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: MV3YZ

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 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 264
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3510572.910862
FMO2-HF: Nuclear repulsion 3401008.215888
FMO2-HF: Total energy -109564.694974
FMO2-MP2: Total energy -109882.000397


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.
-36.365-26.6449.625-9.068-10.279-0.003
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 : 0.052 / q_NPA : 0.007
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].
3A6PHE00.0510.0092.382-9.149-4.2591.190-2.823-3.2570.022
4A7GLU-1-0.845-0.9182.099-25.865-21.2958.367-6.247-6.690-0.026
5A8TYR0-0.0110.0113.543-2.035-1.7740.0680.002-0.3320.001
6A9VAL0-0.011-0.0106.590-0.757-0.7570.0000.0000.0000.000
7A10ARG10.9000.9435.6480.4590.4590.0000.0000.0000.000
8A11ASP-1-0.934-0.9609.1160.9990.9990.0000.0000.0000.000
9A12PHE0-0.076-0.03411.248-0.083-0.0830.0000.0000.0000.000
10A13GLU-1-1.003-0.98311.3090.1000.1000.0000.0000.0000.000
11A14ALA00.0140.00914.934-0.011-0.0110.0000.0000.0000.000
12A15ASP-1-0.826-0.89318.4620.0490.0490.0000.0000.0000.000
13A16ASP-1-0.755-0.85320.2490.0670.0670.0000.0000.0000.000
14A17THR0-0.051-0.05022.822-0.028-0.0280.0000.0000.0000.000
15A18CYS0-0.065-0.01724.9070.0090.0090.0000.0000.0000.000
16A19LEU00.0350.01128.619-0.006-0.0060.0000.0000.0000.000
17A20ALA00.0360.00930.747-0.008-0.0080.0000.0000.0000.000
18A21HIS00.0210.01132.1290.0030.0030.0000.0000.0000.000
19A22CYS0-0.0340.01234.2380.0030.0030.0000.0000.0000.000
20A23TRP00.0230.00234.701-0.005-0.0050.0000.0000.0000.000
21A24VAL00.0060.01330.3580.0070.0070.0000.0000.0000.000
22A25VAL00.006-0.00433.755-0.006-0.0060.0000.0000.0000.000
23A26VAL00.0070.00830.9680.0070.0070.0000.0000.0000.000
24A27ARG10.7640.86433.616-0.028-0.0280.0000.0000.0000.000
25A28LEU0-0.014-0.00632.2820.0040.0040.0000.0000.0000.000
26A29ASP-1-0.763-0.86235.8680.0210.0210.0000.0000.0000.000
27A30GLY00.0460.02936.6150.0010.0010.0000.0000.0000.000
28A31ARG10.9410.96233.185-0.034-0.0340.0000.0000.0000.000
29A32ASN0-0.059-0.04137.363-0.001-0.0010.0000.0000.0000.000
30A33PHE00.0740.02638.484-0.002-0.0020.0000.0000.0000.000
31A34HIS0-0.0250.01542.435-0.002-0.0020.0000.0000.0000.000
32A35ARG10.9370.95841.247-0.014-0.0140.0000.0000.0000.000
33A36PHE0-0.023-0.00340.439-0.001-0.0010.0000.0000.0000.000
34A37ALA00.0480.02543.776-0.003-0.0030.0000.0000.0000.000
35A38GLU-1-0.911-0.94747.0220.0100.0100.0000.0000.0000.000
36A39LYS10.8800.92945.168-0.007-0.0070.0000.0000.0000.000
37A40HIS0-0.0220.01042.505-0.004-0.0040.0000.0000.0000.000
38A41ASN0-0.062-0.02847.8280.0000.0000.0000.0000.0000.000
39A42PHE00.008-0.00344.876-0.001-0.0010.0000.0000.0000.000
40A43ALA00.0020.00350.9120.0010.0010.0000.0000.0000.000
41A44LYS10.9400.98949.893-0.004-0.0040.0000.0000.0000.000
42A45PRO0-0.008-0.01655.056-0.001-0.0010.0000.0000.0000.000
43A46ASN0-0.032-0.03352.4000.0010.0010.0000.0000.0000.000
44A47ASP-1-0.734-0.83450.018-0.011-0.0110.0000.0000.0000.000
45A48SER00.016-0.01050.3060.0000.0000.0000.0000.0000.000
46A49ARG10.8590.92249.1380.0110.0110.0000.0000.0000.000
47A50ALA00.0180.00746.141-0.002-0.0020.0000.0000.0000.000
48A51LEU00.0130.00345.324-0.001-0.0010.0000.0000.0000.000
49A52GLN0-0.012-0.01645.935-0.003-0.0030.0000.0000.0000.000
50A53LEU00.0220.03941.175-0.002-0.0020.0000.0000.0000.000
51A54MET0-0.0160.00840.214-0.004-0.0040.0000.0000.0000.000
52A55THR0-0.001-0.00141.015-0.001-0.0010.0000.0000.0000.000
53A56LYS10.9631.01941.0640.0430.0430.0000.0000.0000.000
54A57CYS0-0.067-0.02037.265-0.005-0.0050.0000.0000.0000.000
55A58ALA00.0200.00137.144-0.004-0.0040.0000.0000.0000.000
56A59GLN0-0.042-0.04138.040-0.002-0.0020.0000.0000.0000.000
57A60THR0-0.001-0.00634.814-0.005-0.0050.0000.0000.0000.000
58A61VAL0-0.046-0.02232.652-0.006-0.0060.0000.0000.0000.000
59A62MET0-0.073-0.04433.809-0.002-0.0020.0000.0000.0000.000
60A63GLU-1-0.913-0.93035.969-0.059-0.0590.0000.0000.0000.000
61A64GLU-1-0.947-0.95731.192-0.101-0.1010.0000.0000.0000.000
62A65LEU0-0.063-0.01928.461-0.008-0.0080.0000.0000.0000.000
63A66GLU-1-0.849-0.92128.857-0.103-0.1030.0000.0000.0000.000
64A67ASP-1-0.830-0.91832.139-0.043-0.0430.0000.0000.0000.000
65A68ILE00.0100.02833.0650.0080.0080.0000.0000.0000.000
66A69VAL0-0.020-0.01136.206-0.003-0.0030.0000.0000.0000.000
67A70ILE0-0.023-0.00639.7660.0000.0000.0000.0000.0000.000
68A71ALA00.0140.00639.3170.0010.0010.0000.0000.0000.000
69A72TYR0-0.029-0.03041.0450.0000.0000.0000.0000.0000.000
70A73GLY00.0600.03342.0550.0020.0020.0000.0000.0000.000
71A74GLN0-0.070-0.04643.486-0.002-0.0020.0000.0000.0000.000
72A75SER00.0270.00344.6790.0010.0010.0000.0000.0000.000
73A76ASP-1-0.886-0.94542.0600.0010.0010.0000.0000.0000.000
74A77GLU-1-0.812-0.89039.9790.0120.0120.0000.0000.0000.000
75A78TYR00.016-0.01838.593-0.004-0.0040.0000.0000.0000.000
76A79SER0-0.041-0.00237.8130.0040.0040.0000.0000.0000.000
77A80PHE00.0050.00134.869-0.004-0.0040.0000.0000.0000.000
78A81VAL0-0.011-0.00335.7290.0040.0040.0000.0000.0000.000
79A82PHE00.0300.01330.917-0.004-0.0040.0000.0000.0000.000
80A83LYS10.8520.92434.8520.0490.0490.0000.0000.0000.000
81A84ARG10.8710.93034.476-0.003-0.0030.0000.0000.0000.000
82A85LYS10.8680.93434.5640.0290.0290.0000.0000.0000.000
83A86THR0-0.039-0.03530.264-0.006-0.0060.0000.0000.0000.000
84A87ASN0-0.003-0.03726.6990.0100.0100.0000.0000.0000.000
85A88TRP0-0.018-0.00126.787-0.001-0.0010.0000.0000.0000.000
86A89PHE00.1030.03321.211-0.019-0.0190.0000.0000.0000.000
87A90LYS10.9210.96421.0200.1030.1030.0000.0000.0000.000
88A91ARG10.7800.88723.9950.0150.0150.0000.0000.0000.000
89A92ARG10.8730.93817.488-0.063-0.0630.0000.0000.0000.000
90A93ALA00.0510.01223.697-0.013-0.0130.0000.0000.0000.000
91A94SER0-0.018-0.04021.225-0.017-0.0170.0000.0000.0000.000
92A95LYS10.8500.94919.1090.0950.0950.0000.0000.0000.000
93A96PHE00.0300.01723.550-0.010-0.0100.0000.0000.0000.000
94A97MET0-0.0060.00225.610-0.002-0.0020.0000.0000.0000.000
95A98THR00.003-0.01322.812-0.009-0.0090.0000.0000.0000.000
96A99HIS00.0010.03022.928-0.002-0.0020.0000.0000.0000.000
97A100VAL00.0150.01526.783-0.004-0.0040.0000.0000.0000.000
98A101ALA00.011-0.00328.551-0.002-0.0020.0000.0000.0000.000
99A102SER0-0.040-0.03226.738-0.004-0.0040.0000.0000.0000.000
100A103GLN00.0540.04528.8660.0010.0010.0000.0000.0000.000
101A104PHE00.0310.02330.945-0.001-0.0010.0000.0000.0000.000
102A105ALA0-0.001-0.00731.4140.0000.0000.0000.0000.0000.000
103A106SER0-0.039-0.02930.339-0.002-0.0020.0000.0000.0000.000
104A107SER0-0.028-0.03132.830-0.002-0.0020.0000.0000.0000.000
105A108TYR00.030-0.01135.9780.0010.0010.0000.0000.0000.000
106A109VAL0-0.033-0.02135.4730.0020.0020.0000.0000.0000.000
107A110PHE0-0.048-0.01336.143-0.001-0.0010.0000.0000.0000.000
108A111TYR00.007-0.01237.977-0.001-0.0010.0000.0000.0000.000
109A112TRP0-0.0010.00041.0620.0040.0040.0000.0000.0000.000
110A113ARG10.9530.95242.9010.0390.0390.0000.0000.0000.000
111A114ASP-1-0.902-0.93644.188-0.042-0.0420.0000.0000.0000.000
112A115TYR0-0.030-0.01944.4000.0010.0010.0000.0000.0000.000
113A116PHE0-0.070-0.03845.5360.0030.0030.0000.0000.0000.000
114A117GLU-1-0.941-0.95948.062-0.027-0.0270.0000.0000.0000.000
115A118ASP-1-0.918-0.95550.236-0.021-0.0210.0000.0000.0000.000
116A119GLN0-0.079-0.02947.4550.0020.0020.0000.0000.0000.000
117A120PRO00.0310.01845.905-0.002-0.0020.0000.0000.0000.000
118A121LEU00.0070.00738.9350.0030.0030.0000.0000.0000.000
119A122LEU0-0.016-0.02342.143-0.001-0.0010.0000.0000.0000.000
120A123TYR0-0.007-0.01637.8380.0020.0020.0000.0000.0000.000
121A124PRO00.0320.02434.1570.0000.0000.0000.0000.0000.000
122A125PRO0-0.0160.00135.5690.0050.0050.0000.0000.0000.000
123A126GLY00.0000.00133.343-0.002-0.0020.0000.0000.0000.000
124A127PHE0-0.006-0.02232.6570.0000.0000.0000.0000.0000.000
125A128ASP-1-0.907-0.93132.0350.0440.0440.0000.0000.0000.000
126A129GLY00.0450.01831.436-0.006-0.0060.0000.0000.0000.000
127A130ARG10.8550.92730.898-0.031-0.0310.0000.0000.0000.000
128A131VAL00.0270.00029.006-0.009-0.0090.0000.0000.0000.000
129A132VAL0-0.0210.00231.6960.0090.0090.0000.0000.0000.000
130A133VAL0-0.003-0.00631.525-0.006-0.0060.0000.0000.0000.000
131A134TYR0-0.009-0.00134.7720.0050.0050.0000.0000.0000.000
132A135PRO00.0410.01737.994-0.004-0.0040.0000.0000.0000.000
133A136SER0-0.016-0.01039.171-0.004-0.0040.0000.0000.0000.000
134A137ASN00.1280.04442.3210.0010.0010.0000.0000.0000.000
135A138GLN0-0.016-0.00644.328-0.003-0.0030.0000.0000.0000.000
136A139THR00.0530.02842.1560.0010.0010.0000.0000.0000.000
137A140LEU0-0.0160.00339.8370.0010.0010.0000.0000.0000.000
138A141LYS10.8930.93842.783-0.004-0.0040.0000.0000.0000.000
139A142ASP-1-0.830-0.91746.2030.0150.0150.0000.0000.0000.000
140A143TYR0-0.030-0.01639.8200.0030.0030.0000.0000.0000.000
141A144LEU00.031-0.00242.1560.0000.0000.0000.0000.0000.000
142A145SER00.0190.01045.1550.0000.0000.0000.0000.0000.000
143A146TRP0-0.0160.01341.9220.0000.0000.0000.0000.0000.000
144A147ARG10.7570.84942.047-0.016-0.0160.0000.0000.0000.000
145A148GLN00.0520.01146.1900.0000.0000.0000.0000.0000.000
146A149ALA0-0.045-0.02649.3670.0000.0000.0000.0000.0000.000
147A150ASP-1-0.831-0.91046.6410.0180.0180.0000.0000.0000.000
148A151CYS00.0140.02348.883-0.001-0.0010.0000.0000.0000.000
149A152HIS0-0.0040.00250.365-0.001-0.0010.0000.0000.0000.000
150A153ILE0-0.015-0.01852.8300.0000.0000.0000.0000.0000.000
151A154ASN0-0.017-0.01549.5690.0010.0010.0000.0000.0000.000
152A155ASN00.0620.05153.040-0.001-0.0010.0000.0000.0000.000
153A156LEU0-0.0350.00154.777-0.001-0.0010.0000.0000.0000.000
154A157TYR0-0.012-0.00755.4120.0000.0000.0000.0000.0000.000
155A158ASN0-0.004-0.03852.4660.0000.0000.0000.0000.0000.000
156A159THR0-0.007-0.01356.473-0.001-0.0010.0000.0000.0000.000
157A160VAL00.0280.00959.2180.0000.0000.0000.0000.0000.000
158A161PHE0-0.028-0.01556.3840.0000.0000.0000.0000.0000.000
159A162TRP0-0.002-0.02154.1280.0000.0000.0000.0000.0000.000
160A163ALA00.0260.04459.952-0.001-0.0010.0000.0000.0000.000
161A164LEU00.006-0.00863.4200.0000.0000.0000.0000.0000.000
162A165ILE0-0.054-0.01359.1960.0000.0000.0000.0000.0000.000
163A166GLN0-0.087-0.04259.788-0.001-0.0010.0000.0000.0000.000
164A167GLN0-0.015-0.00363.7520.0000.0000.0000.0000.0000.000
165A168SER00.005-0.00367.0840.0000.0000.0000.0000.0000.000
166A169GLY0-0.0050.02266.4060.0000.0000.0000.0000.0000.000
167A170LEU0-0.054-0.01865.3580.0010.0010.0000.0000.0000.000
168A171THR00.021-0.02262.3530.0000.0000.0000.0000.0000.000
169A172PRO00.0550.00657.6660.0000.0000.0000.0000.0000.000
170A173VAL00.0180.00859.8170.0010.0010.0000.0000.0000.000
171A174GLN00.0340.03260.7940.0000.0000.0000.0000.0000.000
172A175ALA00.0260.01561.2620.0000.0000.0000.0000.0000.000
173A176GLN0-0.016-0.00456.9530.0000.0000.0000.0000.0000.000
174A177GLY00.005-0.00360.5020.0010.0010.0000.0000.0000.000
175A178ARG10.8420.92463.286-0.010-0.0100.0000.0000.0000.000
176A179LEU00.0210.00760.8460.0000.0000.0000.0000.0000.000
177A180GLN0-0.0240.01160.2010.0000.0000.0000.0000.0000.000
178A181GLY0-0.008-0.00461.3010.0000.0000.0000.0000.0000.000
179A182THR0-0.055-0.02162.882-0.001-0.0010.0000.0000.0000.000
180A183LEU0-0.007-0.02862.0630.0010.0010.0000.0000.0000.000
181A184ALA0-0.013-0.02260.665-0.001-0.0010.0000.0000.0000.000
182A185ALA00.0180.00462.424-0.001-0.0010.0000.0000.0000.000
183A186ASP-1-0.785-0.88765.7410.0110.0110.0000.0000.0000.000
184A187LYS10.8880.94859.106-0.014-0.0140.0000.0000.0000.000
185A188ASN0-0.028-0.01564.437-0.001-0.0010.0000.0000.0000.000
186A189GLU-1-0.885-0.92965.6660.0050.0050.0000.0000.0000.000
187A190ILE00.0310.01666.4080.0000.0000.0000.0000.0000.000
188A191LEU0-0.033-0.00662.4710.0000.0000.0000.0000.0000.000
189A192PHE0-0.033-0.00867.133-0.001-0.0010.0000.0000.0000.000
190A193SER0-0.037-0.03370.137-0.001-0.0010.0000.0000.0000.000
191A194GLU-1-0.890-0.93969.6280.0070.0070.0000.0000.0000.000
192A195PHE0-0.033-0.02667.0960.0000.0000.0000.0000.0000.000
193A196ASN0-0.057-0.00469.910-0.001-0.0010.0000.0000.0000.000
194A197ILE00.0140.00064.541-0.001-0.0010.0000.0000.0000.000
195A198ASN0-0.002-0.00966.6180.0010.0010.0000.0000.0000.000
196A199TYR00.1050.04457.239-0.001-0.0010.0000.0000.0000.000
197A200ASN0-0.057-0.04161.9190.0000.0000.0000.0000.0000.000
198A201ASN0-0.042-0.02063.020-0.001-0.0010.0000.0000.0000.000
199A202GLU-1-0.856-0.91759.206-0.004-0.0040.0000.0000.0000.000
200A203LEU0-0.0030.00956.1880.0000.0000.0000.0000.0000.000
201A204PRO00.033-0.00255.6310.0010.0010.0000.0000.0000.000
202A205MET0-0.033-0.00850.2750.0010.0010.0000.0000.0000.000
203A206TYR00.0390.02151.7050.0000.0000.0000.0000.0000.000
204A207ARG10.8390.93453.4850.0040.0040.0000.0000.0000.000
205A208LYS10.8290.91452.9680.0010.0010.0000.0000.0000.000
206A209GLY00.1010.08449.0980.0010.0010.0000.0000.0000.000
207A210THR0-0.033-0.02846.292-0.002-0.0020.0000.0000.0000.000
208A211VAL0-0.024-0.00345.7970.0010.0010.0000.0000.0000.000
209A212LEU0-0.0100.00741.669-0.002-0.0020.0000.0000.0000.000
210A213ILE00.0310.00743.5330.0010.0010.0000.0000.0000.000
211A214TRP0-0.032-0.02037.877-0.002-0.0020.0000.0000.0000.000
212A215GLN00.0090.00244.3640.0020.0020.0000.0000.0000.000
213A216LYS10.9180.95345.2900.0390.0390.0000.0000.0000.000
214A217VAL00.0670.04147.8480.0020.0020.0000.0000.0000.000
215A218ASP-1-0.962-0.99248.871-0.041-0.0410.0000.0000.0000.000
216A219GLU-1-0.794-0.85649.253-0.052-0.0520.0000.0000.0000.000
217A220VAL00.005-0.00752.294-0.002-0.0020.0000.0000.0000.000
218A221MET0-0.0090.00950.6230.0000.0000.0000.0000.0000.000
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