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: MVYNZ

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 OptHSide
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 -2611591.774002
FMO2-HF: Nuclear repulsion 2524262.124382
FMO2-HF: Total energy -87329.64962
FMO2-MP2: Total energy -87580.752481


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.
-17.136-10.73719.252-11.689-13.961-0.052
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 : -0.002 / q_NPA : -0.027
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].
3A3PHE00.020-0.0013.7881.4633.008-0.012-0.818-0.7150.003
4A4ALA0-0.073-0.0436.2090.3550.3550.0000.0000.0000.000
5A5ALA00.0310.0207.810-0.173-0.1730.0000.0000.0000.000
6A6GLY0-0.025-0.0169.431-0.045-0.0450.0000.0000.0000.000
7A7LYS10.9150.9578.7990.1570.1570.0000.0000.0000.000
8A8ASP-1-0.786-0.8936.454-1.146-1.1460.0000.0000.0000.000
9A9ASP-1-0.846-0.9121.966-15.787-14.7976.157-3.698-3.449-0.052
10A10LEU0-0.052-0.0051.9380.8511.1234.496-2.785-1.983-0.003
11A11CYS0-0.157-0.0702.9071.4101.3124.715-1.851-2.7650.000
12A12THR00.0380.0274.237-0.238-0.2200.000-0.015-0.0030.000
13A14SER00.0380.0327.2790.0620.0620.0000.0000.0000.000
14A15ASN00.029-0.01410.6850.1090.1090.0000.0000.0000.000
15A16LYS10.9560.99113.066-0.100-0.1000.0000.0000.0000.000
16A17THR0-0.038-0.04715.730-0.018-0.0180.0000.0000.0000.000
17A18GLU-1-0.945-0.97818.8600.0150.0150.0000.0000.0000.000
18A19SER0-0.060-0.03021.0230.0030.0030.0000.0000.0000.000
19A20SER00.0190.03716.003-0.005-0.0050.0000.0000.0000.000
20A21PRO00.0130.00914.181-0.004-0.0040.0000.0000.0000.000
21A22GLU-1-0.836-0.88110.0520.2860.2860.0000.0000.0000.000
22A23THR0-0.048-0.0399.6610.0860.0860.0000.0000.0000.000
23A24VAL00.0260.0083.176-0.387-0.1270.049-0.078-0.2310.000
24A25ASP-1-0.811-0.8856.1720.0690.0690.0000.0000.0000.000
25A27SER0-0.023-0.0265.9260.0310.0310.0000.0000.0000.000
26A28SER0-0.002-0.0109.660-0.087-0.0870.0000.0000.0000.000
27A29LYS10.8340.9186.1000.4260.4260.0000.0000.0000.000
28A30LYS10.8970.9539.1420.1080.1080.0000.0000.0000.000
29A31LEU00.0030.0165.429-0.005-0.0050.0000.0000.0000.000
30A32THR00.0240.0019.5120.0450.0450.0000.0000.0000.000
31A33THR0-0.026-0.0238.1040.0530.0530.0000.0000.0000.000
32A34VAL00.0260.0096.048-0.034-0.0340.0000.0000.0000.000
33A35PRO0-0.0100.0122.293-0.906-0.4732.142-0.839-1.7360.003
34A36THR00.0310.0084.0810.2010.4250.001-0.045-0.1810.000
35A37GLY00.025-0.0022.836-0.9800.7770.519-0.976-1.3000.000
36A38ILE0-0.019-0.0082.650-1.703-0.8381.170-0.583-1.451-0.003
37A39PRO00.0570.0433.672-0.549-0.4160.015-0.001-0.1470.000
38A40THR00.0100.0037.001-0.092-0.0920.0000.0000.0000.000
39A41SER0-0.107-0.07810.025-0.053-0.0530.0000.0000.0000.000
40A42THR0-0.035-0.0367.190-0.085-0.0850.0000.0000.0000.000
41A43GLU-1-0.846-0.9039.7630.1650.1650.0000.0000.0000.000
42A44LYS10.9060.96410.848-0.073-0.0730.0000.0000.0000.000
43A45LEU00.0270.0185.2440.0080.0080.0000.0000.0000.000
44A46GLN0-0.0100.0027.605-0.050-0.0500.0000.0000.0000.000
45A47LEU00.0330.0085.4460.0500.0500.0000.0000.0000.000
46A48ASN00.0320.0268.901-0.015-0.0150.0000.0000.0000.000
47A49TYR0-0.024-0.02611.708-0.036-0.0360.0000.0000.0000.000
48A50ASN0-0.032-0.0068.918-0.113-0.1130.0000.0000.0000.000
49A51GLN0-0.011-0.02912.354-0.020-0.0200.0000.0000.0000.000
50A52LEU00.0300.0508.881-0.004-0.0040.0000.0000.0000.000
51A53THR00.0440.01413.025-0.004-0.0040.0000.0000.0000.000
52A54GLY00.002-0.00714.646-0.010-0.0100.0000.0000.0000.000
53A55ILE00.000-0.00112.1130.0230.0230.0000.0000.0000.000
54A56PRO00.0290.02710.887-0.037-0.0370.0000.0000.0000.000
55A57PRO00.0170.00213.2220.0540.0540.0000.0000.0000.000
56A58THR00.0300.00512.879-0.006-0.0060.0000.0000.0000.000
57A59ALA0-0.043-0.0189.5200.0780.0780.0000.0000.0000.000
58A60PHE00.0340.0069.0030.1590.1590.0000.0000.0000.000
59A61GLN00.0250.02211.175-0.019-0.0190.0000.0000.0000.000
60A62GLY00.008-0.00811.183-0.069-0.0690.0000.0000.0000.000
61A63LEU0-0.0050.0247.822-0.070-0.0700.0000.0000.0000.000
62A64THR0-0.012-0.01911.795-0.066-0.0660.0000.0000.0000.000
63A65LYS10.8520.91013.835-0.279-0.2790.0000.0000.0000.000
64A66LEU00.0140.0259.732-0.017-0.0170.0000.0000.0000.000
65A67THR0-0.034-0.01513.799-0.036-0.0360.0000.0000.0000.000
66A68TYR0-0.0130.00112.682-0.026-0.0260.0000.0000.0000.000
67A69LEU00.0270.01010.6630.0580.0580.0000.0000.0000.000
68A70ASN0-0.021-0.00611.582-0.032-0.0320.0000.0000.0000.000
69A71LEU00.035-0.00210.8240.0450.0450.0000.0000.0000.000
70A72ASP-1-0.756-0.85813.4950.0830.0830.0000.0000.0000.000
71A73SER0-0.060-0.03714.775-0.006-0.0060.0000.0000.0000.000
72A74ASN0-0.037-0.01812.291-0.009-0.0090.0000.0000.0000.000
73A75GLN0-0.044-0.03215.761-0.020-0.0200.0000.0000.0000.000
74A76LEU00.0190.01514.0470.0000.0000.0000.0000.0000.000
75A77GLN0-0.0030.00117.954-0.017-0.0170.0000.0000.0000.000
76A78TYR0-0.025-0.02319.947-0.010-0.0100.0000.0000.0000.000
77A79LEU00.0180.01517.2320.0150.0150.0000.0000.0000.000
78A80PRO0-0.0030.00917.040-0.020-0.0200.0000.0000.0000.000
79A81VAL00.010-0.03320.0590.0060.0060.0000.0000.0000.000
80A82GLY00.0420.03221.4150.0080.0080.0000.0000.0000.000
81A83VAL0-0.055-0.01315.4440.0180.0180.0000.0000.0000.000
82A84PHE00.0540.01014.9930.0380.0380.0000.0000.0000.000
83A85ASP-1-0.882-0.93617.9590.1920.1920.0000.0000.0000.000
84A86GLN0-0.054-0.03816.415-0.012-0.0120.0000.0000.0000.000
85A87LEU0-0.0180.00513.4740.0120.0120.0000.0000.0000.000
86A88LYS10.9800.97717.133-0.223-0.2230.0000.0000.0000.000
87A89ASN0-0.084-0.05417.952-0.040-0.0400.0000.0000.0000.000
88A90LEU0-0.0310.00414.653-0.004-0.0040.0000.0000.0000.000
89A91ASN00.0150.01318.458-0.016-0.0160.0000.0000.0000.000
90A92GLU-1-0.843-0.93517.6980.0880.0880.0000.0000.0000.000
91A93LEU00.0110.00415.9910.0300.0300.0000.0000.0000.000
92A94ARG10.7440.85816.119-0.106-0.1060.0000.0000.0000.000
93A95LEU00.0320.01016.2020.0280.0280.0000.0000.0000.000
94A96ASP-1-0.733-0.83518.4210.0670.0670.0000.0000.0000.000
95A97PHE0-0.056-0.03619.0580.0060.0060.0000.0000.0000.000
96A98ASN0-0.0090.00116.5530.0070.0070.0000.0000.0000.000
97A99LYS10.8760.93520.317-0.051-0.0510.0000.0000.0000.000
98A100LEU00.0450.03619.8430.0000.0000.0000.0000.0000.000
99A101LYS10.9260.94423.458-0.059-0.0590.0000.0000.0000.000
100A102SER0-0.019-0.00725.842-0.003-0.0030.0000.0000.0000.000
101A103LEU00.0530.02023.2850.0070.0070.0000.0000.0000.000
102A104PRO0-0.0100.00722.117-0.010-0.0100.0000.0000.0000.000
103A105PRO00.0290.00025.4350.0000.0000.0000.0000.0000.000
104A106ARG10.9400.96326.555-0.103-0.1030.0000.0000.0000.000
105A107VAL0-0.024-0.00521.2680.0090.0090.0000.0000.0000.000
106A108PHE00.1010.04521.1520.0150.0150.0000.0000.0000.000
107A109ASP-1-0.848-0.92223.9220.1110.1110.0000.0000.0000.000
108A110ARG10.9210.97122.527-0.160-0.1600.0000.0000.0000.000
109A111LEU0-0.025-0.00119.3040.0080.0080.0000.0000.0000.000
110A112THR00.0440.01022.766-0.007-0.0070.0000.0000.0000.000
111A113ASN0-0.086-0.03922.746-0.022-0.0220.0000.0000.0000.000
112A114LEU0-0.0100.00620.3060.0000.0000.0000.0000.0000.000
113A115THR00.0150.01623.158-0.005-0.0050.0000.0000.0000.000
114A116ALA00.0120.01221.904-0.011-0.0110.0000.0000.0000.000
115A117LEU00.0190.01121.5570.0160.0160.0000.0000.0000.000
116A118TYR0-0.066-0.03520.522-0.016-0.0160.0000.0000.0000.000
117A119LEU0-0.017-0.02121.1970.0130.0130.0000.0000.0000.000
118A120GLU-1-0.745-0.84223.4610.0390.0390.0000.0000.0000.000
119A121TYR0-0.025-0.00423.5250.0050.0050.0000.0000.0000.000
120A122ASN0-0.020-0.00721.4290.0080.0080.0000.0000.0000.000
121A123GLN0-0.012-0.01025.063-0.009-0.0090.0000.0000.0000.000
122A124LEU00.0130.00325.231-0.001-0.0010.0000.0000.0000.000
123A125GLN0-0.001-0.01128.647-0.006-0.0060.0000.0000.0000.000
124A126SER0-0.055-0.01330.999-0.002-0.0020.0000.0000.0000.000
125A127ILE00.0130.00629.2610.0040.0040.0000.0000.0000.000
126A128PRO00.0060.00228.190-0.005-0.0050.0000.0000.0000.000
127A129LYS10.9660.96431.468-0.060-0.0600.0000.0000.0000.000
128A130GLY00.0830.04632.9770.0040.0040.0000.0000.0000.000
129A131VAL0-0.105-0.03727.1770.0050.0050.0000.0000.0000.000
130A132PHE00.0570.00426.8290.0080.0080.0000.0000.0000.000
131A133ASP-1-0.850-0.91629.9860.0760.0760.0000.0000.0000.000
132A134LYS10.8020.88128.263-0.103-0.1030.0000.0000.0000.000
133A135LEU0-0.0250.01125.2430.0030.0030.0000.0000.0000.000
134A136VAL00.0520.01028.571-0.005-0.0050.0000.0000.0000.000
135A137ASN0-0.093-0.07827.315-0.012-0.0120.0000.0000.0000.000
136A138LEU0-0.0100.02325.3510.0000.0000.0000.0000.0000.000
137A139GLU-1-0.804-0.90227.4650.0660.0660.0000.0000.0000.000
138A140THR0-0.018-0.01425.778-0.005-0.0050.0000.0000.0000.000
139A141LEU00.0260.01726.4890.0080.0080.0000.0000.0000.000
140A142TRP0-0.004-0.01325.172-0.013-0.0130.0000.0000.0000.000
141A143LEU00.0330.01126.1190.0070.0070.0000.0000.0000.000
142A144ARG10.8250.89527.141-0.036-0.0360.0000.0000.0000.000
143A145GLU-1-0.852-0.92928.1180.0320.0320.0000.0000.0000.000
144A146ASN0-0.0030.02926.4600.0060.0060.0000.0000.0000.000
145A147LYS10.8110.87329.955-0.040-0.0400.0000.0000.0000.000
146A148LEU00.0210.03630.8700.0000.0000.0000.0000.0000.000
147A149GLN00.0140.01234.212-0.005-0.0050.0000.0000.0000.000
148A150SER00.010-0.00137.085-0.002-0.0020.0000.0000.0000.000
149A151VAL0-0.009-0.00534.2340.0030.0030.0000.0000.0000.000
150A152PRO0-0.055-0.03634.875-0.002-0.0020.0000.0000.0000.000
151A153ASP-1-0.907-0.96137.8560.0440.0440.0000.0000.0000.000
152A154GLY00.0820.01739.3180.0020.0020.0000.0000.0000.000
153A155ALA0-0.095-0.02934.2300.0030.0030.0000.0000.0000.000
154A156PHE00.035-0.01832.1330.0050.0050.0000.0000.0000.000
155A157ASP-1-0.830-0.88335.2960.0490.0490.0000.0000.0000.000
156A158SER0-0.0110.00633.704-0.003-0.0030.0000.0000.0000.000
157A159LEU0-0.077-0.02730.2840.0030.0030.0000.0000.0000.000
158A160THR0-0.016-0.01633.575-0.002-0.0020.0000.0000.0000.000
159A161LYS10.8190.90629.556-0.075-0.0750.0000.0000.0000.000
160A162VAL0-0.0370.01030.4170.0000.0000.0000.0000.0000.000
161A163GLU-1-0.937-0.95331.8280.0400.0400.0000.0000.0000.000
162A164MET0-0.076-0.04330.457-0.005-0.0050.0000.0000.0000.000
163A165LEU00.0360.01530.9060.0050.0050.0000.0000.0000.000
164A166GLN0-0.049-0.00729.656-0.006-0.0060.0000.0000.0000.000
165A167LEU00.0620.01331.1130.0040.0040.0000.0000.0000.000
166A168HIS0-0.064-0.04833.375-0.001-0.0010.0000.0000.0000.000
167A169ASN0-0.021-0.02832.6520.0020.0020.0000.0000.0000.000
168A170ASN00.0250.00631.3470.0040.0040.0000.0000.0000.000
169A171PRO0-0.0310.01834.791-0.002-0.0020.0000.0000.0000.000
170A172TRP0-0.018-0.02634.3640.0020.0020.0000.0000.0000.000
171A173ASP-1-0.829-0.91739.7240.0250.0250.0000.0000.0000.000
172A174CYS0-0.156-0.07140.2170.0030.0030.0000.0000.0000.000
173A175ALA00.0030.00045.479-0.001-0.0010.0000.0000.0000.000
174A221CYS0-0.0540.02543.225-0.001-0.0010.0000.0000.0000.000
175A177SER00.0620.01746.7260.0000.0000.0000.0000.0000.000
176A178ASP-1-0.887-0.98141.6200.0400.0400.0000.0000.0000.000
177A179ILE0-0.0410.00141.2060.0020.0020.0000.0000.0000.000
178A180ILE0-0.011-0.00643.3130.0000.0000.0000.0000.0000.000
179A181TYR0-0.046-0.02637.9180.0000.0000.0000.0000.0000.000
180A182LEU00.0300.01637.5800.0000.0000.0000.0000.0000.000
181A183ARG10.8590.94241.071-0.027-0.0270.0000.0000.0000.000
182A184THR0-0.027-0.04044.197-0.002-0.0020.0000.0000.0000.000
183A185PHE0-0.0080.00237.121-0.001-0.0010.0000.0000.0000.000
184A186ILE00.024-0.01238.9350.0000.0000.0000.0000.0000.000
185A187ALA0-0.070-0.03241.698-0.001-0.0010.0000.0000.0000.000
186A188LYS10.9140.96843.886-0.036-0.0360.0000.0000.0000.000
187A189ASN0-0.006-0.00140.014-0.001-0.0010.0000.0000.0000.000
188A190THR0-0.012-0.03340.4220.0020.0020.0000.0000.0000.000
189A191ASP-1-0.902-0.92741.7440.0240.0240.0000.0000.0000.000
190A192LYS10.8410.90539.512-0.036-0.0360.0000.0000.0000.000
191A193ILE00.0030.01534.6820.0020.0020.0000.0000.0000.000
192A194SER00.0400.00934.556-0.004-0.0040.0000.0000.0000.000
193A195GLY00.000-0.01634.3380.0030.0030.0000.0000.0000.000
194A196MET00.0160.03935.4260.0010.0010.0000.0000.0000.000
195A197GLU-1-0.864-0.92837.4750.0220.0220.0000.0000.0000.000
196A198SER0-0.038-0.00236.693-0.001-0.0010.0000.0000.0000.000
197A199ALA0-0.040-0.00238.082-0.001-0.0010.0000.0000.0000.000
198A200GLN00.0260.00138.963-0.002-0.0020.0000.0000.0000.000
199A202ASN00.0380.00040.719-0.003-0.0030.0000.0000.0000.000
200A203GLY0-0.0140.00041.899-0.001-0.0010.0000.0000.0000.000
201A204THR0-0.030-0.01744.017-0.002-0.0020.0000.0000.0000.000
202A205SER00.0110.00744.3220.0010.0010.0000.0000.0000.000
203A206THR0-0.014-0.00245.8570.0000.0000.0000.0000.0000.000
204A207ALA00.0640.03243.7560.0010.0010.0000.0000.0000.000
205A208VAL00.040-0.00840.3900.0000.0000.0000.0000.0000.000
206A209LYS10.8900.93543.514-0.020-0.0200.0000.0000.0000.000
207A210ASP-1-0.828-0.88745.1070.0190.0190.0000.0000.0000.000
208A211VAL0-0.025-0.01046.080-0.001-0.0010.0000.0000.0000.000
209A212LYS10.8880.94048.933-0.017-0.0170.0000.0000.0000.000
210A213THR00.0660.01648.5690.0000.0000.0000.0000.0000.000
211A214GLU-1-0.814-0.89351.2080.0250.0250.0000.0000.0000.000
212A215PRO0-0.052-0.04754.0560.0000.0000.0000.0000.0000.000
213A216ILE00.0110.00548.3940.0000.0000.0000.0000.0000.000
214A217LYS10.8290.90950.807-0.025-0.0250.0000.0000.0000.000
215A218ASN0-0.0140.00151.6080.0010.0010.0000.0000.0000.000
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