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: 98Z52

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 OptH
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 -2747273.057564
FMO2-HF: Nuclear repulsion 2661781.39712
FMO2-HF: Total energy -85491.660444
FMO2-MP2: Total energy -85743.034946


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.
-2.727-0.952-0.028-0.655-1.0920.004
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 : -0.013 / q_NPA : -0.029
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].
3A3LYS10.8710.9523.7181.3592.995-0.027-0.643-0.9660.004
4A4ARG10.8310.9085.2850.2400.379-0.001-0.012-0.1260.000
5A5VAL0-0.0070.0008.2440.0330.0330.0000.0000.0000.000
6A6LEU0-0.0280.00611.8900.0570.0570.0000.0000.0000.000
7A7MET0-0.030-0.01614.596-0.004-0.0040.0000.0000.0000.000
8A8VAL00.000-0.00317.6260.0150.0150.0000.0000.0000.000
9A9VAL0-0.009-0.01020.9100.0030.0030.0000.0000.0000.000
10A10THR0-0.017-0.03824.0700.0070.0070.0000.0000.0000.000
11A11ASN00.014-0.01226.057-0.005-0.0050.0000.0000.0000.000
12A12HIS0-0.0360.00229.4650.0040.0040.0000.0000.0000.000
13A13THR00.0330.00732.930-0.001-0.0010.0000.0000.0000.000
14A14THR0-0.047-0.04235.7430.0020.0020.0000.0000.0000.000
15A15ILE00.0320.04438.096-0.002-0.0020.0000.0000.0000.000
16A16THR00.0180.00141.2040.0020.0020.0000.0000.0000.000
17A17ASP-1-0.915-0.96743.683-0.048-0.0480.0000.0000.0000.000
18A18ASP-1-0.951-0.99645.443-0.050-0.0500.0000.0000.0000.000
19A19HIS10.8510.95842.0900.0520.0520.0000.0000.0000.000
20A20LYS10.9340.97338.4230.0590.0590.0000.0000.0000.000
21A21THR0-0.047-0.03834.953-0.002-0.0020.0000.0000.0000.000
22A22GLY00.0120.00132.0550.0020.0020.0000.0000.0000.000
23A23LEU00.0290.01524.919-0.001-0.0010.0000.0000.0000.000
24A24TRP00.006-0.00128.8290.0090.0090.0000.0000.0000.000
25A25LEU00.0310.01325.549-0.009-0.0090.0000.0000.0000.000
26A26GLU-1-0.898-0.94725.496-0.131-0.1310.0000.0000.0000.000
27A27GLH0-0.053-0.07824.794-0.013-0.0130.0000.0000.0000.000
28A28PHE0-0.028-0.00518.833-0.015-0.0150.0000.0000.0000.000
29A29ALA00.0370.00620.736-0.021-0.0210.0000.0000.0000.000
30A30VAL0-0.0010.00620.910-0.012-0.0120.0000.0000.0000.000
31A31PRO0-0.022-0.02519.330-0.013-0.0130.0000.0000.0000.000
32A32TYR00.0170.01915.464-0.033-0.0330.0000.0000.0000.000
33A33LEU00.0230.01915.859-0.037-0.0370.0000.0000.0000.000
34A34VAL00.0220.01816.455-0.014-0.0140.0000.0000.0000.000
35A35PHE0-0.053-0.04712.645-0.036-0.0360.0000.0000.0000.000
36A36GLN00.0160.00311.857-0.114-0.1140.0000.0000.0000.000
37A37GLU-1-0.953-0.97312.241-0.222-0.2220.0000.0000.0000.000
38A38LYS10.8480.93511.2880.4180.4180.0000.0000.0000.000
39A39GLY0-0.047-0.0178.829-0.065-0.0650.0000.0000.0000.000
40A40TYR0-0.033-0.0236.985-0.236-0.2360.0000.0000.0000.000
41A41ASP-1-0.872-0.9235.6900.0760.0760.0000.0000.0000.000
42A42VAL00.0240.0077.6650.0500.0500.0000.0000.0000.000
43A43LYS10.8520.92311.3880.2180.2180.0000.0000.0000.000
44A44VAL0-0.002-0.01113.393-0.003-0.0030.0000.0000.0000.000
45A45ALA0-0.012-0.00917.0100.0170.0170.0000.0000.0000.000
46A46SER00.008-0.00119.3060.0000.0000.0000.0000.0000.000
47A47ILE00.0030.01522.9460.0010.0010.0000.0000.0000.000
48A48GLN0-0.032-0.03525.3780.0040.0040.0000.0000.0000.000
49A49GLY0-0.032-0.00322.7750.0050.0050.0000.0000.0000.000
50A50GLY0-0.041-0.01723.0960.0070.0070.0000.0000.0000.000
51A51GLU-1-0.929-0.95224.426-0.099-0.0990.0000.0000.0000.000
52A52VAL0-0.041-0.02024.2870.0050.0050.0000.0000.0000.000
53A53PRO0-0.0310.01327.2680.0020.0020.0000.0000.0000.000
54A54LEU00.023-0.00227.425-0.005-0.0050.0000.0000.0000.000
55A55ASP-1-0.836-0.91331.099-0.075-0.0750.0000.0000.0000.000
56A56PRO00.0600.02033.738-0.001-0.0010.0000.0000.0000.000
57A57ARG10.8940.94136.3120.0670.0670.0000.0000.0000.000
58A58SER0-0.061-0.01831.262-0.003-0.0030.0000.0000.0000.000
59A59ILE0-0.025-0.02331.447-0.005-0.0050.0000.0000.0000.000
60A60ASN0-0.036-0.04433.0720.0010.0010.0000.0000.0000.000
61A61GLU-1-0.935-0.94533.616-0.063-0.0630.0000.0000.0000.000
62A62LYS10.8830.96129.4650.0870.0870.0000.0000.0000.000
63A63ASP-1-0.816-0.90226.805-0.099-0.0990.0000.0000.0000.000
64A64PRO0-0.021-0.02727.314-0.006-0.0060.0000.0000.0000.000
65A65SER0-0.039-0.00723.008-0.007-0.0070.0000.0000.0000.000
66A66TRP00.019-0.00422.460-0.013-0.0130.0000.0000.0000.000
67A67ALA00.0410.03523.594-0.005-0.0050.0000.0000.0000.000
68A68GLU-1-0.917-0.97117.758-0.188-0.1880.0000.0000.0000.000
69A69ALA0-0.021-0.00619.933-0.009-0.0090.0000.0000.0000.000
70A70GLU-1-0.874-0.97120.864-0.111-0.1110.0000.0000.0000.000
71A71ALA0-0.050-0.02621.5490.0070.0070.0000.0000.0000.000
72A72ALA00.0330.01418.3860.0040.0040.0000.0000.0000.000
73A73LEU0-0.032-0.01020.0550.0030.0030.0000.0000.0000.000
74A74LYS10.9340.96922.8990.1140.1140.0000.0000.0000.000
75A75HIS0-0.066-0.03118.8770.0000.0000.0000.0000.0000.000
76A76THR0-0.0050.02219.729-0.009-0.0090.0000.0000.0000.000
77A77ALA00.0210.00416.9700.0120.0120.0000.0000.0000.000
78A78ARG10.9530.97419.0780.0920.0920.0000.0000.0000.000
79A79LEU0-0.045-0.01219.1330.0000.0000.0000.0000.0000.000
80A80SER0-0.0070.00118.3370.0130.0130.0000.0000.0000.000
81A81LYS10.9190.94419.3700.0760.0760.0000.0000.0000.000
82A82ASP-1-0.916-0.95215.606-0.089-0.0890.0000.0000.0000.000
83A83ASP-1-0.818-0.90714.952-0.153-0.1530.0000.0000.0000.000
84A84ALA0-0.024-0.01015.686-0.025-0.0250.0000.0000.0000.000
85A85HIS10.8540.92813.8520.1300.1300.0000.0000.0000.000
86A86GLY00.0140.0099.7810.0270.0270.0000.0000.0000.000
87A87PHE00.0040.0138.8500.0720.0720.0000.0000.0000.000
88A88ASP-1-0.869-0.9397.758-1.586-1.5860.0000.0000.0000.000
89A89ALA00.0250.00611.0080.0620.0620.0000.0000.0000.000
90A90ILE0-0.0260.00614.1880.0070.0070.0000.0000.0000.000
91A91PHE00.005-0.01117.0330.0060.0060.0000.0000.0000.000
92A92LEU0-0.010-0.00419.1090.0110.0110.0000.0000.0000.000
93A93PRO00.011-0.01321.3380.0100.0100.0000.0000.0000.000
94A94GLY00.0350.02324.3500.0060.0060.0000.0000.0000.000
95A95GLY00.0370.01728.1340.0000.0000.0000.0000.0000.000
96A96HIS10.7990.84931.1540.0790.0790.0000.0000.0000.000
97A97GLY00.0410.04032.2840.0030.0030.0000.0000.0000.000
98A98THR00.0360.00228.0730.0030.0030.0000.0000.0000.000
99A99MET0-0.033-0.00430.770-0.003-0.0030.0000.0000.0000.000
100A100PHE0-0.048-0.03333.8030.0040.0040.0000.0000.0000.000
101A101ASP-1-0.780-0.86329.758-0.103-0.1030.0000.0000.0000.000
102A102PHE0-0.009-0.01725.010-0.004-0.0040.0000.0000.0000.000
103A103PRO0-0.0090.01229.370-0.002-0.0020.0000.0000.0000.000
104A104ASP-1-0.902-0.95831.653-0.077-0.0770.0000.0000.0000.000
105A105ASN0-0.0190.00726.8730.0000.0000.0000.0000.0000.000
106A106GLU-1-0.764-0.90127.645-0.092-0.0920.0000.0000.0000.000
107A107THR0-0.056-0.02522.750-0.002-0.0020.0000.0000.0000.000
108A108LEU00.0240.00322.658-0.008-0.0080.0000.0000.0000.000
109A109GLN0-0.029-0.01324.019-0.008-0.0080.0000.0000.0000.000
110A110TYR0-0.045-0.01521.044-0.005-0.0050.0000.0000.0000.000
111A111VAL00.0190.00018.653-0.006-0.0060.0000.0000.0000.000
112A112LEU0-0.002-0.00320.364-0.018-0.0180.0000.0000.0000.000
113A113GLN0-0.028-0.01722.071-0.005-0.0050.0000.0000.0000.000
114A114GLN0-0.005-0.00718.958-0.004-0.0040.0000.0000.0000.000
115A115PHE00.0200.01014.585-0.013-0.0130.0000.0000.0000.000
116A116ALA0-0.038-0.02018.499-0.022-0.0220.0000.0000.0000.000
117A117GLU-1-0.888-0.94821.138-0.124-0.1240.0000.0000.0000.000
118A118ASP-1-0.922-0.95616.165-0.189-0.1890.0000.0000.0000.000
119A119GLY0-0.078-0.02916.589-0.038-0.0380.0000.0000.0000.000
120A120ARG10.9190.9669.8600.4370.4370.0000.0000.0000.000
121A121ILE0-0.0040.00213.4200.0530.0530.0000.0000.0000.000
122A122ILE00.0160.01216.896-0.005-0.0050.0000.0000.0000.000
123A123ALA00.008-0.00319.7360.0130.0130.0000.0000.0000.000
124A124ALA0-0.0010.01021.3370.0030.0030.0000.0000.0000.000
125A125VAL00.0230.01024.1850.0060.0060.0000.0000.0000.000
126A126CSD-1-0.760-0.80826.511-0.103-0.1030.0000.0000.0000.000
127A127HIS10.7440.81130.2310.1000.1000.0000.0000.0000.000
128A128GLY00.0560.05826.6500.0030.0030.0000.0000.0000.000
129A129PRO0-0.012-0.02927.283-0.002-0.0020.0000.0000.0000.000
130A130SER00.0200.00328.6510.0040.0040.0000.0000.0000.000
131A131GLY0-0.009-0.00326.8970.0050.0050.0000.0000.0000.000
132A132LEU0-0.010-0.02024.854-0.001-0.0010.0000.0000.0000.000
133A133VAL0-0.058-0.00628.3180.0050.0050.0000.0000.0000.000
134A134ASN00.003-0.01431.3130.0070.0070.0000.0000.0000.000
135A135ALA00.0250.03826.6070.0020.0020.0000.0000.0000.000
136A136THR0-0.035-0.02628.1050.0010.0010.0000.0000.0000.000
137A137TYR00.0340.02624.010-0.011-0.0110.0000.0000.0000.000
138A138LYS10.9130.94325.9610.0890.0890.0000.0000.0000.000
139A139ASP-1-0.936-0.96628.252-0.081-0.0810.0000.0000.0000.000
140A140GLY0-0.0040.00830.7990.0050.0050.0000.0000.0000.000
141A141THR0-0.072-0.03530.6390.0040.0040.0000.0000.0000.000
142A142PRO00.008-0.00430.224-0.007-0.0070.0000.0000.0000.000
143A143ILE00.0420.02224.4430.0000.0000.0000.0000.0000.000
144A144VAL0-0.026-0.02027.904-0.006-0.0060.0000.0000.0000.000
145A145LYS10.9590.98829.8260.0790.0790.0000.0000.0000.000
146A146GLY0-0.045-0.02731.119-0.003-0.0030.0000.0000.0000.000
147A147LYS10.8820.96724.1530.1610.1610.0000.0000.0000.000
148A148THR0-0.041-0.02629.1690.0090.0090.0000.0000.0000.000
149A149VAL0-0.042-0.02328.203-0.011-0.0110.0000.0000.0000.000
150A150THR0-0.017-0.02529.1150.0110.0110.0000.0000.0000.000
151A151SER0-0.003-0.02030.213-0.007-0.0070.0000.0000.0000.000
152A152PHE0-0.020-0.00532.1490.0050.0050.0000.0000.0000.000
153A153THR0-0.035-0.03034.4150.0040.0040.0000.0000.0000.000
154A154ASP-1-0.753-0.87937.735-0.069-0.0690.0000.0000.0000.000
155A155GLU-1-0.978-1.00040.890-0.058-0.0580.0000.0000.0000.000
156A156GLU-1-0.726-0.84636.594-0.084-0.0840.0000.0000.0000.000
157A157GLU-1-0.747-0.84038.003-0.077-0.0770.0000.0000.0000.000
158A158ARG10.9300.96140.6570.0580.0580.0000.0000.0000.000
159A159GLU-1-0.894-0.91742.654-0.056-0.0560.0000.0000.0000.000
160A160VAL0-0.080-0.04839.1400.0010.0010.0000.0000.0000.000
161A161GLY00.0200.02042.5680.0010.0010.0000.0000.0000.000
162A162LEU0-0.032-0.02639.6730.0010.0010.0000.0000.0000.000
163A163ASP-1-0.833-0.93042.275-0.056-0.0560.0000.0000.0000.000
164A164VAL0-0.039-0.02143.2460.0000.0000.0000.0000.0000.000
165A165HIS0-0.039-0.01643.0900.0010.0010.0000.0000.0000.000
166A166MET0-0.058-0.01538.417-0.005-0.0050.0000.0000.0000.000
167A167PRO00.0020.01338.0500.0030.0030.0000.0000.0000.000
168A168PHE0-0.009-0.00834.4460.0010.0010.0000.0000.0000.000
169A169LEU00.0350.02439.312-0.002-0.0020.0000.0000.0000.000
170A170LEU00.0370.01331.8700.0000.0000.0000.0000.0000.000
171A171GLU-1-0.748-0.85535.925-0.076-0.0760.0000.0000.0000.000
172A172SER0-0.092-0.07537.0140.0010.0010.0000.0000.0000.000
173A173THR0-0.030-0.02536.4220.0030.0030.0000.0000.0000.000
174A174LEU00.0030.00031.345-0.001-0.0010.0000.0000.0000.000
175A175ARG10.8950.94735.0110.0700.0700.0000.0000.0000.000
176A176LEU0-0.056-0.01437.5510.0020.0020.0000.0000.0000.000
177A177ARG10.8290.92134.3100.0810.0810.0000.0000.0000.000
178A178GLY0-0.020-0.01635.153-0.002-0.0020.0000.0000.0000.000
179A179ALA00.0140.02532.454-0.002-0.0020.0000.0000.0000.000
180A180ASN0-0.048-0.02233.1940.0110.0110.0000.0000.0000.000
181A181PHE0-0.015-0.01333.325-0.005-0.0050.0000.0000.0000.000
182A182VAL0-0.013-0.00432.1300.0060.0060.0000.0000.0000.000
183A183ARG10.8420.92033.8140.0670.0670.0000.0000.0000.000
184A184GLY00.0660.04535.1560.0030.0030.0000.0000.0000.000
185A185GLY00.003-0.00136.1800.0020.0020.0000.0000.0000.000
186A186LYS10.8850.94837.2660.0520.0520.0000.0000.0000.000
187A187TRP0-0.055-0.04235.9550.0000.0000.0000.0000.0000.000
188A188THR0-0.072-0.03435.3010.0010.0010.0000.0000.0000.000
189A189ASP-1-0.830-0.88028.917-0.130-0.1300.0000.0000.0000.000
190A190PHE00.0100.01030.7830.0040.0040.0000.0000.0000.000
191A191SER00.0390.00625.679-0.008-0.0080.0000.0000.0000.000
192A192VAL0-0.071-0.03426.7210.0050.0050.0000.0000.0000.000
193A193ARG10.7870.84917.8460.2540.2540.0000.0000.0000.000
194A194ASP-1-0.814-0.88224.192-0.122-0.1220.0000.0000.0000.000
195A195GLY00.023-0.00321.993-0.006-0.0060.0000.0000.0000.000
196A196ASN00.0340.01918.422-0.033-0.0330.0000.0000.0000.000
197A197LEU0-0.0350.00219.970-0.019-0.0190.0000.0000.0000.000
198A198ILE00.0010.00018.8530.0170.0170.0000.0000.0000.000
199A199THR00.0200.01022.8830.0030.0030.0000.0000.0000.000
200A200GLY00.0650.02825.8420.0030.0030.0000.0000.0000.000
201A201GLN00.0050.00927.6830.0000.0000.0000.0000.0000.000
202A202ASN0-0.010-0.02030.5700.0000.0000.0000.0000.0000.000
203A203PRO00.0220.02129.297-0.008-0.0080.0000.0000.0000.000
204A204GLN00.1200.05028.823-0.010-0.0100.0000.0000.0000.000
205A205SER00.0010.00028.2250.0010.0010.0000.0000.0000.000
206A206SER0-0.037-0.01424.414-0.016-0.0160.0000.0000.0000.000
207A207ARG11.0401.01522.2370.1390.1390.0000.0000.0000.000
208A208SER0-0.020-0.01522.430-0.022-0.0220.0000.0000.0000.000
209A209THR0-0.016-0.02822.121-0.010-0.0100.0000.0000.0000.000
210A210ALA00.012-0.00418.629-0.024-0.0240.0000.0000.0000.000
211A211GLU-1-0.864-0.94217.998-0.283-0.2830.0000.0000.0000.000
212A212LYS10.8100.90718.3570.1550.1550.0000.0000.0000.000
213A213VAL0-0.037-0.01014.818-0.018-0.0180.0000.0000.0000.000
214A214VAL00.0350.02113.536-0.079-0.0790.0000.0000.0000.000
215A215ALA00.0160.02513.584-0.049-0.0490.0000.0000.0000.000
216A216ALA0-0.018-0.01614.826-0.012-0.0120.0000.0000.0000.000
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