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: QYQMY

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2740555.347823
FMO2-HF: Nuclear repulsion 2653266.948364
FMO2-HF: Total energy -87288.399459
FMO2-MP2: Total energy -87546.001727


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.
-28.418-25.62817.315-10.89-9.216-0.083
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 : -0.033 / q_NPA : -0.040
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].
3A4PHE00.008-0.0133.404-4.310-2.1820.026-1.200-0.9540.000
4A5ALA00.0610.0452.7950.5731.2600.065-0.256-0.4960.000
5A6GLU-1-0.952-0.9744.8360.3960.544-0.001-0.012-0.1350.000
6A7LYS10.8280.9307.4712.0162.0160.0000.0000.0000.000
7A8VAL00.0120.0178.988-0.195-0.1950.0000.0000.0000.000
8A9ALA0-0.0010.00211.0760.0750.0750.0000.0000.0000.000
9A10ILE00.0300.02612.7460.0710.0710.0000.0000.0000.000
10A11ILE0-0.0010.00012.646-0.005-0.0050.0000.0000.0000.000
11A12THR00.0620.04516.6790.0670.0670.0000.0000.0000.000
12A13GLY00.0300.01220.015-0.020-0.0200.0000.0000.0000.000
13A14SER0-0.020-0.02117.2450.0200.0200.0000.0000.0000.000
14A15SER00.0230.02018.956-0.012-0.0120.0000.0000.0000.000
15A16ASN0-0.077-0.05521.2300.0530.0530.0000.0000.0000.000
16A17GLY00.0730.03420.734-0.036-0.0360.0000.0000.0000.000
17A18ILE00.0550.03918.025-0.044-0.0440.0000.0000.0000.000
18A19GLY00.0770.04516.809-0.097-0.0970.0000.0000.0000.000
19A20ARG10.8600.94716.1890.3450.3450.0000.0000.0000.000
20A21ALA00.0180.00414.773-0.075-0.0750.0000.0000.0000.000
21A22THR00.002-0.02212.505-0.145-0.1450.0000.0000.0000.000
22A23ALA0-0.0110.00211.228-0.289-0.2890.0000.0000.0000.000
23A24VAL00.0110.00510.581-0.219-0.2190.0000.0000.0000.000
24A25LEU0-0.051-0.0117.148-0.160-0.1600.0000.0000.0000.000
25A26PHE00.054-0.0046.688-0.728-0.7280.0000.0000.0000.000
26A27ALA0-0.0080.0105.782-1.144-1.1440.0000.0000.0000.000
27A28ARG10.9220.9595.5351.0621.0620.0000.0000.0000.000
28A29GLU-1-0.853-0.9112.476-10.289-6.3411.925-2.462-3.412-0.023
29A30GLY00.0120.0341.735-16.403-20.63015.283-6.997-4.059-0.060
30A31ALA0-0.034-0.0053.3511.5821.6880.0170.037-0.1600.000
31A32LYS10.8270.9176.5011.6531.6530.0000.0000.0000.000
32A33VAL00.012-0.0039.4450.0890.0890.0000.0000.0000.000
33A34THR00.0210.01112.0810.1820.1820.0000.0000.0000.000
34A35ILE0-0.027-0.00414.968-0.037-0.0370.0000.0000.0000.000
35A36THR00.003-0.03117.4430.0650.0650.0000.0000.0000.000
36A37GLY0-0.010-0.01121.163-0.015-0.0150.0000.0000.0000.000
37A38ARG10.8790.92624.3440.2670.2670.0000.0000.0000.000
38A39HIS00.0010.00327.0080.0190.0190.0000.0000.0000.000
39A40ALA00.0710.02425.706-0.022-0.0220.0000.0000.0000.000
40A41GLU-1-0.880-0.93424.978-0.221-0.2210.0000.0000.0000.000
41A42ARG10.8910.94524.6690.2460.2460.0000.0000.0000.000
42A43LEU00.0150.00319.999-0.023-0.0230.0000.0000.0000.000
43A44GLU-1-0.784-0.86220.243-0.387-0.3870.0000.0000.0000.000
44A45GLU-1-0.879-0.92120.484-0.318-0.3180.0000.0000.0000.000
45A46THR0-0.068-0.06016.1410.0050.0050.0000.0000.0000.000
46A47ARG10.8530.91616.2070.2820.2820.0000.0000.0000.000
47A48GLN0-0.027-0.03016.1310.0060.0060.0000.0000.0000.000
48A49GLN0-0.053-0.03815.390-0.029-0.0290.0000.0000.0000.000
49A50ILE0-0.026-0.00910.888-0.032-0.0320.0000.0000.0000.000
50A51LEU0-0.008-0.00112.1560.0160.0160.0000.0000.0000.000
51A52ALA0-0.0040.00913.9250.0750.0750.0000.0000.0000.000
52A53ALA0-0.090-0.0379.6690.0600.0600.0000.0000.0000.000
53A54GLY0-0.005-0.0059.6290.0810.0810.0000.0000.0000.000
54A55VAL0-0.066-0.0217.9430.0840.0840.0000.0000.0000.000
55A56SER00.0300.00810.2930.0190.0190.0000.0000.0000.000
56A57GLU-1-0.834-0.93912.306-0.387-0.3870.0000.0000.0000.000
57A58GLN0-0.021-0.00913.878-0.061-0.0610.0000.0000.0000.000
58A59ASN0-0.028-0.0078.1640.0480.0480.0000.0000.0000.000
59A60VAL00.0200.01111.602-0.208-0.2080.0000.0000.0000.000
60A61ASN00.0000.00514.0910.1730.1730.0000.0000.0000.000
61A62SER00.008-0.00817.218-0.063-0.0630.0000.0000.0000.000
62A63VAL00.0240.02319.7950.0440.0440.0000.0000.0000.000
63A64VAL00.0080.00722.581-0.015-0.0150.0000.0000.0000.000
64A65ALA00.0370.01925.6500.0210.0210.0000.0000.0000.000
65A66ASP-1-0.801-0.85527.197-0.281-0.2810.0000.0000.0000.000
66A67VAL00.0670.02524.7980.0080.0080.0000.0000.0000.000
67A68THR0-0.063-0.05227.6480.0030.0030.0000.0000.0000.000
68A69THR0-0.061-0.02830.8740.0170.0170.0000.0000.0000.000
69A70ASP-1-0.834-0.90930.558-0.267-0.2670.0000.0000.0000.000
70A71ALA00.0760.02830.514-0.013-0.0130.0000.0000.0000.000
71A72GLY00.0080.01028.447-0.012-0.0120.0000.0000.0000.000
72A73GLN0-0.049-0.04626.149-0.025-0.0250.0000.0000.0000.000
73A74ASP-1-0.801-0.89525.492-0.329-0.3290.0000.0000.0000.000
74A75GLU-1-0.914-0.92825.277-0.328-0.3280.0000.0000.0000.000
75A76ILE0-0.047-0.02620.905-0.034-0.0340.0000.0000.0000.000
76A77LEU0-0.028-0.01221.078-0.056-0.0560.0000.0000.0000.000
77A78SER0-0.014-0.03021.804-0.021-0.0210.0000.0000.0000.000
78A79THR0-0.004-0.01521.552-0.025-0.0250.0000.0000.0000.000
79A80THR00.0080.00716.552-0.050-0.0500.0000.0000.0000.000
80A81LEU0-0.038-0.00517.846-0.041-0.0410.0000.0000.0000.000
81A82GLY0-0.0170.01120.0370.0180.0180.0000.0000.0000.000
82A83LYS10.8660.92417.6120.4560.4560.0000.0000.0000.000
83A84PHE0-0.038-0.04014.082-0.033-0.0330.0000.0000.0000.000
84A85GLY00.0040.01915.732-0.040-0.0400.0000.0000.0000.000
85A86LYS10.8020.87911.8381.2011.2010.0000.0000.0000.000
86A87LEU00.012-0.00115.500-0.056-0.0560.0000.0000.0000.000
87A88ASP-1-0.787-0.85512.173-1.232-1.2320.0000.0000.0000.000
88A89ILE00.0050.00310.2970.0320.0320.0000.0000.0000.000
89A90LEU00.0060.02214.3600.0170.0170.0000.0000.0000.000
90A91VAL00.0050.00814.3460.0320.0320.0000.0000.0000.000
91A92ASN0-0.033-0.03217.4780.0340.0340.0000.0000.0000.000
92A93ASN0-0.014-0.01619.7020.0440.0440.0000.0000.0000.000
93A94ALA00.0040.01721.6480.0170.0170.0000.0000.0000.000
94A95GLY00.003-0.00424.9580.0210.0210.0000.0000.0000.000
95A109GLN00.0400.02741.1880.0040.0040.0000.0000.0000.000
96A110SER0-0.035-0.04544.238-0.002-0.0020.0000.0000.0000.000
97A111ILE00.0850.03043.482-0.007-0.0070.0000.0000.0000.000
98A112GLU-1-0.785-0.86943.005-0.142-0.1420.0000.0000.0000.000
99A113SER0-0.021-0.01039.970-0.010-0.0100.0000.0000.0000.000
100A114TYR0-0.0130.01538.698-0.016-0.0160.0000.0000.0000.000
101A115ASP-1-0.862-0.93438.384-0.178-0.1780.0000.0000.0000.000
102A116ALA0-0.062-0.03036.876-0.013-0.0130.0000.0000.0000.000
103A117THR0-0.039-0.03833.958-0.019-0.0190.0000.0000.0000.000
104A118LEU00.0360.01033.469-0.022-0.0220.0000.0000.0000.000
105A119ASN0-0.0120.00333.602-0.018-0.0180.0000.0000.0000.000
106A120LEU0-0.002-0.00828.333-0.016-0.0160.0000.0000.0000.000
107A121ASN0-0.034-0.02929.003-0.040-0.0400.0000.0000.0000.000
108A122LEU00.0180.01729.125-0.016-0.0160.0000.0000.0000.000
109A123ARG10.9590.98630.3700.2120.2120.0000.0000.0000.000
110A124SER0-0.047-0.03328.417-0.014-0.0140.0000.0000.0000.000
111A125VAL00.0340.03224.976-0.020-0.0200.0000.0000.0000.000
112A126ILE00.0040.01826.525-0.020-0.0200.0000.0000.0000.000
113A127ALA0-0.042-0.01928.776-0.003-0.0030.0000.0000.0000.000
114A128LEU00.0350.01922.2610.0000.0000.0000.0000.0000.000
115A129THR00.013-0.02223.631-0.033-0.0330.0000.0000.0000.000
116A130LYS10.9030.95325.0060.2680.2680.0000.0000.0000.000
117A131LYS10.7980.88826.3150.3040.3040.0000.0000.0000.000
118A132ALA00.0250.01421.163-0.003-0.0030.0000.0000.0000.000
119A133VAL00.0190.00722.440-0.024-0.0240.0000.0000.0000.000
120A134PRO00.0240.02123.510-0.015-0.0150.0000.0000.0000.000
121A135HIS00.0480.01320.450-0.007-0.0070.0000.0000.0000.000
122A136LEU0-0.0120.00317.479-0.036-0.0360.0000.0000.0000.000
123A137SER00.003-0.00619.648-0.017-0.0170.0000.0000.0000.000
124A138SER0-0.078-0.02820.6810.0280.0280.0000.0000.0000.000
125A139THR0-0.052-0.04115.6730.0280.0280.0000.0000.0000.000
126A140LYS10.8820.94916.3870.3070.3070.0000.0000.0000.000
127A141GLY00.0490.02215.774-0.062-0.0620.0000.0000.0000.000
128A142GLU-1-0.818-0.89113.792-0.875-0.8750.0000.0000.0000.000
129A143ILE0-0.0070.00716.745-0.036-0.0360.0000.0000.0000.000
130A144VAL0-0.017-0.01415.1540.0290.0290.0000.0000.0000.000
131A145ASN0-0.016-0.02318.404-0.029-0.0290.0000.0000.0000.000
132A146ILE00.0140.01317.9950.0080.0080.0000.0000.0000.000
133A147SER0-0.007-0.03322.0260.0400.0400.0000.0000.0000.000
134A148SER00.0360.00025.2920.0000.0000.0000.0000.0000.000
135A149ILE00.0170.03827.0910.0110.0110.0000.0000.0000.000
136A150ALA0-0.034-0.02429.2290.0220.0220.0000.0000.0000.000
137A151SER0-0.063-0.03430.0850.0260.0260.0000.0000.0000.000
138A152GLY00.0570.00230.924-0.012-0.0120.0000.0000.0000.000
139A153LEU0-0.044-0.00733.2100.0080.0080.0000.0000.0000.000
140A154HIS10.8710.92832.7700.2050.2050.0000.0000.0000.000
141A155ALA00.0200.02037.709-0.005-0.0050.0000.0000.0000.000
142A156THR00.001-0.02034.460-0.001-0.0010.0000.0000.0000.000
143A157PRO00.0200.00337.667-0.005-0.0050.0000.0000.0000.000
144A158ASP-1-0.878-0.92737.505-0.152-0.1520.0000.0000.0000.000
145A159PHE0-0.040-0.02133.846-0.007-0.0070.0000.0000.0000.000
146A160PRO00.0170.02836.520-0.010-0.0100.0000.0000.0000.000
147A161TYR00.016-0.02537.561-0.005-0.0050.0000.0000.0000.000
148A162TYR00.0070.00127.414-0.008-0.0080.0000.0000.0000.000
149A163SER00.025-0.01132.622-0.014-0.0140.0000.0000.0000.000
150A164ILE00.0100.01433.653-0.009-0.0090.0000.0000.0000.000
151A165ALA0-0.0030.00432.646-0.005-0.0050.0000.0000.0000.000
152A166LYS10.8670.93425.8220.3670.3670.0000.0000.0000.000
153A167ALA00.0420.03330.061-0.012-0.0120.0000.0000.0000.000
154A168ALA0-0.039-0.01932.336-0.001-0.0010.0000.0000.0000.000
155A169ILE00.0000.00326.220-0.009-0.0090.0000.0000.0000.000
156A170ASP-1-0.805-0.84627.554-0.342-0.3420.0000.0000.0000.000
157A171GLN0-0.021-0.01128.821-0.002-0.0020.0000.0000.0000.000
158A172TYR00.015-0.00126.1660.0110.0110.0000.0000.0000.000
159A173THR0-0.0010.00123.708-0.025-0.0250.0000.0000.0000.000
160A174ARG10.8650.93026.4530.2520.2520.0000.0000.0000.000
161A175ASN0-0.009-0.00728.5240.0090.0090.0000.0000.0000.000
162A176THR00.003-0.02626.424-0.005-0.0050.0000.0000.0000.000
163A177ALA0-0.0030.02424.856-0.010-0.0100.0000.0000.0000.000
164A178ILE0-0.019-0.01225.7660.0020.0020.0000.0000.0000.000
165A179ASP-1-0.929-0.96528.759-0.263-0.2630.0000.0000.0000.000
166A180LEU00.028-0.01124.4030.0000.0000.0000.0000.0000.000
167A181ILE0-0.0170.02022.375-0.020-0.0200.0000.0000.0000.000
168A182GLN0-0.058-0.02425.1100.0160.0160.0000.0000.0000.000
169A183HIS0-0.043-0.01925.3660.0140.0140.0000.0000.0000.000
170A184GLY0-0.038-0.02022.117-0.026-0.0260.0000.0000.0000.000
171A185ILE0-0.0260.00319.966-0.068-0.0680.0000.0000.0000.000
172A186ARG10.7720.89015.3930.8230.8230.0000.0000.0000.000
173A187VAL00.0020.00619.269-0.070-0.0700.0000.0000.0000.000
174A188ASN00.001-0.01118.7530.1010.1010.0000.0000.0000.000
175A189SER00.0220.01020.880-0.030-0.0300.0000.0000.0000.000
176A190ILE00.0240.02116.8200.0030.0030.0000.0000.0000.000
177A191SER0-0.005-0.00921.421-0.003-0.0030.0000.0000.0000.000
178A192PRO0-0.0040.01021.8520.0200.0200.0000.0000.0000.000
179A193GLY00.0370.00423.6980.0270.0270.0000.0000.0000.000
180A194LEU0-0.034-0.01226.152-0.013-0.0130.0000.0000.0000.000
181A195VAL0-0.007-0.00821.331-0.011-0.0110.0000.0000.0000.000
182A196ALA0-0.013-0.00524.2950.0130.0130.0000.0000.0000.000
183A197THR0-0.007-0.02522.113-0.036-0.0360.0000.0000.0000.000
184A198GLY00.0100.01721.617-0.035-0.0350.0000.0000.0000.000
185A213PHE00.0350.00633.2990.0020.0020.0000.0000.0000.000
186A214TYR00.0690.02137.217-0.005-0.0050.0000.0000.0000.000
187A215SER00.0420.02939.144-0.002-0.0020.0000.0000.0000.000
188A216THR00.0260.00535.1200.0000.0000.0000.0000.0000.000
189A217MET0-0.013-0.01130.906-0.011-0.0110.0000.0000.0000.000
190A218ALA0-0.0130.00635.113-0.003-0.0030.0000.0000.0000.000
191A219THR00.0570.01337.267-0.001-0.0010.0000.0000.0000.000
192A220MET0-0.069-0.00929.244-0.003-0.0030.0000.0000.0000.000
193A221LYS10.8450.89830.4460.1070.1070.0000.0000.0000.000
194A222GLU-1-0.969-0.96434.097-0.102-0.1020.0000.0000.0000.000
195A223CYS0-0.030-0.00934.090-0.002-0.0020.0000.0000.0000.000
196A224VAL0-0.026-0.00927.872-0.014-0.0140.0000.0000.0000.000
197A225PRO00.0470.04430.4390.0070.0070.0000.0000.0000.000
198A226ALA0-0.0120.00125.9750.0090.0090.0000.0000.0000.000
199A227GLY0-0.032-0.01227.8910.0090.0090.0000.0000.0000.000
200A228VAL0-0.021-0.01724.3190.0130.0130.0000.0000.0000.000
201A229MET0-0.0180.00225.922-0.015-0.0150.0000.0000.0000.000
202A230GLY00.0940.06322.786-0.006-0.0060.0000.0000.0000.000
203A231GLN0-0.024-0.02519.1040.0180.0180.0000.0000.0000.000
204A232PRO00.005-0.01217.959-0.048-0.0480.0000.0000.0000.000
205A233GLN00.044-0.00114.074-0.039-0.0390.0000.0000.0000.000
206A234ASP-1-0.802-0.88614.428-0.496-0.4960.0000.0000.0000.000
207A235ILE0-0.036-0.02416.233-0.032-0.0320.0000.0000.0000.000
208A236ALA0-0.0050.00612.368-0.061-0.0610.0000.0000.0000.000
209A237GLU-1-0.813-0.9219.648-1.645-1.6450.0000.0000.0000.000
210A238VAL0-0.019-0.00311.986-0.087-0.0870.0000.0000.0000.000
211A239ILE0-0.011-0.01113.124-0.004-0.0040.0000.0000.0000.000
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