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: 94662

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 OptH
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 -4656273.988313
FMO2-HF: Nuclear repulsion 4538675.517388
FMO2-HF: Total energy -117598.470925
FMO2-MP2: Total energy -117952.034007


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.
-47.837-46.27627.968-15.379-14.15-0.047
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 : -0.036 / q_NPA : -0.040
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].
3A6LEU0-0.0610.0032.194-6.752-3.2784.975-4.093-4.3550.026
4A7LEU00.012-0.0102.149-7.231-6.5732.764-1.187-2.2340.019
5A8PRO00.0000.0162.186-5.201-4.7642.710-1.563-1.585-0.019
6A9LYS10.9320.9774.279-0.2100.010-0.001-0.029-0.1900.000
7A10THR0-0.016-0.0422.491-0.2781.9010.479-1.134-1.5250.003
8A11PHE0-0.003-0.0074.9010.7470.825-0.001-0.004-0.0730.000
9A12ARG10.9540.9874.417-1.148-1.095-0.001-0.008-0.0440.000
10A13THR00.0340.0169.0300.1430.1430.0000.0000.0000.000
11A14LYS10.9380.97512.3130.0620.0620.0000.0000.0000.000
12A15SER0-0.040-0.02814.6950.0270.0270.0000.0000.0000.000
13A16GLY0-0.004-0.00311.3120.0220.0220.0000.0000.0000.000
14A17LYS10.8360.9159.5820.2070.2070.0000.0000.0000.000
15A18GLU-1-0.823-0.8601.647-28.000-33.53817.043-7.361-4.144-0.076
16A19ILE0-0.0160.0045.5930.2390.2390.0000.0000.0000.000
17A20SER00.0390.0096.052-0.518-0.5180.0000.0000.0000.000
18A21ILE0-0.001-0.0108.4030.1130.1130.0000.0000.0000.000
19A22ALA00.0170.01711.2850.0120.0120.0000.0000.0000.000
20A23LEU0-0.041-0.01314.1120.0260.0260.0000.0000.0000.000
21A24GLY00.023-0.00317.6820.0080.0080.0000.0000.0000.000
22A25THR0-0.018-0.01719.9100.0070.0070.0000.0000.0000.000
23A26GLY00.0110.02423.2760.0070.0070.0000.0000.0000.000
24A27THR0-0.044-0.02125.2130.0030.0030.0000.0000.0000.000
25A28LYS10.8640.93828.2400.0570.0570.0000.0000.0000.000
26A29TRP00.0050.00331.2190.0030.0030.0000.0000.0000.000
27A30LYS10.9190.97633.2800.0440.0440.0000.0000.0000.000
28A31GLN00.0180.01837.0020.0010.0010.0000.0000.0000.000
29A32ALA0-0.0030.00040.6120.0020.0020.0000.0000.0000.000
30A33GLN00.012-0.02534.598-0.003-0.0030.0000.0000.0000.000
31A34THR00.0120.00837.023-0.002-0.0020.0000.0000.0000.000
32A35ILE0-0.0010.01538.4810.0000.0000.0000.0000.0000.000
33A36ASN0-0.038-0.03934.580-0.004-0.0040.0000.0000.0000.000
34A37ASP-1-0.933-0.95534.873-0.046-0.0460.0000.0000.0000.000
35A38VAL00.0200.00832.028-0.002-0.0020.0000.0000.0000.000
36A39SER00.0340.01231.6610.0010.0010.0000.0000.0000.000
37A40THR00.0410.00231.718-0.004-0.0040.0000.0000.0000.000
38A41GLU-1-0.921-0.94331.179-0.074-0.0740.0000.0000.0000.000
39A42LEU0-0.022-0.00625.645-0.007-0.0070.0000.0000.0000.000
40A43VAL00.002-0.00827.097-0.009-0.0090.0000.0000.0000.000
41A44ASP-1-0.885-0.94227.263-0.082-0.0820.0000.0000.0000.000
42A45ASN0-0.033-0.01623.982-0.006-0.0060.0000.0000.0000.000
43A46ILE0-0.004-0.01221.715-0.013-0.0130.0000.0000.0000.000
44A47LEU00.0060.00622.611-0.013-0.0130.0000.0000.0000.000
45A48LEU0-0.038-0.00223.913-0.008-0.0080.0000.0000.0000.000
46A49GLY00.0410.00620.843-0.008-0.0080.0000.0000.0000.000
47A50LEU00.0020.00518.323-0.023-0.0230.0000.0000.0000.000
48A51LYS10.9380.97319.8720.0980.0980.0000.0000.0000.000
49A52LEU0-0.101-0.06120.545-0.002-0.0020.0000.0000.0000.000
50A53GLY00.0110.01616.935-0.006-0.0060.0000.0000.0000.000
51A54PHE0-0.021-0.00215.070-0.048-0.0480.0000.0000.0000.000
52A55ARG10.8730.92712.5300.3060.3060.0000.0000.0000.000
53A56HIS00.0000.02910.6290.0270.0270.0000.0000.0000.000
54A57ILE00.0050.01214.0880.0190.0190.0000.0000.0000.000
55A58ASP-1-0.785-0.87816.541-0.154-0.1540.0000.0000.0000.000
56A59THR0-0.008-0.02418.3740.0140.0140.0000.0000.0000.000
57A60ALA00.0160.00321.542-0.001-0.0010.0000.0000.0000.000
58A61GLU-1-0.744-0.82824.262-0.030-0.0300.0000.0000.0000.000
59A62ALA0-0.026-0.03327.4530.0010.0010.0000.0000.0000.000
60A63TYR00.0080.02022.0590.0000.0000.0000.0000.0000.000
61A64ASN0-0.048-0.03127.9190.0030.0030.0000.0000.0000.000
62A65THR00.0440.00025.3150.0020.0020.0000.0000.0000.000
63A66GLN00.0450.03825.150-0.007-0.0070.0000.0000.0000.000
64A67LYS10.9680.99426.8580.0420.0420.0000.0000.0000.000
65A68GLU-1-0.767-0.88427.867-0.066-0.0660.0000.0000.0000.000
66A69VAL00.0200.00822.027-0.005-0.0050.0000.0000.0000.000
67A70GLY00.0280.02124.964-0.005-0.0050.0000.0000.0000.000
68A71GLU-1-0.992-1.00426.843-0.054-0.0540.0000.0000.0000.000
69A72ALA0-0.008-0.00724.5390.0010.0010.0000.0000.0000.000
70A73LEU0-0.031-0.02420.653-0.006-0.0060.0000.0000.0000.000
71A74LYS10.8900.96124.3860.0540.0540.0000.0000.0000.000
72A75ARG10.9380.96227.8270.0720.0720.0000.0000.0000.000
73A76THR0-0.0400.00122.424-0.004-0.0040.0000.0000.0000.000
74A77ASP-1-0.864-0.92525.108-0.078-0.0780.0000.0000.0000.000
75A78VAL0-0.134-0.06318.229-0.005-0.0050.0000.0000.0000.000
76A79PRO00.0630.03119.5680.0060.0060.0000.0000.0000.000
77A80ARG10.8980.93817.4110.0910.0910.0000.0000.0000.000
78A81GLU-1-0.892-0.95817.680-0.091-0.0910.0000.0000.0000.000
79A82ASP-1-0.865-0.91214.928-0.222-0.2220.0000.0000.0000.000
80A83ILE0-0.051-0.02514.413-0.069-0.0690.0000.0000.0000.000
81A84TRP0-0.040-0.02411.134-0.004-0.0040.0000.0000.0000.000
82A85VAL0-0.009-0.01414.271-0.005-0.0050.0000.0000.0000.000
83A86THR00.0510.01014.7100.0180.0180.0000.0000.0000.000
84A87THR0-0.009-0.02817.4740.0000.0000.0000.0000.0000.000
85A88LYS10.8010.87619.3150.1220.1220.0000.0000.0000.000
86A89TYR00.0660.03922.9530.0020.0020.0000.0000.0000.000
87A90SER0-0.027-0.02126.218-0.001-0.0010.0000.0000.0000.000
88A91PRO00.0190.01027.8280.0030.0030.0000.0000.0000.000
89A92GLY00.0720.01930.8610.0030.0030.0000.0000.0000.000
90A93TRP0-0.034-0.01725.753-0.001-0.0010.0000.0000.0000.000
91A94GLY00.0260.01231.6480.0000.0000.0000.0000.0000.000
92A95SER0-0.042-0.01434.6290.0020.0020.0000.0000.0000.000
93A96ILE0-0.0060.00036.2400.0030.0030.0000.0000.0000.000
94A97LYS10.8050.91436.3910.0100.0100.0000.0000.0000.000
95A98ALA00.0030.01332.989-0.002-0.0020.0000.0000.0000.000
96A99TYR0-0.003-0.01133.5010.0010.0010.0000.0000.0000.000
97A100SER0-0.012-0.02431.8920.0010.0010.0000.0000.0000.000
98A101LYS10.9450.95934.2430.0090.0090.0000.0000.0000.000
99A102SER00.0320.01733.4520.0020.0020.0000.0000.0000.000
100A103PRO00.0150.00628.019-0.004-0.0040.0000.0000.0000.000
101A104SER00.0450.02628.858-0.002-0.0020.0000.0000.0000.000
102A105ASP-1-0.851-0.90630.507-0.006-0.0060.0000.0000.0000.000
103A106SER0-0.083-0.05828.191-0.005-0.0050.0000.0000.0000.000
104A107ILE00.0120.00225.082-0.005-0.0050.0000.0000.0000.000
105A108ASP-1-0.856-0.92827.373-0.007-0.0070.0000.0000.0000.000
106A109LYS10.7970.90330.0670.0320.0320.0000.0000.0000.000
107A110ALA0-0.025-0.01025.084-0.005-0.0050.0000.0000.0000.000
108A111LEU00.0020.00224.489-0.007-0.0070.0000.0000.0000.000
109A112ALA0-0.018-0.00227.187-0.003-0.0030.0000.0000.0000.000
110A113GLN0-0.101-0.06028.911-0.005-0.0050.0000.0000.0000.000
111A114LEU00.015-0.00422.781-0.005-0.0050.0000.0000.0000.000
112A115GLY0-0.058-0.01726.173-0.006-0.0060.0000.0000.0000.000
113A116VAL0-0.055-0.01522.601-0.003-0.0030.0000.0000.0000.000
114A117ASP-1-0.893-0.95324.608-0.013-0.0130.0000.0000.0000.000
115A118TYR00.019-0.00817.4220.0170.0170.0000.0000.0000.000
116A119VAL00.0040.00419.871-0.018-0.0180.0000.0000.0000.000
117A120ASP-1-0.765-0.87814.321-0.120-0.1200.0000.0000.0000.000
118A121LEU00.0220.01513.3160.0290.0290.0000.0000.0000.000
119A122PHE00.0150.00416.489-0.014-0.0140.0000.0000.0000.000
120A123LEU0-0.022-0.00716.3560.0160.0160.0000.0000.0000.000
121A124ILE00.0360.01420.413-0.002-0.0020.0000.0000.0000.000
122A125HIS0-0.018-0.02422.545-0.004-0.0040.0000.0000.0000.000
123A126SER00.006-0.00124.199-0.005-0.0050.0000.0000.0000.000
124A127PRO00.0430.02724.4200.0060.0060.0000.0000.0000.000
125A128PHE0-0.047-0.02326.5960.0050.0050.0000.0000.0000.000
126A129PHE0-0.033-0.00527.741-0.002-0.0020.0000.0000.0000.000
127A130THR00.0140.00732.6130.0030.0030.0000.0000.0000.000
128A131THR00.024-0.00834.880-0.002-0.0020.0000.0000.0000.000
129A132GLU-1-0.784-0.87536.417-0.007-0.0070.0000.0000.0000.000
130A133GLN0-0.087-0.05035.1240.0010.0010.0000.0000.0000.000
131A134THR00.035-0.00331.709-0.001-0.0010.0000.0000.0000.000
132A135HIS0-0.081-0.03534.6520.0030.0030.0000.0000.0000.000
133A136GLY0-0.009-0.00637.3030.0020.0020.0000.0000.0000.000
134A137TYR00.0050.00531.6670.0010.0010.0000.0000.0000.000
135A138THR00.0540.02232.078-0.004-0.0040.0000.0000.0000.000
136A139LEU00.015-0.00325.0180.0000.0000.0000.0000.0000.000
137A140GLU-1-0.845-0.93327.2760.0180.0180.0000.0000.0000.000
138A141GLN00.0760.04628.1580.0010.0010.0000.0000.0000.000
139A142ALA0-0.019-0.01127.8690.0010.0010.0000.0000.0000.000
140A143TRP0-0.040-0.02218.677-0.012-0.0120.0000.0000.0000.000
141A144GLU-1-0.902-0.95324.9750.0450.0450.0000.0000.0000.000
142A145ALA0-0.006-0.00227.3950.0040.0040.0000.0000.0000.000
143A146LEU0-0.036-0.02621.491-0.002-0.0020.0000.0000.0000.000
144A147VAL0-0.006-0.00322.5920.0070.0070.0000.0000.0000.000
145A148GLU-1-0.940-0.97024.0470.0620.0620.0000.0000.0000.000
146A149ALA0-0.026-0.00724.4700.0010.0010.0000.0000.0000.000
147A150LYS10.8760.94616.746-0.170-0.1700.0000.0000.0000.000
148A151LYS10.9270.96922.345-0.080-0.0800.0000.0000.0000.000
149A152ALA0-0.031-0.00524.6780.0030.0030.0000.0000.0000.000
150A153GLY0-0.035-0.00922.349-0.005-0.0050.0000.0000.0000.000
151A154LYS10.9380.97723.118-0.020-0.0200.0000.0000.0000.000
152A155VAL0-0.0030.00119.255-0.018-0.0180.0000.0000.0000.000
153A156ARG10.7500.88712.7240.0540.0540.0000.0000.0000.000
154A157GLU-1-0.906-0.96012.7180.2840.2840.0000.0000.0000.000
155A158ILE00.0180.01616.088-0.035-0.0350.0000.0000.0000.000
156A159GLY00.038-0.00916.4470.0210.0210.0000.0000.0000.000
157A160ILE0-0.047-0.00817.5730.0010.0010.0000.0000.0000.000
158A161SER0-0.0070.00318.170-0.017-0.0170.0000.0000.0000.000
159A162ASN0-0.022-0.02320.4770.0060.0060.0000.0000.0000.000
160A163ALA00.0110.01919.9620.0080.0080.0000.0000.0000.000
161A164ALA00.0560.00920.763-0.009-0.0090.0000.0000.0000.000
162A165ILE00.008-0.00820.3460.0060.0060.0000.0000.0000.000
163A166PRO00.0520.01922.1670.0080.0080.0000.0000.0000.000
164A167HIS00.0250.02023.2310.0030.0030.0000.0000.0000.000
165A168LEU00.000-0.00717.5160.0060.0060.0000.0000.0000.000
166A169GLU-1-0.941-0.96021.1590.0290.0290.0000.0000.0000.000
167A170LYS10.8960.94623.383-0.003-0.0030.0000.0000.0000.000
168A171LEU0-0.0030.00720.3530.0030.0030.0000.0000.0000.000
169A172PHE0-0.014-0.00816.9410.0080.0080.0000.0000.0000.000
170A173ALA0-0.020-0.00721.8610.0090.0090.0000.0000.0000.000
171A174ALA00.0020.01125.2510.0010.0010.0000.0000.0000.000
172A175SER0-0.054-0.02421.5790.0030.0030.0000.0000.0000.000
173A176PRO0-0.0260.00423.5830.0030.0030.0000.0000.0000.000
174A177SER0-0.011-0.02822.075-0.001-0.0010.0000.0000.0000.000
175A178PRO00.050-0.00617.670-0.006-0.0060.0000.0000.0000.000
176A179GLU-1-0.938-0.94817.0290.2260.2260.0000.0000.0000.000
177A180TYR0-0.031-0.02917.510-0.004-0.0040.0000.0000.0000.000
178A181TYR00.0320.02916.231-0.024-0.0240.0000.0000.0000.000
179A182PRO0-0.0270.00016.5270.0090.0090.0000.0000.0000.000
180A183VAL00.002-0.00311.4340.0220.0220.0000.0000.0000.000
181A184VAL0-0.014-0.00411.374-0.014-0.0140.0000.0000.0000.000
182A185ASN0-0.004-0.02513.4900.0210.0210.0000.0000.0000.000
183A186GLN0-0.055-0.01815.226-0.005-0.0050.0000.0000.0000.000
184A187ILE0-0.0100.00116.8600.0220.0220.0000.0000.0000.000
185A188GLU-1-0.751-0.85418.794-0.097-0.0970.0000.0000.0000.000
186A189PHE0-0.012-0.01716.5980.0010.0010.0000.0000.0000.000
187A190HIS0-0.013-0.02619.356-0.010-0.0100.0000.0000.0000.000
188A191PRO00.0230.01120.6710.0050.0050.0000.0000.0000.000
189A192PHE00.0030.02222.3830.0040.0040.0000.0000.0000.000
190A193LEU0-0.018-0.00423.2660.0100.0100.0000.0000.0000.000
191A194GLN00.0050.00119.724-0.014-0.0140.0000.0000.0000.000
192A195ASN0-0.042-0.03819.038-0.012-0.0120.0000.0000.0000.000
193A196GLN00.0630.03820.7530.0090.0090.0000.0000.0000.000
194A197SER00.0440.02322.0050.0100.0100.0000.0000.0000.000
195A198LYS10.9940.97422.2400.0230.0230.0000.0000.0000.000
196A199ASN0-0.048-0.01820.344-0.003-0.0030.0000.0000.0000.000
197A200ILE00.0390.03017.698-0.002-0.0020.0000.0000.0000.000
198A201VAL00.0650.03113.6030.0020.0020.0000.0000.0000.000
199A202ARG11.0130.99913.9410.0600.0600.0000.0000.0000.000
200A203PHE00.0110.01314.4390.0030.0030.0000.0000.0000.000
201A204CYS0-0.049-0.02713.0060.0270.0270.0000.0000.0000.000
202A205GLN0-0.032-0.0169.7770.0320.0320.0000.0000.0000.000
203A206GLU-1-0.955-0.97410.139-0.058-0.0580.0000.0000.0000.000
204A207HIS10.8320.92712.6230.0090.0090.0000.0000.0000.000
205A208GLY00.0150.0219.3200.0510.0510.0000.0000.0000.000
206A209ILE0-0.071-0.02610.3130.0690.0690.0000.0000.0000.000
207A210LEU0-0.017-0.0077.006-0.052-0.0520.0000.0000.0000.000
208A211VAL00.0260.0139.6460.0260.0260.0000.0000.0000.000
209A212GLU-1-0.829-0.93011.418-0.291-0.2910.0000.0000.0000.000
210A213ALA0-0.008-0.00313.3970.0320.0320.0000.0000.0000.000
211A214PHE0-0.006-0.00616.072-0.011-0.0110.0000.0000.0000.000
212A215SER0-0.014-0.02619.0410.0070.0070.0000.0000.0000.000
213A216PRO00.0590.03917.2160.0100.0100.0000.0000.0000.000
214A217LEU0-0.036-0.02919.5030.0040.0040.0000.0000.0000.000
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