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: 98J92

Calculation Name: 4OO8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OO8

Chain ID: D

ChEMBL ID:

UniProt ID: Q99ZW2

Base Structure: X-ray

Registration Date: 2023-09-24

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 1172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -36516124.402934
FMO2-HF: Nuclear repulsion 36048154.165713
FMO2-HF: Total energy -467970.23722
FMO2-MP2: Total energy -469362.247315


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:3:LYS)


Summations of interaction energy for fragment #1(D:3:LYS)
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.
75.62368.19345.098-17.573-20.092-0.178
Interaction energy analysis for fragmet #1(D:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.816 / q_NPA : 0.912
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].
3D5TYR0-0.085-0.1202.565-3.6282.2971.342-2.823-4.444-0.013
4D6SER00.0760.0454.5441.4701.524-0.001-0.011-0.0420.000
5D7ILE0-0.042-0.0297.481-0.944-0.9440.0000.0000.0000.000
6D8GLY00.0070.0329.6651.5331.5330.0000.0000.0000.000
7D9LEU0-0.047-0.04913.222-0.109-0.1090.0000.0000.0000.000
8D10ALA00.0410.01515.8910.6660.6660.0000.0000.0000.000
9D11ILE0-0.015-0.00618.9660.2430.2430.0000.0000.0000.000
10D12GLY00.0550.02721.5340.5020.5020.0000.0000.0000.000
11D13THR0-0.056-0.04524.998-0.203-0.2030.0000.0000.0000.000
12D14ASN00.0100.01126.9740.2040.2040.0000.0000.0000.000
13D15SER0-0.0020.00122.7560.0610.0610.0000.0000.0000.000
14D16VAL0-0.0040.00917.1410.0170.0170.0000.0000.0000.000
15D17GLY00.0170.02517.960-0.383-0.3830.0000.0000.0000.000
16D18TRP0-0.018-0.01910.717-0.971-0.9710.0000.0000.0000.000
17D19ALA00.0280.00211.6220.5730.5730.0000.0000.0000.000
18D20VAL0-0.020-0.0014.844-1.041-1.0410.0000.0000.0000.000
19D21ILE00.0000.0008.0971.3431.3430.0000.0000.0000.000
20D22THR0-0.062-0.0714.845-4.099-4.0990.0000.0000.0000.000
21D23ASP-1-0.749-0.8656.401-31.673-31.6730.0000.0000.0000.000
22D24GLU-1-0.832-0.8897.974-25.756-25.7560.0000.0000.0000.000
23D25TYR00.0490.03210.5710.7530.7530.0000.0000.0000.000
24D26LYS10.9290.9999.69821.60221.6020.0000.0000.0000.000
25D27VAL00.0250.0088.902-2.491-2.4910.0000.0000.0000.000
26D28PRO0-0.0230.0105.3091.3971.3970.0000.0000.0000.000
27D29SER00.0440.0178.0020.9930.9930.0000.0000.0000.000
28D30LYS10.8810.9384.12343.31043.420-0.001-0.006-0.1030.000
29D31LYS10.9310.9499.73426.99026.9900.0000.0000.0000.000
30D32PHE00.0250.0279.428-1.142-1.1420.0000.0000.0000.000
31D33LYS10.9930.98513.71616.45916.4590.0000.0000.0000.000
32D34VAL0-0.040-0.01916.586-0.295-0.2950.0000.0000.0000.000
33D35LEU0-0.041-0.01719.8130.4180.4180.0000.0000.0000.000
34D36GLY00.036-0.00122.3560.1050.1050.0000.0000.0000.000
35D37ASN0-0.0100.01126.037-0.317-0.3170.0000.0000.0000.000
36D38THR00.0290.02826.3320.1960.1960.0000.0000.0000.000
37D39ASP-1-0.767-0.89027.228-10.419-10.4190.0000.0000.0000.000
38D40ARG10.9130.98322.23312.36012.3600.0000.0000.0000.000
39D41HIS10.8930.92221.54112.00712.0070.0000.0000.0000.000
40D42SER0-0.0250.00017.126-0.630-0.6300.0000.0000.0000.000
41D43ILE00.0220.01816.7110.7670.7670.0000.0000.0000.000
42D44LYS10.9280.96713.17418.89418.8940.0000.0000.0000.000
43D45LYS10.8050.90913.46817.90917.9090.0000.0000.0000.000
44D46ASN00.0470.01512.131-2.463-2.4630.0000.0000.0000.000
45D47LEU0-0.036-0.0116.2690.3020.3020.0000.0000.0000.000
46D48ILE00.0430.00810.218-1.025-1.0250.0000.0000.0000.000
47D49GLY00.007-0.00213.0620.8580.8580.0000.0000.0000.000
48D50ALA00.0070.00816.069-0.171-0.1710.0000.0000.0000.000
49D51LEU0-0.062-0.00218.6090.4400.4400.0000.0000.0000.000
50D52LEU00.0270.00520.3170.3140.3140.0000.0000.0000.000
51D53PHE0-0.079-0.04922.9200.1260.1260.0000.0000.0000.000
52D54ASP-1-0.761-0.86526.361-9.885-9.8850.0000.0000.0000.000
53D55SER0-0.028-0.03729.545-0.169-0.1690.0000.0000.0000.000
54D56GLY0-0.0060.01531.0060.0920.0920.0000.0000.0000.000
55D57GLU-1-0.920-0.95932.034-8.327-8.3270.0000.0000.0000.000
56D58THR00.006-0.00835.340-0.115-0.1150.0000.0000.0000.000
57D59ALA00.0190.00037.4310.0810.0810.0000.0000.0000.000
58D60GLU-1-0.935-0.96439.464-7.129-7.1290.0000.0000.0000.000
59D61ALA00.0930.03742.5610.1890.1890.0000.0000.0000.000
60D62THR0-0.009-0.01340.1880.2060.2060.0000.0000.0000.000
61D63ARG10.9450.97043.0347.4107.4100.0000.0000.0000.000
62D64LEU00.0570.02345.2010.1480.1480.0000.0000.0000.000
63D65LYS11.0031.00345.2717.1487.1480.0000.0000.0000.000
64D66ARG10.8980.97042.8247.4477.4470.0000.0000.0000.000
65D67THR0-0.022-0.02348.0420.1530.1530.0000.0000.0000.000
66D68ALA00.0250.01650.9310.1410.1410.0000.0000.0000.000
67D69ARG10.9760.99045.7786.9186.9180.0000.0000.0000.000
68D70ARG10.9440.97447.1866.7146.7140.0000.0000.0000.000
69D71ARG10.9940.99653.7885.9135.9130.0000.0000.0000.000
70D72TYR00.0040.00655.3690.1550.1550.0000.0000.0000.000
71D73THR0-0.043-0.00955.2760.0850.0850.0000.0000.0000.000
72D74ARG10.9870.97953.6695.9365.9360.0000.0000.0000.000
73D75ARG10.9070.97359.8025.2925.2920.0000.0000.0000.000
74D76LYS10.9570.97759.3865.4535.4530.0000.0000.0000.000
75D77ASN00.0550.01259.4790.0830.0830.0000.0000.0000.000
76D78ARG10.8790.96962.5375.1195.1190.0000.0000.0000.000
77D79ILE0-0.0140.00066.0900.0610.0610.0000.0000.0000.000
78D80LEU00.0140.00363.7620.0480.0480.0000.0000.0000.000
79D81TYR00.0180.00863.158-0.006-0.0060.0000.0000.0000.000
80D82LEU0-0.0020.00868.9490.0490.0490.0000.0000.0000.000
81D83GLN0-0.044-0.03870.5060.0510.0510.0000.0000.0000.000
82D84GLU-1-0.946-0.95769.446-4.626-4.6260.0000.0000.0000.000
83D85ILE0-0.044-0.02372.5150.0530.0530.0000.0000.0000.000
84D86PHE00.013-0.00975.3490.0560.0560.0000.0000.0000.000
85D87SER0-0.043-0.01574.6620.0710.0710.0000.0000.0000.000
86D88ASN0-0.020-0.00476.7790.0790.0790.0000.0000.0000.000
87D89GLU-1-0.818-0.93679.730-3.795-3.7950.0000.0000.0000.000
88D90MET0-0.082-0.03278.3270.0320.0320.0000.0000.0000.000
89D91ALA00.0310.01679.8420.0300.0300.0000.0000.0000.000
90D92LYS10.8990.96381.4493.8413.8410.0000.0000.0000.000
91D93VAL0-0.057-0.01184.0240.0440.0440.0000.0000.0000.000
92D94ASP-1-0.850-0.96681.589-3.976-3.9760.0000.0000.0000.000
93D95ASP-1-0.890-0.92780.446-4.033-4.0330.0000.0000.0000.000
94D96SER0-0.0080.00277.743-0.064-0.0640.0000.0000.0000.000
95D97PHE0-0.008-0.00477.201-0.043-0.0430.0000.0000.0000.000
96D98PHE00.027-0.01973.096-0.042-0.0420.0000.0000.0000.000
97D99HIS00.0200.01272.814-0.062-0.0620.0000.0000.0000.000
98D100ARG10.8360.93773.0204.0364.0360.0000.0000.0000.000
99D101LEU0-0.042-0.01272.102-0.040-0.0400.0000.0000.0000.000
100D102GLU-1-1.007-1.00467.779-4.841-4.8410.0000.0000.0000.000
101D103GLU-1-0.771-0.88168.558-4.537-4.5370.0000.0000.0000.000
102D104SER0-0.062-0.02870.602-0.011-0.0110.0000.0000.0000.000
103D105PHE0-0.083-0.04663.605-0.021-0.0210.0000.0000.0000.000
104D106LEU0-0.024-0.01766.520-0.038-0.0380.0000.0000.0000.000
105D107VAL0-0.003-0.01869.0520.0550.0550.0000.0000.0000.000
106D108GLU-1-0.911-0.96871.603-4.131-4.1310.0000.0000.0000.000
107D109GLU-1-0.960-0.97972.547-4.474-4.4740.0000.0000.0000.000
108D110ASP-1-0.840-0.91868.215-4.726-4.7260.0000.0000.0000.000
109D111LYS10.8040.93171.4294.3674.3670.0000.0000.0000.000
110D112LYS10.8670.92570.4614.5844.5840.0000.0000.0000.000
111D113HIS0-0.037-0.01375.0810.0770.0770.0000.0000.0000.000
112D114GLU-1-0.808-0.91377.859-3.989-3.9890.0000.0000.0000.000
113D115ARG10.8850.94377.2443.9643.9640.0000.0000.0000.000
114D116HIS0-0.043-0.01677.516-0.063-0.0630.0000.0000.0000.000
115D117PRO00.0090.00375.5930.0030.0030.0000.0000.0000.000
116D118ILE0-0.014-0.00877.649-0.007-0.0070.0000.0000.0000.000
117D119PHE0-0.057-0.04280.0250.0170.0170.0000.0000.0000.000
118D120GLY00.0570.03082.282-0.032-0.0320.0000.0000.0000.000
119D121ASN0-0.021-0.02783.823-0.017-0.0170.0000.0000.0000.000
120D122ILE00.0310.01384.735-0.028-0.0280.0000.0000.0000.000
121D123VAL0-0.004-0.00885.935-0.008-0.0080.0000.0000.0000.000
122D124ASP-1-0.816-0.90586.608-3.677-3.6770.0000.0000.0000.000
123D125GLU-1-0.799-0.90680.422-4.056-4.0560.0000.0000.0000.000
124D126VAL00.001-0.00984.289-0.029-0.0290.0000.0000.0000.000
125D127ALA00.0200.01686.1410.0100.0100.0000.0000.0000.000
126D128TYR0-0.056-0.03780.410-0.001-0.0010.0000.0000.0000.000
127D129HIS00.004-0.00878.689-0.011-0.0110.0000.0000.0000.000
128D130GLU-1-0.929-0.94483.823-3.741-3.7410.0000.0000.0000.000
129D131LYS10.8820.95387.1233.6623.6620.0000.0000.0000.000
130D132TYR0-0.093-0.06483.0780.0240.0240.0000.0000.0000.000
131D133PRO00.0670.06482.402-0.055-0.0550.0000.0000.0000.000
132D134THR0-0.057-0.04678.069-0.091-0.0910.0000.0000.0000.000
133D135ILE00.033-0.00375.1160.0310.0310.0000.0000.0000.000
134D136TYR00.002-0.02273.088-0.021-0.0210.0000.0000.0000.000
135D137HIS00.1170.09179.527-0.008-0.0080.0000.0000.0000.000
136D138LEU0-0.046-0.00780.1360.0410.0410.0000.0000.0000.000
137D139ARG10.7980.87573.9944.3344.3340.0000.0000.0000.000
138D140LYS10.9480.98181.2063.7943.7940.0000.0000.0000.000
139D141LYS10.9410.98783.8883.7253.7250.0000.0000.0000.000
140D142LEU0-0.005-0.00981.8450.0420.0420.0000.0000.0000.000
141D143VAL0-0.030-0.00682.332-0.005-0.0050.0000.0000.0000.000
142D144ASP-1-0.905-0.95885.310-3.709-3.7090.0000.0000.0000.000
143D145SER0-0.051-0.03488.8660.0540.0540.0000.0000.0000.000
144D146THR00.007-0.00889.912-0.030-0.0300.0000.0000.0000.000
145D147ASP-1-0.907-0.93392.381-3.452-3.4520.0000.0000.0000.000
146D148LYS10.9360.98489.9583.5823.5820.0000.0000.0000.000
147D149ALA0-0.019-0.00686.3850.0110.0110.0000.0000.0000.000
148D150ASP-1-0.758-0.86984.814-3.842-3.8420.0000.0000.0000.000
149D151LEU00.0800.03781.644-0.037-0.0370.0000.0000.0000.000
150D152ARG10.8540.90680.4553.8173.8170.0000.0000.0000.000
151D153LEU0-0.028-0.02279.875-0.060-0.0600.0000.0000.0000.000
152D154ILE00.0220.01980.515-0.049-0.0490.0000.0000.0000.000
153D155TYR00.0310.02571.806-0.082-0.0820.0000.0000.0000.000
154D156LEU00.0210.01075.327-0.077-0.0770.0000.0000.0000.000
155D157ALA0-0.0050.00575.554-0.067-0.0670.0000.0000.0000.000
156D158LEU00.0540.02575.787-0.056-0.0560.0000.0000.0000.000
157D159ALA00.014-0.00172.002-0.084-0.0840.0000.0000.0000.000
158D160HIS0-0.064-0.02571.058-0.098-0.0980.0000.0000.0000.000
159D161MET00.0080.01671.294-0.070-0.0700.0000.0000.0000.000
160D162ILE00.0270.03668.312-0.091-0.0910.0000.0000.0000.000
161D163LYS10.8650.92465.4564.7884.7880.0000.0000.0000.000
162D164PHE0-0.136-0.10065.595-0.149-0.1490.0000.0000.0000.000
163D165ARG10.9450.99262.1885.0955.0950.0000.0000.0000.000
164D166GLY00.0400.04167.1980.0440.0440.0000.0000.0000.000
165D167HIS0-0.061-0.01864.082-0.122-0.1220.0000.0000.0000.000
166D168PHE0-0.020-0.03363.2140.0250.0250.0000.0000.0000.000
167D169LEU0-0.064-0.04461.631-0.077-0.0770.0000.0000.0000.000
168D170ILE00.0010.00064.873-0.018-0.0180.0000.0000.0000.000
169D171GLU-1-0.939-0.94766.688-4.855-4.8550.0000.0000.0000.000
170D172GLY00.0720.04268.7140.0320.0320.0000.0000.0000.000
171D173ASP-1-0.954-0.97572.372-4.387-4.3870.0000.0000.0000.000
172D174LEU0-0.063-0.03375.5500.0060.0060.0000.0000.0000.000
173D175ASN00.0160.00177.507-0.007-0.0070.0000.0000.0000.000
174D176PRO0-0.058-0.02881.2810.0000.0000.0000.0000.0000.000
175D177ASP-1-0.880-0.94082.990-3.747-3.7470.0000.0000.0000.000
176D178ASN0-0.073-0.02882.1560.0870.0870.0000.0000.0000.000
177D179SER0-0.017-0.01783.173-0.037-0.0370.0000.0000.0000.000
178D180ASP-1-0.839-0.91185.116-3.639-3.6390.0000.0000.0000.000
179D181VAL00.018-0.00883.259-0.001-0.0010.0000.0000.0000.000
180D182ASP-1-0.812-0.90885.812-3.687-3.6870.0000.0000.0000.000
181D183LYS10.8520.90489.0403.5543.5540.0000.0000.0000.000
182D184LEU0-0.009-0.00584.5490.0140.0140.0000.0000.0000.000
183D185PHE0-0.0060.00284.533-0.029-0.0290.0000.0000.0000.000
184D186ILE00.0130.00486.9700.0010.0010.0000.0000.0000.000
185D187GLN00.0150.01687.647-0.023-0.0230.0000.0000.0000.000
186D188LEU00.0000.02582.798-0.002-0.0020.0000.0000.0000.000
187D189VAL0-0.025-0.01086.869-0.006-0.0060.0000.0000.0000.000
188D190GLN0-0.027-0.02889.0630.0040.0040.0000.0000.0000.000
189D191THR0-0.009-0.02187.2580.0280.0280.0000.0000.0000.000
190D192TYR0-0.003-0.01584.238-0.035-0.0350.0000.0000.0000.000
191D193ASN00.006-0.01488.188-0.027-0.0270.0000.0000.0000.000
192D194GLN0-0.0060.01691.6160.0370.0370.0000.0000.0000.000
193D195LEU0-0.020-0.00486.2520.0120.0120.0000.0000.0000.000
194D196PHE0-0.069-0.03484.570-0.028-0.0280.0000.0000.0000.000
195D197GLU-1-0.891-0.94790.537-3.400-3.4000.0000.0000.0000.000
196D198GLU-1-0.983-0.96492.088-3.441-3.4410.0000.0000.0000.000
197D199ASN0-0.112-0.06989.7470.0020.0020.0000.0000.0000.000
198D200PRO00.0310.03490.286-0.049-0.0490.0000.0000.0000.000
199D201ILE0-0.018-0.01886.649-0.005-0.0050.0000.0000.0000.000
200D202ASN0-0.020-0.01791.006-0.010-0.0100.0000.0000.0000.000
201D203ALA00.013-0.00691.210-0.034-0.0340.0000.0000.0000.000
202D204SER0-0.003-0.00792.7110.0470.0470.0000.0000.0000.000
203D205GLY0-0.016-0.00994.362-0.007-0.0070.0000.0000.0000.000
204D206VAL0-0.0150.00589.073-0.017-0.0170.0000.0000.0000.000
205D207ASP-1-0.815-0.91488.658-3.680-3.6800.0000.0000.0000.000
206D208ALA00.0180.00186.102-0.055-0.0550.0000.0000.0000.000
207D209LYS10.9430.99284.7113.7423.7420.0000.0000.0000.000
208D210ALA0-0.0480.02784.347-0.067-0.0670.0000.0000.0000.000
209D211ILE0-0.040-0.02081.924-0.066-0.0660.0000.0000.0000.000
210D212LEU00.0310.00779.863-0.075-0.0750.0000.0000.0000.000
211D213SER0-0.027-0.05179.120-0.067-0.0670.0000.0000.0000.000
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1159D1353THR0-0.015-0.04512.2330.1720.1720.0000.0000.0000.000
1160D1354GLY00.015-0.00115.328-0.019-0.0190.0000.0000.0000.000
1161D1355LEU0-0.048-0.01810.4730.3530.3530.0000.0000.0000.000
1162D1356TYR0-0.044-0.02010.1890.0200.0200.0000.0000.0000.000
1163D1357GLU-1-0.799-0.88516.174-13.886-13.8860.0000.0000.0000.000
1164D1358THR0-0.034-0.02719.790-0.081-0.0810.0000.0000.0000.000
1165D1359ARG10.7710.87222.46912.99012.9900.0000.0000.0000.000
1166D1360ILE00.005-0.00925.4520.0590.0590.0000.0000.0000.000
1167D1361ASP-1-0.809-0.90529.076-9.262-9.2620.0000.0000.0000.000
1168D1362LEU0-0.041-0.02831.8240.1320.1320.0000.0000.0000.000
1169D1363SER0-0.015-0.00734.9470.3400.3400.0000.0000.0000.000
1170D1364GLN00.0200.00534.4700.2420.2420.0000.0000.0000.000
1171D1365LEU0-0.061-0.02334.7480.1420.1420.0000.0000.0000.000
1172D1366GLY0-0.0260.00038.5490.2470.2470.0000.0000.0000.000