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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: XR1N8

Calculation Name: 1SFS-A-Xray13

Preferred Name:

Target Type:

Ligand Name: phosphate ion

ligand 3-letter code: PO4

PDB ID: 1SFS

Chain ID: A

ChEMBL ID:

UniProt ID: P84136

Base Structure: X-ray

Registration Date: 2017-12-04

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20171117
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 214
LigandCharge PO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2645321.070748
FMO2-HF: Nuclear repulsion 2561999.633552
FMO2-HF: Total energy -83321.437196
FMO2-MP2: Total energy -83567.871367


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(A:3:ACE)


Summations of interaction energy for fragment #1(A:3:ACE)
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.
0.3541.291-0.007-0.447-0.4820
Interaction energy analysis for fragmet #1(A:3:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.017
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].
3A5ILE0-0.078-0.0303.8681.3162.027-0.010-0.335-0.3650.000
4A6TRP00.0680.0197.074-0.095-0.0950.0000.0000.0000.000
5A7GLY00.024-0.0059.8230.1040.1040.0000.0000.0000.000
6A8VAL00.0090.02613.302-0.014-0.0140.0000.0000.0000.000
7A9ASP-1-0.813-0.89016.414-0.309-0.3090.0000.0000.0000.000
8A10SER00.0570.03019.3990.0080.0080.0000.0000.0000.000
9A11ALA00.0510.03023.0730.0000.0000.0000.0000.0000.000
10A12GLN00.0080.01126.4090.0050.0050.0000.0000.0000.000
11A13VAL00.0030.00526.401-0.011-0.0110.0000.0000.0000.000
12A14VAL0-0.0120.00423.1090.0040.0040.0000.0000.0000.000
13A15THR00.0230.01526.2210.0060.0060.0000.0000.0000.000
14A16ASP-1-0.786-0.86827.017-0.075-0.0750.0000.0000.0000.000
15A17GLN00.0120.00527.201-0.003-0.0030.0000.0000.0000.000
16A18LEU00.0280.03024.1870.0010.0010.0000.0000.0000.000
17A19PHE00.016-0.00419.759-0.008-0.0080.0000.0000.0000.000
18A20GLN00.0300.00422.560-0.003-0.0030.0000.0000.0000.000
19A200CYS0-0.0270.00422.0120.0110.0110.0000.0000.0000.000
20A22VAL00.0620.02118.3650.0000.0000.0000.0000.0000.000
21A23ARG10.8420.94019.2050.0610.0610.0000.0000.0000.000
22A24THR0-0.137-0.08919.6360.0100.0100.0000.0000.0000.000
23A25GLU-1-0.900-0.93621.398-0.048-0.0480.0000.0000.0000.000
24A26LEU0-0.096-0.05516.620-0.001-0.0010.0000.0000.0000.000
25A27GLY00.016-0.01214.9430.0000.0000.0000.0000.0000.000
26A28TYR0-0.025-0.02614.8530.0080.0080.0000.0000.0000.000
27A29PRO0-0.0170.02213.886-0.041-0.0410.0000.0000.0000.000
28A30LYS10.8480.89410.9590.2970.2970.0000.0000.0000.000
29A31PHE0-0.037-0.02410.5290.0310.0310.0000.0000.0000.000
30A32TRP00.043-0.00215.530-0.014-0.0140.0000.0000.0000.000
31A33GLY0-0.028-0.01818.2770.0160.0160.0000.0000.0000.000
32A34ARG10.7650.86219.6490.1610.1610.0000.0000.0000.000
33A35TYR00.0740.03423.423-0.005-0.0050.0000.0000.0000.000
34A36LEU0-0.043-0.04226.3730.0110.0110.0000.0000.0000.000
35A37SER0-0.040-0.02828.5840.0090.0090.0000.0000.0000.000
36A38GLU-1-0.864-0.92630.929-0.095-0.0950.0000.0000.0000.000
37A39VAL0-0.042-0.00531.7940.0050.0050.0000.0000.0000.000
38A40PRO00.034-0.00133.687-0.002-0.0020.0000.0000.0000.000
39A41ASN0-0.030-0.01435.088-0.001-0.0010.0000.0000.0000.000
40A42VAL0-0.0180.00229.698-0.002-0.0020.0000.0000.0000.000
41A43SER0-0.013-0.01228.540-0.009-0.0090.0000.0000.0000.000
42A44GLU-1-0.818-0.90229.539-0.087-0.0870.0000.0000.0000.000
43A45GLY0-0.032-0.00829.200-0.011-0.0110.0000.0000.0000.000
44A46LEU0-0.046-0.01925.1210.0040.0040.0000.0000.0000.000
45A47THR00.0360.01129.3940.0090.0090.0000.0000.0000.000
46A48ARG10.9210.95030.0470.0730.0730.0000.0000.0000.000
47A49ASP-1-0.873-0.93930.537-0.070-0.0700.0000.0000.0000.000
48A50GLU-1-0.793-0.87126.621-0.128-0.1280.0000.0000.0000.000
49A51ILE00.004-0.00125.465-0.006-0.0060.0000.0000.0000.000
50A52VAL0-0.0090.00225.888-0.004-0.0040.0000.0000.0000.000
51A53ARG10.8600.91426.6020.0920.0920.0000.0000.0000.000
52A54ILE0-0.0010.00421.393-0.001-0.0010.0000.0000.0000.000
53A55ARG10.9230.95022.2710.1170.1170.0000.0000.0000.000
54A56ASN0-0.057-0.00723.0940.0100.0100.0000.0000.0000.000
55A57TYR0-0.099-0.08121.3720.0090.0090.0000.0000.0000.000
56A58GLY00.0120.02119.477-0.002-0.0020.0000.0000.0000.000
57A59VAL0-0.091-0.02617.310-0.020-0.0200.0000.0000.0000.000
58A60LYS10.8800.94915.7050.2240.2240.0000.0000.0000.000
59A61VAL00.0500.00918.226-0.021-0.0210.0000.0000.0000.000
60A62LEU0-0.0080.00015.479-0.006-0.0060.0000.0000.0000.000
61A63PRO0-0.0110.00019.2570.0090.0090.0000.0000.0000.000
62A64ILE00.0380.02620.808-0.012-0.0120.0000.0000.0000.000
63A65TYR0-0.003-0.01623.8320.0190.0190.0000.0000.0000.000
64A66ASN00.0710.00526.948-0.004-0.0040.0000.0000.0000.000
65A67ALA0-0.0050.02228.6510.0050.0050.0000.0000.0000.000
66A68PHE0-0.098-0.06927.4390.0070.0070.0000.0000.0000.000
67A69ARG10.8820.93930.3010.1040.1040.0000.0000.0000.000
68A70GLU-1-0.819-0.89132.711-0.088-0.0880.0000.0000.0000.000
69A71ALA0-0.042-0.01829.780-0.001-0.0010.0000.0000.0000.000
70A72VAL00.0700.04931.675-0.001-0.0010.0000.0000.0000.000
71A73GLY00.0160.00234.5370.0030.0030.0000.0000.0000.000
72A74TYR0-0.005-0.00734.137-0.003-0.0030.0000.0000.0000.000
73A75ALA00.009-0.01035.816-0.003-0.0030.0000.0000.0000.000
74A76ASN0-0.012-0.01235.8780.0010.0010.0000.0000.0000.000
75A77GLY00.0660.04332.551-0.004-0.0040.0000.0000.0000.000
76A78GLN0-0.028-0.02332.636-0.002-0.0020.0000.0000.0000.000
77A79VAL0-0.041-0.01434.838-0.001-0.0010.0000.0000.0000.000
78A80ALA00.0120.01931.118-0.001-0.0010.0000.0000.0000.000
79A81ALA00.0500.02230.336-0.004-0.0040.0000.0000.0000.000
80A82ARG10.9070.94531.3460.0710.0710.0000.0000.0000.000
81A83ASN00.0070.00433.8490.0040.0040.0000.0000.0000.000
82A84ALA00.0160.01628.4080.0000.0000.0000.0000.0000.000
83A85VAL00.0140.00029.942-0.001-0.0010.0000.0000.0000.000
84A86PHE0-0.074-0.02731.3040.0040.0040.0000.0000.0000.000
85A87HIS00.0440.01131.2210.0040.0040.0000.0000.0000.000
86A88ALA00.0310.01628.2360.0010.0010.0000.0000.0000.000
87A89ARG10.9240.95429.8100.0860.0860.0000.0000.0000.000
88A90ARG10.9631.00932.5550.0780.0780.0000.0000.0000.000
89A91LEU0-0.026-0.01928.8890.0060.0060.0000.0000.0000.000
90A92GLY0-0.068-0.02530.4190.0000.0000.0000.0000.0000.000
91A93ILE00.0060.01724.870-0.002-0.0020.0000.0000.0000.000
92A94PRO0-0.0320.00025.0900.0050.0050.0000.0000.0000.000
93A95LYS10.9710.98026.1960.0740.0740.0000.0000.0000.000
94A96ASN0-0.010-0.01423.504-0.001-0.0010.0000.0000.0000.000
95A97LYS10.8290.92420.3060.1600.1600.0000.0000.0000.000
96A98LEU00.0020.00117.2470.0120.0120.0000.0000.0000.000
97A99LEU0-0.043-0.01221.3230.0050.0050.0000.0000.0000.000
98A100PHE0-0.001-0.00216.581-0.001-0.0010.0000.0000.0000.000
99A101ALA0-0.0080.00822.2590.0120.0120.0000.0000.0000.000
100A102ASN0-0.046-0.03523.490-0.028-0.0280.0000.0000.0000.000
101A103ILE0-0.021-0.00923.9680.0160.0160.0000.0000.0000.000
102A104GLU-1-0.849-0.92924.433-0.153-0.1530.0000.0000.0000.000
103A105ASP-1-0.880-0.95424.502-0.132-0.1320.0000.0000.0000.000
104A106PHE0-0.067-0.03126.2460.0080.0080.0000.0000.0000.000
105A107PHE0-0.081-0.03529.0960.0060.0060.0000.0000.0000.000
106A108ALA00.0220.02330.427-0.002-0.0020.0000.0000.0000.000
107A109VAL0-0.088-0.06627.407-0.007-0.0070.0000.0000.0000.000
108A110ASP-1-0.715-0.84430.681-0.083-0.0830.0000.0000.0000.000
109A111ALA0-0.018-0.02329.797-0.008-0.0080.0000.0000.0000.000
110A112ALA0-0.042-0.02930.837-0.003-0.0030.0000.0000.0000.000
111A113TRP0-0.0170.01427.351-0.005-0.0050.0000.0000.0000.000
112A114ILE00.0250.00725.452-0.006-0.0060.0000.0000.0000.000
113A115ALA00.0050.01228.278-0.005-0.0050.0000.0000.0000.000
114A116ALA0-0.0060.00330.2710.0000.0000.0000.0000.0000.000
115A117TRP0-0.066-0.01924.3750.0080.0080.0000.0000.0000.000
116A118VAL00.0260.00325.055-0.003-0.0030.0000.0000.0000.000
117A119GLU-1-0.946-0.98627.643-0.080-0.0800.0000.0000.0000.000
118A120THR0-0.093-0.06730.9570.0080.0080.0000.0000.0000.000
119A121LEU0-0.0310.00026.1280.0040.0040.0000.0000.0000.000
120A122TYR00.0440.06327.2820.0050.0050.0000.0000.0000.000
121A123PRO0-0.004-0.00929.5360.0010.0010.0000.0000.0000.000
122A124THR0-0.131-0.08829.9910.0040.0040.0000.0000.0000.000
123A125GLY0-0.012-0.01228.6380.0030.0030.0000.0000.0000.000
124A126TYR0-0.068-0.04425.801-0.001-0.0010.0000.0000.0000.000
125A127ARG10.8860.94017.9310.2300.2300.0000.0000.0000.000
126A128PRO00.0250.00523.166-0.010-0.0100.0000.0000.0000.000
127A129GLY00.0510.02620.179-0.017-0.0170.0000.0000.0000.000
128A130LEU0-0.011-0.01419.8320.0270.0270.0000.0000.0000.000
129A131TYR00.000-0.00118.277-0.024-0.0240.0000.0000.0000.000
130A132ALA00.0560.03019.3710.0290.0290.0000.0000.0000.000
131A133ASP-1-0.795-0.88519.215-0.238-0.2380.0000.0000.0000.000
132A134PRO0-0.059-0.03517.1760.0210.0210.0000.0000.0000.000
133A135THR0-0.115-0.06619.1040.0170.0170.0000.0000.0000.000
134A136LYS10.9360.97321.8840.1290.1290.0000.0000.0000.000
135A137GLY00.0090.01425.072-0.008-0.0080.0000.0000.0000.000
136A138ASP-1-0.800-0.92126.892-0.098-0.0980.0000.0000.0000.000
137A139PHE0-0.019-0.00220.580-0.002-0.0020.0000.0000.0000.000
138A140ALA0-0.006-0.00822.490-0.001-0.0010.0000.0000.0000.000
139A141ALA00.0570.03323.8460.0010.0010.0000.0000.0000.000
140A142ALA00.0800.05027.1730.0040.0040.0000.0000.0000.000
141A143TYR0-0.048-0.08820.213-0.006-0.0060.0000.0000.0000.000
142A144CYS-1-0.722-0.88023.418-0.138-0.1380.0000.0000.0000.000
143A145GLU-1-0.881-0.89025.422-0.069-0.0690.0000.0000.0000.000
144A146ALA0-0.031-0.03426.9460.0060.0060.0000.0000.0000.000
145A147VAL0-0.030-0.01922.9620.0060.0060.0000.0000.0000.000
146A148SER0-0.073-0.02526.2930.0090.0090.0000.0000.0000.000
147A149ARG10.7740.87328.9310.0770.0770.0000.0000.0000.000
148A150ASN00.0240.00629.4150.0060.0060.0000.0000.0000.000
149A151ASN00.0760.04624.349-0.012-0.0120.0000.0000.0000.000
150A152GLN0-0.007-0.01324.844-0.017-0.0170.0000.0000.0000.000
151A153VAL00.0060.00923.887-0.011-0.0110.0000.0000.0000.000
152A154ALA00.0690.04320.869-0.017-0.0170.0000.0000.0000.000
153A155VAL0-0.118-0.04320.029-0.017-0.0170.0000.0000.0000.000
154A156GLN0-0.042-0.04220.500-0.023-0.0230.0000.0000.0000.000
155A157ALA00.0240.03120.983-0.015-0.0150.0000.0000.0000.000
156A158VAL0-0.060-0.02115.008-0.019-0.0190.0000.0000.0000.000
157A159ILE00.0110.00816.1020.0150.0150.0000.0000.0000.000
158A160TRP0-0.087-0.05114.659-0.066-0.0660.0000.0000.0000.000
159A161SER00.0360.00813.9760.0660.0660.0000.0000.0000.000
160A162ALA0-0.003-0.00515.056-0.057-0.0570.0000.0000.0000.000
161A163ALA00.0580.05916.2890.0360.0360.0000.0000.0000.000
162A164PRO00.0250.00813.376-0.042-0.0420.0000.0000.0000.000
163A165ARG10.9500.95714.9130.1650.1650.0000.0000.0000.000
164A166PRO0-0.064-0.02212.7900.0330.0330.0000.0000.0000.000
165A167GLY00.0680.03815.7790.0360.0360.0000.0000.0000.000
166A168THR0-0.0090.00515.105-0.027-0.0270.0000.0000.0000.000
167A169THR0-0.031-0.01512.3750.0120.0120.0000.0000.0000.000
168A170LYS10.9470.96714.6210.0270.0270.0000.0000.0000.000
169A171GLU-1-0.835-0.91710.592-0.186-0.1860.0000.0000.0000.000
170A172GLN0-0.036-0.0309.9450.0310.0310.0000.0000.0000.000
171A173LYS10.8750.93710.7260.1070.1070.0000.0000.0000.000
172A174ALA00.0170.0477.898-0.001-0.0010.0000.0000.0000.000
173A175PRO0-0.0010.0108.0860.1200.1200.0000.0000.0000.000
174A176ARG10.9660.9734.288-0.328-0.314-0.001-0.0160.0020.000
175A177TYR0-0.031-0.0373.818-0.1970.0150.004-0.096-0.1190.000
176A178GLN0-0.093-0.0515.5600.4270.4270.0000.0000.0000.000
177A179PRO0-0.0210.0118.5890.1270.1270.0000.0000.0000.000
178A180ALA00.002-0.01011.5380.0430.0430.0000.0000.0000.000
179A181ALA0-0.004-0.01214.139-0.045-0.0450.0000.0000.0000.000
180A182PRO00.0370.02715.9590.0180.0180.0000.0000.0000.000
181A183PRO0-0.049-0.02318.645-0.008-0.0080.0000.0000.0000.000
182A184CYS-1-0.878-0.91620.046-0.126-0.1260.0000.0000.0000.000
183A185SER0-0.075-0.02618.720-0.028-0.0280.0000.0000.0000.000
184A186ALA00.1250.05016.620-0.001-0.0010.0000.0000.0000.000
185A187ASN0-0.092-0.01714.204-0.021-0.0210.0000.0000.0000.000
186A188VAL00.0480.02212.000-0.013-0.0130.0000.0000.0000.000
187A189TRP0-0.032-0.01010.266-0.133-0.1330.0000.0000.0000.000
188A190VAL00.0270.01210.447-0.152-0.1520.0000.0000.0000.000
189A191TRP0-0.018-0.0088.1340.0120.0120.0000.0000.0000.000
190A192GLN00.0700.03711.903-0.049-0.0490.0000.0000.0000.000
191A193TYR0-0.053-0.01610.8270.0100.0100.0000.0000.0000.000
192A194GLY00.001-0.02113.5340.0590.0590.0000.0000.0000.000
193A195ARG10.8600.91116.5320.1810.1810.0000.0000.0000.000
194A196ASP-1-0.884-0.94519.936-0.134-0.1340.0000.0000.0000.000
195A197ALA0-0.031-0.02519.3170.0110.0110.0000.0000.0000.000
196A198GLU-1-0.951-0.95721.060-0.077-0.0770.0000.0000.0000.000
197A199VAL0-0.058-0.03521.3370.0070.0070.0000.0000.0000.000
198A201PRO0-0.0090.01922.976-0.010-0.0100.0000.0000.0000.000
199A202VAL0-0.059-0.03319.014-0.004-0.0040.0000.0000.0000.000
200A203ASP-1-0.759-0.86318.272-0.204-0.2040.0000.0000.0000.000
201A204THR0-0.055-0.03613.6190.0050.0050.0000.0000.0000.000
202A205ASN0-0.036-0.03812.412-0.026-0.0260.0000.0000.0000.000
203A206LEU0-0.034-0.0136.016-0.076-0.0760.0000.0000.0000.000
204A207ALA00.0070.0017.6700.1590.1590.0000.0000.0000.000
205A208ASP-1-0.775-0.8596.456-1.662-1.6620.0000.0000.0000.000
206A209ARG10.9810.9696.2900.4740.4740.0000.0000.0000.000
207A210ARG10.8560.9198.5050.6630.6630.0000.0000.0000.000
208A211LEU00.0120.00511.0340.0950.0950.0000.0000.0000.000
209A212LEU0-0.007-0.01210.7560.0810.0810.0000.0000.0000.000
210A213ASP-1-0.885-0.92913.898-0.149-0.1490.0000.0000.0000.000
211A214PHE0-0.096-0.04916.0840.0440.0440.0000.0000.0000.000
212A215LEU00.0140.01215.1900.0090.0090.0000.0000.0000.000
213A216TYR-1-0.819-0.91018.638-0.153-0.1530.0000.0000.0000.000
214A217PO4-2-1.804-1.92732.578-0.162-0.1620.0000.0000.0000.000