FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 6NZ3Z

Calculation Name: 4YB9-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YB9

Chain ID: D

ChEMBL ID:

UniProt ID: P58353

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 437
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7782527.620408
FMO2-HF: Nuclear repulsion 7615147.85446
FMO2-HF: Total energy -167379.765948
FMO2-MP2: Total energy -167867.43729


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:19:LEU)


Summations of interaction energy for fragment #1(D:19:LEU)
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.
-4.0660.3170.69-1.93-3.143-0.002
Interaction energy analysis for fragmet #1(D:19:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / 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].
3D21THR00.0210.0063.072-4.187-1.6190.065-1.213-1.420-0.001
4D22LEU0-0.005-0.0032.550-1.1350.1810.625-0.560-1.381-0.001
5D23ILE0-0.012-0.0084.0710.1760.6750.000-0.157-0.3420.000
6D24ALA00.0260.0126.0450.2820.2820.0000.0000.0000.000
7D25ALA0-0.0150.0087.5210.1400.1400.0000.0000.0000.000
8D26PHE0-0.018-0.0037.5670.0910.0910.0000.0000.0000.000
9D27GLY00.0420.01611.3000.0320.0320.0000.0000.0000.000
10D28SER0-0.003-0.01812.7320.0290.0290.0000.0000.0000.000
11D29SER0-0.0030.00115.2650.0100.0100.0000.0000.0000.000
12D30PHE00.0260.02514.6990.0120.0120.0000.0000.0000.000
13D31GLN00.0060.01916.5350.0220.0220.0000.0000.0000.000
14D32TYR00.0020.00318.9240.0140.0140.0000.0000.0000.000
15D33GLY00.0330.00619.9680.0080.0080.0000.0000.0000.000
16D34TYR0-0.054-0.02919.8270.0070.0070.0000.0000.0000.000
17D35ASN0-0.020-0.03821.7190.0110.0110.0000.0000.0000.000
18D36VAL0-0.0520.00024.4310.0020.0020.0000.0000.0000.000
19D37ALA00.0360.01624.6310.0030.0030.0000.0000.0000.000
20D38ALA0-0.025-0.00824.9940.0040.0040.0000.0000.0000.000
21D39ILE0-0.027-0.00926.8570.0040.0040.0000.0000.0000.000
22D40ASN00.005-0.01029.640-0.001-0.0010.0000.0000.0000.000
23D41SER0-0.0160.00129.9940.0000.0000.0000.0000.0000.000
24D42PRO00.0200.01330.1370.0010.0010.0000.0000.0000.000
25D43SER0-0.053-0.03733.0880.0000.0000.0000.0000.0000.000
26D44GLU-1-0.966-0.97435.6820.0120.0120.0000.0000.0000.000
27D45PHE00.0930.04234.8770.0000.0000.0000.0000.0000.000
28D46MET0-0.052-0.01333.7810.0000.0000.0000.0000.0000.000
29D47LYS10.8860.94537.828-0.005-0.0050.0000.0000.0000.000
30D48ASP-1-0.831-0.91240.9730.0140.0140.0000.0000.0000.000
31D49PHE0-0.026-0.00239.437-0.001-0.0010.0000.0000.0000.000
32D50TYR0-0.047-0.05837.2470.0000.0000.0000.0000.0000.000
33D51ALA00.0160.00842.607-0.001-0.0010.0000.0000.0000.000
34D52TYR00.0500.02042.2510.0000.0000.0000.0000.0000.000
35D53THR0-0.048-0.02542.9360.0000.0000.0000.0000.0000.000
36D54TYR0-0.074-0.03445.581-0.001-0.0010.0000.0000.0000.000
37D55TYR00.0900.04548.1870.0000.0000.0000.0000.0000.000
38D56ASP-1-0.902-0.94747.9360.0170.0170.0000.0000.0000.000
39D57ARG10.7430.85644.458-0.017-0.0170.0000.0000.0000.000
40D58VAL0-0.044-0.00750.876-0.001-0.0010.0000.0000.0000.000
41D59GLY0-0.0300.00153.491-0.001-0.0010.0000.0000.0000.000
42D60GLU-1-0.963-0.98355.4880.0050.0050.0000.0000.0000.000
43D61TYR00.027-0.00451.5760.0000.0000.0000.0000.0000.000
44D62MET0-0.0500.00145.041-0.001-0.0010.0000.0000.0000.000
45D63ASN00.0290.00750.540-0.001-0.0010.0000.0000.0000.000
46D64GLU-1-0.807-0.91149.0870.0040.0040.0000.0000.0000.000
47D65PHE0-0.0260.00047.842-0.001-0.0010.0000.0000.0000.000
48D66TYR0-0.005-0.01447.366-0.001-0.0010.0000.0000.0000.000
49D67LEU00.0600.02743.5650.0000.0000.0000.0000.0000.000
50D68THR0-0.015-0.00743.3730.0000.0000.0000.0000.0000.000
51D69LEU0-0.045-0.00442.620-0.001-0.0010.0000.0000.0000.000
52D70LEU00.0270.00841.510-0.001-0.0010.0000.0000.0000.000
53D71TRP00.0420.01834.4120.0000.0000.0000.0000.0000.000
54D72SER00.023-0.00737.899-0.001-0.0010.0000.0000.0000.000
55D73VAL0-0.043-0.00238.015-0.002-0.0020.0000.0000.0000.000
56D74THR0-0.0070.01734.647-0.001-0.0010.0000.0000.0000.000
57D75VAL00.0060.02833.039-0.001-0.0010.0000.0000.0000.000
58D76SER0-0.017-0.03433.004-0.003-0.0030.0000.0000.0000.000
59D77MET00.023-0.01234.359-0.004-0.0040.0000.0000.0000.000
60D78PHE00.0040.03224.732-0.002-0.0020.0000.0000.0000.000
61D79PRO0-0.022-0.00329.786-0.004-0.0040.0000.0000.0000.000
62D80PHE0-0.0020.00030.798-0.003-0.0030.0000.0000.0000.000
63D81GLY00.0280.00530.929-0.001-0.0010.0000.0000.0000.000
64D82GLY00.0210.00527.933-0.003-0.0030.0000.0000.0000.000
65D83PHE00.001-0.01528.883-0.005-0.0050.0000.0000.0000.000
66D84LEU0-0.0020.01031.470-0.003-0.0030.0000.0000.0000.000
67D85GLY00.0400.00828.1250.0000.0000.0000.0000.0000.000
68D86SER0-0.088-0.03927.151-0.005-0.0050.0000.0000.0000.000
69D87LEU0-0.029-0.02028.171-0.004-0.0040.0000.0000.0000.000
70D88MET0-0.026-0.00728.9530.0000.0000.0000.0000.0000.000
71D89VAL00.0280.01024.421-0.001-0.0010.0000.0000.0000.000
72D90GLY0-0.0110.00427.187-0.002-0.0020.0000.0000.0000.000
73D91PRO00.0110.00329.689-0.002-0.0020.0000.0000.0000.000
74D92LEU00.0460.04026.2000.0010.0010.0000.0000.0000.000
75D93VAL00.0310.01523.210-0.001-0.0010.0000.0000.0000.000
76D94ASN0-0.077-0.03525.119-0.010-0.0100.0000.0000.0000.000
77D95ASN0-0.034-0.01427.6430.0040.0040.0000.0000.0000.000
78D96LEU00.0270.02124.2620.0010.0010.0000.0000.0000.000
79D97GLY00.0550.03522.597-0.002-0.0020.0000.0000.0000.000
80D98ARG10.7520.83018.8110.1070.1070.0000.0000.0000.000
81D99LYS10.8450.90513.8690.1040.1040.0000.0000.0000.000
82D100GLY00.0620.04017.6780.0110.0110.0000.0000.0000.000
83D101THR0-0.023-0.02820.6770.0130.0130.0000.0000.0000.000
84D102LEU00.0130.01115.3610.0060.0060.0000.0000.0000.000
85D103LEU00.0060.00715.6540.0110.0110.0000.0000.0000.000
86D104PHE00.0000.00219.0110.0130.0130.0000.0000.0000.000
87D105ASN00.035-0.00420.123-0.003-0.0030.0000.0000.0000.000
88D106ASN0-0.016-0.01416.5790.0150.0150.0000.0000.0000.000
89D107ILE00.007-0.01020.1070.0130.0130.0000.0000.0000.000
90D108PHE0-0.046-0.01422.5350.0050.0050.0000.0000.0000.000
91D109SER00.025-0.02421.6500.0000.0000.0000.0000.0000.000
92D110ILE0-0.019-0.00620.5680.0050.0050.0000.0000.0000.000
93D111VAL00.0160.02224.4320.0040.0040.0000.0000.0000.000
94D112PRO00.0020.00426.3410.0020.0020.0000.0000.0000.000
95D113ALA0-0.0080.00724.3070.0010.0010.0000.0000.0000.000
96D114LEU00.0070.00026.3710.0040.0040.0000.0000.0000.000
97D115LEU0-0.036-0.01428.6510.0000.0000.0000.0000.0000.000
98D116MET0-0.025-0.02227.308-0.002-0.0020.0000.0000.0000.000
99D117GLY0-0.0090.00229.2690.0010.0010.0000.0000.0000.000
100D118PHE00.0040.00230.0490.0030.0030.0000.0000.0000.000
101D119SER00.000-0.01733.391-0.003-0.0030.0000.0000.0000.000
102D120GLU-1-0.937-0.96134.5570.0430.0430.0000.0000.0000.000
103D121LEU0-0.023-0.00836.306-0.001-0.0010.0000.0000.0000.000
104D122ALA0-0.042-0.01039.131-0.001-0.0010.0000.0000.0000.000
105D123LYS10.9490.95839.787-0.013-0.0130.0000.0000.0000.000
106D124SER00.0800.05437.9000.0000.0000.0000.0000.0000.000
107D125PHE0-0.025-0.03638.289-0.002-0.0020.0000.0000.0000.000
108D126GLU-1-0.952-0.95937.4770.0110.0110.0000.0000.0000.000
109D127MET0-0.005-0.01035.053-0.001-0.0010.0000.0000.0000.000
110D128ILE00.0520.04533.2730.0010.0010.0000.0000.0000.000
111D129ILE0-0.0130.00033.908-0.003-0.0030.0000.0000.0000.000
112D130VAL0-0.004-0.01334.804-0.003-0.0030.0000.0000.0000.000
113D131ALA00.0110.01530.636-0.002-0.0020.0000.0000.0000.000
114D132ARG10.8630.91228.4950.0050.0050.0000.0000.0000.000
115D133VAL00.0080.01330.284-0.005-0.0050.0000.0000.0000.000
116D134LEU0-0.012-0.00329.521-0.005-0.0050.0000.0000.0000.000
117D135VAL00.0510.01324.579-0.004-0.0040.0000.0000.0000.000
118D136GLY00.0320.01225.644-0.007-0.0070.0000.0000.0000.000
119D137ILE0-0.059-0.01927.011-0.008-0.0080.0000.0000.0000.000
120D138CYS0-0.043-0.01122.903-0.008-0.0080.0000.0000.0000.000
121D139ALA00.0540.04922.284-0.012-0.0120.0000.0000.0000.000
122D140GLY0-0.0050.01222.964-0.012-0.0120.0000.0000.0000.000
123D141LEU0-0.0320.00223.409-0.008-0.0080.0000.0000.0000.000
124D142SER0-0.036-0.04318.869-0.014-0.0140.0000.0000.0000.000
125D143SER0-0.017-0.02619.532-0.021-0.0210.0000.0000.0000.000
126D144ASN0-0.056-0.02321.119-0.005-0.0050.0000.0000.0000.000
127D145VAL0-0.010-0.01518.984-0.010-0.0100.0000.0000.0000.000
128D146VAL00.0220.01714.228-0.015-0.0150.0000.0000.0000.000
129D147PRO00.0190.01015.919-0.029-0.0290.0000.0000.0000.000
130D148MET0-0.035-0.00117.595-0.003-0.0030.0000.0000.0000.000
131D149TYR0-0.027-0.04412.509-0.008-0.0080.0000.0000.0000.000
132D150LEU00.0220.00010.184-0.016-0.0160.0000.0000.0000.000
133D151GLY00.0150.01314.245-0.014-0.0140.0000.0000.0000.000
134D152GLU-1-0.814-0.87617.378-0.117-0.1170.0000.0000.0000.000
135D153LEU0-0.043-0.02312.5300.0090.0090.0000.0000.0000.000
136D154ALA0-0.0040.02813.393-0.014-0.0140.0000.0000.0000.000
137D155PRO00.0360.02113.2960.0360.0360.0000.0000.0000.000
138D156LYS10.8210.88416.2990.1160.1160.0000.0000.0000.000
139D157ASN0-0.008-0.01318.9900.0040.0040.0000.0000.0000.000
140D158TRP0-0.031-0.0069.215-0.001-0.0010.0000.0000.0000.000
141D159ARG10.9260.95815.0040.1700.1700.0000.0000.0000.000
142D160GLY00.0330.00616.194-0.012-0.0120.0000.0000.0000.000
143D161ALA00.0450.03012.9250.0070.0070.0000.0000.0000.000
144D162LEU0-0.002-0.00113.742-0.020-0.0200.0000.0000.0000.000
145D163GLY0-0.002-0.00414.6570.0100.0100.0000.0000.0000.000
146D164VAL00.0340.01016.6210.0190.0190.0000.0000.0000.000
147D165VAL0-0.0060.01510.9340.0040.0040.0000.0000.0000.000
148D166PRO00.0090.00113.9490.0000.0000.0000.0000.0000.000
149D167GLN00.0400.01415.2480.0220.0220.0000.0000.0000.000
150D168LEU00.0270.00712.6870.0170.0170.0000.0000.0000.000
151D169PHE00.002-0.0108.8680.0040.0040.0000.0000.0000.000
152D170ILE0-0.0060.00914.8140.0290.0290.0000.0000.0000.000
153D171THR00.007-0.00318.4730.0150.0150.0000.0000.0000.000
154D172ILE00.0250.00612.8710.0170.0170.0000.0000.0000.000
155D173GLY00.0090.00016.8800.0220.0220.0000.0000.0000.000
156D174ILE0-0.038-0.01618.6030.0160.0160.0000.0000.0000.000
157D175LEU00.0110.00918.1080.0090.0090.0000.0000.0000.000
158D176VAL0-0.018-0.01716.3630.0130.0130.0000.0000.0000.000
159D177ALA00.0230.00319.7500.0120.0120.0000.0000.0000.000
160D178GLN0-0.006-0.00722.9420.0020.0020.0000.0000.0000.000
161D179ILE0-0.015-0.00919.3870.0040.0040.0000.0000.0000.000
162D180PHE0-0.022-0.01919.4150.0110.0110.0000.0000.0000.000
163D181GLY00.000-0.00424.4630.0020.0020.0000.0000.0000.000
164D182LEU00.0080.01026.974-0.005-0.0050.0000.0000.0000.000
165D183ARG10.8300.87628.779-0.015-0.0150.0000.0000.0000.000
166D184SER0-0.037-0.01230.2240.0010.0010.0000.0000.0000.000
167D185LEU0-0.081-0.03624.6270.0070.0070.0000.0000.0000.000
168D186LEU0-0.026-0.00625.5220.0030.0030.0000.0000.0000.000
169D187ALA0-0.049-0.00929.494-0.003-0.0030.0000.0000.0000.000
170D188ASN00.0550.01431.839-0.001-0.0010.0000.0000.0000.000
171D189GLU-1-0.871-0.94834.9140.0290.0290.0000.0000.0000.000
172D190GLU-1-0.935-0.97334.6730.0410.0410.0000.0000.0000.000
173D191GLY00.0220.01631.6190.0040.0040.0000.0000.0000.000
174D192TRP00.007-0.00230.4620.0020.0020.0000.0000.0000.000
175D193PRO00.0250.01130.646-0.001-0.0010.0000.0000.0000.000
176D194ILE0-0.008-0.00126.3180.0020.0020.0000.0000.0000.000
177D195LEU0-0.0190.01225.5010.0040.0040.0000.0000.0000.000
178D196LEU00.0090.00425.659-0.003-0.0030.0000.0000.0000.000
179D197GLY00.0310.01425.837-0.003-0.0030.0000.0000.0000.000
180D198LEU0-0.005-0.00120.9350.0070.0070.0000.0000.0000.000
181D199THR00.0130.00720.9900.0020.0020.0000.0000.0000.000
182D200GLY0-0.006-0.01020.649-0.008-0.0080.0000.0000.0000.000
183D201ILE0-0.021-0.00116.8430.0100.0100.0000.0000.0000.000
184D202PRO0-0.009-0.01015.0780.0210.0210.0000.0000.0000.000
185D203ALA00.0150.01814.988-0.011-0.0110.0000.0000.0000.000
186D204VAL00.016-0.00616.385-0.004-0.0040.0000.0000.0000.000
187D205LEU0-0.0110.00510.2130.0230.0230.0000.0000.0000.000
188D206GLN0-0.007-0.00311.6960.0470.0470.0000.0000.0000.000
189D207LEU0-0.033-0.03112.558-0.022-0.0220.0000.0000.0000.000
190D208LEU0-0.0150.01112.4130.0000.0000.0000.0000.0000.000
191D209PHE0-0.015-0.0227.8120.0840.0840.0000.0000.0000.000
192D210LEU0-0.0020.0089.893-0.072-0.0720.0000.0000.0000.000
193D211PRO00.0120.00311.565-0.036-0.0360.0000.0000.0000.000
194D212PHE00.0330.0366.966-0.018-0.0180.0000.0000.0000.000
195D213PHE0-0.0060.0064.918-0.050-0.0500.0000.0000.0000.000
196D214PRO0-0.009-0.00110.4260.0550.0550.0000.0000.0000.000
197D215GLU-1-0.802-0.87713.576-0.091-0.0910.0000.0000.0000.000
198D216SER0-0.021-0.03816.745-0.019-0.0190.0000.0000.0000.000
199D217PRO00.0360.00217.8070.0180.0180.0000.0000.0000.000
200D218ARG10.7970.89220.9960.1140.1140.0000.0000.0000.000
201D219TYR0-0.025-0.02022.2400.0090.0090.0000.0000.0000.000
202D220LEU00.0210.00220.6140.0100.0100.0000.0000.0000.000
203D221LEU00.0320.01824.4150.0090.0090.0000.0000.0000.000
204D222ILE0-0.064-0.01126.8400.0070.0070.0000.0000.0000.000
205D223GLN0-0.066-0.04727.1010.0050.0050.0000.0000.0000.000
206D224LYS10.8410.90826.2330.0460.0460.0000.0000.0000.000
207D225LYS10.8540.93628.5060.0540.0540.0000.0000.0000.000
208D226ASP-1-0.819-0.88325.914-0.042-0.0420.0000.0000.0000.000
209D227GLU-1-0.818-0.90025.846-0.064-0.0640.0000.0000.0000.000
210D228ALA00.002-0.00325.539-0.007-0.0070.0000.0000.0000.000
211D229ALA00.0180.02822.470-0.004-0.0040.0000.0000.0000.000
212D230ALA00.0120.00821.025-0.012-0.0120.0000.0000.0000.000
213D231LYS10.8610.91320.8150.0570.0570.0000.0000.0000.000
214D232SER0-0.064-0.04619.911-0.010-0.0100.0000.0000.0000.000
215D233ALA0-0.021-0.01116.679-0.011-0.0110.0000.0000.0000.000
216D234LEU00.0090.00416.017-0.028-0.0280.0000.0000.0000.000
217D235ARG10.9330.96516.2570.0880.0880.0000.0000.0000.000
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219D237LEU0-0.0190.01210.055-0.059-0.0590.0000.0000.0000.000
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