Manual

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

tag_button

FMODB ID: 98K22

Calculation Name: 3HXQ-A-Xray372

Preferred Name: von Willebrand factor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3HXQ

Chain ID: A

ChEMBL ID: CHEMBL2021748

UniProt ID: P04275

Base Structure: X-ray

Registration Date: 2023-09-23

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2465298.098624
FMO2-HF: Nuclear repulsion 2385274.906453
FMO2-HF: Total energy -80023.192171
FMO2-MP2: Total energy -80258.368753


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:502:PRO)


Summations of interaction energy for fragment #1(A:502:PRO)
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.
-2.673-1.1450.004-0.623-0.9090.001
Interaction energy analysis for fragmet #1(A:502:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.026
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].
3A504LEU0-0.047-0.0233.677-1.0790.2990.005-0.616-0.7670.001
4A505HIS0-0.107-0.0604.4430.4310.581-0.001-0.007-0.1420.000
5A506ASP-1-0.860-0.9057.520-0.559-0.5590.0000.0000.0000.000
6A507PHE0-0.005-0.0228.881-0.037-0.0370.0000.0000.0000.000
7A508TYR00.010-0.00410.8190.1580.1580.0000.0000.0000.000
8A509CYS0-0.098-0.00612.8250.1440.1440.0000.0000.0000.000
9A510SER00.007-0.00315.7430.1010.1010.0000.0000.0000.000
10A511ARG10.7830.87513.0840.5980.5980.0000.0000.0000.000
11A512LEU0-0.073-0.03019.4200.0180.0180.0000.0000.0000.000
12A513LEU00.0270.00818.5430.0160.0160.0000.0000.0000.000
13A514ASP-1-0.753-0.84022.520-0.193-0.1930.0000.0000.0000.000
14A515LEU00.0240.01018.7500.0100.0100.0000.0000.0000.000
15A516VAL0-0.029-0.03122.7490.0100.0100.0000.0000.0000.000
16A517PHE00.0470.02318.9070.0060.0060.0000.0000.0000.000
17A518LEU0-0.034-0.02523.8460.0170.0170.0000.0000.0000.000
18A519LEU00.0260.00524.424-0.002-0.0020.0000.0000.0000.000
19A520ASP-1-0.715-0.82326.368-0.057-0.0570.0000.0000.0000.000
20A521GLY00.0680.04328.360-0.002-0.0020.0000.0000.0000.000
21A522SER0-0.059-0.04630.7130.0090.0090.0000.0000.0000.000
22A523SER0-0.024-0.01531.854-0.003-0.0030.0000.0000.0000.000
23A524ARG10.7860.87630.1330.0220.0220.0000.0000.0000.000
24A525LEU00.0160.03225.4470.0020.0020.0000.0000.0000.000
25A526SER00.011-0.01029.1760.0010.0010.0000.0000.0000.000
26A527GLU-1-0.896-0.95729.559-0.080-0.0800.0000.0000.0000.000
27A528ALA00.0350.00828.224-0.009-0.0090.0000.0000.0000.000
28A529GLU-1-0.811-0.88625.367-0.045-0.0450.0000.0000.0000.000
29A530PHE00.001-0.00224.822-0.017-0.0170.0000.0000.0000.000
30A531GLU-1-0.842-0.91625.989-0.145-0.1450.0000.0000.0000.000
31A532VAL00.0230.01020.554-0.022-0.0220.0000.0000.0000.000
32A533LEU0-0.026-0.00821.130-0.029-0.0290.0000.0000.0000.000
33A534LYS10.7640.87221.8210.1000.1000.0000.0000.0000.000
34A535ALA00.0140.00220.838-0.027-0.0270.0000.0000.0000.000
35A536PHE0-0.0080.00514.090-0.037-0.0370.0000.0000.0000.000
36A537VAL00.011-0.00117.716-0.051-0.0510.0000.0000.0000.000
37A538VAL0-0.025-0.02819.748-0.031-0.0310.0000.0000.0000.000
38A539ASP-1-0.740-0.85014.865-0.660-0.6600.0000.0000.0000.000
39A540MET00.0340.03514.953-0.046-0.0460.0000.0000.0000.000
40A541MET0-0.119-0.06216.622-0.008-0.0080.0000.0000.0000.000
41A542GLU-1-0.850-0.90617.677-0.352-0.3520.0000.0000.0000.000
42A543ARG10.8530.9219.9721.0311.0310.0000.0000.0000.000
43A544LEU0-0.021-0.01115.348-0.041-0.0410.0000.0000.0000.000
44A545ARG10.9170.97518.1640.3740.3740.0000.0000.0000.000
45A546ILE0-0.024-0.02020.6220.0380.0380.0000.0000.0000.000
46A547SER0-0.013-0.01923.6860.0230.0230.0000.0000.0000.000
47A548GLN0-0.066-0.04926.6550.0100.0100.0000.0000.0000.000
48A549LYS10.9230.95528.1040.1740.1740.0000.0000.0000.000
49A550TRP00.0320.02721.800-0.005-0.0050.0000.0000.0000.000
50A551VAL00.1020.06919.6350.0120.0120.0000.0000.0000.000
51A552ARG10.6670.80523.0390.1920.1920.0000.0000.0000.000
52A553VAL00.0460.01522.520-0.012-0.0120.0000.0000.0000.000
53A554ALA0-0.046-0.02725.2090.0190.0190.0000.0000.0000.000
54A555VAL00.0200.01125.141-0.013-0.0130.0000.0000.0000.000
55A556VAL0-0.042-0.02627.5240.0130.0130.0000.0000.0000.000
56A557GLU-1-0.793-0.86628.713-0.090-0.0900.0000.0000.0000.000
57A558TYR0-0.064-0.04927.3310.0020.0020.0000.0000.0000.000
58A559HIS00.024-0.00632.2180.0050.0050.0000.0000.0000.000
59A560ASP-1-0.947-0.97235.146-0.045-0.0450.0000.0000.0000.000
60A561GLY00.011-0.00136.8250.0020.0020.0000.0000.0000.000
61A562SER0-0.029-0.02433.567-0.002-0.0020.0000.0000.0000.000
62A563HIS0-0.0100.00934.0830.0060.0060.0000.0000.0000.000
63A564ALA0-0.004-0.01432.152-0.008-0.0080.0000.0000.0000.000
64A565TYR00.0210.01930.7020.0050.0050.0000.0000.0000.000
65A566ILE0-0.051-0.01327.579-0.002-0.0020.0000.0000.0000.000
66A567GLY00.0390.01730.4130.0000.0000.0000.0000.0000.000
67A568LEU00.0100.00926.937-0.003-0.0030.0000.0000.0000.000
68A569LYS10.8550.90830.0470.1160.1160.0000.0000.0000.000
69A570ASP-1-0.763-0.85931.250-0.142-0.1420.0000.0000.0000.000
70A571ARG10.8520.92432.1520.1490.1490.0000.0000.0000.000
71A572LYS10.9020.95031.7260.1410.1410.0000.0000.0000.000
72A573ARG10.9510.97030.4140.1430.1430.0000.0000.0000.000
73A574PRO00.0960.02024.8700.0060.0060.0000.0000.0000.000
74A575SER00.0190.01525.923-0.010-0.0100.0000.0000.0000.000
75A576GLU-1-0.861-0.90327.446-0.138-0.1380.0000.0000.0000.000
76A577LEU0-0.0070.00226.8230.0060.0060.0000.0000.0000.000
77A578ARG10.8760.91721.8720.3250.3250.0000.0000.0000.000
78A579ARG10.8660.93425.7440.1410.1410.0000.0000.0000.000
79A580ILE0-0.028-0.01628.9320.0100.0100.0000.0000.0000.000
80A581ALA00.0140.00625.1840.0090.0090.0000.0000.0000.000
81A582SER00.009-0.00626.5130.0080.0080.0000.0000.0000.000
82A583GLN0-0.014-0.01427.6270.0130.0130.0000.0000.0000.000
83A584VAL0-0.037-0.00328.4220.0110.0110.0000.0000.0000.000
84A585LYS10.9590.97030.7560.0850.0850.0000.0000.0000.000
85A586TYR00.005-0.00331.128-0.002-0.0020.0000.0000.0000.000
86A587ALA0-0.010-0.00532.7550.0040.0040.0000.0000.0000.000
87A588GLY00.0090.01133.8730.0050.0050.0000.0000.0000.000
88A589SER0-0.039-0.02434.6850.0070.0070.0000.0000.0000.000
89A590GLN0-0.019-0.01435.8010.0020.0020.0000.0000.0000.000
90A591VAL0-0.032-0.03436.4760.0040.0040.0000.0000.0000.000
91A592ALA00.0680.04631.867-0.003-0.0030.0000.0000.0000.000
92A593SER0-0.041-0.03632.9430.0010.0010.0000.0000.0000.000
93A594THR00.034-0.01728.952-0.005-0.0050.0000.0000.0000.000
94A595SER0-0.066-0.07631.343-0.006-0.0060.0000.0000.0000.000
95A596GLU-1-0.757-0.88134.016-0.060-0.0600.0000.0000.0000.000
96A597VAL00.0720.05229.926-0.003-0.0030.0000.0000.0000.000
97A598LEU0-0.0130.00927.705-0.009-0.0090.0000.0000.0000.000
98A599LYS10.7750.87631.4470.0520.0520.0000.0000.0000.000
99A600TYR00.0500.01832.831-0.003-0.0030.0000.0000.0000.000
100A601THR00.014-0.01828.378-0.007-0.0070.0000.0000.0000.000
101A602LEU0-0.054-0.01231.799-0.004-0.0040.0000.0000.0000.000
102A603PHE0-0.046-0.03733.7260.0020.0020.0000.0000.0000.000
103A604GLN0-0.0090.01935.5490.0020.0020.0000.0000.0000.000
104A605ILE0-0.032-0.00329.639-0.002-0.0020.0000.0000.0000.000
105A606PHE00.0350.01626.848-0.004-0.0040.0000.0000.0000.000
106A607SER0-0.035-0.00732.9180.0070.0070.0000.0000.0000.000
107A608LYS10.9280.95336.1190.0910.0910.0000.0000.0000.000
108A609ILE00.0320.01231.453-0.006-0.0060.0000.0000.0000.000
109A610ASP-1-0.800-0.88632.421-0.130-0.1300.0000.0000.0000.000
110A611ARG10.7140.84525.2570.2290.2290.0000.0000.0000.000
111A612PRO0-0.010-0.01429.617-0.009-0.0090.0000.0000.0000.000
112A613GLU-1-0.798-0.89126.816-0.182-0.1820.0000.0000.0000.000
113A614ALA00.0010.02924.853-0.012-0.0120.0000.0000.0000.000
114A615SER00.005-0.01821.0230.0320.0320.0000.0000.0000.000
115A616ARG10.7850.89223.5560.1550.1550.0000.0000.0000.000
116A617ILE00.0330.02218.5440.0140.0140.0000.0000.0000.000
117A618ALA0-0.008-0.00622.669-0.006-0.0060.0000.0000.0000.000
118A619LEU00.0220.01317.9820.0090.0090.0000.0000.0000.000
119A620LEU0-0.035-0.01821.7590.0060.0060.0000.0000.0000.000
120A621LEU00.0300.02219.2610.0090.0090.0000.0000.0000.000
121A622MET0-0.033-0.00822.6840.0160.0160.0000.0000.0000.000
122A623ALA00.0540.01824.1520.0030.0030.0000.0000.0000.000
123A624SER0-0.051-0.04026.5430.0120.0120.0000.0000.0000.000
124A625GLN0-0.003-0.01329.6810.0000.0000.0000.0000.0000.000
125A626GLU-1-0.701-0.76632.536-0.046-0.0460.0000.0000.0000.000
126A627PRO00.0590.01535.2370.0050.0050.0000.0000.0000.000
127A628GLN00.0340.00937.747-0.002-0.0020.0000.0000.0000.000
128A629ARG10.9260.96138.9210.0160.0160.0000.0000.0000.000
129A630MET00.0300.02537.7920.0000.0000.0000.0000.0000.000
130A631SER0-0.028-0.03635.428-0.002-0.0020.0000.0000.0000.000
131A632ARG10.8880.95037.1070.0240.0240.0000.0000.0000.000
132A633ASN0-0.007-0.00638.5210.0010.0010.0000.0000.0000.000
133A634PHE00.0570.03628.967-0.002-0.0020.0000.0000.0000.000
134A635VAL00.0300.00933.030-0.005-0.0050.0000.0000.0000.000
135A636ARG10.9540.98433.9010.0420.0420.0000.0000.0000.000
136A637TYR00.011-0.00233.620-0.002-0.0020.0000.0000.0000.000
137A638VAL00.0540.03228.253-0.006-0.0060.0000.0000.0000.000
138A639GLN0-0.046-0.03430.436-0.006-0.0060.0000.0000.0000.000
139A640GLY0-0.028-0.01232.785-0.002-0.0020.0000.0000.0000.000
140A641LEU0-0.004-0.00528.750-0.003-0.0030.0000.0000.0000.000
141A642LYS10.9280.96628.6270.0550.0550.0000.0000.0000.000
142A643LYS10.9000.94329.6590.0570.0570.0000.0000.0000.000
143A644LYS10.7990.91531.6350.0960.0960.0000.0000.0000.000
144A645LYS10.9290.97122.8780.1600.1600.0000.0000.0000.000
145A646VAL0-0.035-0.01426.362-0.014-0.0140.0000.0000.0000.000
146A647ILE0-0.0020.00520.6200.0190.0190.0000.0000.0000.000
147A648VAL0-0.042-0.03223.803-0.006-0.0060.0000.0000.0000.000
148A649ILE00.0440.02717.4260.0110.0110.0000.0000.0000.000
149A650PRO0-0.050-0.02720.786-0.005-0.0050.0000.0000.0000.000
150A651VAL00.0470.02017.546-0.005-0.0050.0000.0000.0000.000
151A652GLY0-0.029-0.02519.8530.0030.0030.0000.0000.0000.000
152A653ILE00.0030.00320.4570.0140.0140.0000.0000.0000.000
153A654GLY00.0830.04522.1740.0000.0000.0000.0000.0000.000
154A655PRO0-0.050-0.04724.114-0.003-0.0030.0000.0000.0000.000
155A656HIS00.0290.03227.0670.0000.0000.0000.0000.0000.000
156A657ALA00.0290.04924.897-0.007-0.0070.0000.0000.0000.000
157A658ASN00.033-0.00226.8260.0170.0170.0000.0000.0000.000
158A659LEU00.0480.01624.381-0.005-0.0050.0000.0000.0000.000
159A660LYS10.9220.96627.0620.0110.0110.0000.0000.0000.000
160A661GLN0-0.028-0.00229.034-0.004-0.0040.0000.0000.0000.000
161A662ILE00.0450.03522.573-0.007-0.0070.0000.0000.0000.000
162A663ARG11.0341.01724.165-0.049-0.0490.0000.0000.0000.000
163A664LEU0-0.099-0.03225.957-0.001-0.0010.0000.0000.0000.000
164A665ILE00.0300.01624.075-0.001-0.0010.0000.0000.0000.000
165A666GLU-1-0.803-0.89820.561-0.022-0.0220.0000.0000.0000.000
166A667LYS10.9080.95424.2020.0050.0050.0000.0000.0000.000
167A668GLN0-0.074-0.03127.3510.0020.0020.0000.0000.0000.000
168A669ALA0-0.021-0.02625.3700.0000.0000.0000.0000.0000.000
169A670PRO00.0380.01822.702-0.004-0.0040.0000.0000.0000.000
170A671GLU-1-0.812-0.89018.383-0.179-0.1790.0000.0000.0000.000
171A672ASN0-0.100-0.04619.852-0.034-0.0340.0000.0000.0000.000
172A673LYS10.9430.98612.0900.1910.1910.0000.0000.0000.000
173A674ALA0-0.024-0.01818.332-0.029-0.0290.0000.0000.0000.000
174A675PHE00.0000.00211.272-0.001-0.0010.0000.0000.0000.000
175A676VAL0-0.058-0.04116.670-0.008-0.0080.0000.0000.0000.000
176A677LEU00.0180.02814.9110.0220.0220.0000.0000.0000.000
177A678SER00.0220.00218.420-0.001-0.0010.0000.0000.0000.000
178A679SER0-0.066-0.08019.9200.0030.0030.0000.0000.0000.000
179A680VAL00.0310.00719.656-0.010-0.0100.0000.0000.0000.000
180A681ASP-1-0.830-0.88019.025-0.049-0.0490.0000.0000.0000.000
181A682GLU-1-0.834-0.90314.4560.0930.0930.0000.0000.0000.000
182A683LEU0-0.046-0.02514.387-0.028-0.0280.0000.0000.0000.000
183A684GLU-1-0.848-0.91813.717-0.371-0.3710.0000.0000.0000.000
184A685GLN0-0.073-0.05111.525-0.041-0.0410.0000.0000.0000.000
185A686GLN0-0.021-0.0039.6460.0280.0280.0000.0000.0000.000
186A687ARG10.7620.86410.6250.3640.3640.0000.0000.0000.000
187A688ASP-1-0.767-0.8555.926-2.406-2.4060.0000.0000.0000.000
188A689GLU-1-0.845-0.9216.357-0.849-0.8490.0000.0000.0000.000
189A690ILE0-0.036-0.0157.7460.1880.1880.0000.0000.0000.000
190A691VAL0-0.025-0.02710.5670.0840.0840.0000.0000.0000.000
191A692SER0-0.003-0.0187.613-0.024-0.0240.0000.0000.0000.000
192A693TYR0-0.048-0.0359.9810.1850.1850.0000.0000.0000.000
193A694LEU0-0.019-0.02712.1490.1020.1020.0000.0000.0000.000
194A696ASP-1-0.811-0.93510.403-0.860-0.8600.0000.0000.0000.000
195A697LEU0-0.0410.00413.9070.0780.0780.0000.0000.0000.000
196A698ALA0-0.062-0.01417.0350.0630.0630.0000.0000.0000.000
197A699PRO00.0410.04017.939-0.035-0.0350.0000.0000.0000.000
198A700GLU-1-0.796-0.89616.292-0.437-0.4370.0000.0000.0000.000
199A701ALA0-0.027-0.01319.8770.0320.0320.0000.0000.0000.000
200A702PRO0-0.044-0.01823.2030.0080.0080.0000.0000.0000.000