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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: LN1M9

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1918331.098179
FMO2-HF: Nuclear repulsion 1840730.533185
FMO2-HF: Total energy -77600.564994
FMO2-MP2: Total energy -77823.422377


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.
-46.855-33.83836.783-17.323-32.477-0.033
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 : -0.026 / q_NPA : 0.017
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].
3A3ILE00.0200.0022.524-5.315-1.5671.538-2.260-3.026-0.009
4A4GLU-1-0.843-0.8954.949-1.992-1.913-0.001-0.011-0.0670.000
5A5THR00.005-0.0148.395-0.099-0.0990.0000.0000.0000.000
6A6THR0-0.0520.00411.0490.1100.1100.0000.0000.0000.000
7A7PRO00.0780.02314.6880.0090.0090.0000.0000.0000.000
8A8GLU-1-0.808-0.90513.032-1.010-1.0100.0000.0000.0000.000
9A9SER0-0.015-0.01214.118-0.058-0.0580.0000.0000.0000.000
10A10ARG10.8660.90616.5060.3300.3300.0000.0000.0000.000
11A11TYR00.007-0.01019.357-0.024-0.0240.0000.0000.0000.000
12A12LEU00.0050.02121.4960.0060.0060.0000.0000.0000.000
13A13ALA0-0.041-0.01824.997-0.002-0.0020.0000.0000.0000.000
14A14GLN0-0.012-0.00426.9310.0170.0170.0000.0000.0000.000
15A15ILE0-0.040-0.02929.381-0.007-0.0070.0000.0000.0000.000
16A16GLY0-0.013-0.00529.7700.0120.0120.0000.0000.0000.000
17A17ASP-1-0.834-0.89927.260-0.216-0.2160.0000.0000.0000.000
18A18SER0-0.020-0.03124.743-0.003-0.0030.0000.0000.0000.000
19A19VAL0-0.0050.01820.692-0.013-0.0130.0000.0000.0000.000
20A20SER00.014-0.00218.5160.0090.0090.0000.0000.0000.000
21A21LEU0-0.0120.02214.721-0.013-0.0130.0000.0000.0000.000
22A22THR0-0.012-0.00612.877-0.004-0.0040.0000.0000.0000.000
23A23CYS0-0.0260.0017.258-0.194-0.1940.0000.0000.0000.000
24A24SER00.0330.0087.4280.1780.1780.0000.0000.0000.000
25A25THR0-0.014-0.0232.260-1.279-0.7472.348-0.844-2.035-0.003
26A26THR0-0.042-0.0304.1760.4630.685-0.001-0.016-0.2050.000
27A27GLY0-0.036-0.0322.988-4.337-2.3470.237-1.095-1.133-0.010
28A28CYS0-0.020-0.0102.590-3.6811.4066.733-3.041-8.7790.001
29A29GLU-1-0.924-0.9454.0700.4050.4570.005-0.032-0.0250.000
30A30SER0-0.015-0.0237.329-0.345-0.3450.0000.0000.0000.000
31A31PRO0-0.0150.0044.5540.2060.407-0.001-0.015-0.1850.000
32A32PHE0-0.023-0.0055.778-0.212-0.2120.0000.0000.0000.000
33A33PHE00.011-0.0065.437-0.492-0.4920.0000.0000.0000.000
34A34SER0-0.034-0.0127.7450.2900.2900.0000.0000.0000.000
35A35TRP00.016-0.0099.653-0.191-0.1910.0000.0000.0000.000
36A36ARG10.8070.88811.2540.6290.6290.0000.0000.0000.000
37A37THR00.008-0.01214.640-0.031-0.0310.0000.0000.0000.000
38A38GLN00.0780.02516.818-0.020-0.0200.0000.0000.0000.000
39A39ILE0-0.055-0.02518.0740.0240.0240.0000.0000.0000.000
40A40ASP-1-0.856-0.91615.709-0.345-0.3450.0000.0000.0000.000
41A41SER00.0040.02618.5380.0220.0220.0000.0000.0000.000
42A42PRO0-0.011-0.01919.896-0.024-0.0240.0000.0000.0000.000
43A43LEU00.0290.01715.903-0.002-0.0020.0000.0000.0000.000
44A44ASN0-0.077-0.02219.9430.0020.0020.0000.0000.0000.000
45A45GLY00.0910.05320.7800.0010.0010.0000.0000.0000.000
46A46LYS10.8850.95119.9640.2220.2220.0000.0000.0000.000
47A47VAL00.0300.01913.506-0.019-0.0190.0000.0000.0000.000
48A48THR0-0.063-0.03615.2260.0720.0720.0000.0000.0000.000
49A49ASN0-0.0150.00411.069-0.133-0.1330.0000.0000.0000.000
50A50GLU-1-0.910-0.96612.276-0.223-0.2230.0000.0000.0000.000
51A51GLY00.0690.04711.987-0.102-0.1020.0000.0000.0000.000
52A52THR0-0.056-0.0227.0440.0820.0820.0000.0000.0000.000
53A53THR00.0240.0087.614-0.495-0.4950.0000.0000.0000.000
54A54SER0-0.012-0.0029.4800.1760.1760.0000.0000.0000.000
55A55THR00.019-0.00210.935-0.059-0.0590.0000.0000.0000.000
56A56LEU0-0.0100.00014.1180.0390.0390.0000.0000.0000.000
57A57THR00.001-0.00416.164-0.005-0.0050.0000.0000.0000.000
58A58MET0-0.073-0.04118.9450.0190.0190.0000.0000.0000.000
59A59ASN00.0060.02522.5560.0080.0080.0000.0000.0000.000
60A60PRO0-0.0100.00325.8950.0090.0090.0000.0000.0000.000
61A61VAL0-0.018-0.00324.109-0.004-0.0040.0000.0000.0000.000
62A62SER00.0600.00326.4440.0190.0190.0000.0000.0000.000
63A63PHE00.0790.02426.863-0.019-0.0190.0000.0000.0000.000
64A64GLY0-0.047-0.01626.068-0.005-0.0050.0000.0000.0000.000
65A65ASN0-0.006-0.03222.0870.0010.0010.0000.0000.0000.000
66A66GLU-1-0.756-0.81322.642-0.229-0.2290.0000.0000.0000.000
67A67HIS10.8360.92219.6960.3070.3070.0000.0000.0000.000
68A68SER00.0380.02117.288-0.021-0.0210.0000.0000.0000.000
69A69TYR0-0.034-0.03115.0770.0140.0140.0000.0000.0000.000
70A70LEU0-0.009-0.01211.831-0.045-0.0450.0000.0000.0000.000
71A72THR0-0.014-0.0196.422-0.057-0.0570.0000.0000.0000.000
72A73ALA00.0470.0242.658-0.4350.2060.318-0.264-0.695-0.001
73A74THR0-0.030-0.0292.557-5.147-2.9371.566-1.571-2.205-0.019
74A76GLU-1-0.778-0.8854.1354.9175.3870.0040.050-0.5230.001
75A77SER0-0.059-0.0375.656-0.706-0.7060.0000.0000.0000.000
76A78ARG10.8150.8961.895-23.252-29.66018.092-5.899-5.7850.006
77A79LYS10.8940.9282.475-0.7770.4481.768-0.940-2.054-0.009
78A80LEU0-0.051-0.0162.617-2.5810.2214.176-1.411-5.5670.010
79A81GLU-1-0.774-0.8723.866-1.448-1.2820.0010.026-0.1930.000
80A82LYS10.7980.8967.0751.1541.1540.0000.0000.0000.000
81A83GLY00.0070.0089.4420.0170.0170.0000.0000.0000.000
82A84ILE0-0.027-0.01312.994-0.007-0.0070.0000.0000.0000.000
83A85GLN00.0440.03415.7520.0100.0100.0000.0000.0000.000
84A86VAL0-0.030-0.01818.8010.0020.0020.0000.0000.0000.000
85A87GLU-1-0.828-0.88821.313-0.275-0.2750.0000.0000.0000.000
86A88ILE0-0.029-0.02424.966-0.005-0.0050.0000.0000.0000.000
87A89TYR00.0350.02427.8050.0080.0080.0000.0000.0000.000
88A90SER0-0.037-0.04231.519-0.005-0.0050.0000.0000.0000.000
89A91PHE00.0600.01734.3880.0060.0060.0000.0000.0000.000
90A92PRO00.0270.02636.7750.0020.0020.0000.0000.0000.000
91A93LYS10.8130.88838.6010.1110.1110.0000.0000.0000.000
92A94ASP-1-0.853-0.91142.397-0.109-0.1090.0000.0000.0000.000
93A95PRO0-0.010-0.01245.1450.0010.0010.0000.0000.0000.000
94A96GLU-1-0.951-0.96647.510-0.078-0.0780.0000.0000.0000.000
95A97ILE0-0.030-0.03450.8050.0000.0000.0000.0000.0000.000
96A98HIS00.0140.01754.3110.0010.0010.0000.0000.0000.000
97A99LEU0-0.001-0.01156.9510.0000.0000.0000.0000.0000.000
98A100SER0-0.036-0.03560.5180.0010.0010.0000.0000.0000.000
99A101GLY0-0.016-0.00862.4290.0020.0020.0000.0000.0000.000
100A102PRO0-0.033-0.00665.485-0.001-0.0010.0000.0000.0000.000
101A103LEU00.0000.01865.3470.0000.0000.0000.0000.0000.000
102A104GLU-1-0.770-0.88168.104-0.041-0.0410.0000.0000.0000.000
103A105ALA00.0090.00070.802-0.001-0.0010.0000.0000.0000.000
104A106GLY0-0.0040.00071.4720.0010.0010.0000.0000.0000.000
105A107LYS10.7930.88469.2320.0430.0430.0000.0000.0000.000
106A108PRO0-0.035-0.02267.780-0.001-0.0010.0000.0000.0000.000
107A109ILE0-0.017-0.00863.4550.0000.0000.0000.0000.0000.000
108A110THR00.0120.00859.275-0.001-0.0010.0000.0000.0000.000
109A111VAL0-0.0080.01256.6740.0010.0010.0000.0000.0000.000
110A112LYS10.8350.90452.2590.0710.0710.0000.0000.0000.000
111A113CYS0-0.049-0.00550.538-0.001-0.0010.0000.0000.0000.000
112A114SER00.0260.00948.6090.0010.0010.0000.0000.0000.000
113A115VAL00.0400.01343.134-0.001-0.0010.0000.0000.0000.000
114A116ALA00.0170.01643.1580.0010.0010.0000.0000.0000.000
115A117ASP-1-0.806-0.87938.242-0.118-0.1180.0000.0000.0000.000
116A118VAL00.0030.01337.544-0.008-0.0080.0000.0000.0000.000
117A119TYR0-0.087-0.06430.0780.0050.0050.0000.0000.0000.000
118A120PRO00.0310.00832.799-0.006-0.0060.0000.0000.0000.000
119A121PHE00.0540.00335.1560.0030.0030.0000.0000.0000.000
120A122ASP-1-0.798-0.88535.289-0.146-0.1460.0000.0000.0000.000
121A123ARG10.7330.82833.1760.1680.1680.0000.0000.0000.000
122A124LEU0-0.042-0.00937.9730.0000.0000.0000.0000.0000.000
123A125GLU-1-0.788-0.87741.048-0.094-0.0940.0000.0000.0000.000
124A126ILE0-0.036-0.01644.495-0.001-0.0010.0000.0000.0000.000
125A127ASP-1-0.784-0.89047.244-0.090-0.0900.0000.0000.0000.000
126A128LEU0-0.010-0.02650.3020.0000.0000.0000.0000.0000.000
127A129LEU0-0.014-0.00251.9590.0010.0010.0000.0000.0000.000
128A130LYS10.8340.90756.1970.0560.0560.0000.0000.0000.000
129A131GLY00.0030.00357.9290.0030.0030.0000.0000.0000.000
130A132ASP-1-0.909-0.95356.121-0.068-0.0680.0000.0000.0000.000
131A133HIS0-0.019-0.01256.594-0.001-0.0010.0000.0000.0000.000
132A134LEU00.0280.01451.8440.0000.0000.0000.0000.0000.000
133A135MET0-0.084-0.03356.0940.0020.0020.0000.0000.0000.000
134A136LYS10.8720.92853.2430.0730.0730.0000.0000.0000.000
135A137SER0-0.024-0.01149.4150.0000.0000.0000.0000.0000.000
136A138GLN0-0.078-0.05147.8960.0070.0070.0000.0000.0000.000
137A139GLU-1-0.872-0.92244.197-0.104-0.1040.0000.0000.0000.000
138A140PHE0-0.022-0.03042.3880.0050.0050.0000.0000.0000.000
139A141LEU00.0070.00540.470-0.005-0.0050.0000.0000.0000.000
140A142GLU-1-0.954-0.95440.925-0.098-0.0980.0000.0000.0000.000
141A143ASP-1-0.830-0.93039.929-0.106-0.1060.0000.0000.0000.000
142A144ALA0-0.037-0.01941.0270.0000.0000.0000.0000.0000.000
143A145ASP-1-0.844-0.90937.541-0.117-0.1170.0000.0000.0000.000
144A146ARG10.8500.89131.5490.1580.1580.0000.0000.0000.000
145A147LYS10.7810.87628.8560.1780.1780.0000.0000.0000.000
146A148SER0-0.0080.00734.8770.0000.0000.0000.0000.0000.000
147A149LEU0-0.086-0.03734.8030.0010.0010.0000.0000.0000.000
148A150GLU-1-0.879-0.93438.548-0.091-0.0910.0000.0000.0000.000
149A151THR0-0.035-0.02942.294-0.004-0.0040.0000.0000.0000.000
150A152LYS10.8150.93242.0160.1080.1080.0000.0000.0000.000
151A153SER0-0.026-0.04445.9200.0010.0010.0000.0000.0000.000
152A154LEU0-0.036-0.00949.4210.0000.0000.0000.0000.0000.000
153A155GLU-1-0.749-0.86751.759-0.068-0.0680.0000.0000.0000.000
154A156VAL0-0.040-0.01455.406-0.001-0.0010.0000.0000.0000.000
155A157THR0-0.005-0.02058.2890.0000.0000.0000.0000.0000.000
156A158PHE0-0.025-0.00962.1020.0000.0000.0000.0000.0000.000
157A159THR00.0250.02264.6190.0010.0010.0000.0000.0000.000
158A160PRO0-0.0080.01766.526-0.001-0.0010.0000.0000.0000.000
159A161VAL00.0120.00067.9670.0020.0020.0000.0000.0000.000
160A162ILE00.0300.01170.297-0.001-0.0010.0000.0000.0000.000
161A163GLU-1-0.855-0.94870.027-0.045-0.0450.0000.0000.0000.000
162A164ASP-1-0.811-0.90566.129-0.054-0.0540.0000.0000.0000.000
163A165ILE0-0.0210.00366.352-0.002-0.0020.0000.0000.0000.000
164A166GLY00.0180.02666.1130.0010.0010.0000.0000.0000.000
165A167LYS10.7980.90362.8490.0510.0510.0000.0000.0000.000
166A168VAL0-0.006-0.01857.4460.0000.0000.0000.0000.0000.000
167A169LEU0-0.0050.00557.763-0.001-0.0010.0000.0000.0000.000
168A170VAL0-0.012-0.00652.462-0.001-0.0010.0000.0000.0000.000
169A172ARG10.9110.94547.4530.0860.0860.0000.0000.0000.000
170A173ALA00.0230.01843.5980.0020.0020.0000.0000.0000.000
171A174LYS10.7800.87042.5100.0950.0950.0000.0000.0000.000
172A175LEU00.0390.01035.5820.0010.0010.0000.0000.0000.000
173A176HIS00.004-0.00136.528-0.007-0.0070.0000.0000.0000.000
174A177ILE00.007-0.00232.285-0.002-0.0020.0000.0000.0000.000
175A178ASP-1-0.852-0.92431.069-0.231-0.2310.0000.0000.0000.000
176A179GLU-1-0.823-0.87530.471-0.176-0.1760.0000.0000.0000.000
177A180MET0-0.127-0.06227.696-0.006-0.0060.0000.0000.0000.000
178A181ASP-1-0.832-0.90432.847-0.147-0.1470.0000.0000.0000.000
179A182SER0-0.102-0.04936.1900.0050.0050.0000.0000.0000.000
180A183VAL0-0.068-0.03839.4150.0070.0070.0000.0000.0000.000
181A184PRO00.0040.00438.654-0.006-0.0060.0000.0000.0000.000
182A185THR00.0200.02136.6050.0010.0010.0000.0000.0000.000
183A186VAL0-0.045-0.02838.9980.0050.0050.0000.0000.0000.000
184A187ARG10.8280.92439.2440.1220.1220.0000.0000.0000.000
185A188GLN00.019-0.00244.4220.0020.0020.0000.0000.0000.000
186A189ALA00.0140.03148.2130.0000.0000.0000.0000.0000.000
187A190VAL00.006-0.01851.1830.0010.0010.0000.0000.0000.000
188A191LYS10.9050.95554.9360.0580.0580.0000.0000.0000.000
189A192GLU-1-0.826-0.90058.356-0.055-0.0550.0000.0000.0000.000
190A193LEU0-0.043-0.02861.6680.0010.0010.0000.0000.0000.000
191A194GLN0-0.042-0.03564.5900.0030.0030.0000.0000.0000.000
192A195VAL00.0240.00367.0750.0000.0000.0000.0000.0000.000
193A196ASP-1-1.010-0.99270.540-0.041-0.0410.0000.0000.0000.000