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: 7276K

Calculation Name: 4PO4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PO4

Chain ID: A

ChEMBL ID:

UniProt ID: A0A088

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2613036.379135
FMO2-HF: Nuclear repulsion 2525705.840182
FMO2-HF: Total energy -87330.538953
FMO2-MP2: Total energy -87582.068024


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: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.
-22.292-15.83617.881-9.723-14.611-0.044
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 : 0 / q_Mulliken : -0.007 / q_NPA : -0.024
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].
3A3PHE00.0160.0173.8571.7623.170-0.012-0.713-0.6820.001
4A4ALA0-0.065-0.0386.2760.2540.2540.0000.0000.0000.000
5A5ALA00.0310.0227.646-0.192-0.1920.0000.0000.0000.000
6A6GLY0-0.019-0.0099.491-0.038-0.0380.0000.0000.0000.000
7A7LYS10.8790.9408.834-0.030-0.0300.0000.0000.0000.000
8A8ASP-1-0.749-0.8666.662-0.969-0.9690.0000.0000.0000.000
9A9ASP-1-0.852-0.9221.956-15.886-15.4996.467-3.504-3.350-0.048
10A10LEU0-0.070-0.0152.2960.2941.3061.113-0.916-1.2090.000
11A11CYS0-0.102-0.0492.9771.0181.4253.021-1.222-2.2060.001
12A12THR00.0210.0044.582-0.315-0.349-0.001-0.0090.0440.000
13A14SER00.0240.0237.4970.0950.0950.0000.0000.0000.000
14A15ASN00.039-0.00511.1680.1270.1270.0000.0000.0000.000
15A16LYS10.9690.99613.129-0.179-0.1790.0000.0000.0000.000
16A17THR0-0.011-0.03015.791-0.017-0.0170.0000.0000.0000.000
17A18GLU-1-0.954-0.98419.3250.0400.0400.0000.0000.0000.000
18A19SER0-0.053-0.01721.298-0.003-0.0030.0000.0000.0000.000
19A20SER00.0020.01817.1640.0010.0010.0000.0000.0000.000
20A21PRO00.0510.03214.9070.0030.0030.0000.0000.0000.000
21A22GLU-1-0.849-0.91010.2220.3960.3960.0000.0000.0000.000
22A23THR0-0.053-0.0339.9980.0710.0710.0000.0000.0000.000
23A24VAL00.014-0.0023.593-0.241-0.0780.009-0.044-0.1280.000
24A25ASP-1-0.788-0.8816.610-0.090-0.0900.0000.0000.0000.000
25A27SER0-0.020-0.0235.8300.0300.0300.0000.0000.0000.000
26A28SER00.014-0.0059.689-0.096-0.0960.0000.0000.0000.000
27A29LYS10.7910.9096.2720.5970.5970.0000.0000.0000.000
28A30LYS10.8880.9399.1830.1900.1900.0000.0000.0000.000
29A31LEU00.0130.0285.5090.0180.0180.0000.0000.0000.000
30A32THR00.025-0.0029.6790.0620.0620.0000.0000.0000.000
31A33THR0-0.025-0.0178.1890.0740.0740.0000.0000.0000.000
32A34VAL00.0310.0075.969-0.076-0.0760.0000.0000.0000.000
33A35PRO0-0.0120.0112.337-0.876-0.2321.487-0.679-1.4520.004
34A36THR00.002-0.0123.074-0.5260.6510.174-0.662-0.688-0.006
35A37GLY00.0480.0112.435-4.086-2.4513.660-2.487-2.8070.006
36A38ILE0-0.0110.0002.762-2.371-2.7041.9330.366-1.966-0.002
37A39PRO00.0400.0313.426-0.395-0.4050.0300.147-0.1670.000
38A40THR0-0.005-0.0016.789-0.152-0.1520.0000.0000.0000.000
39A41SER0-0.080-0.0649.998-0.063-0.0630.0000.0000.0000.000
40A42THR0-0.022-0.0347.466-0.111-0.1110.0000.0000.0000.000
41A43GLU-1-0.805-0.8779.9180.1900.1900.0000.0000.0000.000
42A44LYS10.8700.95211.280-0.080-0.0800.0000.0000.0000.000
43A45LEU00.0110.0165.5570.0270.0270.0000.0000.0000.000
44A46GLN00.0020.0087.923-0.039-0.0390.0000.0000.0000.000
45A47LEU00.0340.0075.5430.0070.0070.0000.0000.0000.000
46A48ASN00.0190.0298.885-0.019-0.0190.0000.0000.0000.000
47A49TYR0-0.011-0.01711.821-0.047-0.0470.0000.0000.0000.000
48A50ASN0-0.062-0.0388.899-0.124-0.1240.0000.0000.0000.000
49A51GLN0-0.013-0.02812.659-0.011-0.0110.0000.0000.0000.000
50A52LEU00.0180.0319.1770.0040.0040.0000.0000.0000.000
51A53THR00.0280.00313.3260.0110.0110.0000.0000.0000.000
52A54GLY0-0.004-0.00614.924-0.001-0.0010.0000.0000.0000.000
53A55ILE00.0100.00712.0010.0080.0080.0000.0000.0000.000
54A56PRO00.0130.01811.004-0.025-0.0250.0000.0000.0000.000
55A57PRO00.034-0.01312.9700.0510.0510.0000.0000.0000.000
56A58THR00.0130.00711.961-0.002-0.0020.0000.0000.0000.000
57A59ALA0-0.036-0.0049.0170.1010.1010.0000.0000.0000.000
58A60PHE00.0730.0148.3640.1630.1630.0000.0000.0000.000
59A61GLN00.0100.02410.7840.0040.0040.0000.0000.0000.000
60A62GLY00.0200.00410.960-0.071-0.0710.0000.0000.0000.000
61A63LEU0-0.031-0.0027.300-0.061-0.0610.0000.0000.0000.000
62A64THR0-0.024-0.01911.319-0.085-0.0850.0000.0000.0000.000
63A65LYS10.8390.92013.135-0.348-0.3480.0000.0000.0000.000
64A66LEU0-0.034-0.0069.922-0.035-0.0350.0000.0000.0000.000
65A67THR0-0.027-0.02513.875-0.042-0.0420.0000.0000.0000.000
66A68TYR0-0.038-0.03713.128-0.032-0.0320.0000.0000.0000.000
67A69LEU00.0200.00910.7610.0570.0570.0000.0000.0000.000
68A70ASN0-0.009-0.00111.895-0.039-0.0390.0000.0000.0000.000
69A71LEU00.0430.00910.8580.0370.0370.0000.0000.0000.000
70A72ASP-1-0.741-0.84113.3650.0370.0370.0000.0000.0000.000
71A73SER0-0.051-0.03115.125-0.019-0.0190.0000.0000.0000.000
72A74ASN0-0.050-0.03212.254-0.036-0.0360.0000.0000.0000.000
73A75GLN0-0.013-0.01116.288-0.003-0.0030.0000.0000.0000.000
74A76LEU00.0230.02214.1320.0030.0030.0000.0000.0000.000
75A77GLN00.0070.00118.117-0.009-0.0090.0000.0000.0000.000
76A78TYR0-0.024-0.02019.893-0.004-0.0040.0000.0000.0000.000
77A79LEU00.0180.01217.0330.0110.0110.0000.0000.0000.000
78A80PRO00.0080.01116.868-0.017-0.0170.0000.0000.0000.000
79A81VAL00.015-0.01619.9390.0050.0050.0000.0000.0000.000
80A82GLY00.0400.02721.0800.0100.0100.0000.0000.0000.000
81A83VAL0-0.067-0.02215.3540.0210.0210.0000.0000.0000.000
82A84PHE00.0760.02414.8750.0360.0360.0000.0000.0000.000
83A85ASP-1-0.856-0.92817.9180.1810.1810.0000.0000.0000.000
84A86GLN0-0.048-0.03916.019-0.006-0.0060.0000.0000.0000.000
85A87LEU0-0.026-0.00913.2980.0160.0160.0000.0000.0000.000
86A88LYS10.9840.98217.070-0.238-0.2380.0000.0000.0000.000
87A89ASN0-0.052-0.02417.932-0.044-0.0440.0000.0000.0000.000
88A90LEU0-0.0390.00614.701-0.006-0.0060.0000.0000.0000.000
89A91ASN0-0.014-0.00118.590-0.022-0.0220.0000.0000.0000.000
90A92GLU-1-0.779-0.86717.8590.0630.0630.0000.0000.0000.000
91A93LEU0-0.021-0.01016.0490.0290.0290.0000.0000.0000.000
92A94ARG10.7480.85916.426-0.070-0.0700.0000.0000.0000.000
93A95LEU00.0340.00516.0730.0220.0220.0000.0000.0000.000
94A96ASP-1-0.733-0.84118.2670.0370.0370.0000.0000.0000.000
95A97PHE0-0.044-0.02419.188-0.002-0.0020.0000.0000.0000.000
96A98ASN0-0.031-0.01616.659-0.003-0.0030.0000.0000.0000.000
97A99LYS10.8770.93320.628-0.002-0.0020.0000.0000.0000.000
98A100LEU00.0260.03419.8380.0010.0010.0000.0000.0000.000
99A101LYS10.9410.95423.524-0.029-0.0290.0000.0000.0000.000
100A102SER0-0.059-0.01925.900-0.002-0.0020.0000.0000.0000.000
101A103LEU00.0600.02323.1080.0050.0050.0000.0000.0000.000
102A104PRO00.0040.00622.053-0.007-0.0070.0000.0000.0000.000
103A105PRO00.0160.00225.3780.0000.0000.0000.0000.0000.000
104A106ARG10.9510.96826.844-0.099-0.0990.0000.0000.0000.000
105A107VAL0-0.0250.00421.1750.0100.0100.0000.0000.0000.000
106A108PHE00.0920.03220.8970.0160.0160.0000.0000.0000.000
107A109ASP-1-0.810-0.90923.6890.1080.1080.0000.0000.0000.000
108A110ARG10.8580.92622.221-0.166-0.1660.0000.0000.0000.000
109A111LEU0-0.0180.00919.3170.0070.0070.0000.0000.0000.000
110A112THR00.0320.00222.932-0.007-0.0070.0000.0000.0000.000
111A113ASN0-0.069-0.03922.853-0.021-0.0210.0000.0000.0000.000
112A114LEU0-0.0270.00220.487-0.002-0.0020.0000.0000.0000.000
113A115THR00.0520.03423.469-0.005-0.0050.0000.0000.0000.000
114A116ALA00.0020.00722.373-0.011-0.0110.0000.0000.0000.000
115A117LEU00.001-0.00121.4990.0150.0150.0000.0000.0000.000
116A118TYR0-0.067-0.05420.869-0.016-0.0160.0000.0000.0000.000
117A119LEU00.0200.00121.1150.0120.0120.0000.0000.0000.000
118A120GLU-1-0.741-0.86123.3450.0160.0160.0000.0000.0000.000
119A121TYR0-0.038-0.01723.6370.0010.0010.0000.0000.0000.000
120A122ASN0-0.035-0.01521.3340.0020.0020.0000.0000.0000.000
121A123GLN0-0.009-0.00725.161-0.007-0.0070.0000.0000.0000.000
122A124LEU00.0120.01425.1980.0000.0000.0000.0000.0000.000
123A125GLN00.024-0.00428.724-0.004-0.0040.0000.0000.0000.000
124A126SER0-0.048-0.01931.190-0.001-0.0010.0000.0000.0000.000
125A127ILE00.0400.01429.1680.0030.0030.0000.0000.0000.000
126A128PRO0-0.034-0.01128.220-0.004-0.0040.0000.0000.0000.000
127A129LYS10.9750.97131.491-0.048-0.0480.0000.0000.0000.000
128A130GLY00.0850.04833.2540.0030.0030.0000.0000.0000.000
129A131VAL0-0.127-0.05426.9820.0060.0060.0000.0000.0000.000
130A132PHE00.0680.01626.5250.0080.0080.0000.0000.0000.000
131A133ASP-1-0.852-0.91429.6470.0730.0730.0000.0000.0000.000
132A134LYS10.8120.90228.250-0.099-0.0990.0000.0000.0000.000
133A135LEU0-0.0370.00325.2150.0040.0040.0000.0000.0000.000
134A136VAL00.0330.00628.614-0.005-0.0050.0000.0000.0000.000
135A137ASN0-0.058-0.05227.314-0.011-0.0110.0000.0000.0000.000
136A138LEU0-0.0280.00125.689-0.001-0.0010.0000.0000.0000.000
137A139GLU-1-0.810-0.90727.7850.0630.0630.0000.0000.0000.000
138A140THR0-0.018-0.01026.326-0.007-0.0070.0000.0000.0000.000
139A141LEU00.0100.00826.5210.0080.0080.0000.0000.0000.000
140A142TRP0-0.025-0.02425.287-0.013-0.0130.0000.0000.0000.000
141A143LEU00.0480.00826.0620.0050.0050.0000.0000.0000.000
142A144ARG10.8340.91627.416-0.015-0.0150.0000.0000.0000.000
143A145GLU-1-0.826-0.89528.0960.0080.0080.0000.0000.0000.000
144A146ASN0-0.055-0.01626.4650.0030.0030.0000.0000.0000.000
145A147LYS10.8220.88030.000-0.019-0.0190.0000.0000.0000.000
146A148LEU00.0100.02730.7140.0010.0010.0000.0000.0000.000
147A149GLN0-0.0020.01034.197-0.004-0.0040.0000.0000.0000.000
148A150SER0-0.031-0.02637.256-0.001-0.0010.0000.0000.0000.000
149A151VAL00.003-0.00534.2300.0020.0020.0000.0000.0000.000
150A152PRO0-0.065-0.04034.696-0.002-0.0020.0000.0000.0000.000
151A153ASP-1-0.836-0.92937.7500.0390.0390.0000.0000.0000.000
152A154GLY00.0070.00239.0490.0030.0030.0000.0000.0000.000
153A155ALA0-0.056-0.02234.1470.0030.0030.0000.0000.0000.000
154A156PHE00.026-0.00831.8850.0040.0040.0000.0000.0000.000
155A157ASP-1-0.837-0.89835.1300.0440.0440.0000.0000.0000.000
156A158SER0-0.030-0.02233.771-0.002-0.0020.0000.0000.0000.000
157A159LEU0-0.070-0.01830.4900.0030.0030.0000.0000.0000.000
158A160THR0-0.031-0.03033.719-0.002-0.0020.0000.0000.0000.000
159A161LYS10.8110.91429.393-0.076-0.0760.0000.0000.0000.000
160A162VAL0-0.073-0.01430.463-0.001-0.0010.0000.0000.0000.000
161A163GLU-1-0.871-0.91932.1850.0360.0360.0000.0000.0000.000
162A164MET0-0.107-0.05130.899-0.006-0.0060.0000.0000.0000.000
163A165LEU00.0280.01331.0140.0050.0050.0000.0000.0000.000
164A166GLN0-0.044-0.00829.696-0.005-0.0050.0000.0000.0000.000
165A167LEU00.0380.00231.2260.0030.0030.0000.0000.0000.000
166A168HIS00.0050.00933.277-0.003-0.0030.0000.0000.0000.000
167A169ASN0-0.050-0.05632.5540.0020.0020.0000.0000.0000.000
168A170ASN00.0310.01331.2370.0030.0030.0000.0000.0000.000
169A171PRO0-0.0240.02134.846-0.002-0.0020.0000.0000.0000.000
170A172TRP0-0.026-0.03134.3740.0020.0020.0000.0000.0000.000
171A173ASP-1-0.826-0.91639.6670.0150.0150.0000.0000.0000.000
172A174CYS0-0.103-0.05840.1950.0030.0030.0000.0000.0000.000
173A175ALA0-0.009-0.00445.800-0.001-0.0010.0000.0000.0000.000
174A221CYS0-0.0180.03343.207-0.001-0.0010.0000.0000.0000.000
175A177SER00.038-0.00446.2720.0000.0000.0000.0000.0000.000
176A178ASP-1-0.856-0.94541.4850.0320.0320.0000.0000.0000.000
177A179ILE0-0.0160.00141.1970.0020.0020.0000.0000.0000.000
178A180ILE0-0.026-0.00543.3070.0000.0000.0000.0000.0000.000
179A181TYR0-0.025-0.01337.750-0.001-0.0010.0000.0000.0000.000
180A182LEU00.0300.02137.3340.0000.0000.0000.0000.0000.000
181A183ARG10.8480.92940.840-0.021-0.0210.0000.0000.0000.000
182A184THR0-0.018-0.02944.063-0.002-0.0020.0000.0000.0000.000
183A185PHE0-0.016-0.00637.049-0.001-0.0010.0000.0000.0000.000
184A186ILE00.039-0.01039.0870.0000.0000.0000.0000.0000.000
185A187ALA0-0.047-0.03141.673-0.001-0.0010.0000.0000.0000.000
186A188LYS10.8930.96043.786-0.033-0.0330.0000.0000.0000.000
187A189ASN00.0000.00640.069-0.001-0.0010.0000.0000.0000.000
188A190THR0-0.015-0.03940.8220.0010.0010.0000.0000.0000.000
189A191ASP-1-0.935-0.95841.3120.0200.0200.0000.0000.0000.000
190A192LYS10.8680.92539.711-0.034-0.0340.0000.0000.0000.000
191A193ILE0-0.0060.01334.9450.0020.0020.0000.0000.0000.000
192A194SER00.0780.02734.588-0.003-0.0030.0000.0000.0000.000
193A195GLY00.012-0.00234.5390.0020.0020.0000.0000.0000.000
194A196MET0-0.0220.03035.600-0.001-0.0010.0000.0000.0000.000
195A197GLU-1-0.823-0.89937.6150.0150.0150.0000.0000.0000.000
196A198SER0-0.065-0.03036.432-0.001-0.0010.0000.0000.0000.000
197A199ALA0-0.0010.01237.978-0.001-0.0010.0000.0000.0000.000
198A200GLN0-0.028-0.01938.861-0.001-0.0010.0000.0000.0000.000
199A202ASN00.019-0.00540.957-0.003-0.0030.0000.0000.0000.000
200A203GLY0-0.015-0.00142.0530.0000.0000.0000.0000.0000.000
201A204THR0-0.029-0.00744.099-0.001-0.0010.0000.0000.0000.000
202A205SER00.0240.01244.2090.0000.0000.0000.0000.0000.000
203A206THR0-0.016-0.00445.9090.0000.0000.0000.0000.0000.000
204A207ALA00.0890.03843.5300.0010.0010.0000.0000.0000.000
205A208VAL00.021-0.01340.5210.0000.0000.0000.0000.0000.000
206A209LYS10.8630.92743.603-0.013-0.0130.0000.0000.0000.000
207A210ASP-1-0.835-0.89445.1140.0130.0130.0000.0000.0000.000
208A211VAL0-0.005-0.00346.014-0.001-0.0010.0000.0000.0000.000
209A212LYS10.8600.92148.909-0.011-0.0110.0000.0000.0000.000
210A213THR00.0740.03048.4320.0000.0000.0000.0000.0000.000
211A214GLU-1-0.794-0.88750.9990.0200.0200.0000.0000.0000.000
212A215PRO0-0.050-0.03853.9980.0000.0000.0000.0000.0000.000
213A216ILE00.0270.02148.2300.0000.0000.0000.0000.0000.000
214A217LYS10.7950.88350.753-0.021-0.0210.0000.0000.0000.000
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