FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: JQ169

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:

Apendix: None


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 195
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1918310.411673
FMO2-HF: Nuclear repulsion 1840713.675147
FMO2-HF: Total energy -77596.736526
FMO2-MP2: Total energy -77819.868075


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.
-36.495-15.57923.538-14.462-29.989-0.04
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 : 0.020 / q_NPA : 0.016
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].
3A3ILE00.0310.0262.935-5.845-1.2200.268-2.311-2.5810.002
4A4GLU-1-0.942-0.9744.971-0.790-0.716-0.001-0.007-0.0650.000
5A5THR0-0.014-0.0198.441-0.102-0.1020.0000.0000.0000.000
6A6THR00.0180.04711.2880.0580.0580.0000.0000.0000.000
7A7PRO00.0220.00514.922-0.017-0.0170.0000.0000.0000.000
8A8GLU-1-0.853-0.94213.634-0.436-0.4360.0000.0000.0000.000
9A9SER0-0.006-0.01314.642-0.019-0.0190.0000.0000.0000.000
10A10ARG10.8790.93216.8950.1760.1760.0000.0000.0000.000
11A11TYR00.000-0.00819.757-0.012-0.0120.0000.0000.0000.000
12A12LEU00.0280.05021.9810.0020.0020.0000.0000.0000.000
13A13ALA0-0.034-0.03124.761-0.001-0.0010.0000.0000.0000.000
14A14GLN00.0090.02126.7120.0130.0130.0000.0000.0000.000
15A15ILE0-0.030-0.02629.460-0.007-0.0070.0000.0000.0000.000
16A16GLY0-0.044-0.02329.9200.0070.0070.0000.0000.0000.000
17A17ASP-1-0.865-0.93227.771-0.142-0.1420.0000.0000.0000.000
18A18SER0-0.025-0.02725.426-0.010-0.0100.0000.0000.0000.000
19A19VAL0-0.004-0.00220.794-0.003-0.0030.0000.0000.0000.000
20A20SER00.006-0.01118.571-0.005-0.0050.0000.0000.0000.000
21A21LEU0-0.0310.00514.8850.0040.0040.0000.0000.0000.000
22A22THR0-0.007-0.02313.017-0.035-0.0350.0000.0000.0000.000
23A23CYS0-0.035-0.0027.337-0.108-0.1080.0000.0000.0000.000
24A24SER00.0600.0357.4500.0630.0630.0000.0000.0000.000
25A25THR00.0080.0052.479-1.1430.0160.658-0.474-1.3440.000
26A26THR0-0.0030.0023.6760.5690.9640.001-0.105-0.2910.000
27A27GLY0-0.066-0.0552.409-4.376-2.4932.193-1.698-2.377-0.020
28A28CYS-1-0.822-0.8952.485-2.3420.6121.353-1.502-2.806-0.014
29A29GLU-1-0.999-0.9813.8650.3170.3830.015-0.016-0.0650.000
30A30SER0-0.062-0.0437.315-0.119-0.1190.0000.0000.0000.000
31A31PRO00.0660.0384.466-0.0390.157-0.001-0.014-0.1810.000
32A32PHE0-0.089-0.0485.7520.1500.1500.0000.0000.0000.000
33A33PHE00.015-0.0085.518-0.349-0.3490.0000.0000.0000.000
34A34SER0-0.051-0.0237.7870.1760.1760.0000.0000.0000.000
35A35TRP00.0200.0109.830-0.081-0.0810.0000.0000.0000.000
36A36ARG10.8950.94311.8630.4220.4220.0000.0000.0000.000
37A37THR00.0140.00515.090-0.014-0.0140.0000.0000.0000.000
38A38GLN00.0940.03217.330-0.016-0.0160.0000.0000.0000.000
39A39ILE0-0.064-0.02518.3120.0140.0140.0000.0000.0000.000
40A40ASP-1-0.912-0.95416.321-0.264-0.2640.0000.0000.0000.000
41A41SER0-0.0030.01619.0970.0190.0190.0000.0000.0000.000
42A42PRO0-0.033-0.03020.435-0.020-0.0200.0000.0000.0000.000
43A43LEU00.0540.03615.8250.0020.0020.0000.0000.0000.000
44A44ASN0-0.061-0.01120.0110.0070.0070.0000.0000.0000.000
45A45GLY00.1070.06220.7390.0050.0050.0000.0000.0000.000
46A46LYS10.8750.93619.9080.2160.2160.0000.0000.0000.000
47A47VAL00.0210.00513.464-0.001-0.0010.0000.0000.0000.000
48A48THR0-0.087-0.03815.6480.0320.0320.0000.0000.0000.000
49A49ASN00.0330.02411.445-0.055-0.0550.0000.0000.0000.000
50A50GLU-1-0.942-0.97313.001-0.361-0.3610.0000.0000.0000.000
51A51GLY00.0500.03211.901-0.040-0.0400.0000.0000.0000.000
52A52THR00.0250.0137.1010.0200.0200.0000.0000.0000.000
53A53THR00.0210.0007.663-0.271-0.2710.0000.0000.0000.000
54A54SER0-0.045-0.0149.8620.1250.1250.0000.0000.0000.000
55A55THR00.033-0.00411.288-0.003-0.0030.0000.0000.0000.000
56A56LEU0-0.041-0.01014.5770.0270.0270.0000.0000.0000.000
57A57THR00.004-0.00316.3220.0150.0150.0000.0000.0000.000
58A58MET0-0.055-0.03519.6040.0090.0090.0000.0000.0000.000
59A59ASN0-0.0120.04722.5930.0120.0120.0000.0000.0000.000
60A60PRO0-0.030-0.01225.9500.0020.0020.0000.0000.0000.000
61A61VAL00.0060.00524.961-0.005-0.0050.0000.0000.0000.000
62A62SER00.0570.00626.4090.0150.0150.0000.0000.0000.000
63A63PHE00.1330.04827.041-0.012-0.0120.0000.0000.0000.000
64A64GLY0-0.072-0.02626.342-0.002-0.0020.0000.0000.0000.000
65A65ASN0-0.018-0.04822.117-0.001-0.0010.0000.0000.0000.000
66A66GLU-1-0.822-0.87122.871-0.145-0.1450.0000.0000.0000.000
67A67HIS10.8630.93220.2310.2070.2070.0000.0000.0000.000
68A68SER00.0210.02717.392-0.002-0.0020.0000.0000.0000.000
69A69TYR0-0.049-0.04915.1760.0080.0080.0000.0000.0000.000
70A70LEU0-0.010-0.03011.774-0.011-0.0110.0000.0000.0000.000
71A72THR0-0.050-0.0386.0500.0470.0470.0000.0000.0000.000
72A73ALA00.0360.0182.430-0.517-0.1821.227-0.557-1.0040.002
73A74THR0-0.070-0.0512.610-4.171-2.3030.986-1.017-1.837-0.014
74A75CYS-1-0.736-0.8612.634-2.372-0.7317.717-2.661-6.696-0.014
75A76GLU-1-0.872-0.9333.9081.9602.3940.0080.074-0.5160.000
76A77SER0-0.118-0.0716.495-0.316-0.3160.0000.0000.0000.000
77A78ARG10.8250.9172.281-10.170-9.4984.043-1.439-3.2760.011
78A79LYS10.9570.9932.621-2.341-1.1372.249-1.130-2.323-0.014
79A80LEU0-0.055-0.0132.724-2.9660.3072.822-1.607-4.4880.021
80A81GLU-1-0.867-0.9414.002-1.134-0.9970.0000.002-0.1390.000
81A82LYS10.8810.9377.3620.6520.6520.0000.0000.0000.000
82A83GLY0-0.0080.0079.603-0.058-0.0580.0000.0000.0000.000
83A84ILE00.0020.01513.0230.0130.0130.0000.0000.0000.000
84A85GLN0-0.008-0.00215.856-0.002-0.0020.0000.0000.0000.000
85A86VAL0-0.035-0.02718.999-0.002-0.0020.0000.0000.0000.000
86A87GLU-1-0.852-0.92221.514-0.141-0.1410.0000.0000.0000.000
87A88ILE0-0.032-0.02025.168-0.006-0.0060.0000.0000.0000.000
88A89TYR00.0320.01727.9970.0050.0050.0000.0000.0000.000
89A90SER0-0.030-0.02131.762-0.007-0.0070.0000.0000.0000.000
90A91PHE00.0540.01234.6840.0040.0040.0000.0000.0000.000
91A92PRO0-0.027-0.00737.3650.0010.0010.0000.0000.0000.000
92A93LYS10.9090.96238.9500.0740.0740.0000.0000.0000.000
93A94ASP-1-0.894-0.93542.785-0.067-0.0670.0000.0000.0000.000
94A95PRO00.0610.01345.784-0.001-0.0010.0000.0000.0000.000
95A96GLU-1-0.985-0.99347.730-0.052-0.0520.0000.0000.0000.000
96A97ILE00.002-0.00450.9480.0010.0010.0000.0000.0000.000
97A98HIS0-0.037-0.02754.3530.0010.0010.0000.0000.0000.000
98A99LEU0-0.001-0.00157.0490.0010.0010.0000.0000.0000.000
99A100SER0-0.037-0.02560.6310.0000.0000.0000.0000.0000.000
100A101GLY0-0.025-0.00162.6490.0010.0010.0000.0000.0000.000
101A102PRO0-0.041-0.01965.2960.0000.0000.0000.0000.0000.000
102A103LEU00.0250.03966.2210.0000.0000.0000.0000.0000.000
103A104GLU-1-0.913-0.96968.178-0.026-0.0260.0000.0000.0000.000
104A105ALA0-0.011-0.01771.1750.0000.0000.0000.0000.0000.000
105A106GLY00.0060.00671.6200.0010.0010.0000.0000.0000.000
106A107LYS10.9240.97370.2160.0280.0280.0000.0000.0000.000
107A108PRO0-0.069-0.04067.524-0.001-0.0010.0000.0000.0000.000
108A109ILE0-0.023-0.01563.6370.0000.0000.0000.0000.0000.000
109A110THR00.013-0.04059.1710.0000.0000.0000.0000.0000.000
110A111VAL0-0.0130.00456.5270.0000.0000.0000.0000.0000.000
111A112LYS10.9350.96052.5170.0470.0470.0000.0000.0000.000
112A113CYS-1-0.902-0.99251.008-0.052-0.0520.0000.0000.0000.000
113A114SER00.032-0.02548.6590.0000.0000.0000.0000.0000.000
114A115VAL00.0680.02743.694-0.001-0.0010.0000.0000.0000.000
115A116ALA0-0.013-0.00243.5600.0000.0000.0000.0000.0000.000
116A117ASP-1-0.904-0.97338.560-0.083-0.0830.0000.0000.0000.000
117A118VAL00.0360.01438.045-0.005-0.0050.0000.0000.0000.000
118A119TYR0-0.114-0.05930.2550.0030.0030.0000.0000.0000.000
119A120PRO00.007-0.00332.966-0.004-0.0040.0000.0000.0000.000
120A121PHE00.0700.00835.3210.0020.0020.0000.0000.0000.000
121A122ASP-1-0.849-0.93135.961-0.083-0.0830.0000.0000.0000.000
122A123ARG10.8820.96934.5910.0890.0890.0000.0000.0000.000
123A124LEU0-0.059-0.03838.1450.0000.0000.0000.0000.0000.000
124A125GLU-1-0.914-0.94941.276-0.053-0.0530.0000.0000.0000.000
125A126ILE0-0.020-0.01344.739-0.002-0.0020.0000.0000.0000.000
126A127ASP-1-0.840-0.93747.512-0.050-0.0500.0000.0000.0000.000
127A128LEU00.0130.00550.5680.0000.0000.0000.0000.0000.000
128A129LEU0-0.017-0.03452.0410.0010.0010.0000.0000.0000.000
129A130LYS10.8930.95355.9990.0320.0320.0000.0000.0000.000
130A131GLY0-0.022-0.00458.6280.0010.0010.0000.0000.0000.000
131A132ASP-1-0.939-0.97156.629-0.038-0.0380.0000.0000.0000.000
132A133HIS0-0.063-0.04357.3260.0000.0000.0000.0000.0000.000
133A134LEU00.0380.03151.9490.0000.0000.0000.0000.0000.000
134A135MET0-0.102-0.03556.2110.0020.0020.0000.0000.0000.000
135A136LYS10.8880.93353.7400.0430.0430.0000.0000.0000.000
136A137SER00.0660.05149.8050.0000.0000.0000.0000.0000.000
137A138GLN0-0.074-0.03348.0880.0030.0030.0000.0000.0000.000
138A139GLU-1-0.869-0.92644.759-0.057-0.0570.0000.0000.0000.000
139A140PHE0-0.028-0.03942.6160.0020.0020.0000.0000.0000.000
140A141LEU0-0.004-0.00240.819-0.004-0.0040.0000.0000.0000.000
141A142GLU-1-0.950-0.96441.217-0.056-0.0560.0000.0000.0000.000
142A143ASP-1-0.896-0.97639.967-0.068-0.0680.0000.0000.0000.000
143A144ALA0-0.097-0.04540.566-0.001-0.0010.0000.0000.0000.000
144A145ASP-1-0.849-0.92538.880-0.074-0.0740.0000.0000.0000.000
145A146ARG10.9090.94632.2520.0920.0920.0000.0000.0000.000
146A147LYS10.7850.88928.2130.1310.1310.0000.0000.0000.000
147A148SER00.0030.02734.520-0.003-0.0030.0000.0000.0000.000
148A149LEU0-0.037-0.00235.833-0.001-0.0010.0000.0000.0000.000
149A150GLU-1-0.928-0.95838.548-0.063-0.0630.0000.0000.0000.000
150A151THR0-0.024-0.02742.215-0.002-0.0020.0000.0000.0000.000
151A152LYS10.8590.96542.5960.0680.0680.0000.0000.0000.000
152A153SER0-0.009-0.00245.9380.0010.0010.0000.0000.0000.000
153A154LEU00.0220.03749.5270.0000.0000.0000.0000.0000.000
154A155GLU-1-0.911-0.96251.897-0.042-0.0420.0000.0000.0000.000
155A156VAL0-0.018-0.00655.6520.0010.0010.0000.0000.0000.000
156A157THR00.0220.02958.5700.0000.0000.0000.0000.0000.000
157A158PHE0-0.039-0.01462.2910.0000.0000.0000.0000.0000.000
158A159THR00.0070.01964.7250.0000.0000.0000.0000.0000.000
159A160PRO00.0080.03566.6920.0000.0000.0000.0000.0000.000
160A161VAL00.018-0.01468.1720.0010.0010.0000.0000.0000.000
161A162ILE00.041-0.00270.395-0.001-0.0010.0000.0000.0000.000
162A163GLU-1-0.920-0.96269.900-0.026-0.0260.0000.0000.0000.000
163A164ASP-1-0.856-0.94866.262-0.031-0.0310.0000.0000.0000.000
164A165ILE0-0.030-0.00366.339-0.001-0.0010.0000.0000.0000.000
165A166GLY00.0420.03266.3750.0010.0010.0000.0000.0000.000
166A167LYS10.8250.92963.0330.0300.0300.0000.0000.0000.000
167A168VAL00.014-0.00657.6290.0000.0000.0000.0000.0000.000
168A169LEU0-0.021-0.00157.7250.0000.0000.0000.0000.0000.000
169A170VAL0-0.066-0.05852.540-0.001-0.0010.0000.0000.0000.000
170A171CYS-1-0.854-0.80650.655-0.052-0.0520.0000.0000.0000.000
171A172ARG10.8900.89747.8500.0500.0500.0000.0000.0000.000
172A173ALA00.0480.04044.1000.0010.0010.0000.0000.0000.000
173A174LYS10.8950.92942.8190.0540.0540.0000.0000.0000.000
174A175LEU00.0250.00635.7130.0000.0000.0000.0000.0000.000
175A176HIS0-0.0160.00237.531-0.005-0.0050.0000.0000.0000.000
176A177ILE0-0.007-0.01632.105-0.001-0.0010.0000.0000.0000.000
177A178ASP-1-0.890-0.95331.840-0.114-0.1140.0000.0000.0000.000
178A179GLU-1-0.901-0.95230.900-0.091-0.0910.0000.0000.0000.000
179A180MET0-0.165-0.07028.0400.0010.0010.0000.0000.0000.000
180A181ASP-1-0.816-0.90033.016-0.079-0.0790.0000.0000.0000.000
181A182SER0-0.077-0.04036.2120.0030.0030.0000.0000.0000.000
182A183VAL0-0.115-0.06239.5400.0040.0040.0000.0000.0000.000
183A184PRO00.0280.02039.101-0.003-0.0030.0000.0000.0000.000
184A185THR00.0150.00437.130-0.001-0.0010.0000.0000.0000.000
185A186VAL0-0.070-0.03939.5740.0030.0030.0000.0000.0000.000
186A187ARG10.8640.96139.3880.0780.0780.0000.0000.0000.000
187A188GLN00.0370.00944.8130.0020.0020.0000.0000.0000.000
188A189ALA00.0290.04748.534-0.001-0.0010.0000.0000.0000.000
189A190VAL0-0.006-0.01351.5060.0010.0010.0000.0000.0000.000
190A191LYS10.9150.96655.1300.0380.0380.0000.0000.0000.000
191A192GLU-1-0.889-0.95858.369-0.034-0.0340.0000.0000.0000.000
192A193LEU0-0.051-0.01561.7470.0000.0000.0000.0000.0000.000
193A194GLN0-0.015-0.01764.5930.0020.0020.0000.0000.0000.000
194A195VAL0-0.014-0.02367.1350.0000.0000.0000.0000.0000.000
195A196ASP-1-0.982-0.97170.704-0.026-0.0260.0000.0000.0000.000