FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 49RZN

Calculation Name: 4K51-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 4K51

Chain ID: A

ChEMBL ID:
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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:


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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2614518.823178
FMO2-HF: Nuclear repulsion 2528643.803158
FMO2-HF: Total energy -85875.020019
FMO2-MP2: Total energy -86130.561071


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.
-1.5760.8366.019-2.731-5.7-0.017
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 : -0.006 / q_NPA : -0.018
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].
3A280ALA00.0470.0201.823-0.574-0.3274.968-2.124-3.091-0.010
4A281ASN00.0920.0302.400-2.094-0.2961.050-0.575-2.273-0.007
5A282TYR0-0.0160.0013.8151.1751.4530.002-0.021-0.2590.000
6A283TYR00.029-0.0035.8240.8400.8400.0000.0000.0000.000
7A284GLU-1-0.905-0.9506.853-2.102-2.1020.0000.0000.0000.000
8A285ASN0-0.018-0.0217.6040.4290.4290.0000.0000.0000.000
9A286LEU0-0.010-0.0079.4690.2560.2560.0000.0000.0000.000
10A287VAL00.0160.01611.1530.1740.1740.0000.0000.0000.000
11A288LYS10.9310.97310.9131.2461.2460.0000.0000.0000.000
12A289VAL00.0080.01213.5150.0980.0980.0000.0000.0000.000
13A290PHE00.0380.00814.7580.0750.0750.0000.0000.0000.000
14A291PHE0-0.054-0.00717.0760.0460.0460.0000.0000.0000.000
15A292VAL0-0.018-0.01918.1410.0410.0410.0000.0000.0000.000
16A293SER0-0.073-0.05419.2090.0290.0290.0000.0000.0000.000
17A294GLY00.0170.03321.7160.0300.0300.0000.0000.0000.000
18A295ASP-1-0.817-0.88220.751-0.220-0.2200.0000.0000.0000.000
19A296PRO00.0480.01120.510-0.043-0.0430.0000.0000.0000.000
20A297LEU00.0730.02920.507-0.036-0.0360.0000.0000.0000.000
21A298LEU00.0010.03517.887-0.008-0.0080.0000.0000.0000.000
22A299HIS0-0.0110.04016.376-0.048-0.0480.0000.0000.0000.000
23A300THR00.0240.01315.723-0.082-0.0820.0000.0000.0000.000
24A301THR0-0.028-0.05615.625-0.008-0.0080.0000.0000.0000.000
25A302ALA0-0.013-0.02012.033-0.011-0.0110.0000.0000.0000.000
26A303TRP00.0280.01911.262-0.189-0.1890.0000.0000.0000.000
27A304LYS10.9230.96512.1470.2340.2340.0000.0000.0000.000
28A305LYS10.8460.93110.2170.2960.2960.0000.0000.0000.000
29A306PHE00.0050.0116.111-0.027-0.0270.0000.0000.0000.000
30A307TYR00.022-0.0158.323-0.081-0.0810.0000.0000.0000.000
31A308LYS10.9680.99611.1330.3650.3650.0000.0000.0000.000
32A309LEU00.0000.0094.304-0.0380.051-0.001-0.011-0.0770.000
33A310TYR00.0170.0597.8600.1400.1400.0000.0000.0000.000
34A311SER00.013-0.0188.7890.0800.0800.0000.0000.0000.000
35A312THR0-0.153-0.1038.7460.0940.0940.0000.0000.0000.000
36A313ASN0-0.018-0.0136.5260.0510.0510.0000.0000.0000.000
37A314PRO00.0590.0319.527-0.011-0.0110.0000.0000.0000.000
38A315ARG10.8270.9119.0530.4190.4190.0000.0000.0000.000
39A316ALA00.0330.02111.435-0.073-0.0730.0000.0000.0000.000
40A317THR00.0390.03313.1180.0600.0600.0000.0000.0000.000
41A318GLU-1-0.853-0.93515.564-0.302-0.3020.0000.0000.0000.000
42A319GLU-1-0.898-0.95717.367-0.406-0.4060.0000.0000.0000.000
43A320GLU-1-0.901-0.94813.058-0.774-0.7740.0000.0000.0000.000
44A321PHE00.0170.01113.470-0.028-0.0280.0000.0000.0000.000
45A322LYS10.9701.05016.3820.2760.2760.0000.0000.0000.000
46A323THR00.0150.06316.7290.0280.0280.0000.0000.0000.000
47A324TYR0-0.0280.01110.865-0.058-0.0580.0000.0000.0000.000
48A325SER0-0.014-0.06215.8210.0050.0050.0000.0000.0000.000
49A326SER0-0.011-0.05418.2710.0370.0370.0000.0000.0000.000
50A327THR0-0.041-0.06416.9440.0190.0190.0000.0000.0000.000
51A328ILE0-0.051-0.02514.4490.0160.0160.0000.0000.0000.000
52A329PHE00.004-0.00218.4800.0260.0260.0000.0000.0000.000
53A330LEU00.0320.02522.0690.0240.0240.0000.0000.0000.000
54A331SER0-0.0020.01719.3620.0310.0310.0000.0000.0000.000
55A332ALA0-0.0060.01121.8950.0180.0180.0000.0000.0000.000
56A333ILE00.0120.01123.5430.0220.0220.0000.0000.0000.000
57A334SER0-0.093-0.05524.7770.0140.0140.0000.0000.0000.000
58A335THR0-0.031-0.02724.195-0.008-0.0080.0000.0000.0000.000
59A336GLN00.0390.01526.4210.0030.0030.0000.0000.0000.000
60A337LEU0-0.002-0.01429.129-0.001-0.0010.0000.0000.0000.000
61A338ASP-1-0.827-0.92929.062-0.155-0.1550.0000.0000.0000.000
62A339GLU-1-0.908-0.93730.737-0.127-0.1270.0000.0000.0000.000
63A340ILE00.004-0.00832.7910.0010.0010.0000.0000.0000.000
64A341PRO0-0.0070.01531.6530.0070.0070.0000.0000.0000.000
65A342SER0-0.044-0.04734.8750.0030.0030.0000.0000.0000.000
66A343ILE0-0.018-0.00936.4710.0050.0050.0000.0000.0000.000
67A344GLY00.0220.03034.4650.0030.0030.0000.0000.0000.000
68A345TYR0-0.026-0.01827.9600.0060.0060.0000.0000.0000.000
69A346ASP-1-0.778-0.90926.848-0.122-0.1220.0000.0000.0000.000
70A347PRO0-0.005-0.00825.7630.0110.0110.0000.0000.0000.000
71A348HIS10.8550.91722.3740.1690.1690.0000.0000.0000.000
72A349LEU00.0170.02021.838-0.006-0.0060.0000.0000.0000.000
73A350ARG10.9390.95118.9700.0200.0200.0000.0000.0000.000
74A351MET00.0380.03316.359-0.004-0.0040.0000.0000.0000.000
75A352TYR00.024-0.00117.736-0.034-0.0340.0000.0000.0000.000
76A353ARG10.9580.97818.293-0.065-0.0650.0000.0000.0000.000
77A354LEU0-0.051-0.01712.0380.0300.0300.0000.0000.0000.000
78A355LEU0-0.035-0.01713.190-0.027-0.0270.0000.0000.0000.000
79A356ASN0-0.084-0.04214.7840.0030.0030.0000.0000.0000.000
80A357LEU0-0.0270.00917.496-0.001-0.0010.0000.0000.0000.000
81A358ASP-1-0.896-0.95420.3340.0100.0100.0000.0000.0000.000
82A359ALA0-0.056-0.02923.6820.0110.0110.0000.0000.0000.000
83A360LYS10.9240.96324.1390.0880.0880.0000.0000.0000.000
84A361PRO0-0.0060.00922.0310.0050.0050.0000.0000.0000.000
85A362THR00.0320.03424.5850.0010.0010.0000.0000.0000.000
86A363ARG10.7870.86725.9540.1680.1680.0000.0000.0000.000
87A364LYS10.9890.99026.8970.1090.1090.0000.0000.0000.000
88A365GLU-1-0.913-0.98326.114-0.116-0.1160.0000.0000.0000.000
89A366MET0-0.039-0.00220.492-0.012-0.0120.0000.0000.0000.000
90A367LEU00.0450.01723.278-0.014-0.0140.0000.0000.0000.000
91A368GLN0-0.025-0.00125.586-0.006-0.0060.0000.0000.0000.000
92A369SER0-0.070-0.05121.949-0.008-0.0080.0000.0000.0000.000
93A370ILE0-0.041-0.03020.176-0.011-0.0110.0000.0000.0000.000
94A371ILE0-0.020-0.00122.303-0.003-0.0030.0000.0000.0000.000
95A372GLU-1-0.939-0.97425.443-0.110-0.1100.0000.0000.0000.000
96A373ASP-1-0.865-0.85418.924-0.214-0.2140.0000.0000.0000.000
97A374GLU-1-0.933-0.97921.966-0.186-0.1860.0000.0000.0000.000
98A375SER0-0.082-0.09317.510-0.019-0.0190.0000.0000.0000.000
99A376ILE0-0.0200.01316.983-0.046-0.0460.0000.0000.0000.000
100A377TYR00.0910.02319.308-0.006-0.0060.0000.0000.0000.000
101A378GLY00.0290.02622.5520.0110.0110.0000.0000.0000.000
102A379LYS10.7850.86918.8560.2650.2650.0000.0000.0000.000
103A380VAL0-0.036-0.01121.830-0.024-0.0240.0000.0000.0000.000
104A381ASP-1-0.863-0.92823.314-0.281-0.2810.0000.0000.0000.000
105A382GLU-1-0.833-0.94825.874-0.173-0.1730.0000.0000.0000.000
106A383GLU-1-0.863-0.93228.886-0.209-0.2090.0000.0000.0000.000
107A384LEU0-0.015-0.01124.0600.0050.0050.0000.0000.0000.000
108A385LYS10.8250.93926.4330.1990.1990.0000.0000.0000.000
109A386GLU-1-0.925-0.95429.763-0.140-0.1400.0000.0000.0000.000
110A387LEU0-0.017-0.01528.7620.0070.0070.0000.0000.0000.000
111A388TYR0-0.013-0.01929.2340.0030.0030.0000.0000.0000.000
112A389ASP-1-0.877-0.94931.245-0.113-0.1130.0000.0000.0000.000
113A390ILE00.016-0.00134.5950.0070.0070.0000.0000.0000.000
114A391ILE0-0.054-0.03831.2000.0060.0060.0000.0000.0000.000
115A392GLU-1-0.865-0.89730.939-0.151-0.1510.0000.0000.0000.000
116A393VAL0-0.085-0.02434.3080.0060.0060.0000.0000.0000.000
117A394ASN0-0.066-0.01936.7850.0130.0130.0000.0000.0000.000
118A395PHE0-0.0040.00938.088-0.002-0.0020.0000.0000.0000.000
119A396ASP-1-0.804-0.90739.924-0.081-0.0810.0000.0000.0000.000
120A397VAL0-0.018-0.00842.801-0.004-0.0040.0000.0000.0000.000
121A398ASP-1-0.945-0.96844.026-0.082-0.0820.0000.0000.0000.000
122A399THR0-0.029-0.03142.9200.0030.0030.0000.0000.0000.000
123A400VAL0-0.0050.00339.434-0.004-0.0040.0000.0000.0000.000
124A401LYS10.7870.88740.2980.1020.1020.0000.0000.0000.000
125A402GLN00.0620.02941.515-0.004-0.0040.0000.0000.0000.000
126A403GLN0-0.0090.00739.494-0.001-0.0010.0000.0000.0000.000
127A404LEU00.004-0.00834.908-0.006-0.0060.0000.0000.0000.000
128A405GLU-1-0.949-0.96336.915-0.124-0.1240.0000.0000.0000.000
129A406ASN00.022-0.01338.157-0.006-0.0060.0000.0000.0000.000
130A407LEU0-0.0080.02032.636-0.008-0.0080.0000.0000.0000.000
131A408LEU00.0550.01432.299-0.014-0.0140.0000.0000.0000.000
132A409VAL0-0.0120.02932.918-0.011-0.0110.0000.0000.0000.000
133A410LYS10.9420.97032.0670.1520.1520.0000.0000.0000.000
134A411LEU00.0270.00027.561-0.014-0.0140.0000.0000.0000.000
135A412SER0-0.045-0.03828.243-0.021-0.0210.0000.0000.0000.000
136A413SER0-0.069-0.02928.5510.0010.0010.0000.0000.0000.000
137A414LYS10.8610.95624.4310.2510.2510.0000.0000.0000.000
138A415THR00.008-0.01020.2200.0030.0030.0000.0000.0000.000
139A416TYR0-0.017-0.01719.877-0.011-0.0110.0000.0000.0000.000
140A417PHE00.0330.01121.285-0.002-0.0020.0000.0000.0000.000
141A418SER00.0510.01024.6940.0000.0000.0000.0000.0000.000
142A419GLN0-0.040-0.01518.817-0.018-0.0180.0000.0000.0000.000
143A420TYR00.001-0.05818.816-0.014-0.0140.0000.0000.0000.000
144A421ILE00.0040.01925.1660.0200.0200.0000.0000.0000.000
145A422ALA0-0.022-0.01527.9070.0150.0150.0000.0000.0000.000
146A423PRO00.0350.03125.1840.0130.0130.0000.0000.0000.000
147A424LEU00.0350.00528.2680.0130.0130.0000.0000.0000.000
148A425ARG10.9020.96029.7330.2020.2020.0000.0000.0000.000
149A426ASP-1-0.889-0.94831.170-0.172-0.1720.0000.0000.0000.000
150A427VAL0-0.031-0.00329.6470.0150.0150.0000.0000.0000.000
151A428ILE00.0040.00532.9320.0120.0120.0000.0000.0000.000
152A429MET00.0250.01335.4750.0080.0080.0000.0000.0000.000
153A430ARG10.8420.94734.6960.1460.1460.0000.0000.0000.000
154A431ARG10.8640.90833.5540.1420.1420.0000.0000.0000.000
155A432VAL0-0.006-0.00838.3770.0070.0070.0000.0000.0000.000
156A433PHE00.0280.00240.0350.0070.0070.0000.0000.0000.000
157A434VAL00.0500.03839.5710.0060.0060.0000.0000.0000.000
158A435ALA00.0230.05342.4790.0060.0060.0000.0000.0000.000
159A436ALA0-0.006-0.01044.2750.0050.0050.0000.0000.0000.000
160A437SER0-0.141-0.11345.2940.0050.0050.0000.0000.0000.000
161A438GLN0-0.014-0.01344.2020.0040.0040.0000.0000.0000.000
162A439LYS10.8650.96148.7600.0780.0780.0000.0000.0000.000
163A440PHE0-0.022-0.02849.4450.0030.0030.0000.0000.0000.000
164A441THR00.0240.03652.0640.0010.0010.0000.0000.0000.000
165A442THR0-0.007-0.02553.9310.0000.0000.0000.0000.0000.000
166A443VAL0-0.0060.01851.0930.0020.0020.0000.0000.0000.000
167A444SER0-0.0050.01153.546-0.002-0.0020.0000.0000.0000.000
168A445GLN00.1120.03550.297-0.002-0.0020.0000.0000.0000.000
169A446SER0-0.047-0.00849.910-0.005-0.0050.0000.0000.0000.000
170A447GLU-1-0.928-0.98550.599-0.074-0.0740.0000.0000.0000.000
171A448LEU00.0180.01546.818-0.003-0.0030.0000.0000.0000.000
172A449TYR00.0680.00645.768-0.004-0.0040.0000.0000.0000.000
173A450LYS10.9621.04345.3840.0830.0830.0000.0000.0000.000
174A451LEU0-0.016-0.01245.752-0.004-0.0040.0000.0000.0000.000
175A452ALA00.0210.01642.140-0.003-0.0030.0000.0000.0000.000
176A453THR0-0.060-0.06941.242-0.006-0.0060.0000.0000.0000.000
177A454LEU0-0.031-0.01436.4290.0040.0040.0000.0000.0000.000
178A455PRO00.0150.01238.3330.0000.0000.0000.0000.0000.000
179A456ALA00.026-0.01036.269-0.007-0.0070.0000.0000.0000.000
180A457PRO00.0240.03332.2570.0010.0010.0000.0000.0000.000
181A458LEU0-0.104-0.05331.973-0.008-0.0080.0000.0000.0000.000
182A459ASP-1-0.925-0.94235.349-0.143-0.1430.0000.0000.0000.000
183A460LEU00.013-0.00235.777-0.006-0.0060.0000.0000.0000.000
184A461SER00.0240.00739.4920.0080.0080.0000.0000.0000.000
185A462ALA00.027-0.00642.447-0.001-0.0010.0000.0000.0000.000
186A463TRP00.0630.02841.6510.0040.0040.0000.0000.0000.000
187A464ASP-1-0.892-0.94238.800-0.138-0.1380.0000.0000.0000.000
188A465ILE0-0.056-0.02240.080-0.002-0.0020.0000.0000.0000.000
189A466GLU-1-0.891-0.94741.912-0.087-0.0870.0000.0000.0000.000
190A467LYS10.9510.97337.1840.1300.1300.0000.0000.0000.000
191A468SER0-0.001-0.00736.8480.0010.0010.0000.0000.0000.000
192A469LEU0-0.0070.00539.0440.0000.0000.0000.0000.0000.000
193A470LEU0-0.004-0.01942.0540.0030.0030.0000.0000.0000.000
194A471GLN0-0.089-0.02834.9700.0050.0050.0000.0000.0000.000
195A472ALA00.012-0.01238.5130.0000.0000.0000.0000.0000.000
196A473ALA0-0.039-0.01439.4460.0040.0040.0000.0000.0000.000
197A474VAL0-0.0190.00138.2530.0040.0040.0000.0000.0000.000
198A475GLU-1-0.899-0.94834.278-0.139-0.1390.0000.0000.0000.000
199A476ASP-1-0.959-0.97838.334-0.075-0.0750.0000.0000.0000.000
200A477TYR0-0.041-0.01634.3260.0000.0000.0000.0000.0000.000
201A478VAL0-0.018-0.02140.8330.0020.0020.0000.0000.0000.000
202A479SER00.0050.00744.1710.0020.0020.0000.0000.0000.000
203A480ILE00.0100.00845.8500.0020.0020.0000.0000.0000.000
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