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: 7GRZK

Calculation Name: 4Y66-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: D

ChEMBL ID:

UniProt ID: E2RTU1

Base Structure: X-ray

Registration Date: 2023-06-20

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 210
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1502564.916424
FMO2-HF: Nuclear repulsion 1418905.599639
FMO2-HF: Total energy -83659.316785
FMO2-MP2: Total energy -83898.687402


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(D:8:ALA)


Summations of interaction energy for fragment #1(D:8:ALA)
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.
-3.438-1.2537.866-4.296-5.753-0.015
Interaction energy analysis for fragmet #1(D:8:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.008
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].
3D10ALA00.0730.0273.593-0.9670.3150.004-0.531-0.7540.001
4D11ALA0-0.034-0.0071.935-1.554-2.6195.285-2.077-2.142-0.003
5D12VAL0-0.011-0.0053.530-0.2420.0350.008-0.006-0.2790.000
6D13LYS10.8530.9246.1580.0100.0100.0000.0000.0000.000
7D14GLU-1-0.822-0.9157.3860.6490.6490.0000.0000.0000.000
8D15LEU0-0.0200.0178.412-0.020-0.0200.0000.0000.0000.000
9D16MET0-0.002-0.01810.197-0.006-0.0060.0000.0000.0000.000
10D17GLN00.0140.03011.7450.0400.0400.0000.0000.0000.000
11D18THR0-0.056-0.04412.4150.0060.0060.0000.0000.0000.000
12D19SER0-0.034-0.01414.3710.0070.0070.0000.0000.0000.000
13D20ASN00.0820.04815.896-0.042-0.0420.0000.0000.0000.000
14D21LYS10.9320.97317.8970.0970.0970.0000.0000.0000.000
15D22PRO00.0400.02316.944-0.021-0.0210.0000.0000.0000.000
16D23GLN0-0.042-0.02813.288-0.045-0.0450.0000.0000.0000.000
17D24ASN00.0530.03415.906-0.026-0.0260.0000.0000.0000.000
18D25VAL00.0570.01811.358-0.040-0.0400.0000.0000.0000.000
19D26GLN00.0080.00512.090-0.068-0.0680.0000.0000.0000.000
20D27THR00.0390.01113.818-0.012-0.0120.0000.0000.0000.000
21D28ALA00.0510.0399.6010.0160.0160.0000.0000.0000.000
22D29ILE0-0.0260.0148.243-0.086-0.0860.0000.0000.0000.000
23D30ASN0-0.049-0.03610.5330.0370.0370.0000.0000.0000.000
24D31ASN0-0.021-0.02212.0810.0710.0710.0000.0000.0000.000
25D32THR00.0790.0626.0910.0140.0140.0000.0000.0000.000
26D33GLY0-0.0170.0008.0610.0640.0640.0000.0000.0000.000
27D34SER0-0.053-0.0479.8290.0320.0320.0000.0000.0000.000
28D35LYS10.9180.9525.1410.4940.4940.0000.0000.0000.000
29D36TYR00.0240.0092.704-2.723-1.0322.569-1.682-2.578-0.013
30D37GLY00.0710.0386.5830.1940.1940.0000.0000.0000.000
31D38LYS10.9190.9408.6310.2390.2390.0000.0000.0000.000
32D39THR00.0640.02010.917-0.061-0.0610.0000.0000.0000.000
33D40THR00.0210.0175.2900.1550.1550.0000.0000.0000.000
34D41VAL0-0.025-0.0076.662-0.263-0.2630.0000.0000.0000.000
35D42GLN00.003-0.0017.5730.0020.0020.0000.0000.0000.000
36D43LYS10.8230.9016.5860.4530.4530.0000.0000.0000.000
37D44ALA00.0070.0125.7910.0690.0690.0000.0000.0000.000
38D45LEU0-0.005-0.0067.8110.1600.1600.0000.0000.0000.000
39D46ASP-1-0.821-0.89611.035-0.177-0.1770.0000.0000.0000.000
40D47GLU-1-0.833-0.8998.044-0.270-0.2700.0000.0000.0000.000
41D48LEU0-0.020-0.0198.9760.0830.0830.0000.0000.0000.000
42D49VAL0-0.016-0.00212.3880.0580.0580.0000.0000.0000.000
43D50ALA0-0.032-0.01214.5980.0350.0350.0000.0000.0000.000
44D51GLN0-0.050-0.02610.6190.0610.0610.0000.0000.0000.000
45D52ASN0-0.016-0.00215.9000.0120.0120.0000.0000.0000.000
46D53LEU00.0440.02912.5040.0180.0180.0000.0000.0000.000
47D54CYS0-0.110-0.04713.558-0.047-0.0470.0000.0000.0000.000
48D55ILE00.0380.02915.8710.0180.0180.0000.0000.0000.000
49D56TYR0-0.026-0.03018.056-0.011-0.0110.0000.0000.0000.000
50D65LEU0-0.010-0.00418.520-0.003-0.0030.0000.0000.0000.000
51D66TYR0-0.045-0.05014.9750.0080.0080.0000.0000.0000.000
52D67LEU0-0.017-0.01016.861-0.007-0.0070.0000.0000.0000.000
53D68TRP00.1260.05512.534-0.010-0.0100.0000.0000.0000.000
54D69ASN00.0040.00616.2910.0080.0080.0000.0000.0000.000
55D70GLN0-0.026-0.05019.0970.0280.0280.0000.0000.0000.000
56D71ASN0-0.058-0.03021.8600.0140.0140.0000.0000.0000.000
57D72LEU0-0.036-0.00917.8690.0080.0080.0000.0000.0000.000
58D73LEU0-0.079-0.02619.6020.0150.0150.0000.0000.0000.000
59D74GLU-1-0.924-0.96723.0870.0570.0570.0000.0000.0000.000
60D75VAL0-0.027-0.01026.310-0.003-0.0030.0000.0000.0000.000
61D76LEU0-0.025-0.00429.3050.0020.0020.0000.0000.0000.000
62D77SER0-0.011-0.02631.754-0.005-0.0050.0000.0000.0000.000
63D78ASP-1-0.891-0.95635.4250.0050.0050.0000.0000.0000.000
64D79ALA00.0320.01037.7590.0000.0000.0000.0000.0000.000
65D80GLN00.0500.04233.439-0.002-0.0020.0000.0000.0000.000
66D81LEU00.0160.01632.5020.0020.0020.0000.0000.0000.000
67D82MET00.0160.00935.082-0.001-0.0010.0000.0000.0000.000
68D83GLU-1-0.909-0.94837.2630.0230.0230.0000.0000.0000.000
69D84VAL00.0100.00331.3340.0010.0010.0000.0000.0000.000
70D85ASN0-0.066-0.05034.690-0.002-0.0020.0000.0000.0000.000
71D86ALA00.0160.02636.405-0.001-0.0010.0000.0000.0000.000
72D87GLN00.008-0.00134.1510.0000.0000.0000.0000.0000.000
73D88ILE0-0.007-0.00731.2210.0000.0000.0000.0000.0000.000
74D89ASN0-0.045-0.03334.870-0.003-0.0030.0000.0000.0000.000
75D90ASP-1-0.844-0.90138.3630.0230.0230.0000.0000.0000.000
76D91LEU00.0280.00532.7220.0000.0000.0000.0000.0000.000
77D92LYS10.8490.92735.155-0.005-0.0050.0000.0000.0000.000
78D93ALA00.0210.02337.544-0.001-0.0010.0000.0000.0000.000
79D94GLN0-0.085-0.05637.9780.0010.0010.0000.0000.0000.000
80D95VAL0-0.009-0.01334.3270.0000.0000.0000.0000.0000.000
81D96GLU-1-0.822-0.89037.6080.0060.0060.0000.0000.0000.000
82D97LYS10.9040.96340.381-0.021-0.0210.0000.0000.0000.000
83D98LEU0-0.019-0.02237.6530.0000.0000.0000.0000.0000.000
84D99THR0-0.046-0.02837.6740.0010.0010.0000.0000.0000.000
85D100GLN0-0.039-0.02940.2040.0000.0000.0000.0000.0000.000
86D101GLN00.0300.01243.2410.0000.0000.0000.0000.0000.000
87D102GLY00.0450.03641.3160.0000.0000.0000.0000.0000.000
88D103GLU-1-0.809-0.88442.3030.0060.0060.0000.0000.0000.000
89D104THR0-0.052-0.03644.6890.0000.0000.0000.0000.0000.000
90D105LEU00.0110.01243.4090.0000.0000.0000.0000.0000.000
91D106ARG10.9500.97539.864-0.011-0.0110.0000.0000.0000.000
92D107ILE0-0.054-0.01545.681-0.001-0.0010.0000.0000.0000.000
93D108THR0-0.028-0.03549.3360.0000.0000.0000.0000.0000.000
94D109GLN0-0.073-0.03544.1770.0000.0000.0000.0000.0000.000
95D110ARG10.8570.90047.084-0.007-0.0070.0000.0000.0000.000
96D111ASN0-0.039-0.02950.373-0.001-0.0010.0000.0000.0000.000
97D112LEU0-0.042-0.00851.8190.0000.0000.0000.0000.0000.000
98D113GLU-1-0.864-0.93547.3720.0130.0130.0000.0000.0000.000
99D114ALA0-0.059-0.01752.2590.0000.0000.0000.0000.0000.000
100D115ALA0-0.021-0.00555.131-0.001-0.0010.0000.0000.0000.000
101D116PRO00.0170.02856.3690.0010.0010.0000.0000.0000.000
102D117ILE00.0140.00255.0400.0000.0000.0000.0000.0000.000
103D118THR00.0550.00958.9200.0000.0000.0000.0000.0000.000
104D119GLU-1-0.825-0.90461.3630.0120.0120.0000.0000.0000.000
105D120VAL0-0.016-0.00459.1630.0000.0000.0000.0000.0000.000
106D121LEU00.0570.04162.322-0.001-0.0010.0000.0000.0000.000
107D122LYS10.7980.87563.886-0.012-0.0120.0000.0000.0000.000
108D123GLN0-0.0070.00064.643-0.001-0.0010.0000.0000.0000.000
109D124GLU-1-0.875-0.94161.7400.0080.0080.0000.0000.0000.000
110D125VAL0-0.010-0.01166.340-0.001-0.0010.0000.0000.0000.000
111D126ASP-1-0.816-0.87869.4050.0080.0080.0000.0000.0000.000
112D127GLU-1-0.970-0.98667.1110.0070.0070.0000.0000.0000.000
113D128LEU0-0.0070.00067.431-0.001-0.0010.0000.0000.0000.000
114D129ARG10.7600.85071.350-0.007-0.0070.0000.0000.0000.000
115D130GLN00.0230.00973.4260.0000.0000.0000.0000.0000.000
116D131GLN0-0.032-0.01969.3230.0000.0000.0000.0000.0000.000
117D132VAL0-0.010-0.00374.1370.0000.0000.0000.0000.0000.000
118D133SER00.0210.02476.5960.0000.0000.0000.0000.0000.000
119D134ALA00.019-0.00277.8070.0000.0000.0000.0000.0000.000
120D135ASN0-0.027-0.02075.2570.0000.0000.0000.0000.0000.000
121D136ASP-1-0.860-0.92779.5720.0030.0030.0000.0000.0000.000
122D137GLU-1-0.827-0.90482.3500.0030.0030.0000.0000.0000.000
123D138LYS10.8250.91877.566-0.004-0.0040.0000.0000.0000.000
124D139LEU0-0.012-0.01480.6930.0000.0000.0000.0000.0000.000
125D140ARG10.7420.85084.597-0.003-0.0030.0000.0000.0000.000
126D141LEU00.0220.00387.0470.0000.0000.0000.0000.0000.000
127D142VAL0-0.031-0.01185.0810.0000.0000.0000.0000.0000.000
128D143ARG10.8890.92985.032-0.002-0.0020.0000.0000.0000.000
129D144GLU-1-0.857-0.88790.1010.0020.0020.0000.0000.0000.000
130D145SER0-0.043-0.02192.2040.0000.0000.0000.0000.0000.000
131D146ASN0-0.088-0.04689.5890.0000.0000.0000.0000.0000.000
132D147ALA00.0450.02191.1410.0000.0000.0000.0000.0000.000
133D148ILE0-0.038-0.01684.2450.0000.0000.0000.0000.0000.000
134D149VAL0-0.0110.00386.8450.0000.0000.0000.0000.0000.000
135D150SER00.0200.01183.0830.0000.0000.0000.0000.0000.000
136D151ASP-1-0.860-0.94181.146-0.001-0.0010.0000.0000.0000.000
137D152ALA00.0340.00883.9910.0000.0000.0000.0000.0000.000
138D153ASP-1-0.824-0.90285.6710.0000.0000.0000.0000.0000.000
139D154MET0-0.0030.01587.0980.0000.0000.0000.0000.0000.000
140D155LEU00.0120.01084.3460.0000.0000.0000.0000.0000.000
141D156THR0-0.044-0.04588.7700.0000.0000.0000.0000.0000.000
142D157LEU0-0.0130.01091.3620.0000.0000.0000.0000.0000.000
143D158GLN00.007-0.01589.2230.0000.0000.0000.0000.0000.000
144D159LYS10.8400.90892.3940.0020.0020.0000.0000.0000.000
145D160ASN00.0140.00394.2950.0000.0000.0000.0000.0000.000
146D161TYR0-0.021-0.02196.8950.0000.0000.0000.0000.0000.000
147D162LYS10.9140.95695.8510.0020.0020.0000.0000.0000.000
148D163ASP-1-0.838-0.89897.435-0.002-0.0020.0000.0000.0000.000
149D164ALA00.0180.00899.8430.0000.0000.0000.0000.0000.000
150D165MET00.0090.009101.4240.0000.0000.0000.0000.0000.000
151D166THR0-0.045-0.036100.7470.0000.0000.0000.0000.0000.000
152D167ALA0-0.020-0.003103.3780.0000.0000.0000.0000.0000.000
153D168TRP00.0430.017105.7300.0000.0000.0000.0000.0000.000
154D169ALA00.0150.006106.7730.0000.0000.0000.0000.0000.000
155D170THR0-0.030-0.028106.1720.0000.0000.0000.0000.0000.000
156D171ARG10.9290.958106.4060.0010.0010.0000.0000.0000.000
157D172ARG10.8430.899111.4480.0020.0020.0000.0000.0000.000
158D173ALA0-0.0070.005111.5550.0000.0000.0000.0000.0000.000
159D174LYS10.8370.894112.6060.0020.0020.0000.0000.0000.000
160D175CYS0-0.029-0.010114.6660.0000.0000.0000.0000.0000.000
161D176ARG10.8140.872116.8370.0010.0010.0000.0000.0000.000
162D177GLU-1-0.792-0.868114.216-0.002-0.0020.0000.0000.0000.000
163D178VAL0-0.0180.006118.7640.0000.0000.0000.0000.0000.000
164D179ILE00.010-0.002120.2660.0000.0000.0000.0000.0000.000
165D180ASP-1-0.773-0.884121.069-0.002-0.0020.0000.0000.0000.000
166D181THR0-0.070-0.039122.2210.0000.0000.0000.0000.0000.000
167D182LEU0-0.045-0.024124.7930.0000.0000.0000.0000.0000.000
168D183SER0-0.021-0.026126.6980.0000.0000.0000.0000.0000.000
169D184GLU-1-0.862-0.919126.978-0.002-0.0020.0000.0000.0000.000
170D185GLY0-0.046-0.013129.1810.0000.0000.0000.0000.0000.000
171D186MET0-0.063-0.026130.9890.0000.0000.0000.0000.0000.000
172D187GLY0-0.0050.011132.5720.0000.0000.0000.0000.0000.000
173D188VAL0-0.069-0.039131.6050.0000.0000.0000.0000.0000.000
174D189LYS10.9930.985129.4090.0010.0010.0000.0000.0000.000
175D190PRO00.0590.025124.4160.0000.0000.0000.0000.0000.000
176D191SER0-0.047-0.013125.1200.0000.0000.0000.0000.0000.000
177D192ALA00.0580.023126.5210.0000.0000.0000.0000.0000.000
178D193PHE00.0300.008126.0440.0000.0000.0000.0000.0000.000
179D194MET0-0.038-0.007121.9500.0000.0000.0000.0000.0000.000
180D195ASP-1-0.862-0.931126.096-0.001-0.0010.0000.0000.0000.000
181D196GLN0-0.079-0.038128.3650.0000.0000.0000.0000.0000.000
182D197LEU0-0.056-0.030126.5160.0000.0000.0000.0000.0000.000
183D198GLY0-0.0200.008126.8150.0000.0000.0000.0000.0000.000
184D199LEU0-0.053-0.024121.6470.0000.0000.0000.0000.0000.000
185D200GLU-1-0.936-0.968119.394-0.001-0.0010.0000.0000.0000.000
186D201GLU-1-0.830-0.912117.046-0.001-0.0010.0000.0000.0000.000
187D202GLY00.0300.025117.2110.0000.0000.0000.0000.0000.000
188D203LEU0-0.024-0.015110.8700.0000.0000.0000.0000.0000.000
189D204PRO00.0350.041114.4310.0000.0000.0000.0000.0000.000
190D205MET00.002-0.029109.5030.0000.0000.0000.0000.0000.000
191D206THR00.0250.015110.7510.0000.0000.0000.0000.0000.000
192D207THR00.0880.034109.5230.0000.0000.0000.0000.0000.000
193D208TYR00.0040.020105.0430.0000.0000.0000.0000.0000.000
194D209THR0-0.026-0.019106.1430.0000.0000.0000.0000.0000.000
195D210GLU-1-0.919-0.955105.273-0.001-0.0010.0000.0000.0000.000
196D211MET00.0090.002103.9430.0000.0000.0000.0000.0000.000
197D212LYS10.9040.948101.7940.0020.0020.0000.0000.0000.000
198D213LYS10.8390.915100.5860.0010.0010.0000.0000.0000.000
199D214ALA0-0.0200.00299.8090.0000.0000.0000.0000.0000.000
200D215LEU00.0130.01495.0610.0000.0000.0000.0000.0000.000
201D216PRO00.0540.03595.1990.0000.0000.0000.0000.0000.000
202D217PRO0-0.061-0.03495.8010.0000.0000.0000.0000.0000.000
203D218VAL00.0320.03690.2170.0000.0000.0000.0000.0000.000
204D219ASN0-0.0030.00091.8060.0000.0000.0000.0000.0000.000
205D220VAL00.0250.00988.3990.0000.0000.0000.0000.0000.000
206D221SER0-0.022-0.01587.0030.0000.0000.0000.0000.0000.000
207D222LYS10.8610.93285.8710.0020.0020.0000.0000.0000.000
208D223ALA00.0520.03484.1690.0000.0000.0000.0000.0000.000
209D224ASP-1-0.919-0.96180.838-0.002-0.0020.0000.0000.0000.000
210D225ILE00.0000.01379.3350.0000.0000.0000.0000.0000.000