Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QYV8Y

Calculation Name: 5N9J-Y-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: Y

ChEMBL ID:

UniProt ID: P87310

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2074690.541992
FMO2-HF: Nuclear repulsion 2000384.704831
FMO2-HF: Total energy -74305.83716
FMO2-MP2: Total energy -74525.332891


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(Y:2:PRO)


Summations of interaction energy for fragment #1(Y:2:PRO)
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.
-18.499-3.64414.689-13.198-16.348-0.077
Interaction energy analysis for fragmet #1(Y:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.037
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].
3Y4HIS00.0320.0002.306-2.4072.0261.343-2.416-3.3610.007
4Y5GLY0-0.031-0.0135.393-0.0490.003-0.001-0.004-0.0460.000
5Y6VAL0-0.044-0.0149.0670.0570.0570.0000.0000.0000.000
6Y7ILE00.0320.01211.6940.0170.0170.0000.0000.0000.000
7Y8TYR0-0.006-0.01815.0060.0130.0130.0000.0000.0000.000
8Y9TYR00.0760.02918.2150.0000.0000.0000.0000.0000.000
9Y10SER00.002-0.00921.7130.0030.0030.0000.0000.0000.000
10Y11SER00.0220.01425.1170.0050.0050.0000.0000.0000.000
11Y12PRO00.0330.01027.090-0.001-0.0010.0000.0000.0000.000
12Y13SER00.0110.00128.1900.0010.0010.0000.0000.0000.000
13Y14MET00.005-0.00721.1560.0050.0050.0000.0000.0000.000
14Y15ALA00.0260.00324.6710.0000.0000.0000.0000.0000.000
15Y16THR0-0.069-0.04026.4430.0010.0010.0000.0000.0000.000
16Y17PHE00.0140.01720.3310.0040.0040.0000.0000.0000.000
17Y18LEU00.0260.02720.0720.0020.0020.0000.0000.0000.000
18Y19SER00.0040.00722.4870.0020.0020.0000.0000.0000.000
19Y20PRO00.0150.00524.2800.0020.0020.0000.0000.0000.000
20Y21ALA00.0050.01520.4620.0010.0010.0000.0000.0000.000
21Y22GLN00.0160.00619.0010.0070.0070.0000.0000.0000.000
22Y23ASP-1-0.857-0.91920.691-0.023-0.0230.0000.0000.0000.000
23Y24ASN0-0.033-0.02922.0890.0080.0080.0000.0000.0000.000
24Y25LEU0-0.0110.02415.1720.0020.0020.0000.0000.0000.000
25Y26VAL0-0.010-0.01619.5570.0040.0040.0000.0000.0000.000
26Y27ARG10.9280.96720.6310.0230.0230.0000.0000.0000.000
27Y28THR0-0.088-0.06922.2920.0020.0020.0000.0000.0000.000
28Y29TYR00.0320.01317.502-0.001-0.0010.0000.0000.0000.000
29Y30PHE0-0.044-0.00717.9650.0030.0030.0000.0000.0000.000
30Y31ALA0-0.0080.01016.1620.0060.0060.0000.0000.0000.000
31Y32GLN00.0200.01514.1850.0090.0090.0000.0000.0000.000
32Y33HIS00.0130.00115.429-0.009-0.0090.0000.0000.0000.000
33Y34LEU0-0.014-0.00511.7040.0110.0110.0000.0000.0000.000
34Y35LYS10.8960.95310.349-0.105-0.1050.0000.0000.0000.000
35Y36LYS11.0010.98815.7260.0040.0040.0000.0000.0000.000
36Y37TRP0-0.047-0.02713.1610.0050.0050.0000.0000.0000.000
37Y38VAL00.0660.01116.578-0.002-0.0020.0000.0000.0000.000
38Y39VAL0-0.028-0.01015.7660.0010.0010.0000.0000.0000.000
39Y40GLN0-0.0010.00519.1080.0010.0010.0000.0000.0000.000
40Y41TYR00.0130.01121.911-0.002-0.0020.0000.0000.0000.000
41Y42LYS10.8450.91023.5720.0370.0370.0000.0000.0000.000
42Y43LEU0-0.028-0.01326.849-0.003-0.0030.0000.0000.0000.000
43Y44TYR0-0.104-0.07529.1100.0030.0030.0000.0000.0000.000
44Y45ARG10.9700.97832.1240.0400.0400.0000.0000.0000.000
45Y46ASN00.0220.03334.7690.0020.0020.0000.0000.0000.000
46Y47ALA00.0470.01137.752-0.002-0.0020.0000.0000.0000.000
47Y48VAL0-0.0030.00439.2340.0000.0000.0000.0000.0000.000
48Y49THR0-0.093-0.04737.841-0.002-0.0020.0000.0000.0000.000
49Y50PRO00.0030.03634.321-0.003-0.0030.0000.0000.0000.000
50Y51LYS10.8630.90029.2750.0710.0710.0000.0000.0000.000
51Y52THR00.0080.02628.9580.0020.0020.0000.0000.0000.000
52Y53LEU00.009-0.01123.8140.0000.0000.0000.0000.0000.000
53Y54GLU-1-0.755-0.84424.006-0.038-0.0380.0000.0000.0000.000
54Y55PHE0-0.033-0.02815.806-0.006-0.0060.0000.0000.0000.000
55Y56LEU00.0190.02120.0300.0010.0010.0000.0000.0000.000
56Y57LYS10.8800.95911.1980.1930.1930.0000.0000.0000.000
57Y58GLN00.0660.02216.7850.0010.0010.0000.0000.0000.000
58Y59ASN0-0.031-0.00811.8560.0230.0230.0000.0000.0000.000
59Y60ILE0-0.023-0.02713.1880.0190.0190.0000.0000.0000.000
60Y61ASN00.0120.00915.683-0.006-0.0060.0000.0000.0000.000
61Y62PRO00.000-0.01018.114-0.004-0.0040.0000.0000.0000.000
62Y63SER0-0.0210.02017.1120.0040.0040.0000.0000.0000.000
63Y64MET0-0.0010.01418.557-0.010-0.0100.0000.0000.0000.000
64Y65LEU0-0.037-0.02215.816-0.005-0.0050.0000.0000.0000.000
65Y66ALA00.0140.00220.366-0.005-0.0050.0000.0000.0000.000
66Y67CYS0-0.018-0.00822.927-0.001-0.0010.0000.0000.0000.000
67Y68VAL00.004-0.00724.9140.0020.0020.0000.0000.0000.000
68Y69ASP-1-0.808-0.93527.641-0.061-0.0610.0000.0000.0000.000
69Y70GLU-1-0.973-0.99826.180-0.087-0.0870.0000.0000.0000.000
70Y71ALA0-0.0090.01224.897-0.008-0.0080.0000.0000.0000.000
71Y72THR00.0180.01324.523-0.004-0.0040.0000.0000.0000.000
72Y73MET00.008-0.01318.686-0.004-0.0040.0000.0000.0000.000
73Y74ILE0-0.052-0.01222.4930.0030.0030.0000.0000.0000.000
74Y75ASP-1-0.844-0.91017.856-0.054-0.0540.0000.0000.0000.000
75Y76ALA0-0.019-0.00521.4250.0080.0080.0000.0000.0000.000
76Y77GLU-1-0.864-0.94123.3400.0100.0100.0000.0000.0000.000
77Y78PRO00.054-0.00724.294-0.005-0.0050.0000.0000.0000.000
78Y79GLU-1-0.873-0.92226.926-0.002-0.0020.0000.0000.0000.000
79Y80LEU0-0.015-0.00127.710-0.001-0.0010.0000.0000.0000.000
80Y81GLU-1-0.744-0.85927.526-0.030-0.0300.0000.0000.0000.000
81Y82ASP-1-0.886-0.94230.175-0.012-0.0120.0000.0000.0000.000
82Y83ILE0-0.049-0.02332.7770.0000.0000.0000.0000.0000.000
83Y84ILE00.0060.00130.6560.0000.0000.0000.0000.0000.000
84Y85VAL0-0.0090.00233.607-0.001-0.0010.0000.0000.0000.000
85Y86ARG10.9040.94636.1690.0070.0070.0000.0000.0000.000
86Y87THR0-0.056-0.02337.3580.0000.0000.0000.0000.0000.000
87Y88LYS10.9140.96538.9810.0130.0130.0000.0000.0000.000
88Y89LEU00.0140.00438.678-0.001-0.0010.0000.0000.0000.000
89Y90TRP00.028-0.00333.2740.0000.0000.0000.0000.0000.000
90Y91ASN0-0.0050.01536.7720.0020.0020.0000.0000.0000.000
91Y92PHE00.025-0.00335.691-0.001-0.0010.0000.0000.0000.000
92Y93ARG10.7810.87029.3780.0280.0280.0000.0000.0000.000
93Y94GLN0-0.003-0.00130.2730.0040.0040.0000.0000.0000.000
94Y95SER0-0.053-0.01527.846-0.002-0.0020.0000.0000.0000.000
95Y96PHE0-0.010-0.01423.8030.0010.0010.0000.0000.0000.000
96Y97THR0-0.051-0.03022.7840.0030.0030.0000.0000.0000.000
97Y98ILE00.0120.00617.265-0.005-0.0050.0000.0000.0000.000
98Y99GLU-1-0.865-0.92119.874-0.041-0.0410.0000.0000.0000.000
99Y100GLY00.0460.00218.320-0.005-0.0050.0000.0000.0000.000
100Y101SER0-0.122-0.05416.9110.0140.0140.0000.0000.0000.000
101Y102ILE0-0.0210.00510.878-0.012-0.0120.0000.0000.0000.000
102Y103TYR0-0.017-0.02513.0590.0190.0190.0000.0000.0000.000
103Y104GLU-1-0.819-0.89810.0380.1040.1040.0000.0000.0000.000
104Y105VAL00.003-0.02011.1130.0050.0050.0000.0000.0000.000
105Y106GLY00.0370.02111.250-0.013-0.0130.0000.0000.0000.000
106Y107SER00.0090.0138.6650.0140.0140.0000.0000.0000.000
107Y108PHE00.0210.0006.493-0.024-0.0240.0000.0000.0000.000
108Y109LYS10.8160.9126.346-0.135-0.1350.0000.0000.0000.000
109Y110VAL00.0020.0027.717-0.058-0.0580.0000.0000.0000.000
110Y111ALA0-0.014-0.00710.4380.0360.0360.0000.0000.0000.000
111Y112ILE0-0.0080.01012.672-0.023-0.0230.0000.0000.0000.000
112Y113ALA00.021-0.00816.2570.0170.0170.0000.0000.0000.000
113Y114ASN00.0340.02118.302-0.011-0.0110.0000.0000.0000.000
114Y115VAL00.0070.00519.7390.0000.0000.0000.0000.0000.000
115Y116LEU0-0.076-0.02022.3270.0050.0050.0000.0000.0000.000
116Y117GLN00.0910.04225.650-0.003-0.0030.0000.0000.0000.000
117Y118LYS10.9560.97128.4140.0350.0350.0000.0000.0000.000
118Y119SER00.0200.00629.0210.0030.0030.0000.0000.0000.000
119Y120VAL0-0.0190.01030.0330.0000.0000.0000.0000.0000.000
120Y121TRP0-0.009-0.01424.8530.0020.0020.0000.0000.0000.000
121Y122LYS10.9740.98825.7450.0530.0530.0000.0000.0000.000
122Y123GLY00.0380.05024.078-0.001-0.0010.0000.0000.0000.000
123Y124ILE0-0.0140.01118.762-0.002-0.0020.0000.0000.0000.000
124Y125LEU0-0.036-0.01413.662-0.011-0.0110.0000.0000.0000.000
125Y126PHE00.016-0.01113.7030.0180.0180.0000.0000.0000.000
126Y127HIS0-0.016-0.0246.6850.0290.0290.0000.0000.0000.000
127Y128VAL00.0290.0207.3720.0660.0660.0000.0000.0000.000
128Y129THR0-0.025-0.0033.090-0.776-0.1630.066-0.170-0.5080.001
129Y130TYR0-0.007-0.0163.473-0.3280.2070.013-0.122-0.426-0.001
130Y131ASP-1-0.930-0.9612.752-2.198-0.0510.719-1.188-1.678-0.011
131Y132GLY00.0330.0083.212-0.3030.0040.025-0.053-0.280-0.001
132Y133THR0-0.025-0.0174.205-0.1950.1240.000-0.039-0.2800.000
133Y134GLU-1-0.843-0.9112.355-3.652-0.9254.713-4.129-3.312-0.043
134Y135SER00.0110.0194.675-0.203-0.177-0.001-0.011-0.0140.000
135Y136VAL00.035-0.0087.802-0.012-0.0120.0000.0000.0000.000
136Y137ASP-1-0.860-0.9179.065-0.260-0.2600.0000.0000.0000.000
137Y138LEU0-0.010-0.0069.8360.0350.0350.0000.0000.0000.000
138Y139ALA00.0200.0116.4500.0240.0240.0000.0000.0000.000
139Y140ARG10.8730.9448.3920.3820.3820.0000.0000.0000.000
140Y141PRO00.002-0.01411.1450.0270.0270.0000.0000.0000.000
141Y142ILE00.0370.0329.6850.0290.0290.0000.0000.0000.000
142Y143ILE0-0.008-0.0116.4540.0210.0210.0000.0000.0000.000
143Y144GLN0-0.035-0.01810.6240.0330.0330.0000.0000.0000.000
144Y145GLU-1-0.853-0.90314.145-0.070-0.0700.0000.0000.0000.000
145Y146PHE00.0490.01211.1070.0190.0190.0000.0000.0000.000
146Y147PHE0-0.015-0.01713.4940.0150.0150.0000.0000.0000.000
147Y148LEU0-0.019-0.01115.0710.0160.0160.0000.0000.0000.000
148Y149LYS10.8600.91716.8700.0880.0880.0000.0000.0000.000
149Y150CYS0-0.105-0.05416.3150.0120.0120.0000.0000.0000.000
150Y151PHE0-0.036-0.01314.9350.0080.0080.0000.0000.0000.000
151Y152LEU00.0230.01920.3020.0000.0000.0000.0000.0000.000
152Y153GLN0-0.075-0.03722.866-0.001-0.0010.0000.0000.0000.000
153Y154ASN00.028-0.00124.7390.0060.0060.0000.0000.0000.000
154Y155ASN00.0300.03220.006-0.001-0.0010.0000.0000.0000.000
155Y156LYS10.9580.97623.7520.0510.0510.0000.0000.0000.000
156Y157SER0-0.025-0.01326.8440.0000.0000.0000.0000.0000.000
157Y158VAL0-0.043-0.01624.0130.0030.0030.0000.0000.0000.000
158Y159THR00.0230.01423.154-0.002-0.0020.0000.0000.0000.000
159Y160PRO0-0.045-0.02319.0380.0060.0060.0000.0000.0000.000
160Y161VAL0-0.0040.01021.3980.0040.0040.0000.0000.0000.000
161Y162TYR0-0.034-0.02016.188-0.002-0.0020.0000.0000.0000.000
162Y163GLU-1-0.784-0.87314.156-0.217-0.2170.0000.0000.0000.000
163Y164SER0-0.035-0.00513.827-0.004-0.0040.0000.0000.0000.000
164Y165PHE00.038-0.0019.301-0.030-0.0300.0000.0000.0000.000
165Y166PHE0-0.064-0.0187.4380.1440.1440.0000.0000.0000.000
166Y167ASN0-0.059-0.0582.784-0.5210.7370.267-0.494-1.0320.003
167Y168GLN00.0130.0013.3500.3021.6210.002-0.655-0.6660.001
168Y169PRO00.0880.0461.936-7.413-8.9017.053-3.066-2.500-0.027
169Y170ARG10.8410.9153.2111.5102.3150.160-0.248-0.716-0.002
170Y171HIS00.0910.0383.180-2.951-1.2230.331-0.601-1.458-0.004
171Y172SER0-0.055-0.0184.357-0.206-0.132-0.001-0.002-0.0710.000
172Y173LEU00.0340.0267.120-0.079-0.0790.0000.0000.0000.000
173Y174ASP-1-0.781-0.9108.334-0.092-0.0920.0000.0000.0000.000
174Y175SER0-0.024-0.02410.8510.0030.0030.0000.0000.0000.000
175Y176LYS10.9320.95514.3710.0950.0950.0000.0000.0000.000
176Y177LEU00.0120.01811.3220.0120.0120.0000.0000.0000.000
177Y178LEU00.005-0.00113.7330.0130.0130.0000.0000.0000.000
178Y179LEU00.0100.01215.5810.0190.0190.0000.0000.0000.000
179Y180GLN00.0380.01517.5330.0200.0200.0000.0000.0000.000
180Y181LEU0-0.022-0.00914.7800.0070.0070.0000.0000.0000.000
181Y182PHE00.014-0.00818.6610.0140.0140.0000.0000.0000.000
182Y183LYS10.8720.95421.4570.1100.1100.0000.0000.0000.000
183Y184GLN0-0.054-0.03819.2930.0180.0180.0000.0000.0000.000
184Y185ARG10.7850.89719.3140.1650.1650.0000.0000.0000.000
185Y186ILE0-0.063-0.00724.0740.0110.0110.0000.0000.0000.000