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: P5J6Z

Calculation Name: 3SO6-A-Xray21

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SO6

Chain ID: A

ChEMBL ID:

UniProt ID: D3ZAR1

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1469410.88355
FMO2-HF: Nuclear repulsion 1408552.450614
FMO2-HF: Total energy -60858.432936
FMO2-MP2: Total energy -61031.534566


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:42:MET)


Summations of interaction energy for fragment #1(A:42:MET)
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.
-37.761-50.62263.962-22.376-28.72-0.074
Interaction energy analysis for fragmet #1(A:42:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.009
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].
3A44GLY00.008-0.0192.480-5.853-3.2861.574-1.876-2.265-0.014
4A45MET0-0.053-0.0162.9150.3781.1260.095-0.137-0.7060.000
5A46VAL00.0220.0105.1220.3010.345-0.0010.000-0.0420.000
6A47PHE0-0.031-0.0125.9440.0790.0790.0000.0000.0000.000
7A48SER00.0350.02210.7150.0770.0770.0000.0000.0000.000
8A49LEU0-0.025-0.00111.8160.0250.0250.0000.0000.0000.000
9A50LYS10.9370.96815.8710.1880.1880.0000.0000.0000.000
10A51TYR0-0.0070.01317.668-0.006-0.0060.0000.0000.0000.000
11A52LEU0-0.034-0.02719.2370.0120.0120.0000.0000.0000.000
12A53GLY00.0310.01720.3080.0120.0120.0000.0000.0000.000
13A54MET0-0.035-0.00220.199-0.007-0.0070.0000.0000.0000.000
14A55THR0-0.027-0.00821.7660.0040.0040.0000.0000.0000.000
15A56LEU00.0900.05422.3850.0010.0010.0000.0000.0000.000
16A57VAL0-0.057-0.03220.589-0.007-0.0070.0000.0000.0000.000
17A58GLU-1-0.863-0.94223.9040.0090.0090.0000.0000.0000.000
18A59ARG10.8760.92323.611-0.003-0.0030.0000.0000.0000.000
19A60PRO00.0550.03518.678-0.005-0.0050.0000.0000.0000.000
20A61LYS10.8900.94615.392-0.138-0.1380.0000.0000.0000.000
21A62GLY00.0820.03718.374-0.002-0.0020.0000.0000.0000.000
22A63GLU-1-0.824-0.89419.628-0.065-0.0650.0000.0000.0000.000
23A64GLU-1-0.728-0.82420.471-0.010-0.0100.0000.0000.0000.000
24A65LEU0-0.091-0.02321.235-0.005-0.0050.0000.0000.0000.000
25A66SER00.045-0.00718.150-0.001-0.0010.0000.0000.0000.000
26A67ALA00.0020.02120.088-0.010-0.0100.0000.0000.0000.000
27A68ALA00.0060.00822.391-0.005-0.0050.0000.0000.0000.000
28A69ALA00.0500.02321.194-0.002-0.0020.0000.0000.0000.000
29A70VAL00.0540.02618.888-0.005-0.0050.0000.0000.0000.000
30A71LYS10.8420.91421.8550.0490.0490.0000.0000.0000.000
31A72ARG10.8740.92825.1330.0290.0290.0000.0000.0000.000
32A73ILE00.0250.02320.541-0.001-0.0010.0000.0000.0000.000
33A74VAL0-0.003-0.01222.670-0.004-0.0040.0000.0000.0000.000
34A75ALA0-0.040-0.01625.0350.0000.0000.0000.0000.0000.000
35A76THR00.0160.01727.2900.0030.0030.0000.0000.0000.000
36A77ALA00.0720.04625.0840.0010.0010.0000.0000.0000.000
37A78LYS10.8740.92627.2180.0810.0810.0000.0000.0000.000
38A79ALA00.0240.03229.5760.0010.0010.0000.0000.0000.000
39A80SER0-0.034-0.00329.2740.0020.0020.0000.0000.0000.000
40A81GLY00.0490.03131.6400.0030.0030.0000.0000.0000.000
41A82LYS10.9240.97629.7460.0610.0610.0000.0000.0000.000
42A83LYS10.9330.96327.3980.0840.0840.0000.0000.0000.000
43A84LEU00.0050.00722.2200.0020.0020.0000.0000.0000.000
44A85GLN00.0380.06121.197-0.002-0.0020.0000.0000.0000.000
45A86LYS10.8590.92919.7670.1360.1360.0000.0000.0000.000
46A87VAL00.0350.02314.8240.0160.0160.0000.0000.0000.000
47A88THR0-0.027-0.01212.072-0.037-0.0370.0000.0000.0000.000
48A89LEU00.0040.0049.1890.0430.0430.0000.0000.0000.000
49A90LYS10.9220.9687.0230.8940.8940.0000.0000.0000.000
50A91VAL0-0.004-0.0092.546-0.1830.2650.371-0.146-0.6740.001
51A92SER00.002-0.0112.861-3.637-2.1650.888-1.072-1.287-0.004
52A93PRO00.0390.0112.312-0.367-1.0765.926-1.157-4.0600.005
53A94ARG10.9220.9724.906-1.247-1.1110.005-0.063-0.0780.000
54A95GLY0-0.008-0.0037.061-0.209-0.2090.0000.0000.0000.000
55A96ILE0-0.033-0.0036.912-0.053-0.0530.0000.0000.0000.000
56A97ILE0-0.027-0.0018.8300.0400.0400.0000.0000.0000.000
57A98LEU00.0020.01011.115-0.107-0.1070.0000.0000.0000.000
58A99THR00.0530.01513.7260.0340.0340.0000.0000.0000.000
59A100ASP-1-0.731-0.82016.079-0.143-0.1430.0000.0000.0000.000
60A101SER0-0.049-0.06017.519-0.004-0.0040.0000.0000.0000.000
61A102LEU0-0.079-0.02318.9540.0020.0020.0000.0000.0000.000
62A103THR00.011-0.01922.2190.0050.0050.0000.0000.0000.000
63A104SER0-0.0090.00618.5030.0110.0110.0000.0000.0000.000
64A105GLN00.0410.03218.9460.0070.0070.0000.0000.0000.000
65A106LEU0-0.045-0.03015.494-0.020-0.0200.0000.0000.0000.000
66A107ILE0-0.0180.00717.2990.0090.0090.0000.0000.0000.000
67A108GLU-1-0.722-0.84816.2240.0190.0190.0000.0000.0000.000
68A109ASN00.0000.00712.472-0.012-0.0120.0000.0000.0000.000
69A110VAL00.0070.00311.7580.0260.0260.0000.0000.0000.000
70A111SER00.002-0.01211.1890.0780.0780.0000.0000.0000.000
71A112ILE00.0620.0076.775-0.080-0.0800.0000.0000.0000.000
72A113TYR0-0.033-0.01410.389-0.024-0.0240.0000.0000.0000.000
73A114ARG10.7400.87313.693-0.103-0.1030.0000.0000.0000.000
74A115ILE0-0.041-0.0019.262-0.049-0.0490.0000.0000.0000.000
75A116SER0-0.067-0.03712.7190.0420.0420.0000.0000.0000.000
76A117TYR00.0470.00413.2100.0180.0180.0000.0000.0000.000
77A118CYS0-0.061-0.0249.474-0.036-0.0360.0000.0000.0000.000
78A119THR0-0.029-0.02211.9880.0070.0070.0000.0000.0000.000
79A120ALA00.0480.03713.334-0.032-0.0320.0000.0000.0000.000
80A121ASP-1-0.790-0.88414.732-0.072-0.0720.0000.0000.0000.000
81A122LYS11.0060.98518.4030.0570.0570.0000.0000.0000.000
82A123MET0-0.025-0.00521.218-0.001-0.0010.0000.0000.0000.000
83A124HIS0-0.0340.00121.711-0.007-0.0070.0000.0000.0000.000
84A125ASP-1-0.831-0.90319.592-0.161-0.1610.0000.0000.0000.000
85A126LYS10.8540.91018.4130.1270.1270.0000.0000.0000.000
86A127VAL0-0.039-0.02817.402-0.021-0.0210.0000.0000.0000.000
87A128PHE00.0390.0299.450-0.015-0.0150.0000.0000.0000.000
88A129ALA00.000-0.01313.7820.0100.0100.0000.0000.0000.000
89A130TYR00.003-0.01211.339-0.016-0.0160.0000.0000.0000.000
90A131ILE00.003-0.00313.411-0.012-0.0120.0000.0000.0000.000
91A132ALA00.014-0.00414.2270.0310.0310.0000.0000.0000.000
92A133GLN00.0130.02216.069-0.032-0.0320.0000.0000.0000.000
93A134SER0-0.023-0.00818.2940.0110.0110.0000.0000.0000.000
94A135GLN00.012-0.00419.3680.0030.0030.0000.0000.0000.000
95A136GLN0-0.006-0.00920.9180.0070.0070.0000.0000.0000.000
96A137ASN0-0.0010.00724.007-0.002-0.0020.0000.0000.0000.000
97A138GLU-1-0.874-0.94123.7260.0490.0490.0000.0000.0000.000
98A139SER0-0.0340.04824.177-0.001-0.0010.0000.0000.0000.000
99A140LEU00.016-0.00520.2810.0080.0080.0000.0000.0000.000
100A141GLU-1-0.708-0.82019.208-0.015-0.0150.0000.0000.0000.000
101A142CYS0-0.100-0.04617.3650.0000.0000.0000.0000.0000.000
102A143HIS00.0770.04715.601-0.022-0.0220.0000.0000.0000.000
103A144ALA00.016-0.00415.756-0.015-0.0150.0000.0000.0000.000
104A145PHE00.0290.00914.109-0.007-0.0070.0000.0000.0000.000
105A146LEU00.0010.00116.598-0.005-0.0050.0000.0000.0000.000
106A147CYS0-0.0080.02714.624-0.032-0.0320.0000.0000.0000.000
107A148THR00.000-0.02117.0810.0290.0290.0000.0000.0000.000
108A149LYS10.9580.96817.9860.2560.2560.0000.0000.0000.000
109A150ARG11.0301.03517.1520.1560.1560.0000.0000.0000.000
110A151LYN0-0.006-0.02315.6840.0010.0010.0000.0000.0000.000
111A152VAL0-0.0120.00812.931-0.048-0.0480.0000.0000.0000.000
112A153ALA00.0810.04712.086-0.060-0.0600.0000.0000.0000.000
113A154GLN00.0440.03011.837-0.033-0.0330.0000.0000.0000.000
114A155ALA00.0230.0239.337-0.010-0.0100.0000.0000.0000.000
115A156VAL0-0.0010.0137.587-0.189-0.1890.0000.0000.0000.000
116A157THR00.021-0.0146.797-0.089-0.0890.0000.0000.0000.000
117A158LEU00.0060.0067.5040.0860.0860.0000.0000.0000.000
118A159THR0-0.029-0.0212.589-0.395-0.0430.855-0.206-1.0000.001
119A160VAL00.001-0.0142.527-2.061-1.1701.144-0.764-1.271-0.012
120A161ALA00.0020.0194.7250.4620.556-0.001-0.003-0.0900.000
121A162GLN00.0370.0062.698-6.713-3.5493.944-2.089-5.018-0.018
122A163ALA00.0420.0212.491-0.4251.4412.197-1.541-2.522-0.003
123A164PHE0-0.006-0.0113.6640.153-0.9660.0501.398-0.329-0.001
124A165LYS10.8950.9596.849-0.180-0.1800.0000.0000.0000.000
125A166VAL00.0290.0182.395-1.608-0.3100.653-0.452-1.4990.001
126A167ALA0-0.009-0.0135.486-0.523-0.5230.0000.0000.0000.000
127A168PHE0-0.017-0.0047.710-0.250-0.2500.0000.0000.0000.000
128A169GLU-1-0.776-0.8718.102-0.263-0.2630.0000.0000.0000.000
129A170PHE0-0.013-0.0124.180-0.116-0.005-0.001-0.010-0.1000.000
130A171TRP0-0.032-0.0119.599-0.002-0.0020.0000.0000.0000.000
131A172GLN00.0440.03012.896-0.030-0.0300.0000.0000.0000.000
132A173VAL0-0.0310.01311.651-0.012-0.0120.0000.0000.0000.000
133A174SER0-0.001-0.00614.4440.0060.0060.0000.0000.0000.000
134A175LEU0-0.0120.00910.5010.0080.0080.0000.0000.0000.000
135A176VAL0-0.003-0.00911.0770.0080.0080.0000.0000.0000.000
136A177PRO00.0070.0207.3540.0030.0030.0000.0000.0000.000
137A178ARG00.1660.0924.336-1.356-1.2280.000-0.056-0.0720.000
138A1HOH0-0.0120.00117.2530.0030.0030.0000.0000.0000.000
139A2HOH0-0.042-0.03017.396-0.007-0.0070.0000.0000.0000.000
140A3HOH00.0090.00818.8890.0020.0020.0000.0000.0000.000
141A4HOH0-0.008-0.00910.7210.0190.0190.0000.0000.0000.000
142A5HOH0-0.066-0.04922.7150.0020.0020.0000.0000.0000.000
143A6HOH0-0.037-0.03313.099-0.015-0.0150.0000.0000.0000.000
144A7HOH00.0070.00516.1460.0020.0020.0000.0000.0000.000
145A8HOH0-0.004-0.00621.0370.0010.0010.0000.0000.0000.000
146A9HOH00.0170.01024.8680.0010.0010.0000.0000.0000.000
147A10HOH0-0.0190.00216.186-0.004-0.0040.0000.0000.0000.000
148A11HOH00.0180.01125.5710.0020.0020.0000.0000.0000.000
149A12HOH00.0040.00511.846-0.004-0.0040.0000.0000.0000.000
150A14HOH00.0320.02123.041-0.002-0.0020.0000.0000.0000.000
151A15HOH0-0.028-0.02218.6390.0010.0010.0000.0000.0000.000
152A16HOH0-0.003-0.01412.7080.0100.0100.0000.0000.0000.000
153A18HOH0-0.019-0.01524.7160.0040.0040.0000.0000.0000.000
154A20HOH0-0.052-0.03721.1450.0050.0050.0000.0000.0000.000
155A21HOH0-0.006-0.01020.533-0.005-0.0050.0000.0000.0000.000
156A22HOH00.0250.01023.8950.0000.0000.0000.0000.0000.000
157A25HOH0-0.002-0.00222.8960.0000.0000.0000.0000.0000.000
158A26HOH00.0070.00413.0640.0080.0080.0000.0000.0000.000
159A27HOH0-0.044-0.03121.5850.0050.0050.0000.0000.0000.000
160A28HOH00.0010.00317.1200.0030.0030.0000.0000.0000.000
161A29HOH0-0.033-0.0248.242-0.045-0.0450.0000.0000.0000.000
162A31HOH0-0.026-0.03422.9660.0010.0010.0000.0000.0000.000
163A32HOH0-0.023-0.01831.2390.0010.0010.0000.0000.0000.000
164A33HOH00.0380.02218.217-0.001-0.0010.0000.0000.0000.000
165A35HOH0-0.036-0.01715.342-0.001-0.0010.0000.0000.0000.000
166A36HOH00.0290.01913.0500.0130.0130.0000.0000.0000.000
167A37HOH00.000-0.00817.0750.0080.0080.0000.0000.0000.000
168A38HOH0-0.057-0.04618.6950.0100.0100.0000.0000.0000.000
169A39HOH00.0330.01724.310-0.002-0.0020.0000.0000.0000.000
170A40HOH0-0.0110.00724.9830.0020.0020.0000.0000.0000.000
171A41HOH0-0.014-0.03026.3140.0020.0020.0000.0000.0000.000
172A179HOH00.0420.03232.304-0.001-0.0010.0000.0000.0000.000
173A180HOH00.0210.00913.478-0.007-0.0070.0000.0000.0000.000
174A181HOH00.0040.0041.649-1.617-13.19121.015-6.521-2.919-0.034
175A182HOH0-0.036-0.02722.8000.0010.0010.0000.0000.0000.000
176A187HOH0-0.064-0.04322.774-0.003-0.0030.0000.0000.0000.000
177A188HOH0-0.016-0.02618.0090.0030.0030.0000.0000.0000.000
178A190HOH00.0090.00427.383-0.001-0.0010.0000.0000.0000.000
179A191HOH00.0010.0137.246-0.026-0.0260.0000.0000.0000.000
180A196HOH00.0100.01715.9450.0090.0090.0000.0000.0000.000
181A197HOH00.0110.02020.1800.0060.0060.0000.0000.0000.000
182A198HOH0-0.060-0.06924.674-0.002-0.0020.0000.0000.0000.000
183A202HOH0-0.019-0.01128.9910.0000.0000.0000.0000.0000.000
184A203HOH0-0.050-0.03412.949-0.001-0.0010.0000.0000.0000.000
185A205HOH00.000-0.00514.121-0.015-0.0150.0000.0000.0000.000
186A206HOH0-0.0030.00427.4870.0010.0010.0000.0000.0000.000
187A207HOH00.0140.01322.8900.0040.0040.0000.0000.0000.000
188A208HOH0-0.052-0.04210.3010.0250.0250.0000.0000.0000.000
189A211HOH00.0180.0171.932-5.061-7.9957.790-2.449-2.406-0.023
190A215HOH0-0.005-0.0059.876-0.017-0.0170.0000.0000.0000.000
191A216HOH00.0430.02416.7420.0100.0100.0000.0000.0000.000
192A218HOH00.0330.02416.7480.0100.0100.0000.0000.0000.000
193A219HOH0-0.032-0.02716.8250.0030.0030.0000.0000.0000.000
194A222HOH00.0350.02927.528-0.002-0.0020.0000.0000.0000.000
195A224HOH0-0.020-0.01815.6140.0050.0050.0000.0000.0000.000
196A225HOH00.0110.01112.183-0.010-0.0100.0000.0000.0000.000
197A229HOH0-0.029-0.0321.805-8.180-18.34117.457-5.084-2.2120.027
198A232HOH0-0.058-0.0493.5980.0470.3640.001-0.148-0.1700.000
199A233HOH0-0.037-0.02521.5720.0030.0030.0000.0000.0000.000
200A234HOH00.006-0.00424.618-0.003-0.0030.0000.0000.0000.000
201A235HOH0-0.029-0.0299.5850.0270.0270.0000.0000.0000.000
202A236HOH0-0.030-0.04023.798-0.002-0.0020.0000.0000.0000.000
203A237HOH0-0.046-0.03326.597-0.002-0.0020.0000.0000.0000.000
204A240HOH0-0.107-0.10027.2270.0000.0000.0000.0000.0000.000
205A241HOH00.0840.09329.131-0.001-0.0010.0000.0000.0000.000
206A245HOH0-0.021-0.01327.6280.0000.0000.0000.0000.0000.000
207A247HOH00.0400.02926.108-0.003-0.0030.0000.0000.0000.000
208A250HOH00.0500.03731.533-0.002-0.0020.0000.0000.0000.000
209A255HOH0-0.046-0.04119.251-0.005-0.0050.0000.0000.0000.000
210A257HOH0-0.042-0.03719.0610.0040.0040.0000.0000.0000.000
211A258HOH0-0.007-0.02321.1650.0020.0020.0000.0000.0000.000
212A259HOH0-0.019-0.02920.1270.0040.0040.0000.0000.0000.000
213A260HOH00.0180.01320.0750.0080.0080.0000.0000.0000.000
214A261HOH00.005-0.00818.555-0.002-0.0020.0000.0000.0000.000
215A262HOH00.0050.01322.1790.0030.0030.0000.0000.0000.000
216A265HOH0-0.035-0.02535.2670.0010.0010.0000.0000.0000.000
217A268HOH0-0.023-0.0259.256-0.002-0.0020.0000.0000.0000.000
218A271HOH0-0.026-0.02430.8840.0010.0010.0000.0000.0000.000
219A275HOH0-0.019-0.02317.1610.0090.0090.0000.0000.0000.000
220A280HOH0-0.004-0.01113.531-0.001-0.0010.0000.0000.0000.000
221A282HOH00.0220.01528.0940.0010.0010.0000.0000.0000.000
222A292HOH0-0.024-0.02626.9520.0010.0010.0000.0000.0000.000
223A293HOH0-0.052-0.03128.507-0.001-0.0010.0000.0000.0000.000
224A294HOH00.013-0.00722.972-0.001-0.0010.0000.0000.0000.000
225A296HOH0-0.040-0.02622.7510.0000.0000.0000.0000.0000.000
226A297HOH0-0.027-0.02818.172-0.006-0.0060.0000.0000.0000.000
227A300HOH0-0.021-0.03623.0840.0010.0010.0000.0000.0000.000
228A302HOH0-0.029-0.01524.2340.0030.0030.0000.0000.0000.000
229A303HOH00.0320.02414.9710.0150.0150.0000.0000.0000.000