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: 3J84L

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2456463.390515
FMO2-HF: Nuclear repulsion 2376441.894179
FMO2-HF: Total energy -80021.496336
FMO2-MP2: Total energy -80256.743389


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.
-2.762-1.2760.002-0.632-0.8560.001
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 : -0.018 / q_NPA : -0.034
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].
3A504LEU0-0.055-0.0223.708-0.4481.0380.002-0.632-0.8560.001
4A505HIS0-0.075-0.0384.9560.5370.5370.0000.0000.0000.000
5A506ASP-1-0.877-0.9237.698-0.517-0.5170.0000.0000.0000.000
6A507PHE00.002-0.0098.8690.0320.0320.0000.0000.0000.000
7A508TYR00.030-0.00510.6840.1640.1640.0000.0000.0000.000
8A509CYS0-0.084-0.00212.7970.1530.1530.0000.0000.0000.000
9A510SER00.0220.01215.4330.0920.0920.0000.0000.0000.000
10A511ARG10.9150.95412.5860.6150.6150.0000.0000.0000.000
11A512LEU0-0.074-0.03319.7390.0160.0160.0000.0000.0000.000
12A513LEU00.0400.00818.5230.0080.0080.0000.0000.0000.000
13A514ASP-1-0.797-0.88022.373-0.199-0.1990.0000.0000.0000.000
14A515LEU00.019-0.00118.8460.0050.0050.0000.0000.0000.000
15A516VAL0-0.020-0.01822.8670.0120.0120.0000.0000.0000.000
16A517PHE00.0200.00519.239-0.003-0.0030.0000.0000.0000.000
17A518LEU0-0.036-0.01823.9950.0210.0210.0000.0000.0000.000
18A519LEU00.018-0.00724.399-0.006-0.0060.0000.0000.0000.000
19A520ASP-1-0.749-0.83526.344-0.082-0.0820.0000.0000.0000.000
20A521GLY00.0860.03928.281-0.003-0.0030.0000.0000.0000.000
21A522SER0-0.069-0.05230.4770.0100.0100.0000.0000.0000.000
22A523SER0-0.030-0.01731.630-0.004-0.0040.0000.0000.0000.000
23A524ARG10.8230.91329.4820.0450.0450.0000.0000.0000.000
24A525LEU00.0230.03625.2920.0010.0010.0000.0000.0000.000
25A526SER00.0170.00228.7970.0050.0050.0000.0000.0000.000
26A527GLU-1-0.879-0.94729.737-0.097-0.0970.0000.0000.0000.000
27A528ALA00.0360.00427.580-0.011-0.0110.0000.0000.0000.000
28A529GLU-1-0.863-0.93925.152-0.081-0.0810.0000.0000.0000.000
29A530PHE0-0.003-0.00524.661-0.018-0.0180.0000.0000.0000.000
30A531GLU-1-0.869-0.94525.772-0.166-0.1660.0000.0000.0000.000
31A532VAL00.0150.00720.397-0.022-0.0220.0000.0000.0000.000
32A533LEU0-0.0190.00320.979-0.035-0.0350.0000.0000.0000.000
33A534LYS10.8000.89621.4380.1190.1190.0000.0000.0000.000
34A535ALA00.0230.01620.622-0.024-0.0240.0000.0000.0000.000
35A536PHE0-0.022-0.05613.971-0.039-0.0390.0000.0000.0000.000
36A537VAL00.0190.00817.588-0.050-0.0500.0000.0000.0000.000
37A538VAL0-0.033-0.03119.497-0.032-0.0320.0000.0000.0000.000
38A539ASP-1-0.854-0.92115.168-0.621-0.6210.0000.0000.0000.000
39A540MET00.0170.03114.965-0.059-0.0590.0000.0000.0000.000
40A541MET0-0.099-0.05216.5180.0010.0010.0000.0000.0000.000
41A542GLU-1-1.014-1.00317.259-0.405-0.4050.0000.0000.0000.000
42A543ARG10.9200.9729.7201.2121.2120.0000.0000.0000.000
43A544LEU0-0.050-0.02715.426-0.035-0.0350.0000.0000.0000.000
44A545ARG10.9110.96818.1750.3540.3540.0000.0000.0000.000
45A546ILE0-0.007-0.01120.6700.0310.0310.0000.0000.0000.000
46A547SER0-0.011-0.01723.8480.0230.0230.0000.0000.0000.000
47A548GLN0-0.060-0.04426.8540.0010.0010.0000.0000.0000.000
48A549LYS10.9260.96228.3470.1650.1650.0000.0000.0000.000
49A550TRP00.0190.00722.687-0.004-0.0040.0000.0000.0000.000
50A551VAL00.0930.07319.6420.0120.0120.0000.0000.0000.000
51A552ARG10.7440.86723.0490.1990.1990.0000.0000.0000.000
52A553VAL00.0510.02422.401-0.011-0.0110.0000.0000.0000.000
53A554ALA0-0.032-0.02225.1940.0200.0200.0000.0000.0000.000
54A555VAL00.0050.00625.322-0.015-0.0150.0000.0000.0000.000
55A556VAL0-0.034-0.02427.6070.0150.0150.0000.0000.0000.000
56A557GLU-1-0.828-0.89828.500-0.113-0.1130.0000.0000.0000.000
57A558TYR0-0.033-0.04126.6110.0110.0110.0000.0000.0000.000
58A559HIS00.0060.01032.0840.0050.0050.0000.0000.0000.000
59A560ASP-1-0.967-0.98334.881-0.061-0.0610.0000.0000.0000.000
60A561GLY00.0300.01236.6890.0030.0030.0000.0000.0000.000
61A562SER0-0.037-0.02833.484-0.003-0.0030.0000.0000.0000.000
62A563HIS0-0.0120.00234.1830.0060.0060.0000.0000.0000.000
63A564ALA0-0.014-0.01932.380-0.009-0.0090.0000.0000.0000.000
64A565TYR00.0230.02430.5630.0050.0050.0000.0000.0000.000
65A566ILE0-0.036-0.01127.5450.0010.0010.0000.0000.0000.000
66A567GLY00.0670.04230.412-0.002-0.0020.0000.0000.0000.000
67A568LEU00.0220.00827.066-0.004-0.0040.0000.0000.0000.000
68A569LYS10.8790.92030.1630.1210.1210.0000.0000.0000.000
69A570ASP-1-0.844-0.92231.782-0.144-0.1440.0000.0000.0000.000
70A571ARG10.8620.94032.0890.1490.1490.0000.0000.0000.000
71A572LYS11.0011.01931.7180.1520.1520.0000.0000.0000.000
72A573ARG10.9790.98630.1000.1560.1560.0000.0000.0000.000
73A574PRO00.1050.03724.7170.0040.0040.0000.0000.0000.000
74A575SER00.0160.00326.161-0.004-0.0040.0000.0000.0000.000
75A576GLU-1-0.982-0.99327.148-0.142-0.1420.0000.0000.0000.000
76A577LEU0-0.039-0.01126.6390.0060.0060.0000.0000.0000.000
77A578ARG11.0371.00321.9840.3180.3180.0000.0000.0000.000
78A579ARG10.9410.99525.8980.1470.1470.0000.0000.0000.000
79A580ILE0-0.020-0.00929.0790.0090.0090.0000.0000.0000.000
80A581ALA00.0140.01325.2640.0090.0090.0000.0000.0000.000
81A582SER00.0170.00226.7670.0060.0060.0000.0000.0000.000
82A583GLN0-0.038-0.02727.7940.0110.0110.0000.0000.0000.000
83A584VAL0-0.017-0.00328.3340.0100.0100.0000.0000.0000.000
84A585LYS10.9500.96630.7310.0970.0970.0000.0000.0000.000
85A586TYR00.0170.01830.970-0.002-0.0020.0000.0000.0000.000
86A587ALA0-0.0150.00532.8360.0060.0060.0000.0000.0000.000
87A588GLY00.0510.02433.4580.0060.0060.0000.0000.0000.000
88A589SER0-0.043-0.01334.7140.0080.0080.0000.0000.0000.000
89A590GLN00.0180.00435.6590.0000.0000.0000.0000.0000.000
90A591VAL0-0.053-0.04936.0830.0040.0040.0000.0000.0000.000
91A592ALA00.0750.05531.256-0.003-0.0030.0000.0000.0000.000
92A593SER0-0.026-0.01132.5250.0010.0010.0000.0000.0000.000
93A594THR00.038-0.01428.898-0.005-0.0050.0000.0000.0000.000
94A595SER0-0.062-0.07331.341-0.006-0.0060.0000.0000.0000.000
95A596GLU-1-0.895-0.94634.067-0.072-0.0720.0000.0000.0000.000
96A597VAL00.0550.05230.014-0.002-0.0020.0000.0000.0000.000
97A598LEU0-0.008-0.00527.843-0.008-0.0080.0000.0000.0000.000
98A599LYS10.9050.96131.5180.0660.0660.0000.0000.0000.000
99A600TYR00.0290.00133.0000.0010.0010.0000.0000.0000.000
100A601THR00.016-0.00828.687-0.005-0.0050.0000.0000.0000.000
101A602LEU0-0.044-0.01031.970-0.002-0.0020.0000.0000.0000.000
102A603PHE0-0.075-0.06033.7530.0030.0030.0000.0000.0000.000
103A604GLN0-0.0160.00235.3920.0020.0020.0000.0000.0000.000
104A605ILE0-0.040-0.00229.758-0.001-0.0010.0000.0000.0000.000
105A606PHE00.0300.01227.132-0.003-0.0030.0000.0000.0000.000
106A607SER0-0.0250.00033.1760.0070.0070.0000.0000.0000.000
107A608LYS10.9730.96236.4560.0970.0970.0000.0000.0000.000
108A609ILE00.0050.00631.781-0.006-0.0060.0000.0000.0000.000
109A610ASP-1-0.923-0.96732.249-0.135-0.1350.0000.0000.0000.000
110A611ARG10.8570.92925.7110.2240.2240.0000.0000.0000.000
111A612PRO0-0.020-0.01329.396-0.010-0.0100.0000.0000.0000.000
112A613GLU-1-0.892-0.94327.682-0.166-0.1660.0000.0000.0000.000
113A614ALA0-0.0260.01124.877-0.013-0.0130.0000.0000.0000.000
114A615SER00.0300.00921.4380.0250.0250.0000.0000.0000.000
115A616ARG10.8630.95023.6500.1580.1580.0000.0000.0000.000
116A617ILE00.0420.02118.5760.0090.0090.0000.0000.0000.000
117A618ALA0-0.012-0.00522.670-0.004-0.0040.0000.0000.0000.000
118A619LEU00.0340.01417.6460.0070.0070.0000.0000.0000.000
119A620LEU0-0.037-0.02421.5330.0100.0100.0000.0000.0000.000
120A621LEU00.0380.01719.2210.0040.0040.0000.0000.0000.000
121A622MET0-0.067-0.03122.7780.0190.0190.0000.0000.0000.000
122A623ALA00.0370.02323.931-0.001-0.0010.0000.0000.0000.000
123A624SER0-0.031-0.02326.2730.0140.0140.0000.0000.0000.000
124A625GLN0-0.049-0.03729.6190.0000.0000.0000.0000.0000.000
125A626GLU-1-0.722-0.79732.308-0.062-0.0620.0000.0000.0000.000
126A627PRO00.0630.01834.8080.0050.0050.0000.0000.0000.000
127A628GLN00.0680.01737.608-0.002-0.0020.0000.0000.0000.000
128A629ARG10.9070.95838.8280.0280.0280.0000.0000.0000.000
129A630MET00.0180.00837.8900.0010.0010.0000.0000.0000.000
130A631SER0-0.032-0.02435.366-0.002-0.0020.0000.0000.0000.000
131A632ARG10.9200.96537.1010.0340.0340.0000.0000.0000.000
132A633ASN0-0.050-0.02638.5990.0030.0030.0000.0000.0000.000
133A634PHE00.0740.03129.025-0.002-0.0020.0000.0000.0000.000
134A635VAL00.0450.02032.948-0.006-0.0060.0000.0000.0000.000
135A636ARG10.9510.98533.7940.0530.0530.0000.0000.0000.000
136A637TYR00.0380.00933.376-0.001-0.0010.0000.0000.0000.000
137A638VAL00.0450.03728.378-0.006-0.0060.0000.0000.0000.000
138A639GLN0-0.038-0.03630.345-0.006-0.0060.0000.0000.0000.000
139A640GLY0-0.053-0.02932.610-0.002-0.0020.0000.0000.0000.000
140A641LEU00.0280.00828.556-0.002-0.0020.0000.0000.0000.000
141A642LYS10.9060.95528.5560.0700.0700.0000.0000.0000.000
142A643LYS10.9120.95129.8070.0680.0680.0000.0000.0000.000
143A644LYS10.8150.93731.8600.1010.1010.0000.0000.0000.000
144A645LYS10.9430.97423.4670.1580.1580.0000.0000.0000.000
145A646VAL0-0.046-0.02626.160-0.012-0.0120.0000.0000.0000.000
146A647ILE00.0080.01820.2900.0180.0180.0000.0000.0000.000
147A648VAL0-0.031-0.02123.326-0.005-0.0050.0000.0000.0000.000
148A649ILE00.0100.01117.0200.0080.0080.0000.0000.0000.000
149A650PRO0-0.046-0.03320.369-0.005-0.0050.0000.0000.0000.000
150A651VAL00.0390.02417.571-0.006-0.0060.0000.0000.0000.000
151A652GLY0-0.028-0.02819.7520.0100.0100.0000.0000.0000.000
152A653ILE00.0540.04119.8540.0090.0090.0000.0000.0000.000
153A654GLY00.0640.03721.8870.0030.0030.0000.0000.0000.000
154A655PRO0-0.014-0.02224.2270.0010.0010.0000.0000.0000.000
155A656HIS00.0030.00026.6380.0040.0040.0000.0000.0000.000
156A657ALA00.0320.04424.513-0.006-0.0060.0000.0000.0000.000
157A658ASN00.024-0.01126.4080.0170.0170.0000.0000.0000.000
158A659LEU00.0800.04424.247-0.005-0.0050.0000.0000.0000.000
159A660LYS10.9170.96926.7890.0310.0310.0000.0000.0000.000
160A661GLN0-0.025-0.00728.882-0.006-0.0060.0000.0000.0000.000
161A662ILE00.0850.05722.215-0.006-0.0060.0000.0000.0000.000
162A663ARG11.0401.01924.703-0.015-0.0150.0000.0000.0000.000
163A664LEU0-0.113-0.04925.8260.0010.0010.0000.0000.0000.000
164A665ILE00.031-0.00624.3950.0010.0010.0000.0000.0000.000
165A666GLU-1-0.885-0.93720.538-0.057-0.0570.0000.0000.0000.000
166A667LYS10.9020.95724.0910.0250.0250.0000.0000.0000.000
167A668GLN0-0.093-0.03827.0730.0020.0020.0000.0000.0000.000
168A669ALA0-0.016-0.01624.8100.0040.0040.0000.0000.0000.000
169A670PRO00.0650.03322.886-0.003-0.0030.0000.0000.0000.000
170A671GLU-1-0.898-0.95118.363-0.193-0.1930.0000.0000.0000.000
171A672ASN0-0.088-0.02420.127-0.039-0.0390.0000.0000.0000.000
172A673LYS11.0201.01311.9110.2460.2460.0000.0000.0000.000
173A674ALA00.012-0.00618.244-0.023-0.0230.0000.0000.0000.000
174A675PHE0-0.018-0.00311.4050.0120.0120.0000.0000.0000.000
175A676VAL0-0.040-0.02716.375-0.005-0.0050.0000.0000.0000.000
176A677LEU00.0070.01514.4890.0200.0200.0000.0000.0000.000
177A678SER00.0080.00517.9220.0030.0030.0000.0000.0000.000
178A679SER0-0.018-0.02719.3300.0010.0010.0000.0000.0000.000
179A680VAL00.019-0.00719.222-0.017-0.0170.0000.0000.0000.000
180A681ASP-1-0.881-0.92918.934-0.104-0.1040.0000.0000.0000.000
181A682GLU-1-0.894-0.95214.151-0.018-0.0180.0000.0000.0000.000
182A683LEU0-0.023-0.02514.036-0.043-0.0430.0000.0000.0000.000
183A684GLU-1-0.926-0.97813.369-0.432-0.4320.0000.0000.0000.000
184A685GLN0-0.019-0.01611.194-0.112-0.1120.0000.0000.0000.000
185A686GLN00.0080.0109.104-0.065-0.0650.0000.0000.0000.000
186A687ARG10.8490.98010.1430.4620.4620.0000.0000.0000.000
187A688ASP-1-0.766-0.8855.921-2.643-2.6430.0000.0000.0000.000
188A689GLU-1-0.867-0.9275.319-1.626-1.6260.0000.0000.0000.000
189A690ILE0-0.038-0.0147.6050.2350.2350.0000.0000.0000.000
190A691VAL0-0.031-0.04010.8560.1120.1120.0000.0000.0000.000
191A692SER0-0.001-0.0027.5990.0270.0270.0000.0000.0000.000
192A693TYR00.0100.0149.9760.2060.2060.0000.0000.0000.000
193A694LEU0-0.025-0.02311.9570.1170.1170.0000.0000.0000.000
194A696ASP-1-0.876-0.9529.657-0.926-0.9260.0000.0000.0000.000
195A697LEU0-0.050-0.01413.3120.0890.0890.0000.0000.0000.000
196A698ALA0-0.122-0.05416.5440.0640.0640.0000.0000.0000.000
197A699PRO0-0.003-0.00717.789-0.026-0.0260.0000.0000.0000.000
198A700GLU-1-0.902-0.95617.104-0.398-0.3980.0000.0000.0000.000
199A701ALA0-0.058-0.03620.0400.0260.0260.0000.0000.0000.000
200A702PRO00.0130.02323.339-0.002-0.0020.0000.0000.0000.000