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: 53L7Z

Calculation Name: 2WD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CU62

Base Structure: X-ray

Registration Date: 2023-06-21

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1812317.120247
FMO2-HF: Nuclear repulsion 1742421.452006
FMO2-HF: Total energy -69895.668242
FMO2-MP2: Total energy -70099.762211


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:499:ARG)


Summations of interaction energy for fragment #1(A:499:ARG)
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.
5.3337.65412.761-7.851-7.233-0.07
Interaction energy analysis for fragmet #1(A:499:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.938 / q_NPA : 0.954
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].
3A501ALA0-0.032-0.0262.7734.0497.1200.146-1.220-1.9970.007
4A502GLU-1-0.823-0.9031.789-59.549-60.62012.617-6.610-4.937-0.077
5A503ILE00.0400.0354.4482.5192.683-0.001-0.016-0.1480.000
6A504MET0-0.054-0.0096.9772.9242.9240.0000.0000.0000.000
7A505GLU-1-0.913-0.9587.491-20.655-20.6550.0000.0000.0000.000
8A506SER00.012-0.0028.0452.3922.3920.0000.0000.0000.000
9A507ILE0-0.009-0.01110.6551.6811.6810.0000.0000.0000.000
10A508LYS10.8240.91212.61416.82316.8230.0000.0000.0000.000
11A509ARG10.9530.96913.38317.05817.0580.0000.0000.0000.000
12A510LEU0-0.005-0.00414.3210.9470.9470.0000.0000.0000.000
13A511TYR00.0050.01216.7321.2801.2800.0000.0000.0000.000
14A512PRO00.0570.03818.489-0.169-0.1690.0000.0000.0000.000
15A513GLY0-0.024-0.02319.350-0.410-0.4100.0000.0000.0000.000
16A514SER00.0020.00220.7130.2530.2530.0000.0000.0000.000
17A515VAL00.0070.01414.229-0.041-0.0410.0000.0000.0000.000
18A516TYR0-0.048-0.01616.985-0.034-0.0340.0000.0000.0000.000
19A517GLY00.0710.02913.184-0.292-0.2920.0000.0000.0000.000
20A518ARG10.7920.8986.08331.27331.2730.0000.0000.0000.000
21A519LEU00.044-0.00312.6490.5700.5700.0000.0000.0000.000
22A520ILE0-0.027-0.0099.7040.8210.8210.0000.0000.0000.000
23A521ASP-1-0.873-0.95711.898-20.841-20.8410.0000.0000.0000.000
24A522LEU0-0.0020.02914.8570.8880.8880.0000.0000.0000.000
25A523CYS0-0.045-0.02017.8831.0351.0350.0000.0000.0000.000
26A524GLN00.018-0.01217.993-1.411-1.4110.0000.0000.0000.000
27A525PRO0-0.0070.02219.7400.6940.6940.0000.0000.0000.000
28A526THR0-0.024-0.01523.0370.0780.0780.0000.0000.0000.000
29A527GLN00.000-0.00526.2050.0970.0970.0000.0000.0000.000
30A528LYS11.0250.99922.27212.80212.8020.0000.0000.0000.000
31A529LYS10.9470.97624.5839.4099.4090.0000.0000.0000.000
32A530TYR00.0480.00725.6840.0040.0040.0000.0000.0000.000
33A531GLN0-0.0260.00420.436-0.299-0.2990.0000.0000.0000.000
34A532ILE00.0460.02320.206-0.787-0.7870.0000.0000.0000.000
35A533ALA00.0300.01821.512-0.286-0.2860.0000.0000.0000.000
36A534VAL00.0180.00219.964-0.160-0.1600.0000.0000.0000.000
37A535THR0-0.0340.00016.331-0.622-0.6220.0000.0000.0000.000
38A536LYS10.8930.96017.79213.91213.9120.0000.0000.0000.000
39A537VAL0-0.059-0.03420.143-0.111-0.1110.0000.0000.0000.000
40A538LEU0-0.0040.00717.6510.0030.0030.0000.0000.0000.000
41A539GLY00.0220.01116.221-0.352-0.3520.0000.0000.0000.000
42A540LYS10.9570.95611.70022.04722.0470.0000.0000.0000.000
43A541ASN00.0290.01413.717-1.587-1.5870.0000.0000.0000.000
44A542MET0-0.019-0.00213.1310.8380.8380.0000.0000.0000.000
45A543ASP-1-0.863-0.9417.762-31.747-31.7470.0000.0000.0000.000
46A544ALA0-0.043-0.01711.063-0.835-0.8350.0000.0000.0000.000
47A545ILE00.0080.00410.0180.9700.9700.0000.0000.0000.000
48A546ILE00.0160.01913.8900.8320.8320.0000.0000.0000.000
49A547VAL0-0.003-0.00417.040-0.197-0.1970.0000.0000.0000.000
50A548ASP-1-0.869-0.93519.300-11.587-11.5870.0000.0000.0000.000
51A549SER00.0290.00022.6540.4210.4210.0000.0000.0000.000
52A550GLU-1-0.813-0.93622.280-12.682-12.6820.0000.0000.0000.000
53A551LYS10.8610.93322.68511.65011.6500.0000.0000.0000.000
54A552THR0-0.0020.01119.639-0.566-0.5660.0000.0000.0000.000
55A553GLY00.0560.02518.384-0.818-0.8180.0000.0000.0000.000
56A554ARG10.8760.93618.19611.38011.3800.0000.0000.0000.000
57A555ASP-1-0.831-0.90919.486-13.745-13.7450.0000.0000.0000.000
58A556CYS0-0.031-0.00814.723-0.911-0.9110.0000.0000.0000.000
59A557ILE0-0.017-0.00814.528-1.338-1.3380.0000.0000.0000.000
60A558GLN0-0.073-0.02915.727-0.371-0.3710.0000.0000.0000.000
61A559TYR00.0460.00810.759-1.230-1.2300.0000.0000.0000.000
62A560ILE0-0.018-0.01210.565-0.942-0.9420.0000.0000.0000.000
63A561LYS10.9210.94912.23715.14115.1410.0000.0000.0000.000
64A562GLU-1-0.890-0.93214.587-16.366-16.3660.0000.0000.0000.000
65A563GLN0-0.055-0.0269.9291.4591.4590.0000.0000.0000.000
66A564ARG10.9060.96410.32221.66021.6600.0000.0000.0000.000
67A565GLY0-0.0010.0127.914-2.447-2.4470.0000.0000.0000.000
68A566GLU-1-0.996-1.0114.718-46.322-46.165-0.001-0.005-0.1510.000
69A567PRO0-0.013-0.0127.8060.7820.7820.0000.0000.0000.000
70A568GLU-1-0.816-0.8917.508-34.517-34.5170.0000.0000.0000.000
71A569THR0-0.078-0.03911.4991.9431.9430.0000.0000.0000.000
72A570PHE00.0430.00812.900-0.528-0.5280.0000.0000.0000.000
73A571LEU0-0.033-0.01116.7720.7550.7550.0000.0000.0000.000
74A572PRO00.0170.01319.773-0.131-0.1310.0000.0000.0000.000
75A573LEU00.008-0.01022.2280.5000.5000.0000.0000.0000.000
76A574ASP-1-0.810-0.90124.492-11.181-11.1810.0000.0000.0000.000
77A575TYR00.0120.01226.1520.4480.4480.0000.0000.0000.000
78A576LEU0-0.114-0.03922.8590.1090.1090.0000.0000.0000.000
79A577GLU-1-0.902-0.94826.276-9.589-9.5890.0000.0000.0000.000
80A578VAL0-0.047-0.01326.485-0.098-0.0980.0000.0000.0000.000
81A579LYS10.9530.96829.4019.7629.7620.0000.0000.0000.000
82A580PRO00.005-0.00831.615-0.247-0.2470.0000.0000.0000.000
83A581THR0-0.031-0.02131.0610.0410.0410.0000.0000.0000.000
84A582ASP-1-0.884-0.95233.492-7.932-7.9320.0000.0000.0000.000
85A583GLU-1-0.943-0.98736.491-7.891-7.8910.0000.0000.0000.000
86A584LYS11.0361.02737.8017.4417.4410.0000.0000.0000.000
87A585LEU0-0.054-0.02935.3150.0330.0330.0000.0000.0000.000
88A586ARG10.7430.84433.1998.7318.7310.0000.0000.0000.000
89A587GLU-1-0.889-0.93838.138-7.009-7.0090.0000.0000.0000.000
90A588LEU0-0.099-0.04838.0450.1570.1570.0000.0000.0000.000
91A589LYS10.9530.97839.7046.7746.7740.0000.0000.0000.000
92A590GLY00.0310.01538.7430.1240.1240.0000.0000.0000.000
93A591ALA00.0020.01133.785-0.181-0.1810.0000.0000.0000.000
94A592LYS10.9600.98032.4499.4209.4200.0000.0000.0000.000
95A593LEU00.007-0.00131.249-0.347-0.3470.0000.0000.0000.000
96A594VAL0-0.005-0.00325.084-0.104-0.1040.0000.0000.0000.000
97A595ILE00.0370.00325.979-0.291-0.2910.0000.0000.0000.000
98A596ASP-1-0.785-0.83927.411-9.484-9.4840.0000.0000.0000.000
99A597VAL0-0.048-0.03026.0040.1620.1620.0000.0000.0000.000
100A598ILE0-0.049-0.01621.755-0.426-0.4260.0000.0000.0000.000
101A599ARG10.9290.97223.14812.39712.3970.0000.0000.0000.000
102A600TYR0-0.021-0.01822.346-0.487-0.4870.0000.0000.0000.000
103A601GLU-1-0.972-0.97121.254-12.433-12.4330.0000.0000.0000.000
104A602PRO00.1140.05421.649-0.444-0.4440.0000.0000.0000.000
105A603PRO00.025-0.01124.893-0.236-0.2360.0000.0000.0000.000
106A604HIS00.0670.01024.7030.4310.4310.0000.0000.0000.000
107A605ILE0-0.0160.00920.6080.0030.0030.0000.0000.0000.000
108A606LYS10.9400.96923.8259.4249.4240.0000.0000.0000.000
109A607LYS10.8850.94325.85110.79710.7970.0000.0000.0000.000
110A608ALA00.0720.03120.412-0.051-0.0510.0000.0000.0000.000
111A609LEU0-0.003-0.00521.440-0.410-0.4100.0000.0000.0000.000
112A610GLN0-0.032-0.02623.693-0.005-0.0050.0000.0000.0000.000
113A611TYR00.0030.01220.2470.3750.3750.0000.0000.0000.000
114A612ALA0-0.029-0.00320.633-0.122-0.1220.0000.0000.0000.000
115A613CYS0-0.088-0.02622.432-0.040-0.0400.0000.0000.0000.000
116A614GLY00.0230.01425.2950.2540.2540.0000.0000.0000.000
117A615ASN0-0.013-0.02028.544-0.108-0.1080.0000.0000.0000.000
118A616ALA0-0.052-0.01427.4470.1990.1990.0000.0000.0000.000
119A617LEU00.0410.01829.4200.1220.1220.0000.0000.0000.000
120A618VAL0-0.045-0.02228.145-0.362-0.3620.0000.0000.0000.000
121A619CYS0-0.0050.00630.2000.2600.2600.0000.0000.0000.000
122A620ASP-1-0.858-0.92531.093-9.189-9.1890.0000.0000.0000.000
123A621ASN00.0470.01231.852-0.265-0.2650.0000.0000.0000.000
124A622VAL00.009-0.01330.168-0.066-0.0660.0000.0000.0000.000
125A623GLU-1-0.931-0.97332.657-7.952-7.9520.0000.0000.0000.000
126A624ASP-1-0.862-0.93235.784-8.046-8.0460.0000.0000.0000.000
127A625ALA0-0.055-0.04531.5360.0380.0380.0000.0000.0000.000
128A626ARG10.9730.98733.6288.4878.4870.0000.0000.0000.000
129A627ARG10.9960.99635.1247.3537.3530.0000.0000.0000.000
130A628ILE00.003-0.00136.1890.1910.1910.0000.0000.0000.000
131A629ALA0-0.047-0.00233.609-0.054-0.0540.0000.0000.0000.000
132A630PHE0-0.048-0.06032.592-0.006-0.0060.0000.0000.0000.000
133A631GLY00.0280.03737.7810.1370.1370.0000.0000.0000.000
134A632GLY0-0.0190.00440.3240.2000.2000.0000.0000.0000.000
135A633HIS00.0600.02241.755-0.145-0.1450.0000.0000.0000.000
136A634GLN0-0.0090.00937.833-0.039-0.0390.0000.0000.0000.000
137A635ARG10.9400.97134.5908.6938.6930.0000.0000.0000.000
138A636HIS10.8450.91634.2618.4278.4270.0000.0000.0000.000
139A637LYS10.9250.97023.98012.48912.4890.0000.0000.0000.000
140A638THR00.0220.00930.2600.1380.1380.0000.0000.0000.000
141A639VAL0-0.049-0.01624.596-0.233-0.2330.0000.0000.0000.000
142A640ALA00.0730.06127.8920.2770.2770.0000.0000.0000.000
143A641LEU0-0.007-0.01326.676-0.536-0.5360.0000.0000.0000.000
144A642ASP-1-0.880-0.93825.359-11.309-11.3090.0000.0000.0000.000
145A643GLY0-0.042-0.03322.745-0.485-0.4850.0000.0000.0000.000
146A644THR0-0.031-0.01123.265-0.342-0.3420.0000.0000.0000.000
147A645LEU0-0.041-0.02923.3510.2100.2100.0000.0000.0000.000
148A646PHE00.0380.02126.4370.0620.0620.0000.0000.0000.000
149A647GLN0-0.008-0.01525.004-0.257-0.2570.0000.0000.0000.000
150A648LYS10.9880.97929.53110.19810.1980.0000.0000.0000.000
151A649SER00.0320.00928.4660.2710.2710.0000.0000.0000.000
152A650GLY00.0000.01031.6710.1670.1670.0000.0000.0000.000
153A651VAL0-0.0050.00625.4720.0210.0210.0000.0000.0000.000
154A652ILE00.0500.02127.8590.0870.0870.0000.0000.0000.000
155A653SER0-0.050-0.02522.572-0.537-0.5370.0000.0000.0000.000
156A654GLY00.0560.01523.0880.3350.3350.0000.0000.0000.000
157A655GLY00.0590.04320.566-0.425-0.4250.0000.0000.0000.000
158A656ALA00.0370.00820.150-0.647-0.6470.0000.0000.0000.000
159A657SER0-0.012-0.00519.111-0.052-0.0520.0000.0000.0000.000
160A658ASP-1-0.845-0.92315.476-18.357-18.3570.0000.0000.0000.000
161A659LEU0-0.083-0.04315.996-0.923-0.9230.0000.0000.0000.000
162A660LYS10.9990.98517.83513.46913.4690.0000.0000.0000.000
163A661ALA0-0.031-0.01714.274-0.088-0.0880.0000.0000.0000.000
164A662LYS10.9600.97712.30019.24119.2410.0000.0000.0000.000
165A663ALA00.0020.00514.165-0.596-0.5960.0000.0000.0000.000
166A664ARG10.9700.98513.61819.27119.2710.0000.0000.0000.000
167A665ARG10.9200.9709.61927.03427.0340.0000.0000.0000.000
168A666TRP0-0.070-0.04613.4500.0480.0480.0000.0000.0000.000
169A667ASP-1-0.894-0.94516.624-14.459-14.4590.0000.0000.0000.000
170A668GLU-1-0.893-0.96211.180-23.419-23.4190.0000.0000.0000.000
171A669LYS10.9140.98313.38516.43816.4380.0000.0000.0000.000
172A670ALA0-0.062-0.05014.9470.6790.6790.0000.0000.0000.000
173A671VAL00.0090.01016.6350.6510.6510.0000.0000.0000.000
174A672ASP-1-0.828-0.93112.696-19.895-19.8950.0000.0000.0000.000
175A673LYS10.8280.92016.38813.25013.2500.0000.0000.0000.000
176A674LEU0-0.033-0.01219.6090.6340.6340.0000.0000.0000.000
177A675LYS10.9071.00312.16520.16920.1690.0000.0000.0000.000