Manual

About

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: XYNJ2

Calculation Name: 3PO8-A-Xray33

Preferred Name:

Target Type:

Ligand Name: phosphate ion

ligand 3-letter code: PO4

PDB ID: 3PO8

Chain ID: A

ChEMBL ID:

UniProt ID: P71590

Base Structure: X-ray

Registration Date: 2018-09-07

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 Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 213
LigandCharge PO4=-3
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -981842.438517
FMO2-HF: Nuclear repulsion 934969.326044
FMO2-HF: Total energy -46873.112472
FMO2-MP2: Total energy -47007.392424


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:2:ACE)


Summations of interaction energy for fragment #1(A:2: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.
19.168-6.66626.8472.453-3.466-0.019
Interaction energy analysis for fragmet #1(A:2:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : -0.068
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].
3A4THR0-0.057-0.0103.8590.9952.064-0.015-0.598-0.456-0.002
4A5SER00.0080.0137.4920.0130.0130.0000.0000.0000.000
5A6VAL00.0520.02510.8320.0740.0740.0000.0000.0000.000
6A7THR0-0.037-0.03314.2390.0340.0340.0000.0000.0000.000
7A8LEU0-0.031-0.00117.5410.0150.0150.0000.0000.0000.000
8A9GLN00.0100.00621.0160.0020.0020.0000.0000.0000.000
9A10LEU0-0.020-0.00823.7890.0060.0060.0000.0000.0000.000
10A11ASP-1-0.871-0.92927.466-0.090-0.0900.0000.0000.0000.000
11A12ASP-1-0.771-0.84229.466-0.087-0.0870.0000.0000.0000.000
12A13GLY00.0140.02131.5640.0070.0070.0000.0000.0000.000
13A14SER0-0.079-0.05730.642-0.001-0.0010.0000.0000.0000.000
14A15GLY00.0230.02027.700-0.001-0.0010.0000.0000.0000.000
15A16ARG10.8110.88326.0300.1060.1060.0000.0000.0000.000
16A17THR00.0260.00320.646-0.003-0.0030.0000.0000.0000.000
17A18TYR0-0.090-0.04220.1220.0120.0120.0000.0000.0000.000
18A19GLN00.0140.03714.2210.0250.0250.0000.0000.0000.000
19A20LEU00.0120.02315.0400.0250.0250.0000.0000.0000.000
20A21ARG10.9080.94814.9380.1710.1710.0000.0000.0000.000
21A22GLU-1-0.826-0.88612.307-0.491-0.4910.0000.0000.0000.000
22A23GLY00.0110.00814.8340.0590.0590.0000.0000.0000.000
23A24SER00.0080.02217.919-0.008-0.0080.0000.0000.0000.000
24A25ASN00.0010.01617.7190.0020.0020.0000.0000.0000.000
25A26ILE00.0100.01021.7600.0050.0050.0000.0000.0000.000
26A27ILE00.0130.00523.668-0.002-0.0020.0000.0000.0000.000
27A28GLY00.0600.01326.9820.0070.0070.0000.0000.0000.000
28A29ARG10.8650.95630.7470.0730.0730.0000.0000.0000.000
29A30GLY0-0.023-0.01333.2000.0050.0050.0000.0000.0000.000
30A31GLN00.003-0.00432.248-0.003-0.0030.0000.0000.0000.000
31A32ASP-1-0.867-0.93530.667-0.105-0.1050.0000.0000.0000.000
32A33ALA0-0.0110.03028.242-0.010-0.0100.0000.0000.0000.000
33A34GLN00.0480.05122.6480.0040.0040.0000.0000.0000.000
34A35PHE00.0140.02724.032-0.004-0.0040.0000.0000.0000.000
35A36ARG10.8910.96026.0280.0980.0980.0000.0000.0000.000
36A37LEU00.0390.00828.3310.0020.0020.0000.0000.0000.000
37A38PRO0-0.047-0.01031.7960.0040.0040.0000.0000.0000.000
38A39ASP-1-0.664-0.80534.653-0.074-0.0740.0000.0000.0000.000
39A40THR0-0.019-0.03336.565-0.002-0.0020.0000.0000.0000.000
40A41GLY0-0.0100.01238.0870.0020.0020.0000.0000.0000.000
41A42VAL0-0.0360.00831.928-0.001-0.0010.0000.0000.0000.000
42A43SER00.001-0.03534.0710.0020.0020.0000.0000.0000.000
43A44ARG10.6880.83733.6440.0640.0640.0000.0000.0000.000
44A45ARG10.8940.93928.5960.1070.1070.0000.0000.0000.000
45A46HIS00.0830.06430.2420.0050.0050.0000.0000.0000.000
46A47LEU00.0310.01724.7390.0020.0020.0000.0000.0000.000
47A48GLU-1-0.810-0.88823.628-0.168-0.1680.0000.0000.0000.000
48A49ILE0-0.003-0.00418.3230.0010.0010.0000.0000.0000.000
49A50ARG10.7620.85018.8820.1620.1620.0000.0000.0000.000
50A51TRP0-0.020-0.0109.9130.0230.0230.0000.0000.0000.000
51A52ASP-1-0.730-0.85411.865-0.525-0.5250.0000.0000.0000.000
52A53GLY00.0070.0098.867-0.062-0.0620.0000.0000.0000.000
53A54GLN0-0.045-0.0175.802-0.746-0.7460.0000.0000.0000.000
54A55VAL00.0310.0089.3100.0970.0970.0000.0000.0000.000
55A56ALA0-0.0090.00013.025-0.010-0.0100.0000.0000.0000.000
56A57LEU0-0.007-0.00415.9370.0370.0370.0000.0000.0000.000
57A58LEU0-0.0110.00019.248-0.005-0.0050.0000.0000.0000.000
58A59ALA00.0130.00122.4160.0120.0120.0000.0000.0000.000
59A60ASP-1-0.734-0.82025.701-0.097-0.0970.0000.0000.0000.000
60A61LEU0-0.077-0.03827.6950.0010.0010.0000.0000.0000.000
61A62ASN00.0160.01330.8980.0060.0060.0000.0000.0000.000
62A63SER0-0.004-0.00232.8650.0060.0060.0000.0000.0000.000
63A64THR0-0.028-0.02634.8300.0050.0050.0000.0000.0000.000
64A65ASN0-0.043-0.01936.8750.0070.0070.0000.0000.0000.000
65A66GLY00.0780.07734.0230.0020.0020.0000.0000.0000.000
66A67THR0-0.014-0.02427.876-0.004-0.0040.0000.0000.0000.000
67A68THR00.0230.02330.2340.0030.0030.0000.0000.0000.000
68A69VAL00.0080.00123.761-0.008-0.0080.0000.0000.0000.000
69A70ASN00.0440.02823.9450.0050.0050.0000.0000.0000.000
70A71ASN0-0.034-0.01428.1070.0060.0060.0000.0000.0000.000
71A72ALA00.0290.04829.1540.0080.0080.0000.0000.0000.000
72A73PRO00.0160.01030.281-0.007-0.0070.0000.0000.0000.000
73A74VAL0-0.029-0.00826.8300.0000.0000.0000.0000.0000.000
74A75GLN00.0260.06529.1030.0080.0080.0000.0000.0000.000
75A76GLU-1-0.774-0.89423.930-0.145-0.1450.0000.0000.0000.000
76A77TRP0-0.031-0.01321.8220.0190.0190.0000.0000.0000.000
77A78GLN00.0090.01715.883-0.003-0.0030.0000.0000.0000.000
78A79LEU0-0.0020.00317.9140.0140.0140.0000.0000.0000.000
79A80ALA00.0100.01716.558-0.033-0.0330.0000.0000.0000.000
80A81ASP-1-0.810-0.92015.490-0.207-0.2070.0000.0000.0000.000
81A82GLY00.0130.01517.4000.0290.0290.0000.0000.0000.000
82A83ASP-1-0.733-0.83120.574-0.135-0.1350.0000.0000.0000.000
83A84VAL00.009-0.00122.574-0.009-0.0090.0000.0000.0000.000
84A85ILE00.0050.00422.5220.0080.0080.0000.0000.0000.000
85A86ARG10.7850.89326.6500.0880.0880.0000.0000.0000.000
86A87LEU00.0330.01428.6810.0000.0000.0000.0000.0000.000
87A88GLY00.0270.01732.0960.0000.0000.0000.0000.0000.000
88A89HIS10.7760.86135.4820.0680.0680.0000.0000.0000.000
89A90SER00.0150.01130.9810.0010.0010.0000.0000.0000.000
90A91GLU-1-0.795-0.87829.642-0.083-0.0830.0000.0000.0000.000
91A92ILE0-0.007-0.00623.468-0.003-0.0030.0000.0000.0000.000
92A93ILE00.0240.02522.110-0.001-0.0010.0000.0000.0000.000
93A94VAL00.0040.00017.880-0.018-0.0180.0000.0000.0000.000
94A95ARG10.8730.92517.1840.1810.1810.0000.0000.0000.000
95A96MET0-0.0030.01412.016-0.032-0.0320.0000.0000.0000.000
96A97HIS0-0.071-0.03011.0460.1170.1170.0000.0000.0000.000
97A98PRO00.0180.0057.274-0.178-0.1780.0000.0000.0000.000
98A99LEU0-0.067-0.0315.7490.2490.2490.0000.0000.0000.000
99A100THR-1-0.883-0.8915.488-0.192-0.1920.0000.0000.0000.000
100A101PO4-3-2.245-2.52737.670-0.217-0.2170.0000.0000.0000.000
101A104HOH0-0.047-0.03232.5440.0010.0010.0000.0000.0000.000
102A107HOH00.0010.0521.8447.795-7.25317.607-0.922-1.636-0.004
103A109HOH0-0.051-0.03834.1890.0020.0020.0000.0000.0000.000
104A111HOH00.0470.02041.260-0.001-0.0010.0000.0000.0000.000
105A115HOH0-0.023-0.01517.119-0.004-0.0040.0000.0000.0000.000
106A119HOH0-0.022-0.02234.2910.0010.0010.0000.0000.0000.000
107A120HOH0-0.016-0.0167.4880.0080.0080.0000.0000.0000.000
108A122HOH0-0.006-0.00826.1000.0050.0050.0000.0000.0000.000
109A123HOH0-0.015-0.00841.4980.0000.0000.0000.0000.0000.000
110A130HOH0-0.060-0.03915.5020.0130.0130.0000.0000.0000.000
111A136HOH0-0.052-0.03311.4790.0170.0170.0000.0000.0000.000
112A138HOH0-0.013-0.0016.247-0.081-0.0810.0000.0000.0000.000
113A139HOH0-0.041-0.02214.7830.0050.0050.0000.0000.0000.000
114A140HOH0-0.046-0.03628.079-0.003-0.0030.0000.0000.0000.000
115A141HOH00.0180.01625.758-0.002-0.0020.0000.0000.0000.000
116A149HOH0-0.025-0.01338.9000.0000.0000.0000.0000.0000.000
117A165HOH0-0.049-0.04934.5860.0010.0010.0000.0000.0000.000
118A171HOH0-0.037-0.02233.2100.0020.0020.0000.0000.0000.000
119A181HOH00.0270.02244.041-0.001-0.0010.0000.0000.0000.000
120A192HOH0-0.061-0.03939.2000.0010.0010.0000.0000.0000.000
121A193HOH0-0.046-0.02035.3540.0010.0010.0000.0000.0000.000
122A198HOH0-0.014-0.01036.0030.0010.0010.0000.0000.0000.000
123A201HOH0-0.005-0.02026.8400.0030.0030.0000.0000.0000.000
124A214HOH00.0010.0053.2340.1480.2620.009-0.052-0.0710.000
125A222HOH00.0210.0145.209-0.041-0.0410.0000.0000.0000.000
126A226HOH0-0.022-0.02341.0030.0000.0000.0000.0000.0000.000
127A235HOH0-0.041-0.04420.2560.0050.0050.0000.0000.0000.000
128A236HOH0-0.0130.00440.3690.0010.0010.0000.0000.0000.000
129A237HOH00.0170.00639.724-0.001-0.0010.0000.0000.0000.000
130A250HOH0-0.041-0.0379.8740.0160.0160.0000.0000.0000.000
131A251HOH0-0.005-0.03126.7190.0010.0010.0000.0000.0000.000
132A255HOH00.0350.04824.4440.0070.0070.0000.0000.0000.000
133A258HOH0-0.106-0.06133.518-0.001-0.0010.0000.0000.0000.000
134A260HOH0-0.003-0.01027.3390.0020.0020.0000.0000.0000.000
135A261HOH0-0.020-0.02033.1550.0020.0020.0000.0000.0000.000
136A262HOH0-0.0020.00328.7280.0030.0030.0000.0000.0000.000
137A263HOH00.014-0.00137.301-0.001-0.0010.0000.0000.0000.000
138A264HOH00.0080.00534.5850.0000.0000.0000.0000.0000.000
139A265HOH00.001-0.00131.8750.0010.0010.0000.0000.0000.000
140A266HOH00.0150.00927.1560.0020.0020.0000.0000.0000.000
141A267HOH0-0.014-0.00419.4560.0110.0110.0000.0000.0000.000
142A268HOH0-0.020-0.01636.2910.0010.0010.0000.0000.0000.000
143A269HOH00.0380.03018.9820.0040.0040.0000.0000.0000.000
144A270HOH0-0.002-0.00335.189-0.002-0.0020.0000.0000.0000.000
145A271HOH0-0.012-0.00820.4010.0010.0010.0000.0000.0000.000
146A272HOH0-0.005-0.01035.038-0.002-0.0020.0000.0000.0000.000
147A273HOH0-0.007-0.00914.139-0.013-0.0130.0000.0000.0000.000
148A274HOH0-0.022-0.01218.8260.0010.0010.0000.0000.0000.000
149A275HOH00.0350.02413.8370.0040.0040.0000.0000.0000.000
150A276HOH0-0.0060.00132.8920.0010.0010.0000.0000.0000.000
151A277HOH0-0.063-0.04821.1720.0070.0070.0000.0000.0000.000
152A278HOH0-0.068-0.06510.9250.0030.0030.0000.0000.0000.000
153A279HOH00.0090.01618.3330.0170.0170.0000.0000.0000.000
154A280HOH0-0.018-0.01716.012-0.005-0.0050.0000.0000.0000.000
155A281HOH00.010-0.00312.979-0.037-0.0370.0000.0000.0000.000
156A282HOH0-0.030-0.01929.425-0.001-0.0010.0000.0000.0000.000
157A283HOH00.0080.01515.267-0.001-0.0010.0000.0000.0000.000
158A284HOH0-0.007-0.02532.7230.0020.0020.0000.0000.0000.000
159A285HOH0-0.059-0.04320.8180.0080.0080.0000.0000.0000.000
160A286HOH0-0.058-0.04534.1550.0010.0010.0000.0000.0000.000
161A288HOH00.0440.02031.266-0.002-0.0020.0000.0000.0000.000
162A289HOH0-0.025-0.01414.9540.0210.0210.0000.0000.0000.000
163A290HOH00.0360.02213.3590.0000.0000.0000.0000.0000.000
164A291HOH0-0.025-0.01439.0580.0010.0010.0000.0000.0000.000
165A294HOH0-0.039-0.03229.3520.0020.0020.0000.0000.0000.000
166A295HOH00.0450.03432.401-0.003-0.0030.0000.0000.0000.000
167A296HOH0-0.024-0.02531.177-0.001-0.0010.0000.0000.0000.000
168A297HOH0-0.035-0.02827.3620.0030.0030.0000.0000.0000.000
169A298HOH0-0.008-0.00724.7830.0070.0070.0000.0000.0000.000
170A299HOH0-0.071-0.08632.4070.0010.0010.0000.0000.0000.000
171A301HOH0-0.025-0.02333.1870.0010.0010.0000.0000.0000.000
172A302HOH0-0.060-0.08128.534-0.001-0.0010.0000.0000.0000.000
173A303HOH0-0.047-0.03024.9200.0010.0010.0000.0000.0000.000
174A305HOH0-0.024-0.01841.2510.0010.0010.0000.0000.0000.000
175A306HOH0-0.023-0.0209.7170.0160.0160.0000.0000.0000.000
176A308HOH00.0250.01023.9970.0030.0030.0000.0000.0000.000
177A311HOH0-0.018-0.02024.355-0.006-0.0060.0000.0000.0000.000
178A312HOH0-0.007-0.01228.3210.0030.0030.0000.0000.0000.000
179A313HOH0-0.003-0.00237.9010.0020.0020.0000.0000.0000.000
180A314HOH0-0.005-0.0156.624-0.353-0.3530.0000.0000.0000.000
181A315HOH0-0.066-0.07624.6580.0050.0050.0000.0000.0000.000
182A316HOH0-0.069-0.04238.1260.0010.0010.0000.0000.0000.000
183A317HOH0-0.048-0.03624.0060.0030.0030.0000.0000.0000.000
184A319HOH00.0200.01536.622-0.001-0.0010.0000.0000.0000.000
185A320HOH00.0190.01811.8160.0220.0220.0000.0000.0000.000
186A321HOH0-0.028-0.01918.5990.0010.0010.0000.0000.0000.000
187A322HOH00.0580.04224.216-0.006-0.0060.0000.0000.0000.000
188A323HOH00.0610.08126.7890.0040.0040.0000.0000.0000.000
189A324HOH00.0320.01212.069-0.038-0.0380.0000.0000.0000.000
190A325HOH0-0.040-0.02435.7780.0020.0020.0000.0000.0000.000
191A326HOH00.003-0.00329.1070.0020.0020.0000.0000.0000.000
192A327HOH00.004-0.00326.3100.0040.0040.0000.0000.0000.000
193A328HOH0-0.032-0.01812.9330.0300.0300.0000.0000.0000.000
194A329HOH0-0.003-0.00833.312-0.002-0.0020.0000.0000.0000.000
195A330HOH0-0.0300.0112.25012.1620.1939.2464.025-1.303-0.013
196A331HOH00.0210.01228.865-0.001-0.0010.0000.0000.0000.000
197A333HOH0-0.001-0.0137.5020.0000.0000.0000.0000.0000.000
198A334HOH00.0130.0069.581-0.029-0.0290.0000.0000.0000.000
199A337HOH0-0.036-0.02226.2670.0050.0050.0000.0000.0000.000
200A338HOH00.0170.02233.9430.0020.0020.0000.0000.0000.000
201A340HOH0-0.013-0.02536.464-0.002-0.0020.0000.0000.0000.000
202A341HOH0-0.013-0.01840.6110.0010.0010.0000.0000.0000.000
203A343HOH0-0.031-0.04132.9390.0010.0010.0000.0000.0000.000
204A346HOH0-0.082-0.06229.156-0.003-0.0030.0000.0000.0000.000
205A348HOH0-0.026-0.02317.0260.0140.0140.0000.0000.0000.000
206A350HOH0-0.042-0.0309.976-0.043-0.0430.0000.0000.0000.000
207A351HOH0-0.055-0.04434.2070.0010.0010.0000.0000.0000.000
208A352HOH0-0.033-0.02541.6420.0000.0000.0000.0000.0000.000
209A353HOH0-0.056-0.02818.8730.0060.0060.0000.0000.0000.000
210A355HOH0-0.039-0.03334.7220.0010.0010.0000.0000.0000.000
211A356HOH0-0.014-0.0158.0760.1090.1090.0000.0000.0000.000
212A357HOH0-0.013-0.01613.3400.0250.0250.0000.0000.0000.000
213A359HOH00.006-0.01011.627-0.031-0.0310.0000.0000.0000.000