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: 72RRK

Calculation Name: 3VXG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VXG

Chain ID: A

ChEMBL ID:

UniProt ID: Q76L36

Base Structure: X-ray

Registration Date: 2023-09-20

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 304
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4670422.321835
FMO2-HF: Nuclear repulsion 4552821.973087
FMO2-HF: Total energy -117600.348748
FMO2-MP2: Total energy -117953.787114


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:4:SER)


Summations of interaction energy for fragment #1(A:4:SER)
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.
-41.9-44.16633.54-16.683-14.589-0.032
Interaction energy analysis for fragmet #1(A:4:SER)
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 : -0.027
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].
3A6LEU0-0.0320.0102.074-8.180-5.1545.316-4.069-4.2730.034
4A7LEU00.008-0.0092.376-6.825-5.0691.231-1.027-1.9600.017
5A8PRO0-0.0010.0131.949-5.577-7.4656.897-2.722-2.286-0.029
6A9LYS10.8460.9504.153-0.0260.209-0.001-0.019-0.2150.000
7A10THR00.002-0.0212.210-1.0541.5801.434-1.846-2.2220.005
8A11PHE0-0.011-0.0284.7360.3790.476-0.001-0.007-0.0890.000
9A12ARG10.8720.9253.9850.9040.998-0.001-0.012-0.0800.000
10A13THR00.0230.0269.0360.1350.1350.0000.0000.0000.000
11A14LYS10.8400.91612.4290.0490.0490.0000.0000.0000.000
12A15SER0-0.050-0.04414.7320.0120.0120.0000.0000.0000.000
13A16GLY00.0040.00611.3350.0060.0060.0000.0000.0000.000
14A17LYS10.8020.8859.7070.1190.1190.0000.0000.0000.000
15A18GLU-1-0.792-0.8421.616-21.948-30.16818.665-6.981-3.464-0.059
16A19ILE0-0.0210.0055.4020.2850.2850.0000.0000.0000.000
17A20SER00.0320.0036.062-0.285-0.2850.0000.0000.0000.000
18A21ILE0-0.011-0.0088.5740.0680.0680.0000.0000.0000.000
19A22ALA00.0240.02411.748-0.012-0.0120.0000.0000.0000.000
20A23LEU0-0.046-0.01814.4120.0170.0170.0000.0000.0000.000
21A24GLY00.0290.00817.9900.0040.0040.0000.0000.0000.000
22A25THR0-0.033-0.04920.0310.0010.0010.0000.0000.0000.000
23A26GLY00.0150.01723.3760.0030.0030.0000.0000.0000.000
24A27THR0-0.041-0.02625.3320.0020.0020.0000.0000.0000.000
25A28LYS10.7890.88728.5000.0230.0230.0000.0000.0000.000
26A29TRP00.0200.00431.5120.0020.0020.0000.0000.0000.000
27A30LYS10.8810.94734.5130.0120.0120.0000.0000.0000.000
28A31GLN00.0070.01437.3520.0000.0000.0000.0000.0000.000
29A32ALA00.0080.00240.0770.0010.0010.0000.0000.0000.000
30A33GLN00.021-0.01933.893-0.001-0.0010.0000.0000.0000.000
31A34THR0-0.0110.00137.201-0.001-0.0010.0000.0000.0000.000
32A35ILE00.0160.02838.7150.0000.0000.0000.0000.0000.000
33A36ASN0-0.004-0.02334.108-0.001-0.0010.0000.0000.0000.000
34A37ASP-1-0.902-0.95434.490-0.019-0.0190.0000.0000.0000.000
35A38VAL00.0100.01732.018-0.001-0.0010.0000.0000.0000.000
36A39SER00.0580.02831.8200.0000.0000.0000.0000.0000.000
37A40THR00.025-0.00731.689-0.002-0.0020.0000.0000.0000.000
38A41GLU-1-0.925-0.94931.059-0.036-0.0360.0000.0000.0000.000
39A42LEU0-0.0100.00425.611-0.004-0.0040.0000.0000.0000.000
40A43VAL0-0.012-0.01027.045-0.004-0.0040.0000.0000.0000.000
41A44ASP-1-0.773-0.87727.145-0.045-0.0450.0000.0000.0000.000
42A45ASN0-0.045-0.03024.393-0.005-0.0050.0000.0000.0000.000
43A46ILE00.004-0.00421.725-0.007-0.0070.0000.0000.0000.000
44A47LEU00.0000.01222.460-0.010-0.0100.0000.0000.0000.000
45A48LEU0-0.052-0.01423.993-0.006-0.0060.0000.0000.0000.000
46A49GLY00.0400.00420.751-0.005-0.0050.0000.0000.0000.000
47A50LEU0-0.0120.00018.618-0.016-0.0160.0000.0000.0000.000
48A51LYS10.9270.97720.0970.0580.0580.0000.0000.0000.000
49A52LEU0-0.094-0.04520.4830.0000.0000.0000.0000.0000.000
50A53GLY00.0270.01216.813-0.003-0.0030.0000.0000.0000.000
51A54PHE0-0.035-0.00715.027-0.032-0.0320.0000.0000.0000.000
52A55ARG10.8630.91712.3360.1990.1990.0000.0000.0000.000
53A56HIS0-0.0100.00410.956-0.018-0.0180.0000.0000.0000.000
54A57ILE00.0060.01913.9450.0160.0160.0000.0000.0000.000
55A58ASP-1-0.764-0.86116.889-0.039-0.0390.0000.0000.0000.000
56A59THR0-0.008-0.01018.5530.0040.0040.0000.0000.0000.000
57A60ALA00.0370.01721.7330.0030.0030.0000.0000.0000.000
58A61GLU-1-0.737-0.81024.455-0.001-0.0010.0000.0000.0000.000
59A62ALA0-0.017-0.02527.682-0.001-0.0010.0000.0000.0000.000
60A63TYR0-0.0540.00321.1540.0030.0030.0000.0000.0000.000
61A64ASN0-0.009-0.01227.9590.0000.0000.0000.0000.0000.000
62A65THR00.0570.03126.4910.0000.0000.0000.0000.0000.000
63A66GLN00.0410.02525.762-0.003-0.0030.0000.0000.0000.000
64A67LYS10.8830.94126.7960.0180.0180.0000.0000.0000.000
65A68GLU-1-0.743-0.86427.794-0.029-0.0290.0000.0000.0000.000
66A69VAL00.0220.01321.859-0.004-0.0040.0000.0000.0000.000
67A70GLY00.0250.02124.762-0.004-0.0040.0000.0000.0000.000
68A71GLU-1-0.895-0.95026.794-0.026-0.0260.0000.0000.0000.000
69A72ALA0-0.010-0.00424.508-0.001-0.0010.0000.0000.0000.000
70A73LEU0-0.020-0.02620.486-0.004-0.0040.0000.0000.0000.000
71A74LYS10.8270.93124.4570.0300.0300.0000.0000.0000.000
72A75ARG10.7810.88327.3570.0430.0430.0000.0000.0000.000
73A76THR0-0.0020.00722.449-0.004-0.0040.0000.0000.0000.000
74A77ASP-1-0.890-0.93824.811-0.057-0.0570.0000.0000.0000.000
75A78VAL0-0.102-0.04218.294-0.004-0.0040.0000.0000.0000.000
76A79PRO00.0410.00919.8030.0040.0040.0000.0000.0000.000
77A80ARG10.8650.91917.4130.0450.0450.0000.0000.0000.000
78A81GLU-1-0.815-0.92818.078-0.051-0.0510.0000.0000.0000.000
79A82ASP-1-0.831-0.87115.245-0.204-0.2040.0000.0000.0000.000
80A83ILE0-0.042-0.01914.726-0.045-0.0450.0000.0000.0000.000
81A84TRP00.0080.00111.6100.0030.0030.0000.0000.0000.000
82A85VAL0-0.015-0.01514.0510.0030.0030.0000.0000.0000.000
83A86THR00.0340.01614.9770.0140.0140.0000.0000.0000.000
84A87THR0-0.003-0.01417.541-0.004-0.0040.0000.0000.0000.000
85A88LYS10.8060.87919.3980.0380.0380.0000.0000.0000.000
86A89TYR00.0550.03923.202-0.002-0.0020.0000.0000.0000.000
87A90SER0-0.037-0.02926.479-0.001-0.0010.0000.0000.0000.000
88A91PRO00.0070.00327.7110.0000.0000.0000.0000.0000.000
89A92GLY00.0580.00830.6780.0010.0010.0000.0000.0000.000
90A93TRP0-0.055-0.03625.470-0.002-0.0020.0000.0000.0000.000
91A94GLY00.0050.00731.292-0.001-0.0010.0000.0000.0000.000
92A95SER0-0.037-0.02034.1930.0000.0000.0000.0000.0000.000
93A96ILE0-0.0230.00435.5850.0010.0010.0000.0000.0000.000
94A97LYS10.8330.91335.929-0.005-0.0050.0000.0000.0000.000
95A98ALA0-0.0130.00433.197-0.002-0.0020.0000.0000.0000.000
96A99TYR0-0.0110.00033.6580.0000.0000.0000.0000.0000.000
97A100SER0-0.026-0.04431.9940.0000.0000.0000.0000.0000.000
98A101LYS10.8720.92234.170-0.008-0.0080.0000.0000.0000.000
99A102SER00.0470.00532.8470.0020.0020.0000.0000.0000.000
100A103PRO00.0260.01027.445-0.003-0.0030.0000.0000.0000.000
101A104SER00.0440.01228.6150.0000.0000.0000.0000.0000.000
102A105ASP-1-0.891-0.90130.2380.0110.0110.0000.0000.0000.000
103A106SER0-0.053-0.04928.436-0.003-0.0030.0000.0000.0000.000
104A107ILE00.0120.01224.824-0.004-0.0040.0000.0000.0000.000
105A108ASP-1-0.764-0.86927.1090.0140.0140.0000.0000.0000.000
106A109LYS10.7930.89529.7820.0010.0010.0000.0000.0000.000
107A110ALA0-0.019-0.00725.193-0.004-0.0040.0000.0000.0000.000
108A111LEU0-0.0080.00724.231-0.005-0.0050.0000.0000.0000.000
109A112ALA00.0000.00827.171-0.003-0.0030.0000.0000.0000.000
110A113GLN0-0.098-0.05628.999-0.002-0.0020.0000.0000.0000.000
111A114LEU00.023-0.00622.936-0.004-0.0040.0000.0000.0000.000
112A115GLY0-0.037-0.00826.715-0.004-0.0040.0000.0000.0000.000
113A116VAL0-0.053-0.02923.156-0.004-0.0040.0000.0000.0000.000
114A117ASP-1-0.798-0.89023.689-0.002-0.0020.0000.0000.0000.000
115A118TYR0-0.057-0.04316.7010.0090.0090.0000.0000.0000.000
116A119VAL00.0100.01119.631-0.014-0.0140.0000.0000.0000.000
117A120ASP-1-0.733-0.86114.204-0.058-0.0580.0000.0000.0000.000
118A121LEU0-0.0070.00113.4060.0290.0290.0000.0000.0000.000
119A122PHE00.0410.01216.508-0.014-0.0140.0000.0000.0000.000
120A123LEU0-0.030-0.00716.3840.0130.0130.0000.0000.0000.000
121A124ILE00.0230.01220.455-0.006-0.0060.0000.0000.0000.000
122A125HIS00.0360.00122.4670.0010.0010.0000.0000.0000.000
123A126SER00.0180.00824.108-0.004-0.0040.0000.0000.0000.000
124A127PRO00.0150.01523.9790.0040.0040.0000.0000.0000.000
125A128PHE0-0.048-0.02226.1340.0020.0020.0000.0000.0000.000
126A129PHE0-0.046-0.01327.298-0.002-0.0020.0000.0000.0000.000
127A130THR00.017-0.00332.1890.0010.0010.0000.0000.0000.000
128A131THR00.0460.01234.853-0.001-0.0010.0000.0000.0000.000
129A132GLU-1-0.797-0.88736.2170.0060.0060.0000.0000.0000.000
130A133GLN0-0.060-0.02134.6590.0000.0000.0000.0000.0000.000
131A134THR00.0570.01531.418-0.001-0.0010.0000.0000.0000.000
132A135HIS0-0.053-0.01934.2940.0010.0010.0000.0000.0000.000
133A136GLY00.0040.00536.4350.0010.0010.0000.0000.0000.000
134A137TYR0-0.029-0.00631.4780.0020.0020.0000.0000.0000.000
135A138THR00.014-0.02231.224-0.002-0.0020.0000.0000.0000.000
136A139LEU00.004-0.00524.6720.0000.0000.0000.0000.0000.000
137A140GLU-1-0.768-0.86426.7210.0340.0340.0000.0000.0000.000
138A141GLN00.0690.04427.6840.0020.0020.0000.0000.0000.000
139A142ALA0-0.042-0.02927.4180.0010.0010.0000.0000.0000.000
140A143TRP0-0.027-0.01518.341-0.008-0.0080.0000.0000.0000.000
141A144GLU-1-0.874-0.94424.7440.0520.0520.0000.0000.0000.000
142A145ALA0-0.017-0.00926.9600.0030.0030.0000.0000.0000.000
143A146LEU0-0.015-0.01221.135-0.002-0.0020.0000.0000.0000.000
144A147VAL0-0.0230.00022.0830.0080.0080.0000.0000.0000.000
145A148GLU-1-0.790-0.89023.6300.0760.0760.0000.0000.0000.000
146A149ALA0-0.026-0.01124.413-0.001-0.0010.0000.0000.0000.000
147A150LYS10.8350.91315.765-0.205-0.2050.0000.0000.0000.000
148A151LYS10.8040.89021.938-0.077-0.0770.0000.0000.0000.000
149A152ALA0-0.048-0.01524.136-0.001-0.0010.0000.0000.0000.000
150A153GLY0-0.016-0.00122.170-0.007-0.0070.0000.0000.0000.000
151A154LYS10.8150.88722.448-0.030-0.0300.0000.0000.0000.000
152A155VAL00.0100.00419.021-0.013-0.0130.0000.0000.0000.000
153A156ARG10.7840.89912.6440.0120.0120.0000.0000.0000.000
154A157GLU-1-0.831-0.91511.8290.3840.3840.0000.0000.0000.000
155A158ILE00.0330.02015.685-0.032-0.0320.0000.0000.0000.000
156A159GLY00.042-0.00515.9190.0240.0240.0000.0000.0000.000
157A160ILE0-0.054-0.01217.363-0.007-0.0070.0000.0000.0000.000
158A161SER0-0.007-0.01018.156-0.006-0.0060.0000.0000.0000.000
159A162ASN0-0.002-0.00920.4320.0000.0000.0000.0000.0000.000
160A163ALA00.0160.02219.7500.0010.0010.0000.0000.0000.000
161A164ALA00.0490.00920.586-0.006-0.0060.0000.0000.0000.000
162A165ILE00.0150.00419.9510.0060.0060.0000.0000.0000.000
163A166PRO00.0490.01321.8630.0070.0070.0000.0000.0000.000
164A167HIS00.0120.01722.9160.0030.0030.0000.0000.0000.000
165A168LEU00.0170.00517.0340.0050.0050.0000.0000.0000.000
166A169GLU-1-0.959-0.97020.6270.0390.0390.0000.0000.0000.000
167A170LYS10.8790.92522.921-0.021-0.0210.0000.0000.0000.000
168A171LEU0-0.0040.00520.0000.0020.0020.0000.0000.0000.000
169A172PHE0-0.012-0.00516.3810.0070.0070.0000.0000.0000.000
170A173ALA0-0.022-0.01021.4350.0060.0060.0000.0000.0000.000
171A174ALA0-0.0180.00324.8160.0000.0000.0000.0000.0000.000
172A175SER0-0.015-0.01621.1700.0040.0040.0000.0000.0000.000
173A176PRO0-0.030-0.00523.2120.0030.0030.0000.0000.0000.000
174A177SER0-0.023-0.05321.5860.0020.0020.0000.0000.0000.000
175A178PRO00.041-0.00717.190-0.002-0.0020.0000.0000.0000.000
176A179GLU-1-0.873-0.87716.7270.1990.1990.0000.0000.0000.000
177A180TYR0-0.073-0.06517.521-0.002-0.0020.0000.0000.0000.000
178A181TYR00.0340.03216.092-0.021-0.0210.0000.0000.0000.000
179A182PRO0-0.049-0.01216.3320.0130.0130.0000.0000.0000.000
180A183VAL00.0110.00011.2170.0170.0170.0000.0000.0000.000
181A184VAL0-0.021-0.01211.1510.0080.0080.0000.0000.0000.000
182A185ASN00.001-0.01513.3580.0000.0000.0000.0000.0000.000
183A186GLN0-0.043-0.03715.178-0.010-0.0100.0000.0000.0000.000
184A187ILE0-0.0200.00116.5400.0040.0040.0000.0000.0000.000
185A188GLU-1-0.721-0.84118.827-0.036-0.0360.0000.0000.0000.000
186A189PHE0-0.006-0.00316.397-0.001-0.0010.0000.0000.0000.000
187A190HIS0-0.001-0.02619.275-0.003-0.0030.0000.0000.0000.000
188A191PRO00.0330.01420.5240.0000.0000.0000.0000.0000.000
189A192PHE0-0.0180.01422.3830.0000.0000.0000.0000.0000.000
190A193LEU00.004-0.00123.1030.0040.0040.0000.0000.0000.000
191A194GLN0-0.0250.00219.397-0.009-0.0090.0000.0000.0000.000
192A195ASN0-0.002-0.02018.589-0.008-0.0080.0000.0000.0000.000
193A196GLN00.0500.04020.1300.0060.0060.0000.0000.0000.000
194A197SER00.0330.01921.5610.0060.0060.0000.0000.0000.000
195A198LYS10.9980.98421.6990.0100.0100.0000.0000.0000.000
196A199ASN0-0.035-0.02819.8150.0000.0000.0000.0000.0000.000
197A200ILE0-0.0020.02117.566-0.007-0.0070.0000.0000.0000.000
198A201VAL00.0670.03613.2620.0060.0060.0000.0000.0000.000
199A202ARG10.8590.90813.4760.0540.0540.0000.0000.0000.000
200A203PHE00.0250.01113.910-0.003-0.0030.0000.0000.0000.000
201A204CYS0-0.054-0.03312.5970.0250.0250.0000.0000.0000.000
202A205GLN0-0.008-0.0069.1030.0320.0320.0000.0000.0000.000
203A206GLU-1-0.852-0.9099.777-0.055-0.0550.0000.0000.0000.000
204A207HIS10.8270.92312.364-0.011-0.0110.0000.0000.0000.000
205A208GLY00.0270.0318.7200.0540.0540.0000.0000.0000.000
206A209ILE0-0.064-0.0239.5740.1030.1030.0000.0000.0000.000
207A210LEU0-0.025-0.0087.159-0.071-0.0710.0000.0000.0000.000
208A211VAL00.0240.0089.4770.0080.0080.0000.0000.0000.000
209A212GLU-1-0.788-0.89011.254-0.072-0.0720.0000.0000.0000.000
210A213ALA0-0.010-0.00313.4990.0050.0050.0000.0000.0000.000
211A214PHE0-0.007-0.00716.219-0.006-0.0060.0000.0000.0000.000
212A215SER0-0.005-0.01719.2010.0010.0010.0000.0000.0000.000
213A216PRO00.0500.03717.2590.0020.0020.0000.0000.0000.000
214A217LEU0-0.020-0.02119.9440.0000.0000.0000.0000.0000.000
215A218ALA00.0320.02422.5510.0020.0020.0000.0000.0000.000
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