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

tag_button

FMODB ID: MN4KZ

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 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 221
LigandCharge CSD=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2749501.798647
FMO2-HF: Nuclear repulsion 2664009.034917
FMO2-HF: Total energy -85492.76373
FMO2-MP2: Total energy -85744.214164


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.
-6.956-4.705-0.023-1.042-1.1850.006
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 : -0.022 / q_NPA : -0.016
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].
3A3LYS10.8460.9363.6491.1803.431-0.023-1.042-1.1850.006
4A4ARG10.7730.8654.9901.6881.6880.0000.0000.0000.000
5A5VAL0-0.016-0.0067.6700.2740.2740.0000.0000.0000.000
6A6LEU0-0.0240.00911.3860.0430.0430.0000.0000.0000.000
7A7MET0-0.025-0.01013.9480.0230.0230.0000.0000.0000.000
8A8VAL00.000-0.00316.9780.0290.0290.0000.0000.0000.000
9A9VAL0-0.012-0.01320.0230.0110.0110.0000.0000.0000.000
10A10THR0-0.005-0.03023.1190.0180.0180.0000.0000.0000.000
11A11ASN00.002-0.02224.810-0.012-0.0120.0000.0000.0000.000
12A12HIS0-0.044-0.00628.2400.0110.0110.0000.0000.0000.000
13A13THR00.0360.00231.757-0.006-0.0060.0000.0000.0000.000
14A14THR0-0.040-0.02834.5240.0020.0020.0000.0000.0000.000
15A15ILE00.0070.03237.370-0.003-0.0030.0000.0000.0000.000
16A16THR00.0270.00040.1770.0040.0040.0000.0000.0000.000
17A17ASP-1-0.878-0.95342.561-0.096-0.0960.0000.0000.0000.000
18A18ASP-1-0.903-0.94144.297-0.105-0.1050.0000.0000.0000.000
19A19HIS10.8480.93141.3120.1090.1090.0000.0000.0000.000
20A20LYS10.8630.92737.6020.1150.1150.0000.0000.0000.000
21A21THR0-0.055-0.04833.958-0.006-0.0060.0000.0000.0000.000
22A22GLY00.0260.01131.0390.0060.0060.0000.0000.0000.000
23A23LEU00.0320.01723.996-0.002-0.0020.0000.0000.0000.000
24A24TRP0-0.015-0.00828.2030.0200.0200.0000.0000.0000.000
25A25LEU00.0250.01525.170-0.022-0.0220.0000.0000.0000.000
26A26GLU-1-0.885-0.94525.236-0.316-0.3160.0000.0000.0000.000
27A27GLH0-0.048-0.06924.701-0.028-0.0280.0000.0000.0000.000
28A28PHE0-0.022-0.00517.823-0.029-0.0290.0000.0000.0000.000
29A29ALA00.0320.00620.616-0.050-0.0500.0000.0000.0000.000
30A30VAL00.0100.01020.946-0.033-0.0330.0000.0000.0000.000
31A31PRO0-0.021-0.02319.044-0.036-0.0360.0000.0000.0000.000
32A32TYR00.0110.01313.746-0.051-0.0510.0000.0000.0000.000
33A33LEU00.0210.02015.924-0.089-0.0890.0000.0000.0000.000
34A34VAL00.0230.01716.540-0.048-0.0480.0000.0000.0000.000
35A35PHE0-0.060-0.05112.580-0.084-0.0840.0000.0000.0000.000
36A36GLN00.0210.00912.016-0.269-0.2690.0000.0000.0000.000
37A37GLU-1-0.952-0.97512.629-0.656-0.6560.0000.0000.0000.000
38A38LYS10.7930.89711.3721.1721.1720.0000.0000.0000.000
39A39GLY0-0.039-0.0138.891-0.207-0.2070.0000.0000.0000.000
40A40TYR0-0.030-0.0247.351-0.370-0.3700.0000.0000.0000.000
41A41ASP-1-0.831-0.8915.158-1.672-1.6720.0000.0000.0000.000
42A42VAL00.0140.0007.2970.1460.1460.0000.0000.0000.000
43A43LYS10.8470.91310.7320.5120.5120.0000.0000.0000.000
44A44VAL0-0.002-0.00912.1040.0330.0330.0000.0000.0000.000
45A45ALA0-0.013-0.01115.7630.0460.0460.0000.0000.0000.000
46A46SER00.0140.00618.1440.0020.0020.0000.0000.0000.000
47A47ILE00.0020.01321.8970.0070.0070.0000.0000.0000.000
48A48GLN0-0.045-0.04424.4560.0150.0150.0000.0000.0000.000
49A49GLY0-0.0210.00221.8370.0150.0150.0000.0000.0000.000
50A50GLY0-0.037-0.01422.1650.0170.0170.0000.0000.0000.000
51A51GLU-1-0.857-0.91223.339-0.219-0.2190.0000.0000.0000.000
52A52VAL0-0.030-0.01123.0830.0130.0130.0000.0000.0000.000
53A53PRO0-0.0340.00526.1070.0010.0010.0000.0000.0000.000
54A54LEU00.0230.00126.445-0.012-0.0120.0000.0000.0000.000
55A55ASP-1-0.839-0.89530.164-0.165-0.1650.0000.0000.0000.000
56A56PRO00.0640.02632.997-0.006-0.0060.0000.0000.0000.000
57A57ARG10.8860.93835.5880.1540.1540.0000.0000.0000.000
58A58SER0-0.055-0.02731.016-0.008-0.0080.0000.0000.0000.000
59A59ILE0-0.009-0.01630.630-0.014-0.0140.0000.0000.0000.000
60A60ASN0-0.056-0.04532.5760.0010.0010.0000.0000.0000.000
61A61GLU-1-0.937-0.94833.438-0.166-0.1660.0000.0000.0000.000
62A62LYS10.8150.90328.9660.2150.2150.0000.0000.0000.000
63A63ASP-1-0.795-0.85526.980-0.281-0.2810.0000.0000.0000.000
64A64PRO0-0.023-0.03027.273-0.012-0.0120.0000.0000.0000.000
65A65SER0-0.057-0.04723.276-0.016-0.0160.0000.0000.0000.000
66A66TRP00.023-0.00922.518-0.028-0.0280.0000.0000.0000.000
67A67ALA00.0130.01823.145-0.005-0.0050.0000.0000.0000.000
68A68GLU-1-0.902-0.96017.060-0.503-0.5030.0000.0000.0000.000
69A69ALA0-0.016-0.00419.265-0.015-0.0150.0000.0000.0000.000
70A70GLU-1-0.786-0.90620.244-0.250-0.2500.0000.0000.0000.000
71A71ALA0-0.028-0.01420.7480.0210.0210.0000.0000.0000.000
72A72ALA00.0200.00717.3450.0170.0170.0000.0000.0000.000
73A73LEU0-0.023-0.00619.0980.0110.0110.0000.0000.0000.000
74A74LYS10.8620.92621.8280.2470.2470.0000.0000.0000.000
75A75HIS0-0.086-0.04017.9870.0050.0050.0000.0000.0000.000
76A76THR00.0040.03118.631-0.021-0.0210.0000.0000.0000.000
77A77ALA00.0210.00416.0990.0390.0390.0000.0000.0000.000
78A78ARG10.9510.97418.2190.1470.1470.0000.0000.0000.000
79A79LEU0-0.043-0.01218.2320.0020.0020.0000.0000.0000.000
80A80SER0-0.041-0.05418.1820.0360.0360.0000.0000.0000.000
81A81LYS10.8780.91118.9950.0870.0870.0000.0000.0000.000
82A82ASP-1-0.873-0.90515.877-0.091-0.0910.0000.0000.0000.000
83A83ASP-1-0.814-0.89614.304-0.373-0.3730.0000.0000.0000.000
84A84ALA0-0.035-0.01115.484-0.060-0.0600.0000.0000.0000.000
85A85HIS10.8020.89514.1480.1680.1680.0000.0000.0000.000
86A86GLY00.0400.02410.1270.0300.0300.0000.0000.0000.000
87A87PHE00.0070.0128.937-0.135-0.1350.0000.0000.0000.000
88A88ASP-1-0.831-0.9047.971-2.287-2.2870.0000.0000.0000.000
89A89ALA00.015-0.00411.1570.1330.1330.0000.0000.0000.000
90A90ILE0-0.0220.00713.657-0.032-0.0320.0000.0000.0000.000
91A91PHE00.000-0.01416.4830.0220.0220.0000.0000.0000.000
92A92LEU0-0.006-0.00318.6180.0130.0130.0000.0000.0000.000
93A93PRO00.008-0.01120.9000.0220.0220.0000.0000.0000.000
94A94GLY00.0360.02423.9710.0160.0160.0000.0000.0000.000
95A95GLY00.0410.01827.744-0.002-0.0020.0000.0000.0000.000
96A96HIS10.8250.88130.6960.1740.1740.0000.0000.0000.000
97A97GLY00.0450.04031.3580.0080.0080.0000.0000.0000.000
98A98THR00.029-0.00427.3590.0080.0080.0000.0000.0000.000
99A99MET0-0.031-0.00130.011-0.002-0.0020.0000.0000.0000.000
100A100PHE0-0.050-0.03732.9800.0100.0100.0000.0000.0000.000
101A101ASP-1-0.786-0.86628.656-0.206-0.2060.0000.0000.0000.000
102A102PHE0-0.002-0.01424.305-0.006-0.0060.0000.0000.0000.000
103A103PRO0-0.0110.01528.762-0.001-0.0010.0000.0000.0000.000
104A104ASP-1-0.879-0.95031.228-0.134-0.1340.0000.0000.0000.000
105A105ASN0-0.0260.00426.2720.0060.0060.0000.0000.0000.000
106A106GLU-1-0.714-0.84727.012-0.132-0.1320.0000.0000.0000.000
107A107THR0-0.038-0.02922.3380.0000.0000.0000.0000.0000.000
108A108LEU00.0030.00322.362-0.014-0.0140.0000.0000.0000.000
109A109GLN0-0.033-0.01823.826-0.010-0.0100.0000.0000.0000.000
110A110TYR0-0.040-0.01420.914-0.004-0.0040.0000.0000.0000.000
111A111VAL00.0200.00218.431-0.003-0.0030.0000.0000.0000.000
112A112LEU0-0.001-0.00220.332-0.026-0.0260.0000.0000.0000.000
113A113GLN0-0.018-0.01022.1940.0030.0030.0000.0000.0000.000
114A114GLN00.0020.00219.1230.0240.0240.0000.0000.0000.000
115A115PHE00.0410.01414.389-0.005-0.0050.0000.0000.0000.000
116A116ALA0-0.023-0.00818.662-0.027-0.0270.0000.0000.0000.000
117A117GLU-1-0.880-0.95221.280-0.143-0.1430.0000.0000.0000.000
118A118ASP-1-0.855-0.91216.121-0.231-0.2310.0000.0000.0000.000
119A119GLY0-0.072-0.03016.438-0.040-0.0400.0000.0000.0000.000
120A120ARG10.8040.88810.6210.5060.5060.0000.0000.0000.000
121A121ILE0-0.015-0.00313.7100.0800.0800.0000.0000.0000.000
122A122ILE00.0050.00517.042-0.018-0.0180.0000.0000.0000.000
123A123ALA00.013-0.00119.2370.0230.0230.0000.0000.0000.000
124A124ALA00.0090.01420.9330.0020.0020.0000.0000.0000.000
125A125VAL00.0200.00823.7070.0110.0110.0000.0000.0000.000
126A126CSD-1-0.790-0.82226.133-0.229-0.2290.0000.0000.0000.000
127A127HIS10.7690.80829.8550.2150.2150.0000.0000.0000.000
128A128GLY00.0540.06426.1690.0100.0100.0000.0000.0000.000
129A129PRO0-0.009-0.02726.7160.0000.0000.0000.0000.0000.000
130A130SER00.017-0.00728.1010.0110.0110.0000.0000.0000.000
131A131GLY0-0.009-0.00226.3770.0130.0130.0000.0000.0000.000
132A132LEU0-0.012-0.02124.4170.0030.0030.0000.0000.0000.000
133A133VAL0-0.058-0.00928.0310.0120.0120.0000.0000.0000.000
134A134ASN00.0080.00131.0300.0130.0130.0000.0000.0000.000
135A135ALA00.0150.03326.5270.0070.0070.0000.0000.0000.000
136A136THR0-0.033-0.03228.1800.0000.0000.0000.0000.0000.000
137A137TYR00.0250.02323.678-0.011-0.0110.0000.0000.0000.000
138A138LYS10.8760.93525.9110.0990.0990.0000.0000.0000.000
139A139ASP-1-0.871-0.92928.346-0.111-0.1110.0000.0000.0000.000
140A140GLY0-0.0090.00930.9020.0070.0070.0000.0000.0000.000
141A141THR0-0.095-0.06130.8600.0000.0000.0000.0000.0000.000
142A142PRO00.002-0.00930.364-0.012-0.0120.0000.0000.0000.000
143A143ILE00.0280.01724.506-0.001-0.0010.0000.0000.0000.000
144A144VAL0-0.017-0.01427.939-0.011-0.0110.0000.0000.0000.000
145A145LYS10.9600.99029.9050.1290.1290.0000.0000.0000.000
146A146GLY0-0.033-0.02031.189-0.004-0.0040.0000.0000.0000.000
147A147LYS10.7960.91525.3120.2700.2700.0000.0000.0000.000
148A148THR0-0.044-0.03629.5300.0150.0150.0000.0000.0000.000
149A149VAL0-0.042-0.02228.393-0.022-0.0220.0000.0000.0000.000
150A150THR0-0.020-0.03029.2350.0190.0190.0000.0000.0000.000
151A151SER0-0.005-0.02230.022-0.011-0.0110.0000.0000.0000.000
152A152PHE0-0.011-0.00531.7060.0080.0080.0000.0000.0000.000
153A153THR0-0.026-0.03634.0160.0100.0100.0000.0000.0000.000
154A154ASP-1-0.768-0.89237.322-0.143-0.1430.0000.0000.0000.000
155A155GLU-1-0.893-0.93640.442-0.135-0.1350.0000.0000.0000.000
156A156GLU-1-0.694-0.81136.365-0.191-0.1910.0000.0000.0000.000
157A157GLU-1-0.763-0.85337.468-0.166-0.1660.0000.0000.0000.000
158A158ARG10.9140.95240.2630.1270.1270.0000.0000.0000.000
159A159GLU-1-0.868-0.89142.313-0.132-0.1320.0000.0000.0000.000
160A160VAL0-0.068-0.03838.9010.0020.0020.0000.0000.0000.000
161A161GLY00.0180.02142.2620.0030.0030.0000.0000.0000.000
162A162LEU0-0.043-0.03539.2200.0040.0040.0000.0000.0000.000
163A163ASP-1-0.825-0.92541.797-0.117-0.1170.0000.0000.0000.000
164A164VAL0-0.038-0.02242.7780.0010.0010.0000.0000.0000.000
165A165HIS0-0.043-0.01542.4070.0040.0040.0000.0000.0000.000
166A166MET0-0.059-0.01837.866-0.009-0.0090.0000.0000.0000.000
167A167PRO0-0.0010.01337.3040.0060.0060.0000.0000.0000.000
168A168PHE0-0.002-0.00833.8900.0040.0040.0000.0000.0000.000
169A169LEU00.0230.01938.741-0.006-0.0060.0000.0000.0000.000
170A170LEU00.0410.03231.3290.0020.0020.0000.0000.0000.000
171A171GLU-1-0.728-0.83035.504-0.159-0.1590.0000.0000.0000.000
172A172SER0-0.067-0.06536.5870.0040.0040.0000.0000.0000.000
173A173THR0-0.031-0.03236.1860.0080.0080.0000.0000.0000.000
174A174LEU0-0.010-0.00830.9850.0010.0010.0000.0000.0000.000
175A175ARG10.8650.91634.8130.1460.1460.0000.0000.0000.000
176A176LEU0-0.044-0.01037.5850.0050.0050.0000.0000.0000.000
177A177ARG10.8210.90934.2920.1470.1470.0000.0000.0000.000
178A178GLY0-0.024-0.01835.272-0.001-0.0010.0000.0000.0000.000
179A179ALA00.0070.02332.612-0.003-0.0030.0000.0000.0000.000
180A180ASN0-0.053-0.02433.4240.0210.0210.0000.0000.0000.000
181A181PHE0-0.010-0.01233.578-0.012-0.0120.0000.0000.0000.000
182A182VAL0-0.008-0.00332.5980.0110.0110.0000.0000.0000.000
183A183ARG10.8080.89934.1750.1540.1540.0000.0000.0000.000
184A184GLY00.0770.04735.4380.0060.0060.0000.0000.0000.000
185A185GLY00.0060.00136.5390.0070.0070.0000.0000.0000.000
186A186LYS10.7940.88937.2460.1230.1230.0000.0000.0000.000
187A187TRP0-0.077-0.06235.615-0.002-0.0020.0000.0000.0000.000
188A188THR0-0.070-0.02835.229-0.001-0.0010.0000.0000.0000.000
189A189ASP-1-0.812-0.85828.959-0.318-0.3180.0000.0000.0000.000
190A190PHE00.0040.00430.9150.0070.0070.0000.0000.0000.000
191A191SER00.0430.00326.077-0.013-0.0130.0000.0000.0000.000
192A192VAL0-0.081-0.03527.1510.0080.0080.0000.0000.0000.000
193A193ARG10.7940.83418.3770.5080.5080.0000.0000.0000.000
194A194ASP-1-0.765-0.84624.623-0.234-0.2340.0000.0000.0000.000
195A195GLY00.024-0.00122.308-0.001-0.0010.0000.0000.0000.000
196A196ASN00.0400.02118.272-0.078-0.0780.0000.0000.0000.000
197A197LEU0-0.0200.01120.174-0.032-0.0320.0000.0000.0000.000
198A198ILE0-0.007-0.00619.2290.0260.0260.0000.0000.0000.000
199A199THR00.0240.01223.2380.0050.0050.0000.0000.0000.000
200A200GLY00.0610.02425.8500.0010.0010.0000.0000.0000.000
201A201GLN0-0.019-0.01427.5030.0030.0030.0000.0000.0000.000
202A202ASN0-0.018-0.02430.2770.0000.0000.0000.0000.0000.000
203A203PRO00.0310.03229.103-0.019-0.0190.0000.0000.0000.000
204A204GLN00.1240.05928.703-0.025-0.0250.0000.0000.0000.000
205A205SER0-0.005-0.00728.139-0.002-0.0020.0000.0000.0000.000
206A206SER0-0.038-0.01524.325-0.030-0.0300.0000.0000.0000.000
207A207ARG10.9740.98121.1400.4290.4290.0000.0000.0000.000
208A208SER0-0.018-0.01922.436-0.048-0.0480.0000.0000.0000.000
209A209THR0-0.020-0.03621.951-0.016-0.0160.0000.0000.0000.000
210A210ALA00.012-0.00118.606-0.039-0.0390.0000.0000.0000.000
211A211GLU-1-0.801-0.90918.201-0.674-0.6740.0000.0000.0000.000
212A212LYS10.7980.89618.5720.3530.3530.0000.0000.0000.000
213A213VAL0-0.025-0.00314.838-0.020-0.0200.0000.0000.0000.000
214A214VAL00.0300.01713.612-0.111-0.1110.0000.0000.0000.000
215A215ALA00.0120.02013.815-0.085-0.0850.0000.0000.0000.000
216A216ALA0-0.017-0.01015.098-0.017-0.0170.0000.0000.0000.000
217A217LEU0-0.029-0.02510.312-0.029-0.0290.0000.0000.0000.000
218A218GLU-1-0.841-0.92410.400-1.130-1.1300.0000.0000.0000.000
219A219GLU-1-0.852-0.88211.403-0.567-0.5670.0000.0000.0000.000
220A220ARG10.7900.90910.5170.9210.9210.0000.0000.0000.000
221A221GLU-1-0.903-0.9315.881-3.727-3.7270.0000.0000.0000.000