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: 6NZRZ

Calculation Name: 5TCB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TCB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HZE4

Base Structure: X-ray

Registration Date: 2023-06-22

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 253
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3262489.862467
FMO2-HF: Nuclear repulsion 3166481.343916
FMO2-HF: Total energy -96008.518551
FMO2-MP2: Total energy -96295.533703


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:48:GLY)


Summations of interaction energy for fragment #1(A:48:GLY)
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.
-3.093-0.8095.105-3.554-3.834-0.009
Interaction energy analysis for fragmet #1(A:48:GLY)
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 : -0.003
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].
3A50SER00.043-0.0063.8710.6101.699-0.006-0.545-0.5380.002
4A51SER0-0.020-0.0156.7390.8470.8470.0000.0000.0000.000
5A52VAL0-0.018-0.0067.438-0.331-0.3310.0000.0000.0000.000
6A53ALA00.0380.0199.3550.1820.1820.0000.0000.0000.000
7A54PHE0-0.004-0.00910.522-0.004-0.0040.0000.0000.0000.000
8A55TRP0-0.021-0.01714.644-0.002-0.0020.0000.0000.0000.000
9A56TYR00.020-0.01215.9990.0070.0070.0000.0000.0000.000
10A57ALA00.0090.02120.4560.0250.0250.0000.0000.0000.000
11A58GLU-1-0.811-0.89423.036-0.104-0.1040.0000.0000.0000.000
12A59ARG10.7580.84724.7780.1050.1050.0000.0000.0000.000
13A60PRO00.0640.04920.141-0.007-0.0070.0000.0000.0000.000
14A61PRO00.0010.00720.7530.0000.0000.0000.0000.0000.000
15A62LEU00.0350.00819.595-0.047-0.0470.0000.0000.0000.000
16A63ALA00.0060.01119.057-0.053-0.0530.0000.0000.0000.000
17A64GLU-1-0.870-0.92919.489-0.387-0.3870.0000.0000.0000.000
18A65LEU0-0.013-0.02215.940-0.065-0.0650.0000.0000.0000.000
19A66SER0-0.062-0.04514.697-0.109-0.1090.0000.0000.0000.000
20A67GLN0-0.047-0.01714.773-0.087-0.0870.0000.0000.0000.000
21A68PHE0-0.068-0.01911.159-0.055-0.0550.0000.0000.0000.000
22A69ASP-1-0.821-0.8706.491-4.361-4.3610.0000.0000.0000.000
23A70TRP0-0.020-0.0252.530-0.2820.0332.922-1.566-1.670-0.009
24A71VAL00.0330.0148.0700.1320.1320.0000.0000.0000.000
25A72VAL0-0.0190.00710.4760.1060.1060.0000.0000.0000.000
26A73LEU00.0170.01112.746-0.003-0.0030.0000.0000.0000.000
27A74GLU-1-0.747-0.84716.3710.0260.0260.0000.0000.0000.000
28A75ALA00.002-0.01018.995-0.012-0.0120.0000.0000.0000.000
29A76ALA0-0.043-0.02120.443-0.004-0.0040.0000.0000.0000.000
30A77HIS0-0.051-0.02622.2140.0020.0020.0000.0000.0000.000
31A78LEU0-0.0130.01718.797-0.017-0.0170.0000.0000.0000.000
32A79LYS10.8360.90722.8470.1220.1220.0000.0000.0000.000
33A80PRO00.0430.00321.758-0.020-0.0200.0000.0000.0000.000
34A81ALA0-0.0080.00521.663-0.016-0.0160.0000.0000.0000.000
35A82ASP-1-0.787-0.88321.242-0.206-0.2060.0000.0000.0000.000
36A83VAL0-0.025-0.01016.456-0.048-0.0480.0000.0000.0000.000
37A84GLY0-0.036-0.01417.299-0.042-0.0420.0000.0000.0000.000
38A85TYR00.0810.03318.632-0.034-0.0340.0000.0000.0000.000
39A86LEU0-0.009-0.01315.015-0.039-0.0390.0000.0000.0000.000
40A87LYS10.8410.91613.6950.1640.1640.0000.0000.0000.000
41A88GLU-1-0.994-0.99615.294-0.316-0.3160.0000.0000.0000.000
42A89GLN0-0.069-0.02916.693-0.002-0.0020.0000.0000.0000.000
43A90GLY0-0.036-0.00713.428-0.054-0.0540.0000.0000.0000.000
44A91SER0-0.043-0.01111.228-0.186-0.1860.0000.0000.0000.000
45A92THR0-0.029-0.0277.2670.2370.2370.0000.0000.0000.000
46A93PRO0-0.0320.0019.8770.0010.0010.0000.0000.0000.000
47A94PHE0-0.026-0.0336.0160.1540.1540.0000.0000.0000.000
48A95ALA0-0.001-0.00311.838-0.026-0.0260.0000.0000.0000.000
49A96TYR0-0.030-0.04214.6380.0620.0620.0000.0000.0000.000
50A97LEU0-0.042-0.02616.404-0.001-0.0010.0000.0000.0000.000
51A98SER00.0620.05617.5780.0490.0490.0000.0000.0000.000
52A99VAL0-0.004-0.01717.697-0.001-0.0010.0000.0000.0000.000
53A100GLY00.0140.00420.6250.0000.0000.0000.0000.0000.000
54A101GLU-1-0.861-0.89023.1350.0890.0890.0000.0000.0000.000
55A102PHE0-0.025-0.00324.3740.0010.0010.0000.0000.0000.000
56A103ASP-1-0.851-0.92923.9580.0520.0520.0000.0000.0000.000
57A104GLY0-0.012-0.02126.991-0.006-0.0060.0000.0000.0000.000
58A105ASP-1-0.817-0.90730.6640.0230.0230.0000.0000.0000.000
59A106ALA0-0.015-0.01934.3650.0050.0050.0000.0000.0000.000
60A107ALA0-0.020-0.01436.7610.0030.0030.0000.0000.0000.000
61A108ALA00.0290.02132.4930.0010.0010.0000.0000.0000.000
62A109ILE00.0210.02131.5620.0040.0040.0000.0000.0000.000
63A110ALA0-0.064-0.03433.7670.0060.0060.0000.0000.0000.000
64A111ASP-1-0.961-0.97135.4650.0250.0250.0000.0000.0000.000
65A112SER0-0.018-0.02431.5640.0040.0040.0000.0000.0000.000
66A113GLY0-0.021-0.00833.3120.0060.0060.0000.0000.0000.000
67A114LEU0-0.025-0.01429.0100.0080.0080.0000.0000.0000.000
68A115ALA00.0480.02633.0510.0070.0070.0000.0000.0000.000
69A116ARG10.8770.93435.641-0.088-0.0880.0000.0000.0000.000
70A117GLY00.001-0.00332.2540.0050.0050.0000.0000.0000.000
71A118LYS10.8640.93631.670-0.051-0.0510.0000.0000.0000.000
72A119SER0-0.026-0.00231.1030.0000.0000.0000.0000.0000.000
73A120ALA0-0.036-0.01133.125-0.003-0.0030.0000.0000.0000.000
74A121VAL0-0.013-0.01230.669-0.002-0.0020.0000.0000.0000.000
75A122ARG10.8040.87933.395-0.105-0.1050.0000.0000.0000.000
76A123ASN0-0.027-0.02032.410-0.001-0.0010.0000.0000.0000.000
77A124GLN00.0350.03031.3660.0070.0070.0000.0000.0000.000
78A125ALA00.0740.04928.925-0.007-0.0070.0000.0000.0000.000
79A126TRP00.019-0.00230.9220.0040.0040.0000.0000.0000.000
80A127ASN0-0.070-0.03829.738-0.005-0.0050.0000.0000.0000.000
81A128SER00.0400.01426.634-0.003-0.0030.0000.0000.0000.000
82A129GLN0-0.022-0.01728.456-0.004-0.0040.0000.0000.0000.000
83A130VAL00.0540.04027.2050.0070.0070.0000.0000.0000.000
84A131MET0-0.0340.00326.884-0.015-0.0150.0000.0000.0000.000
85A132ASP-1-0.855-0.91928.1710.1570.1570.0000.0000.0000.000
86A133LEU00.0210.00622.9620.0000.0000.0000.0000.0000.000
87A134ALA0-0.018-0.01426.7110.0160.0160.0000.0000.0000.000
88A135ALA0-0.0120.01029.455-0.006-0.0060.0000.0000.0000.000
89A136PRO0-0.014-0.01629.5430.0050.0050.0000.0000.0000.000
90A137SER00.004-0.00329.7250.0060.0060.0000.0000.0000.000
91A138TRP00.0440.02723.907-0.013-0.0130.0000.0000.0000.000
92A139ARG10.8400.90925.006-0.234-0.2340.0000.0000.0000.000
93A140ALA0-0.006-0.00924.9120.0090.0090.0000.0000.0000.000
94A141HIS00.0190.01325.350-0.005-0.0050.0000.0000.0000.000
95A142LEU00.0090.01921.255-0.008-0.0080.0000.0000.0000.000
96A143LEU0-0.020-0.00320.9920.0050.0050.0000.0000.0000.000
97A144LYS10.8480.91722.626-0.069-0.0690.0000.0000.0000.000
98A145ARG10.8150.87219.665-0.041-0.0410.0000.0000.0000.000
99A146ALA00.0400.02218.363-0.018-0.0180.0000.0000.0000.000
100A147ALA00.0360.01819.439-0.014-0.0140.0000.0000.0000.000
101A148GLU-1-0.847-0.90021.8470.0260.0260.0000.0000.0000.000
102A149LEU0-0.0040.00617.519-0.026-0.0260.0000.0000.0000.000
103A150ARG10.8690.89217.761-0.172-0.1720.0000.0000.0000.000
104A151LYS10.7630.86218.732-0.067-0.0670.0000.0000.0000.000
105A152GLN0-0.041-0.01920.242-0.031-0.0310.0000.0000.0000.000
106A153GLY0-0.0030.01718.285-0.032-0.0320.0000.0000.0000.000
107A154TYR00.0330.00914.327-0.054-0.0540.0000.0000.0000.000
108A155ALA00.0280.01710.4000.0540.0540.0000.0000.0000.000
109A156GLY00.005-0.00610.0280.1370.1370.0000.0000.0000.000
110A157LEU0-0.045-0.01711.071-0.114-0.1140.0000.0000.0000.000
111A158PHE00.0300.01310.3820.1140.1140.0000.0000.0000.000
112A159LEU0-0.042-0.02112.375-0.050-0.0500.0000.0000.0000.000
113A160ASP-1-0.697-0.82614.4750.1850.1850.0000.0000.0000.000
114A161THR00.020-0.02016.7570.0280.0280.0000.0000.0000.000
115A162LEU0-0.036-0.01014.6420.0020.0020.0000.0000.0000.000
116A163ASP-1-0.822-0.91418.9740.2320.2320.0000.0000.0000.000
117A164SER00.023-0.02121.395-0.014-0.0140.0000.0000.0000.000
118A165PHE0-0.061-0.02921.963-0.022-0.0220.0000.0000.0000.000
119A166GLN0-0.010-0.02423.895-0.027-0.0270.0000.0000.0000.000
120A167LEU00.0160.00827.065-0.013-0.0130.0000.0000.0000.000
121A168GLN0-0.036-0.02829.221-0.022-0.0220.0000.0000.0000.000
122A169ALA0-0.046-0.01831.364-0.001-0.0010.0000.0000.0000.000
123A170GLU-1-0.750-0.85833.0370.1210.1210.0000.0000.0000.000
124A171GLU-1-0.799-0.88432.9740.1220.1220.0000.0000.0000.000
125A172ARG10.8180.88132.771-0.102-0.1020.0000.0000.0000.000
126A173ARG10.8110.92028.582-0.132-0.1320.0000.0000.0000.000
127A174GLU-1-0.684-0.79527.8790.2680.2680.0000.0000.0000.000
128A175GLY0-0.022-0.01528.2510.0140.0140.0000.0000.0000.000
129A176GLN0-0.009-0.02727.3310.0140.0140.0000.0000.0000.000
130A177ARG10.7490.84022.718-0.313-0.3130.0000.0000.0000.000
131A178ARG10.8910.92123.557-0.207-0.2070.0000.0000.0000.000
132A179ALA0-0.048-0.00724.9670.0150.0150.0000.0000.0000.000
133A180LEU00.0540.02919.5960.0050.0050.0000.0000.0000.000
134A181ALA00.0550.02720.0330.0280.0280.0000.0000.0000.000
135A182SER0-0.043-0.03420.5110.0220.0220.0000.0000.0000.000
136A183PHE0-0.011-0.00718.808-0.001-0.0010.0000.0000.0000.000
137A184LEU00.0400.02215.6900.0020.0020.0000.0000.0000.000
138A185ALA00.0410.01517.3930.0420.0420.0000.0000.0000.000
139A186GLN0-0.107-0.05119.228-0.007-0.0070.0000.0000.0000.000
140A187LEU00.0290.00616.138-0.019-0.0190.0000.0000.0000.000
141A188HIS00.0290.01711.589-0.109-0.1090.0000.0000.0000.000
142A189ARG10.8960.95816.310-0.339-0.3390.0000.0000.0000.000
143A190GLN0-0.100-0.05519.486-0.033-0.0330.0000.0000.0000.000
144A191GLU-1-0.741-0.83116.7980.1470.1470.0000.0000.0000.000
145A192PRO00.0170.01214.7450.0330.0330.0000.0000.0000.000
146A193GLY0-0.037-0.01713.8210.0460.0460.0000.0000.0000.000
147A194LEU0-0.064-0.02012.526-0.084-0.0840.0000.0000.0000.000
148A195LYS10.9570.9735.221-1.674-1.6740.0000.0000.0000.000
149A196LEU00.0030.0179.149-0.202-0.2020.0000.0000.0000.000
150A197PHE00.012-0.0057.3110.4400.4400.0000.0000.0000.000
151A198PHE00.0220.0058.689-0.192-0.1920.0000.0000.0000.000
152A199ASN00.004-0.00710.8250.0450.0450.0000.0000.0000.000
153A200ARG10.8390.90213.575-0.183-0.1830.0000.0000.0000.000
154A201GLY00.0770.03414.1330.1000.1000.0000.0000.0000.000
155A202PHE00.011-0.00313.6950.0560.0560.0000.0000.0000.000
156A203GLU-1-0.882-0.92817.2950.3360.3360.0000.0000.0000.000
157A204VAL0-0.017-0.02217.114-0.032-0.0320.0000.0000.0000.000
158A205LEU00.0230.02011.9830.0250.0250.0000.0000.0000.000
159A206PRO0-0.008-0.00215.7900.0600.0600.0000.0000.0000.000
160A207GLU-1-0.883-0.90618.3100.3550.3550.0000.0000.0000.000
161A208LEU0-0.079-0.03115.359-0.037-0.0370.0000.0000.0000.000
162A209PRO00.0370.02014.1710.1560.1560.0000.0000.0000.000
163A210GLY0-0.002-0.01311.207-0.082-0.0820.0000.0000.0000.000
164A211VAL0-0.065-0.02311.6610.0170.0170.0000.0000.0000.000
165A212ALA00.0020.0118.940-0.004-0.0040.0000.0000.0000.000
166A213SER0-0.054-0.0464.5910.2100.219-0.001-0.005-0.0020.000
167A214ALA00.0190.0013.6052.5743.0750.010-0.118-0.3930.000
168A215VAL0-0.014-0.0085.520-0.592-0.5920.0000.0000.0000.000
169A216ALA00.0080.0138.928-0.111-0.1110.0000.0000.0000.000
170A217VAL00.004-0.01610.6980.0700.0700.0000.0000.0000.000
171A218GLU-1-0.795-0.82413.810-0.032-0.0320.0000.0000.0000.000
172A219SER0-0.029-0.04616.6850.0380.0380.0000.0000.0000.000
173A220ILE0-0.095-0.04913.9900.0320.0320.0000.0000.0000.000
174A221HIS0-0.083-0.06717.3620.0220.0220.0000.0000.0000.000
175A222ALA0-0.0030.01119.7520.0080.0080.0000.0000.0000.000
176A223GLY00.0910.03920.073-0.007-0.0070.0000.0000.0000.000
177A224TRP0-0.006-0.00822.110-0.013-0.0130.0000.0000.0000.000
178A225ASP-1-0.778-0.86624.4600.0300.0300.0000.0000.0000.000
179A226ALA00.009-0.01426.191-0.006-0.0060.0000.0000.0000.000
180A227ALA0-0.043-0.00628.1010.0000.0000.0000.0000.0000.000
181A228ALA0-0.050-0.03231.040-0.003-0.0030.0000.0000.0000.000
182A229GLY0-0.0100.00431.091-0.005-0.0050.0000.0000.0000.000
183A230GLN0-0.024-0.00629.700-0.006-0.0060.0000.0000.0000.000
184A231TYR00.0420.01323.8920.0030.0030.0000.0000.0000.000
185A232ARG10.7650.86325.798-0.002-0.0020.0000.0000.0000.000
186A233GLU-1-0.803-0.88024.090-0.038-0.0380.0000.0000.0000.000
187A234VAL0-0.039-0.01320.3930.0080.0080.0000.0000.0000.000
188A235PRO0-0.0100.00323.778-0.004-0.0040.0000.0000.0000.000
189A236GLN0-0.029-0.01623.913-0.007-0.0070.0000.0000.0000.000
190A237ASP-1-0.864-0.94225.0590.0750.0750.0000.0000.0000.000
191A238ASP-1-0.855-0.93322.5710.1110.1110.0000.0000.0000.000
192A239ARG10.7650.84420.3820.0210.0210.0000.0000.0000.000
193A240ASP-1-0.895-0.94320.7860.1150.1150.0000.0000.0000.000
194A241TRP0-0.039-0.02520.0240.0310.0310.0000.0000.0000.000
195A242LEU0-0.004-0.00916.9330.0410.0410.0000.0000.0000.000
196A243LYS10.8690.92917.797-0.130-0.1300.0000.0000.0000.000
197A244GLY0-0.0040.00118.0600.0320.0320.0000.0000.0000.000
198A245HIS00.0070.00516.5680.0750.0750.0000.0000.0000.000
199A246LEU00.012-0.00312.7170.1000.1000.0000.0000.0000.000
200A247ASP-1-0.796-0.87113.3400.3330.3330.0000.0000.0000.000
201A248ALA0-0.0110.00115.1820.0450.0450.0000.0000.0000.000
202A249LEU0-0.011-0.00510.5730.0940.0940.0000.0000.0000.000
203A250ARG10.8930.92210.714-0.059-0.0590.0000.0000.0000.000
204A251ALA0-0.066-0.02711.7650.0510.0510.0000.0000.0000.000
205A252GLN0-0.096-0.04310.9320.0490.0490.0000.0000.0000.000
206A253GLY0-0.015-0.0058.8260.2290.2290.0000.0000.0000.000
207A254MET0-0.0340.0096.6001.1181.1180.0000.0000.0000.000
208A255PRO00.000-0.0072.494-1.692-1.4082.182-1.285-1.181-0.002
209A256ILE00.0090.0154.419-0.271-0.200-0.001-0.031-0.0400.000
210A257VAL0-0.017-0.0076.108-0.358-0.3580.0000.0000.0000.000
211A258ALA0-0.0080.0038.5610.1010.1010.0000.0000.0000.000
212A259ILE00.0190.01912.148-0.112-0.1120.0000.0000.0000.000
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