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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3J63L

Calculation Name: 1VSC-A-Xray372

Preferred Name: Vascular cell adhesion protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1VSC

Chain ID: A

ChEMBL ID: CHEMBL3735

UniProt ID: P19320

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptHSide
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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1918994.770205
FMO2-HF: Nuclear repulsion 1841395.214622
FMO2-HF: Total energy -77599.555583
FMO2-MP2: Total energy -77822.503999


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:PHE)


Summations of interaction energy for fragment #1(A:1:PHE)
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.
-38.164-17.70326.518-14.823-32.157-0.038
Interaction energy analysis for fragmet #1(A:1:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.013
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].
3A3ILE00.0250.0112.689-6.316-1.4750.715-2.495-3.060-0.005
4A4GLU-1-0.907-0.9514.752-1.131-1.026-0.001-0.017-0.0880.000
5A5THR0-0.013-0.0268.198-0.122-0.1220.0000.0000.0000.000
6A6THR0-0.0330.02110.9240.1040.1040.0000.0000.0000.000
7A7PRO00.0560.00314.562-0.006-0.0060.0000.0000.0000.000
8A8GLU-1-0.823-0.91413.054-0.816-0.8160.0000.0000.0000.000
9A9SER00.012-0.01114.298-0.052-0.0520.0000.0000.0000.000
10A10ARG10.8680.92316.5720.2910.2910.0000.0000.0000.000
11A11TYR00.009-0.00119.390-0.008-0.0080.0000.0000.0000.000
12A12LEU00.0280.04721.679-0.001-0.0010.0000.0000.0000.000
13A13ALA0-0.038-0.03224.4400.0040.0040.0000.0000.0000.000
14A14GLN0-0.019-0.00226.4400.0120.0120.0000.0000.0000.000
15A15ILE0-0.035-0.02829.219-0.005-0.0050.0000.0000.0000.000
16A16GLY0-0.025-0.01829.7200.0100.0100.0000.0000.0000.000
17A17ASP-1-0.844-0.91227.376-0.188-0.1880.0000.0000.0000.000
18A18SER0-0.005-0.01724.602-0.007-0.0070.0000.0000.0000.000
19A19VAL0-0.023-0.01320.471-0.003-0.0030.0000.0000.0000.000
20A20SER0-0.004-0.01618.300-0.002-0.0020.0000.0000.0000.000
21A21LEU0-0.0020.02614.664-0.007-0.0070.0000.0000.0000.000
22A22THR00.0160.01212.730-0.015-0.0150.0000.0000.0000.000
23A23CYS0-0.0310.0007.110-0.189-0.1890.0000.0000.0000.000
24A24SER00.0430.0167.3640.1370.1370.0000.0000.0000.000
25A25THR0-0.022-0.0162.293-1.419-0.7782.323-0.832-2.132-0.001
26A26THR00.0040.0073.5510.6381.0750.001-0.118-0.3210.000
27A27GLY0-0.028-0.0302.449-4.767-2.5011.966-1.845-2.387-0.022
28A28CYS0-0.014-0.0032.385-2.5701.1389.137-3.659-9.1860.005
29A29GLU-1-0.933-0.9523.8340.4040.4640.020-0.018-0.0620.000
30A30SER0-0.004-0.0147.350-0.412-0.4120.0000.0000.0000.000
31A31PRO0-0.0050.0034.5880.0580.267-0.001-0.015-0.1930.000
32A32PHE0-0.041-0.0176.001-0.222-0.2220.0000.0000.0000.000
33A33PHE00.018-0.0085.154-0.450-0.4500.0000.0000.0000.000
34A34SER0-0.029-0.0107.8600.2540.2540.0000.0000.0000.000
35A35TRP00.001-0.0019.841-0.200-0.2000.0000.0000.0000.000
36A36ARG10.8370.90311.6240.7830.7830.0000.0000.0000.000
37A37THR00.0190.00715.007-0.038-0.0380.0000.0000.0000.000
38A38GLN00.0820.02817.131-0.023-0.0230.0000.0000.0000.000
39A39ILE0-0.052-0.02018.1230.0110.0110.0000.0000.0000.000
40A40ASP-1-0.868-0.92616.149-0.468-0.4680.0000.0000.0000.000
41A41SER00.0120.02218.9570.0340.0340.0000.0000.0000.000
42A42PRO0-0.038-0.03220.334-0.026-0.0260.0000.0000.0000.000
43A43LEU00.0390.02615.913-0.004-0.0040.0000.0000.0000.000
44A44ASN0-0.063-0.02519.9690.0120.0120.0000.0000.0000.000
45A45GLY00.0980.05420.6330.0040.0040.0000.0000.0000.000
46A46LYS10.8800.94120.0010.2080.2080.0000.0000.0000.000
47A47VAL00.0250.01113.531-0.005-0.0050.0000.0000.0000.000
48A48THR0-0.051-0.01915.6550.0540.0540.0000.0000.0000.000
49A49ASN0-0.0060.00911.258-0.102-0.1020.0000.0000.0000.000
50A50GLU-1-0.917-0.95512.908-0.128-0.1280.0000.0000.0000.000
51A51GLY00.0590.03211.941-0.045-0.0450.0000.0000.0000.000
52A52THR0-0.041-0.0237.1730.0190.0190.0000.0000.0000.000
53A53THR00.0640.0357.622-0.383-0.3830.0000.0000.0000.000
54A54SER0-0.040-0.0149.7300.1330.1330.0000.0000.0000.000
55A55THR00.031-0.00411.147-0.046-0.0460.0000.0000.0000.000
56A56LEU0-0.0270.00014.3990.0370.0370.0000.0000.0000.000
57A57THR00.004-0.00716.1680.0030.0030.0000.0000.0000.000
58A58MET0-0.047-0.02719.1350.0100.0100.0000.0000.0000.000
59A59ASN0-0.0130.04622.4250.0110.0110.0000.0000.0000.000
60A60PRO0-0.008-0.00525.7760.0070.0070.0000.0000.0000.000
61A61VAL0-0.019-0.00524.001-0.009-0.0090.0000.0000.0000.000
62A62SER00.057-0.00226.2210.0190.0190.0000.0000.0000.000
63A63PHE00.1490.05526.882-0.020-0.0200.0000.0000.0000.000
64A64GLY0-0.066-0.02026.241-0.008-0.0080.0000.0000.0000.000
65A65ASN0-0.007-0.03521.9500.0000.0000.0000.0000.0000.000
66A66GLU-1-0.794-0.83522.700-0.237-0.2370.0000.0000.0000.000
67A67HIS10.8450.92520.1140.3280.3280.0000.0000.0000.000
68A68SER00.0300.02617.134-0.010-0.0100.0000.0000.0000.000
69A69TYR0-0.056-0.04615.0540.0070.0070.0000.0000.0000.000
70A70LEU0-0.007-0.02411.682-0.039-0.0390.0000.0000.0000.000
71A72THR0-0.020-0.0256.086-0.141-0.1410.0000.0000.0000.000
72A73ALA00.0300.0152.383-0.401-0.0701.348-0.574-1.106-0.001
73A74THR0-0.030-0.0212.456-5.685-4.0371.522-1.165-2.006-0.017
74A76GLU-1-0.798-0.8953.8963.0943.6030.0060.035-0.5490.001
75A77SER0-0.042-0.0246.520-0.416-0.4160.0000.0000.0000.000
76A78ARG10.8070.9062.445-12.010-10.5983.433-1.418-3.4270.006
77A79LYS10.9100.9422.557-1.911-0.3981.904-1.173-2.243-0.015
78A80LEU0-0.051-0.0092.671-2.4970.1404.144-1.549-5.2320.011
79A81GLU-1-0.796-0.8833.861-1.455-1.3110.0010.020-0.1650.000
80A82LYS10.8350.9087.1391.0211.0210.0000.0000.0000.000
81A83GLY0-0.0150.0049.380-0.014-0.0140.0000.0000.0000.000
82A84ILE0-0.0080.00512.8070.0160.0160.0000.0000.0000.000
83A85GLN00.0270.02915.598-0.010-0.0100.0000.0000.0000.000
84A86VAL0-0.022-0.02618.8090.0040.0040.0000.0000.0000.000
85A87GLU-1-0.856-0.91821.280-0.261-0.2610.0000.0000.0000.000
86A88ILE0-0.024-0.01824.928-0.002-0.0020.0000.0000.0000.000
87A89TYR00.0260.01827.7650.0050.0050.0000.0000.0000.000
88A90SER0-0.035-0.03031.520-0.004-0.0040.0000.0000.0000.000
89A91PHE00.0670.01234.4490.0040.0040.0000.0000.0000.000
90A92PRO0-0.021-0.00137.1190.0030.0030.0000.0000.0000.000
91A93LYS10.8390.91238.7020.1060.1060.0000.0000.0000.000
92A94ASP-1-0.881-0.91542.537-0.095-0.0950.0000.0000.0000.000
93A95PRO00.006-0.00445.5210.0000.0000.0000.0000.0000.000
94A96GLU-1-0.961-0.98847.479-0.074-0.0740.0000.0000.0000.000
95A97ILE0-0.061-0.03350.7090.0000.0000.0000.0000.0000.000
96A98HIS0-0.001-0.00354.1110.0010.0010.0000.0000.0000.000
97A99LEU0-0.006-0.00156.8220.0000.0000.0000.0000.0000.000
98A100SER0-0.033-0.02460.4020.0010.0010.0000.0000.0000.000
99A101GLY0-0.0100.00262.4370.0010.0010.0000.0000.0000.000
100A102PRO0-0.042-0.02065.079-0.001-0.0010.0000.0000.0000.000
101A103LEU00.0010.03865.4720.0000.0000.0000.0000.0000.000
102A104GLU-1-0.788-0.88567.933-0.039-0.0390.0000.0000.0000.000
103A105ALA0-0.004-0.01570.927-0.001-0.0010.0000.0000.0000.000
104A106GLY00.0110.00871.3580.0010.0010.0000.0000.0000.000
105A107LYS10.8100.89969.4760.0410.0410.0000.0000.0000.000
106A108PRO0-0.052-0.03167.259-0.001-0.0010.0000.0000.0000.000
107A109ILE0-0.015-0.00763.2540.0000.0000.0000.0000.0000.000
108A110THR0-0.007-0.03858.8870.0000.0000.0000.0000.0000.000
109A111VAL0-0.0050.00756.3110.0000.0000.0000.0000.0000.000
110A112LYS10.8600.91152.5770.0690.0690.0000.0000.0000.000
111A113CYS0-0.072-0.02350.621-0.001-0.0010.0000.0000.0000.000
112A114SER00.0220.00648.486-0.001-0.0010.0000.0000.0000.000
113A115VAL00.0400.02343.1820.0010.0010.0000.0000.0000.000
114A116ALA00.0150.01843.352-0.001-0.0010.0000.0000.0000.000
115A117ASP-1-0.823-0.89738.361-0.112-0.1120.0000.0000.0000.000
116A118VAL00.0280.02137.830-0.006-0.0060.0000.0000.0000.000
117A119TYR0-0.093-0.05030.2130.0030.0030.0000.0000.0000.000
118A120PRO00.0260.00232.712-0.004-0.0040.0000.0000.0000.000
119A121PHE00.0710.01235.1080.0030.0030.0000.0000.0000.000
120A122ASP-1-0.796-0.89135.498-0.146-0.1460.0000.0000.0000.000
121A123ARG10.7450.86633.3410.1620.1620.0000.0000.0000.000
122A124LEU0-0.048-0.02637.8980.0020.0020.0000.0000.0000.000
123A125GLU-1-0.803-0.88441.028-0.090-0.0900.0000.0000.0000.000
124A126ILE0-0.056-0.02944.4810.0000.0000.0000.0000.0000.000
125A127ASP-1-0.788-0.89247.256-0.083-0.0830.0000.0000.0000.000
126A128LEU0-0.027-0.01850.2980.0000.0000.0000.0000.0000.000
127A129LEU0-0.004-0.02351.5850.0010.0010.0000.0000.0000.000
128A130LYS10.8760.92155.7150.0510.0510.0000.0000.0000.000
129A131GLY0-0.0120.00658.3360.0020.0020.0000.0000.0000.000
130A132ASP-1-0.963-0.97856.313-0.059-0.0590.0000.0000.0000.000
131A133HIS0-0.025-0.02357.0170.0000.0000.0000.0000.0000.000
132A134LEU00.0290.02351.6840.0000.0000.0000.0000.0000.000
133A135MET0-0.082-0.02855.9260.0020.0020.0000.0000.0000.000
134A136LYS10.8820.92353.4330.0700.0700.0000.0000.0000.000
135A137SER00.0390.03749.4470.0010.0010.0000.0000.0000.000
136A138GLN0-0.105-0.05347.8410.0050.0050.0000.0000.0000.000
137A139GLU-1-0.849-0.91444.420-0.100-0.1000.0000.0000.0000.000
138A140PHE0-0.019-0.03142.4840.0050.0050.0000.0000.0000.000
139A141LEU00.0110.01240.617-0.005-0.0050.0000.0000.0000.000
140A142GLU-1-0.957-0.97241.039-0.106-0.1060.0000.0000.0000.000
141A143ASP-1-0.845-0.94339.753-0.111-0.1110.0000.0000.0000.000
142A144ALA0-0.064-0.02740.432-0.003-0.0030.0000.0000.0000.000
143A145ASP-1-0.861-0.91538.112-0.125-0.1250.0000.0000.0000.000
144A146ARG10.8590.90331.7600.1630.1630.0000.0000.0000.000
145A147LYS10.7670.87728.2310.2090.2090.0000.0000.0000.000
146A148SER0-0.008-0.00434.3840.0000.0000.0000.0000.0000.000
147A149LEU0-0.048-0.02034.6190.0000.0000.0000.0000.0000.000
148A150GLU-1-0.891-0.92638.382-0.094-0.0940.0000.0000.0000.000
149A151THR0-0.013-0.03042.054-0.003-0.0030.0000.0000.0000.000
150A152LYS10.7920.91842.2430.1090.1090.0000.0000.0000.000
151A153SER0-0.007-0.02445.7400.0010.0010.0000.0000.0000.000
152A154LEU00.0150.02249.3210.0000.0000.0000.0000.0000.000
153A155GLU-1-0.811-0.89051.677-0.066-0.0660.0000.0000.0000.000
154A156VAL0-0.0020.00255.4360.0000.0000.0000.0000.0000.000
155A157THR00.0350.03158.3420.0000.0000.0000.0000.0000.000
156A158PHE0-0.029-0.00862.0650.0000.0000.0000.0000.0000.000
157A159THR00.0270.02364.4830.0000.0000.0000.0000.0000.000
158A160PRO0-0.0020.02166.3710.0000.0000.0000.0000.0000.000
159A161VAL00.017-0.00667.9070.0010.0010.0000.0000.0000.000
160A162ILE00.0410.00070.115-0.001-0.0010.0000.0000.0000.000
161A163GLU-1-0.872-0.94469.511-0.041-0.0410.0000.0000.0000.000
162A164ASP-1-0.838-0.91165.926-0.049-0.0490.0000.0000.0000.000
163A165ILE0-0.0180.01166.052-0.001-0.0010.0000.0000.0000.000
164A166GLY00.0510.03566.0780.0010.0010.0000.0000.0000.000
165A167LYS10.7810.89162.7540.0450.0450.0000.0000.0000.000
166A168VAL0-0.007-0.00957.2630.0000.0000.0000.0000.0000.000
167A169LEU00.0000.00657.5850.0000.0000.0000.0000.0000.000
168A170VAL0-0.016-0.02252.198-0.001-0.0010.0000.0000.0000.000
169A172ARG10.9530.96647.6390.0770.0770.0000.0000.0000.000
170A173ALA00.0080.01943.9910.0000.0000.0000.0000.0000.000
171A174LYS10.7840.85242.5700.0890.0890.0000.0000.0000.000
172A175LEU00.0280.00235.520-0.001-0.0010.0000.0000.0000.000
173A176HIS0-0.0010.01236.585-0.005-0.0050.0000.0000.0000.000
174A177ILE00.002-0.01832.090-0.005-0.0050.0000.0000.0000.000
175A178ASP-1-0.862-0.93631.477-0.193-0.1930.0000.0000.0000.000
176A179GLU-1-0.800-0.87530.507-0.162-0.1620.0000.0000.0000.000
177A180MET0-0.159-0.06828.041-0.003-0.0030.0000.0000.0000.000
178A181ASP-1-0.824-0.91232.669-0.123-0.1230.0000.0000.0000.000
179A182SER0-0.086-0.03435.8660.0030.0030.0000.0000.0000.000
180A183VAL0-0.068-0.04239.1980.0060.0060.0000.0000.0000.000
181A184PRO00.0060.01138.786-0.004-0.0040.0000.0000.0000.000
182A185THR00.0150.01136.9090.0020.0020.0000.0000.0000.000
183A186VAL0-0.067-0.03739.2640.0030.0030.0000.0000.0000.000
184A187ARG10.8660.94339.4010.1090.1090.0000.0000.0000.000
185A188GLN00.022-0.00744.5220.0010.0010.0000.0000.0000.000
186A189ALA00.0190.03348.2470.0000.0000.0000.0000.0000.000
187A190VAL00.005-0.01351.2290.0000.0000.0000.0000.0000.000
188A191LYS10.9160.95754.8460.0540.0540.0000.0000.0000.000
189A192GLU-1-0.845-0.91158.096-0.048-0.0480.0000.0000.0000.000
190A193LEU0-0.025-0.01761.4660.0000.0000.0000.0000.0000.000
191A194GLN0-0.044-0.04464.3200.0020.0020.0000.0000.0000.000
192A195VAL00.003-0.02066.8590.0000.0000.0000.0000.0000.000
193A196ASP-1-0.988-0.97470.433-0.036-0.0360.0000.0000.0000.000