FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 72G7K

Calculation Name: 3OTC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OTC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NWX6

Base Structure: X-ray

Registration Date: 2023-06-21

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 264
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3524094.718586
FMO2-HF: Nuclear repulsion 3414529.257394
FMO2-HF: Total energy -109565.461192
FMO2-MP2: Total energy -109882.940685


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:4:SER)


Summations of interaction energy for fragment #1(A:4:SER)
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.
-42.105-39.53419.543-12.817-9.297-0.062
Interaction energy analysis for fragmet #1(A:4:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / 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].
3A6PHE00.0470.0073.206-4.164-0.1500.047-2.180-1.8810.004
4A7GLU-1-0.806-0.8691.675-38.406-40.15219.479-10.536-7.197-0.067
5A8TYR00.0000.0223.974-1.347-1.0440.017-0.101-0.2190.001
6A9VAL0-0.012-0.0127.136-0.333-0.3330.0000.0000.0000.000
7A10ARG10.9010.9405.3482.4792.4790.0000.0000.0000.000
8A11ASP-1-0.933-0.9559.0440.0830.0830.0000.0000.0000.000
9A12PHE0-0.075-0.03411.4260.0650.0650.0000.0000.0000.000
10A13GLU-1-0.975-0.98710.624-0.821-0.8210.0000.0000.0000.000
11A14ALA0-0.0060.00514.5140.0060.0060.0000.0000.0000.000
12A15ASP-1-0.808-0.89718.131-0.307-0.3070.0000.0000.0000.000
13A16ASP-1-0.736-0.84020.281-0.226-0.2260.0000.0000.0000.000
14A17THR0-0.062-0.05022.611-0.010-0.0100.0000.0000.0000.000
15A18CYS0-0.054-0.00824.8160.0250.0250.0000.0000.0000.000
16A19LEU00.0350.02028.489-0.006-0.0060.0000.0000.0000.000
17A20ALA00.0530.02430.634-0.004-0.0040.0000.0000.0000.000
18A21HIS00.0160.00431.9510.0060.0060.0000.0000.0000.000
19A22CYS0-0.0220.02534.1300.0110.0110.0000.0000.0000.000
20A23TRP00.0110.00234.384-0.014-0.0140.0000.0000.0000.000
21A24VAL0-0.0060.00530.1080.0050.0050.0000.0000.0000.000
22A25VAL0-0.007-0.00633.549-0.004-0.0040.0000.0000.0000.000
23A26VAL00.0130.01630.6740.0010.0010.0000.0000.0000.000
24A27ARG10.7770.86333.4240.0970.0970.0000.0000.0000.000
25A28LEU0-0.0230.00231.903-0.006-0.0060.0000.0000.0000.000
26A29ASP-1-0.768-0.85835.478-0.090-0.0900.0000.0000.0000.000
27A30GLY00.0600.01336.705-0.005-0.0050.0000.0000.0000.000
28A31ARG10.9360.96933.0200.1080.1080.0000.0000.0000.000
29A32ASN0-0.057-0.04337.376-0.001-0.0010.0000.0000.0000.000
30A33PHE00.0140.01638.1930.0020.0020.0000.0000.0000.000
31A34HIS0-0.0100.01242.2880.0000.0000.0000.0000.0000.000
32A35ARG10.9260.95440.4890.0770.0770.0000.0000.0000.000
33A36PHE0-0.013-0.00540.1870.0010.0010.0000.0000.0000.000
34A37ALA00.0380.01643.7040.0000.0000.0000.0000.0000.000
35A38GLU-1-0.907-0.94246.983-0.054-0.0540.0000.0000.0000.000
36A39LYS10.8770.93145.2640.0630.0630.0000.0000.0000.000
37A40HIS00.0130.02942.228-0.002-0.0020.0000.0000.0000.000
38A41ASN0-0.059-0.03147.6310.0010.0010.0000.0000.0000.000
39A42PHE0-0.019-0.01644.6490.0000.0000.0000.0000.0000.000
40A43ALA00.0130.00750.7450.0030.0030.0000.0000.0000.000
41A44LYS10.9230.96749.7570.0610.0610.0000.0000.0000.000
42A45PRO00.0160.01355.4160.0020.0020.0000.0000.0000.000
43A46ASN0-0.058-0.03352.418-0.004-0.0040.0000.0000.0000.000
44A47ASP-1-0.716-0.83650.013-0.071-0.0710.0000.0000.0000.000
45A48SER00.0220.00150.106-0.002-0.0020.0000.0000.0000.000
46A49ARG10.8520.92548.7200.0710.0710.0000.0000.0000.000
47A50ALA00.0220.01845.795-0.005-0.0050.0000.0000.0000.000
48A51LEU00.0020.00045.080-0.005-0.0050.0000.0000.0000.000
49A52GLN00.0090.00145.703-0.005-0.0050.0000.0000.0000.000
50A53LEU00.0080.03041.031-0.005-0.0050.0000.0000.0000.000
51A54MET0-0.0170.01040.027-0.010-0.0100.0000.0000.0000.000
52A55THR00.003-0.01240.857-0.004-0.0040.0000.0000.0000.000
53A56LYS10.8900.97141.0650.1200.1200.0000.0000.0000.000
54A57CYS0-0.064-0.01837.208-0.009-0.0090.0000.0000.0000.000
55A58ALA00.0070.00037.070-0.010-0.0100.0000.0000.0000.000
56A59GLN0-0.026-0.03837.959-0.004-0.0040.0000.0000.0000.000
57A60THR00.002-0.00234.789-0.005-0.0050.0000.0000.0000.000
58A61VAL0-0.032-0.02132.670-0.011-0.0110.0000.0000.0000.000
59A62MET0-0.071-0.04033.744-0.005-0.0050.0000.0000.0000.000
60A63GLU-1-0.841-0.89836.000-0.146-0.1460.0000.0000.0000.000
61A64GLU-1-0.918-0.94731.244-0.234-0.2340.0000.0000.0000.000
62A65LEU0-0.070-0.02328.300-0.023-0.0230.0000.0000.0000.000
63A66GLU-1-0.856-0.92028.359-0.257-0.2570.0000.0000.0000.000
64A67ASP-1-0.811-0.91731.845-0.173-0.1730.0000.0000.0000.000
65A68ILE0-0.0080.01732.8480.0100.0100.0000.0000.0000.000
66A69VAL0-0.029-0.01835.6130.0020.0020.0000.0000.0000.000
67A70ILE0-0.023-0.01139.2900.0060.0060.0000.0000.0000.000
68A71ALA00.0160.01038.871-0.006-0.0060.0000.0000.0000.000
69A72TYR0-0.055-0.06340.6150.0050.0050.0000.0000.0000.000
70A73GLY00.0600.03441.774-0.004-0.0040.0000.0000.0000.000
71A74GLN0-0.036-0.03543.4530.0060.0060.0000.0000.0000.000
72A75SER00.0220.01544.643-0.002-0.0020.0000.0000.0000.000
73A76ASP-1-0.860-0.93442.033-0.087-0.0870.0000.0000.0000.000
74A77GLU-1-0.822-0.89340.024-0.094-0.0940.0000.0000.0000.000
75A78TYR00.012-0.01238.2890.0000.0000.0000.0000.0000.000
76A79SER0-0.0180.00837.455-0.006-0.0060.0000.0000.0000.000
77A80PHE00.006-0.00334.8660.0010.0010.0000.0000.0000.000
78A81VAL0-0.0010.00235.829-0.001-0.0010.0000.0000.0000.000
79A82PHE00.0390.02430.563-0.001-0.0010.0000.0000.0000.000
80A83LYS10.8460.92034.4000.1600.1600.0000.0000.0000.000
81A84ARG10.8450.90534.0700.0880.0880.0000.0000.0000.000
82A85LYS10.8590.92134.2250.1170.1170.0000.0000.0000.000
83A86THR0-0.037-0.01629.787-0.014-0.0140.0000.0000.0000.000
84A87ASN0-0.009-0.03726.113-0.011-0.0110.0000.0000.0000.000
85A88TRP0-0.026-0.00625.902-0.021-0.0210.0000.0000.0000.000
86A89PHE00.0790.02321.044-0.039-0.0390.0000.0000.0000.000
87A90LYS10.9500.96720.7290.3260.3260.0000.0000.0000.000
88A91ARG10.7550.85023.6330.1730.1730.0000.0000.0000.000
89A92ARG10.8420.93617.5230.3280.3280.0000.0000.0000.000
90A93ALA00.0500.01023.517-0.007-0.0070.0000.0000.0000.000
91A94SER0-0.010-0.03821.449-0.011-0.0110.0000.0000.0000.000
92A95LYS10.8720.96819.2590.4360.4360.0000.0000.0000.000
93A96PHE00.0070.01323.361-0.002-0.0020.0000.0000.0000.000
94A97MET0-0.0070.00125.8970.0100.0100.0000.0000.0000.000
95A98THR0-0.022-0.03322.406-0.002-0.0020.0000.0000.0000.000
96A99HIS0-0.0070.02923.0100.0100.0100.0000.0000.0000.000
97A100VAL00.0270.01726.6690.0090.0090.0000.0000.0000.000
98A101ALA00.0230.00528.4610.0090.0090.0000.0000.0000.000
99A102SER0-0.048-0.04026.4880.0050.0050.0000.0000.0000.000
100A103GLN00.0320.03228.5810.0140.0140.0000.0000.0000.000
101A104PHE00.0310.01930.8250.0110.0110.0000.0000.0000.000
102A105ALA0-0.002-0.01131.2920.0100.0100.0000.0000.0000.000
103A106SER0-0.036-0.03130.2070.0050.0050.0000.0000.0000.000
104A107SER0-0.023-0.02332.8250.0080.0080.0000.0000.0000.000
105A108TYR00.041-0.00435.9700.0100.0100.0000.0000.0000.000
106A109VAL0-0.040-0.02634.9240.0090.0090.0000.0000.0000.000
107A110PHE0-0.048-0.01235.9400.0050.0050.0000.0000.0000.000
108A111TYR00.006-0.01237.8060.0060.0060.0000.0000.0000.000
109A112TRP0-0.017-0.00840.8010.0060.0060.0000.0000.0000.000
110A113ARG10.9000.91442.6610.1020.1020.0000.0000.0000.000
111A114ASP-1-0.855-0.91543.828-0.115-0.1150.0000.0000.0000.000
112A115TYR0-0.020-0.01244.3730.0020.0020.0000.0000.0000.000
113A116PHE0-0.056-0.03445.4290.0060.0060.0000.0000.0000.000
114A117GLU-1-0.917-0.94147.784-0.082-0.0820.0000.0000.0000.000
115A118ASP-1-0.893-0.94849.720-0.072-0.0720.0000.0000.0000.000
116A119GLN0-0.057-0.01647.3380.0040.0040.0000.0000.0000.000
117A120PRO00.0300.01645.661-0.005-0.0050.0000.0000.0000.000
118A121LEU00.0080.01638.6660.0020.0020.0000.0000.0000.000
119A122LEU0-0.006-0.01842.040-0.002-0.0020.0000.0000.0000.000
120A123TYR0-0.012-0.01237.9730.0040.0040.0000.0000.0000.000
121A124PRO00.0370.02634.2360.0020.0020.0000.0000.0000.000
122A125PRO0-0.0010.00836.1060.0030.0030.0000.0000.0000.000
123A126GLY0-0.005-0.00833.608-0.010-0.0100.0000.0000.0000.000
124A127PHE0-0.011-0.01732.8630.0080.0080.0000.0000.0000.000
125A128ASP-1-0.883-0.90732.141-0.114-0.1140.0000.0000.0000.000
126A129GLY00.0530.01230.930-0.003-0.0030.0000.0000.0000.000
127A130ARG10.8320.90330.5320.0970.0970.0000.0000.0000.000
128A131VAL00.028-0.00229.178-0.006-0.0060.0000.0000.0000.000
129A132VAL0-0.0260.00331.8450.0090.0090.0000.0000.0000.000
130A133VAL00.011-0.00231.337-0.008-0.0080.0000.0000.0000.000
131A134TYR00.0040.00334.7040.0100.0100.0000.0000.0000.000
132A135PRO00.0390.01138.143-0.005-0.0050.0000.0000.0000.000
133A136SER0-0.029-0.02339.0690.0000.0000.0000.0000.0000.000
134A137ASN00.1220.05142.424-0.005-0.0050.0000.0000.0000.000
135A138GLN00.0100.00744.230-0.001-0.0010.0000.0000.0000.000
136A139THR00.0430.02242.1710.0000.0000.0000.0000.0000.000
137A140LEU0-0.0070.00839.740-0.001-0.0010.0000.0000.0000.000
138A141LYS10.8800.93342.6930.0620.0620.0000.0000.0000.000
139A142ASP-1-0.829-0.88845.686-0.059-0.0590.0000.0000.0000.000
140A143TYR0-0.012-0.01839.4790.0020.0020.0000.0000.0000.000
141A144LEU00.020-0.00241.5430.0000.0000.0000.0000.0000.000
142A145SER0-0.011-0.01844.8690.0020.0020.0000.0000.0000.000
143A146TRP00.0230.01942.0200.0000.0000.0000.0000.0000.000
144A147ARG10.7260.83341.7680.0770.0770.0000.0000.0000.000
145A148GLN00.0400.00845.9960.0030.0030.0000.0000.0000.000
146A149ALA0-0.021-0.01749.1960.0020.0020.0000.0000.0000.000
147A150ASP-1-0.825-0.89946.377-0.062-0.0620.0000.0000.0000.000
148A151CYS00.0110.02748.6370.0010.0010.0000.0000.0000.000
149A152HIS00.0180.02550.0400.0010.0010.0000.0000.0000.000
150A153ILE0-0.023-0.01352.5650.0020.0020.0000.0000.0000.000
151A154ASN0-0.033-0.02449.3600.0030.0030.0000.0000.0000.000
152A155ASN00.0620.04352.6920.0010.0010.0000.0000.0000.000
153A156LEU0-0.0450.00054.4710.0020.0020.0000.0000.0000.000
154A157TYR0-0.0020.00055.2940.0030.0030.0000.0000.0000.000
155A158ASN0-0.008-0.02752.4630.0020.0020.0000.0000.0000.000
156A159THR0-0.010-0.02756.3860.0000.0000.0000.0000.0000.000
157A160VAL00.0230.01659.1790.0010.0010.0000.0000.0000.000
158A161PHE0-0.014-0.00956.2310.0010.0010.0000.0000.0000.000
159A162TRP00.010-0.02753.8720.0010.0010.0000.0000.0000.000
160A163ALA00.0320.05059.7530.0000.0000.0000.0000.0000.000
161A164LEU0-0.003-0.01363.2750.0010.0010.0000.0000.0000.000
162A165ILE0-0.046-0.01258.8100.0010.0010.0000.0000.0000.000
163A166GLN0-0.108-0.06159.3330.0000.0000.0000.0000.0000.000
164A167GLN0-0.028-0.01363.5030.0000.0000.0000.0000.0000.000
165A168SER00.0010.00166.8190.0010.0010.0000.0000.0000.000
166A169GLY0-0.0070.01866.4320.0010.0010.0000.0000.0000.000
167A170LEU0-0.059-0.01965.0230.0010.0010.0000.0000.0000.000
168A171THR00.024-0.02662.157-0.002-0.0020.0000.0000.0000.000
169A172PRO00.0500.00357.5870.0010.0010.0000.0000.0000.000
170A173VAL00.0260.01859.7430.0000.0000.0000.0000.0000.000
171A174GLN00.0380.04160.8600.0000.0000.0000.0000.0000.000
172A175ALA00.0330.02461.0240.0010.0010.0000.0000.0000.000
173A176GLN0-0.0060.00257.236-0.001-0.0010.0000.0000.0000.000
174A177GLY0-0.012-0.01360.5520.0000.0000.0000.0000.0000.000
175A178ARG10.8070.89463.6600.0300.0300.0000.0000.0000.000
176A179LEU00.0210.01460.8900.0000.0000.0000.0000.0000.000
177A180GLN0-0.0250.00660.141-0.001-0.0010.0000.0000.0000.000
178A181GLY00.0070.00561.4090.0020.0020.0000.0000.0000.000
179A182THR0-0.058-0.02762.8970.0000.0000.0000.0000.0000.000
180A183LEU0-0.008-0.02062.011-0.002-0.0020.0000.0000.0000.000
181A184ALA0-0.018-0.02360.338-0.001-0.0010.0000.0000.0000.000
182A185ALA00.0150.00462.107-0.001-0.0010.0000.0000.0000.000
183A186ASP-1-0.764-0.88665.590-0.031-0.0310.0000.0000.0000.000
184A187LYS10.8810.95259.1670.0370.0370.0000.0000.0000.000
185A188ASN0-0.001-0.00464.207-0.002-0.0020.0000.0000.0000.000
186A189GLU-1-0.888-0.91865.397-0.030-0.0300.0000.0000.0000.000
187A190ILE00.0330.01666.2090.0000.0000.0000.0000.0000.000
188A191LEU0-0.038-0.01262.1260.0000.0000.0000.0000.0000.000
189A192PHE0-0.031-0.00366.7680.0000.0000.0000.0000.0000.000
190A193SER0-0.047-0.05669.9950.0000.0000.0000.0000.0000.000
191A194GLU-1-0.875-0.93469.397-0.030-0.0300.0000.0000.0000.000
192A195PHE0-0.032-0.02966.6660.0000.0000.0000.0000.0000.000
193A196ASN0-0.053-0.00769.669-0.001-0.0010.0000.0000.0000.000
194A197ILE00.0010.00264.175-0.001-0.0010.0000.0000.0000.000
195A198ASN00.0410.01966.6550.0000.0000.0000.0000.0000.000
196A199TYR00.0770.02557.075-0.002-0.0020.0000.0000.0000.000
197A200ASN0-0.074-0.05961.850-0.003-0.0030.0000.0000.0000.000
198A201ASN0-0.037-0.02663.155-0.001-0.0010.0000.0000.0000.000
199A202GLU-1-0.825-0.90259.029-0.054-0.0540.0000.0000.0000.000
200A203LEU00.0110.01955.971-0.001-0.0010.0000.0000.0000.000
201A204PRO00.001-0.01155.470-0.001-0.0010.0000.0000.0000.000
202A205MET0-0.029-0.01450.062-0.001-0.0010.0000.0000.0000.000
203A206TYR00.005-0.00551.406-0.002-0.0020.0000.0000.0000.000
204A207ARG10.8120.91753.1380.0530.0530.0000.0000.0000.000
205A208LYS10.8310.92252.4540.0620.0620.0000.0000.0000.000
206A209GLY00.0930.07948.481-0.002-0.0020.0000.0000.0000.000
207A210THR0-0.037-0.01945.9990.0040.0040.0000.0000.0000.000
208A211VAL0-0.0040.00145.346-0.005-0.0050.0000.0000.0000.000
209A212LEU0-0.029-0.00341.4000.0000.0000.0000.0000.0000.000
210A213ILE00.0380.01243.079-0.003-0.0030.0000.0000.0000.000
211A214TRP0-0.039-0.01637.2730.0040.0040.0000.0000.0000.000
212A215GLN00.0130.00743.7520.0050.0050.0000.0000.0000.000
213A216LYS10.9080.95344.6820.1050.1050.0000.0000.0000.000
214A217VAL00.0770.04747.5650.0050.0050.0000.0000.0000.000
215A218ASP-1-0.919-0.98048.560-0.091-0.0910.0000.0000.0000.000
216A219GLU-1-0.757-0.83848.528-0.110-0.1100.0000.0000.0000.000
217A220VAL00.0120.00851.886-0.001-0.0010.0000.0000.0000.000
218A221MET0-0.0210.00049.9930.0000.0000.0000.0000.0000.000
219A222THR0-0.007-0.01055.5510.0020.0020.0000.0000.0000.000
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