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: 2NN2R

Calculation Name: 3TCV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TCV

Chain ID: A

ChEMBL ID:

UniProt ID: Q2YIN4

Base Structure: X-ray

Registration Date: 2023-09-21

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2870206.706004
FMO2-HF: Nuclear repulsion 2781183.676934
FMO2-HF: Total energy -89023.02907
FMO2-MP2: Total energy -89287.562999


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:LEU)


Summations of interaction energy for fragment #1(A:4:LEU)
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.
-5.778-0.2951.716-2.136-5.064-0.007
Interaction energy analysis for fragmet #1(A:4:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / 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].
3A6ASN00.009-0.0073.236-2.481-0.4060.034-0.871-1.2390.000
4A7TRP0-0.062-0.0162.555-1.5960.3180.559-0.648-1.825-0.002
5A8THR0-0.004-0.0064.4820.1040.1770.000-0.026-0.0470.000
6A9PRO0-0.009-0.0087.852-0.050-0.0500.0000.0000.0000.000
7A10ARG10.8470.9427.6110.4790.4790.0000.0000.0000.000
8A11PRO00.0130.00311.2430.0180.0180.0000.0000.0000.000
9A12LYS10.9120.96614.7670.1300.1300.0000.0000.0000.000
10A13PRO00.0110.01217.1930.0170.0170.0000.0000.0000.000
11A14GLU-1-0.847-0.92919.143-0.129-0.1290.0000.0000.0000.000
12A15ARG10.8240.89122.5390.1010.1010.0000.0000.0000.000
13A16LYS10.8530.93222.4620.0700.0700.0000.0000.0000.000
14A17ILE00.0320.00926.540-0.003-0.0030.0000.0000.0000.000
15A18PHE0-0.018-0.00121.7230.0030.0030.0000.0000.0000.000
16A19GLU-1-0.761-0.85426.841-0.032-0.0320.0000.0000.0000.000
17A20GLY00.0210.01928.5210.0020.0020.0000.0000.0000.000
18A21ARG10.8650.93329.5620.0150.0150.0000.0000.0000.000
19A22TYR0-0.082-0.06831.0080.0020.0020.0000.0000.0000.000
20A23VAL0-0.0090.00029.281-0.001-0.0010.0000.0000.0000.000
21A24ARG10.8290.89930.6690.0380.0380.0000.0000.0000.000
22A25LEU0-0.036-0.00525.430-0.002-0.0020.0000.0000.0000.000
23A26GLU-1-0.753-0.84429.123-0.042-0.0420.0000.0000.0000.000
24A27PRO00.0020.00627.830-0.002-0.0020.0000.0000.0000.000
25A28LEU0-0.033-0.00829.7280.0060.0060.0000.0000.0000.000
26A29ASN00.013-0.00432.1390.0010.0010.0000.0000.0000.000
27A30ALA00.0770.03935.3710.0030.0030.0000.0000.0000.000
28A31GLN0-0.012-0.01038.3360.0030.0030.0000.0000.0000.000
29A32LYS10.8360.90036.0870.0440.0440.0000.0000.0000.000
30A33HIS00.019-0.02033.7210.0000.0000.0000.0000.0000.000
31A34GLY00.0460.03138.4270.0000.0000.0000.0000.0000.000
32A35ASP-1-0.868-0.92540.332-0.039-0.0390.0000.0000.0000.000
33A36GLU-1-0.833-0.92540.471-0.035-0.0350.0000.0000.0000.000
34A37LEU0-0.026-0.01335.115-0.001-0.0010.0000.0000.0000.000
35A38PHE00.0260.01539.025-0.001-0.0010.0000.0000.0000.000
36A39ALA00.0210.03041.6150.0000.0000.0000.0000.0000.000
37A40ALA00.0040.00938.9320.0000.0000.0000.0000.0000.000
38A41SER0-0.093-0.05338.204-0.002-0.0020.0000.0000.0000.000
39A42SER0-0.038-0.02739.948-0.001-0.0010.0000.0000.0000.000
40A43VAL0-0.016-0.00241.2840.0020.0020.0000.0000.0000.000
41A44GLU-1-0.913-0.96444.168-0.033-0.0330.0000.0000.0000.000
42A45ASP-1-0.808-0.87041.539-0.042-0.0420.0000.0000.0000.000
43A46ALA0-0.006-0.00340.526-0.003-0.0030.0000.0000.0000.000
44A47GLU-1-0.849-0.94539.848-0.052-0.0520.0000.0000.0000.000
45A48GLN00.0010.00239.851-0.003-0.0030.0000.0000.0000.000
46A49ARG10.7170.84136.7170.0420.0420.0000.0000.0000.000
47A50PHE00.027-0.00135.306-0.005-0.0050.0000.0000.0000.000
48A51THR0-0.059-0.01935.841-0.003-0.0030.0000.0000.0000.000
49A52TRP0-0.049-0.03931.559-0.003-0.0030.0000.0000.0000.000
50A53LEU0-0.0500.00130.517-0.007-0.0070.0000.0000.0000.000
51A54PHE00.033-0.00426.5810.0030.0030.0000.0000.0000.000
52A55GLU-1-0.791-0.86631.644-0.084-0.0840.0000.0000.0000.000
53A56THR00.0250.00635.0940.0000.0000.0000.0000.0000.000
54A57PRO0-0.0070.01138.645-0.001-0.0010.0000.0000.0000.000
55A58PRO0-0.047-0.01139.4880.0010.0010.0000.0000.0000.000
56A59ALA00.0620.02942.3100.0020.0020.0000.0000.0000.000
57A60THR0-0.032-0.06045.7370.0020.0020.0000.0000.0000.000
58A61ARG10.8040.86642.4550.0430.0430.0000.0000.0000.000
59A62ALA00.012-0.00144.329-0.002-0.0020.0000.0000.0000.000
60A63GLU-1-0.852-0.90244.274-0.045-0.0450.0000.0000.0000.000
61A64PHE0-0.005-0.00437.075-0.003-0.0030.0000.0000.0000.000
62A65GLU-1-0.803-0.88239.673-0.053-0.0530.0000.0000.0000.000
63A66PRO0-0.0010.00139.471-0.003-0.0030.0000.0000.0000.000
64A67TRP0-0.046-0.01931.601-0.002-0.0020.0000.0000.0000.000
65A68LEU00.0120.03034.884-0.004-0.0040.0000.0000.0000.000
66A69ASP-1-0.818-0.87435.337-0.067-0.0670.0000.0000.0000.000
67A70LYS10.9620.97431.1760.0910.0910.0000.0000.0000.000
68A71ALA0-0.015-0.00830.852-0.006-0.0060.0000.0000.0000.000
69A72SER0-0.026-0.04330.490-0.003-0.0030.0000.0000.0000.000
70A73LYS10.7870.87431.5360.0640.0640.0000.0000.0000.000
71A74SER0-0.064-0.02026.788-0.004-0.0040.0000.0000.0000.000
72A75ASP-1-0.848-0.92324.125-0.121-0.1210.0000.0000.0000.000
73A76ASP-1-0.829-0.88820.205-0.205-0.2050.0000.0000.0000.000
74A77PRO0-0.001-0.01923.3880.0030.0030.0000.0000.0000.000
75A78LEU0-0.0240.02122.5240.0100.0100.0000.0000.0000.000
76A79PHE00.029-0.00224.8760.0000.0000.0000.0000.0000.000
77A80PHE0-0.045-0.02323.8600.0060.0060.0000.0000.0000.000
78A81ALA00.0150.01428.7920.0000.0000.0000.0000.0000.000
79A82VAL0-0.027-0.01929.4320.0000.0000.0000.0000.0000.000
80A83ILE0-0.007-0.00931.9420.0020.0020.0000.0000.0000.000
81A84ASP-1-0.763-0.86334.076-0.032-0.0320.0000.0000.0000.000
82A85LYS10.7770.86833.4200.0270.0270.0000.0000.0000.000
83A86ALA0-0.059-0.01437.1020.0020.0020.0000.0000.0000.000
84A87SER0-0.019-0.04739.9510.0010.0010.0000.0000.0000.000
85A88GLY0-0.005-0.00239.6220.0010.0010.0000.0000.0000.000
86A89LYS10.8550.93640.0330.0280.0280.0000.0000.0000.000
87A90VAL0-0.023-0.01835.564-0.002-0.0020.0000.0000.0000.000
88A91ALA00.0050.00035.5630.0010.0010.0000.0000.0000.000
89A92GLY00.006-0.01333.8340.0000.0000.0000.0000.0000.000
90A93ARG10.7780.89430.4200.0800.0800.0000.0000.0000.000
91A94GLN0-0.004-0.00424.8990.0050.0050.0000.0000.0000.000
92A95ALA00.0230.00624.8350.0030.0030.0000.0000.0000.000
93A96LEU0-0.0090.01418.635-0.004-0.0040.0000.0000.0000.000
94A97MET0-0.043-0.01319.7620.0150.0150.0000.0000.0000.000
95A98ARG10.7750.85516.2430.2190.2190.0000.0000.0000.000
96A99ILE0-0.026-0.01416.008-0.028-0.0280.0000.0000.0000.000
97A100ASP-1-0.787-0.87311.601-0.551-0.5510.0000.0000.0000.000
98A101PRO00.0360.00111.434-0.067-0.0670.0000.0000.0000.000
99A102ALA0-0.036-0.00110.526-0.069-0.0690.0000.0000.0000.000
100A103ASN0-0.055-0.0506.918-0.362-0.3620.0000.0000.0000.000
101A104GLY00.0060.0166.930-0.081-0.0810.0000.0000.0000.000
102A105VAL0-0.002-0.0068.9630.0240.0240.0000.0000.0000.000
103A106ILE0-0.0020.00211.0740.0270.0270.0000.0000.0000.000
104A107GLU-1-0.777-0.87614.776-0.172-0.1720.0000.0000.0000.000
105A108ILE0-0.059-0.01417.7930.0110.0110.0000.0000.0000.000
106A109GLY00.0690.01620.8330.0020.0020.0000.0000.0000.000
107A110SER0-0.023-0.03123.7550.0090.0090.0000.0000.0000.000
108A111ILE0-0.0070.01124.5110.0050.0050.0000.0000.0000.000
109A112TYR0-0.052-0.03628.5020.0020.0020.0000.0000.0000.000
110A113TRP0-0.027-0.02426.4090.0030.0030.0000.0000.0000.000
111A114GLY00.0930.04233.4330.0010.0010.0000.0000.0000.000
112A115PRO00.016-0.00936.8350.0000.0000.0000.0000.0000.000
113A116LEU0-0.0060.00838.5200.0020.0020.0000.0000.0000.000
114A117ILE00.0220.00832.3790.0010.0010.0000.0000.0000.000
115A118SER0-0.0450.00033.814-0.001-0.0010.0000.0000.0000.000
116A119ARG10.9170.93631.7300.0550.0550.0000.0000.0000.000
117A120ARG10.9210.97134.1820.0300.0300.0000.0000.0000.000
118A121PRO00.0230.00131.798-0.004-0.0040.0000.0000.0000.000
119A122ALA00.0720.03730.589-0.002-0.0020.0000.0000.0000.000
120A123ALA00.0320.02730.184-0.003-0.0030.0000.0000.0000.000
121A124THR0-0.0020.00026.135-0.006-0.0060.0000.0000.0000.000
122A125GLU-1-0.751-0.87325.766-0.037-0.0370.0000.0000.0000.000
123A126ALA00.0100.01425.869-0.003-0.0030.0000.0000.0000.000
124A127GLN00.0530.02020.147-0.016-0.0160.0000.0000.0000.000
125A128PHE00.001-0.00121.217-0.008-0.0080.0000.0000.0000.000
126A129LEU0-0.033-0.01521.227-0.003-0.0030.0000.0000.0000.000
127A130PHE00.0240.01020.414-0.002-0.0020.0000.0000.0000.000
128A131MET0-0.0260.02816.597-0.015-0.0150.0000.0000.0000.000
129A132GLN00.0390.00716.5210.0010.0010.0000.0000.0000.000
130A133TYR0-0.0030.00517.056-0.001-0.0010.0000.0000.0000.000
131A134VAL00.0420.01413.382-0.008-0.0080.0000.0000.0000.000
132A135PHE00.004-0.00110.531-0.028-0.0280.0000.0000.0000.000
133A136ASP-1-0.806-0.87712.377-0.023-0.0230.0000.0000.0000.000
134A137VAL0-0.081-0.03314.9550.0180.0180.0000.0000.0000.000
135A138LEU0-0.030-0.00613.7940.0010.0010.0000.0000.0000.000
136A139GLY00.0030.01310.153-0.044-0.0440.0000.0000.0000.000
137A140TYR0-0.081-0.0598.306-0.116-0.1160.0000.0000.0000.000
138A141ARG10.9470.9652.788-0.5840.8371.123-0.591-1.953-0.005
139A142ARG10.7090.8237.6890.3640.3640.0000.0000.0000.000
140A143TYR00.007-0.01310.2000.0020.0020.0000.0000.0000.000
141A144GLU-1-0.745-0.86813.983-0.277-0.2770.0000.0000.0000.000
142A145TRP00.004-0.00816.2460.0200.0200.0000.0000.0000.000
143A146GLU-1-0.851-0.90519.777-0.155-0.1550.0000.0000.0000.000
144A147CYS0-0.043-0.01921.9410.0090.0090.0000.0000.0000.000
145A148HIS00.0540.03025.634-0.005-0.0050.0000.0000.0000.000
146A149ASN00.0710.02527.6310.0010.0010.0000.0000.0000.000
147A150GLU-1-0.860-0.93528.532-0.066-0.0660.0000.0000.0000.000
148A151ASN0-0.0050.01229.3710.0090.0090.0000.0000.0000.000
149A152GLY00.0260.00229.644-0.003-0.0030.0000.0000.0000.000
150A153PRO0-0.037-0.03630.3310.0000.0000.0000.0000.0000.000
151A154SER00.0240.02426.855-0.002-0.0020.0000.0000.0000.000
152A155ARG10.9660.98925.0930.0880.0880.0000.0000.0000.000
153A156ARG10.9720.98125.6570.0550.0550.0000.0000.0000.000
154A157ALA0-0.040-0.01027.0900.0030.0030.0000.0000.0000.000
155A158ALA00.0460.03021.8570.0010.0010.0000.0000.0000.000
156A159GLU-1-0.833-0.92322.212-0.082-0.0820.0000.0000.0000.000
157A160ARG10.8180.92823.3670.0510.0510.0000.0000.0000.000
158A161PHE0-0.055-0.03422.0530.0080.0080.0000.0000.0000.000
159A162GLY00.0420.02219.7790.0010.0010.0000.0000.0000.000
160A163PHE0-0.033-0.00217.331-0.003-0.0030.0000.0000.0000.000
161A164ARG10.8750.92914.3130.1230.1230.0000.0000.0000.000
162A165PHE00.002-0.00917.289-0.015-0.0150.0000.0000.0000.000
163A166GLU-1-0.781-0.83613.335-0.260-0.2600.0000.0000.0000.000
164A167GLY00.0050.00617.697-0.001-0.0010.0000.0000.0000.000
165A168ILE0-0.045-0.03220.678-0.001-0.0010.0000.0000.0000.000
166A169PHE0-0.0100.01317.9740.0030.0030.0000.0000.0000.000
167A170ARG10.9630.96923.7870.1100.1100.0000.0000.0000.000
168A171GLN0-0.026-0.02527.418-0.004-0.0040.0000.0000.0000.000
169A172HIS0-0.046-0.00422.667-0.009-0.0090.0000.0000.0000.000
170A173MET0-0.006-0.00926.787-0.003-0.0030.0000.0000.0000.000
171A174VAL00.0220.01929.4130.0050.0050.0000.0000.0000.000
172A175VAL00.010-0.00530.675-0.002-0.0020.0000.0000.0000.000
173A176LYS10.8220.90633.8340.0730.0730.0000.0000.0000.000
174A177GLY00.0230.01537.4290.0030.0030.0000.0000.0000.000
175A178ARG10.8630.94535.7320.0690.0690.0000.0000.0000.000
176A179ASN00.024-0.01031.752-0.005-0.0050.0000.0000.0000.000
177A180ARG10.8240.87924.9000.1240.1240.0000.0000.0000.000
178A181ASP-1-0.783-0.87027.880-0.101-0.1010.0000.0000.0000.000
179A182THR0-0.049-0.01022.5440.0070.0070.0000.0000.0000.000
180A183ALA0-0.023-0.00223.268-0.005-0.0050.0000.0000.0000.000
181A184TRP00.0150.01417.859-0.002-0.0020.0000.0000.0000.000
182A185PHE0-0.047-0.04217.9340.0110.0110.0000.0000.0000.000
183A186SER0-0.055-0.04313.016-0.013-0.0130.0000.0000.0000.000
184A187VAL00.0230.03013.4920.0240.0240.0000.0000.0000.000
185A188LEU00.011-0.0048.265-0.042-0.0420.0000.0000.0000.000
186A189ASP-1-0.807-0.9095.460-0.376-0.3760.0000.0000.0000.000
187A190SER0-0.074-0.0527.6730.0810.0810.0000.0000.0000.000
188A191GLU-1-0.843-0.9199.272-0.113-0.1130.0000.0000.0000.000
189A192TRP0-0.018-0.02112.0540.0170.0170.0000.0000.0000.000
190A193PRO00.0150.01212.2090.0110.0110.0000.0000.0000.000
191A194ALA00.0220.01415.2830.0070.0070.0000.0000.0000.000
192A195LEU00.0070.00916.7620.0020.0020.0000.0000.0000.000
193A196LYS10.8070.89417.6900.0160.0160.0000.0000.0000.000
194A197GLN00.001-0.01218.6520.0040.0040.0000.0000.0000.000
195A198ALA00.0030.01621.5220.0010.0010.0000.0000.0000.000
196A199TYR0-0.017-0.03221.005-0.002-0.0020.0000.0000.0000.000
197A200GLN0-0.046-0.02522.6830.0030.0030.0000.0000.0000.000
198A201ALA00.0070.00925.6180.0020.0020.0000.0000.0000.000
199A202TRP0-0.038-0.01727.172-0.003-0.0030.0000.0000.0000.000
200A203LEU00.003-0.01226.1780.0000.0000.0000.0000.0000.000
201A204ALA00.0070.02729.7620.0000.0000.0000.0000.0000.000
202A205PRO00.0390.01431.678-0.001-0.0010.0000.0000.0000.000
203A206GLU-1-0.840-0.92734.5030.0000.0000.0000.0000.0000.000
204A207ASN0-0.035-0.01432.0520.0030.0030.0000.0000.0000.000
205A208PHE0-0.016-0.00332.411-0.003-0.0030.0000.0000.0000.000
206A209ASP-1-0.838-0.91837.597-0.010-0.0100.0000.0000.0000.000
207A210SER00.011-0.00641.259-0.001-0.0010.0000.0000.0000.000
208A211ALA0-0.024-0.00143.915-0.001-0.0010.0000.0000.0000.000
209A212GLY0-0.0100.00240.251-0.002-0.0020.0000.0000.0000.000
210A213GLN0-0.004-0.01038.839-0.005-0.0050.0000.0000.0000.000
211A214GLN00.0050.00533.0430.0000.0000.0000.0000.0000.000
212A215LYS10.8120.90235.8110.0060.0060.0000.0000.0000.000
213A216LYS10.9440.99130.6410.0050.0050.0000.0000.0000.000
214A217THR0-0.052-0.05630.891-0.003-0.0030.0000.0000.0000.000
215A218LEU0-0.021-0.01524.2940.0020.0020.0000.0000.0000.000
216A219GLN00.027-0.01025.9300.0020.0020.0000.0000.0000.000
217A220GLU-1-0.747-0.85126.593-0.013-0.0130.0000.0000.0000.000
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