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: M372Z

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 OptHSide
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 -1499224.713709
FMO2-HF: Nuclear repulsion 1415566.87231
FMO2-HF: Total energy -83657.8414
FMO2-MP2: Total energy -83897.459435


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.
-1.157-0.63311.502-5.497-6.53-0.017
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 : 0.025 / q_NPA : -0.004
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].
3D10ALA00.0740.0163.198-1.0000.4400.015-0.605-0.8500.001
4D11ALA0-0.022-0.0061.7980.994-1.8908.725-3.110-2.730-0.005
5D12VAL0-0.020-0.0093.474-0.450-0.1140.0100.009-0.3560.000
6D13LYS10.8570.9355.8720.2540.2540.0000.0000.0000.000
7D14GLU-1-0.852-0.9297.1320.5010.5010.0000.0000.0000.000
8D15LEU0-0.0380.0128.1630.0160.0160.0000.0000.0000.000
9D16MET0-0.009-0.0209.864-0.005-0.0050.0000.0000.0000.000
10D17GLN00.0160.03111.6400.0360.0360.0000.0000.0000.000
11D18THR0-0.058-0.05411.9780.0000.0000.0000.0000.0000.000
12D19SER0-0.0100.00314.1490.0170.0170.0000.0000.0000.000
13D20ASN00.0700.03815.545-0.042-0.0420.0000.0000.0000.000
14D21LYS10.9360.96717.8290.0880.0880.0000.0000.0000.000
15D22PRO00.0310.01816.630-0.024-0.0240.0000.0000.0000.000
16D23GLN0-0.080-0.05613.265-0.043-0.0430.0000.0000.0000.000
17D24ASN00.0540.04015.578-0.032-0.0320.0000.0000.0000.000
18D25VAL00.0860.02911.765-0.053-0.0530.0000.0000.0000.000
19D26GLN0-0.027-0.01912.420-0.067-0.0670.0000.0000.0000.000
20D27THR00.0750.02114.029-0.002-0.0020.0000.0000.0000.000
21D28ALA00.0070.0199.4950.0080.0080.0000.0000.0000.000
22D29ILE0-0.054-0.0018.384-0.038-0.0380.0000.0000.0000.000
23D30ASN0-0.030-0.01410.4360.0620.0620.0000.0000.0000.000
24D31ASN0-0.023-0.03211.6020.0460.0460.0000.0000.0000.000
25D32THR00.0760.0874.942-0.084-0.0840.0000.0000.0000.000
26D33GLY0-0.058-0.0468.1530.1310.1310.0000.0000.0000.000
27D34SER00.012-0.0268.946-0.018-0.0180.0000.0000.0000.000
28D35LYS10.9761.0014.5270.1660.241-0.001-0.002-0.0720.000
29D36TYR0-0.005-0.0082.691-2.307-0.7502.753-1.789-2.522-0.013
30D37GLY00.0460.0236.7380.1600.1600.0000.0000.0000.000
31D38LYS10.9390.9569.5790.2770.2770.0000.0000.0000.000
32D39THR00.0600.01111.170-0.072-0.0720.0000.0000.0000.000
33D40THR00.0050.0005.4450.1160.1160.0000.0000.0000.000
34D41VAL00.0020.0146.696-0.254-0.2540.0000.0000.0000.000
35D42GLN00.0090.0007.756-0.017-0.0170.0000.0000.0000.000
36D43LYS10.8430.9097.0220.4300.4300.0000.0000.0000.000
37D44ALA0-0.0100.0036.1070.0580.0580.0000.0000.0000.000
38D45LEU00.032-0.0058.2270.1160.1160.0000.0000.0000.000
39D46ASP-1-0.848-0.90811.144-0.189-0.1890.0000.0000.0000.000
40D47GLU-1-0.850-0.9078.871-0.254-0.2540.0000.0000.0000.000
41D48LEU0-0.037-0.0229.1520.0600.0600.0000.0000.0000.000
42D49VAL00.0100.00912.6470.0630.0630.0000.0000.0000.000
43D50ALA0-0.038-0.01015.1770.0350.0350.0000.0000.0000.000
44D51GLN0-0.038-0.01911.2500.0360.0360.0000.0000.0000.000
45D52ASN0-0.022-0.00816.4080.0090.0090.0000.0000.0000.000
46D53LEU00.0240.00912.5360.0160.0160.0000.0000.0000.000
47D54CYS0-0.104-0.05213.717-0.056-0.0560.0000.0000.0000.000
48D55ILE00.0110.01516.1210.0240.0240.0000.0000.0000.000
49D56TYR00.0300.02318.330-0.008-0.0080.0000.0000.0000.000
50D65LEU0-0.019-0.00518.422-0.002-0.0020.0000.0000.0000.000
51D66TYR0-0.041-0.05515.0870.0120.0120.0000.0000.0000.000
52D67LEU0-0.033-0.00316.471-0.016-0.0160.0000.0000.0000.000
53D68TRP00.1220.05512.283-0.014-0.0140.0000.0000.0000.000
54D69ASN00.0160.02216.4490.0220.0220.0000.0000.0000.000
55D70GLN0-0.029-0.05319.2570.0270.0270.0000.0000.0000.000
56D71ASN0-0.056-0.02722.0300.0170.0170.0000.0000.0000.000
57D72LEU0-0.044-0.01317.7890.0080.0080.0000.0000.0000.000
58D73LEU0-0.079-0.02819.3580.0140.0140.0000.0000.0000.000
59D74GLU-1-0.916-0.95122.9230.0360.0360.0000.0000.0000.000
60D75VAL0-0.018-0.01226.213-0.003-0.0030.0000.0000.0000.000
61D76LEU0-0.031-0.00529.2510.0030.0030.0000.0000.0000.000
62D77SER00.015-0.00731.906-0.004-0.0040.0000.0000.0000.000
63D78ASP-1-0.887-0.95835.564-0.004-0.0040.0000.0000.0000.000
64D79ALA00.0030.00537.8080.0000.0000.0000.0000.0000.000
65D80GLN00.0510.01533.798-0.001-0.0010.0000.0000.0000.000
66D81LEU00.0140.02732.4730.0020.0020.0000.0000.0000.000
67D82MET00.0230.00735.197-0.001-0.0010.0000.0000.0000.000
68D83GLU-1-0.897-0.94037.1070.0180.0180.0000.0000.0000.000
69D84VAL0-0.0070.00231.3250.0010.0010.0000.0000.0000.000
70D85ASN0-0.059-0.05334.6210.0000.0000.0000.0000.0000.000
71D86ALA00.0320.03836.159-0.001-0.0010.0000.0000.0000.000
72D87GLN00.0100.00133.475-0.001-0.0010.0000.0000.0000.000
73D88ILE00.015-0.00431.2430.0000.0000.0000.0000.0000.000
74D89ASN0-0.112-0.06834.970-0.002-0.0020.0000.0000.0000.000
75D90ASP-1-0.890-0.93838.3810.0200.0200.0000.0000.0000.000
76D91LEU00.0100.00232.6860.0010.0010.0000.0000.0000.000
77D92LYS10.9020.94834.538-0.001-0.0010.0000.0000.0000.000
78D93ALA00.0490.03737.088-0.001-0.0010.0000.0000.0000.000
79D94GLN0-0.077-0.03737.7370.0020.0020.0000.0000.0000.000
80D95VAL0-0.008-0.01234.0710.0000.0000.0000.0000.0000.000
81D96GLU-1-0.863-0.91937.3690.0070.0070.0000.0000.0000.000
82D97LYS10.9070.95840.022-0.021-0.0210.0000.0000.0000.000
83D98LEU0-0.020-0.03037.5730.0000.0000.0000.0000.0000.000
84D99THR00.0030.01337.4010.0000.0000.0000.0000.0000.000
85D100GLN0-0.003-0.00540.0250.0000.0000.0000.0000.0000.000
86D101GLN00.0270.01643.1010.0000.0000.0000.0000.0000.000
87D102GLY00.0460.03241.1010.0000.0000.0000.0000.0000.000
88D103GLU-1-0.866-0.92542.1340.0100.0100.0000.0000.0000.000
89D104THR0-0.069-0.04844.2800.0000.0000.0000.0000.0000.000
90D105LEU0-0.005-0.01143.5360.0000.0000.0000.0000.0000.000
91D106ARG10.9120.95139.526-0.014-0.0140.0000.0000.0000.000
92D107ILE0-0.042-0.00845.315-0.001-0.0010.0000.0000.0000.000
93D108THR0-0.008-0.01349.0260.0000.0000.0000.0000.0000.000
94D109GLN0-0.053-0.01944.1740.0000.0000.0000.0000.0000.000
95D110ARG10.9200.94846.898-0.010-0.0100.0000.0000.0000.000
96D111ASN0-0.039-0.03250.115-0.001-0.0010.0000.0000.0000.000
97D112LEU0-0.041-0.01451.6170.0000.0000.0000.0000.0000.000
98D113GLU-1-0.887-0.93247.4260.0180.0180.0000.0000.0000.000
99D114ALA0-0.077-0.02852.3450.0000.0000.0000.0000.0000.000
100D115ALA0-0.022-0.00355.038-0.001-0.0010.0000.0000.0000.000
101D116PRO00.0290.02856.1780.0010.0010.0000.0000.0000.000
102D117ILE00.016-0.00255.2710.0000.0000.0000.0000.0000.000
103D118THR00.0780.01458.6970.0000.0000.0000.0000.0000.000
104D119GLU-1-0.837-0.91161.1530.0140.0140.0000.0000.0000.000
105D120VAL00.0120.00759.0290.0000.0000.0000.0000.0000.000
106D121LEU00.0070.02862.096-0.001-0.0010.0000.0000.0000.000
107D122LYS10.8200.88563.685-0.014-0.0140.0000.0000.0000.000
108D123GLN0-0.014-0.00564.416-0.001-0.0010.0000.0000.0000.000
109D124GLU-1-0.872-0.93861.1750.0110.0110.0000.0000.0000.000
110D125VAL0-0.024-0.01966.031-0.001-0.0010.0000.0000.0000.000
111D126ASP-1-0.814-0.87869.0770.0100.0100.0000.0000.0000.000
112D127GLU-1-0.968-0.98466.8050.0100.0100.0000.0000.0000.000
113D128LEU00.0170.00366.991-0.001-0.0010.0000.0000.0000.000
114D129ARG10.7690.86270.951-0.010-0.0100.0000.0000.0000.000
115D130GLN0-0.036-0.02273.3740.0000.0000.0000.0000.0000.000
116D131GLN0-0.0310.00069.8520.0000.0000.0000.0000.0000.000
117D132VAL00.007-0.00573.8610.0000.0000.0000.0000.0000.000
118D133SER00.0220.02376.3510.0000.0000.0000.0000.0000.000
119D134ALA00.0460.01977.9000.0000.0000.0000.0000.0000.000
120D135ASN0-0.031-0.03575.2430.0000.0000.0000.0000.0000.000
121D136ASP-1-0.863-0.91579.1640.0050.0050.0000.0000.0000.000
122D137GLU-1-0.853-0.92782.0090.0050.0050.0000.0000.0000.000
123D138LYS10.8370.92177.025-0.006-0.0060.0000.0000.0000.000
124D139LEU00.013-0.00480.4130.0000.0000.0000.0000.0000.000
125D140ARG10.7520.87484.146-0.005-0.0050.0000.0000.0000.000
126D141LEU00.0350.01087.0890.0000.0000.0000.0000.0000.000
127D142VAL0-0.059-0.02184.7220.0000.0000.0000.0000.0000.000
128D143ARG10.9500.96184.392-0.003-0.0030.0000.0000.0000.000
129D144GLU-1-0.879-0.90589.6440.0040.0040.0000.0000.0000.000
130D145SER0-0.032-0.02191.5300.0000.0000.0000.0000.0000.000
131D146ASN0-0.107-0.05289.2950.0000.0000.0000.0000.0000.000
132D147ALA00.0480.02191.0190.0000.0000.0000.0000.0000.000
133D148ILE0-0.068-0.03684.1730.0000.0000.0000.0000.0000.000
134D149VAL0-0.017-0.00186.9570.0000.0000.0000.0000.0000.000
135D150SER0-0.001-0.00183.0370.0000.0000.0000.0000.0000.000
136D151ASP-1-0.830-0.92680.4470.0010.0010.0000.0000.0000.000
137D152ALA0-0.001-0.01183.5120.0000.0000.0000.0000.0000.000
138D153ASP-1-0.836-0.92285.1330.0010.0010.0000.0000.0000.000
139D154MET0-0.0150.00086.8800.0000.0000.0000.0000.0000.000
140D155LEU00.0050.01184.3540.0000.0000.0000.0000.0000.000
141D156THR0-0.050-0.03288.3250.0000.0000.0000.0000.0000.000
142D157LEU00.0010.01391.1340.0000.0000.0000.0000.0000.000
143D158GLN00.012-0.00289.3460.0000.0000.0000.0000.0000.000
144D159LYS10.8490.90492.0900.0000.0000.0000.0000.0000.000
145D160ASN00.0120.00093.9620.0000.0000.0000.0000.0000.000
146D161TYR0-0.007-0.00596.7120.0000.0000.0000.0000.0000.000
147D162LYS10.9000.95395.6740.0010.0010.0000.0000.0000.000
148D163ASP-1-0.820-0.88897.356-0.001-0.0010.0000.0000.0000.000
149D164ALA0-0.0050.00099.7950.0000.0000.0000.0000.0000.000
150D165MET00.0050.011101.3810.0000.0000.0000.0000.0000.000
151D166THR0-0.058-0.053100.4580.0000.0000.0000.0000.0000.000
152D167ALA0-0.006-0.002103.1060.0000.0000.0000.0000.0000.000
153D168TRP00.0370.024105.5600.0000.0000.0000.0000.0000.000
154D169ALA0-0.006-0.011106.1740.0000.0000.0000.0000.0000.000
155D170THR0-0.011-0.019105.9770.0000.0000.0000.0000.0000.000
156D171ARG10.9440.964106.2650.0000.0000.0000.0000.0000.000
157D172ARG10.8340.895111.0660.0000.0000.0000.0000.0000.000
158D173ALA0-0.0140.001111.0840.0000.0000.0000.0000.0000.000
159D174LYS10.8500.904112.6210.0010.0010.0000.0000.0000.000
160D175CYS0-0.048-0.024114.3850.0000.0000.0000.0000.0000.000
161D176ARG10.9070.921116.6320.0010.0010.0000.0000.0000.000
162D177GLU-1-0.796-0.858113.692-0.001-0.0010.0000.0000.0000.000
163D178VAL0-0.034-0.014118.0820.0000.0000.0000.0000.0000.000
164D179ILE0-0.019-0.019120.0270.0000.0000.0000.0000.0000.000
165D180ASP-1-0.806-0.885120.915-0.001-0.0010.0000.0000.0000.000
166D181THR0-0.028-0.005122.2940.0000.0000.0000.0000.0000.000
167D182LEU0-0.040-0.027124.5160.0000.0000.0000.0000.0000.000
168D183SER0-0.005-0.008126.3670.0000.0000.0000.0000.0000.000
169D184GLU-1-0.880-0.949126.468-0.001-0.0010.0000.0000.0000.000
170D185GLY0-0.053-0.015129.1490.0000.0000.0000.0000.0000.000
171D186MET0-0.092-0.038130.9950.0000.0000.0000.0000.0000.000
172D187GLY00.0130.016132.1430.0000.0000.0000.0000.0000.000
173D188VAL0-0.042-0.025131.3790.0000.0000.0000.0000.0000.000
174D189LYS10.9970.991128.7300.0000.0000.0000.0000.0000.000
175D190PRO00.0710.041124.0230.0000.0000.0000.0000.0000.000
176D191SER0-0.058-0.038125.1840.0000.0000.0000.0000.0000.000
177D192ALA0-0.012-0.003126.1410.0000.0000.0000.0000.0000.000
178D193PHE00.0690.017125.3880.0000.0000.0000.0000.0000.000
179D194MET0-0.042-0.025121.5390.0000.0000.0000.0000.0000.000
180D195ASP-1-0.864-0.922125.9400.0000.0000.0000.0000.0000.000
181D196GLN0-0.129-0.053128.1030.0000.0000.0000.0000.0000.000
182D197LEU0-0.056-0.046126.1260.0000.0000.0000.0000.0000.000
183D198GLY00.0060.023126.2970.0000.0000.0000.0000.0000.000
184D199LEU0-0.077-0.034121.3170.0000.0000.0000.0000.0000.000
185D200GLU-1-0.913-0.950119.1560.0000.0000.0000.0000.0000.000
186D201GLU-1-0.849-0.906116.2690.0000.0000.0000.0000.0000.000
187D202GLY00.0200.017116.2360.0000.0000.0000.0000.0000.000
188D203LEU0-0.027-0.015110.4280.0000.0000.0000.0000.0000.000
189D204PRO00.0300.039113.7830.0000.0000.0000.0000.0000.000
190D205MET00.014-0.023109.3410.0000.0000.0000.0000.0000.000
191D206THR00.0300.009110.4780.0000.0000.0000.0000.0000.000
192D207THR00.0720.015109.4860.0000.0000.0000.0000.0000.000
193D208TYR00.0460.047104.9560.0000.0000.0000.0000.0000.000
194D209THR0-0.018-0.012105.7240.0000.0000.0000.0000.0000.000
195D210GLU-1-0.925-0.959105.1240.0000.0000.0000.0000.0000.000
196D211MET0-0.015-0.023103.8420.0000.0000.0000.0000.0000.000
197D212LYS10.9150.966101.0230.0010.0010.0000.0000.0000.000
198D213LYS10.8470.93099.9820.0000.0000.0000.0000.0000.000
199D214ALA0-0.034-0.01999.1120.0000.0000.0000.0000.0000.000
200D215LEU00.0280.01994.7840.0000.0000.0000.0000.0000.000
201D216PRO00.0400.04095.0800.0000.0000.0000.0000.0000.000
202D217PRO0-0.026-0.02195.7230.0000.0000.0000.0000.0000.000
203D218VAL00.0340.03689.9820.0000.0000.0000.0000.0000.000
204D219ASN0-0.015-0.01491.4260.0000.0000.0000.0000.0000.000
205D220VAL00.0570.02887.8270.0000.0000.0000.0000.0000.000
206D221SER0-0.032-0.03286.7720.0000.0000.0000.0000.0000.000
207D222LYS10.8460.94985.8310.0000.0000.0000.0000.0000.000
208D223ALA00.014-0.01083.9740.0000.0000.0000.0000.0000.000
209D224ASP-1-0.868-0.92779.9720.0000.0000.0000.0000.0000.000
210D225ILE00.0100.01879.4380.0000.0000.0000.0000.0000.000