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: YV6Q2

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2931342.297697
FMO2-HF: Nuclear repulsion 2838608.98383
FMO2-HF: Total energy -92733.313867
FMO2-MP2: Total energy -93004.314736


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.
-3.097-0.6220.219-0.973-1.720
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 : 0.042 / q_NPA : 0.007
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-1-0.863-0.9523.782-4.327-2.9750.009-0.516-0.8460.001
4A31LEU00.025-0.0025.0480.5340.568-0.001-0.008-0.0240.000
5A32ALA00.0370.0276.5920.3590.3590.0000.0000.0000.000
6A33LYS10.9050.9624.5481.3501.426-0.001-0.017-0.0580.000
7A34LEU0-0.002-0.0056.7010.5730.5730.0000.0000.0000.000
8A35MET00.0030.0069.7400.2620.2620.0000.0000.0000.000
9A36GLN0-0.0140.0008.8230.0960.0960.0000.0000.0000.000
10A37ILE0-0.016-0.0029.3670.1440.1440.0000.0000.0000.000
11A38ALA00.0230.02512.2360.1320.1320.0000.0000.0000.000
12A39ALA0-0.022-0.00414.9290.0810.0810.0000.0000.0000.000
13A40LEU0-0.026-0.00916.7630.0450.0450.0000.0000.0000.000
14A41LYS10.8350.88319.0790.2420.2420.0000.0000.0000.000
15A42GLY00.0330.03622.5100.0160.0160.0000.0000.0000.000
16A43ASN0-0.030-0.02223.922-0.003-0.0030.0000.0000.0000.000
17A44GLU-1-0.794-0.88621.956-0.269-0.2690.0000.0000.0000.000
18A45GLU-1-0.831-0.92224.745-0.173-0.1730.0000.0000.0000.000
19A46VAL0-0.005-0.01419.6550.0070.0070.0000.0000.0000.000
20A47LEU00.0140.02222.6980.0090.0090.0000.0000.0000.000
21A48ASP-1-0.828-0.92517.678-0.443-0.4430.0000.0000.0000.000
22A49VAL00.024-0.01519.9530.0280.0280.0000.0000.0000.000
23A50ALA0-0.019-0.00319.145-0.022-0.0220.0000.0000.0000.000
24A51THR0-0.048-0.02118.722-0.024-0.0240.0000.0000.0000.000
25A52GLY00.0330.00918.186-0.041-0.0410.0000.0000.0000.000
26A53GLY0-0.027-0.02217.7910.0150.0150.0000.0000.0000.000
27A54GLY00.0420.02018.308-0.001-0.0010.0000.0000.0000.000
28A55HIS0-0.076-0.05612.741-0.031-0.0310.0000.0000.0000.000
29A56VAL00.0300.01012.826-0.098-0.0980.0000.0000.0000.000
30A57ALA00.0520.02415.068-0.008-0.0080.0000.0000.0000.000
31A58ASN0-0.0240.00116.1210.0580.0580.0000.0000.0000.000
32A59ALA0-0.032-0.01313.8310.0010.0010.0000.0000.0000.000
33A60PHE00.041-0.00513.903-0.001-0.0010.0000.0000.0000.000
34A61ALA0-0.0090.01017.7980.0320.0320.0000.0000.0000.000
35A62PRO00.0200.01318.9060.0360.0360.0000.0000.0000.000
36A63PHE0-0.041-0.01416.3920.0170.0170.0000.0000.0000.000
37A64VAL0-0.039-0.01320.2270.0140.0140.0000.0000.0000.000
38A65LYS10.8800.96122.9550.1920.1920.0000.0000.0000.000
39A66LYS10.8390.89625.7480.1780.1780.0000.0000.0000.000
40A67VAL00.0140.01821.104-0.010-0.0100.0000.0000.0000.000
41A68VAL0-0.040-0.01124.2570.0180.0180.0000.0000.0000.000
42A69ALA0-0.0050.00322.563-0.018-0.0180.0000.0000.0000.000
43A70PHE00.0200.00122.9510.0220.0220.0000.0000.0000.000
44A71ASP-1-0.765-0.89321.959-0.213-0.2130.0000.0000.0000.000
45A72LEU00.0100.01124.8970.0120.0120.0000.0000.0000.000
46A73THR0-0.028-0.01727.1460.0070.0070.0000.0000.0000.000
47A74GLU-1-0.828-0.92527.994-0.139-0.1390.0000.0000.0000.000
48A75ASP-1-0.926-0.96228.504-0.109-0.1090.0000.0000.0000.000
49A76ILE0-0.044-0.01722.850-0.007-0.0070.0000.0000.0000.000
50A77LEU0-0.005-0.00124.503-0.020-0.0200.0000.0000.0000.000
51A78LYS10.9040.95426.2810.1020.1020.0000.0000.0000.000
52A79VAL0-0.0160.00021.962-0.006-0.0060.0000.0000.0000.000
53A80ALA00.0010.00921.570-0.017-0.0170.0000.0000.0000.000
54A81ARG10.8940.93822.5670.1380.1380.0000.0000.0000.000
55A82ALA0-0.0010.01525.049-0.004-0.0040.0000.0000.0000.000
56A83PHE00.003-0.00116.306-0.019-0.0190.0000.0000.0000.000
57A84ILE0-0.043-0.02620.338-0.014-0.0140.0000.0000.0000.000
58A85GLU-1-0.895-0.95322.251-0.178-0.1780.0000.0000.0000.000
59A86GLY0-0.0040.00724.2570.0110.0110.0000.0000.0000.000
60A87ASN0-0.115-0.06419.1140.0070.0070.0000.0000.0000.000
61A88GLY0-0.0230.00222.806-0.008-0.0080.0000.0000.0000.000
62A89HIS0-0.017-0.00319.8180.0210.0210.0000.0000.0000.000
63A90GLN00.006-0.01124.9520.0030.0030.0000.0000.0000.000
64A91GLN0-0.063-0.02423.9900.0120.0120.0000.0000.0000.000
65A92VAL00.008-0.00423.145-0.011-0.0110.0000.0000.0000.000
66A93GLU-1-0.904-0.93726.302-0.134-0.1340.0000.0000.0000.000
67A94TYR00.0260.00824.011-0.008-0.0080.0000.0000.0000.000
68A95VAL0-0.006-0.00527.3320.0140.0140.0000.0000.0000.000
69A96GLN00.0300.01027.683-0.011-0.0110.0000.0000.0000.000
70A97GLY0-0.038-0.04028.5360.0080.0080.0000.0000.0000.000
71A98ASP-1-0.891-0.94927.552-0.104-0.1040.0000.0000.0000.000
72A99ALA00.0150.00223.780-0.003-0.0030.0000.0000.0000.000
73A101GLN0-0.0170.00229.0850.0070.0070.0000.0000.0000.000
74A102MET0-0.038-0.01225.109-0.010-0.0100.0000.0000.0000.000
75A103PRO0-0.0030.01429.9640.0060.0060.0000.0000.0000.000
76A104PHE0-0.036-0.03127.542-0.004-0.0040.0000.0000.0000.000
77A105THR00.0350.00832.2390.0050.0050.0000.0000.0000.000
78A106ASP-1-0.823-0.91332.144-0.089-0.0890.0000.0000.0000.000
79A107GLU-1-0.978-0.97830.778-0.088-0.0880.0000.0000.0000.000
80A108ARG10.9050.95829.5330.1490.1490.0000.0000.0000.000
81A109PHE0-0.015-0.01925.091-0.006-0.0060.0000.0000.0000.000
82A110HIS00.0120.01024.3160.0020.0020.0000.0000.0000.000
83A111ILE0-0.021-0.00718.554-0.001-0.0010.0000.0000.0000.000
84A112VAL00.0350.03720.5630.0080.0080.0000.0000.0000.000
85A113THR0-0.006-0.00715.756-0.015-0.0150.0000.0000.0000.000
86A114CYS00.0030.01415.9790.0390.0390.0000.0000.0000.000
87A115ARG10.9350.9626.7091.4161.4160.0000.0000.0000.000
88A116ILE0-0.074-0.03710.2610.0120.0120.0000.0000.0000.000
89A117ALA00.0460.02713.2390.0460.0460.0000.0000.0000.000
90A118ALA00.0690.02316.5550.0340.0340.0000.0000.0000.000
91A119HIS10.7900.88714.8570.1300.1300.0000.0000.0000.000
92A120HIS10.8290.90218.2260.1190.1190.0000.0000.0000.000
93A121PHE0-0.0080.01220.6620.0050.0050.0000.0000.0000.000
94A122PRO00.0730.04323.2770.0110.0110.0000.0000.0000.000
95A123ASN0-0.034-0.03426.2960.0070.0070.0000.0000.0000.000
96A124PRO00.0150.01821.933-0.008-0.0080.0000.0000.0000.000
97A125ALA00.0950.02923.850-0.010-0.0100.0000.0000.0000.000
98A126SER00.0230.01525.857-0.002-0.0020.0000.0000.0000.000
99A127PHE00.0260.02119.675-0.009-0.0090.0000.0000.0000.000
100A128VAL0-0.019-0.00621.672-0.013-0.0130.0000.0000.0000.000
101A129SER00.0720.02624.154-0.004-0.0040.0000.0000.0000.000
102A130GLU-1-0.822-0.89327.252-0.093-0.0930.0000.0000.0000.000
103A131ALA0-0.010-0.01623.023-0.008-0.0080.0000.0000.0000.000
104A132TYR00.0430.02025.083-0.007-0.0070.0000.0000.0000.000
105A133ARG10.7630.87526.9150.0930.0930.0000.0000.0000.000
106A134VAL0-0.012-0.00226.4260.0010.0010.0000.0000.0000.000
107A135LEU0-0.0260.01622.956-0.009-0.0090.0000.0000.0000.000
108A136LYS10.8790.94427.3010.1490.1490.0000.0000.0000.000
109A137LYS10.9200.95427.8740.0750.0750.0000.0000.0000.000
110A138GLY00.006-0.00326.826-0.003-0.0030.0000.0000.0000.000
111A139GLY0-0.037-0.00224.464-0.015-0.0150.0000.0000.0000.000
112A140GLN0-0.019-0.01817.755-0.002-0.0020.0000.0000.0000.000
113A141LEU00.0220.01918.270-0.017-0.0170.0000.0000.0000.000
114A142LEU0-0.025-0.01513.818-0.011-0.0110.0000.0000.0000.000
115A143LEU0-0.0010.00114.741-0.028-0.0280.0000.0000.0000.000
116A144VAL0-0.011-0.0148.763-0.032-0.0320.0000.0000.0000.000
117A145ASP-1-0.733-0.86410.860-0.127-0.1270.0000.0000.0000.000
118A146ASN0-0.056-0.02210.2710.0560.0560.0000.0000.0000.000
119A147SER0-0.023-0.02111.528-0.044-0.0440.0000.0000.0000.000
120A148ALA00.0110.02313.3710.0590.0590.0000.0000.0000.000
121A149PRO0-0.080-0.06115.6400.0160.0160.0000.0000.0000.000
122A150GLU-1-0.723-0.84817.2050.1520.1520.0000.0000.0000.000
123A151ASN0-0.017-0.00420.027-0.028-0.0280.0000.0000.0000.000
124A152ASP-1-0.759-0.89521.5290.1350.1350.0000.0000.0000.000
125A153ALA00.0140.02323.867-0.006-0.0060.0000.0000.0000.000
126A154PHE0-0.022-0.03519.1050.0110.0110.0000.0000.0000.000
127A155ASP-1-0.781-0.84419.2990.1440.1440.0000.0000.0000.000
128A156VAL00.0530.01920.355-0.008-0.0080.0000.0000.0000.000
129A157PHE0-0.024-0.00519.695-0.010-0.0100.0000.0000.0000.000
130A158TYR0-0.001-0.00313.083-0.003-0.0030.0000.0000.0000.000
131A159ASN00.0480.01118.607-0.029-0.0290.0000.0000.0000.000
132A160TYR0-0.0140.00620.074-0.015-0.0150.0000.0000.0000.000
133A161VAL00.0220.00118.560-0.013-0.0130.0000.0000.0000.000
134A162GLU-1-0.944-0.98115.4310.1280.1280.0000.0000.0000.000
135A163LYS10.8400.93818.940-0.034-0.0340.0000.0000.0000.000
136A164GLU-1-0.942-0.96922.3490.0430.0430.0000.0000.0000.000
137A165ARG10.8580.94415.867-0.026-0.0260.0000.0000.0000.000
138A166ASP-1-0.825-0.91619.734-0.066-0.0660.0000.0000.0000.000
139A167DTY00.0320.01921.7170.0010.0010.0000.0000.0000.000
140A168SER0-0.042-0.03922.299-0.004-0.0040.0000.0000.0000.000
141A169HIS0-0.039-0.01817.269-0.031-0.0310.0000.0000.0000.000
142A170HIS0-0.029-0.01121.2500.0130.0130.0000.0000.0000.000
143A171ARG10.7730.85620.518-0.062-0.0620.0000.0000.0000.000
144A172ALA0-0.025-0.00115.358-0.025-0.0250.0000.0000.0000.000
145A173TRP00.0390.01617.2430.0310.0310.0000.0000.0000.000
146A174LYS10.7810.88316.503-0.123-0.1230.0000.0000.0000.000
147A175LYS10.8550.89012.555-0.434-0.4340.0000.0000.0000.000
148A176SER0-0.029-0.05116.653-0.034-0.0340.0000.0000.0000.000
149A177ASP-1-0.780-0.89220.1470.0600.0600.0000.0000.0000.000
150A178TRP00.019-0.01016.107-0.033-0.0330.0000.0000.0000.000
151A179LEU0-0.019-0.00918.402-0.017-0.0170.0000.0000.0000.000
152A180LYS10.9640.98820.911-0.066-0.0660.0000.0000.0000.000
153A181MET00.0230.01520.933-0.012-0.0120.0000.0000.0000.000
154A182LEU0-0.065-0.02818.420-0.016-0.0160.0000.0000.0000.000
155A183GLU-1-0.928-0.96323.0420.0070.0070.0000.0000.0000.000
156A184GLU-1-0.966-0.98625.832-0.002-0.0020.0000.0000.0000.000
157A185ALA0-0.056-0.02225.837-0.003-0.0030.0000.0000.0000.000
158A186GLY0-0.019-0.00527.626-0.007-0.0070.0000.0000.0000.000
159A187PHE0-0.085-0.04822.826-0.011-0.0110.0000.0000.0000.000
160A188GLU-1-0.918-0.96024.108-0.032-0.0320.0000.0000.0000.000
161A189LEU0-0.067-0.04116.547-0.021-0.0210.0000.0000.0000.000
162A190GLU-1-0.824-0.89718.414-0.136-0.1360.0000.0000.0000.000
163A191GLU-1-0.874-0.92513.417-0.186-0.1860.0000.0000.0000.000
164A192LEU0-0.002-0.00912.201-0.054-0.0540.0000.0000.0000.000
165A193HIS0-0.057-0.0348.2150.1820.1820.0000.0000.0000.000
166A194CYS0-0.022-0.0168.376-0.214-0.2140.0000.0000.0000.000
167A195PHE0-0.022-0.0203.029-1.211-0.4600.213-0.395-0.568-0.001
168A196HIS0-0.004-0.0244.777-0.800-0.779-0.001-0.004-0.0160.000
169A197LYS10.9160.9664.1720.2510.4920.000-0.033-0.2080.000
170A198THR00.0240.0086.453-0.208-0.2080.0000.0000.0000.000
171A199PHE0-0.061-0.0199.424-0.043-0.0430.0000.0000.0000.000
172A200ILE00.0800.04011.9990.0190.0190.0000.0000.0000.000
173A201PHE0-0.010-0.01614.913-0.039-0.0390.0000.0000.0000.000
174A202GLU-1-0.727-0.86917.7800.0610.0610.0000.0000.0000.000
175A203ASP-1-0.821-0.91015.4470.0610.0610.0000.0000.0000.000
176A204TRP0-0.121-0.08213.742-0.030-0.0300.0000.0000.0000.000
177A205CYS0-0.016-0.00816.060-0.029-0.0290.0000.0000.0000.000
178A206ASP-1-0.785-0.88619.7740.0100.0100.0000.0000.0000.000
179A207ARG10.8550.94412.412-0.027-0.0270.0000.0000.0000.000
180A208MET0-0.058-0.01918.621-0.027-0.0270.0000.0000.0000.000
181A209ASN0-0.060-0.02020.9450.0040.0040.0000.0000.0000.000
182A210VAL00.0120.01722.1610.0030.0030.0000.0000.0000.000
183A211THR00.0430.02824.8810.0030.0030.0000.0000.0000.000
184A212THR00.021-0.01927.3680.0080.0080.0000.0000.0000.000
185A213GLU-1-0.880-0.94128.6880.0350.0350.0000.0000.0000.000
186A214LYS10.9280.98326.083-0.033-0.0330.0000.0000.0000.000
187A215LYS10.7900.87523.220-0.031-0.0310.0000.0000.0000.000
188A216GLN0-0.041-0.01925.5150.0110.0110.0000.0000.0000.000
189A217GLU-1-0.892-0.93828.1560.0640.0640.0000.0000.0000.000
190A218LEU00.0140.00621.2000.0110.0110.0000.0000.0000.000
191A219SER00.0210.00223.6700.0210.0210.0000.0000.0000.000
192A220ASP-1-0.872-0.92424.6720.1030.1030.0000.0000.0000.000
193A221PHE00.002-0.01324.0250.0070.0070.0000.0000.0000.000
194A222ILE0-0.007-0.00620.1720.0100.0100.0000.0000.0000.000
195A223LYS10.9861.00224.003-0.111-0.1110.0000.0000.0000.000
196A224SER0-0.090-0.01425.7190.0040.0040.0000.0000.0000.000
197A225LYS10.8160.92824.363-0.138-0.1380.0000.0000.0000.000
198A226PRO00.0700.03126.7410.0050.0050.0000.0000.0000.000
199A227THR00.0590.01625.0930.0140.0140.0000.0000.0000.000
200A228GLU-1-0.904-0.93623.4750.2050.2050.0000.0000.0000.000
201A229TYR00.027-0.01121.4860.0300.0300.0000.0000.0000.000
202A230TYR0-0.009-0.03919.8810.0370.0370.0000.0000.0000.000
203A231GLN0-0.005-0.00119.0930.0370.0370.0000.0000.0000.000
204A232LYS10.8870.96515.520-0.381-0.3810.0000.0000.0000.000
205A233PHE0-0.050-0.03714.7500.0710.0710.0000.0000.0000.000
206A234LYS10.8340.91913.583-0.547-0.5470.0000.0000.0000.000
207A235ILE00.0120.01916.0960.0210.0210.0000.0000.0000.000
208A236VAL00.0000.01917.111-0.008-0.0080.0000.0000.0000.000
209A237VAL0-0.027-0.01619.621-0.012-0.0120.0000.0000.0000.000
210A238GLU-1-0.930-0.96721.5590.1940.1940.0000.0000.0000.000
211A239ASP-1-0.904-0.95124.6550.1090.1090.0000.0000.0000.000
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