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: 1N2JZ

Calculation Name: 1VL5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VL5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KAF6

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2939667.413269
FMO2-HF: Nuclear repulsion 2846932.552054
FMO2-HF: Total energy -92734.861215
FMO2-MP2: Total energy -93006.001696


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:28:GLY)


Summations of interaction energy for fragment #1(A:28:GLY)
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.
-8.993-6.5525.533-4.12-3.854-0.031
Interaction energy analysis for fragmet #1(A:28:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / q_NPA : 0.032
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].
3A30ASP-1-0.843-0.9242.011-13.749-12.0255.080-3.688-3.117-0.029
4A31LEU00.0520.0094.8000.3280.374-0.001-0.010-0.0360.000
5A32ALA00.0330.0315.8930.4650.4650.0000.0000.0000.000
6A33LYS10.8290.9243.8193.1933.3890.000-0.056-0.1390.000
7A34LEU00.003-0.0105.9760.7810.7810.0000.0000.0000.000
8A35MET0-0.0030.0038.9900.3710.3710.0000.0000.0000.000
9A36GLN0-0.021-0.0057.8110.0360.0360.0000.0000.0000.000
10A37ILE0-0.028-0.0108.7190.2040.2040.0000.0000.0000.000
11A38ALA00.0110.01211.4810.2110.2110.0000.0000.0000.000
12A39ALA0-0.044-0.00914.1100.1340.1340.0000.0000.0000.000
13A40LEU0-0.0150.00216.1310.0760.0760.0000.0000.0000.000
14A41LYS10.8420.88718.4980.4230.4230.0000.0000.0000.000
15A42GLY00.0330.03821.7900.0340.0340.0000.0000.0000.000
16A43ASN0-0.039-0.02723.1890.0050.0050.0000.0000.0000.000
17A44GLU-1-0.800-0.89321.558-0.427-0.4270.0000.0000.0000.000
18A45GLU-1-0.772-0.87424.179-0.254-0.2540.0000.0000.0000.000
19A46VAL0-0.008-0.01218.944-0.001-0.0010.0000.0000.0000.000
20A47LEU00.0020.00622.0940.0260.0260.0000.0000.0000.000
21A48ASP-1-0.773-0.84817.356-0.687-0.6870.0000.0000.0000.000
22A49VAL00.0300.00319.9090.0460.0460.0000.0000.0000.000
23A50ALA0-0.012-0.00319.058-0.044-0.0440.0000.0000.0000.000
24A51THR0-0.053-0.03818.119-0.022-0.0220.0000.0000.0000.000
25A52GLY00.0320.01117.808-0.036-0.0360.0000.0000.0000.000
26A53GLY0-0.027-0.00917.5540.0330.0330.0000.0000.0000.000
27A54GLY00.0310.00518.4860.0120.0120.0000.0000.0000.000
28A55HIS0-0.073-0.04513.369-0.019-0.0190.0000.0000.0000.000
29A56VAL00.0160.00812.406-0.126-0.1260.0000.0000.0000.000
30A57ALA00.0530.01814.506-0.019-0.0190.0000.0000.0000.000
31A58ASN00.003-0.00215.9930.0600.0600.0000.0000.0000.000
32A59ALA0-0.039-0.01112.4860.0070.0070.0000.0000.0000.000
33A60PHE00.055-0.01113.065-0.004-0.0040.0000.0000.0000.000
34A61ALA00.0030.01516.6850.0420.0420.0000.0000.0000.000
35A62PRO0-0.0030.00217.6920.0380.0380.0000.0000.0000.000
36A63PHE0-0.042-0.01915.5460.0190.0190.0000.0000.0000.000
37A64VAL0-0.058-0.02319.384-0.008-0.0080.0000.0000.0000.000
38A65LYS10.8760.94422.0950.2920.2920.0000.0000.0000.000
39A66LYS10.7990.88924.6540.2650.2650.0000.0000.0000.000
40A67VAL00.0030.01620.133-0.028-0.0280.0000.0000.0000.000
41A68VAL0-0.025-0.00823.2740.0340.0340.0000.0000.0000.000
42A69ALA00.0290.02322.273-0.031-0.0310.0000.0000.0000.000
43A70PHE0-0.008-0.01122.7600.0370.0370.0000.0000.0000.000
44A71ASP-1-0.782-0.90921.818-0.329-0.3290.0000.0000.0000.000
45A72LEU00.0170.01424.7570.0210.0210.0000.0000.0000.000
46A73THR0-0.044-0.03126.9860.0140.0140.0000.0000.0000.000
47A74GLU-1-0.831-0.92827.762-0.166-0.1660.0000.0000.0000.000
48A75ASP-1-0.876-0.92728.985-0.127-0.1270.0000.0000.0000.000
49A76ILE0-0.026-0.00122.669-0.001-0.0010.0000.0000.0000.000
50A77LEU0-0.014-0.00724.318-0.019-0.0190.0000.0000.0000.000
51A78LYS10.8250.91226.1150.1180.1180.0000.0000.0000.000
52A79VAL00.0000.00821.680-0.001-0.0010.0000.0000.0000.000
53A80ALA00.0170.01421.394-0.013-0.0130.0000.0000.0000.000
54A81ARG10.8230.86622.3780.1550.1550.0000.0000.0000.000
55A82ALA0-0.012-0.00224.867-0.002-0.0020.0000.0000.0000.000
56A83PHE0-0.015-0.00215.748-0.006-0.0060.0000.0000.0000.000
57A84ILE0-0.0080.00419.951-0.014-0.0140.0000.0000.0000.000
58A85GLU-1-0.844-0.89221.760-0.181-0.1810.0000.0000.0000.000
59A86GLY0-0.0100.00623.8060.0150.0150.0000.0000.0000.000
60A87ASN0-0.104-0.05818.9190.0100.0100.0000.0000.0000.000
61A88GLY0-0.0100.00721.865-0.009-0.0090.0000.0000.0000.000
62A89HIS0-0.0020.00818.4720.0180.0180.0000.0000.0000.000
63A90GLN0-0.026-0.03223.714-0.010-0.0100.0000.0000.0000.000
64A91GLN0-0.043-0.02323.0260.0170.0170.0000.0000.0000.000
65A92VAL0-0.015-0.00222.109-0.020-0.0200.0000.0000.0000.000
66A93GLU-1-0.801-0.87425.306-0.206-0.2060.0000.0000.0000.000
67A94TYR00.0420.00724.179-0.028-0.0280.0000.0000.0000.000
68A95VAL0-0.018-0.00727.3890.0190.0190.0000.0000.0000.000
69A96GLN00.0550.02827.740-0.012-0.0120.0000.0000.0000.000
70A97GLY0-0.037-0.04028.4480.0090.0090.0000.0000.0000.000
71A98ASP-1-0.838-0.91426.821-0.213-0.2130.0000.0000.0000.000
72A99ALA0-0.016-0.02523.433-0.009-0.0090.0000.0000.0000.000
73A101GLN0-0.035-0.00328.6580.0080.0080.0000.0000.0000.000
74A102MET0-0.038-0.01524.819-0.006-0.0060.0000.0000.0000.000
75A103PRO0-0.0210.01129.6280.0070.0070.0000.0000.0000.000
76A104PHE0-0.018-0.03227.3290.0010.0010.0000.0000.0000.000
77A105THR00.0150.00332.0810.0050.0050.0000.0000.0000.000
78A106ASP-1-0.809-0.90831.852-0.196-0.1960.0000.0000.0000.000
79A107GLU-1-0.840-0.90930.150-0.205-0.2050.0000.0000.0000.000
80A108ARG10.7890.90929.0620.2480.2480.0000.0000.0000.000
81A109PHE0-0.006-0.00924.7460.0010.0010.0000.0000.0000.000
82A110HIS00.001-0.00823.932-0.001-0.0010.0000.0000.0000.000
83A111ILE0-0.014-0.00718.161-0.018-0.0180.0000.0000.0000.000
84A112VAL00.0220.02620.3090.0330.0330.0000.0000.0000.000
85A113THR0-0.009-0.03715.356-0.042-0.0420.0000.0000.0000.000
86A114CYS0-0.037-0.01215.6660.0840.0840.0000.0000.0000.000
87A115ARG10.9140.9336.4841.7621.7620.0000.0000.0000.000
88A116ILE0-0.080-0.0419.9150.0630.0630.0000.0000.0000.000
89A117ALA00.0260.02312.8880.1040.1040.0000.0000.0000.000
90A118ALA00.0930.03316.4740.0600.0600.0000.0000.0000.000
91A119HIS10.7960.89215.0610.3330.3330.0000.0000.0000.000
92A120HIS10.8350.89818.0360.2560.2560.0000.0000.0000.000
93A121PHE00.0030.01320.4190.0170.0170.0000.0000.0000.000
94A122PRO00.0660.03623.4620.0040.0040.0000.0000.0000.000
95A123ASN0-0.017-0.02626.4180.0130.0130.0000.0000.0000.000
96A124PRO00.0180.00921.844-0.009-0.0090.0000.0000.0000.000
97A125ALA00.0790.03023.731-0.020-0.0200.0000.0000.0000.000
98A126SER00.0190.01625.656-0.004-0.0040.0000.0000.0000.000
99A127PHE00.0350.03119.268-0.006-0.0060.0000.0000.0000.000
100A128VAL00.0040.00821.207-0.018-0.0180.0000.0000.0000.000
101A129SER0-0.002-0.01823.7960.0000.0000.0000.0000.0000.000
102A130GLU-1-0.738-0.83926.965-0.203-0.2030.0000.0000.0000.000
103A131ALA0-0.018-0.02122.778-0.003-0.0030.0000.0000.0000.000
104A132TYR0-0.005-0.01224.8480.0010.0010.0000.0000.0000.000
105A133ARG10.7500.84226.6980.2080.2080.0000.0000.0000.000
106A134VAL0-0.006-0.00626.2030.0060.0060.0000.0000.0000.000
107A135LEU0-0.0270.01222.449-0.005-0.0050.0000.0000.0000.000
108A136LYS10.8070.90126.8090.2750.2750.0000.0000.0000.000
109A137LYS10.8900.93427.4790.1760.1760.0000.0000.0000.000
110A138GLY0-0.020-0.00326.3960.0030.0030.0000.0000.0000.000
111A139GLY0-0.0320.00424.057-0.025-0.0250.0000.0000.0000.000
112A140GLN0-0.020-0.02217.6980.0070.0070.0000.0000.0000.000
113A141LEU00.0210.01918.212-0.014-0.0140.0000.0000.0000.000
114A142LEU0-0.028-0.01513.669-0.045-0.0450.0000.0000.0000.000
115A143LEU00.0020.00814.521-0.007-0.0070.0000.0000.0000.000
116A144VAL0-0.002-0.0078.614-0.111-0.1110.0000.0000.0000.000
117A145ASP-1-0.747-0.85011.119-0.353-0.3530.0000.0000.0000.000
118A146ASN0-0.001-0.00410.413-0.133-0.1330.0000.0000.0000.000
119A147SER0-0.051-0.05011.960-0.047-0.0470.0000.0000.0000.000
120A148ALA00.0070.00913.7700.0820.0820.0000.0000.0000.000
121A149PRO0-0.065-0.05616.151-0.004-0.0040.0000.0000.0000.000
122A150GLU-1-0.679-0.81617.388-0.124-0.1240.0000.0000.0000.000
123A151ASN00.0020.01120.118-0.002-0.0020.0000.0000.0000.000
124A152ASP-1-0.754-0.88322.023-0.011-0.0110.0000.0000.0000.000
125A153ALA00.0130.02424.533-0.002-0.0020.0000.0000.0000.000
126A154PHE0-0.001-0.02419.7110.0110.0110.0000.0000.0000.000
127A155ASP-1-0.795-0.83519.822-0.047-0.0470.0000.0000.0000.000
128A156VAL00.0530.01820.884-0.006-0.0060.0000.0000.0000.000
129A157PHE0-0.0040.00320.349-0.002-0.0020.0000.0000.0000.000
130A158TYR0-0.062-0.05813.7270.0070.0070.0000.0000.0000.000
131A159ASN00.001-0.00719.390-0.025-0.0250.0000.0000.0000.000
132A160TYR0-0.055-0.03420.906-0.008-0.0080.0000.0000.0000.000
133A161VAL00.0080.00019.007-0.001-0.0010.0000.0000.0000.000
134A162GLU-1-0.772-0.87814.7250.0110.0110.0000.0000.0000.000
135A163LYS10.8420.93219.2940.0580.0580.0000.0000.0000.000
136A164GLU-1-0.815-0.87522.6150.0160.0160.0000.0000.0000.000
137A165ARG10.8190.91415.563-0.005-0.0050.0000.0000.0000.000
138A166ASP-1-0.800-0.88519.334-0.131-0.1310.0000.0000.0000.000
139A167DTY00.0240.01221.591-0.012-0.0120.0000.0000.0000.000
140A168SER0-0.041-0.04721.866-0.013-0.0130.0000.0000.0000.000
141A169HIS0-0.035-0.00917.821-0.043-0.0430.0000.0000.0000.000
142A170HIS0-0.050-0.00521.5550.0290.0290.0000.0000.0000.000
143A171ARG10.7760.83520.9260.1250.1250.0000.0000.0000.000
144A172ALA0-0.0140.00615.934-0.041-0.0410.0000.0000.0000.000
145A173TRP00.0240.00317.3190.0480.0480.0000.0000.0000.000
146A174LYS10.7390.86016.7730.0340.0340.0000.0000.0000.000
147A175LYS10.8030.86812.8410.0570.0570.0000.0000.0000.000
148A176SER0-0.013-0.03616.846-0.026-0.0260.0000.0000.0000.000
149A177ASP-1-0.745-0.87220.232-0.145-0.1450.0000.0000.0000.000
150A178TRP00.015-0.00715.887-0.021-0.0210.0000.0000.0000.000
151A179LEU0-0.0050.00218.351-0.016-0.0160.0000.0000.0000.000
152A180LYS10.8270.90520.6020.1470.1470.0000.0000.0000.000
153A181MET0-0.005-0.00420.9310.0010.0010.0000.0000.0000.000
154A182LEU0-0.046-0.01618.169-0.011-0.0110.0000.0000.0000.000
155A183GLU-1-0.878-0.93522.807-0.160-0.1600.0000.0000.0000.000
156A184GLU-1-0.887-0.93925.593-0.144-0.1440.0000.0000.0000.000
157A185ALA0-0.048-0.01625.4680.0100.0100.0000.0000.0000.000
158A186GLY00.0000.01027.572-0.002-0.0020.0000.0000.0000.000
159A187PHE0-0.058-0.03622.629-0.011-0.0110.0000.0000.0000.000
160A188GLU-1-0.911-0.94923.745-0.220-0.2200.0000.0000.0000.000
161A189LEU0-0.069-0.04516.184-0.038-0.0380.0000.0000.0000.000
162A190GLU-1-0.796-0.86017.800-0.452-0.4520.0000.0000.0000.000
163A191GLU-1-0.841-0.92812.826-0.865-0.8650.0000.0000.0000.000
164A192LEU0-0.010-0.00911.885-0.047-0.0470.0000.0000.0000.000
165A193HIS0-0.010-0.0087.590-0.148-0.1480.0000.0000.0000.000
166A194CYS0-0.015-0.0168.025-0.070-0.0700.0000.0000.0000.000
167A195PHE00.009-0.0052.693-0.934-0.4590.454-0.366-0.562-0.002
168A196HIS00.0100.0035.119-0.189-0.1890.0000.0000.0000.000
169A197LYS10.8620.9295.2300.9830.9830.0000.0000.0000.000
170A198THR00.013-0.0037.498-0.255-0.2550.0000.0000.0000.000
171A199PHE0-0.0320.00010.2580.0370.0370.0000.0000.0000.000
172A200ILE00.0620.03012.436-0.024-0.0240.0000.0000.0000.000
173A201PHE0-0.003-0.00915.169-0.053-0.0530.0000.0000.0000.000
174A202GLU-1-0.695-0.81018.0150.1270.1270.0000.0000.0000.000
175A203ASP-1-0.815-0.92515.6350.3160.3160.0000.0000.0000.000
176A204TRP0-0.137-0.07213.884-0.024-0.0240.0000.0000.0000.000
177A205CYS0-0.0190.00316.257-0.057-0.0570.0000.0000.0000.000
178A206ASP-1-0.784-0.87920.0020.0850.0850.0000.0000.0000.000
179A207ARG10.8610.93113.285-0.214-0.2140.0000.0000.0000.000
180A208MET0-0.056-0.01518.671-0.043-0.0430.0000.0000.0000.000
181A209ASN0-0.072-0.03321.1630.0020.0020.0000.0000.0000.000
182A210VAL00.0120.01922.676-0.003-0.0030.0000.0000.0000.000
183A211THR00.0710.03125.1710.0130.0130.0000.0000.0000.000
184A212THR00.029-0.00527.6820.0060.0060.0000.0000.0000.000
185A213GLU-1-0.924-0.95029.0110.0540.0540.0000.0000.0000.000
186A214LYS10.8450.91226.523-0.026-0.0260.0000.0000.0000.000
187A215LYS10.7770.85423.302-0.110-0.1100.0000.0000.0000.000
188A216GLN0-0.031-0.02625.7270.0200.0200.0000.0000.0000.000
189A217GLU-1-0.887-0.94928.3290.0570.0570.0000.0000.0000.000
190A218LEU00.0040.00121.8370.0050.0050.0000.0000.0000.000
191A219SER00.0260.01724.2340.0200.0200.0000.0000.0000.000
192A220ASP-1-0.820-0.89925.2350.1270.1270.0000.0000.0000.000
193A221PHE00.0390.02825.2190.0020.0020.0000.0000.0000.000
194A222ILE0-0.029-0.01120.6140.0000.0000.0000.0000.0000.000
195A223LYS10.8690.93224.500-0.135-0.1350.0000.0000.0000.000
196A224SER0-0.070-0.03726.3900.0010.0010.0000.0000.0000.000
197A225LYS10.7870.91125.143-0.113-0.1130.0000.0000.0000.000
198A226PRO00.0480.02027.4480.0120.0120.0000.0000.0000.000
199A227THR00.0440.01625.8920.0110.0110.0000.0000.0000.000
200A228GLU-1-0.815-0.91524.1060.1590.1590.0000.0000.0000.000
201A229TYR0-0.012-0.01121.9790.0140.0140.0000.0000.0000.000
202A230TYR00.013-0.00520.4830.0360.0360.0000.0000.0000.000
203A231GLN0-0.009-0.00419.7510.0340.0340.0000.0000.0000.000
204A232LYS10.9030.97615.599-0.156-0.1560.0000.0000.0000.000
205A233PHE0-0.046-0.03715.5880.0450.0450.0000.0000.0000.000
206A234LYS10.8180.90514.227-0.420-0.4200.0000.0000.0000.000
207A235ILE0-0.0140.01216.9860.0440.0440.0000.0000.0000.000
208A236VAL00.0030.01017.860-0.008-0.0080.0000.0000.0000.000
209A237VAL0-0.034-0.02620.461-0.016-0.0160.0000.0000.0000.000
210A238GLU-1-0.903-0.94922.6190.3480.3480.0000.0000.0000.000
211A239ASP-1-0.909-0.95325.5590.1860.1860.0000.0000.0000.000
212A240GLY0-0.027-0.00428.230-0.016-0.0160.0000.0000.0000.000
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