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: NN36Q

Calculation Name: 3P0L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P0L

Chain ID: A

ChEMBL ID:

UniProt ID: P49675

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2523815.624271
FMO2-HF: Nuclear repulsion 2438795.84844
FMO2-HF: Total energy -85019.77583
FMO2-MP2: Total energy -85262.570962


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(A:64:SER)


Summations of interaction energy for fragment #1(A:64:SER)
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.
-2.1080.1490.013-1.311-0.960.004
Interaction energy analysis for fragmet #1(A:64:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.015
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].
3A66THR0-0.033-0.0243.501-3.215-0.9580.013-1.311-0.9600.004
4A67LEU0-0.012-0.0086.2460.5120.5120.0000.0000.0000.000
5A68TYR0-0.009-0.0079.353-0.208-0.2080.0000.0000.0000.000
6A69SER00.006-0.02313.2210.0950.0950.0000.0000.0000.000
7A70ASP-1-0.854-0.94316.690-0.253-0.2530.0000.0000.0000.000
8A71GLN0-0.0060.00419.4960.0200.0200.0000.0000.0000.000
9A72GLU-1-0.841-0.90015.666-0.599-0.5990.0000.0000.0000.000
10A73LEU00.000-0.00314.680-0.007-0.0070.0000.0000.0000.000
11A74ALA00.0430.02718.3380.0210.0210.0000.0000.0000.000
12A75TYR0-0.030-0.02220.4420.0100.0100.0000.0000.0000.000
13A76LEU0-0.018-0.02514.5920.0060.0060.0000.0000.0000.000
14A77GLN0-0.082-0.03419.3260.0210.0210.0000.0000.0000.000
15A78GLN00.0890.05421.9000.0220.0220.0000.0000.0000.000
16A79GLY00.003-0.00221.7670.0160.0160.0000.0000.0000.000
17A80GLU-1-0.896-0.95019.090-0.248-0.2480.0000.0000.0000.000
18A81GLU-1-0.874-0.92822.921-0.137-0.1370.0000.0000.0000.000
19A82ALA0-0.027-0.00826.1940.0170.0170.0000.0000.0000.000
20A83MET0-0.007-0.01022.7330.0100.0100.0000.0000.0000.000
21A84GLN0-0.007-0.00723.1760.0280.0280.0000.0000.0000.000
22A85LYS10.8620.91827.4860.0910.0910.0000.0000.0000.000
23A86ALA0-0.0150.00029.4790.0100.0100.0000.0000.0000.000
24A87LEU00.013-0.01525.8930.0090.0090.0000.0000.0000.000
25A88GLY00.0190.01830.3440.0100.0100.0000.0000.0000.000
26A89ILE0-0.048-0.03132.8260.0080.0080.0000.0000.0000.000
27A90LEU0-0.057-0.02531.3970.0050.0050.0000.0000.0000.000
28A91SER00.010-0.00133.0480.0060.0060.0000.0000.0000.000
29A92ASN0-0.059-0.01035.0680.0070.0070.0000.0000.0000.000
30A93GLN00.0720.01538.330-0.003-0.0030.0000.0000.0000.000
31A94GLU-1-0.906-0.94840.163-0.032-0.0320.0000.0000.0000.000
32A95GLY00.0340.01743.765-0.001-0.0010.0000.0000.0000.000
33A96TRP0-0.039-0.01438.1210.0000.0000.0000.0000.0000.000
34A97LYN00.0090.01644.5660.0020.0020.0000.0000.0000.000
35A98LYS10.8570.90446.0450.0400.0400.0000.0000.0000.000
36A99GLU-1-0.835-0.89345.946-0.052-0.0520.0000.0000.0000.000
37A100SER0-0.003-0.01046.5460.0010.0010.0000.0000.0000.000
38A101GLN0-0.020-0.01847.3800.0000.0000.0000.0000.0000.000
39A102GLN00.0160.01845.8730.0010.0010.0000.0000.0000.000
40A103ASP-1-0.834-0.91648.602-0.039-0.0390.0000.0000.0000.000
41A104ASN0-0.053-0.02545.0310.0020.0020.0000.0000.0000.000
42A105GLY00.0430.03345.4130.0000.0000.0000.0000.0000.000
43A106ASP-1-0.799-0.86942.469-0.059-0.0590.0000.0000.0000.000
44A107LYS10.8200.89442.9950.0520.0520.0000.0000.0000.000
45A108VAL00.0180.02442.313-0.004-0.0040.0000.0000.0000.000
46A109MET0-0.0020.00242.1680.0050.0050.0000.0000.0000.000
47A110SER00.024-0.00742.833-0.005-0.0050.0000.0000.0000.000
48A111LYS10.8130.90341.0800.0540.0540.0000.0000.0000.000
49A112VAL0-0.0160.00042.504-0.004-0.0040.0000.0000.0000.000
50A113VAL00.0160.02037.4470.0030.0030.0000.0000.0000.000
51A114PRO00.016-0.00640.642-0.002-0.0020.0000.0000.0000.000
52A115ASP-1-0.812-0.89236.986-0.070-0.0700.0000.0000.0000.000
53A116VAL0-0.046-0.01636.032-0.004-0.0040.0000.0000.0000.000
54A117GLY00.0420.02639.1770.0000.0000.0000.0000.0000.000
55A118LYS10.7050.84541.6950.0600.0600.0000.0000.0000.000
56A119VAL0-0.0060.01437.649-0.004-0.0040.0000.0000.0000.000
57A120PHE0-0.004-0.00439.3330.0060.0060.0000.0000.0000.000
58A121ARG10.8360.90237.1180.0590.0590.0000.0000.0000.000
59A122LEU00.0380.03637.7140.0050.0050.0000.0000.0000.000
60A123GLU-1-0.832-0.88137.840-0.067-0.0670.0000.0000.0000.000
61A124VAL00.0490.02437.5290.0040.0040.0000.0000.0000.000
62A125VAL0-0.025-0.00837.718-0.002-0.0020.0000.0000.0000.000
63A126VAL00.0510.02335.5300.0020.0020.0000.0000.0000.000
64A127ASP-1-0.864-0.92237.065-0.051-0.0510.0000.0000.0000.000
65A128GLN00.016-0.00134.262-0.002-0.0020.0000.0000.0000.000
66A129PRO00.0390.02430.815-0.002-0.0020.0000.0000.0000.000
67A130MET00.0040.01625.340-0.003-0.0030.0000.0000.0000.000
68A131GLU-1-0.826-0.93623.806-0.146-0.1460.0000.0000.0000.000
69A132ARG10.8170.91726.6420.0830.0830.0000.0000.0000.000
70A133LEU00.001-0.00329.502-0.004-0.0040.0000.0000.0000.000
71A134TYR0-0.028-0.02320.114-0.014-0.0140.0000.0000.0000.000
72A135GLU-1-0.810-0.90424.919-0.147-0.1470.0000.0000.0000.000
73A136GLU-1-0.814-0.89425.897-0.124-0.1240.0000.0000.0000.000
74A137LEU0-0.039-0.01728.0910.0010.0010.0000.0000.0000.000
75A138VAL0-0.052-0.04422.953-0.006-0.0060.0000.0000.0000.000
76A139GLU-1-0.993-0.97920.899-0.254-0.2540.0000.0000.0000.000
77A140ARG10.7850.85623.2040.1280.1280.0000.0000.0000.000
78A141MET0-0.0110.01225.3350.0100.0100.0000.0000.0000.000
79A142GLU-1-0.789-0.87925.873-0.215-0.2150.0000.0000.0000.000
80A143ALA00.0050.01528.7090.0090.0090.0000.0000.0000.000
81A144MET0-0.016-0.01430.8740.0120.0120.0000.0000.0000.000
82A145GLY00.0170.00532.8830.0080.0080.0000.0000.0000.000
83A146GLU-1-0.881-0.91533.684-0.112-0.1120.0000.0000.0000.000
84A147TRP0-0.042-0.01632.5740.0110.0110.0000.0000.0000.000
85A148ASN00.0070.00335.8530.0120.0120.0000.0000.0000.000
86A149PRO00.0430.01238.563-0.003-0.0030.0000.0000.0000.000
87A150ASN0-0.051-0.03339.5790.0000.0000.0000.0000.0000.000
88A151VAL0-0.064-0.03534.836-0.003-0.0030.0000.0000.0000.000
89A152LYS10.9620.99337.5780.1030.1030.0000.0000.0000.000
90A153GLU-1-0.922-0.97332.735-0.145-0.1450.0000.0000.0000.000
91A154ILE0-0.017-0.00928.637-0.001-0.0010.0000.0000.0000.000
92A155LYS10.8440.91427.8880.1810.1810.0000.0000.0000.000
93A156VAL0-0.029-0.03121.255-0.005-0.0050.0000.0000.0000.000
94A157LEU0-0.048-0.01424.361-0.002-0.0020.0000.0000.0000.000
95A158GLN00.0310.01217.2280.0300.0300.0000.0000.0000.000
96A159LYS10.9480.97116.6600.4130.4130.0000.0000.0000.000
97A160ILE00.0250.01814.645-0.049-0.0490.0000.0000.0000.000
98A161GLY00.0660.04211.0440.0320.0320.0000.0000.0000.000
99A162LYS10.8410.9018.1531.2781.2780.0000.0000.0000.000
100A163ASP-1-0.744-0.83913.481-0.375-0.3750.0000.0000.0000.000
101A164THR00.0060.01316.4460.0620.0620.0000.0000.0000.000
102A165PHE0-0.036-0.03317.607-0.052-0.0520.0000.0000.0000.000
103A166ILE00.0210.02420.2470.0310.0310.0000.0000.0000.000
104A167THR0-0.0180.00223.497-0.008-0.0080.0000.0000.0000.000
105A168HIS0-0.002-0.01326.5590.0030.0030.0000.0000.0000.000
106A169GLU-1-0.804-0.88530.053-0.159-0.1590.0000.0000.0000.000
107A170LEU00.0100.01432.4420.0080.0080.0000.0000.0000.000
108A171ALA00.0280.00235.9690.0000.0000.0000.0000.0000.000
109A172ALA0-0.0050.00538.5900.0010.0010.0000.0000.0000.000
110A173GLU-1-0.911-0.96441.965-0.079-0.0790.0000.0000.0000.000
111A174ALA0-0.036-0.01144.9000.0010.0010.0000.0000.0000.000
112A175ALA00.002-0.00945.9280.0030.0030.0000.0000.0000.000
113A176GLY00.0090.01348.4020.0030.0030.0000.0000.0000.000
114A177ASN0-0.043-0.03149.0480.0000.0000.0000.0000.0000.000
115A178LEU00.0170.00950.421-0.001-0.0010.0000.0000.0000.000
116A179VAL0-0.072-0.02745.4500.0000.0000.0000.0000.0000.000
117A180GLY00.0520.02246.681-0.002-0.0020.0000.0000.0000.000
118A181PRO00.0290.02142.829-0.002-0.0020.0000.0000.0000.000
119A182ARG10.8510.90439.9360.0850.0850.0000.0000.0000.000
120A183ASP-1-0.749-0.82535.495-0.129-0.1290.0000.0000.0000.000
121A184PHE0-0.0090.00532.8490.0050.0050.0000.0000.0000.000
122A185VAL00.0470.02528.847-0.007-0.0070.0000.0000.0000.000
123A186SER0-0.034-0.03628.4650.0130.0130.0000.0000.0000.000
124A187VAL00.0110.03222.401-0.016-0.0160.0000.0000.0000.000
125A188ARG10.7860.86023.4430.2220.2220.0000.0000.0000.000
126A189CYS0-0.002-0.00320.081-0.050-0.0500.0000.0000.0000.000
127A190ALA00.0020.01520.1620.0330.0330.0000.0000.0000.000
128A191LYS10.8810.93716.6710.3060.3060.0000.0000.0000.000
129A192ARG10.8890.89616.0520.3740.3740.0000.0000.0000.000
130A193ARG10.8880.95219.1730.1110.1110.0000.0000.0000.000
131A194GLY00.0190.01820.6540.0220.0220.0000.0000.0000.000
132A195SER00.0160.00721.546-0.002-0.0020.0000.0000.0000.000
133A196THR00.001-0.00824.2940.0030.0030.0000.0000.0000.000
134A197CYS0-0.047-0.01523.394-0.018-0.0180.0000.0000.0000.000
135A198VAL0-0.030-0.02123.5550.0170.0170.0000.0000.0000.000
136A199LEU00.0140.03823.625-0.022-0.0220.0000.0000.0000.000
137A200ALA0-0.011-0.02024.6490.0220.0220.0000.0000.0000.000
138A201GLY00.0600.01125.427-0.022-0.0220.0000.0000.0000.000
139A202MET0-0.060-0.01327.1730.0200.0200.0000.0000.0000.000
140A203ALA00.0090.00128.615-0.015-0.0150.0000.0000.0000.000
141A204THR0-0.016-0.03025.835-0.008-0.0080.0000.0000.0000.000
142A205ASP-1-0.829-0.90628.893-0.150-0.1500.0000.0000.0000.000
143A206PHE0-0.034-0.01222.901-0.010-0.0100.0000.0000.0000.000
144A207GLY00.0270.00427.7020.0060.0060.0000.0000.0000.000
145A208ASN0-0.057-0.02325.9930.0190.0190.0000.0000.0000.000
146A209MET0-0.062-0.01528.8950.0010.0010.0000.0000.0000.000
147A210PRO00.0510.02630.9460.0040.0040.0000.0000.0000.000
148A211GLU-1-0.896-0.93434.341-0.106-0.1060.0000.0000.0000.000
149A212GLN00.011-0.01434.8400.0020.0020.0000.0000.0000.000
150A213LYS10.9210.94539.5040.0880.0880.0000.0000.0000.000
151A214GLY00.0160.00243.3420.0020.0020.0000.0000.0000.000
152A215VAL0-0.0360.00739.2150.0040.0040.0000.0000.0000.000
153A216ILE0-0.041-0.00740.994-0.002-0.0020.0000.0000.0000.000
154A217ARG10.8060.86733.9490.1360.1360.0000.0000.0000.000
155A218ALA0-0.0160.00737.6930.0050.0050.0000.0000.0000.000
156A219GLU-1-0.783-0.89734.985-0.117-0.1170.0000.0000.0000.000
157A220HIS10.8150.90432.0440.1410.1410.0000.0000.0000.000
158A221GLY00.1040.06033.113-0.005-0.0050.0000.0000.0000.000
159A222PRO0-0.012-0.02531.038-0.006-0.0060.0000.0000.0000.000
160A223THR0-0.038-0.00430.6900.0130.0130.0000.0000.0000.000
161A224CYS0-0.074-0.03428.429-0.011-0.0110.0000.0000.0000.000
162A225MET00.0200.01128.9620.0160.0160.0000.0000.0000.000
163A226VAL0-0.024-0.00228.452-0.012-0.0120.0000.0000.0000.000
164A227LEU00.0140.00827.0910.0090.0090.0000.0000.0000.000
165A228HIS00.0310.00028.351-0.010-0.0100.0000.0000.0000.000
166A229PRO00.0430.02129.0740.0040.0040.0000.0000.0000.000
167A230LEU0-0.022-0.00632.0910.0040.0040.0000.0000.0000.000
168A231ALA0-0.008-0.02235.8370.0030.0030.0000.0000.0000.000
169A232GLY00.0210.02336.9090.0040.0040.0000.0000.0000.000
170A233SER0-0.065-0.04136.9620.0010.0010.0000.0000.0000.000
171A234PRO00.0610.01832.087-0.004-0.0040.0000.0000.0000.000
172A235SER0-0.018-0.00332.937-0.005-0.0050.0000.0000.0000.000
173A236LYS10.8500.93735.4020.0420.0420.0000.0000.0000.000
174A237THR00.012-0.00431.268-0.002-0.0020.0000.0000.0000.000
175A238LYS10.7670.87834.0320.0700.0700.0000.0000.0000.000
176A239LEU00.0240.01432.993-0.006-0.0060.0000.0000.0000.000
177A240THR0-0.047-0.04733.2330.0070.0070.0000.0000.0000.000
178A241TRP00.011-0.00332.982-0.006-0.0060.0000.0000.0000.000
179A242LEU00.0000.01433.0960.0070.0070.0000.0000.0000.000
180A243LEU0-0.011-0.00333.763-0.009-0.0090.0000.0000.0000.000
181A244SER00.0170.00735.3160.0070.0070.0000.0000.0000.000
182A245ILE0-0.020-0.02735.822-0.008-0.0080.0000.0000.0000.000
183A246ASP-1-0.820-0.88638.236-0.077-0.0770.0000.0000.0000.000
184A247LEU00.008-0.01839.867-0.004-0.0040.0000.0000.0000.000
185A248LYS10.8500.92538.7810.0980.0980.0000.0000.0000.000
186A249GLY00.0320.00443.546-0.001-0.0010.0000.0000.0000.000
187A250TRP0-0.006-0.00147.0360.0000.0000.0000.0000.0000.000
188A251LEU0-0.0160.00646.7000.0030.0030.0000.0000.0000.000
189A252PRO00.0210.00450.4460.0000.0000.0000.0000.0000.000
190A253LYS11.0120.99549.9940.0470.0470.0000.0000.0000.000
191A254SER0-0.017-0.00150.176-0.002-0.0020.0000.0000.0000.000
192A255ILE00.0870.03149.468-0.001-0.0010.0000.0000.0000.000
193A256ILE00.0390.02745.122-0.002-0.0020.0000.0000.0000.000
194A257ASN00.002-0.00846.043-0.004-0.0040.0000.0000.0000.000
195A258GLN00.0290.02346.707-0.001-0.0010.0000.0000.0000.000
196A259VAL00.0200.01245.125-0.001-0.0010.0000.0000.0000.000
197A260LEU00.0270.02040.620-0.003-0.0030.0000.0000.0000.000
198A261SER0-0.002-0.02442.455-0.003-0.0030.0000.0000.0000.000
199A262GLN0-0.046-0.03744.093-0.002-0.0020.0000.0000.0000.000
200A263THR00.0230.01739.844-0.002-0.0020.0000.0000.0000.000
201A264GLN0-0.065-0.03637.2630.0000.0000.0000.0000.0000.000
202A265VAL0-0.005-0.01340.176-0.002-0.0020.0000.0000.0000.000
203A266ASP-1-0.836-0.88542.463-0.070-0.0700.0000.0000.0000.000
204A267PHE00.0180.00133.2000.0000.0000.0000.0000.0000.000
205A268ALA00.0090.00738.238-0.002-0.0020.0000.0000.0000.000
206A269ASN0-0.006-0.00839.3200.0020.0020.0000.0000.0000.000
207A270HIS00.0010.00139.2920.0020.0020.0000.0000.0000.000
208A271LEU00.0480.02633.294-0.001-0.0010.0000.0000.0000.000
209A272ARG10.7650.83337.0810.0630.0630.0000.0000.0000.000
210A273LYS10.8050.90639.3730.0800.0800.0000.0000.0000.000
211A274ARG10.7970.89833.6370.1080.1080.0000.0000.0000.000
212A275LEU0-0.039-0.01932.982-0.001-0.0010.0000.0000.0000.000
213A276GLU-1-0.831-0.88736.287-0.064-0.0640.0000.0000.0000.000