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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6Y16Z

Calculation Name: 4P5P-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 4P5P

Chain ID: A

ChEMBL ID:

UniProt ID: A0Q664

Base Structure: X-ray

Registration Date: 2023-09-23

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 225
LigandCharge CSD=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2796184.356405
FMO2-HF: Nuclear repulsion 2708681.376064
FMO2-HF: Total energy -87502.980341
FMO2-MP2: Total energy -87757.904292


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-10.465-3.8427.204-4.332-9.497-0.041
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.033
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].
3A3ASN00.0240.0143.045-2.9630.9520.321-1.758-2.479-0.010
4A4VAL0-0.015-0.0124.7700.2220.272-0.001-0.007-0.0420.000
5A5LEU00.0070.0218.3810.0770.0770.0000.0000.0000.000
6A6MET0-0.044-0.01711.3980.0800.0800.0000.0000.0000.000
7A7VAL00.000-0.00214.386-0.033-0.0330.0000.0000.0000.000
8A8THR00.002-0.00817.7310.0250.0250.0000.0000.0000.000
9A9THR0-0.022-0.04221.014-0.017-0.0170.0000.0000.0000.000
10A10SER00.008-0.01224.350-0.004-0.0040.0000.0000.0000.000
11A11HIS0-0.046-0.00826.446-0.006-0.0060.0000.0000.0000.000
12A12ASP-1-0.796-0.91229.854-0.018-0.0180.0000.0000.0000.000
13A13VAL0-0.0270.00331.9100.0040.0040.0000.0000.0000.000
14A14MET0-0.0100.01034.724-0.002-0.0020.0000.0000.0000.000
15A15GLY00.0360.01736.3930.0010.0010.0000.0000.0000.000
16A16ASN0-0.035-0.02538.390-0.004-0.0040.0000.0000.0000.000
17A17SER0-0.048-0.01239.9730.0010.0010.0000.0000.0000.000
18A18ASN00.000-0.01840.768-0.004-0.0040.0000.0000.0000.000
19A19GLU-1-0.928-0.96137.2790.0140.0140.0000.0000.0000.000
20A20LYS10.8890.94034.3210.0140.0140.0000.0000.0000.000
21A21THR0-0.028-0.05131.9270.0050.0050.0000.0000.0000.000
22A22GLY00.0340.01228.751-0.006-0.0060.0000.0000.0000.000
23A23LEU0-0.044-0.03021.6450.0050.0050.0000.0000.0000.000
24A24TRP00.0460.02125.476-0.001-0.0010.0000.0000.0000.000
25A25LEU00.0360.02422.0450.0120.0120.0000.0000.0000.000
26A26SER00.0560.02321.7620.0090.0090.0000.0000.0000.000
27A27GLH0-0.071-0.08221.1300.0230.0230.0000.0000.0000.000
28A28LEU00.0000.01516.4880.0080.0080.0000.0000.0000.000
29A29THR00.011-0.02016.9860.0450.0450.0000.0000.0000.000
30A30HIS10.7910.87517.238-0.140-0.1400.0000.0000.0000.000
31A31PRO00.009-0.00416.0470.0490.0490.0000.0000.0000.000
32A32TYR00.0470.02910.8360.0980.0980.0000.0000.0000.000
33A33TYR00.019-0.01912.2990.0940.0940.0000.0000.0000.000
34A34SER0-0.062-0.01013.8340.0270.0270.0000.0000.0000.000
35A35ILE0-0.020-0.0159.2670.0810.0810.0000.0000.0000.000
36A36ILE00.0130.0397.5220.2810.2810.0000.0000.0000.000
37A37ASP-1-0.807-0.9026.8122.1662.1660.0000.0000.0000.000
38A38LYS10.9280.9534.347-0.1480.104-0.001-0.029-0.2220.000
39A39ASN0-0.059-0.0222.529-4.449-3.3311.932-0.806-2.245-0.008
40A40ILE0-0.015-0.0032.4970.3920.9504.260-1.532-3.286-0.022
41A41ASN00.0340.0123.516-1.087-0.3630.687-0.212-1.199-0.001
42A42ILE0-0.059-0.0304.748-1.001-0.9950.0060.012-0.0240.000
43A43ASP-1-0.799-0.8458.474-0.504-0.5040.0000.0000.0000.000
44A44ILE0-0.022-0.02410.6600.0150.0150.0000.0000.0000.000
45A45VAL0-0.029-0.00714.364-0.038-0.0380.0000.0000.0000.000
46A46SER00.0130.01117.0680.0270.0270.0000.0000.0000.000
47A47ILE00.0120.00420.698-0.027-0.0270.0000.0000.0000.000
48A48MET0-0.013-0.01723.066-0.018-0.0180.0000.0000.0000.000
49A49GLY0-0.0010.01122.063-0.012-0.0120.0000.0000.0000.000
50A50GLY0-0.037-0.01123.0520.0120.0120.0000.0000.0000.000
51A51GLU-1-0.937-0.95123.763-0.032-0.0320.0000.0000.0000.000
52A52ILE0-0.044-0.03120.0850.0000.0000.0000.0000.0000.000
53A53PRO0-0.0040.02324.7110.0090.0090.0000.0000.0000.000
54A54ILE00.010-0.00925.0290.0060.0060.0000.0000.0000.000
55A55ASP-1-0.808-0.87827.8090.0230.0230.0000.0000.0000.000
56A56PRO00.0640.03430.2550.0070.0070.0000.0000.0000.000
57A57ASN0-0.032-0.02732.5650.0060.0060.0000.0000.0000.000
58A58SER0-0.118-0.06227.6390.0080.0080.0000.0000.0000.000
59A59VAL0-0.016-0.02227.3100.0090.0090.0000.0000.0000.000
60A60ALA0-0.0260.01529.916-0.002-0.0020.0000.0000.0000.000
61A61GLN0-0.064-0.02530.443-0.002-0.0020.0000.0000.0000.000
62A62GLU-1-0.886-0.94329.4930.0670.0670.0000.0000.0000.000
63A63ASP-1-0.814-0.90124.2230.1500.1500.0000.0000.0000.000
64A64TYR00.0250.01920.2320.0060.0060.0000.0000.0000.000
65A65TYR0-0.015-0.02417.8570.0100.0100.0000.0000.0000.000
66A66ASN00.0670.01820.6240.0110.0110.0000.0000.0000.000
67A67ASP-1-0.829-0.91322.7180.0670.0670.0000.0000.0000.000
68A68LYS10.8470.93016.234-0.201-0.2010.0000.0000.0000.000
69A69PHE00.008-0.01215.754-0.005-0.0050.0000.0000.0000.000
70A70LEU00.0160.00919.174-0.017-0.0170.0000.0000.0000.000
71A71ALA0-0.022-0.00921.589-0.017-0.0170.0000.0000.0000.000
72A72ASP-1-0.874-0.93015.1910.0450.0450.0000.0000.0000.000
73A73ASP-1-0.848-0.92518.723-0.025-0.0250.0000.0000.0000.000
74A74ASN0-0.043-0.01712.960-0.049-0.0490.0000.0000.0000.000
75A75LEU0-0.013-0.00513.527-0.013-0.0130.0000.0000.0000.000
76A76LYS10.8440.91317.285-0.014-0.0140.0000.0000.0000.000
77A77ASN0-0.016-0.02319.5060.0010.0010.0000.0000.0000.000
78A78ILE00.0190.02214.429-0.012-0.0120.0000.0000.0000.000
79A79MET0-0.0130.00019.010-0.004-0.0040.0000.0000.0000.000
80A80LYS10.9350.99221.8610.0500.0500.0000.0000.0000.000
81A81ASN0-0.086-0.04722.183-0.003-0.0030.0000.0000.0000.000
82A82SER00.0140.01719.519-0.022-0.0220.0000.0000.0000.000
83A83THR00.0300.00916.456-0.016-0.0160.0000.0000.0000.000
84A84SER0-0.025-0.01818.9430.0130.0130.0000.0000.0000.000
85A85LEU00.022-0.00217.074-0.034-0.0340.0000.0000.0000.000
86A86ARG10.7810.88818.5780.1250.1250.0000.0000.0000.000
87A87ASP-1-0.871-0.94219.109-0.227-0.2270.0000.0000.0000.000
88A88VAL0-0.0140.01413.619-0.041-0.0410.0000.0000.0000.000
89A89ASN0-0.028-0.03113.1820.1140.1140.0000.0000.0000.000
90A90ILE00.0360.00312.333-0.098-0.0980.0000.0000.0000.000
91A91LYS10.8050.88711.9810.3670.3670.0000.0000.0000.000
92A92GLU-1-0.896-0.9328.200-1.373-1.3730.0000.0000.0000.000
93A93TYR0-0.096-0.0696.991-0.549-0.5490.0000.0000.0000.000
94A94ASP-1-0.825-0.9065.899-1.773-1.7730.0000.0000.0000.000
95A95ALA0-0.029-0.0338.9900.2740.2740.0000.0000.0000.000
96A96ILE0-0.0210.00911.135-0.083-0.0830.0000.0000.0000.000
97A97ILE0-0.036-0.02113.1230.0590.0590.0000.0000.0000.000
98A98PHE00.0210.00015.802-0.020-0.0200.0000.0000.0000.000
99A99ALA00.0170.00319.2640.0240.0240.0000.0000.0000.000
100A100GLY00.0530.01420.844-0.016-0.0160.0000.0000.0000.000
101A101GLY00.0250.00824.652-0.004-0.0040.0000.0000.0000.000
102A102HIS10.8640.91327.708-0.033-0.0330.0000.0000.0000.000
103A103GLY00.0520.04829.161-0.004-0.0040.0000.0000.0000.000
104A104THR00.004-0.02224.917-0.006-0.0060.0000.0000.0000.000
105A105MET0-0.0230.00427.593-0.005-0.0050.0000.0000.0000.000
106A106TRP0-0.015-0.01030.727-0.002-0.0020.0000.0000.0000.000
107A107ASP-1-0.790-0.87226.788-0.048-0.0480.0000.0000.0000.000
108A108PHE0-0.015-0.02421.958-0.012-0.0120.0000.0000.0000.000
109A109PRO00.0400.03726.495-0.009-0.0090.0000.0000.0000.000
110A110ASN00.001-0.00728.879-0.002-0.0020.0000.0000.0000.000
111A111ASN00.0110.02224.205-0.021-0.0210.0000.0000.0000.000
112A112ALA00.1010.03925.497-0.004-0.0040.0000.0000.0000.000
113A113ASN00.0160.00821.116-0.034-0.0340.0000.0000.0000.000
114A114ILE00.0220.03120.798-0.022-0.0220.0000.0000.0000.000
115A115HIS0-0.029-0.01521.341-0.014-0.0140.0000.0000.0000.000
116A116SER0-0.009-0.01522.007-0.009-0.0090.0000.0000.0000.000
117A117LYS10.8720.93716.6300.2740.2740.0000.0000.0000.000
118A118VAL00.0400.01817.369-0.024-0.0240.0000.0000.0000.000
119A119LEU0-0.013-0.00418.9990.0030.0030.0000.0000.0000.000
120A120ASP-1-0.856-0.90815.968-0.390-0.3900.0000.0000.0000.000
121A121ILE00.002-0.00412.404-0.021-0.0210.0000.0000.0000.000
122A122TYR00.0220.00515.7140.0310.0310.0000.0000.0000.000
123A123ALA0-0.0230.00118.8120.0260.0260.0000.0000.0000.000
124A124LYS10.8430.93011.1440.7340.7340.0000.0000.0000.000
125A125ASN0-0.046-0.02614.7140.0310.0310.0000.0000.0000.000
126A126GLY00.0380.01913.2780.0520.0520.0000.0000.0000.000
127A127VAL0-0.044-0.02512.7330.0470.0470.0000.0000.0000.000
128A128ILE00.0090.00814.340-0.062-0.0620.0000.0000.0000.000
129A129GLY00.0350.01916.7630.0380.0380.0000.0000.0000.000
130A130ALA0-0.027-0.00818.084-0.028-0.0280.0000.0000.0000.000
131A131ILE00.0160.01421.0280.0160.0160.0000.0000.0000.000
132A132CSD-1-0.777-0.80623.2170.0440.0440.0000.0000.0000.000
133A133HIS10.7860.80026.845-0.040-0.0400.0000.0000.0000.000
134A134GLY00.0470.04223.556-0.011-0.0110.0000.0000.0000.000
135A135VAL0-0.050-0.02723.944-0.013-0.0130.0000.0000.0000.000
136A136ALA00.0420.00625.412-0.007-0.0070.0000.0000.0000.000
137A137ALA0-0.077-0.02822.532-0.009-0.0090.0000.0000.0000.000
138A138LEU0-0.019-0.03421.135-0.014-0.0140.0000.0000.0000.000
139A139ILE0-0.0070.02725.126-0.001-0.0010.0000.0000.0000.000
140A140ASN0-0.008-0.01328.3250.0050.0050.0000.0000.0000.000
141A141VAL0-0.0200.00823.160-0.010-0.0100.0000.0000.0000.000
142A142LYS10.8440.91226.4500.0450.0450.0000.0000.0000.000
143A143ASP-1-0.743-0.87626.921-0.056-0.0560.0000.0000.0000.000
144A144ASN0-0.015-0.02027.932-0.007-0.0070.0000.0000.0000.000
145A145ASN0-0.061-0.02629.884-0.001-0.0010.0000.0000.0000.000
146A146GLY00.0120.00931.6370.0060.0060.0000.0000.0000.000
147A147GLN0-0.026-0.00731.7870.0090.0090.0000.0000.0000.000
148A148ASN00.0720.04229.557-0.010-0.0100.0000.0000.0000.000
149A149ILE00.0210.01822.8690.0070.0070.0000.0000.0000.000
150A150ILE00.0030.00725.3650.0090.0090.0000.0000.0000.000
151A151ARG10.8380.92627.6920.0250.0250.0000.0000.0000.000
152A152ASP-1-0.929-0.98130.3660.0250.0250.0000.0000.0000.000
153A153LYS10.8220.92824.423-0.015-0.0150.0000.0000.0000.000
154A154GLU-1-0.929-0.95128.3850.0920.0920.0000.0000.0000.000
155A155VAL0-0.048-0.02226.1910.0070.0070.0000.0000.0000.000
156A156THR0-0.008-0.03126.8590.0010.0010.0000.0000.0000.000
157A157GLY00.0260.00227.615-0.005-0.0050.0000.0000.0000.000
158A158PHE0-0.020-0.00828.7040.0030.0030.0000.0000.0000.000
159A159SER00.000-0.01031.041-0.007-0.0070.0000.0000.0000.000
160A160ASN0-0.019-0.03234.439-0.005-0.0050.0000.0000.0000.000
161A161ASN0-0.071-0.03537.768-0.006-0.0060.0000.0000.0000.000
162A162GLU-1-0.737-0.82433.1440.0750.0750.0000.0000.0000.000
163A163GLU-1-0.726-0.84134.8040.0280.0280.0000.0000.0000.000
164A164LYS10.9390.97237.280-0.034-0.0340.0000.0000.0000.000
165A165ILE0-0.077-0.02638.842-0.002-0.0020.0000.0000.0000.000
166A166VAL0-0.051-0.03035.6440.0000.0000.0000.0000.0000.000
167A167GLY0-0.0120.00639.015-0.003-0.0030.0000.0000.0000.000
168A168LEU00.014-0.00336.285-0.003-0.0030.0000.0000.0000.000
169A169THR0-0.020-0.01639.177-0.002-0.0020.0000.0000.0000.000
170A170ASP-1-0.940-0.96840.6220.0060.0060.0000.0000.0000.000
171A171VAL0-0.043-0.00738.695-0.003-0.0030.0000.0000.0000.000
172A172VAL0-0.048-0.02335.091-0.004-0.0040.0000.0000.0000.000
173A173PRO0-0.040-0.01334.9630.0000.0000.0000.0000.0000.000
174A174PHE00.004-0.00931.430-0.002-0.0020.0000.0000.0000.000
175A175SER00.0270.01136.1650.0020.0020.0000.0000.0000.000
176A176LEU00.003-0.00628.949-0.002-0.0020.0000.0000.0000.000
177A177GLU-1-0.786-0.88733.0250.0430.0430.0000.0000.0000.000
178A178ASP-1-0.823-0.91334.4370.0210.0210.0000.0000.0000.000
179A179SER00.008-0.00433.517-0.002-0.0020.0000.0000.0000.000
180A180LEU0-0.044-0.02128.657-0.003-0.0030.0000.0000.0000.000
181A181VAL0-0.010-0.00332.4410.0000.0000.0000.0000.0000.000
182A182GLU-1-0.972-0.97835.600-0.005-0.0050.0000.0000.0000.000
183A183ALA0-0.077-0.03131.628-0.004-0.0040.0000.0000.0000.000
184A184GLY0-0.004-0.00633.088-0.003-0.0030.0000.0000.0000.000
185A185ALA0-0.050-0.00730.1890.0040.0040.0000.0000.0000.000
186A186LYS10.8730.92631.543-0.055-0.0550.0000.0000.0000.000
187A187TYR00.0300.00031.1890.0080.0080.0000.0000.0000.000
188A188SER0-0.0290.00031.6660.0040.0040.0000.0000.0000.000
189A189SER00.0320.01331.9820.0010.0010.0000.0000.0000.000
190A190ALA0-0.0310.00032.217-0.001-0.0010.0000.0000.0000.000
191A191SER00.003-0.02333.970-0.006-0.0060.0000.0000.0000.000
192A192GLU-1-0.857-0.92234.7330.0700.0700.0000.0000.0000.000
193A193TRP0-0.060-0.04532.4000.0030.0030.0000.0000.0000.000
194A194GLN0-0.040-0.00232.1180.0060.0060.0000.0000.0000.000
195A195SER0-0.062-0.03025.920-0.003-0.0030.0000.0000.0000.000
196A196TYR0-0.026-0.03527.4900.0050.0050.0000.0000.0000.000
197A197VAL00.006-0.01121.604-0.004-0.0040.0000.0000.0000.000
198A198LYS10.8320.92924.783-0.109-0.1090.0000.0000.0000.000
199A199SER00.001-0.01820.253-0.002-0.0020.0000.0000.0000.000
200A200ASP-1-0.764-0.85622.9070.0830.0830.0000.0000.0000.000
201A201SER0-0.020-0.04121.840-0.015-0.0150.0000.0000.0000.000
202A202LYS10.8580.94113.618-0.214-0.2140.0000.0000.0000.000
203A203ILE00.0120.01618.185-0.018-0.0180.0000.0000.0000.000
204A204ILE0-0.037-0.02216.8410.0180.0180.0000.0000.0000.000
205A205THR00.0360.01620.706-0.015-0.0150.0000.0000.0000.000
206A206ALA00.014-0.00423.0120.0180.0180.0000.0000.0000.000
207A207GLN00.0430.02624.733-0.008-0.0080.0000.0000.0000.000
208A208ASN00.008-0.00727.287-0.002-0.0020.0000.0000.0000.000
209A209PRO00.0550.02725.7100.0150.0150.0000.0000.0000.000
210A210GLN00.0120.00325.5140.0160.0160.0000.0000.0000.000
211A211SER00.013-0.00625.1660.0110.0110.0000.0000.0000.000
212A212ALA0-0.015-0.00321.1560.0200.0200.0000.0000.0000.000
213A213THR0-0.009-0.01320.0540.0280.0280.0000.0000.0000.000
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