Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3J4ML

Calculation Name: 1VLW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VLW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WXS1

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2337378.642938
FMO2-HF: Nuclear repulsion 2258791.983094
FMO2-HF: Total energy -78586.659844
FMO2-MP2: Total energy -78813.758476


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:HIS)


Summations of interaction energy for fragment #1(A:-1:HIS)
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.
-43.702-41.50721.786-8.843-15.1350.028
Interaction energy analysis for fragmet #1(A:-1:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.093 / q_NPA : 0.012
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].
3A1MET00.0250.0063.862-1.488-0.079-0.009-0.584-0.8160.001
4A2LYS10.9400.9942.005-16.569-19.68314.333-4.766-6.4530.032
5A3MET00.0520.0232.354-6.028-6.3427.112-1.836-4.9630.009
6A4GLU-1-0.893-0.9564.5800.0030.2620.003-0.064-0.1970.000
7A5GLU-1-0.915-0.9787.4211.1481.1480.0000.0000.0000.000
8A6LEU0-0.021-0.0033.280-1.202-0.8520.024-0.082-0.291-0.001
9A7PHE00.016-0.0037.189-0.579-0.5790.0000.0000.0000.000
10A8LYS10.9400.98710.103-1.483-1.4830.0000.0000.0000.000
11A9LYS10.9090.9569.815-0.075-0.0750.0000.0000.0000.000
12A10HIS00.021-0.0048.6990.0070.0070.0000.0000.0000.000
13A11LYS10.8930.96912.522-0.540-0.5400.0000.0000.0000.000
14A12ILE00.0310.01214.5200.0290.0290.0000.0000.0000.000
15A13VAL0-0.010-0.00612.416-0.060-0.0600.0000.0000.0000.000
16A14ALA00.0180.00914.5840.0640.0640.0000.0000.0000.000
17A15VAL0-0.050-0.01816.153-0.075-0.0750.0000.0000.0000.000
18A16LEU00.0440.01517.8160.0530.0530.0000.0000.0000.000
19A17ARG10.8680.96820.0670.2760.2760.0000.0000.0000.000
20A18ALA0-0.019-0.01523.0430.0080.0080.0000.0000.0000.000
21A19ASN0-0.030-0.02225.2890.0000.0000.0000.0000.0000.000
22A20SER00.0380.00926.4700.0060.0060.0000.0000.0000.000
23A21VAL00.0970.06522.092-0.020-0.0200.0000.0000.0000.000
24A22GLU-1-0.889-0.95923.074-0.546-0.5460.0000.0000.0000.000
25A23GLU-1-0.825-0.91124.752-0.369-0.3690.0000.0000.0000.000
26A24ALA00.004-0.01820.720-0.003-0.0030.0000.0000.0000.000
27A25LYS10.9030.96219.6510.7170.7170.0000.0000.0000.000
28A26GLU-1-0.901-0.95220.675-0.452-0.4520.0000.0000.0000.000
29A27LYS10.8690.94121.8010.3940.3940.0000.0000.0000.000
30A28ALA00.000-0.01716.8520.0110.0110.0000.0000.0000.000
31A29LEU0-0.035-0.00517.739-0.048-0.0480.0000.0000.0000.000
32A30ALA00.0150.02219.6790.0050.0050.0000.0000.0000.000
33A31VAL00.008-0.02017.1150.0450.0450.0000.0000.0000.000
34A32PHE0-0.020-0.00412.6730.0210.0210.0000.0000.0000.000
35A33GLU-1-0.852-0.92117.015-0.477-0.4770.0000.0000.0000.000
36A34GLY0-0.040-0.01220.0910.0470.0470.0000.0000.0000.000
37A35GLY0-0.028-0.01817.4150.0630.0630.0000.0000.0000.000
38A36VAL0-0.052-0.02115.1620.0340.0340.0000.0000.0000.000
39A37HIS00.000-0.00910.364-0.113-0.1130.0000.0000.0000.000
40A38LEU0-0.0360.0148.068-0.291-0.2910.0000.0000.0000.000
41A39ILE00.0170.00711.1270.1990.1990.0000.0000.0000.000
42A40GLU-1-0.899-0.96412.533-0.516-0.5160.0000.0000.0000.000
43A41ILE00.0280.01514.3900.1280.1280.0000.0000.0000.000
44A42THR0-0.077-0.06416.067-0.002-0.0020.0000.0000.0000.000
45A43PHE00.067-0.00515.484-0.013-0.0130.0000.0000.0000.000
46A44THR0-0.039-0.02419.4540.0390.0390.0000.0000.0000.000
47A45VAL0-0.077-0.01321.0170.0350.0350.0000.0000.0000.000
48A46PRO00.0110.00422.470-0.029-0.0290.0000.0000.0000.000
49A47ASP-1-0.859-0.92822.713-0.569-0.5690.0000.0000.0000.000
50A48ALA00.0060.01418.281-0.066-0.0660.0000.0000.0000.000
51A49ASP-1-0.895-0.97016.729-0.909-0.9090.0000.0000.0000.000
52A50THR00.0340.03316.967-0.149-0.1490.0000.0000.0000.000
53A51VAL0-0.002-0.00217.693-0.040-0.0400.0000.0000.0000.000
54A52ILE0-0.035-0.02312.338-0.041-0.0410.0000.0000.0000.000
55A53LYS10.9881.00514.0370.9140.9140.0000.0000.0000.000
56A54GLU-1-0.947-0.98215.218-0.878-0.8780.0000.0000.0000.000
57A55LEU0-0.0230.00114.5720.0930.0930.0000.0000.0000.000
58A56SER00.0260.01112.315-0.099-0.0990.0000.0000.0000.000
59A57PHE00.0690.03513.235-0.119-0.1190.0000.0000.0000.000
60A58LEU00.0080.00714.0890.0430.0430.0000.0000.0000.000
61A59LYS10.8800.9335.5605.7775.7770.0000.0000.0000.000
62A60GLU-1-0.989-0.99710.037-1.631-1.6310.0000.0000.0000.000
63A61LYS10.8130.92112.3471.2811.2810.0000.0000.0000.000
64A62GLY00.0050.0109.5620.1750.1750.0000.0000.0000.000
65A63ALA0-0.049-0.0169.4770.0720.0720.0000.0000.0000.000
66A64ILE0-0.028-0.0214.709-0.505-0.436-0.001-0.002-0.0660.000
67A65ILE00.0350.0147.8950.6620.6620.0000.0000.0000.000
68A66GLY00.0400.0319.125-0.524-0.5240.0000.0000.0000.000
69A67ALA0-0.0120.01010.4110.1590.1590.0000.0000.0000.000
70A68GLY00.0470.00512.5650.0970.0970.0000.0000.0000.000
71A69THR0-0.086-0.05715.2500.0040.0040.0000.0000.0000.000
72A70VAL00.0060.02613.718-0.005-0.0050.0000.0000.0000.000
73A71THR0-0.052-0.07716.7320.0760.0760.0000.0000.0000.000
74A72SER00.0760.05218.5060.0260.0260.0000.0000.0000.000
75A73VAL00.1070.02715.153-0.079-0.0790.0000.0000.0000.000
76A74GLU-1-0.915-0.95016.500-0.472-0.4720.0000.0000.0000.000
77A75GLN00.0260.03217.493-0.072-0.0720.0000.0000.0000.000
78A76CYS00.0280.02411.800-0.093-0.0930.0000.0000.0000.000
79A77ARG10.9310.98112.9770.4320.4320.0000.0000.0000.000
80A78LYS10.9990.99914.2540.4790.4790.0000.0000.0000.000
81A79ALA00.0040.00212.539-0.113-0.1130.0000.0000.0000.000
82A80VAL0-0.018-0.0208.847-0.213-0.2130.0000.0000.0000.000
83A81GLU-1-0.979-0.99310.448-1.335-1.3350.0000.0000.0000.000
84A82SER0-0.098-0.06913.1410.0060.0060.0000.0000.0000.000
85A83GLY0-0.0260.0019.390-0.003-0.0030.0000.0000.0000.000
86A84ALA0-0.073-0.0278.685-0.409-0.4090.0000.0000.0000.000
87A85GLU-1-0.894-0.9643.711-10.693-10.1850.004-0.157-0.355-0.001
88A86PHE0-0.067-0.0354.4440.3480.506-0.001-0.013-0.1450.000
89A87ILE00.0260.0186.790-0.022-0.0220.0000.0000.0000.000
90A88VAL00.0110.0069.8880.2660.2660.0000.0000.0000.000
91A89SER0-0.025-0.00312.768-0.077-0.0770.0000.0000.0000.000
92A90PRO0-0.034-0.00916.0550.0640.0640.0000.0000.0000.000
93A91HIS00.0270.00119.0200.0540.0540.0000.0000.0000.000
94A92LEU00.0080.01715.563-0.003-0.0030.0000.0000.0000.000
95A93ASP-1-0.771-0.87116.396-0.142-0.1420.0000.0000.0000.000
96A94GLU-1-0.907-0.98815.5590.1960.1960.0000.0000.0000.000
97A95GLU-1-0.881-0.93215.662-0.071-0.0710.0000.0000.0000.000
98A96ILE0-0.002-0.00312.421-0.069-0.0690.0000.0000.0000.000
99A97SER00.0040.00811.372-0.029-0.0290.0000.0000.0000.000
100A98GLN0-0.056-0.02310.5790.0890.0890.0000.0000.0000.000
101A99PHE00.0620.03411.3790.0040.0040.0000.0000.0000.000
102A100CYS0-0.039-0.0097.408-0.233-0.2330.0000.0000.0000.000
103A101LYS10.8890.9516.628-0.877-0.8770.0000.0000.0000.000
104A102GLU-1-0.931-0.9677.407-0.094-0.0940.0000.0000.0000.000
105A103LYS10.8630.9458.2780.9790.9790.0000.0000.0000.000
106A104GLY00.0140.0194.393-0.613-0.505-0.001-0.012-0.0940.000
107A105VAL0-0.073-0.0462.845-6.654-4.5400.310-1.181-1.242-0.012
108A106PHE0-0.012-0.0153.3760.7251.2950.013-0.140-0.4420.000
109A107TYR00.020-0.0424.955-0.0550.023-0.001-0.006-0.0710.000
110A108MET0-0.064-0.0268.6140.4100.4100.0000.0000.0000.000
111A109PRO00.0110.01011.167-0.119-0.1190.0000.0000.0000.000
112A110GLY0-0.0110.00014.4740.0920.0920.0000.0000.0000.000
113A111VAL0-0.049-0.03017.8170.0160.0160.0000.0000.0000.000
114A112MET00.0250.01220.499-0.012-0.0120.0000.0000.0000.000
115A113THR00.0320.01923.8820.0140.0140.0000.0000.0000.000
116A114PRO00.0890.01323.5800.0270.0270.0000.0000.0000.000
117A115THR0-0.0020.00323.8460.0360.0360.0000.0000.0000.000
118A116GLU-1-0.870-0.94421.7420.1660.1660.0000.0000.0000.000
119A117LEU0-0.0010.01419.4760.0280.0280.0000.0000.0000.000
120A118VAL0-0.007-0.01218.9580.0650.0650.0000.0000.0000.000
121A119LYS10.9330.97219.760-0.142-0.1420.0000.0000.0000.000
122A120ALA00.0510.02915.6720.0180.0180.0000.0000.0000.000
123A121MET0-0.013-0.01615.0350.0620.0620.0000.0000.0000.000
124A122LYS10.9110.96515.510-0.324-0.3240.0000.0000.0000.000
125A123LEU0-0.0130.01614.1000.0130.0130.0000.0000.0000.000
126A124GLY00.003-0.01411.5180.0160.0160.0000.0000.0000.000
127A125HIS10.8070.9089.597-0.357-0.3570.0000.0000.0000.000
128A126THR00.0530.02111.656-0.096-0.0960.0000.0000.0000.000
129A127ILE0-0.0020.0099.172-0.075-0.0750.0000.0000.0000.000
130A128LEU0-0.012-0.00712.335-0.085-0.0850.0000.0000.0000.000
131A129LYS10.9390.95914.9380.0000.0000.0000.0000.0000.000
132A130LEU0-0.044-0.00516.2420.0060.0060.0000.0000.0000.000
133A131PHE0-0.051-0.00719.913-0.052-0.0520.0000.0000.0000.000
134A132PRO00.0470.02721.9400.0100.0100.0000.0000.0000.000
135A133GLY00.056-0.00623.6780.0210.0210.0000.0000.0000.000
136A134GLU-1-0.926-0.99324.665-0.019-0.0190.0000.0000.0000.000
137A135VAL0-0.050-0.00627.6840.0020.0020.0000.0000.0000.000
138A136VAL0-0.0290.00024.4360.0140.0140.0000.0000.0000.000
139A137GLY00.0720.02325.3490.0100.0100.0000.0000.0000.000
140A138PRO00.0210.00725.8560.0330.0330.0000.0000.0000.000
141A139GLN00.037-0.00326.8970.0370.0370.0000.0000.0000.000
142A140PHE00.0020.00722.9320.0130.0130.0000.0000.0000.000
143A141VAL00.0010.00421.6190.0290.0290.0000.0000.0000.000
144A142LYS10.8840.96024.129-0.276-0.2760.0000.0000.0000.000
145A143ALA0-0.015-0.01326.8420.0200.0200.0000.0000.0000.000
146A144MET0-0.017-0.00423.0170.0130.0130.0000.0000.0000.000
147A145LYS10.9210.98721.455-0.605-0.6050.0000.0000.0000.000
148A146GLY00.011-0.01024.5640.0340.0340.0000.0000.0000.000
149A147PRO00.0000.00625.9120.0270.0270.0000.0000.0000.000
150A148PHE0-0.003-0.00820.9500.0200.0200.0000.0000.0000.000
151A149PRO00.0330.03221.0730.0460.0460.0000.0000.0000.000
152A150ASN0-0.029-0.03716.9080.0630.0630.0000.0000.0000.000
153A151VAL0-0.020-0.01216.0980.1620.1620.0000.0000.0000.000
154A152LYS10.8610.94613.624-1.448-1.4480.0000.0000.0000.000
155A153PHE00.0580.01815.3230.0270.0270.0000.0000.0000.000
156A154VAL00.0190.00613.1620.0290.0290.0000.0000.0000.000
157A155PRO00.0180.02016.391-0.053-0.0530.0000.0000.0000.000
158A156THR0-0.023-0.00818.414-0.022-0.0220.0000.0000.0000.000
159A157GLY00.0480.04620.4240.0080.0080.0000.0000.0000.000
160A158GLY00.0370.01624.1390.0270.0270.0000.0000.0000.000
161A159VAL0-0.0140.02621.7120.0260.0260.0000.0000.0000.000
162A160ASN00.025-0.01324.962-0.022-0.0220.0000.0000.0000.000
163A161LEU00.0720.01225.7880.0220.0220.0000.0000.0000.000
164A162ASP-1-0.938-0.96327.4530.0040.0040.0000.0000.0000.000
165A163ASN00.0180.00526.8320.0100.0100.0000.0000.0000.000
166A164VAL00.0100.00822.0100.0310.0310.0000.0000.0000.000
167A203CYS0-0.054-0.01522.2320.0550.0550.0000.0000.0000.000
168A166GLU-1-0.933-0.96225.8510.1570.1570.0000.0000.0000.000
169A167TRP0-0.028-0.03322.7130.0510.0510.0000.0000.0000.000
170A168PHE0-0.009-0.00517.5830.0430.0430.0000.0000.0000.000
171A169LYS10.9450.98522.700-0.149-0.1490.0000.0000.0000.000
172A170ALA0-0.071-0.05424.8970.0230.0230.0000.0000.0000.000
173A171GLY0-0.042-0.00822.1280.0210.0210.0000.0000.0000.000
174A172VAL0-0.049-0.00818.9530.0680.0680.0000.0000.0000.000
175A173LEU0-0.042-0.01011.4470.0140.0140.0000.0000.0000.000
176A174ALA0-0.010-0.01713.739-0.004-0.0040.0000.0000.0000.000
177A175VAL0-0.0030.00215.8540.0020.0020.0000.0000.0000.000
178A176GLY00.0310.02516.848-0.046-0.0460.0000.0000.0000.000
179A177VAL0-0.039-0.02617.9920.0280.0280.0000.0000.0000.000
180A178GLY00.0770.04420.278-0.052-0.0520.0000.0000.0000.000
181A179SER00.000-0.00822.634-0.005-0.0050.0000.0000.0000.000
182A180ALA00.032-0.00325.306-0.008-0.0080.0000.0000.0000.000
183A181LEU0-0.0340.01119.1620.0090.0090.0000.0000.0000.000
184A182VAL00.0510.01320.694-0.009-0.0090.0000.0000.0000.000
185A183LYS10.9190.95823.5980.1850.1850.0000.0000.0000.000
186A184GLY00.0340.03827.2880.0180.0180.0000.0000.0000.000
187A185THR00.0050.00728.394-0.029-0.0290.0000.0000.0000.000
188A186PRO00.0810.03125.7490.0070.0070.0000.0000.0000.000
189A187ASP-1-0.837-0.92326.183-0.299-0.2990.0000.0000.0000.000
190A188GLU-1-0.856-0.93727.983-0.209-0.2090.0000.0000.0000.000
191A189VAL0-0.074-0.03322.6400.0140.0140.0000.0000.0000.000
192A190ARG10.8450.92523.1150.3810.3810.0000.0000.0000.000
193A191GLU-1-0.904-0.95824.011-0.219-0.2190.0000.0000.0000.000
194A192LYS10.8260.90025.3140.2360.2360.0000.0000.0000.000
195A193ALA0-0.005-0.00720.2380.0270.0270.0000.0000.0000.000
196A194LYS10.9600.99121.4840.2940.2940.0000.0000.0000.000
197A195ALA0-0.033-0.01323.2440.0320.0320.0000.0000.0000.000
198A196PHE0-0.013-0.02721.1570.0380.0380.0000.0000.0000.000
199A197VAL0-0.0190.00417.9640.0470.0470.0000.0000.0000.000
200A198GLU-1-0.953-0.98320.5180.0020.0020.0000.0000.0000.000
201A199LYS10.9490.97423.8030.0100.0100.0000.0000.0000.000
202A200ILE0-0.016-0.01818.6980.0310.0310.0000.0000.0000.000
203A201ARG10.8680.95221.1100.0880.0880.0000.0000.0000.000
204A202GLY0-0.0080.00321.9810.0270.0270.0000.0000.0000.000