FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5JGNZ

Calculation Name: 4G3T-A-Xray372

Preferred Name: FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4G3T

Chain ID: A

ChEMBL ID: CHEMBL3797019

UniProt ID: A0R607

Base Structure: X-ray

Registration Date: 2023-09-23

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 336
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5071088.098407
FMO2-HF: Nuclear repulsion 4942165.583602
FMO2-HF: Total energy -128922.514805
FMO2-MP2: Total energy -129303.487874


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:85:ASN)


Summations of interaction energy for fragment #1(A:85:ASN)
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.
-22.889-19.86110.659-7.143-6.544-0.057
Interaction energy analysis for fragmet #1(A:85:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.039
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].
3A87ILE00.0370.0163.867-1.0831.148-0.023-1.219-0.9890.004
4A88HIS0-0.079-0.0553.6860.9791.246-0.001-0.116-0.1500.000
5A89SER00.0150.0098.6460.4240.4240.0000.0000.0000.000
6A90ILE00.010-0.00612.016-0.087-0.0870.0000.0000.0000.000
7A91ASP-1-0.760-0.83614.707-0.578-0.5780.0000.0000.0000.000
8A92SER0-0.020-0.03118.4150.0210.0210.0000.0000.0000.000
9A93GLY0-0.050-0.02021.3610.0540.0540.0000.0000.0000.000
10A94THR0-0.048-0.07019.8840.0270.0270.0000.0000.0000.000
11A95ARG10.8440.91219.8690.3710.3710.0000.0000.0000.000
12A96LEU00.0150.01616.060-0.001-0.0010.0000.0000.0000.000
13A97VAL0-0.024-0.01910.747-0.072-0.0720.0000.0000.0000.000
14A98ASP-1-0.839-0.8899.127-2.186-2.1860.0000.0000.0000.000
15A99VAL0-0.002-0.0205.822-0.596-0.5960.0000.0000.0000.000
16A100ASP-1-0.709-0.8281.911-20.138-21.36510.579-5.193-4.159-0.064
17A101ALA00.001-0.0194.1650.3960.5740.000-0.060-0.1180.000
18A102GLY00.0190.0113.382-0.4420.5620.064-0.428-0.6410.003
19A103VAL0-0.0230.0013.2350.0180.4870.041-0.125-0.3840.000
20A104SER0-0.005-0.0085.0530.1420.248-0.001-0.002-0.1030.000
21A105LEU00.0610.0198.659-0.516-0.5160.0000.0000.0000.000
22A106ASP-1-0.870-0.92011.6890.0860.0860.0000.0000.0000.000
23A107GLN0-0.030-0.0298.016-0.279-0.2790.0000.0000.0000.000
24A108LEU00.0340.0219.045-0.254-0.2540.0000.0000.0000.000
25A109MET0-0.014-0.00811.005-0.023-0.0230.0000.0000.0000.000
26A110LYS10.7580.89112.978-0.004-0.0040.0000.0000.0000.000
27A111ALA00.0230.02111.700-0.009-0.0090.0000.0000.0000.000
28A112ALA00.0300.01613.7230.0020.0020.0000.0000.0000.000
29A113LEU00.0190.01415.7480.0380.0380.0000.0000.0000.000
30A114PRO0-0.025-0.02117.3990.0410.0410.0000.0000.0000.000
31A115HIS0-0.043-0.00815.934-0.012-0.0120.0000.0000.0000.000
32A116GLY00.0400.04420.1320.0150.0150.0000.0000.0000.000
33A117LEU0-0.066-0.01917.5120.0270.0270.0000.0000.0000.000
34A118TRP00.014-0.00918.5860.0030.0030.0000.0000.0000.000
35A119VAL00.017-0.00114.573-0.022-0.0220.0000.0000.0000.000
36A120PRO00.0200.02116.2780.0490.0490.0000.0000.0000.000
37A121VAL00.0080.01218.0660.0340.0340.0000.0000.0000.000
38A122LEU0-0.027-0.00517.3750.0130.0130.0000.0000.0000.000
39A123PRO0-0.0080.00415.0170.0360.0360.0000.0000.0000.000
40A124GLY00.0370.02017.168-0.046-0.0460.0000.0000.0000.000
41A125THR0-0.019-0.02115.5450.0250.0250.0000.0000.0000.000
42A126ARG11.0030.99313.513-0.742-0.7420.0000.0000.0000.000
43A127GLN00.020-0.00410.948-0.084-0.0840.0000.0000.0000.000
44A128VAL0-0.0130.00910.5180.3910.3910.0000.0000.0000.000
45A129THR00.0340.0186.789-0.560-0.5600.0000.0000.0000.000
46A130VAL00.0390.0247.250-0.228-0.2280.0000.0000.0000.000
47A131GLY00.0210.0118.169-0.200-0.2000.0000.0000.0000.000
48A132GLY0-0.009-0.0039.876-0.147-0.1470.0000.0000.0000.000
49A133ALA0-0.028-0.02812.044-0.155-0.1550.0000.0000.0000.000
50A134ILE00.008-0.00111.304-0.114-0.1140.0000.0000.0000.000
51A135GLY00.0480.03513.860-0.056-0.0560.0000.0000.0000.000
52A136CYS0-0.115-0.06115.6860.0560.0560.0000.0000.0000.000
53A137ASP-1-0.751-0.82317.7260.0920.0920.0000.0000.0000.000
54A138ILE0-0.0280.00515.890-0.017-0.0170.0000.0000.0000.000
55A139HIS00.0380.00119.303-0.071-0.0710.0000.0000.0000.000
56A140GLY00.0300.00722.3980.0380.0380.0000.0000.0000.000
57A141LYS10.8270.90723.527-0.158-0.1580.0000.0000.0000.000
58A142ASN00.0470.01922.7130.0210.0210.0000.0000.0000.000
59A143HIS00.0250.04124.749-0.019-0.0190.0000.0000.0000.000
60A144HIS0-0.027-0.02026.618-0.004-0.0040.0000.0000.0000.000
61A145SER0-0.060-0.02828.610-0.016-0.0160.0000.0000.0000.000
62A146ALA0-0.014-0.00123.927-0.021-0.0210.0000.0000.0000.000
63A147GLY00.0160.02824.143-0.014-0.0140.0000.0000.0000.000
64A148SER0-0.034-0.05321.4830.0070.0070.0000.0000.0000.000
65A149PHE00.004-0.01312.942-0.034-0.0340.0000.0000.0000.000
66A150GLY00.0330.00317.856-0.063-0.0630.0000.0000.0000.000
67A151ASN0-0.020-0.00718.975-0.022-0.0220.0000.0000.0000.000
68A152HIS0-0.022-0.00317.962-0.067-0.0670.0000.0000.0000.000
69A153VAL0-0.0160.01014.389-0.081-0.0810.0000.0000.0000.000
70A154ARG10.7670.85316.2400.3570.3570.0000.0000.0000.000
71A155SER00.006-0.00613.9520.0050.0050.0000.0000.0000.000
72A156MET0-0.043-0.01112.457-0.017-0.0170.0000.0000.0000.000
73A157GLU-1-0.793-0.86010.307-0.700-0.7000.0000.0000.0000.000
74A158LEU0-0.034-0.01011.1490.0460.0460.0000.0000.0000.000
75A159LEU0-0.0010.00710.089-0.046-0.0460.0000.0000.0000.000
76A160THR00.022-0.00312.6800.1330.1330.0000.0000.0000.000
77A161ALA00.0050.00016.052-0.001-0.0010.0000.0000.0000.000
78A162ASN0-0.043-0.02917.8790.0170.0170.0000.0000.0000.000
79A163GLY0-0.0010.00615.809-0.020-0.0200.0000.0000.0000.000
80A164GLU-1-0.868-0.89516.100-0.182-0.1820.0000.0000.0000.000
81A165VAL0-0.014-0.01711.9790.0320.0320.0000.0000.0000.000
82A166ARG10.8030.86914.8840.0640.0640.0000.0000.0000.000
83A167HIS0-0.018-0.02415.0030.0330.0330.0000.0000.0000.000
84A168LEU0-0.024-0.00316.1370.0750.0750.0000.0000.0000.000
85A169THR00.0430.00117.241-0.050-0.0500.0000.0000.0000.000
86A170PRO00.0200.00719.7510.0410.0410.0000.0000.0000.000
87A171ALA0-0.007-0.01022.3350.0300.0300.0000.0000.0000.000
88A172GLY00.0280.04123.8220.0010.0010.0000.0000.0000.000
89A173PRO00.0150.00123.8990.0290.0290.0000.0000.0000.000
90A174ASP-1-0.805-0.89021.502-0.152-0.1520.0000.0000.0000.000
91A175SER0-0.015-0.00222.2930.0250.0250.0000.0000.0000.000
92A176ASP-1-0.904-0.95323.445-0.002-0.0020.0000.0000.0000.000
93A177LEU00.0080.00019.4750.0350.0350.0000.0000.0000.000
94A178PHE00.0070.01317.0970.0410.0410.0000.0000.0000.000
95A179TRP00.020-0.01319.4660.0540.0540.0000.0000.0000.000
96A180ALA00.001-0.01222.0360.0390.0390.0000.0000.0000.000
97A181THR0-0.012-0.01615.4630.0730.0730.0000.0000.0000.000
98A182VAL0-0.023-0.00217.4050.0670.0670.0000.0000.0000.000
99A183GLY0-0.020-0.00618.6090.0440.0440.0000.0000.0000.000
100A184GLY00.0200.02119.1190.0200.0200.0000.0000.0000.000
101A185ASN00.0030.00316.1960.0140.0140.0000.0000.0000.000
102A186GLY00.002-0.00714.1350.0940.0940.0000.0000.0000.000
103A187LEU0-0.039-0.02314.816-0.040-0.0400.0000.0000.0000.000
104A188THR0-0.040-0.02516.096-0.060-0.0600.0000.0000.0000.000
105A189GLY00.0860.02614.458-0.083-0.0830.0000.0000.0000.000
106A190ILE0-0.067-0.0187.7630.1480.1480.0000.0000.0000.000
107A191ILE00.0060.0019.624-0.200-0.2000.0000.0000.0000.000
108A192LEU00.0070.0036.7340.3720.3720.0000.0000.0000.000
109A193ARG10.8000.8845.1623.0893.0890.0000.0000.0000.000
110A194ALA0-0.0010.0047.8480.4110.4110.0000.0000.0000.000
111A195THR0-0.0040.01510.264-0.357-0.3570.0000.0000.0000.000
112A196ILE0-0.047-0.03810.8820.2080.2080.0000.0000.0000.000
113A197GLU-1-0.787-0.86414.474-0.436-0.4360.0000.0000.0000.000
114A198MET0-0.058-0.02413.2170.1020.1020.0000.0000.0000.000
115A199THR00.003-0.00518.3350.0370.0370.0000.0000.0000.000
116A200PRO00.0120.00721.342-0.023-0.0230.0000.0000.0000.000
117A201THR0-0.056-0.05122.3120.0500.0500.0000.0000.0000.000
118A202GLU-1-0.790-0.88424.927-0.192-0.1920.0000.0000.0000.000
119A203THR0-0.080-0.06226.2570.0030.0030.0000.0000.0000.000
120A204ALA00.0110.02122.798-0.009-0.0090.0000.0000.0000.000
121A205TYR0-0.073-0.03924.1360.0470.0470.0000.0000.0000.000
122A206PHE00.0280.02024.325-0.008-0.0080.0000.0000.0000.000
123A207ILE0-0.019-0.00929.1010.0030.0030.0000.0000.0000.000
124A208ALA0-0.004-0.00732.4420.0020.0020.0000.0000.0000.000
125A209ASP-1-0.793-0.87934.346-0.002-0.0020.0000.0000.0000.000
126A210GLY0-0.014-0.01736.2890.0080.0080.0000.0000.0000.000
127A211ASP-1-0.816-0.88838.4700.0270.0270.0000.0000.0000.000
128A212VAL0-0.032-0.02140.4680.0090.0090.0000.0000.0000.000
129A213THR0-0.0020.01242.988-0.004-0.0040.0000.0000.0000.000
130A214GLY0-0.017-0.02644.9200.0060.0060.0000.0000.0000.000
131A215SER0-0.068-0.07546.7850.0030.0030.0000.0000.0000.000
132A216LEU00.0300.01941.850-0.001-0.0010.0000.0000.0000.000
133A217ASP-1-0.833-0.90744.1380.0670.0670.0000.0000.0000.000
134A218GLU-1-0.783-0.85546.1170.0570.0570.0000.0000.0000.000
135A219THR0-0.034-0.02239.849-0.006-0.0060.0000.0000.0000.000
136A220ILE00.0290.02640.6320.0000.0000.0000.0000.0000.000
137A221ALA00.0290.02742.456-0.005-0.0050.0000.0000.0000.000
138A222PHE0-0.035-0.02838.680-0.005-0.0050.0000.0000.0000.000
139A223HIS10.7800.89235.902-0.067-0.0670.0000.0000.0000.000
140A224SER0-0.005-0.02339.8760.0010.0010.0000.0000.0000.000
141A225ASP-1-0.837-0.87742.3180.0180.0180.0000.0000.0000.000
142A226GLY00.0210.02140.626-0.006-0.0060.0000.0000.0000.000
143A227SER0-0.051-0.05039.927-0.005-0.0050.0000.0000.0000.000
144A228GLU-1-0.754-0.85535.0040.0420.0420.0000.0000.0000.000
145A229ALA0-0.0130.00035.036-0.004-0.0040.0000.0000.0000.000
146A230ASN0-0.085-0.03635.803-0.015-0.0150.0000.0000.0000.000
147A231TYR0-0.090-0.05933.520-0.004-0.0040.0000.0000.0000.000
148A232THR00.0340.00228.3700.0080.0080.0000.0000.0000.000
149A233TYR0-0.019-0.02023.4600.0210.0210.0000.0000.0000.000
150A234SER0-0.022-0.05729.385-0.002-0.0020.0000.0000.0000.000
151A235SER0-0.032-0.01130.0080.0210.0210.0000.0000.0000.000
152A236ALA00.0270.01332.138-0.012-0.0120.0000.0000.0000.000
153A237TRP0-0.0120.01129.1030.0220.0220.0000.0000.0000.000
154A238PHE00.003-0.00435.302-0.014-0.0140.0000.0000.0000.000
155A239ASP-1-0.746-0.81538.3870.1330.1330.0000.0000.0000.000
156A240ALA00.0690.02439.145-0.005-0.0050.0000.0000.0000.000
157A241ILE0-0.027-0.01039.9520.0020.0020.0000.0000.0000.000
158A242SER0-0.071-0.06243.567-0.006-0.0060.0000.0000.0000.000
159A243LYS10.9931.00246.439-0.088-0.0880.0000.0000.0000.000
160A244PRO00.0120.01148.533-0.003-0.0030.0000.0000.0000.000
161A245PRO0-0.012-0.01750.325-0.001-0.0010.0000.0000.0000.000
162A246LYS10.9790.97947.986-0.080-0.0800.0000.0000.0000.000
163A247LEU00.0090.02243.4530.0030.0030.0000.0000.0000.000
164A248GLY00.019-0.00141.894-0.006-0.0060.0000.0000.0000.000
165A249ARG10.8240.93442.365-0.105-0.1050.0000.0000.0000.000
166A250ALA00.006-0.01038.8960.0110.0110.0000.0000.0000.000
167A251ALA0-0.0110.00637.734-0.009-0.0090.0000.0000.0000.000
168A252ILE0-0.016-0.01636.5400.0120.0120.0000.0000.0000.000
169A253SER0-0.051-0.03033.036-0.007-0.0070.0000.0000.0000.000
170A254ARG10.8870.92732.984-0.022-0.0220.0000.0000.0000.000
171A255GLY00.0530.01731.956-0.002-0.0020.0000.0000.0000.000
172A256SER0-0.0310.00329.475-0.003-0.0030.0000.0000.0000.000
173A257LEU00.0100.01223.6400.0110.0110.0000.0000.0000.000
174A258ALA0-0.027-0.00528.075-0.002-0.0020.0000.0000.0000.000
175A259LYS10.9320.96229.5100.1350.1350.0000.0000.0000.000
176A260LEU00.019-0.01330.8740.0100.0100.0000.0000.0000.000
177A261ASP-1-0.950-0.97832.478-0.086-0.0860.0000.0000.0000.000
178A262GLN00.0560.03433.9120.0040.0040.0000.0000.0000.000
179A263LEU0-0.0400.00029.7710.0130.0130.0000.0000.0000.000
180A264PRO00.0420.02734.231-0.002-0.0020.0000.0000.0000.000
181A265SER00.0880.01935.331-0.004-0.0040.0000.0000.0000.000
182A266LYS10.8680.92635.0350.0290.0290.0000.0000.0000.000
183A267LEU0-0.008-0.00730.6460.0000.0000.0000.0000.0000.000
184A268GLN0-0.007-0.00930.721-0.018-0.0180.0000.0000.0000.000
185A269LYS10.9270.96932.0840.0830.0830.0000.0000.0000.000
186A270ASP-1-0.813-0.88125.724-0.245-0.2450.0000.0000.0000.000
187A271PRO00.0200.02527.1630.0120.0120.0000.0000.0000.000
188A272LEU0-0.0010.00822.6330.0190.0190.0000.0000.0000.000
189A273LYS10.8310.89621.4480.2370.2370.0000.0000.0000.000
190A274PHE00.0070.00517.8830.0460.0460.0000.0000.0000.000
191A308GLY0-0.001-0.01339.9280.0000.0000.0000.0000.0000.000
192A309THR0-0.036-0.01440.3410.0010.0010.0000.0000.0000.000
193A310TYR0-0.039-0.01034.7500.0030.0030.0000.0000.0000.000
194A311ARG10.8570.89839.942-0.020-0.0200.0000.0000.0000.000
195A312ASN00.0120.01137.799-0.004-0.0040.0000.0000.0000.000
196A313LYS10.8940.95735.015-0.055-0.0550.0000.0000.0000.000
197A314VAL00.0220.00932.0560.0030.0030.0000.0000.0000.000
198A315GLN0-0.047-0.01530.1790.0140.0140.0000.0000.0000.000
199A316ASN00.0710.04425.134-0.004-0.0040.0000.0000.0000.000
200A317LEU00.0700.03720.3650.0220.0220.0000.0000.0000.000
201A318THR0-0.014-0.03522.6090.0220.0220.0000.0000.0000.000
202A319GLN0-0.020-0.00624.8050.0060.0060.0000.0000.0000.000
203A320PHE0-0.046-0.00527.0840.0070.0070.0000.0000.0000.000
204A321TYR00.0680.01722.002-0.011-0.0110.0000.0000.0000.000
205A322HIS10.9180.97624.264-0.170-0.1700.0000.0000.0000.000
206A338GLY00.0230.00030.7720.0070.0070.0000.0000.0000.000
207A339PHE0-0.066-0.03630.184-0.029-0.0290.0000.0000.0000.000
208A340LEU00.0210.00929.6210.0220.0220.0000.0000.0000.000
209A341GLN0-0.067-0.03826.004-0.010-0.0100.0000.0000.0000.000
210A342TYR0-0.044-0.04128.9650.0080.0080.0000.0000.0000.000
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