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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: 76Q8K

Calculation Name: 1U9C-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 1U9C

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KWF3

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 221
LigandCharge CSD=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2753281.355228
FMO2-HF: Nuclear repulsion 2667788.269249
FMO2-HF: Total energy -85493.085978
FMO2-MP2: Total energy -85744.583406


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.
-8.214-5.3770.056-1.258-1.635-0.001
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 : -0.011 / q_NPA : -0.011
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].
3A3LYS10.8120.9163.1850.4962.9570.058-1.234-1.285-0.001
4A4ARG10.7970.8834.2411.6031.829-0.001-0.020-0.2050.000
5A5VAL0-0.014-0.0087.2550.3520.3520.0000.0000.0000.000
6A6LEU0-0.0390.00111.0320.0430.0430.0000.0000.0000.000
7A7MET0-0.026-0.01213.3580.0020.0020.0000.0000.0000.000
8A8VAL00.0070.00916.3380.0350.0350.0000.0000.0000.000
9A9VAL0-0.007-0.01019.4540.0080.0080.0000.0000.0000.000
10A10THR00.003-0.03322.6530.0190.0190.0000.0000.0000.000
11A11ASN0-0.006-0.02324.389-0.014-0.0140.0000.0000.0000.000
12A12HIS0-0.0350.00027.8290.0140.0140.0000.0000.0000.000
13A13THR00.012-0.02031.370-0.009-0.0090.0000.0000.0000.000
14A14THR0-0.045-0.02734.1710.0020.0020.0000.0000.0000.000
15A15ILE0-0.0120.01536.698-0.003-0.0030.0000.0000.0000.000
16A16THR00.010-0.02239.7720.0040.0040.0000.0000.0000.000
17A17ASP-1-0.878-0.94842.216-0.100-0.1000.0000.0000.0000.000
18A18ASP-1-0.860-0.90643.839-0.110-0.1100.0000.0000.0000.000
19A19HIS10.8360.92740.8050.1150.1150.0000.0000.0000.000
20A20LYS10.8830.93437.4240.1210.1210.0000.0000.0000.000
21A21THR0-0.078-0.05833.530-0.007-0.0070.0000.0000.0000.000
22A22GLY00.0680.03830.6070.0080.0080.0000.0000.0000.000
23A23LEU00.0250.00923.611-0.001-0.0010.0000.0000.0000.000
24A24TRP0-0.049-0.03027.6220.0230.0230.0000.0000.0000.000
25A25LEU00.0050.00524.937-0.025-0.0250.0000.0000.0000.000
26A26GLU-1-0.830-0.92024.707-0.341-0.3410.0000.0000.0000.000
27A27GLH0-0.025-0.04624.341-0.032-0.0320.0000.0000.0000.000
28A28PHE0-0.019-0.00417.358-0.027-0.0270.0000.0000.0000.000
29A29ALA00.026-0.00420.192-0.057-0.0570.0000.0000.0000.000
30A30VAL00.0060.01320.656-0.035-0.0350.0000.0000.0000.000
31A31PRO0-0.014-0.02019.049-0.041-0.0410.0000.0000.0000.000
32A32TYR0-0.022-0.01513.222-0.043-0.0430.0000.0000.0000.000
33A33LEU00.0060.01215.784-0.095-0.0950.0000.0000.0000.000
34A34VAL00.0050.01116.320-0.061-0.0610.0000.0000.0000.000
35A35PHE0-0.036-0.03712.298-0.092-0.0920.0000.0000.0000.000
36A36GLN0-0.0020.00511.924-0.336-0.3360.0000.0000.0000.000
37A37GLU-1-0.876-0.93413.120-0.711-0.7110.0000.0000.0000.000
38A38LYS10.7980.89211.3291.4831.4830.0000.0000.0000.000
39A39GLY0-0.0260.0029.756-0.222-0.2220.0000.0000.0000.000
40A40TYR0-0.058-0.0377.133-0.417-0.4170.0000.0000.0000.000
41A41ASP-1-0.818-0.8844.739-1.990-1.840-0.001-0.004-0.1450.000
42A42VAL00.0270.0016.8600.1800.1800.0000.0000.0000.000
43A43LYS10.8280.90910.2840.5480.5480.0000.0000.0000.000
44A44VAL00.0190.01311.7880.0570.0570.0000.0000.0000.000
45A45ALA0-0.020-0.01915.3170.0510.0510.0000.0000.0000.000
46A46SER0-0.003-0.00517.6460.0020.0020.0000.0000.0000.000
47A47ILE0-0.0210.00021.4190.0110.0110.0000.0000.0000.000
48A48GLN0-0.031-0.02424.0690.0180.0180.0000.0000.0000.000
49A49GLY0-0.014-0.00221.5630.0170.0170.0000.0000.0000.000
50A50GLY0-0.030-0.01221.8740.0190.0190.0000.0000.0000.000
51A51GLU-1-0.873-0.92022.898-0.234-0.2340.0000.0000.0000.000
52A52VAL0-0.025-0.00722.7870.0120.0120.0000.0000.0000.000
53A53PRO0-0.0190.01225.868-0.002-0.0020.0000.0000.0000.000
54A54LEU00.022-0.00526.279-0.014-0.0140.0000.0000.0000.000
55A55ASP-1-0.828-0.89829.965-0.179-0.1790.0000.0000.0000.000
56A56PRO00.0440.02332.635-0.007-0.0070.0000.0000.0000.000
57A57ARG10.8770.93635.3270.1700.1700.0000.0000.0000.000
58A58SER0-0.042-0.02130.481-0.007-0.0070.0000.0000.0000.000
59A59ILE00.011-0.00430.400-0.015-0.0150.0000.0000.0000.000
60A60ASN0-0.034-0.00932.195-0.001-0.0010.0000.0000.0000.000
61A61GLU-1-0.927-0.96533.342-0.190-0.1900.0000.0000.0000.000
62A62LYS10.7930.87928.7760.2340.2340.0000.0000.0000.000
63A63ASP-1-0.795-0.85426.656-0.328-0.3280.0000.0000.0000.000
64A64PRO0-0.020-0.02726.849-0.013-0.0130.0000.0000.0000.000
65A65SER0-0.052-0.04922.569-0.016-0.0160.0000.0000.0000.000
66A66TRP00.032-0.00421.963-0.027-0.0270.0000.0000.0000.000
67A67ALA00.0090.01422.737-0.004-0.0040.0000.0000.0000.000
68A68GLU-1-0.878-0.94216.325-0.624-0.6240.0000.0000.0000.000
69A69ALA00.0060.00818.976-0.011-0.0110.0000.0000.0000.000
70A70GLU-1-0.820-0.91519.949-0.266-0.2660.0000.0000.0000.000
71A71ALA0-0.020-0.00720.2900.0250.0250.0000.0000.0000.000
72A72ALA00.0280.00717.0910.0230.0230.0000.0000.0000.000
73A73LEU0-0.026-0.01718.8740.0210.0210.0000.0000.0000.000
74A74LYS10.8610.92321.7320.2670.2670.0000.0000.0000.000
75A75HIS0-0.085-0.03717.7160.0020.0020.0000.0000.0000.000
76A76THR00.0120.03718.306-0.017-0.0170.0000.0000.0000.000
77A77ALA00.0260.00715.8270.0450.0450.0000.0000.0000.000
78A78ARG10.9150.96217.8950.1360.1360.0000.0000.0000.000
79A79LEU0-0.021-0.00418.137-0.006-0.0060.0000.0000.0000.000
80A80SER0-0.067-0.06218.0950.0420.0420.0000.0000.0000.000
81A81LYS10.8490.90118.5090.0690.0690.0000.0000.0000.000
82A82ASP-1-0.864-0.91215.535-0.049-0.0490.0000.0000.0000.000
83A83ASP-1-0.800-0.89314.183-0.350-0.3500.0000.0000.0000.000
84A84ALA0-0.037-0.01215.077-0.066-0.0660.0000.0000.0000.000
85A85HIS10.7960.87513.9300.1230.1230.0000.0000.0000.000
86A86GLY00.0390.0249.9440.0150.0150.0000.0000.0000.000
87A87PHE00.0090.0168.450-0.089-0.0890.0000.0000.0000.000
88A88ASP-1-0.825-0.9027.628-2.378-2.3780.0000.0000.0000.000
89A89ALA00.002-0.00710.6780.1710.1710.0000.0000.0000.000
90A90ILE0-0.0090.01413.369-0.032-0.0320.0000.0000.0000.000
91A91PHE00.014-0.00616.2210.0200.0200.0000.0000.0000.000
92A92LEU0-0.011-0.00518.4160.0190.0190.0000.0000.0000.000
93A93PRO00.010-0.00720.5720.0210.0210.0000.0000.0000.000
94A94GLY00.0380.02123.7180.0190.0190.0000.0000.0000.000
95A95GLY00.0250.01827.473-0.004-0.0040.0000.0000.0000.000
96A96HIS10.8240.88430.3330.1860.1860.0000.0000.0000.000
97A97GLY00.0420.03430.8730.0090.0090.0000.0000.0000.000
98A98THR00.0380.00026.7750.0120.0120.0000.0000.0000.000
99A99MET0-0.023-0.00129.377-0.001-0.0010.0000.0000.0000.000
100A100PHE0-0.038-0.02232.1770.0120.0120.0000.0000.0000.000
101A101ASP-1-0.795-0.87328.204-0.212-0.2120.0000.0000.0000.000
102A102PHE00.006-0.00623.689-0.007-0.0070.0000.0000.0000.000
103A103PRO0-0.0320.00027.9590.0010.0010.0000.0000.0000.000
104A104ASP-1-0.840-0.92330.500-0.136-0.1360.0000.0000.0000.000
105A105ASN0-0.0130.01225.9930.0140.0140.0000.0000.0000.000
106A106GLU-1-0.718-0.84227.045-0.117-0.1170.0000.0000.0000.000
107A107THR0-0.027-0.02722.2150.0050.0050.0000.0000.0000.000
108A108LEU0-0.0040.00521.768-0.013-0.0130.0000.0000.0000.000
109A109GLN0-0.032-0.01823.330-0.009-0.0090.0000.0000.0000.000
110A110TYR0-0.062-0.02820.655-0.002-0.0020.0000.0000.0000.000
111A111VAL00.010-0.00218.0400.0000.0000.0000.0000.0000.000
112A112LEU00.0090.00220.169-0.024-0.0240.0000.0000.0000.000
113A113GLN0-0.017-0.01022.0210.0080.0080.0000.0000.0000.000
114A114GLN0-0.013-0.00319.0360.0320.0320.0000.0000.0000.000
115A115PHE00.0350.01013.9950.0020.0020.0000.0000.0000.000
116A116ALA0-0.0100.00018.311-0.029-0.0290.0000.0000.0000.000
117A117GLU-1-0.872-0.94920.994-0.119-0.1190.0000.0000.0000.000
118A118ASP-1-0.824-0.87915.491-0.177-0.1770.0000.0000.0000.000
119A119GLY0-0.025-0.00216.353-0.031-0.0310.0000.0000.0000.000
120A120ARG10.7720.86710.3760.4480.4480.0000.0000.0000.000
121A121ILE0-0.028-0.01013.5410.0730.0730.0000.0000.0000.000
122A122ILE0-0.003-0.00716.769-0.011-0.0110.0000.0000.0000.000
123A123ALA00.0210.00718.8230.0240.0240.0000.0000.0000.000
124A124ALA00.0010.00720.5730.0060.0060.0000.0000.0000.000
125A125VAL00.0240.00923.4350.0030.0030.0000.0000.0000.000
126A126CSD-1-0.783-0.82426.082-0.245-0.2450.0000.0000.0000.000
127A127HIS10.7910.83229.6760.2280.2280.0000.0000.0000.000
128A128GLY00.0570.06425.7850.0140.0140.0000.0000.0000.000
129A129PRO0-0.025-0.03526.4650.0030.0030.0000.0000.0000.000
130A130SER00.016-0.00827.8360.0130.0130.0000.0000.0000.000
131A131GLY00.0030.00726.1180.0160.0160.0000.0000.0000.000
132A132LEU0-0.009-0.01824.1880.0060.0060.0000.0000.0000.000
133A133VAL0-0.060-0.01127.8160.0140.0140.0000.0000.0000.000
134A134ASN0-0.010-0.00630.6690.0140.0140.0000.0000.0000.000
135A135ALA00.0350.03726.3580.0080.0080.0000.0000.0000.000
136A136THR0-0.046-0.03727.968-0.005-0.0050.0000.0000.0000.000
137A137TYR00.0270.02123.010-0.009-0.0090.0000.0000.0000.000
138A138LYS10.8620.92625.5300.0890.0890.0000.0000.0000.000
139A139ASP-1-0.846-0.89328.163-0.103-0.1030.0000.0000.0000.000
140A140GLY00.0070.01530.7510.0080.0080.0000.0000.0000.000
141A141THR0-0.093-0.08029.893-0.003-0.0030.0000.0000.0000.000
142A142PRO00.004-0.00629.817-0.011-0.0110.0000.0000.0000.000
143A143ILE00.0200.01324.1350.0000.0000.0000.0000.0000.000
144A144VAL00.006-0.00127.465-0.014-0.0140.0000.0000.0000.000
145A145LYS10.9150.97729.7490.1270.1270.0000.0000.0000.000
146A146GLY0-0.012-0.01231.371-0.003-0.0030.0000.0000.0000.000
147A147LYS10.7860.89925.5830.2690.2690.0000.0000.0000.000
148A148THR0-0.027-0.02929.2450.0150.0150.0000.0000.0000.000
149A149VAL0-0.048-0.02128.141-0.023-0.0230.0000.0000.0000.000
150A150THR0-0.007-0.02229.0570.0180.0180.0000.0000.0000.000
151A151SER0-0.016-0.02629.795-0.011-0.0110.0000.0000.0000.000
152A152PHE00.001-0.00331.4550.0070.0070.0000.0000.0000.000
153A153THR0-0.023-0.02733.7380.0120.0120.0000.0000.0000.000
154A154ASP-1-0.770-0.89236.999-0.153-0.1530.0000.0000.0000.000
155A155GLU-1-0.896-0.93040.063-0.144-0.1440.0000.0000.0000.000
156A156GLU-1-0.683-0.81336.072-0.207-0.2070.0000.0000.0000.000
157A157GLU-1-0.777-0.86137.015-0.178-0.1780.0000.0000.0000.000
158A158ARG10.9320.97039.9030.1370.1370.0000.0000.0000.000
159A159GLU-1-0.854-0.89242.028-0.144-0.1440.0000.0000.0000.000
160A160VAL0-0.063-0.03638.5910.0020.0020.0000.0000.0000.000
161A161GLY0-0.0020.01041.9100.0020.0020.0000.0000.0000.000
162A162LEU0-0.037-0.03338.8990.0040.0040.0000.0000.0000.000
163A163ASP-1-0.830-0.92441.231-0.124-0.1240.0000.0000.0000.000
164A164VAL0-0.051-0.03242.3090.0010.0010.0000.0000.0000.000
165A165HIS0-0.035-0.01941.8950.0050.0050.0000.0000.0000.000
166A166MET0-0.0480.00037.063-0.009-0.0090.0000.0000.0000.000
167A167PRO0-0.0080.00836.5150.0070.0070.0000.0000.0000.000
168A168PHE0-0.010-0.01633.3470.0040.0040.0000.0000.0000.000
169A169LEU00.0090.01838.238-0.007-0.0070.0000.0000.0000.000
170A170LEU00.0500.03931.4250.0020.0020.0000.0000.0000.000
171A171GLU-1-0.758-0.85235.315-0.171-0.1710.0000.0000.0000.000
172A172SER0-0.062-0.06836.5330.0040.0040.0000.0000.0000.000
173A173THR0-0.050-0.04136.3120.0080.0080.0000.0000.0000.000
174A174LEU0-0.002-0.00330.7210.0020.0020.0000.0000.0000.000
175A175ARG10.8610.91734.5140.1580.1580.0000.0000.0000.000
176A176LEU0-0.035-0.01237.2120.0060.0060.0000.0000.0000.000
177A177ARG10.7970.89733.6770.1500.1500.0000.0000.0000.000
178A178GLY00.005-0.00434.840-0.001-0.0010.0000.0000.0000.000
179A179ALA00.0030.02332.556-0.003-0.0030.0000.0000.0000.000
180A180ASN0-0.032-0.02033.2790.0180.0180.0000.0000.0000.000
181A181PHE0-0.041-0.02533.269-0.012-0.0120.0000.0000.0000.000
182A182VAL0-0.009-0.00332.6500.0130.0130.0000.0000.0000.000
183A183ARG10.8070.88633.8830.1640.1640.0000.0000.0000.000
184A184GLY00.0680.04935.2190.0060.0060.0000.0000.0000.000
185A185GLY00.0170.00636.4390.0110.0110.0000.0000.0000.000
186A186LYS10.7900.88936.8490.1330.1330.0000.0000.0000.000
187A187TRP0-0.072-0.05835.560-0.001-0.0010.0000.0000.0000.000
188A188THR0-0.079-0.02835.305-0.001-0.0010.0000.0000.0000.000
189A189ASP-1-0.792-0.85729.090-0.345-0.3450.0000.0000.0000.000
190A190PHE0-0.0010.01030.8560.0090.0090.0000.0000.0000.000
191A191SER00.0440.01425.949-0.010-0.0100.0000.0000.0000.000
192A192VAL0-0.057-0.01627.0980.0010.0010.0000.0000.0000.000
193A193ARG10.8020.84118.3470.5440.5440.0000.0000.0000.000
194A194ASP-1-0.785-0.85624.360-0.244-0.2440.0000.0000.0000.000
195A195GLY00.0470.01222.1470.0030.0030.0000.0000.0000.000
196A196ASN00.0180.01818.012-0.088-0.0880.0000.0000.0000.000
197A197LEU0-0.0240.01520.025-0.037-0.0370.0000.0000.0000.000
198A198ILE00.001-0.00719.0750.0170.0170.0000.0000.0000.000
199A199THR00.0030.00223.0420.0140.0140.0000.0000.0000.000
200A200GLY00.0560.01725.7500.0000.0000.0000.0000.0000.000
201A201GLN0-0.030-0.02327.4760.0050.0050.0000.0000.0000.000
202A202ASN0-0.042-0.03230.235-0.002-0.0020.0000.0000.0000.000
203A203PRO00.0330.02729.368-0.020-0.0200.0000.0000.0000.000
204A204GLN00.1130.05728.736-0.029-0.0290.0000.0000.0000.000
205A205SER0-0.011-0.00427.982-0.008-0.0080.0000.0000.0000.000
206A206SER0-0.031-0.01224.523-0.034-0.0340.0000.0000.0000.000
207A207ARG10.8470.90320.3230.5380.5380.0000.0000.0000.000
208A208SER0-0.024-0.03522.320-0.053-0.0530.0000.0000.0000.000
209A209THR0-0.016-0.04022.007-0.004-0.0040.0000.0000.0000.000
210A210ALA00.0110.01118.518-0.035-0.0350.0000.0000.0000.000
211A211GLU-1-0.771-0.89818.103-0.755-0.7550.0000.0000.0000.000
212A212LYS10.7800.89318.8240.3910.3910.0000.0000.0000.000
213A213VAL0-0.010-0.00614.619-0.009-0.0090.0000.0000.0000.000
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