0000.000
80A83ASN0-0.004-0.00529.4880.1970.1970.0000.0000.0000.000
81A84ALA00.0160.01424.230-0.075-0.0750.0000.0000.0000.000
82A85VAL00.015-0.00226.058-0.170-0.1700.0000.0000.0000.000
83A86PHE0-0.061-0.02127.4810.1180.1180.0000.0000.0000.000
84A87HIS00.0460.01327.1290.1990.1990.0000.0000.0000.000
85A88ALA00.0430.02724.362-0.068-0.0680.0000.0000.0000.000
86A89ARG10.8980.95625.88710.34110.3410.0000.0000.0000.000
87A90ARG10.9550.99028.8419.6559.6550.0000.0000.0000.000
88A91LEU0-0.015-0.00924.6290.1950.1950.0000.0000.0000.000
89A92GLY0-0.041-0.00626.756-0.121-0.1210.0000.0000.0000.000
90A93ILE0-0.0110.00021.055-0.324-0.3240.0000.0000.0000.000
91A94PRO0-0.0200.00221.6880.3760.3760.0000.0000.0000.000
92A95LYS10.9590.97622.65310.43410.4340.0000.0000.0000.000
93A96ASN0-0.014-0.01520.405-0.101-0.1010.0000.0000.0000.000
94A97LYS10.8330.92217.15616.08716.0870.0000.0000.0000.000
95A98LEU0-0.014-0.00613.7420.5550.5550.0000.0000.0000.000
96A99LEU0-0.025-0.00217.6390.1090.1090.0000.0000.0000.000
97A100PHE0-0.003-0.01112.966-0.041-0.0410.0000.0000.0000.000
98A101ALA0-0.0030.01718.4800.5300.5300.0000.0000.0000.000
99A102ASN0-0.043-0.04019.554-1.241-1.2410.0000.0000.0000.000
100A103ILE0-0.022-0.00720.2910.7640.7640.0000.0000.0000.000
101A104GLU-1-0.773-0.86920.566-13.457-13.4570.0000.0000.0000.000
102A105ASP-1-0.843-0.92221.037-12.959-12.9590.0000.0000.0000.000
103A106PHE0-0.063-0.04122.8630.3490.3490.0000.0000.0000.000
104A107PHE0-0.028-0.00225.2810.3310.3310.0000.0000.0000.000
105A108ALA00.0350.03427.265-0.169-0.1690.0000.0000.0000.000
106A109VAL0-0.074-0.06224.424-0.261-0.2610.0000.0000.0000.000
107A110ASP-1-0.797-0.88827.693-9.806-9.8060.0000.0000.0000.000
108A111ALA00.0330.00227.363-0.335-0.3350.0000.0000.0000.000
109A112ALA0-0.027-0.01028.346-0.120-0.1200.0000.0000.0000.000
110A113TRP00.0010.01323.902-0.244-0.2440.0000.0000.0000.000
111A114ILE00.0190.00022.876-0.260-0.2600.0000.0000.0000.000
112A115ALA00.0170.01125.221-0.307-0.3070.0000.0000.0000.000
113A116ALA00.0050.01227.582-0.059-0.0590.0000.0000.0000.000
114A117TRP0-0.049-0.01820.7810.3610.3610.0000.0000.0000.000
115A118VAL0-0.002-0.01322.219-0.262-0.2620.0000.0000.0000.000
116A119GLU-1-0.862-0.92924.708-10.246-10.2460.0000.0000.0000.000
117A120THR0-0.071-0.04928.1630.4190.4190.0000.0000.0000.000
118A121LEU0-0.0320.00622.5540.1960.1960.0000.0000.0000.000
119A122TYR00.0490.05824.2550.2500.2500.0000.0000.0000.000
120A123PRO00.0120.00826.138-0.015-0.0150.0000.0000.0000.000
121A124THR0-0.124-0.08526.6600.1820.1820.0000.0000.0000.000
122A125GLY00.009-0.01025.5780.1530.1530.0000.0000.0000.000
123A126TYR0-0.053-0.03422.121-0.134-0.1340.0000.0000.0000.000
124A127ARG10.8540.92714.67618.39918.3990.0000.0000.0000.000
125A128PRO00.0220.00519.738-0.269-0.2690.0000.0000.0000.000
126A129GLY00.0550.02516.702-0.809-0.8090.0000.0000.0000.000
127A130LEU0-0.043-0.03116.2821.1331.1330.0000.0000.0000.000
128A131TYR00.0180.01514.427-0.813-0.8130.0000.0000.0000.000
129A132ALA00.0550.03115.8941.1501.1500.0000.0000.0000.000
130A133ASP-1-0.770-0.87315.955-17.989-17.9890.0000.0000.0000.000
131A134PRO0-0.105-0.05814.7690.8360.8360.0000.0000.0000.000
132A135THR0-0.091-0.06316.9480.2960.2960.0000.0000.0000.000
133A136LYS10.8420.91719.66713.20513.2050.0000.0000.0000.000
134A137GLY00.0840.04922.196-0.237-0.2370.0000.0000.0000.000
135A138ASP-1-0.826-0.91724.335-11.096-11.0960.0000.0000.0000.000
136A139PHE0-0.008-0.00818.044-0.094-0.0940.0000.0000.0000.000
137A140ALA00.0190.00820.757-0.146-0.1460.0000.0000.0000.000
138A141ALA00.0120.00821.884-0.028-0.0280.0000.0000.0000.000
139A142ALA00.0330.01925.1890.1290.1290.0000.0000.0000.000
140A143TYR0-0.002-0.04518.8690.0190.0190.0000.0000.0000.000
141A144CYS0-0.061-0.03619.5490.5670.5670.0000.0000.0000.000
142A145GLU-1-0.807-0.87924.138-9.757-9.7570.0000.0000.0000.000
143A146ALA0-0.003-0.00924.8860.3010.3010.0000.0000.0000.000
144A147VAL0-0.048-0.02721.5540.1790.1790.0000.0000.0000.000
145A148SER0-0.058-0.02224.8950.2590.2590.0000.0000.0000.000
146A149ARG10.8060.89028.0489.8949.8940.0000.0000.0000.000
147A150ASN00.0130.00627.8620.1330.1330.0000.0000.0000.000
148A151ASN00.0780.04023.384-0.675-0.6750.0000.0000.0000.000
149A152GLN00.0250.00523.285-1.018-1.0180.0000.0000.0000.000
150A153VAL0-0.019-0.00421.793-0.504-0.5040.0000.0000.0000.000
151A154ALA00.0390.02219.467-0.660-0.6600.0000.0000.0000.000
152A155VAL0-0.065-0.01518.355-0.885-0.8850.0000.0000.0000.000
153A156GLN0-0.024-0.02718.427-1.135-1.1350.0000.0000.0000.000
154A157ALA00.0210.02618.367-0.530-0.5300.0000.0000.0000.000
155A158VAL0-0.053-0.01612.032-0.845-0.8450.0000.0000.0000.000
156A159ILE0-0.021-0.01013.3050.6130.6130.0000.0000.0000.000
157A160TRP0-0.067-0.04310.955-1.718-1.7180.0000.0000.0000.000
158A161SER00.009-0.01410.9002.0212.0210.0000.0000.0000.000
159A162ALA00.0290.01111.592-1.765-1.7650.0000.0000.0000.000
160A163ALA00.0430.04913.4570.7290.7290.0000.0000.0000.000
161A164PRO00.0280.01311.648-1.080-1.0800.0000.0000.0000.000
162A165ARG10.8950.93612.48316.05716.0570.0000.0000.0000.000
163A166PRO0-0.048-0.01711.5201.0121.0120.0000.0000.0000.000
164A167GLY00.0610.04213.9091.1681.1680.0000.0000.0000.000
165A168THR00.0070.01413.136-1.695-1.6950.0000.0000.0000.000
166A169THR0-0.042-0.01510.5150.2860.2860.0000.0000.0000.000
167A170LYS10.9270.95712.66317.26817.2680.0000.0000.0000.000
168A171GLU-1-0.833-0.9048.226-33.234-33.2340.0000.0000.0000.000
169A172GLN0-0.035-0.0318.243-4.187-4.1870.0000.0000.0000.000
170A173LYS10.9140.95610.18420.87620.8760.0000.0000.0000.000
171A174ALA00.0050.0306.3191.1721.1720.0000.0000.0000.000
172A175PRO0-0.0030.0147.121-1.616-1.6160.0000.0000.0000.000
173A176ARG10.9310.9505.07424.25124.2510.0000.0000.0000.000
176A179PRO00.0130.0296.8932.6022.6020.0000.0000.0000.000
177A180ALA00.0110.0029.8390.8320.8320.0000.0000.0000.000
178A181ALA00.0110.00013.037-0.851-0.8510.0000.0000.0000.000
179A182PRO00.0430.02414.8190.7610.7610.0000.0000.0000.000
180A183PRO00.0040.00618.221-0.521-0.5210.0000.0000.0000.000
181A185SER00.0080.01518.241-1.200-1.2000.0000.0000.0000.000
182A186ALA00.1040.04515.5600.5910.5910.0000.0000.0000.000
183A187ASN0-0.060-0.01512.735-1.694-1.6940.0000.0000.0000.000
184A188VAL00.0270.0199.819-0.152-0.1520.0000.0000.0000.000
185A189TRP0-0.013-0.0067.561-3.157-3.1570.0000.0000.0000.000
186A190VAL00.0310.0157.042-3.933-3.9330.0000.0000.0000.000
187A191TRP0-0.024-0.0145.669-0.431-0.4310.0000.0000.0000.000
188A192GLN00.0490.0258.067-1.837-1.8370.0000.0000.0000.000
189A193TYR0-0.037-0.0177.7860.2670.2670.0000.0000.0000.000
190A194GLY00.014-0.01310.6651.3821.3820.0000.0000.0000.000
191A195ARG10.8550.90913.63015.74715.7470.0000.0000.0000.000
192A196ASP-1-0.865-0.94016.637-14.617-14.6170.0000.0000.0000.000
193A197ALA0-0.035-0.01716.2850.3430.3430.0000.0000.0000.000
194A198GLU-1-0.959-0.97018.269-13.720-13.7200.0000.0000.0000.000
195A199VAL0-0.059-0.03119.2480.4900.4900.0000.0000.0000.000
196A201PRO00.0110.02519.871-0.604-0.6040.0000.0000.0000.000
197A202VAL0-0.065-0.03915.821-0.031-0.0310.0000.0000.0000.000
198A203ASP-1-0.746-0.84314.447-17.689-17.6890.0000.0000.0000.000
199A204THR0-0.032-0.03010.784-0.424-0.4240.0000.0000.0000.000
200A205ASN0-0.059-0.0548.363-0.548-0.5480.0000.0000.0000.000
205A210ARG10.8560.9015.86733.95533.9550.0000.0000.0000.000
206A211LEU00.0140.0157.7882.9272.9270.0000.0000.0000.000
207A212LEU00.002-0.0087.9582.2642.2640.0000.0000.0000.000
208A213ASP-1-0.861-0.91610.829-19.886-19.8860.0000.0000.0000.000
209A214PHE0-0.051-0.02813.0851.9301.9300.0000.0000.0000.000
210A215LEU00.0210.01811.5750.7240.7240.0000.0000.0000.000
211A216TYR-1-0.774-0.86915.048-17.143-17.1430.0000.0000.0000.000