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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: ZV4YN

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 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 225
LigandCharge CSD=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2801877.26239
FMO2-HF: Nuclear repulsion 2714374.253358
FMO2-HF: Total energy -87503.009032
FMO2-MP2: Total energy -87757.986577


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.
-9.962-5.12311.503-4.832-11.509-0.045
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 : -0.079 / q_NPA : -0.036
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].
3A3ASN00.007-0.0012.870-3.3500.7730.626-2.059-2.690-0.015
4A4VAL0-0.018-0.0144.7990.2200.276-0.001-0.007-0.0480.000
5A5LEU00.0160.0208.3910.0440.0440.0000.0000.0000.000
6A6MET0-0.037-0.01611.3430.0700.0700.0000.0000.0000.000
7A7VAL0-0.011-0.00314.191-0.045-0.0450.0000.0000.0000.000
8A8THR0-0.005-0.01317.5890.0260.0260.0000.0000.0000.000
9A9THR0-0.022-0.03820.936-0.018-0.0180.0000.0000.0000.000
10A10SER00.002-0.01324.132-0.004-0.0040.0000.0000.0000.000
11A11HIS0-0.039-0.00726.297-0.007-0.0070.0000.0000.0000.000
12A12ASP-1-0.781-0.89029.611-0.014-0.0140.0000.0000.0000.000
13A13VAL0-0.031-0.00631.7430.0040.0040.0000.0000.0000.000
14A14MET0-0.0240.01134.332-0.001-0.0010.0000.0000.0000.000
15A15GLY00.0580.03636.3690.0010.0010.0000.0000.0000.000
16A16ASN0-0.059-0.02638.310-0.004-0.0040.0000.0000.0000.000
17A17SER0-0.039-0.03439.9130.0010.0010.0000.0000.0000.000
18A18ASN0-0.001-0.01640.684-0.004-0.0040.0000.0000.0000.000
19A19GLU-1-0.898-0.94136.8920.0180.0180.0000.0000.0000.000
20A20LYS10.8370.90433.9590.0120.0120.0000.0000.0000.000
21A21THR0-0.025-0.04931.5760.0050.0050.0000.0000.0000.000
22A22GLY00.0510.01428.285-0.007-0.0070.0000.0000.0000.000
23A23LEU0-0.029-0.01821.1650.0060.0060.0000.0000.0000.000
24A24TRP00.0460.01225.053-0.004-0.0040.0000.0000.0000.000
25A25LEU00.0170.01821.5490.0160.0160.0000.0000.0000.000
26A26SER00.0580.02421.4120.0130.0130.0000.0000.0000.000
27A27GLH0-0.068-0.08020.9540.0250.0250.0000.0000.0000.000
28A28LEU0-0.0030.01415.9520.0130.0130.0000.0000.0000.000
29A29THR00.009-0.01516.7380.0530.0530.0000.0000.0000.000
30A30HIS10.8060.88116.845-0.148-0.1480.0000.0000.0000.000
31A31PRO00.009-0.00415.8780.0490.0490.0000.0000.0000.000
32A32TYR00.0240.01510.2660.1020.1020.0000.0000.0000.000
33A33TYR0-0.001-0.02811.9080.1110.1110.0000.0000.0000.000
34A34SER0-0.044-0.00613.2580.0150.0150.0000.0000.0000.000
35A35ILE0-0.014-0.0059.2700.0660.0660.0000.0000.0000.000
36A36ILE00.0120.0347.0110.3010.3010.0000.0000.0000.000
37A37ASP-1-0.815-0.9076.2842.1452.1450.0000.0000.0000.000
38A38LYS10.9310.9553.803-0.0530.3400.002-0.070-0.3240.000
39A39ASN0-0.069-0.0262.511-4.007-3.5012.866-0.740-2.632-0.009
40A40ILE0-0.023-0.0102.5880.4690.7974.263-1.382-3.208-0.020
41A41ASN00.0390.0112.860-1.194-1.5553.722-0.862-2.499-0.002
42A42ILE0-0.060-0.0324.314-1.082-1.2880.0250.288-0.1080.001
43A43ASP-1-0.778-0.8308.104-0.576-0.5760.0000.0000.0000.000
44A44ILE0-0.036-0.03410.2630.0450.0450.0000.0000.0000.000
45A45VAL0-0.037-0.00814.037-0.045-0.0450.0000.0000.0000.000
46A46SER00.0190.01116.9090.0310.0310.0000.0000.0000.000
47A47ILE00.0070.00620.612-0.026-0.0260.0000.0000.0000.000
48A48MET0-0.017-0.00823.193-0.017-0.0170.0000.0000.0000.000
49A49GLY00.0070.01821.852-0.015-0.0150.0000.0000.0000.000
50A50GLY0-0.027-0.00922.8040.0120.0120.0000.0000.0000.000
51A51GLU-1-0.943-0.95623.320-0.035-0.0350.0000.0000.0000.000
52A52ILE0-0.049-0.02219.712-0.001-0.0010.0000.0000.0000.000
53A53PRO00.0040.02224.3630.0090.0090.0000.0000.0000.000
54A54ILE00.002-0.01725.2190.0070.0070.0000.0000.0000.000
55A55ASP-1-0.776-0.86727.6880.0280.0280.0000.0000.0000.000
56A56PRO00.0500.03929.8890.0080.0080.0000.0000.0000.000
57A57ASN0-0.026-0.02732.2320.0050.0050.0000.0000.0000.000
58A58SER0-0.103-0.05727.1760.0080.0080.0000.0000.0000.000
59A59VAL0-0.003-0.01526.8750.0090.0090.0000.0000.0000.000
60A60ALA0-0.0290.01229.505-0.004-0.0040.0000.0000.0000.000
61A61GLN0-0.075-0.04029.907-0.002-0.0020.0000.0000.0000.000
62A62GLU-1-0.898-0.94028.9050.0630.0630.0000.0000.0000.000
63A63ASP-1-0.831-0.90523.4760.1550.1550.0000.0000.0000.000
64A64TYR00.0280.02019.3070.0070.0070.0000.0000.0000.000
65A65TYR0-0.021-0.02217.3520.0110.0110.0000.0000.0000.000
66A66ASN00.0900.03419.9390.0130.0130.0000.0000.0000.000
67A67ASP-1-0.814-0.91322.1510.0650.0650.0000.0000.0000.000
68A68LYS10.8450.92715.912-0.185-0.1850.0000.0000.0000.000
69A69PHE00.008-0.00915.348-0.007-0.0070.0000.0000.0000.000
70A70LEU00.0130.01018.790-0.019-0.0190.0000.0000.0000.000
71A71ALA0-0.020-0.00520.905-0.016-0.0160.0000.0000.0000.000
72A72ASP-1-0.852-0.91614.8260.0100.0100.0000.0000.0000.000
73A73ASP-1-0.817-0.91918.353-0.039-0.0390.0000.0000.0000.000
74A74ASN0-0.053-0.01312.708-0.048-0.0480.0000.0000.0000.000
75A75LEU0-0.017-0.00813.165-0.008-0.0080.0000.0000.0000.000
76A76LYS10.8210.89816.9070.0000.0000.0000.0000.0000.000
77A77ASN0-0.027-0.01618.9490.0020.0020.0000.0000.0000.000
78A78ILE00.0250.00914.301-0.007-0.0070.0000.0000.0000.000
79A79MET0-0.017-0.00818.8420.0000.0000.0000.0000.0000.000
80A80LYS10.9310.98021.6940.0600.0600.0000.0000.0000.000
81A81ASN0-0.085-0.04521.516-0.005-0.0050.0000.0000.0000.000
82A82SER00.0120.01718.960-0.023-0.0230.0000.0000.0000.000
83A83THR00.0010.00216.581-0.018-0.0180.0000.0000.0000.000
84A84SER0-0.032-0.01918.7650.0160.0160.0000.0000.0000.000
85A85LEU00.023-0.00417.121-0.033-0.0330.0000.0000.0000.000
86A86ARG10.7910.87118.6030.1310.1310.0000.0000.0000.000
87A87ASP-1-0.845-0.91418.706-0.220-0.2200.0000.0000.0000.000
88A88VAL00.0010.01313.617-0.040-0.0400.0000.0000.0000.000
89A89ASN0-0.031-0.04313.2170.1230.1230.0000.0000.0000.000
90A90ILE00.0370.01212.493-0.070-0.0700.0000.0000.0000.000
91A91LYS10.7870.87012.1650.3430.3430.0000.0000.0000.000
92A92GLU-1-0.855-0.9127.982-1.244-1.2440.0000.0000.0000.000
93A93TYR0-0.078-0.0546.896-0.603-0.6030.0000.0000.0000.000
94A94ASP-1-0.803-0.8936.167-1.072-1.0720.0000.0000.0000.000
95A95ALA0-0.022-0.0209.1400.2390.2390.0000.0000.0000.000
96A96ILE0-0.0140.00611.149-0.079-0.0790.0000.0000.0000.000
97A97ILE0-0.033-0.01313.0850.0530.0530.0000.0000.0000.000
98A98PHE00.0350.00515.797-0.012-0.0120.0000.0000.0000.000
99A99ALA00.0230.00519.2980.0220.0220.0000.0000.0000.000
100A100GLY00.0440.01220.742-0.018-0.0180.0000.0000.0000.000
101A101GLY00.0110.00624.597-0.003-0.0030.0000.0000.0000.000
102A102HIS10.8300.90427.632-0.039-0.0390.0000.0000.0000.000
103A103GLY00.0520.04029.132-0.004-0.0040.0000.0000.0000.000
104A104THR00.013-0.01624.727-0.006-0.0060.0000.0000.0000.000
105A105MET0-0.0190.00527.412-0.004-0.0040.0000.0000.0000.000
106A106TRP0-0.011-0.00530.448-0.001-0.0010.0000.0000.0000.000
107A107ASP-1-0.789-0.87426.613-0.038-0.0380.0000.0000.0000.000
108A108PHE00.006-0.00821.856-0.012-0.0120.0000.0000.0000.000
109A109PRO00.0410.03126.372-0.008-0.0080.0000.0000.0000.000
110A110ASN0-0.001-0.00729.0800.0010.0010.0000.0000.0000.000
111A111ASN0-0.0090.00124.383-0.021-0.0210.0000.0000.0000.000
112A112ALA00.0920.04125.075-0.005-0.0050.0000.0000.0000.000
113A113ASN00.0000.00520.910-0.032-0.0320.0000.0000.0000.000
114A114ILE00.0310.03820.623-0.020-0.0200.0000.0000.0000.000
115A115HIS0-0.042-0.01921.087-0.015-0.0150.0000.0000.0000.000
116A116SER0-0.018-0.02921.959-0.007-0.0070.0000.0000.0000.000
117A117LYS10.8700.95016.3770.2580.2580.0000.0000.0000.000
118A118VAL00.0310.00817.311-0.016-0.0160.0000.0000.0000.000
119A119LEU0-0.010-0.00419.0760.0090.0090.0000.0000.0000.000
120A120ASP-1-0.837-0.90315.988-0.341-0.3410.0000.0000.0000.000
121A121ILE0-0.011-0.00212.618-0.025-0.0250.0000.0000.0000.000
122A122TYR00.0090.00315.8070.0370.0370.0000.0000.0000.000
123A123ALA0-0.032-0.02119.1010.0230.0230.0000.0000.0000.000
124A124LYS10.8160.92911.4420.5960.5960.0000.0000.0000.000
125A125ASN0-0.041-0.01714.8050.0280.0280.0000.0000.0000.000
126A126GLY00.0470.02813.4310.0570.0570.0000.0000.0000.000
127A127VAL0-0.056-0.03512.5300.0390.0390.0000.0000.0000.000
128A128ILE00.0030.00014.405-0.056-0.0560.0000.0000.0000.000
129A129GLY00.0430.02316.5390.0270.0270.0000.0000.0000.000
130A130ALA0-0.025-0.00917.980-0.029-0.0290.0000.0000.0000.000
131A131ILE00.0000.00721.0160.0180.0180.0000.0000.0000.000
132A132CSD-1-0.784-0.81323.3210.0510.0510.0000.0000.0000.000
133A133HIS10.7990.82726.917-0.048-0.0480.0000.0000.0000.000
134A134GLY00.0500.04123.499-0.010-0.0100.0000.0000.0000.000
135A135VAL0-0.034-0.02723.946-0.012-0.0120.0000.0000.0000.000
136A136ALA00.0510.01725.312-0.007-0.0070.0000.0000.0000.000
137A137ALA0-0.072-0.02622.284-0.009-0.0090.0000.0000.0000.000
138A138LEU0-0.012-0.03420.979-0.013-0.0130.0000.0000.0000.000
139A139ILE0-0.0030.02624.948-0.002-0.0020.0000.0000.0000.000
140A140ASN00.000-0.01328.2710.0040.0040.0000.0000.0000.000
141A141VAL0-0.0220.01323.079-0.010-0.0100.0000.0000.0000.000
142A142LYS10.8530.92126.3120.0320.0320.0000.0000.0000.000
143A143ASP-1-0.739-0.85527.213-0.035-0.0350.0000.0000.0000.000
144A144ASN0-0.024-0.03228.180-0.007-0.0070.0000.0000.0000.000
145A145ASN0-0.065-0.02630.217-0.001-0.0010.0000.0000.0000.000
146A146GLY00.0210.01532.1260.0050.0050.0000.0000.0000.000
147A147GLN0-0.039-0.01231.9510.0080.0080.0000.0000.0000.000
148A148ASN00.0750.03729.598-0.008-0.0080.0000.0000.0000.000
149A149ILE00.0070.00122.7800.0060.0060.0000.0000.0000.000
150A150ILE0-0.0020.00725.3590.0100.0100.0000.0000.0000.000
151A151ARG10.8480.92427.6610.0070.0070.0000.0000.0000.000
152A152ASP-1-0.930-0.97230.2270.0400.0400.0000.0000.0000.000
153A153LYS10.8000.91624.541-0.038-0.0380.0000.0000.0000.000
154A154GLU-1-0.915-0.94628.4220.1000.1000.0000.0000.0000.000
155A155VAL0-0.037-0.01726.3320.0110.0110.0000.0000.0000.000
156A156THR0-0.017-0.02426.7880.0000.0000.0000.0000.0000.000
157A157GLY00.0180.00027.516-0.003-0.0030.0000.0000.0000.000
158A158PHE0-0.020-0.01328.7010.0020.0020.0000.0000.0000.000
159A159SER00.004-0.00531.131-0.008-0.0080.0000.0000.0000.000
160A160ASN0-0.038-0.04134.574-0.005-0.0050.0000.0000.0000.000
161A161ASN0-0.073-0.04137.955-0.007-0.0070.0000.0000.0000.000
162A162GLU-1-0.732-0.82232.7620.0830.0830.0000.0000.0000.000
163A163GLU-1-0.734-0.85134.7570.0360.0360.0000.0000.0000.000
164A164LYS10.9500.98337.163-0.040-0.0400.0000.0000.0000.000
165A165ILE0-0.079-0.03038.574-0.002-0.0020.0000.0000.0000.000
166A166VAL0-0.064-0.03135.3840.0000.0000.0000.0000.0000.000
167A167GLY0-0.0050.00438.717-0.003-0.0030.0000.0000.0000.000
168A168LEU00.010-0.00236.100-0.003-0.0030.0000.0000.0000.000
169A169THR0-0.010-0.01938.997-0.002-0.0020.0000.0000.0000.000
170A170ASP-1-0.959-0.96740.2850.0110.0110.0000.0000.0000.000
171A171VAL0-0.044-0.01438.741-0.003-0.0030.0000.0000.0000.000
172A172VAL0-0.033-0.01534.667-0.003-0.0030.0000.0000.0000.000
173A173PRO0-0.042-0.01634.7320.0000.0000.0000.0000.0000.000
174A174PHE0-0.001-0.00831.203-0.002-0.0020.0000.0000.0000.000
175A175SER00.0220.00135.8960.0030.0030.0000.0000.0000.000
176A176LEU0-0.008-0.01328.625-0.002-0.0020.0000.0000.0000.000
177A177GLU-1-0.793-0.88232.6950.0520.0520.0000.0000.0000.000
178A178ASP-1-0.836-0.91734.5250.0290.0290.0000.0000.0000.000
179A179SER00.021-0.01434.000-0.001-0.0010.0000.0000.0000.000
180A180LEU0-0.063-0.02628.410-0.003-0.0030.0000.0000.0000.000
181A181VAL0-0.0050.00132.3670.0010.0010.0000.0000.0000.000
182A182GLU-1-0.941-0.95435.4850.0050.0050.0000.0000.0000.000
183A183ALA0-0.079-0.03331.309-0.004-0.0040.0000.0000.0000.000
184A184GLY00.000-0.00632.656-0.002-0.0020.0000.0000.0000.000
185A185ALA0-0.027-0.00430.0750.0040.0040.0000.0000.0000.000
186A186LYS10.8810.93131.790-0.074-0.0740.0000.0000.0000.000
187A187TYR00.015-0.01231.2340.0090.0090.0000.0000.0000.000
188A188SER0-0.047-0.00831.2060.0040.0040.0000.0000.0000.000
189A189SER00.0180.00031.8690.0010.0010.0000.0000.0000.000
190A190ALA0-0.0190.00932.4850.0000.0000.0000.0000.0000.000
191A191SER00.004-0.02734.154-0.007-0.0070.0000.0000.0000.000
192A192GLU-1-0.842-0.90234.4050.0750.0750.0000.0000.0000.000
193A193TRP0-0.056-0.04432.1590.0040.0040.0000.0000.0000.000
194A194GLN0-0.0280.00131.6880.0050.0050.0000.0000.0000.000
195A195SER0-0.065-0.04625.704-0.002-0.0020.0000.0000.0000.000
196A196TYR0-0.015-0.02327.5410.0040.0040.0000.0000.0000.000
197A197VAL0-0.006-0.01621.939-0.001-0.0010.0000.0000.0000.000
198A198LYS10.8380.92624.803-0.123-0.1230.0000.0000.0000.000
199A199SER0-0.017-0.02320.2550.0010.0010.0000.0000.0000.000
200A200ASP-1-0.765-0.86522.8710.1000.1000.0000.0000.0000.000
201A201SER0-0.016-0.03622.219-0.012-0.0120.0000.0000.0000.000
202A202LYS10.8420.93813.947-0.313-0.3130.0000.0000.0000.000
203A203ILE00.0160.02318.121-0.005-0.0050.0000.0000.0000.000
204A204ILE0-0.047-0.02616.9840.0210.0210.0000.0000.0000.000
205A205THR00.0220.00520.733-0.018-0.0180.0000.0000.0000.000
206A206ALA00.018-0.00422.9170.0160.0160.0000.0000.0000.000
207A207GLN00.0370.01824.763-0.007-0.0070.0000.0000.0000.000
208A208ASN00.005-0.00527.168-0.002-0.0020.0000.0000.0000.000
209A209PRO00.0420.01125.6320.0150.0150.0000.0000.0000.000
210A210GLN00.0220.00825.2270.0160.0160.0000.0000.0000.000
211A211SER00.003-0.00625.1240.0140.0140.0000.0000.0000.000
212A212ALA0-0.011-0.00521.0160.0220.0220.0000.0000.0000.000
213A213THR0-0.010-0.01119.8110.0320.0320.0000.0000.0000.000
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