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: JL319

Calculation Name: 3TC2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TC2

Chain ID: A

ChEMBL ID:

UniProt ID: Q8S380

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1953974.933226
FMO2-HF: Nuclear repulsion 1882958.619577
FMO2-HF: Total energy -71016.313648
FMO2-MP2: Total energy -71223.084106


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-0.0982.603-0.012-1.139-1.5510.001
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.034
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].
3A4ASP-1-0.918-0.9563.880-1.934-0.057-0.021-0.975-0.8810.001
4A5ALA0-0.009-0.0067.1010.2020.2020.0000.0000.0000.000
5A6THR00.0260.0188.3210.0190.0190.0000.0000.0000.000
6A7PRO0-0.027-0.00510.2420.0780.0780.0000.0000.0000.000
7A8VAL0-0.0190.00012.5680.0240.0240.0000.0000.0000.000
8A9LEU0-0.0030.00214.510-0.029-0.0290.0000.0000.0000.000
9A10ASP-1-0.779-0.87318.1710.0750.0750.0000.0000.0000.000
10A11VAL0-0.045-0.04921.567-0.004-0.0040.0000.0000.0000.000
11A12THR0-0.130-0.08524.472-0.006-0.0060.0000.0000.0000.000
12A13GLY00.0060.00821.893-0.007-0.0070.0000.0000.0000.000
13A14LYS10.8100.91121.152-0.053-0.0530.0000.0000.0000.000
14A15GLU-1-0.862-0.94216.6430.0190.0190.0000.0000.0000.000
15A16LEU0-0.090-0.04516.416-0.006-0.0060.0000.0000.0000.000
16A17ASP-1-0.750-0.87117.5890.0250.0250.0000.0000.0000.000
17A18PRO0-0.016-0.00217.7570.0040.0040.0000.0000.0000.000
18A19ARG10.7600.86119.855-0.017-0.0170.0000.0000.0000.000
19A20LEU0-0.0430.00323.000-0.003-0.0030.0000.0000.0000.000
20A21SER0-0.053-0.04523.9810.0040.0040.0000.0000.0000.000
21A22TYR0-0.0060.00321.732-0.006-0.0060.0000.0000.0000.000
22A23ARG10.8470.92224.882-0.059-0.0590.0000.0000.0000.000
23A24ILE00.0720.04021.1110.0010.0010.0000.0000.0000.000
24A25ILE0-0.014-0.01124.006-0.007-0.0070.0000.0000.0000.000
25A26SER00.0490.01924.6430.0090.0090.0000.0000.0000.000
26A27THR0-0.0080.01024.7420.0050.0050.0000.0000.0000.000
27A28PHE00.0050.01027.079-0.006-0.0060.0000.0000.0000.000
28A29TRP00.0170.00729.9330.0000.0000.0000.0000.0000.000
29A30GLY00.0280.00133.4960.0010.0010.0000.0000.0000.000
30A31ALA00.003-0.01635.1660.0030.0030.0000.0000.0000.000
31A32LEU00.0180.03131.3490.0030.0030.0000.0000.0000.000
32A33GLY00.0540.04730.6160.0080.0080.0000.0000.0000.000
33A34GLY0-0.004-0.00931.3410.0000.0000.0000.0000.0000.000
34A35ASP-1-0.821-0.91828.2150.0830.0830.0000.0000.0000.000
35A36VAL00.0330.01024.161-0.004-0.0040.0000.0000.0000.000
36A37TYR0-0.070-0.03027.559-0.008-0.0080.0000.0000.0000.000
37A38LEU00.0120.02829.0720.0040.0040.0000.0000.0000.000
38A39GLY0-0.007-0.01630.557-0.005-0.0050.0000.0000.0000.000
39A40LYS10.9450.96232.649-0.043-0.0430.0000.0000.0000.000
40A41SER00.0450.03331.8630.0030.0030.0000.0000.0000.000
41A42PRO0-0.038-0.02034.177-0.004-0.0040.0000.0000.0000.000
42A43ASN0-0.041-0.03437.0010.0010.0010.0000.0000.0000.000
43A44SER00.0000.00434.5930.0000.0000.0000.0000.0000.000
44A45ASP-1-0.885-0.93635.8610.0460.0460.0000.0000.0000.000
45A46ALA0-0.0100.01433.867-0.002-0.0020.0000.0000.0000.000
46A47PRO0-0.017-0.01135.449-0.001-0.0010.0000.0000.0000.000
47A48CYS0-0.085-0.03933.781-0.001-0.0010.0000.0000.0000.000
48A49ALA0-0.028-0.01833.2730.0010.0010.0000.0000.0000.000
49A50ASN00.0570.02830.429-0.002-0.0020.0000.0000.0000.000
50A51GLY00.0250.02028.8380.0040.0040.0000.0000.0000.000
51A52VAL00.0200.01724.108-0.005-0.0050.0000.0000.0000.000
52A53PHE0-0.018-0.00327.2870.0030.0030.0000.0000.0000.000
53A54ARG10.8720.93126.863-0.100-0.1000.0000.0000.0000.000
54A55TYR0-0.036-0.00829.646-0.004-0.0040.0000.0000.0000.000
55A56ASN0-0.018-0.03232.3750.0080.0080.0000.0000.0000.000
56A57SER0-0.010-0.01034.955-0.001-0.0010.0000.0000.0000.000
57A58ASP-1-0.856-0.91533.5020.0600.0600.0000.0000.0000.000
58A59VAL0-0.0150.00134.916-0.002-0.0020.0000.0000.0000.000
59A60GLY00.0290.00737.7840.0000.0000.0000.0000.0000.000
60A61PRO0-0.0270.00136.370-0.001-0.0010.0000.0000.0000.000
61A62SER00.010-0.00232.3020.0020.0020.0000.0000.0000.000
62A63GLY0-0.011-0.01629.556-0.001-0.0010.0000.0000.0000.000
63A64THR0-0.034-0.01029.188-0.005-0.0050.0000.0000.0000.000
64A65PRO0-0.022-0.00727.6230.0060.0060.0000.0000.0000.000
65A66VAL0-0.0220.00222.271-0.001-0.0010.0000.0000.0000.000
66A67ARG10.9420.96021.980-0.064-0.0640.0000.0000.0000.000
67A68PHE00.0440.01516.6530.0060.0060.0000.0000.0000.000
68A69ILE00.001-0.00317.529-0.013-0.0130.0000.0000.0000.000
69A70GLY00.0710.03913.5600.0150.0150.0000.0000.0000.000
70A71SER00.0070.00410.866-0.021-0.0210.0000.0000.0000.000
71A72SER0-0.024-0.02113.227-0.007-0.0070.0000.0000.0000.000
72A73SER0-0.046-0.0168.481-0.027-0.0270.0000.0000.0000.000
73A74HIS00.001-0.0107.928-0.028-0.0280.0000.0000.0000.000
74A75PHE00.0150.03010.056-0.018-0.0180.0000.0000.0000.000
75A76GLY00.0170.00112.2350.0080.0080.0000.0000.0000.000
76A77GLN0-0.036-0.03012.940-0.002-0.0020.0000.0000.0000.000
77A78GLY00.0370.02615.2680.0040.0040.0000.0000.0000.000
78A79ILE0-0.032-0.02413.3650.0040.0040.0000.0000.0000.000
79A80PHE0-0.004-0.0019.097-0.018-0.0180.0000.0000.0000.000
80A81GLU-1-0.831-0.9308.9870.4330.4330.0000.0000.0000.000
81A82ASP-1-0.871-0.9334.2752.0522.312-0.001-0.032-0.2270.000
82A83GLU-1-0.826-0.9066.4960.0830.0830.0000.0000.0000.000
83A84LEU0-0.008-0.0037.682-0.001-0.0010.0000.0000.0000.000
84A85LEU0-0.005-0.01410.021-0.063-0.0630.0000.0000.0000.000
85A86ASN00.0230.00713.806-0.001-0.0010.0000.0000.0000.000
86A87ILE00.0090.00416.913-0.002-0.0020.0000.0000.0000.000
87A88GLN00.0350.02019.931-0.008-0.0080.0000.0000.0000.000
88A89PHE00.010-0.00423.6760.0010.0010.0000.0000.0000.000
89A90ALA0-0.032-0.01425.880-0.005-0.0050.0000.0000.0000.000
90A91ILE0-0.051-0.03127.658-0.004-0.0040.0000.0000.0000.000
91A92SER00.0080.00831.364-0.001-0.0010.0000.0000.0000.000
92A93THR00.011-0.00532.8920.0020.0020.0000.0000.0000.000
93A94SER00.0350.01735.631-0.002-0.0020.0000.0000.0000.000
94A95LYS10.9970.97936.003-0.023-0.0230.0000.0000.0000.000
95A96MET00.002-0.00335.2560.0000.0000.0000.0000.0000.000
96A98VAL00.0570.04029.7310.0030.0030.0000.0000.0000.000
97A99SER00.0750.03828.1920.0030.0030.0000.0000.0000.000
98A100TYR00.0120.01127.7040.0040.0040.0000.0000.0000.000
99A101THR0-0.049-0.02128.1310.0030.0030.0000.0000.0000.000
100A102ILE0-0.033-0.00522.7730.0060.0060.0000.0000.0000.000
101A103TRP00.026-0.00920.3220.0020.0020.0000.0000.0000.000
102A104LYS10.8270.90721.542-0.082-0.0820.0000.0000.0000.000
103A105VAL00.0090.00218.6530.0030.0030.0000.0000.0000.000
104A106GLY0-0.032-0.01921.697-0.009-0.0090.0000.0000.0000.000
105A107ASP-1-0.857-0.93724.4520.0860.0860.0000.0000.0000.000
106A108TYR0-0.037-0.03026.2940.0030.0030.0000.0000.0000.000
107A109ASP-1-0.749-0.86227.6060.0660.0660.0000.0000.0000.000
108A110ALA00.010-0.01330.3450.0030.0030.0000.0000.0000.000
109A111SER0-0.087-0.05532.633-0.003-0.0030.0000.0000.0000.000
110A112LEU0-0.099-0.06629.7540.0000.0000.0000.0000.0000.000
111A113GLY0-0.0180.01629.2600.0050.0050.0000.0000.0000.000
112A114THR0-0.045-0.04223.5190.0070.0070.0000.0000.0000.000
113A115MET00.0150.02822.323-0.008-0.0080.0000.0000.0000.000
114A116LEU0-0.022-0.00723.5850.0100.0100.0000.0000.0000.000
115A117LEU00.0140.01820.1760.0040.0040.0000.0000.0000.000
116A118GLU-1-0.824-0.91423.9890.0690.0690.0000.0000.0000.000
117A119THR0-0.060-0.03424.8340.0060.0060.0000.0000.0000.000
118A120GLY0-0.019-0.00726.879-0.004-0.0040.0000.0000.0000.000
119A121GLY0-0.0120.01323.709-0.001-0.0010.0000.0000.0000.000
120A122THR0-0.017-0.02222.215-0.004-0.0040.0000.0000.0000.000
121A123ILE0-0.016-0.02419.5750.0090.0090.0000.0000.0000.000
122A124GLY00.0110.00917.498-0.009-0.0090.0000.0000.0000.000
123A125GLN0-0.094-0.05418.513-0.014-0.0140.0000.0000.0000.000
124A126ALA00.012-0.00717.3150.0100.0100.0000.0000.0000.000
125A127ASP-1-0.811-0.87718.3970.0690.0690.0000.0000.0000.000
126A128SER0-0.051-0.02217.8450.0020.0020.0000.0000.0000.000
127A129SER0-0.026-0.01017.5850.0090.0090.0000.0000.0000.000
128A130TRP0-0.0010.02212.489-0.001-0.0010.0000.0000.0000.000
129A131PHE0-0.024-0.02413.3060.0060.0060.0000.0000.0000.000
130A132LYS10.8160.8965.354-1.302-1.3020.0000.0000.0000.000
131A133ILE0-0.036-0.01510.989-0.035-0.0350.0000.0000.0000.000
132A134VAL00.0610.0309.1670.0780.0780.0000.0000.0000.000
133A135LYS10.8040.88211.710-0.320-0.3200.0000.0000.0000.000
134A136SER0-0.037-0.02714.0630.0480.0480.0000.0000.0000.000
135A137SER0-0.001-0.01616.750-0.002-0.0020.0000.0000.0000.000
136A138GLN0-0.0160.01918.053-0.019-0.0190.0000.0000.0000.000
137A139PHE00.005-0.01020.279-0.001-0.0010.0000.0000.0000.000
138A140GLY0-0.0040.01019.8820.0100.0100.0000.0000.0000.000
139A141TYR00.0100.01114.0140.0030.0030.0000.0000.0000.000
140A142ASN0-0.024-0.03415.559-0.009-0.0090.0000.0000.0000.000
141A143LEU0-0.002-0.00414.9900.0200.0200.0000.0000.0000.000
142A144LEU00.0250.01410.154-0.013-0.0130.0000.0000.0000.000
143A145TYR00.018-0.00513.473-0.016-0.0160.0000.0000.0000.000
144A146CYS0-0.044-0.0109.157-0.041-0.0410.0000.0000.0000.000
145A147PRO00.0210.01811.912-0.037-0.0370.0000.0000.0000.000
146A148VAL0-0.004-0.00612.7480.0050.0050.0000.0000.0000.000
147A149THR00.0160.0039.991-0.018-0.0180.0000.0000.0000.000
148A150THR0-0.001-0.0064.378-0.0100.060-0.001-0.010-0.0590.000
149A151SER0-0.045-0.0096.056-0.088-0.0880.0000.0000.0000.000
150A152SER00.035-0.0153.642-0.2320.1960.012-0.116-0.3250.000
151A153ASP-1-0.810-0.8814.6491.7571.823-0.001-0.006-0.0590.000
152A154ASP-1-0.874-0.9356.5760.1210.1210.0000.0000.0000.000
153A155GLN0-0.032-0.0209.798-0.156-0.1560.0000.0000.0000.000
154A156PHE0-0.053-0.0127.730-0.157-0.1570.0000.0000.0000.000
155A158LEU00.0070.01311.1370.0010.0010.0000.0000.0000.000
156A159LYS10.8800.94213.827-0.450-0.4500.0000.0000.0000.000
157A160VAL00.0140.01516.337-0.038-0.0380.0000.0000.0000.000
158A161GLY00.0470.01118.9510.0080.0080.0000.0000.0000.000
159A162VAL0-0.086-0.04422.323-0.009-0.0090.0000.0000.0000.000
160A163VAL00.0330.03026.071-0.001-0.0010.0000.0000.0000.000
161A164HIS00.012-0.00828.919-0.005-0.0050.0000.0000.0000.000
162A165GLN00.0710.05131.758-0.003-0.0030.0000.0000.0000.000
163A166ASN0-0.016-0.02133.9510.0000.0000.0000.0000.0000.000
164A167GLY00.0360.02836.992-0.003-0.0030.0000.0000.0000.000
165A168LYS10.8740.94133.591-0.062-0.0620.0000.0000.0000.000
166A169ARG10.8780.93729.743-0.079-0.0790.0000.0000.0000.000
167A170ARG10.8160.90327.860-0.088-0.0880.0000.0000.0000.000
168A171LEU00.008-0.00422.4680.0040.0040.0000.0000.0000.000
169A172ALA0-0.013-0.00923.714-0.009-0.0090.0000.0000.0000.000
170A173LEU00.0340.02717.9250.0140.0140.0000.0000.0000.000
171A174VAL0-0.0320.00119.825-0.021-0.0210.0000.0000.0000.000
172A175LYS10.8670.91819.146-0.133-0.1330.0000.0000.0000.000
173A176ASP-1-0.813-0.90719.1860.1900.1900.0000.0000.0000.000
174A177ASN0-0.073-0.03721.595-0.013-0.0130.0000.0000.0000.000
175A178PRO00.0570.04018.388-0.013-0.0130.0000.0000.0000.000
176A179LEU0-0.041-0.02920.552-0.021-0.0210.0000.0000.0000.000
177A180ASP-1-0.794-0.85120.4730.2120.2120.0000.0000.0000.000
178A181VAL0-0.091-0.04919.400-0.022-0.0220.0000.0000.0000.000
179A182SER00.0150.00520.5360.0130.0130.0000.0000.0000.000
180A183PHE00.0310.01817.078-0.010-0.0100.0000.0000.0000.000
181A184LYS10.9830.99122.405-0.067-0.0670.0000.0000.0000.000
182A185GLN00.0580.03325.5970.0000.0000.0000.0000.0000.000
183A186VAL0-0.037-0.01926.623-0.002-0.0020.0000.0000.0000.000
184A187GLN00.0020.01329.630-0.004-0.0040.0000.0000.0000.000