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: 2J45R

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 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 253
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3253166.706536
FMO2-HF: Nuclear repulsion 3157158.368962
FMO2-HF: Total energy -96008.337574
FMO2-MP2: Total energy -96295.47072


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.
-3.481-0.7243.64-3.15-3.247-0.006
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 : 0.016 / q_NPA : -0.002
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].
3A50SER00.028-0.0053.805-0.1411.266-0.013-0.783-0.6110.003
4A51SER0-0.009-0.0136.7720.8580.8580.0000.0000.0000.000
5A52VAL0-0.0070.0007.850-0.308-0.3080.0000.0000.0000.000
6A53ALA00.0320.0199.7970.1520.1520.0000.0000.0000.000
7A54PHE00.002-0.00610.977-0.013-0.0130.0000.0000.0000.000
8A55TRP0-0.013-0.01215.102-0.003-0.0030.0000.0000.0000.000
9A56TYR00.039-0.00116.2440.0060.0060.0000.0000.0000.000
10A57ALA00.0070.01520.5970.0260.0260.0000.0000.0000.000
11A58GLU-1-0.823-0.90423.344-0.103-0.1030.0000.0000.0000.000
12A59ARG10.7690.85925.3320.1060.1060.0000.0000.0000.000
13A60PRO00.0690.04920.480-0.008-0.0080.0000.0000.0000.000
14A61PRO0-0.0070.00121.2480.0040.0040.0000.0000.0000.000
15A62LEU00.0400.01219.887-0.043-0.0430.0000.0000.0000.000
16A63ALA00.0180.01119.399-0.049-0.0490.0000.0000.0000.000
17A64GLU-1-0.862-0.92819.830-0.371-0.3710.0000.0000.0000.000
18A65LEU0-0.025-0.02716.347-0.067-0.0670.0000.0000.0000.000
19A66SER0-0.069-0.04615.037-0.103-0.1030.0000.0000.0000.000
20A67GLN0-0.034-0.01515.018-0.077-0.0770.0000.0000.0000.000
21A68PHE0-0.074-0.02111.671-0.078-0.0780.0000.0000.0000.000
22A69ASP-1-0.806-0.8686.587-4.178-4.1780.0000.0000.0000.000
23A70TRP0-0.021-0.0232.456-0.1950.3271.606-1.037-1.091-0.006
24A71VAL00.0350.0178.4010.1040.1040.0000.0000.0000.000
25A72VAL0-0.0250.00210.7770.0930.0930.0000.0000.0000.000
26A73LEU00.0110.00113.064-0.004-0.0040.0000.0000.0000.000
27A74GLU-1-0.777-0.87916.7040.0180.0180.0000.0000.0000.000
28A75ALA0-0.007-0.01419.056-0.012-0.0120.0000.0000.0000.000
29A76ALA0-0.090-0.05020.558-0.003-0.0030.0000.0000.0000.000
30A77HIS0-0.024-0.01122.9280.0040.0040.0000.0000.0000.000
31A78LEU0-0.0090.01518.842-0.017-0.0170.0000.0000.0000.000
32A79LYS10.8250.89822.9540.1130.1130.0000.0000.0000.000
33A80PRO00.0540.00921.875-0.019-0.0190.0000.0000.0000.000
34A81ALA0-0.010-0.00321.750-0.015-0.0150.0000.0000.0000.000
35A82ASP-1-0.781-0.87521.531-0.190-0.1900.0000.0000.0000.000
36A83VAL0-0.022-0.01016.458-0.043-0.0430.0000.0000.0000.000
37A84GLY0-0.044-0.03017.344-0.041-0.0410.0000.0000.0000.000
38A85TYR00.0740.04018.954-0.021-0.0210.0000.0000.0000.000
39A86LEU0-0.004-0.00815.142-0.040-0.0400.0000.0000.0000.000
40A87LYS10.8260.90913.6700.1340.1340.0000.0000.0000.000
41A88GLU-1-1.004-0.99415.393-0.303-0.3030.0000.0000.0000.000
42A89GLN0-0.062-0.03316.979-0.019-0.0190.0000.0000.0000.000
43A90GLY0-0.034-0.00113.610-0.043-0.0430.0000.0000.0000.000
44A91SER0-0.042-0.01011.275-0.187-0.1870.0000.0000.0000.000
45A92THR0-0.033-0.0217.1880.2230.2230.0000.0000.0000.000
46A93PRO0-0.038-0.0109.906-0.020-0.0200.0000.0000.0000.000
47A94PHE0-0.022-0.0336.1130.1630.1630.0000.0000.0000.000
48A95ALA0-0.018-0.00812.092-0.035-0.0350.0000.0000.0000.000
49A96TYR0-0.036-0.04014.9680.0640.0640.0000.0000.0000.000
50A97LEU0-0.044-0.02916.592-0.002-0.0020.0000.0000.0000.000
51A98SER00.0580.05417.8110.0450.0450.0000.0000.0000.000
52A99VAL0-0.007-0.01217.892-0.002-0.0020.0000.0000.0000.000
53A100GLY00.0310.00820.895-0.002-0.0020.0000.0000.0000.000
54A101GLU-1-0.861-0.88623.4890.0800.0800.0000.0000.0000.000
55A102PHE0-0.031-0.00924.7100.0010.0010.0000.0000.0000.000
56A103ASP-1-0.849-0.92224.6190.0440.0440.0000.0000.0000.000
57A104GLY0-0.015-0.02527.707-0.005-0.0050.0000.0000.0000.000
58A105ASP-1-0.796-0.89631.2500.0190.0190.0000.0000.0000.000
59A106ALA0-0.017-0.01034.9020.0050.0050.0000.0000.0000.000
60A107ALA0-0.029-0.02337.1170.0030.0030.0000.0000.0000.000
61A108ALA00.0070.00932.8130.0010.0010.0000.0000.0000.000
62A109ILE00.0080.00131.8450.0040.0040.0000.0000.0000.000
63A110ALA0-0.066-0.02834.0480.0050.0050.0000.0000.0000.000
64A111ASP-1-0.951-0.96835.9560.0240.0240.0000.0000.0000.000
65A112SER0-0.038-0.02031.7970.0040.0040.0000.0000.0000.000
66A113GLY0-0.013-0.00233.4750.0050.0050.0000.0000.0000.000
67A114LEU0-0.025-0.01929.2860.0090.0090.0000.0000.0000.000
68A115ALA00.0390.02233.3640.0050.0050.0000.0000.0000.000
69A116ARG10.8990.94136.013-0.084-0.0840.0000.0000.0000.000
70A117GLY0-0.002-0.00132.2630.0030.0030.0000.0000.0000.000
71A118LYS10.9230.97431.926-0.049-0.0490.0000.0000.0000.000
72A119SER0-0.031-0.01031.7820.0010.0010.0000.0000.0000.000
73A120ALA0-0.051-0.02533.659-0.003-0.0030.0000.0000.0000.000
74A121VAL0-0.012-0.00131.318-0.002-0.0020.0000.0000.0000.000
75A122ARG10.8160.88933.567-0.096-0.0960.0000.0000.0000.000
76A123ASN0-0.034-0.01832.627-0.002-0.0020.0000.0000.0000.000
77A124GLN00.0270.02431.6840.0090.0090.0000.0000.0000.000
78A125ALA00.0530.03329.189-0.007-0.0070.0000.0000.0000.000
79A126TRP00.0450.00331.2640.0040.0040.0000.0000.0000.000
80A127ASN0-0.064-0.03330.133-0.005-0.0050.0000.0000.0000.000
81A128SER00.0430.00326.823-0.003-0.0030.0000.0000.0000.000
82A129GLN0-0.090-0.04829.414-0.001-0.0010.0000.0000.0000.000
83A130VAL00.0630.03127.7150.0060.0060.0000.0000.0000.000
84A131MET0-0.051-0.00627.123-0.013-0.0130.0000.0000.0000.000
85A132ASP-1-0.821-0.90028.1870.1520.1520.0000.0000.0000.000
86A133LEU00.0210.00723.2610.0010.0010.0000.0000.0000.000
87A134ALA0-0.032-0.02026.9350.0160.0160.0000.0000.0000.000
88A135ALA0-0.0230.00529.620-0.007-0.0070.0000.0000.0000.000
89A136PRO0-0.006-0.01629.6840.0060.0060.0000.0000.0000.000
90A137SER0-0.003-0.00630.0500.0060.0060.0000.0000.0000.000
91A138TRP00.0480.02924.322-0.012-0.0120.0000.0000.0000.000
92A139ARG10.8590.91525.218-0.226-0.2260.0000.0000.0000.000
93A140ALA0-0.018-0.01525.2370.0080.0080.0000.0000.0000.000
94A141HIS00.0200.01525.740-0.004-0.0040.0000.0000.0000.000
95A142LEU00.0110.01321.617-0.006-0.0060.0000.0000.0000.000
96A143LEU0-0.0180.00021.1660.0060.0060.0000.0000.0000.000
97A144LYS10.8610.92322.728-0.070-0.0700.0000.0000.0000.000
98A145ARG10.9240.96321.025-0.043-0.0430.0000.0000.0000.000
99A146ALA00.0420.02318.395-0.016-0.0160.0000.0000.0000.000
100A147ALA00.0310.01819.364-0.010-0.0100.0000.0000.0000.000
101A148GLU-1-0.850-0.90321.7610.0350.0350.0000.0000.0000.000
102A149LEU0-0.0040.00117.769-0.025-0.0250.0000.0000.0000.000
103A150ARG10.8770.89317.494-0.176-0.1760.0000.0000.0000.000
104A151LYS10.7610.86218.507-0.079-0.0790.0000.0000.0000.000
105A152GLN0-0.042-0.01720.400-0.030-0.0300.0000.0000.0000.000
106A153GLY0-0.0260.00718.181-0.030-0.0300.0000.0000.0000.000
107A154TYR00.0340.01414.438-0.046-0.0460.0000.0000.0000.000
108A155ALA00.0250.01410.3240.0490.0490.0000.0000.0000.000
109A156GLY00.0290.00410.1000.1410.1410.0000.0000.0000.000
110A157LEU0-0.051-0.01911.164-0.116-0.1160.0000.0000.0000.000
111A158PHE00.0250.01210.7130.1080.1080.0000.0000.0000.000
112A159LEU0-0.039-0.02512.602-0.045-0.0450.0000.0000.0000.000
113A160ASP-1-0.706-0.83014.8660.1450.1450.0000.0000.0000.000
114A161THR00.006-0.01417.3760.0320.0320.0000.0000.0000.000
115A162LEU0-0.020-0.00714.9460.0090.0090.0000.0000.0000.000
116A163ASP-1-0.851-0.93719.4060.2130.2130.0000.0000.0000.000
117A164SER00.029-0.02121.800-0.013-0.0130.0000.0000.0000.000
118A165PHE0-0.048-0.02222.157-0.021-0.0210.0000.0000.0000.000
119A166GLN0-0.010-0.02123.768-0.022-0.0220.0000.0000.0000.000
120A167LEU00.0160.00927.302-0.012-0.0120.0000.0000.0000.000
121A168GLN0-0.049-0.03229.842-0.021-0.0210.0000.0000.0000.000
122A169ALA0-0.032-0.01431.9340.0000.0000.0000.0000.0000.000
123A170GLU-1-0.710-0.83732.7750.1130.1130.0000.0000.0000.000
124A171GLU-1-0.819-0.89932.9710.1140.1140.0000.0000.0000.000
125A172ARG10.8100.88133.208-0.096-0.0960.0000.0000.0000.000
126A173ARG10.8170.92228.557-0.122-0.1220.0000.0000.0000.000
127A174GLU-1-0.707-0.80827.8700.2570.2570.0000.0000.0000.000
128A175GLY0-0.022-0.01728.4780.0140.0140.0000.0000.0000.000
129A176GLN0-0.011-0.02627.2670.0100.0100.0000.0000.0000.000
130A177ARG10.7740.86322.736-0.299-0.2990.0000.0000.0000.000
131A178ARG10.8850.91923.741-0.196-0.1960.0000.0000.0000.000
132A179ALA0-0.043-0.01024.9940.0170.0170.0000.0000.0000.000
133A180LEU00.0580.03419.8730.0060.0060.0000.0000.0000.000
134A181ALA00.0610.03120.1080.0290.0290.0000.0000.0000.000
135A182SER0-0.036-0.02420.5480.0220.0220.0000.0000.0000.000
136A183PHE0-0.011-0.00919.1640.0030.0030.0000.0000.0000.000
137A184LEU00.0460.02515.8560.0030.0030.0000.0000.0000.000
138A185ALA00.0330.01717.4050.0410.0410.0000.0000.0000.000
139A186GLN0-0.114-0.06119.0640.0020.0020.0000.0000.0000.000
140A187LEU00.0210.00716.247-0.021-0.0210.0000.0000.0000.000
141A188HIS00.0480.02711.586-0.090-0.0900.0000.0000.0000.000
142A189ARG10.9000.95116.240-0.342-0.3420.0000.0000.0000.000
143A190GLN0-0.114-0.06519.207-0.027-0.0270.0000.0000.0000.000
144A191GLU-1-0.761-0.83916.7510.1530.1530.0000.0000.0000.000
145A192PRO00.0280.02014.8210.0420.0420.0000.0000.0000.000
146A193GLY0-0.050-0.02713.4410.0690.0690.0000.0000.0000.000
147A194LEU0-0.060-0.01212.349-0.081-0.0810.0000.0000.0000.000
148A195LYS10.9650.9825.377-1.249-1.2490.0000.0000.0000.000
149A196LEU00.0080.0139.056-0.232-0.2320.0000.0000.0000.000
150A197PHE00.0220.0077.6930.3900.3900.0000.0000.0000.000
151A198PHE00.0240.0028.800-0.190-0.1900.0000.0000.0000.000
152A199ASN00.0100.00211.0100.0350.0350.0000.0000.0000.000
153A200ARG10.8710.93713.145-0.164-0.1640.0000.0000.0000.000
154A201GLY00.0890.02913.8720.0990.0990.0000.0000.0000.000
155A202PHE00.002-0.00513.8090.0490.0490.0000.0000.0000.000
156A203GLU-1-0.877-0.92917.2500.3090.3090.0000.0000.0000.000
157A204VAL0-0.008-0.01717.161-0.020-0.0200.0000.0000.0000.000
158A205LEU00.0120.01512.1540.0240.0240.0000.0000.0000.000
159A206PRO0-0.016-0.00515.8390.0640.0640.0000.0000.0000.000
160A207GLU-1-0.898-0.92917.9290.3570.3570.0000.0000.0000.000
161A208LEU0-0.081-0.03215.542-0.039-0.0390.0000.0000.0000.000
162A209PRO00.0320.01414.3020.1510.1510.0000.0000.0000.000
163A210GLY00.000-0.01211.497-0.086-0.0860.0000.0000.0000.000
164A211VAL0-0.064-0.01811.5130.0500.0500.0000.0000.0000.000
165A212ALA00.0020.0119.371-0.031-0.0310.0000.0000.0000.000
166A213SER0-0.064-0.0474.3740.1360.144-0.001-0.0090.0020.000
167A214ALA00.0210.0003.8752.2752.7040.005-0.080-0.3540.000
168A215VAL0-0.024-0.0075.691-0.481-0.4810.0000.0000.0000.000
169A216ALA0-0.0070.0098.620-0.122-0.1220.0000.0000.0000.000
170A217VAL00.017-0.01110.6010.0750.0750.0000.0000.0000.000
171A218GLU-1-0.808-0.83613.838-0.061-0.0610.0000.0000.0000.000
172A219SER0-0.027-0.05216.8000.0390.0390.0000.0000.0000.000
173A220ILE0-0.099-0.04314.1710.0340.0340.0000.0000.0000.000
174A221HIS0-0.074-0.08017.6130.0320.0320.0000.0000.0000.000
175A222ALA0-0.0080.00619.9070.0140.0140.0000.0000.0000.000
176A223GLY00.0870.03720.291-0.011-0.0110.0000.0000.0000.000
177A224TRP0-0.004-0.00922.194-0.014-0.0140.0000.0000.0000.000
178A225ASP-1-0.804-0.88024.3240.0160.0160.0000.0000.0000.000
179A226ALA00.030-0.00426.202-0.004-0.0040.0000.0000.0000.000
180A227ALA0-0.037-0.00827.978-0.001-0.0010.0000.0000.0000.000
181A228ALA0-0.067-0.03731.163-0.004-0.0040.0000.0000.0000.000
182A229GLY00.0070.01630.389-0.005-0.0050.0000.0000.0000.000
183A230GLN0-0.049-0.02129.949-0.006-0.0060.0000.0000.0000.000
184A231TYR00.0490.00423.9710.0020.0020.0000.0000.0000.000
185A232ARG10.8000.89726.0240.0110.0110.0000.0000.0000.000
186A233GLU-1-0.840-0.89624.127-0.060-0.0600.0000.0000.0000.000
187A234VAL0-0.021-0.01020.4280.0110.0110.0000.0000.0000.000
188A235PRO0-0.0140.00123.831-0.005-0.0050.0000.0000.0000.000
189A236GLN0-0.013-0.02024.287-0.007-0.0070.0000.0000.0000.000
190A237ASP-1-0.889-0.94825.2430.0570.0570.0000.0000.0000.000
191A238ASP-1-0.850-0.93122.5590.0800.0800.0000.0000.0000.000
192A239ARG10.7510.85320.3390.0430.0430.0000.0000.0000.000
193A240ASP-1-0.906-0.95421.1930.0860.0860.0000.0000.0000.000
194A241TRP0-0.040-0.01819.7930.0290.0290.0000.0000.0000.000
195A242LEU00.008-0.00216.8570.0380.0380.0000.0000.0000.000
196A243LYS10.8730.93817.916-0.105-0.1050.0000.0000.0000.000
197A244GLY00.0060.00618.1440.0320.0320.0000.0000.0000.000
198A245HIS00.0160.01016.5850.0770.0770.0000.0000.0000.000
199A246LEU0-0.006-0.01312.7580.0940.0940.0000.0000.0000.000
200A247ASP-1-0.806-0.88013.5720.2880.2880.0000.0000.0000.000
201A248ALA0-0.0190.00215.2310.0470.0470.0000.0000.0000.000
202A249LEU00.005-0.01310.4640.0890.0890.0000.0000.0000.000
203A250ARG10.9010.92610.652-0.020-0.0200.0000.0000.0000.000
204A251ALA0-0.058-0.01611.7040.0590.0590.0000.0000.0000.000
205A252GLN0-0.093-0.03910.9490.0990.0990.0000.0000.0000.000
206A253GLY0-0.012-0.0028.7380.2250.2250.0000.0000.0000.000
207A254MET0-0.056-0.0036.6821.1771.1770.0000.0000.0000.000
208A255PRO00.001-0.0012.292-1.760-1.4382.044-1.225-1.142-0.003
209A256ILE00.0130.0034.568-0.089-0.020-0.001-0.016-0.0510.000
210A257VAL0-0.013-0.0026.002-0.388-0.3880.0000.0000.0000.000
211A258ALA0-0.028-0.0038.4420.1670.1670.0000.0000.0000.000
212A259ILE00.0180.00812.115-0.112-0.1120.0000.0000.0000.000
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