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

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FMODB ID: LN969

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2456680.364413
FMO2-HF: Nuclear repulsion 2376657.764041
FMO2-HF: Total energy -80022.600372
FMO2-MP2: Total energy -80257.815923


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.
-3.483-1.6550.002-0.769-1.0590.002
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 : -0.013 / q_NPA : -0.027
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].
3A504LEU0-0.052-0.0253.629-0.8800.8440.003-0.765-0.9610.002
4A505HIS0-0.091-0.0504.7210.4070.511-0.001-0.004-0.0980.000
5A506ASP-1-0.872-0.9177.629-0.554-0.5540.0000.0000.0000.000
6A507PHE00.007-0.0098.9600.0510.0510.0000.0000.0000.000
7A508TYR00.021-0.01210.8030.1640.1640.0000.0000.0000.000
8A509CYS0-0.0790.00612.5760.1620.1620.0000.0000.0000.000
9A510SER00.0190.00615.4050.0950.0950.0000.0000.0000.000
10A511ARG10.8220.89312.6150.5810.5810.0000.0000.0000.000
11A512LEU0-0.067-0.02919.5160.0140.0140.0000.0000.0000.000
12A513LEU00.0290.00418.2270.0090.0090.0000.0000.0000.000
13A514ASP-1-0.775-0.85422.193-0.203-0.2030.0000.0000.0000.000
14A515LEU00.0250.00418.9300.0060.0060.0000.0000.0000.000
15A516VAL0-0.019-0.01822.8940.0120.0120.0000.0000.0000.000
16A517PHE00.0260.01119.056-0.002-0.0020.0000.0000.0000.000
17A518LEU0-0.031-0.01824.0010.0220.0220.0000.0000.0000.000
18A519LEU00.024-0.00124.468-0.006-0.0060.0000.0000.0000.000
19A520ASP-1-0.737-0.82026.337-0.086-0.0860.0000.0000.0000.000
20A521GLY00.0890.04628.262-0.004-0.0040.0000.0000.0000.000
21A522SER0-0.080-0.06830.5200.0100.0100.0000.0000.0000.000
22A523SER0-0.0060.00131.599-0.005-0.0050.0000.0000.0000.000
23A524ARG10.7980.88929.5450.0500.0500.0000.0000.0000.000
24A525LEU00.0060.02925.3510.0000.0000.0000.0000.0000.000
25A526SER00.008-0.02228.8190.0050.0050.0000.0000.0000.000
26A527GLU-1-0.882-0.95029.702-0.106-0.1060.0000.0000.0000.000
27A528ALA00.0420.00827.593-0.011-0.0110.0000.0000.0000.000
28A529GLU-1-0.814-0.88625.117-0.093-0.0930.0000.0000.0000.000
29A530PHE0-0.011-0.00324.627-0.019-0.0190.0000.0000.0000.000
30A531GLU-1-0.839-0.92225.748-0.178-0.1780.0000.0000.0000.000
31A532VAL00.0140.00420.318-0.023-0.0230.0000.0000.0000.000
32A533LEU0-0.0200.00520.953-0.037-0.0370.0000.0000.0000.000
33A534LYS10.7720.87721.4210.1290.1290.0000.0000.0000.000
34A535ALA00.0060.00620.753-0.025-0.0250.0000.0000.0000.000
35A536PHE0-0.017-0.02613.819-0.037-0.0370.0000.0000.0000.000
36A537VAL00.0160.00617.581-0.049-0.0490.0000.0000.0000.000
37A538VAL0-0.002-0.02019.501-0.033-0.0330.0000.0000.0000.000
38A539ASP-1-0.790-0.86814.736-0.734-0.7340.0000.0000.0000.000
39A540MET00.0470.03515.170-0.060-0.0600.0000.0000.0000.000
40A541MET0-0.108-0.05016.5280.0010.0010.0000.0000.0000.000
41A542GLU-1-0.901-0.93417.675-0.385-0.3850.0000.0000.0000.000
42A543ARG10.8540.93210.1391.1231.1230.0000.0000.0000.000
43A544LEU0-0.037-0.02015.602-0.033-0.0330.0000.0000.0000.000
44A545ARG10.8960.96018.3560.3630.3630.0000.0000.0000.000
45A546ILE0-0.011-0.01120.8420.0330.0330.0000.0000.0000.000
46A547SER0-0.005-0.01424.0310.0240.0240.0000.0000.0000.000
47A548GLN0-0.080-0.05626.7560.0050.0050.0000.0000.0000.000
48A549LYS10.9240.95628.2490.1680.1680.0000.0000.0000.000
49A550TRP00.0370.01721.960-0.004-0.0040.0000.0000.0000.000
50A551VAL00.0950.07519.3940.0120.0120.0000.0000.0000.000
51A552ARG10.6830.81522.7880.1980.1980.0000.0000.0000.000
52A553VAL00.0420.01422.409-0.011-0.0110.0000.0000.0000.000
53A554ALA0-0.037-0.02325.2210.0200.0200.0000.0000.0000.000
54A555VAL00.0110.00625.271-0.016-0.0160.0000.0000.0000.000
55A556VAL0-0.038-0.02727.6160.0160.0160.0000.0000.0000.000
56A557GLU-1-0.816-0.87528.497-0.119-0.1190.0000.0000.0000.000
57A558TYR0-0.018-0.03627.1450.0050.0050.0000.0000.0000.000
58A559HIS00.002-0.00832.0690.0060.0060.0000.0000.0000.000
59A560ASP-1-0.949-0.97534.866-0.063-0.0630.0000.0000.0000.000
60A561GLY00.0100.00336.6900.0030.0030.0000.0000.0000.000
61A562SER0-0.037-0.02733.474-0.003-0.0030.0000.0000.0000.000
62A563HIS0-0.0110.00034.0700.0080.0080.0000.0000.0000.000
63A564ALA0-0.012-0.01732.384-0.009-0.0090.0000.0000.0000.000
64A565TYR00.0140.02530.6020.0040.0040.0000.0000.0000.000
65A566ILE0-0.040-0.01027.5540.0010.0010.0000.0000.0000.000
66A567GLY00.0630.03430.428-0.002-0.0020.0000.0000.0000.000
67A568LEU00.0290.01327.200-0.004-0.0040.0000.0000.0000.000
68A569LYS10.8470.90730.1910.1230.1230.0000.0000.0000.000
69A570ASP-1-0.808-0.88231.707-0.151-0.1510.0000.0000.0000.000
70A571ARG10.8840.94632.1930.1510.1510.0000.0000.0000.000
71A572LYS10.9290.96731.9590.1580.1580.0000.0000.0000.000
72A573ARG10.9680.98230.2640.1590.1590.0000.0000.0000.000
73A574PRO00.1090.03624.8170.0050.0050.0000.0000.0000.000
74A575SER00.0250.00326.254-0.005-0.0050.0000.0000.0000.000
75A576GLU-1-0.905-0.93427.240-0.148-0.1480.0000.0000.0000.000
76A577LEU0-0.033-0.00926.8880.0060.0060.0000.0000.0000.000
77A578ARG10.8990.92621.9060.3450.3450.0000.0000.0000.000
78A579ARG10.8560.92825.9080.1530.1530.0000.0000.0000.000
79A580ILE0-0.019-0.02029.0850.0090.0090.0000.0000.0000.000
80A581ALA00.0160.01425.2500.0090.0090.0000.0000.0000.000
81A582SER00.0290.01326.6770.0050.0050.0000.0000.0000.000
82A583GLN0-0.036-0.00927.7870.0140.0140.0000.0000.0000.000
83A584VAL0-0.016-0.01028.5760.0110.0110.0000.0000.0000.000
84A585LYS10.9560.96730.7150.1010.1010.0000.0000.0000.000
85A586TYR00.004-0.00331.050-0.001-0.0010.0000.0000.0000.000
86A587ALA0-0.029-0.00332.8130.0070.0070.0000.0000.0000.000
87A588GLY00.0540.02733.4310.0060.0060.0000.0000.0000.000
88A589SER0-0.050-0.01834.6360.0080.0080.0000.0000.0000.000
89A590GLN00.0140.00435.6300.0000.0000.0000.0000.0000.000
90A591VAL0-0.044-0.04636.0700.0040.0040.0000.0000.0000.000
91A592ALA00.0720.05631.271-0.003-0.0030.0000.0000.0000.000
92A593SER0-0.040-0.03532.5070.0010.0010.0000.0000.0000.000
93A594THR00.032-0.01428.847-0.004-0.0040.0000.0000.0000.000
94A595SER0-0.061-0.06631.331-0.006-0.0060.0000.0000.0000.000
95A596GLU-1-0.755-0.87134.061-0.074-0.0740.0000.0000.0000.000
96A597VAL00.0630.05829.863-0.002-0.0020.0000.0000.0000.000
97A598LEU0-0.0060.00627.742-0.007-0.0070.0000.0000.0000.000
98A599LYS10.7690.87231.5220.0690.0690.0000.0000.0000.000
99A600TYR00.0380.00432.961-0.003-0.0030.0000.0000.0000.000
100A601THR00.008-0.01828.592-0.005-0.0050.0000.0000.0000.000
101A602LEU0-0.043-0.00531.983-0.002-0.0020.0000.0000.0000.000
102A603PHE0-0.058-0.04533.7700.0030.0030.0000.0000.0000.000
103A604GLN0-0.0040.01435.4960.0020.0020.0000.0000.0000.000
104A605ILE0-0.035-0.00129.810-0.001-0.0010.0000.0000.0000.000
105A606PHE00.0260.00927.223-0.002-0.0020.0000.0000.0000.000
106A607SER0-0.0120.00333.2030.0080.0080.0000.0000.0000.000
107A608LYS10.9500.96436.4330.0960.0960.0000.0000.0000.000
108A609ILE00.002-0.00431.612-0.006-0.0060.0000.0000.0000.000
109A610ASP-1-0.792-0.87431.914-0.138-0.1380.0000.0000.0000.000
110A611ARG10.7600.86325.1370.2300.2300.0000.0000.0000.000
111A612PRO0-0.023-0.01529.270-0.010-0.0100.0000.0000.0000.000
112A613GLU-1-0.843-0.92127.128-0.178-0.1780.0000.0000.0000.000
113A614ALA00.0060.02724.751-0.012-0.0120.0000.0000.0000.000
114A615SER00.0160.01721.1750.0290.0290.0000.0000.0000.000
115A616ARG10.8080.91323.5300.1530.1530.0000.0000.0000.000
116A617ILE00.0410.01618.6750.0100.0100.0000.0000.0000.000
117A618ALA0-0.014-0.00622.695-0.005-0.0050.0000.0000.0000.000
118A619LEU00.0220.01117.7130.0070.0070.0000.0000.0000.000
119A620LEU0-0.035-0.02421.5380.0100.0100.0000.0000.0000.000
120A621LEU00.0200.01419.3400.0030.0030.0000.0000.0000.000
121A622MET0-0.046-0.02122.7640.0210.0210.0000.0000.0000.000
122A623ALA00.0340.01323.904-0.002-0.0020.0000.0000.0000.000
123A624SER0-0.041-0.03526.2410.0140.0140.0000.0000.0000.000
124A625GLN0-0.038-0.02929.591-0.001-0.0010.0000.0000.0000.000
125A626GLU-1-0.720-0.78632.279-0.065-0.0650.0000.0000.0000.000
126A627PRO00.0720.02134.7860.0050.0050.0000.0000.0000.000
127A628GLN00.0590.01637.593-0.001-0.0010.0000.0000.0000.000
128A629ARG10.9120.95638.8060.0280.0280.0000.0000.0000.000
129A630MET00.0170.01137.8420.0010.0010.0000.0000.0000.000
130A631SER0-0.033-0.02935.292-0.003-0.0030.0000.0000.0000.000
131A632ARG10.9020.96037.0890.0350.0350.0000.0000.0000.000
132A633ASN0-0.033-0.02038.5970.0030.0030.0000.0000.0000.000
133A634PHE00.0840.03729.008-0.002-0.0020.0000.0000.0000.000
134A635VAL00.0450.01732.946-0.005-0.0050.0000.0000.0000.000
135A636ARG10.9510.98733.8000.0520.0520.0000.0000.0000.000
136A637TYR00.0320.01233.386-0.001-0.0010.0000.0000.0000.000
137A638VAL00.0480.03428.255-0.006-0.0060.0000.0000.0000.000
138A639GLN0-0.040-0.03830.358-0.005-0.0050.0000.0000.0000.000
139A640GLY0-0.048-0.02532.624-0.001-0.0010.0000.0000.0000.000
140A641LEU00.0200.00428.683-0.002-0.0020.0000.0000.0000.000
141A642LYS10.9080.95528.5610.0660.0660.0000.0000.0000.000
142A643LYS10.9170.95629.8300.0670.0670.0000.0000.0000.000
143A644LYS10.7820.91131.8320.1030.1030.0000.0000.0000.000
144A645LYS10.9530.97723.0820.1610.1610.0000.0000.0000.000
145A646VAL0-0.045-0.02626.222-0.012-0.0120.0000.0000.0000.000
146A647ILE00.0020.01720.2750.0190.0190.0000.0000.0000.000
147A648VAL0-0.030-0.02023.378-0.006-0.0060.0000.0000.0000.000
148A649ILE00.0300.01917.0290.0090.0090.0000.0000.0000.000
149A650PRO0-0.052-0.02820.374-0.007-0.0070.0000.0000.0000.000
150A651VAL00.0370.01917.454-0.007-0.0070.0000.0000.0000.000
151A652GLY0-0.030-0.02619.7280.0110.0110.0000.0000.0000.000
152A653ILE00.0510.04019.8860.0090.0090.0000.0000.0000.000
153A654GLY00.0720.04021.8500.0050.0050.0000.0000.0000.000
154A655PRO0-0.015-0.02524.1820.0020.0020.0000.0000.0000.000
155A656HIS00.0210.01826.5910.0050.0050.0000.0000.0000.000
156A657ALA00.0190.03924.485-0.005-0.0050.0000.0000.0000.000
157A658ASN00.025-0.01226.3740.0180.0180.0000.0000.0000.000
158A659LEU00.0760.04424.332-0.005-0.0050.0000.0000.0000.000
159A660LYS10.9290.97126.7650.0300.0300.0000.0000.0000.000
160A661GLN0-0.025-0.00828.838-0.005-0.0050.0000.0000.0000.000
161A662ILE00.0740.04922.240-0.006-0.0060.0000.0000.0000.000
162A663ARG11.0411.02224.385-0.016-0.0160.0000.0000.0000.000
163A664LEU0-0.131-0.05325.8110.0010.0010.0000.0000.0000.000
164A665ILE00.024-0.00224.2420.0020.0020.0000.0000.0000.000
165A666GLU-1-0.858-0.92720.566-0.052-0.0520.0000.0000.0000.000
166A667LYS10.9070.95824.0900.0220.0220.0000.0000.0000.000
167A668GLN0-0.093-0.03627.0730.0040.0040.0000.0000.0000.000
168A669ALA0-0.017-0.01824.9900.0040.0040.0000.0000.0000.000
169A670PRO00.0640.03223.078-0.004-0.0040.0000.0000.0000.000
170A671GLU-1-0.856-0.92418.270-0.194-0.1940.0000.0000.0000.000
171A672ASN0-0.095-0.03220.146-0.039-0.0390.0000.0000.0000.000
172A673LYS11.0111.00911.5890.2800.2800.0000.0000.0000.000
173A674ALA00.007-0.00618.212-0.024-0.0240.0000.0000.0000.000
174A675PHE0-0.014-0.00411.1170.0160.0160.0000.0000.0000.000
175A676VAL0-0.046-0.03216.353-0.004-0.0040.0000.0000.0000.000
176A677LEU00.0070.01814.3330.0200.0200.0000.0000.0000.000
177A678SER00.0250.00317.8790.0170.0170.0000.0000.0000.000
178A679SER0-0.096-0.09719.2800.0060.0060.0000.0000.0000.000
179A680VAL00.025-0.00419.176-0.019-0.0190.0000.0000.0000.000
180A681ASP-1-0.846-0.88418.919-0.120-0.1200.0000.0000.0000.000
181A682GLU-1-0.856-0.92713.958-0.069-0.0690.0000.0000.0000.000
182A683LEU0-0.015-0.00513.990-0.047-0.0470.0000.0000.0000.000
183A684GLU-1-0.861-0.91713.384-0.482-0.4820.0000.0000.0000.000
184A685GLN0-0.043-0.02811.143-0.101-0.1010.0000.0000.0000.000
185A686GLN0-0.0070.0009.068-0.081-0.0810.0000.0000.0000.000
186A687ARG10.7820.87510.1080.5240.5240.0000.0000.0000.000
187A688ASP-1-0.776-0.8775.878-2.718-2.7180.0000.0000.0000.000
188A689GLU-1-0.844-0.9125.597-1.539-1.5390.0000.0000.0000.000
189A690ILE0-0.045-0.0207.6050.2660.2660.0000.0000.0000.000
190A691VAL0-0.009-0.02110.8030.1260.1260.0000.0000.0000.000
191A692SER0-0.020-0.0247.6930.0050.0050.0000.0000.0000.000
192A693TYR0-0.035-0.0169.9040.2120.2120.0000.0000.0000.000
193A694LEU0-0.016-0.01811.9870.1200.1200.0000.0000.0000.000
194A696ASP-1-0.844-0.9309.642-0.896-0.8960.0000.0000.0000.000
195A697LEU0-0.052-0.00813.2460.0890.0890.0000.0000.0000.000
196A698ALA0-0.112-0.05516.5060.0630.0630.0000.0000.0000.000
197A699PRO00.0140.01017.700-0.023-0.0230.0000.0000.0000.000
198A700GLU-1-0.846-0.92916.493-0.418-0.4180.0000.0000.0000.000
199A701ALA0-0.045-0.02819.8830.0260.0260.0000.0000.0000.000
200A702PRO00.0090.01923.163-0.002-0.0020.0000.0000.0000.000