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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: 1NJ3Z

Calculation Name: 3SHO-A-Xray372

Preferred Name:

Target Type:

Ligand Name: cysteinesulfonic acid

ligand 3-letter code: OCS

PDB ID: 3SHO

Chain ID: A

ChEMBL ID:

UniProt ID: D1C9F1

Base Structure: X-ray

Registration Date: 2023-09-20

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 187
LigandCharge OCS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1788439.311587
FMO2-HF: Nuclear repulsion 1718770.636197
FMO2-HF: Total energy -69668.67539
FMO2-MP2: Total energy -69872.676394


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:96:ASP)


Summations of interaction energy for fragment #1(A:96:ASP)
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.
-20.401-14.6961.066-2.58-4.1910.018
Interaction energy analysis for fragmet #1(A:96:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.868 / q_NPA : -0.946
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].
3A98GLN00.0050.0012.550-22.855-18.6491.015-2.074-3.1470.015
4A99GLN00.008-0.0033.543-13.230-11.8400.052-0.498-0.9450.003
5A100LEU00.0150.0185.583-5.149-5.040-0.001-0.008-0.0990.000
6A101PRO00.0070.0077.702-3.314-3.3140.0000.0000.0000.000
7A102VAL00.0460.0269.352-2.148-2.1480.0000.0000.0000.000
8A103GLN00.005-0.0045.608-1.516-1.5160.0000.0000.0000.000
9A104VAL0-0.010-0.01210.458-1.666-1.6660.0000.0000.0000.000
10A105PHE00.0210.00513.095-1.404-1.4040.0000.0000.0000.000
11A106THR0-0.005-0.00413.604-1.424-1.4240.0000.0000.0000.000
12A107ASN0-0.062-0.04514.352-1.068-1.0680.0000.0000.0000.000
13A108ASP-1-0.818-0.89316.04115.09815.0980.0000.0000.0000.000
14A109ILE0-0.032-0.01517.968-0.852-0.8520.0000.0000.0000.000
15A110GLU-1-0.891-0.94618.59712.90012.9000.0000.0000.0000.000
16A111ASN0-0.029-0.03719.986-0.829-0.8290.0000.0000.0000.000
17A112LEU0-0.0100.00022.208-0.657-0.6570.0000.0000.0000.000
18A113ASN0-0.0180.00223.633-0.921-0.9210.0000.0000.0000.000
19A114GLN0-0.031-0.02522.2370.0060.0060.0000.0000.0000.000
20A115THR0-0.015-0.01925.911-0.379-0.3790.0000.0000.0000.000
21A116LEU00.0120.02728.108-0.393-0.3930.0000.0000.0000.000
22A117ASN0-0.020-0.02127.994-0.455-0.4550.0000.0000.0000.000
23A118GLN0-0.087-0.03528.832-0.130-0.1300.0000.0000.0000.000
24A119THR0-0.026-0.01332.038-0.172-0.1720.0000.0000.0000.000
25A120GLN0-0.001-0.00434.324-0.032-0.0320.0000.0000.0000.000
26A121PRO00.0280.00837.995-0.038-0.0380.0000.0000.0000.000
27A122GLU-1-0.879-0.94540.5527.2187.2180.0000.0000.0000.000
28A123ALA0-0.0050.01039.149-0.103-0.1030.0000.0000.0000.000
29A124ILE0-0.012-0.01235.9900.0270.0270.0000.0000.0000.000
30A125GLU-1-0.874-0.93240.1656.7986.7980.0000.0000.0000.000
31A126ALA00.0130.00043.844-0.112-0.1120.0000.0000.0000.000
32A127ALA0-0.030-0.02840.680-0.079-0.0790.0000.0000.0000.000
33A128VAL00.0220.00141.288-0.038-0.0380.0000.0000.0000.000
34A129GLU-1-0.927-0.96343.6806.3026.3020.0000.0000.0000.000
35A130ALA0-0.089-0.04545.079-0.151-0.1510.0000.0000.0000.000
36A131ILE0-0.032-0.03340.803-0.050-0.0500.0000.0000.0000.000
37A132OCS-1-0.866-0.92545.5006.6206.6200.0000.0000.0000.000
38A133ARG10.9090.97148.209-6.393-6.3930.0000.0000.0000.000
39A134ALA0-0.055-0.00848.232-0.129-0.1290.0000.0000.0000.000
40A135ASP-1-0.977-0.99150.1925.9195.9190.0000.0000.0000.000
41A136HIS0-0.062-0.03747.408-0.029-0.0290.0000.0000.0000.000
42A137VAL00.0390.02742.9620.0250.0250.0000.0000.0000.000
43A138ILE0-0.017-0.01742.9330.0570.0570.0000.0000.0000.000
44A139VAL00.0090.00437.3150.0920.0920.0000.0000.0000.000
45A140VAL0-0.005-0.00337.8350.0300.0300.0000.0000.0000.000
46A141GLY00.0410.01434.2030.1240.1240.0000.0000.0000.000
47A142MET0-0.0190.00733.217-0.022-0.0220.0000.0000.0000.000
48A143GLY00.0270.00629.6210.2140.2140.0000.0000.0000.000
49A144PHE0-0.019-0.01422.9290.0320.0320.0000.0000.0000.000
50A145SER00.0340.00327.1290.2610.2610.0000.0000.0000.000
51A146ALA0-0.0070.02030.003-0.248-0.2480.0000.0000.0000.000
52A147ALA00.0150.00228.208-0.237-0.2370.0000.0000.0000.000
53A148VAL00.0260.01028.629-0.116-0.1160.0000.0000.0000.000
54A149ALA00.0100.01331.118-0.244-0.2440.0000.0000.0000.000
55A150VAL00.0200.00233.072-0.242-0.2420.0000.0000.0000.000
56A151PHE0-0.058-0.02031.727-0.185-0.1850.0000.0000.0000.000
57A152LEU00.0530.02033.882-0.181-0.1810.0000.0000.0000.000
58A153GLY00.0470.01036.272-0.241-0.2410.0000.0000.0000.000
59A154HIS0-0.018-0.00136.441-0.238-0.2380.0000.0000.0000.000
60A155GLY0-0.003-0.00437.563-0.167-0.1670.0000.0000.0000.000
61A156LEU00.0360.00438.739-0.164-0.1640.0000.0000.0000.000
62A157ASN0-0.005-0.00341.829-0.374-0.3740.0000.0000.0000.000
63A158SER0-0.073-0.03540.737-0.186-0.1860.0000.0000.0000.000
64A159LEU0-0.032-0.01340.941-0.106-0.1060.0000.0000.0000.000
65A160GLY00.0040.00044.569-0.159-0.1590.0000.0000.0000.000
66A161ILE0-0.0100.00644.935-0.156-0.1560.0000.0000.0000.000
67A162ARG10.9530.97945.442-6.065-6.0650.0000.0000.0000.000
68A163THR00.0200.00541.588-0.003-0.0030.0000.0000.0000.000
69A164THR0-0.0310.00143.897-0.006-0.0060.0000.0000.0000.000
70A165VAL00.0300.02037.2620.0700.0700.0000.0000.0000.000
71A166LEU0-0.050-0.02439.934-0.057-0.0570.0000.0000.0000.000
72A167THR00.032-0.00834.6830.0690.0690.0000.0000.0000.000
73A168GLU-1-0.980-0.98635.2439.2919.2910.0000.0000.0000.000
74A169GLY00.005-0.00138.003-0.165-0.1650.0000.0000.0000.000
75A170GLY00.0050.00640.375-0.105-0.1050.0000.0000.0000.000
76A171SER0-0.002-0.00943.165-0.061-0.0610.0000.0000.0000.000
77A172THR00.0760.03143.795-0.176-0.1760.0000.0000.0000.000
78A173LEU00.0310.04241.330-0.088-0.0880.0000.0000.0000.000
79A174THR0-0.005-0.00444.831-0.125-0.1250.0000.0000.0000.000
80A175ILE0-0.022-0.01947.835-0.130-0.1300.0000.0000.0000.000
81A176THR00.003-0.00645.941-0.097-0.0970.0000.0000.0000.000
82A177LEU0-0.036-0.01945.627-0.075-0.0750.0000.0000.0000.000
83A178ALA0-0.097-0.05149.168-0.115-0.1150.0000.0000.0000.000
84A179ASN0-0.055-0.02851.817-0.212-0.2120.0000.0000.0000.000
85A180LEU0-0.0280.01047.929-0.016-0.0160.0000.0000.0000.000
86A181ARG10.9510.97152.013-5.950-5.9500.0000.0000.0000.000
87A182PRO00.012-0.00352.5810.0990.0990.0000.0000.0000.000
88A183THR0-0.003-0.00253.2030.0010.0010.0000.0000.0000.000
89A184ASP-1-0.841-0.90548.8986.3556.3550.0000.0000.0000.000
90A185LEU0-0.0010.00743.635-0.016-0.0160.0000.0000.0000.000
91A186MET0-0.041-0.01042.8370.1580.1580.0000.0000.0000.000
92A187ILE00.0290.00637.9990.0690.0690.0000.0000.0000.000
93A188GLY00.0070.00838.0830.0550.0550.0000.0000.0000.000
94A189VAL0-0.004-0.00731.6140.1030.1030.0000.0000.0000.000
95A190SER0-0.036-0.03032.6340.1480.1480.0000.0000.0000.000
96A191VAL00.0080.01427.008-0.063-0.0630.0000.0000.0000.000
97A192TRP00.0010.00823.0130.0510.0510.0000.0000.0000.000
98A193ARG10.8720.93123.488-11.552-11.5520.0000.0000.0000.000
99A194TYR0-0.010-0.07029.071-0.019-0.0190.0000.0000.0000.000
100A195LEU0-0.0050.00730.631-0.236-0.2360.0000.0000.0000.000
101A196ARG11.0000.98633.743-7.971-7.9710.0000.0000.0000.000
102A197ASP-1-0.818-0.90937.4507.7817.7810.0000.0000.0000.000
103A198THR00.009-0.00135.856-0.093-0.0930.0000.0000.0000.000
104A199VAL0-0.005-0.01036.560-0.098-0.0980.0000.0000.0000.000
105A200ALA0-0.025-0.00839.191-0.181-0.1810.0000.0000.0000.000
106A201ALA00.0020.00341.134-0.190-0.1900.0000.0000.0000.000
107A202LEU00.0150.01038.522-0.125-0.1250.0000.0000.0000.000
108A203ALA00.0030.00142.797-0.149-0.1490.0000.0000.0000.000
109A204GLY00.0170.01445.016-0.169-0.1690.0000.0000.0000.000
110A205ALA00.0120.00545.848-0.166-0.1660.0000.0000.0000.000
111A206ALA00.0590.02646.318-0.144-0.1440.0000.0000.0000.000
112A207GLU-1-0.994-1.00848.2306.3616.3610.0000.0000.0000.000
113A208ARG10.8230.91250.118-6.379-6.3790.0000.0000.0000.000
114A209GLY0-0.023-0.00151.839-0.111-0.1110.0000.0000.0000.000
115A210VAL0-0.075-0.02548.261-0.052-0.0520.0000.0000.0000.000
116A211PRO00.0310.02447.9330.1200.1200.0000.0000.0000.000
117A212THR0-0.0020.00343.3020.1440.1440.0000.0000.0000.000
118A213MET00.0020.00639.0690.0540.0540.0000.0000.0000.000
119A214ALA0-0.019-0.00636.6200.1040.1040.0000.0000.0000.000
120A215LEU00.0260.01833.0360.0470.0470.0000.0000.0000.000
121A216THR0-0.050-0.05131.7730.1450.1450.0000.0000.0000.000
122A217ASP-1-0.718-0.82327.36310.62610.6260.0000.0000.0000.000
123A218SER0-0.026-0.01228.9140.0800.0800.0000.0000.0000.000
124A219SER00.0490.02431.466-0.087-0.0870.0000.0000.0000.000
125A220VAL00.005-0.00833.952-0.273-0.2730.0000.0000.0000.000
126A221SER0-0.0170.00032.816-0.156-0.1560.0000.0000.0000.000
127A222PRO0-0.019-0.02934.257-0.210-0.2100.0000.0000.0000.000
128A223PRO00.015-0.00134.842-0.187-0.1870.0000.0000.0000.000
129A224ALA00.0180.01736.055-0.181-0.1810.0000.0000.0000.000
130A225ARG10.8770.93737.985-7.797-7.7970.0000.0000.0000.000
131A226ILE0-0.063-0.02240.647-0.171-0.1710.0000.0000.0000.000
132A227ALA0-0.019-0.01040.533-0.141-0.1410.0000.0000.0000.000
133A228ASP-1-0.843-0.90642.4786.6586.6580.0000.0000.0000.000
134A229HIS0-0.030-0.00541.7440.0930.0930.0000.0000.0000.000
135A230VAL0-0.005-0.00936.2480.1670.1670.0000.0000.0000.000
136A231LEU00.0190.01934.8140.0290.0290.0000.0000.0000.000
137A232VAL0-0.051-0.02530.1360.0990.0990.0000.0000.0000.000
138A233ALA00.0330.01727.6430.0440.0440.0000.0000.0000.000
139A234ALA0-0.0280.00223.3080.0670.0670.0000.0000.0000.000
140A235THR00.0330.00123.3530.1980.1980.0000.0000.0000.000
141A236ARG10.9610.99917.546-14.024-14.0240.0000.0000.0000.000
142A237GLY00.1030.07717.2160.0670.0670.0000.0000.0000.000
143A238VAL0-0.012-0.01711.357-0.001-0.0010.0000.0000.0000.000
144A239GLY0-0.007-0.00112.7221.0791.0790.0000.0000.0000.000
145A240HIS0-0.027-0.02414.464-0.529-0.5290.0000.0000.0000.000
146A241SER0-0.064-0.01416.880-0.914-0.9140.0000.0000.0000.000
147A242LEU0-0.0060.00518.1010.6740.6740.0000.0000.0000.000
148A243SER0-0.017-0.04119.052-0.006-0.0060.0000.0000.0000.000
149A244PRO00.009-0.00320.980-0.434-0.4340.0000.0000.0000.000
150A245VAL00.0090.00821.221-0.569-0.5690.0000.0000.0000.000
151A246GLY00.0490.03024.105-0.396-0.3960.0000.0000.0000.000
152A247LEU00.015-0.00525.980-0.391-0.3910.0000.0000.0000.000
153A248ILE0-0.0110.00227.035-0.386-0.3860.0000.0000.0000.000
154A249ALA0-0.016-0.00527.659-0.337-0.3370.0000.0000.0000.000
155A250VAL00.0530.02729.475-0.297-0.2970.0000.0000.0000.000
156A251VAL0-0.0150.00232.030-0.328-0.3280.0000.0000.0000.000
157A252ASN0-0.009-0.02129.859-0.374-0.3740.0000.0000.0000.000
158A253LEU0-0.0220.00733.634-0.177-0.1770.0000.0000.0000.000
159A254LEU00.012-0.00235.458-0.247-0.2470.0000.0000.0000.000
160A255LEU0-0.026-0.01535.661-0.214-0.2140.0000.0000.0000.000
161A256ALA0-0.050-0.01837.073-0.189-0.1890.0000.0000.0000.000
162A257GLU-1-0.886-0.95539.0157.5187.5180.0000.0000.0000.000
163A258ILE00.002-0.00941.323-0.198-0.1980.0000.0000.0000.000
164A259ALA0-0.038-0.01442.024-0.179-0.1790.0000.0000.0000.000
165A260VAL0-0.048-0.02542.555-0.136-0.1360.0000.0000.0000.000
166A261ARG10.8580.93745.201-6.803-6.8030.0000.0000.0000.000
167A262GLU-1-0.943-0.96447.0796.0636.0630.0000.0000.0000.000
168A263PRO0-0.0120.00447.2900.0730.0730.0000.0000.0000.000
169A264GLU-1-0.915-0.97448.3096.1656.1650.0000.0000.0000.000
170A265ARG10.8660.93846.813-6.644-6.6440.0000.0000.0000.000
171A266ALA00.0510.02545.2360.0430.0430.0000.0000.0000.000
172A267LEU0-0.038-0.02047.2160.0400.0400.0000.0000.0000.000
173A268ALA0-0.024-0.01948.996-0.031-0.0310.0000.0000.0000.000
174A269VAL00.0390.03246.065-0.057-0.0570.0000.0000.0000.000
175A270LEU00.0060.01344.868-0.001-0.0010.0000.0000.0000.000
176A271ARG10.8910.93247.517-6.160-6.1600.0000.0000.0000.000
177A272GLU-1-0.838-0.90851.0595.8825.8820.0000.0000.0000.000
178A273VAL0-0.0030.00445.330-0.038-0.0380.0000.0000.0000.000
179A274ASP-1-0.930-0.96747.7876.7666.7660.0000.0000.0000.000
180A275ARG10.7780.86949.986-5.938-5.9380.0000.0000.0000.000
181A276LEU00.0470.02550.429-0.080-0.0800.0000.0000.0000.000
182A277TYR0-0.0220.00448.666-0.038-0.0380.0000.0000.0000.000
183A278ARG10.8890.93550.751-6.096-6.0960.0000.0000.0000.000
184A279GLU-1-0.983-0.98653.9625.5845.5840.0000.0000.0000.000
185A280GLN0-0.030-0.02554.266-0.023-0.0230.0000.0000.0000.000
186A281GLY0-0.0060.01551.9480.0410.0410.0000.0000.0000.000
187A282MET0-0.069-0.02546.6110.1750.1750.0000.0000.0000.000