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: 766GK

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 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
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2868010.715811
FMO2-HF: Nuclear repulsion 2778988.314474
FMO2-HF: Total energy -89022.401337
FMO2-MP2: Total energy -89286.895786


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.
-4.977-1.1953.544-2.109-5.217-0.004
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 : 0.024 / q_NPA : -0.013
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].
3A6ASN0-0.011-0.0073.234-2.900-0.7630.031-0.878-1.2900.001
4A7TRP0-0.070-0.0202.610-1.6530.2650.498-0.623-1.793-0.002
5A8THR0-0.003-0.0044.4900.1320.2160.000-0.027-0.0570.000
6A9PRO0-0.014-0.0087.862-0.054-0.0540.0000.0000.0000.000
7A10ARG10.8590.9387.9570.4720.4720.0000.0000.0000.000
8A11PRO00.0110.00411.5090.0190.0190.0000.0000.0000.000
9A12LYS10.9931.00415.0460.1330.1330.0000.0000.0000.000
10A13PRO00.0220.02017.1680.0160.0160.0000.0000.0000.000
11A14GLU-1-0.933-0.97519.387-0.121-0.1210.0000.0000.0000.000
12A15ARG10.8360.90922.8470.1000.1000.0000.0000.0000.000
13A16LYS10.9100.96022.8850.0670.0670.0000.0000.0000.000
14A17ILE00.0260.00926.812-0.003-0.0030.0000.0000.0000.000
15A18PHE0-0.049-0.01622.1120.0030.0030.0000.0000.0000.000
16A19GLU-1-0.770-0.84827.099-0.031-0.0310.0000.0000.0000.000
17A20GLY00.0220.01828.7220.0020.0020.0000.0000.0000.000
18A21ARG10.8860.93629.5880.0170.0170.0000.0000.0000.000
19A22TYR0-0.092-0.07131.1520.0020.0020.0000.0000.0000.000
20A23VAL0-0.0040.00829.3970.0000.0000.0000.0000.0000.000
21A24ARG10.8310.88530.9620.0380.0380.0000.0000.0000.000
22A25LEU0-0.038-0.00425.696-0.002-0.0020.0000.0000.0000.000
23A26GLU-1-0.795-0.89229.431-0.043-0.0430.0000.0000.0000.000
24A27PRO0-0.0050.00128.198-0.002-0.0020.0000.0000.0000.000
25A28LEU0-0.026-0.00529.9410.0050.0050.0000.0000.0000.000
26A29ASN00.014-0.00232.1470.0010.0010.0000.0000.0000.000
27A30ALA00.0790.03735.3960.0030.0030.0000.0000.0000.000
28A31GLN0-0.013-0.00838.2170.0020.0020.0000.0000.0000.000
29A32LYS10.8910.94636.2120.0440.0440.0000.0000.0000.000
30A33HIS00.018-0.01333.9040.0000.0000.0000.0000.0000.000
31A34GLY00.0400.02838.4850.0000.0000.0000.0000.0000.000
32A35ASP-1-0.865-0.93240.207-0.039-0.0390.0000.0000.0000.000
33A36GLU-1-0.862-0.94040.648-0.036-0.0360.0000.0000.0000.000
34A37LEU0-0.022-0.01134.940-0.001-0.0010.0000.0000.0000.000
35A38PHE00.0210.00938.887-0.001-0.0010.0000.0000.0000.000
36A39ALA00.0170.02341.4550.0000.0000.0000.0000.0000.000
37A40ALA00.0020.00638.7910.0000.0000.0000.0000.0000.000
38A41SER0-0.090-0.04738.009-0.002-0.0020.0000.0000.0000.000
39A42SER0-0.041-0.01739.815-0.001-0.0010.0000.0000.0000.000
40A43VAL0-0.009-0.00141.1090.0020.0020.0000.0000.0000.000
41A44GLU-1-0.916-0.96644.040-0.033-0.0330.0000.0000.0000.000
42A45ASP-1-0.803-0.86741.974-0.042-0.0420.0000.0000.0000.000
43A46ALA0-0.008-0.00640.436-0.003-0.0030.0000.0000.0000.000
44A47GLU-1-0.854-0.94939.781-0.052-0.0520.0000.0000.0000.000
45A48GLN00.0090.00139.818-0.003-0.0030.0000.0000.0000.000
46A49ARG10.7160.84136.5740.0430.0430.0000.0000.0000.000
47A50PHE00.0210.00135.245-0.005-0.0050.0000.0000.0000.000
48A51THR0-0.041-0.00435.817-0.003-0.0030.0000.0000.0000.000
49A52TRP0-0.038-0.04631.621-0.003-0.0030.0000.0000.0000.000
50A53LEU0-0.062-0.00830.407-0.007-0.0070.0000.0000.0000.000
51A54PHE00.014-0.01626.6010.0020.0020.0000.0000.0000.000
52A55GLU-1-0.829-0.90531.675-0.085-0.0850.0000.0000.0000.000
53A56THR00.012-0.00135.0560.0000.0000.0000.0000.0000.000
54A57PRO0-0.0030.01338.609-0.001-0.0010.0000.0000.0000.000
55A58PRO0-0.044-0.00539.3740.0010.0010.0000.0000.0000.000
56A59ALA00.0770.03842.2220.0020.0020.0000.0000.0000.000
57A60THR0-0.014-0.01545.6160.0020.0020.0000.0000.0000.000
58A61ARG10.8420.89842.2430.0430.0430.0000.0000.0000.000
59A62ALA00.005-0.00544.194-0.002-0.0020.0000.0000.0000.000
60A63GLU-1-0.895-0.96144.209-0.046-0.0460.0000.0000.0000.000
61A64PHE0-0.013-0.00837.202-0.003-0.0030.0000.0000.0000.000
62A65GLU-1-0.815-0.89439.553-0.054-0.0540.0000.0000.0000.000
63A66PRO00.0000.00239.342-0.003-0.0030.0000.0000.0000.000
64A67TRP0-0.034-0.00831.490-0.002-0.0020.0000.0000.0000.000
65A68LEU00.0110.02734.765-0.004-0.0040.0000.0000.0000.000
66A69ASP-1-0.833-0.90535.181-0.066-0.0660.0000.0000.0000.000
67A70LYS10.9560.97131.2010.0900.0900.0000.0000.0000.000
68A71ALA0-0.022-0.01230.721-0.006-0.0060.0000.0000.0000.000
69A72SER0-0.028-0.03930.327-0.003-0.0030.0000.0000.0000.000
70A73LYS10.8070.90131.3630.0650.0650.0000.0000.0000.000
71A74SER0-0.056-0.01426.626-0.004-0.0040.0000.0000.0000.000
72A75ASP-1-0.867-0.93723.959-0.115-0.1150.0000.0000.0000.000
73A76ASP-1-0.846-0.91020.220-0.205-0.2050.0000.0000.0000.000
74A77PRO0-0.006-0.02023.2650.0030.0030.0000.0000.0000.000
75A78LEU0-0.0150.02322.5860.0100.0100.0000.0000.0000.000
76A79PHE00.025-0.00424.6960.0000.0000.0000.0000.0000.000
77A80PHE0-0.040-0.02224.0980.0050.0050.0000.0000.0000.000
78A81ALA00.0170.01228.829-0.001-0.0010.0000.0000.0000.000
79A82VAL0-0.030-0.02229.4950.0000.0000.0000.0000.0000.000
80A83ILE00.003-0.00432.1140.0020.0020.0000.0000.0000.000
81A84ASP-1-0.790-0.89134.396-0.033-0.0330.0000.0000.0000.000
82A85LYS10.7930.87133.7270.0280.0280.0000.0000.0000.000
83A86ALA0-0.049-0.00937.3500.0020.0020.0000.0000.0000.000
84A87SER0-0.037-0.04140.1080.0010.0010.0000.0000.0000.000
85A88GLY0-0.006-0.01339.9260.0010.0010.0000.0000.0000.000
86A89LYS10.9030.96940.3670.0280.0280.0000.0000.0000.000
87A90VAL0-0.012-0.00935.732-0.002-0.0020.0000.0000.0000.000
88A91ALA0-0.009-0.00535.7030.0010.0010.0000.0000.0000.000
89A92GLY00.005-0.01533.7160.0000.0000.0000.0000.0000.000
90A93ARG10.8000.91030.1860.0810.0810.0000.0000.0000.000
91A94GLN0-0.0040.00025.0990.0040.0040.0000.0000.0000.000
92A95ALA00.0160.00624.6090.0030.0030.0000.0000.0000.000
93A96LEU0-0.0030.01618.461-0.004-0.0040.0000.0000.0000.000
94A97MET0-0.026-0.01019.6440.0140.0140.0000.0000.0000.000
95A98ARG10.8060.88016.3820.2190.2190.0000.0000.0000.000
96A99ILE0-0.030-0.00915.890-0.027-0.0270.0000.0000.0000.000
97A100ASP-1-0.785-0.87811.512-0.543-0.5430.0000.0000.0000.000
98A101PRO00.028-0.00511.313-0.066-0.0660.0000.0000.0000.000
99A102ALA0-0.0270.00410.426-0.068-0.0680.0000.0000.0000.000
100A103ASN0-0.055-0.0456.869-0.365-0.3650.0000.0000.0000.000
101A104GLY00.0010.0156.821-0.073-0.0730.0000.0000.0000.000
102A105VAL00.001-0.0068.9140.0260.0260.0000.0000.0000.000
103A106ILE0-0.0090.00010.9750.0250.0250.0000.0000.0000.000
104A107GLU-1-0.774-0.87714.650-0.173-0.1730.0000.0000.0000.000
105A108ILE0-0.070-0.01917.6980.0110.0110.0000.0000.0000.000
106A109GLY00.0570.00720.6990.0020.0020.0000.0000.0000.000
107A110SER0-0.012-0.02323.6610.0090.0090.0000.0000.0000.000
108A111ILE0-0.0110.01324.3810.0050.0050.0000.0000.0000.000
109A112TYR0-0.046-0.03928.3840.0020.0020.0000.0000.0000.000
110A113TRP0-0.029-0.02426.6640.0030.0030.0000.0000.0000.000
111A114GLY00.0850.03833.3020.0010.0010.0000.0000.0000.000
112A115PRO00.020-0.00436.9020.0000.0000.0000.0000.0000.000
113A116LEU0-0.0080.00538.7830.0020.0020.0000.0000.0000.000
114A117ILE00.0170.00932.5880.0010.0010.0000.0000.0000.000
115A118SER0-0.045-0.00434.049-0.001-0.0010.0000.0000.0000.000
116A119ARG10.9170.93431.9090.0560.0560.0000.0000.0000.000
117A120ARG10.9641.00334.4010.0310.0310.0000.0000.0000.000
118A121PRO00.0220.00032.001-0.004-0.0040.0000.0000.0000.000
119A122ALA00.0740.04230.794-0.002-0.0020.0000.0000.0000.000
120A123ALA00.0270.02430.401-0.003-0.0030.0000.0000.0000.000
121A124THR00.001-0.00426.238-0.006-0.0060.0000.0000.0000.000
122A125GLU-1-0.749-0.86725.978-0.038-0.0380.0000.0000.0000.000
123A126ALA00.0100.01526.076-0.003-0.0030.0000.0000.0000.000
124A127GLN00.0540.02920.528-0.016-0.0160.0000.0000.0000.000
125A128PHE00.0100.00221.314-0.008-0.0080.0000.0000.0000.000
126A129LEU0-0.033-0.01721.426-0.003-0.0030.0000.0000.0000.000
127A130PHE00.0270.01320.511-0.002-0.0020.0000.0000.0000.000
128A131MET0-0.0190.02316.734-0.014-0.0140.0000.0000.0000.000
129A132GLN00.019-0.00216.7230.0010.0010.0000.0000.0000.000
130A133TYR0-0.0040.00217.269-0.003-0.0030.0000.0000.0000.000
131A134VAL00.0520.01913.755-0.009-0.0090.0000.0000.0000.000
132A135PHE00.000-0.00210.690-0.028-0.0280.0000.0000.0000.000
133A136ASP-1-0.801-0.88012.539-0.024-0.0240.0000.0000.0000.000
134A137VAL0-0.088-0.03515.0790.0180.0180.0000.0000.0000.000
135A138LEU0-0.033-0.00914.0820.0000.0000.0000.0000.0000.000
136A139GLY00.0020.02010.313-0.045-0.0450.0000.0000.0000.000
137A140TYR0-0.075-0.0518.563-0.117-0.1170.0000.0000.0000.000
138A141ARG10.9680.9752.5470.6190.2623.015-0.581-2.077-0.003
139A142ARG10.7290.8567.7880.3620.3620.0000.0000.0000.000
140A143TYR0-0.006-0.01910.1120.0010.0010.0000.0000.0000.000
141A144GLU-1-0.777-0.89213.853-0.275-0.2750.0000.0000.0000.000
142A145TRP00.010-0.00516.2320.0190.0190.0000.0000.0000.000
143A146GLU-1-0.854-0.93019.819-0.166-0.1660.0000.0000.0000.000
144A147CYS0-0.073-0.03121.9750.0100.0100.0000.0000.0000.000
145A148HIS00.0540.03425.672-0.005-0.0050.0000.0000.0000.000
146A149ASN00.0850.02627.5230.0010.0010.0000.0000.0000.000
147A150GLU-1-0.917-0.97028.593-0.066-0.0660.0000.0000.0000.000
148A151ASN0-0.0200.00629.3430.0090.0090.0000.0000.0000.000
149A152GLY00.022-0.00329.703-0.003-0.0030.0000.0000.0000.000
150A153PRO0-0.040-0.04230.4000.0000.0000.0000.0000.0000.000
151A154SER00.0320.03126.889-0.002-0.0020.0000.0000.0000.000
152A155ARG10.9530.98125.6340.0890.0890.0000.0000.0000.000
153A156ARG10.9690.98325.7310.0560.0560.0000.0000.0000.000
154A157ALA0-0.038-0.01027.1640.0030.0030.0000.0000.0000.000
155A158ALA00.0480.02921.9030.0010.0010.0000.0000.0000.000
156A159GLU-1-0.853-0.93022.282-0.085-0.0850.0000.0000.0000.000
157A160ARG10.8030.91323.4510.0530.0530.0000.0000.0000.000
158A161PHE0-0.050-0.03422.1450.0080.0080.0000.0000.0000.000
159A162GLY00.0180.02319.9790.0010.0010.0000.0000.0000.000
160A163PHE0-0.0370.00117.376-0.003-0.0030.0000.0000.0000.000
161A164ARG10.9370.96015.3810.1210.1210.0000.0000.0000.000
162A165PHE0-0.006-0.00117.376-0.016-0.0160.0000.0000.0000.000
163A166GLU-1-0.793-0.87013.256-0.259-0.2590.0000.0000.0000.000
164A167GLY00.0000.00217.789-0.001-0.0010.0000.0000.0000.000
165A168ILE0-0.044-0.03120.761-0.001-0.0010.0000.0000.0000.000
166A169PHE0-0.0130.00918.2470.0030.0030.0000.0000.0000.000
167A170ARG10.9490.95323.8380.1140.1140.0000.0000.0000.000
168A171GLN0-0.002-0.00827.470-0.006-0.0060.0000.0000.0000.000
169A172HIS0-0.056-0.01822.839-0.009-0.0090.0000.0000.0000.000
170A173MET0-0.004-0.01127.037-0.003-0.0030.0000.0000.0000.000
171A174VAL00.0280.02429.5490.0050.0050.0000.0000.0000.000
172A175VAL00.007-0.00430.737-0.002-0.0020.0000.0000.0000.000
173A176LYS10.8370.92333.9150.0730.0730.0000.0000.0000.000
174A177GLY00.0240.01437.4940.0030.0030.0000.0000.0000.000
175A178ARG10.9150.97836.2840.0690.0690.0000.0000.0000.000
176A179ASN00.0450.00131.816-0.006-0.0060.0000.0000.0000.000
177A180ARG10.8730.93325.0730.1220.1220.0000.0000.0000.000
178A181ASP-1-0.793-0.87527.830-0.100-0.1000.0000.0000.0000.000
179A182THR0-0.050-0.01022.5930.0070.0070.0000.0000.0000.000
180A183ALA0-0.0240.00123.334-0.005-0.0050.0000.0000.0000.000
181A184TRP00.0310.01817.918-0.002-0.0020.0000.0000.0000.000
182A185PHE0-0.038-0.03018.0270.0110.0110.0000.0000.0000.000
183A186SER0-0.061-0.04213.131-0.010-0.0100.0000.0000.0000.000
184A187VAL00.0330.03413.6020.0230.0230.0000.0000.0000.000
185A188LEU00.011-0.0048.416-0.041-0.0410.0000.0000.0000.000
186A189ASP-1-0.834-0.9265.919-0.315-0.3150.0000.0000.0000.000
187A190SER0-0.080-0.0467.7350.0740.0740.0000.0000.0000.000
188A191GLU-1-0.876-0.9489.392-0.112-0.1120.0000.0000.0000.000
189A192TRP0-0.032-0.02712.2130.0160.0160.0000.0000.0000.000
190A193PRO0-0.0020.00412.3340.0100.0100.0000.0000.0000.000
191A194ALA00.0300.01215.3840.0060.0060.0000.0000.0000.000
192A195LEU00.0060.01016.8970.0020.0020.0000.0000.0000.000
193A196LYS10.8230.90817.8350.0160.0160.0000.0000.0000.000
194A197GLN00.0150.00319.1550.0000.0000.0000.0000.0000.000
195A198ALA00.0080.01921.6550.0010.0010.0000.0000.0000.000
196A199TYR0-0.036-0.05821.001-0.001-0.0010.0000.0000.0000.000
197A200GLN0-0.039-0.02022.7340.0040.0040.0000.0000.0000.000
198A201ALA00.0050.00825.7570.0020.0020.0000.0000.0000.000
199A202TRP0-0.055-0.02527.323-0.003-0.0030.0000.0000.0000.000
200A203LEU0-0.005-0.01726.2860.0000.0000.0000.0000.0000.000
201A204ALA00.0080.02829.9270.0000.0000.0000.0000.0000.000
202A205PRO00.0360.00731.820-0.001-0.0010.0000.0000.0000.000
203A206GLU-1-0.864-0.93434.6540.0000.0000.0000.0000.0000.000
204A207ASN0-0.051-0.03632.2840.0030.0030.0000.0000.0000.000
205A208PHE0-0.035-0.01332.675-0.003-0.0030.0000.0000.0000.000
206A209ASP-1-0.842-0.91237.757-0.011-0.0110.0000.0000.0000.000
207A210SER00.000-0.01241.416-0.001-0.0010.0000.0000.0000.000
208A211ALA0-0.0210.00044.048-0.001-0.0010.0000.0000.0000.000
209A212GLY0-0.029-0.01040.430-0.002-0.0020.0000.0000.0000.000
210A213GLN0-0.035-0.03039.025-0.005-0.0050.0000.0000.0000.000
211A214GLN00.0050.00533.2840.0000.0000.0000.0000.0000.000
212A215LYS10.8680.93735.9870.0050.0050.0000.0000.0000.000
213A216LYS10.9460.99230.9970.0040.0040.0000.0000.0000.000
214A217THR0-0.025-0.01930.992-0.003-0.0030.0000.0000.0000.000
215A218LEU0-0.016-0.01524.5200.0020.0020.0000.0000.0000.000
216A219GLN00.018-0.01126.0960.0030.0030.0000.0000.0000.000
217A220GLU-1-0.802-0.89326.742-0.015-0.0150.0000.0000.0000.000
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