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: R9RM8

Calculation Name: 1SPX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SPX

Chain ID: A

ChEMBL ID:

UniProt ID: Q18946

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2740804.42894
FMO2-HF: Nuclear repulsion 2653516.937507
FMO2-HF: Total energy -87287.491433
FMO2-MP2: Total energy -87545.250433


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-24.14-15.6015.932-6.921-7.55-0.062
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.002
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].
3A4PHE00.011-0.0183.337-3.733-1.6640.028-1.068-1.0280.002
4A5ALA00.0680.0512.8510.5541.1740.052-0.227-0.4450.000
5A6GLU-1-0.972-0.9894.8780.3770.506-0.001-0.009-0.1200.000
6A7LYS10.9030.9827.7072.2422.2420.0000.0000.0000.000
7A8VAL00.0010.0039.237-0.243-0.2430.0000.0000.0000.000
8A9ALA00.0100.00611.4310.0910.0910.0000.0000.0000.000
9A10ILE00.0190.02013.0500.0610.0610.0000.0000.0000.000
10A11ILE00.0010.00313.175-0.002-0.0020.0000.0000.0000.000
11A12THR00.0610.03516.9640.0600.0600.0000.0000.0000.000
12A13GLY00.0360.01420.179-0.019-0.0190.0000.0000.0000.000
13A14SER0-0.018-0.01017.4350.0210.0210.0000.0000.0000.000
14A15SER0-0.0060.00819.133-0.013-0.0130.0000.0000.0000.000
15A16ASN0-0.051-0.04321.3290.0590.0590.0000.0000.0000.000
16A17GLY00.0790.03620.709-0.038-0.0380.0000.0000.0000.000
17A18ILE00.0510.05017.877-0.047-0.0470.0000.0000.0000.000
18A19GLY00.0590.02516.796-0.096-0.0960.0000.0000.0000.000
19A20ARG10.8800.96516.2070.3650.3650.0000.0000.0000.000
20A21ALA00.0230.00714.770-0.080-0.0800.0000.0000.0000.000
21A22THR00.012-0.00912.494-0.146-0.1460.0000.0000.0000.000
22A23ALA0-0.0110.00111.194-0.293-0.2930.0000.0000.0000.000
23A24VAL00.0080.00810.750-0.247-0.2470.0000.0000.0000.000
24A25LEU0-0.026-0.0057.272-0.195-0.1950.0000.0000.0000.000
25A26PHE00.045-0.0066.662-0.739-0.7390.0000.0000.0000.000
26A27ALA0-0.0090.0106.017-1.175-1.1750.0000.0000.0000.000
27A28ARG10.9180.9565.7090.8990.8990.0000.0000.0000.000
28A29GLU-1-0.907-0.9492.505-9.700-6.1711.214-1.946-2.797-0.018
29A30GLY0-0.0090.0032.081-14.296-12.2344.629-3.665-3.026-0.046
30A31ALA0-0.043-0.0153.4341.8611.9910.010-0.006-0.1340.000
31A32LYS10.8640.9436.7311.9471.9470.0000.0000.0000.000
32A33VAL00.0340.0159.6950.1260.1260.0000.0000.0000.000
33A34THR00.0390.02812.2820.1990.1990.0000.0000.0000.000
34A35ILE0-0.035-0.00815.252-0.034-0.0340.0000.0000.0000.000
35A36THR00.003-0.02917.6390.0680.0680.0000.0000.0000.000
36A37GLY0-0.014-0.01421.370-0.013-0.0130.0000.0000.0000.000
37A38ARG10.9270.97124.5480.2840.2840.0000.0000.0000.000
38A39HIS0-0.0040.00227.1740.0210.0210.0000.0000.0000.000
39A40ALA00.0750.02625.821-0.023-0.0230.0000.0000.0000.000
40A41GLU-1-0.875-0.93325.069-0.237-0.2370.0000.0000.0000.000
41A42ARG10.8970.95324.6970.2670.2670.0000.0000.0000.000
42A43LEU00.017-0.00220.259-0.024-0.0240.0000.0000.0000.000
43A44GLU-1-0.786-0.87120.336-0.422-0.4220.0000.0000.0000.000
44A45GLU-1-0.920-0.96020.514-0.338-0.3380.0000.0000.0000.000
45A46THR0-0.059-0.06216.3900.0070.0070.0000.0000.0000.000
46A47ARG10.8720.93416.2760.3300.3300.0000.0000.0000.000
47A48GLN0-0.014-0.01716.122-0.006-0.0060.0000.0000.0000.000
48A49GLN0-0.022-0.00615.495-0.044-0.0440.0000.0000.0000.000
49A50ILE0-0.029-0.00910.922-0.034-0.0340.0000.0000.0000.000
50A51LEU0-0.012-0.00712.2000.0040.0040.0000.0000.0000.000
51A52ALA0-0.0030.01114.1720.0760.0760.0000.0000.0000.000
52A53ALA0-0.094-0.0389.7820.0710.0710.0000.0000.0000.000
53A54GLY0-0.006-0.0079.8320.0840.0840.0000.0000.0000.000
54A55VAL0-0.060-0.0157.8290.0620.0620.0000.0000.0000.000
55A56SER00.0260.00410.1480.0640.0640.0000.0000.0000.000
56A57GLU-1-0.862-0.95912.218-0.452-0.4520.0000.0000.0000.000
57A58GLN0-0.042-0.01713.643-0.057-0.0570.0000.0000.0000.000
58A59ASN0-0.056-0.0297.9160.1480.1480.0000.0000.0000.000
59A60VAL00.0230.01311.691-0.205-0.2050.0000.0000.0000.000
60A61ASN0-0.026-0.02214.1620.1790.1790.0000.0000.0000.000
61A62SER00.002-0.01017.334-0.042-0.0420.0000.0000.0000.000
62A63VAL00.0380.02719.9180.0450.0450.0000.0000.0000.000
63A64VAL00.0070.00722.746-0.014-0.0140.0000.0000.0000.000
64A65ALA00.0360.01325.8140.0220.0220.0000.0000.0000.000
65A66ASP-1-0.837-0.86927.417-0.298-0.2980.0000.0000.0000.000
66A67VAL00.0570.01725.1460.0070.0070.0000.0000.0000.000
67A68THR0-0.070-0.08827.9180.0030.0030.0000.0000.0000.000
68A69THR0-0.059-0.02031.1460.0170.0170.0000.0000.0000.000
69A70ASP-1-0.843-0.91530.829-0.284-0.2840.0000.0000.0000.000
70A71ALA00.0950.03930.779-0.014-0.0140.0000.0000.0000.000
71A72GLY0-0.0030.00328.676-0.014-0.0140.0000.0000.0000.000
72A73GLN0-0.029-0.02526.430-0.026-0.0260.0000.0000.0000.000
73A74ASP-1-0.810-0.90625.756-0.346-0.3460.0000.0000.0000.000
74A75GLU-1-0.909-0.93625.304-0.361-0.3610.0000.0000.0000.000
75A76ILE0-0.047-0.01721.131-0.038-0.0380.0000.0000.0000.000
76A77LEU0-0.015-0.01721.342-0.059-0.0590.0000.0000.0000.000
77A78SER0-0.026-0.02722.038-0.026-0.0260.0000.0000.0000.000
78A79THR0-0.002-0.02121.713-0.029-0.0290.0000.0000.0000.000
79A80THR0-0.054-0.00817.344-0.057-0.0570.0000.0000.0000.000
80A81LEU00.0080.00118.032-0.044-0.0440.0000.0000.0000.000
81A82GLY0-0.0200.00820.2390.0160.0160.0000.0000.0000.000
82A83LYS10.8770.94217.7870.5040.5040.0000.0000.0000.000
83A84PHE0-0.037-0.03414.266-0.047-0.0470.0000.0000.0000.000
84A85GLY0-0.0040.01215.883-0.046-0.0460.0000.0000.0000.000
85A86LYS10.8340.91111.7411.2251.2250.0000.0000.0000.000
86A87LEU00.002-0.00515.721-0.058-0.0580.0000.0000.0000.000
87A88ASP-1-0.842-0.89412.507-1.304-1.3040.0000.0000.0000.000
88A89ILE0-0.003-0.00110.5240.0320.0320.0000.0000.0000.000
89A90LEU00.0010.01714.7160.0080.0080.0000.0000.0000.000
90A91VAL00.0020.00314.3500.0340.0340.0000.0000.0000.000
91A92ASN0-0.032-0.03217.4950.0290.0290.0000.0000.0000.000
92A93ASN0-0.009-0.01619.6620.0630.0630.0000.0000.0000.000
93A94ALA00.0000.01521.6140.0160.0160.0000.0000.0000.000
94A95GLY0-0.008-0.00925.0050.0230.0230.0000.0000.0000.000
95A109GLN00.0390.02641.1330.0040.0040.0000.0000.0000.000
96A110SER00.0080.01344.224-0.001-0.0010.0000.0000.0000.000
97A111ILE00.0820.02743.456-0.007-0.0070.0000.0000.0000.000
98A112GLU-1-0.821-0.91542.970-0.147-0.1470.0000.0000.0000.000
99A113SER0-0.023-0.01439.931-0.011-0.0110.0000.0000.0000.000
100A114TYR0-0.0210.00338.667-0.015-0.0150.0000.0000.0000.000
101A115ASP-1-0.851-0.93138.351-0.183-0.1830.0000.0000.0000.000
102A116ALA0-0.062-0.03036.909-0.014-0.0140.0000.0000.0000.000
103A117THR0-0.035-0.02633.841-0.020-0.0200.0000.0000.0000.000
104A118LEU00.0260.00133.436-0.022-0.0220.0000.0000.0000.000
105A119ASN0-0.0120.00633.625-0.020-0.0200.0000.0000.0000.000
106A120LEU00.002-0.00428.397-0.016-0.0160.0000.0000.0000.000
107A121ASN0-0.030-0.02228.964-0.042-0.0420.0000.0000.0000.000
108A122LEU00.0230.02429.093-0.015-0.0150.0000.0000.0000.000
109A123ARG10.9440.97730.4390.2200.2200.0000.0000.0000.000
110A124SER0-0.044-0.03528.796-0.015-0.0150.0000.0000.0000.000
111A125VAL00.0410.03825.042-0.021-0.0210.0000.0000.0000.000
112A126ILE00.0030.01426.762-0.020-0.0200.0000.0000.0000.000
113A127ALA0-0.046-0.02429.111-0.003-0.0030.0000.0000.0000.000
114A128LEU00.0250.01622.4460.0010.0010.0000.0000.0000.000
115A129THR00.030-0.01024.107-0.036-0.0360.0000.0000.0000.000
116A130LYS10.8850.94125.3530.2770.2770.0000.0000.0000.000
117A131LYS10.7890.88626.5570.3250.3250.0000.0000.0000.000
118A132ALA00.0250.01321.464-0.003-0.0030.0000.0000.0000.000
119A133VAL00.0220.01122.766-0.024-0.0240.0000.0000.0000.000
120A134PRO00.0140.01323.846-0.015-0.0150.0000.0000.0000.000
121A135HIS00.0490.01120.711-0.007-0.0070.0000.0000.0000.000
122A136LEU0-0.0100.00717.938-0.036-0.0360.0000.0000.0000.000
123A137SER0-0.003-0.00519.984-0.015-0.0150.0000.0000.0000.000
124A138SER0-0.074-0.02520.8980.0290.0290.0000.0000.0000.000
125A139THR0-0.044-0.03815.6770.0320.0320.0000.0000.0000.000
126A140LYS10.8870.95316.3670.3350.3350.0000.0000.0000.000
127A141GLY00.0530.02416.085-0.058-0.0580.0000.0000.0000.000
128A142GLU-1-0.847-0.92813.502-0.894-0.8940.0000.0000.0000.000
129A143ILE0-0.0100.00116.707-0.037-0.0370.0000.0000.0000.000
130A144VAL0-0.019-0.01115.1210.0320.0320.0000.0000.0000.000
131A145ASN00.002-0.01518.383-0.043-0.0430.0000.0000.0000.000
132A146ILE00.0100.01418.0830.0090.0090.0000.0000.0000.000
133A147SER0-0.005-0.03022.0170.0390.0390.0000.0000.0000.000
134A148SER00.0520.00225.295-0.001-0.0010.0000.0000.0000.000
135A149ILE00.0130.03927.1430.0110.0110.0000.0000.0000.000
136A150ALA0-0.035-0.02729.2570.0230.0230.0000.0000.0000.000
137A151SER0-0.067-0.02530.1440.0250.0250.0000.0000.0000.000
138A152GLY00.0550.00330.948-0.012-0.0120.0000.0000.0000.000
139A153LEU0-0.038-0.00233.2370.0080.0080.0000.0000.0000.000
140A154HIS10.8980.95332.6390.2070.2070.0000.0000.0000.000
141A155ALA00.0140.01337.735-0.005-0.0050.0000.0000.0000.000
142A156THR0-0.016-0.03334.559-0.001-0.0010.0000.0000.0000.000
143A157PRO00.014-0.00537.687-0.006-0.0060.0000.0000.0000.000
144A158ASP-1-0.865-0.91637.585-0.152-0.1520.0000.0000.0000.000
145A159PHE0-0.057-0.03034.041-0.008-0.0080.0000.0000.0000.000
146A160PRO00.0170.01236.522-0.010-0.0100.0000.0000.0000.000
147A161TYR00.021-0.02437.549-0.004-0.0040.0000.0000.0000.000
148A162TYR00.0110.00527.439-0.008-0.0080.0000.0000.0000.000
149A163SER00.022-0.00332.614-0.015-0.0150.0000.0000.0000.000
150A164ILE00.0270.02133.653-0.009-0.0090.0000.0000.0000.000
151A165ALA0-0.0060.00432.544-0.005-0.0050.0000.0000.0000.000
152A166LYS10.8620.94425.9550.3660.3660.0000.0000.0000.000
153A167ALA00.0500.03530.058-0.012-0.0120.0000.0000.0000.000
154A168ALA0-0.041-0.02132.333-0.001-0.0010.0000.0000.0000.000
155A169ILE0-0.0060.00126.205-0.009-0.0090.0000.0000.0000.000
156A170ASP-1-0.820-0.87927.752-0.338-0.3380.0000.0000.0000.000
157A171GLN0-0.027-0.01228.8200.0010.0010.0000.0000.0000.000
158A172TYR00.0130.00026.421-0.006-0.0060.0000.0000.0000.000
159A173THR00.0090.00223.836-0.027-0.0270.0000.0000.0000.000
160A174ARG10.8850.95226.4410.2510.2510.0000.0000.0000.000
161A175ASN0-0.007-0.01428.5210.0090.0090.0000.0000.0000.000
162A176THR0-0.018-0.02626.259-0.005-0.0050.0000.0000.0000.000
163A177ALA00.0080.02824.833-0.010-0.0100.0000.0000.0000.000
164A178ILE0-0.018-0.01125.7500.0020.0020.0000.0000.0000.000
165A179ASP-1-0.933-0.96928.745-0.270-0.2700.0000.0000.0000.000
166A180LEU00.013-0.01224.4750.0000.0000.0000.0000.0000.000
167A181ILE0-0.0200.01822.554-0.020-0.0200.0000.0000.0000.000
168A182GLN0-0.039-0.02325.0840.0120.0120.0000.0000.0000.000
169A183HIS0-0.040-0.01325.6820.0130.0130.0000.0000.0000.000
170A184GLY0-0.046-0.02522.083-0.028-0.0280.0000.0000.0000.000
171A185ILE0-0.029-0.00720.032-0.066-0.0660.0000.0000.0000.000
172A186ARG10.7760.90115.3620.8000.8000.0000.0000.0000.000
173A187VAL00.0150.01719.243-0.069-0.0690.0000.0000.0000.000
174A188ASN00.006-0.00618.6180.1060.1060.0000.0000.0000.000
175A189SER00.0230.01420.873-0.032-0.0320.0000.0000.0000.000
176A190ILE00.0270.02416.8010.0060.0060.0000.0000.0000.000
177A191SER0-0.017-0.01521.440-0.005-0.0050.0000.0000.0000.000
178A192PRO0-0.0040.00821.8630.0220.0220.0000.0000.0000.000
179A193GLY00.0460.00223.7280.0260.0260.0000.0000.0000.000
180A194LEU0-0.031-0.01126.183-0.014-0.0140.0000.0000.0000.000
181A195VAL0-0.001-0.00521.415-0.010-0.0100.0000.0000.0000.000
182A196ALA0-0.020-0.01024.2650.0130.0130.0000.0000.0000.000
183A197THR0-0.046-0.07421.724-0.037-0.0370.0000.0000.0000.000
184A198GLY00.0270.03221.558-0.036-0.0360.0000.0000.0000.000
185A213PHE00.0470.01133.2200.0020.0020.0000.0000.0000.000
186A214TYR00.0650.01837.057-0.005-0.0050.0000.0000.0000.000
187A215SER00.0280.02238.959-0.002-0.0020.0000.0000.0000.000
188A216THR00.0350.00734.6190.0000.0000.0000.0000.0000.000
189A217MET0-0.018-0.01330.850-0.011-0.0110.0000.0000.0000.000
190A218ALA0-0.0140.00434.910-0.003-0.0030.0000.0000.0000.000
191A219THR00.0670.02436.990-0.001-0.0010.0000.0000.0000.000
192A220MET0-0.0850.00029.115-0.003-0.0030.0000.0000.0000.000
193A221LYS10.8210.87130.1640.1030.1030.0000.0000.0000.000
194A222GLU-1-0.967-0.96233.789-0.102-0.1020.0000.0000.0000.000
195A223CYS0-0.032-0.01534.203-0.002-0.0020.0000.0000.0000.000
196A224VAL0-0.035-0.01527.879-0.014-0.0140.0000.0000.0000.000
197A225PRO00.0520.03930.1070.0070.0070.0000.0000.0000.000
198A226ALA0-0.0070.00225.6240.0090.0090.0000.0000.0000.000
199A227GLY0-0.038-0.01527.5640.0090.0090.0000.0000.0000.000
200A228VAL00.006-0.00223.9850.0140.0140.0000.0000.0000.000
201A229MET0-0.0240.00125.684-0.015-0.0150.0000.0000.0000.000
202A230GLY00.0840.04722.791-0.006-0.0060.0000.0000.0000.000
203A231GLN0-0.0090.01019.0450.0150.0150.0000.0000.0000.000
204A232PRO00.014-0.01818.099-0.051-0.0510.0000.0000.0000.000
205A233GLN00.0470.00014.135-0.029-0.0290.0000.0000.0000.000
206A234ASP-1-0.793-0.87414.475-0.487-0.4870.0000.0000.0000.000
207A235ILE0-0.031-0.02116.287-0.030-0.0300.0000.0000.0000.000
208A236ALA0-0.0070.00112.337-0.057-0.0570.0000.0000.0000.000
209A237GLU-1-0.891-0.95110.227-1.394-1.3940.0000.0000.0000.000
210A238VAL0-0.021-0.00712.038-0.082-0.0820.0000.0000.0000.000
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212A240ALA00.0070.0018.374-0.081-0.0810.0000.0000.0000.000
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