FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: YZ6G2

Calculation Name: 4K51-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4K51

Chain ID: A

ChEMBL ID:

UniProt ID: P38249

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:

Apendix: None


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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2622429.006043
FMO2-HF: Nuclear repulsion 2536551.602441
FMO2-HF: Total energy -85877.403602
FMO2-MP2: Total energy -86132.845019


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:278:THR)


Summations of interaction energy for fragment #1(A:278:THR)
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.
-8.392-4.0414.794-3.156-5.987-0.028
Interaction energy analysis for fragmet #1(A:278:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.007
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].
3A280ALA00.0570.0322.273-2.173-0.3251.777-1.356-2.268-0.005
4A281ASN00.038-0.0122.373-6.871-4.6983.017-1.722-3.466-0.023
5A282TYR0-0.0150.0034.1491.3651.6950.000-0.078-0.2530.000
6A283TYR00.0400.0056.0480.6560.6560.0000.0000.0000.000
7A284GLU-1-0.787-0.8606.851-2.833-2.8330.0000.0000.0000.000
8A285ASN0-0.011-0.0107.9610.3430.3430.0000.0000.0000.000
9A286LEU0-0.0060.0039.7350.2640.2640.0000.0000.0000.000
10A287VAL00.0120.01311.1610.1530.1530.0000.0000.0000.000
11A288LYS10.8450.91010.2291.6991.6990.0000.0000.0000.000
12A289VAL00.0110.00913.5460.1000.1000.0000.0000.0000.000
13A290PHE00.0320.00714.7470.0830.0830.0000.0000.0000.000
14A291PHE0-0.0240.01117.5360.0440.0440.0000.0000.0000.000
15A292VAL0-0.012-0.01718.3890.0400.0400.0000.0000.0000.000
16A293SER0-0.077-0.05019.4230.0460.0460.0000.0000.0000.000
17A294GLY00.0130.02421.9640.0320.0320.0000.0000.0000.000
18A295ASP-1-0.808-0.88520.897-0.157-0.1570.0000.0000.0000.000
19A296PRO00.0250.00020.490-0.034-0.0340.0000.0000.0000.000
20A297LEU00.0540.02720.374-0.031-0.0310.0000.0000.0000.000
21A298LEU0-0.032-0.00418.1190.0030.0030.0000.0000.0000.000
22A299HIS0-0.0190.00616.170-0.021-0.0210.0000.0000.0000.000
23A300THR00.0340.01115.421-0.083-0.0830.0000.0000.0000.000
24A301THR0-0.027-0.02415.5710.0000.0000.0000.0000.0000.000
25A302ALA0-0.021-0.01711.8510.0030.0030.0000.0000.0000.000
26A303TRP00.0060.00511.239-0.169-0.1690.0000.0000.0000.000
27A304LYS10.8790.94312.2630.1630.1630.0000.0000.0000.000
28A305LYS10.8350.92910.7620.0700.0700.0000.0000.0000.000
29A306PHE0-0.012-0.0105.9710.0040.0040.0000.0000.0000.000
30A307TYR0-0.003-0.0108.593-0.058-0.0580.0000.0000.0000.000
31A308LYS10.8400.90811.3340.2310.2310.0000.0000.0000.000
32A309LEU0-0.009-0.0015.3750.0750.0750.0000.0000.0000.000
33A310TYR0-0.061-0.0518.2250.1150.1150.0000.0000.0000.000
34A311SER00.001-0.0199.0860.0870.0870.0000.0000.0000.000
35A312THR0-0.071-0.0299.2910.1060.1060.0000.0000.0000.000
36A313ASN0-0.031-0.0086.2440.1590.1590.0000.0000.0000.000
37A314PRO00.010-0.0039.759-0.049-0.0490.0000.0000.0000.000
38A315ARG10.8710.9269.4160.5090.5090.0000.0000.0000.000
39A316ALA00.0250.03411.689-0.084-0.0840.0000.0000.0000.000
40A317THR00.0300.01913.0310.0960.0960.0000.0000.0000.000
41A318GLU-1-0.804-0.89815.906-0.312-0.3120.0000.0000.0000.000
42A319GLU-1-0.901-0.94918.111-0.447-0.4470.0000.0000.0000.000
43A320GLU-1-0.799-0.83712.385-1.077-1.0770.0000.0000.0000.000
44A321PHE00.0120.00013.850-0.023-0.0230.0000.0000.0000.000
45A322LYS10.8650.92716.6690.2970.2970.0000.0000.0000.000
46A323THR0-0.0120.00017.1310.0250.0250.0000.0000.0000.000
47A324TYR0-0.072-0.06410.786-0.041-0.0410.0000.0000.0000.000
48A325SER00.0250.00815.9470.0230.0230.0000.0000.0000.000
49A326SER0-0.010-0.01418.4350.0500.0500.0000.0000.0000.000
50A327THR0-0.021-0.02817.1510.0130.0130.0000.0000.0000.000
51A328ILE0-0.034-0.00914.4890.0260.0260.0000.0000.0000.000
52A329PHE00.023-0.00218.6260.0330.0330.0000.0000.0000.000
53A330LEU00.0370.03422.3260.0260.0260.0000.0000.0000.000
54A331SER00.0260.02820.0660.0110.0110.0000.0000.0000.000
55A332ALA0-0.050-0.00522.0520.0210.0210.0000.0000.0000.000
56A333ILE00.0110.00623.7350.0220.0220.0000.0000.0000.000
57A334SER0-0.050-0.04324.7210.0120.0120.0000.0000.0000.000
58A335THR0-0.057-0.04323.945-0.002-0.0020.0000.0000.0000.000
59A336GLN00.0280.01526.1380.0010.0010.0000.0000.0000.000
60A337LEU00.003-0.00629.1200.0020.0020.0000.0000.0000.000
61A338ASP-1-0.790-0.89429.346-0.115-0.1150.0000.0000.0000.000
62A339GLU-1-0.896-0.92530.618-0.094-0.0940.0000.0000.0000.000
63A340ILE00.001-0.01232.6720.0050.0050.0000.0000.0000.000
64A341PRO00.0300.03031.5370.0070.0070.0000.0000.0000.000
65A342SER0-0.034-0.02534.8550.0050.0050.0000.0000.0000.000
66A343ILE0-0.043-0.02836.5280.0050.0050.0000.0000.0000.000
67A344GLY00.0040.00734.9430.0020.0020.0000.0000.0000.000
68A345TYR0-0.028-0.01327.9730.0030.0030.0000.0000.0000.000
69A346ASP-1-0.701-0.83426.726-0.060-0.0600.0000.0000.0000.000
70A347PRO00.0080.00025.0360.0160.0160.0000.0000.0000.000
71A348HIS10.8100.88322.3310.1210.1210.0000.0000.0000.000
72A349LEU00.0110.01421.8920.0080.0080.0000.0000.0000.000
73A350ARG10.9220.95219.215-0.071-0.0710.0000.0000.0000.000
74A351MET00.0430.02917.0550.0340.0340.0000.0000.0000.000
75A352TYR00.007-0.02417.763-0.016-0.0160.0000.0000.0000.000
76A353ARG10.9990.99918.822-0.229-0.2290.0000.0000.0000.000
77A354LEU0-0.039-0.01012.2210.0510.0510.0000.0000.0000.000
78A355LEU0-0.0040.00013.4400.0150.0150.0000.0000.0000.000
79A356ASN0-0.121-0.05915.3340.0240.0240.0000.0000.0000.000
80A357LEU00.0120.00517.396-0.029-0.0290.0000.0000.0000.000
81A358ASP-1-0.913-0.95820.4620.1220.1220.0000.0000.0000.000
82A359ALA0-0.036-0.02023.8380.0030.0030.0000.0000.0000.000
83A360LYS10.9080.96024.0760.0460.0460.0000.0000.0000.000
84A361PRO0-0.0260.00321.9330.0030.0030.0000.0000.0000.000
85A362THR00.033-0.00224.730-0.003-0.0030.0000.0000.0000.000
86A363ARG10.7410.82426.1190.1510.1510.0000.0000.0000.000
87A364LYS10.9280.96026.8530.0770.0770.0000.0000.0000.000
88A365GLU-1-0.885-0.92726.443-0.057-0.0570.0000.0000.0000.000
89A366MET0-0.044-0.00220.465-0.009-0.0090.0000.0000.0000.000
90A367LEU00.0360.01023.103-0.016-0.0160.0000.0000.0000.000
91A368GLN00.003-0.00825.516-0.007-0.0070.0000.0000.0000.000
92A369SER0-0.031-0.03121.972-0.007-0.0070.0000.0000.0000.000
93A370ILE0-0.053-0.03220.267-0.024-0.0240.0000.0000.0000.000
94A371ILE0-0.0080.00022.591-0.006-0.0060.0000.0000.0000.000
95A372GLU-1-0.865-0.92425.802-0.071-0.0710.0000.0000.0000.000
96A373ASP-1-0.818-0.85319.060-0.158-0.1580.0000.0000.0000.000
97A374GLU-1-0.887-0.94721.813-0.177-0.1770.0000.0000.0000.000
98A375SER0-0.051-0.04118.021-0.026-0.0260.0000.0000.0000.000
99A376ILE0-0.0160.00617.310-0.046-0.0460.0000.0000.0000.000
100A377TYR00.0830.02119.725-0.011-0.0110.0000.0000.0000.000
101A378GLY00.0150.01423.2770.0030.0030.0000.0000.0000.000
102A379LYS10.7340.84718.9970.2600.2600.0000.0000.0000.000
103A380VAL0-0.010-0.00521.727-0.030-0.0300.0000.0000.0000.000
104A381ASP-1-0.762-0.82523.207-0.286-0.2860.0000.0000.0000.000
105A382GLU-1-0.806-0.89825.798-0.184-0.1840.0000.0000.0000.000
106A383GLU-1-0.804-0.89529.138-0.222-0.2220.0000.0000.0000.000
107A384LEU0-0.011-0.00924.0870.0040.0040.0000.0000.0000.000
108A385LYS10.7910.89526.5270.1990.1990.0000.0000.0000.000
109A386GLU-1-0.787-0.88029.913-0.152-0.1520.0000.0000.0000.000
110A387LEU0-0.009-0.00828.6450.0070.0070.0000.0000.0000.000
111A388TYR00.015-0.00729.2110.0050.0050.0000.0000.0000.000
112A389ASP-1-0.852-0.91631.226-0.103-0.1030.0000.0000.0000.000
113A390ILE00.020-0.00134.6700.0070.0070.0000.0000.0000.000
114A391ILE0-0.049-0.03031.2060.0050.0050.0000.0000.0000.000
115A392GLU-1-0.845-0.87530.910-0.135-0.1350.0000.0000.0000.000
116A393VAL0-0.092-0.03834.4170.0070.0070.0000.0000.0000.000
117A394ASN0-0.075-0.04137.2050.0130.0130.0000.0000.0000.000
118A395PHE0-0.0070.00037.817-0.003-0.0030.0000.0000.0000.000
119A396ASP-1-0.815-0.91439.888-0.075-0.0750.0000.0000.0000.000
120A397VAL0-0.014-0.00142.685-0.005-0.0050.0000.0000.0000.000
121A398ASP-1-0.862-0.92943.983-0.080-0.0800.0000.0000.0000.000
122A399THR0-0.023-0.03043.0060.0010.0010.0000.0000.0000.000
123A400VAL00.002-0.00339.031-0.005-0.0050.0000.0000.0000.000
124A401LYS10.8090.92040.0510.0980.0980.0000.0000.0000.000
125A402GLN00.0520.01441.290-0.004-0.0040.0000.0000.0000.000
126A403GLN0-0.0220.01139.094-0.001-0.0010.0000.0000.0000.000
127A404LEU00.013-0.00134.856-0.008-0.0080.0000.0000.0000.000
128A405GLU-1-0.942-0.97137.090-0.131-0.1310.0000.0000.0000.000
129A406ASN00.007-0.01538.377-0.007-0.0070.0000.0000.0000.000
130A407LEU0-0.0080.01531.921-0.009-0.0090.0000.0000.0000.000
131A408LEU00.0390.01232.435-0.016-0.0160.0000.0000.0000.000
132A409VAL0-0.0160.01833.058-0.014-0.0140.0000.0000.0000.000
133A410LYS10.7910.88932.2000.1630.1630.0000.0000.0000.000
134A411LEU0-0.006-0.01527.763-0.017-0.0170.0000.0000.0000.000
135A412SER0-0.015-0.03428.431-0.022-0.0220.0000.0000.0000.000
136A413SER0-0.066-0.01629.305-0.004-0.0040.0000.0000.0000.000
137A414LYS10.7510.87724.7750.2570.2570.0000.0000.0000.000
138A415THR00.012-0.00920.7920.0050.0050.0000.0000.0000.000
139A416TYR0-0.019-0.04219.925-0.012-0.0120.0000.0000.0000.000
140A417PHE00.0330.00721.3840.0020.0020.0000.0000.0000.000
141A418SER00.0340.00824.2880.0040.0040.0000.0000.0000.000
142A419GLN0-0.043-0.02218.569-0.013-0.0130.0000.0000.0000.000
143A420TYR00.002-0.03818.758-0.008-0.0080.0000.0000.0000.000
144A421ILE00.0030.02025.1500.0240.0240.0000.0000.0000.000
145A422ALA00.0070.00628.4890.0170.0170.0000.0000.0000.000
146A423PRO00.0320.02025.5750.0150.0150.0000.0000.0000.000
147A424LEU00.0310.00928.2560.0150.0150.0000.0000.0000.000
148A425ARG10.8790.93929.7830.2010.2010.0000.0000.0000.000
149A426ASP-1-0.832-0.90831.823-0.164-0.1640.0000.0000.0000.000
150A427VAL0-0.041-0.00629.5550.0150.0150.0000.0000.0000.000
151A428ILE0-0.005-0.00432.7600.0130.0130.0000.0000.0000.000
152A429MET0-0.0010.00135.3080.0080.0080.0000.0000.0000.000
153A430ARG10.7920.87835.4450.1270.1270.0000.0000.0000.000
154A431ARG10.8700.92533.6390.1260.1260.0000.0000.0000.000
155A432VAL00.003-0.00238.2950.0080.0080.0000.0000.0000.000
156A433PHE00.007-0.00839.3190.0080.0080.0000.0000.0000.000
157A434VAL0-0.0100.00439.6960.0060.0060.0000.0000.0000.000
158A435ALA00.0390.03842.4410.0060.0060.0000.0000.0000.000
159A436ALA0-0.014-0.01244.4570.0040.0040.0000.0000.0000.000
160A437SER0-0.076-0.06245.4250.0050.0050.0000.0000.0000.000
161A438GLN0-0.023-0.00843.8420.0040.0040.0000.0000.0000.000
162A439LYS10.8080.92148.7990.0750.0750.0000.0000.0000.000
163A440PHE0-0.032-0.01948.9230.0010.0010.0000.0000.0000.000
164A441THR00.0000.00652.1990.0010.0010.0000.0000.0000.000
165A442THR00.004-0.00754.1850.0000.0000.0000.0000.0000.000
166A443VAL0-0.0020.02550.8180.0010.0010.0000.0000.0000.000
167A444SER00.0170.01153.857-0.001-0.0010.0000.0000.0000.000
168A445GLN0-0.013-0.04550.1120.0010.0010.0000.0000.0000.000
169A446SER0-0.043-0.01549.793-0.005-0.0050.0000.0000.0000.000
170A447GLU-1-0.915-0.96750.328-0.071-0.0710.0000.0000.0000.000
171A448LEU00.0300.01746.566-0.003-0.0030.0000.0000.0000.000
172A449TYR0-0.009-0.06445.581-0.005-0.0050.0000.0000.0000.000
173A450LYS10.9440.99545.3080.0850.0850.0000.0000.0000.000
174A451LEU0-0.033-0.01545.476-0.003-0.0030.0000.0000.0000.000
175A452ALA00.0320.01241.956-0.003-0.0030.0000.0000.0000.000
176A453THR0-0.044-0.03540.992-0.007-0.0070.0000.0000.0000.000
177A454LEU0-0.019-0.00136.2230.0040.0040.0000.0000.0000.000
178A455PRO00.0170.01638.716-0.001-0.0010.0000.0000.0000.000
179A456ALA00.028-0.00536.367-0.009-0.0090.0000.0000.0000.000
180A457PRO0-0.019-0.00432.4510.0040.0040.0000.0000.0000.000
181A458LEU0-0.066-0.03431.511-0.010-0.0100.0000.0000.0000.000
182A459ASP-1-0.914-0.94235.171-0.149-0.1490.0000.0000.0000.000
183A460LEU0-0.003-0.02036.347-0.008-0.0080.0000.0000.0000.000
184A461SER00.0270.02439.6340.0090.0090.0000.0000.0000.000
185A462ALA00.016-0.00442.647-0.001-0.0010.0000.0000.0000.000
186A463TRP00.0170.00941.5440.0060.0060.0000.0000.0000.000
187A464ASP-1-0.869-0.94038.912-0.139-0.1390.0000.0000.0000.000
188A465ILE0-0.039-0.01440.065-0.002-0.0020.0000.0000.0000.000
189A466GLU-1-0.789-0.84741.859-0.083-0.0830.0000.0000.0000.000
190A467LYS10.9570.97637.2950.1380.1380.0000.0000.0000.000
191A468SER0-0.006-0.00136.6690.0030.0030.0000.0000.0000.000
192A469LEU0-0.0060.00439.0160.0020.0020.0000.0000.0000.000
193A470LEU0-0.022-0.02941.9730.0040.0040.0000.0000.0000.000
194A471GLN0-0.086-0.04735.5290.0030.0030.0000.0000.0000.000
195A472ALA00.003-0.01138.5100.0010.0010.0000.0000.0000.000
196A473ALA0-0.032-0.01139.5620.0050.0050.0000.0000.0000.000
197A474VAL0-0.043-0.01938.5500.0050.0050.0000.0000.0000.000
198A475GLU-1-0.803-0.85535.144-0.116-0.1160.0000.0000.0000.000
199A476ASP-1-0.870-0.91438.770-0.054-0.0540.0000.0000.0000.000
200A477TYR0-0.008-0.02334.5690.0000.0000.0000.0000.0000.000
201A478VAL0-0.020-0.00540.3710.0000.0000.0000.0000.0000.000
202A479SER00.0150.00943.8290.0020.0020.0000.0000.0000.000
203A480ILE0-0.010-0.00345.6720.0010.0010.0000.0000.0000.000
204A481THR0-0.044-0.01349.1720.0030.0030.0000.0000.0000.000
205A482ILE00.003-0.01147.300-0.001-0.0010.0000.0000.0000.000
206A483ASP-1-0.867-0.92450.655-0.070-0.0700.0000.0000.0000.000
207A484HIS00.0450.05952.4420.0020.0020.0000.0000.0000.000
208A485GLU-1-0.867-0.94756.028-0.056-0.0560.0000.0000.0000.000
209A486SER0-0.140-0.08558.4980.0010.0010.0000.0000.0000.000
210A487ALA00.0200.01555.3330.0000.0000.0000.0000.0000.000
211A488LYS10.8640.93454.3040.0530.0530.0000.0000.0000.000
212A489VAL00.0380.03148.739-0.001-0.0010.0000.0000.0000.000
213A490THR0-0.040-0.03652.1330.0010.0010.0000.0000.0000.000
214A491PHE00.0110.01046.128-0.001-0.0010.0000.0000.0000.000
215A492ALA00.0120.00650.3690.0030.0030.0000.0000.0000.000
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