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: 72YZK

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 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 253
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3249859.153797
FMO2-HF: Nuclear repulsion 3153851.36083
FMO2-HF: Total energy -96007.792968
FMO2-MP2: Total energy -96294.847862


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.
-3.916-1.112.753-2.702-2.856-0.005
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 : 0.009 / q_NPA : -0.007
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].
3A50SER00.0350.0013.8050.1271.482-0.013-0.751-0.5910.003
4A51SER00.001-0.0026.7720.8460.8460.0000.0000.0000.000
5A52VAL0-0.0030.0027.865-0.303-0.3030.0000.0000.0000.000
6A53ALA00.0300.0189.7950.1480.1480.0000.0000.0000.000
7A54PHE00.006-0.00611.089-0.008-0.0080.0000.0000.0000.000
8A55TRP0-0.022-0.01515.102-0.007-0.0070.0000.0000.0000.000
9A56TYR00.043-0.00416.3320.0110.0110.0000.0000.0000.000
10A57ALA00.0110.02120.5980.0260.0260.0000.0000.0000.000
11A58GLU-1-0.877-0.94123.343-0.093-0.0930.0000.0000.0000.000
12A59ARG10.8180.89225.3310.1040.1040.0000.0000.0000.000
13A60PRO00.0650.04520.526-0.010-0.0100.0000.0000.0000.000
14A61PRO0-0.0030.00621.2500.0050.0050.0000.0000.0000.000
15A62LEU00.0330.00819.768-0.043-0.0430.0000.0000.0000.000
16A63ALA00.0280.01819.396-0.045-0.0450.0000.0000.0000.000
17A64GLU-1-0.877-0.94319.827-0.358-0.3580.0000.0000.0000.000
18A65LEU0-0.031-0.02816.259-0.068-0.0680.0000.0000.0000.000
19A66SER0-0.068-0.03915.035-0.107-0.1070.0000.0000.0000.000
20A67GLN0-0.025-0.01115.015-0.082-0.0820.0000.0000.0000.000
21A68PHE0-0.078-0.02311.630-0.080-0.0800.0000.0000.0000.000
22A69ASP-1-0.806-0.8866.137-4.308-4.3080.0000.0000.0000.000
23A70TRP0-0.023-0.0182.668-0.3010.3790.652-0.618-0.714-0.004
24A71VAL00.0320.0158.3990.0870.0870.0000.0000.0000.000
25A72VAL0-0.029-0.00210.7120.1030.1030.0000.0000.0000.000
26A73LEU00.0120.00013.064-0.009-0.0090.0000.0000.0000.000
27A74GLU-1-0.845-0.90916.7040.0270.0270.0000.0000.0000.000
28A75ALA0-0.001-0.02119.079-0.010-0.0100.0000.0000.0000.000
29A76ALA0-0.099-0.03920.558-0.002-0.0020.0000.0000.0000.000
30A77HIS0-0.011-0.00722.9850.0000.0000.0000.0000.0000.000
31A78LEU0-0.0190.00718.888-0.019-0.0190.0000.0000.0000.000
32A79LYS10.8940.94422.9520.0840.0840.0000.0000.0000.000
33A80PRO00.0430.00121.876-0.018-0.0180.0000.0000.0000.000
34A81ALA0-0.010-0.00321.747-0.013-0.0130.0000.0000.0000.000
35A82ASP-1-0.801-0.89321.483-0.175-0.1750.0000.0000.0000.000
36A83VAL0-0.020-0.00916.471-0.042-0.0420.0000.0000.0000.000
37A84GLY0-0.040-0.02817.340-0.036-0.0360.0000.0000.0000.000
38A85TYR00.0580.03318.949-0.037-0.0370.0000.0000.0000.000
39A86LEU0-0.005-0.01015.127-0.038-0.0380.0000.0000.0000.000
40A87LYS10.8530.93013.6740.0770.0770.0000.0000.0000.000
41A88GLU-1-0.999-0.99115.389-0.272-0.2720.0000.0000.0000.000
42A89GLN0-0.047-0.02917.021-0.028-0.0280.0000.0000.0000.000
43A90GLY0-0.0380.00013.598-0.046-0.0460.0000.0000.0000.000
44A91SER0-0.0360.00011.268-0.173-0.1730.0000.0000.0000.000
45A92THR0-0.038-0.0287.1990.2310.2310.0000.0000.0000.000
46A93PRO0-0.047-0.0129.903-0.026-0.0260.0000.0000.0000.000
47A94PHE0-0.012-0.0266.1180.1720.1720.0000.0000.0000.000
48A95ALA0-0.020-0.01012.091-0.043-0.0430.0000.0000.0000.000
49A96TYR0-0.022-0.04014.9680.0690.0690.0000.0000.0000.000
50A97LEU0-0.039-0.02516.5970.0000.0000.0000.0000.0000.000
51A98SER00.0380.03817.8130.0430.0430.0000.0000.0000.000
52A99VAL0-0.013-0.01417.9380.0000.0000.0000.0000.0000.000
53A100GLY00.0310.00820.898-0.002-0.0020.0000.0000.0000.000
54A101GLU-1-0.862-0.88623.4920.0750.0750.0000.0000.0000.000
55A102PHE0-0.025-0.01024.7130.0030.0030.0000.0000.0000.000
56A103ASP-1-0.832-0.91224.6020.0470.0470.0000.0000.0000.000
57A104GLY0-0.023-0.02527.709-0.004-0.0040.0000.0000.0000.000
58A105ASP-1-0.795-0.88931.2520.0200.0200.0000.0000.0000.000
59A106ALA0-0.015-0.01334.9040.0060.0060.0000.0000.0000.000
60A107ALA0-0.035-0.02837.1190.0040.0040.0000.0000.0000.000
61A108ALA00.0020.00932.8050.0010.0010.0000.0000.0000.000
62A109ILE00.0140.00231.6780.0040.0040.0000.0000.0000.000
63A110ALA0-0.068-0.02334.0490.0060.0060.0000.0000.0000.000
64A111ASP-1-0.949-0.96535.8970.0300.0300.0000.0000.0000.000
65A112SER0-0.041-0.03031.8270.0040.0040.0000.0000.0000.000
66A113GLY0-0.015-0.00333.4760.0060.0060.0000.0000.0000.000
67A114LEU0-0.021-0.01929.3060.0090.0090.0000.0000.0000.000
68A115ALA00.0410.02433.3660.0050.0050.0000.0000.0000.000
69A116ARG10.8970.93936.016-0.086-0.0860.0000.0000.0000.000
70A117GLY0-0.003-0.00132.2650.0030.0030.0000.0000.0000.000
71A118LYS10.9210.96931.929-0.051-0.0510.0000.0000.0000.000
72A119SER0-0.024-0.00731.8020.0010.0010.0000.0000.0000.000
73A120ALA0-0.055-0.02533.663-0.003-0.0030.0000.0000.0000.000
74A121VAL0-0.024-0.00731.341-0.002-0.0020.0000.0000.0000.000
75A122ARG10.8260.90433.773-0.090-0.0900.0000.0000.0000.000
76A123ASN0-0.024-0.01432.713-0.002-0.0020.0000.0000.0000.000
77A124GLN00.0610.04231.6660.0100.0100.0000.0000.0000.000
78A125ALA00.0370.02829.190-0.007-0.0070.0000.0000.0000.000
79A126TRP00.038-0.00131.2600.0050.0050.0000.0000.0000.000
80A127ASN0-0.056-0.02930.106-0.005-0.0050.0000.0000.0000.000
81A128SER00.0570.01026.582-0.002-0.0020.0000.0000.0000.000
82A129GLN0-0.129-0.07129.425-0.002-0.0020.0000.0000.0000.000
83A130VAL00.0700.03927.7790.0070.0070.0000.0000.0000.000
84A131MET0-0.041-0.00327.163-0.013-0.0130.0000.0000.0000.000
85A132ASP-1-0.848-0.91728.1900.1520.1520.0000.0000.0000.000
86A133LEU00.0200.00423.6750.0020.0020.0000.0000.0000.000
87A134ALA0-0.020-0.01326.9380.0170.0170.0000.0000.0000.000
88A135ALA0-0.031-0.00329.623-0.006-0.0060.0000.0000.0000.000
89A136PRO00.002-0.01529.6870.0060.0060.0000.0000.0000.000
90A137SER0-0.012-0.00830.0520.0070.0070.0000.0000.0000.000
91A138TRP00.0500.03024.315-0.011-0.0110.0000.0000.0000.000
92A139ARG10.8530.90925.219-0.231-0.2310.0000.0000.0000.000
93A140ALA0-0.010-0.01125.2380.0100.0100.0000.0000.0000.000
94A141HIS00.0170.01525.698-0.001-0.0010.0000.0000.0000.000
95A142LEU00.0130.01221.588-0.004-0.0040.0000.0000.0000.000
96A143LEU0-0.0090.00621.1840.0080.0080.0000.0000.0000.000
97A144LYS10.8460.92222.728-0.083-0.0830.0000.0000.0000.000
98A145ARG10.9680.97821.226-0.061-0.0610.0000.0000.0000.000
99A146ALA00.0500.02818.392-0.014-0.0140.0000.0000.0000.000
100A147ALA00.0170.01019.364-0.007-0.0070.0000.0000.0000.000
101A148GLU-1-0.881-0.93321.7600.0520.0520.0000.0000.0000.000
102A149LEU00.0070.00817.789-0.025-0.0250.0000.0000.0000.000
103A150ARG10.8790.91017.485-0.203-0.2030.0000.0000.0000.000
104A151LYS10.7910.88918.505-0.106-0.1060.0000.0000.0000.000
105A152GLN0-0.041-0.02020.209-0.030-0.0300.0000.0000.0000.000
106A153GLY0-0.0170.00918.178-0.030-0.0300.0000.0000.0000.000
107A154TYR00.010-0.00114.402-0.026-0.0260.0000.0000.0000.000
108A155ALA00.0190.00910.3060.0500.0500.0000.0000.0000.000
109A156GLY00.0260.00010.0990.1630.1630.0000.0000.0000.000
110A157LEU0-0.049-0.01811.162-0.128-0.1280.0000.0000.0000.000
111A158PHE00.0210.01210.7600.1110.1110.0000.0000.0000.000
112A159LEU0-0.042-0.02512.604-0.045-0.0450.0000.0000.0000.000
113A160ASP-1-0.707-0.83614.8680.1350.1350.0000.0000.0000.000
114A161THR00.012-0.00617.3790.0360.0360.0000.0000.0000.000
115A162LEU0-0.030-0.01314.9540.0120.0120.0000.0000.0000.000
116A163ASP-1-0.890-0.95019.4100.1930.1930.0000.0000.0000.000
117A164SER00.038-0.01921.795-0.014-0.0140.0000.0000.0000.000
118A165PHE0-0.056-0.02522.213-0.021-0.0210.0000.0000.0000.000
119A166GLN0-0.003-0.01223.879-0.022-0.0220.0000.0000.0000.000
120A167LEU00.0140.01627.297-0.012-0.0120.0000.0000.0000.000
121A168GLN0-0.054-0.03929.824-0.020-0.0200.0000.0000.0000.000
122A169ALA0-0.018-0.01631.9290.0000.0000.0000.0000.0000.000
123A170GLU-1-0.720-0.84432.7620.1050.1050.0000.0000.0000.000
124A171GLU-1-0.924-0.96032.9670.1090.1090.0000.0000.0000.000
125A172ARG10.8930.93933.454-0.093-0.0930.0000.0000.0000.000
126A173ARG10.8590.93528.553-0.114-0.1140.0000.0000.0000.000
127A174GLU-1-0.726-0.82728.0090.2490.2490.0000.0000.0000.000
128A175GLY0-0.024-0.01928.4820.0150.0150.0000.0000.0000.000
129A176GLN00.000-0.00927.1950.0130.0130.0000.0000.0000.000
130A177ARG10.7690.86522.734-0.291-0.2910.0000.0000.0000.000
131A178ARG10.9050.93523.745-0.188-0.1880.0000.0000.0000.000
132A179ALA0-0.041-0.01024.9980.0180.0180.0000.0000.0000.000
133A180LEU00.0530.03519.8040.0080.0080.0000.0000.0000.000
134A181ALA00.0630.03020.1110.0310.0310.0000.0000.0000.000
135A182SER0-0.032-0.01820.5510.0250.0250.0000.0000.0000.000
136A183PHE0-0.010-0.00719.2960.0050.0050.0000.0000.0000.000
137A184LEU00.0460.02315.9480.0060.0060.0000.0000.0000.000
138A185ALA00.0330.01817.4070.0460.0460.0000.0000.0000.000
139A186GLN0-0.114-0.06019.0660.0040.0040.0000.0000.0000.000
140A187LEU00.0150.00416.170-0.019-0.0190.0000.0000.0000.000
141A188HIS00.0530.02412.126-0.070-0.0700.0000.0000.0000.000
142A189ARG10.9050.95716.241-0.354-0.3540.0000.0000.0000.000
143A190GLN0-0.121-0.07819.207-0.030-0.0300.0000.0000.0000.000
144A191GLU-1-0.755-0.84616.7150.1920.1920.0000.0000.0000.000
145A192PRO00.0220.01914.8350.0490.0490.0000.0000.0000.000
146A193GLY0-0.050-0.02813.4390.0820.0820.0000.0000.0000.000
147A194LEU0-0.059-0.01112.330-0.077-0.0770.0000.0000.0000.000
148A195LYS10.9660.9825.095-1.662-1.6620.0000.0000.0000.000
149A196LEU00.0090.0129.056-0.247-0.2470.0000.0000.0000.000
150A197PHE00.0230.0097.6940.3960.3960.0000.0000.0000.000
151A198PHE00.0210.0038.803-0.189-0.1890.0000.0000.0000.000
152A199ASN00.0040.00611.0050.0210.0210.0000.0000.0000.000
153A200ARG10.9050.93913.149-0.141-0.1410.0000.0000.0000.000
154A201GLY00.0980.03513.8670.0980.0980.0000.0000.0000.000
155A202PHE0-0.013-0.01013.7730.0470.0470.0000.0000.0000.000
156A203GLU-1-0.907-0.95917.2460.2950.2950.0000.0000.0000.000
157A204VAL0-0.006-0.02017.132-0.017-0.0170.0000.0000.0000.000
158A205LEU00.0100.01312.1650.0240.0240.0000.0000.0000.000
159A206PRO0-0.016-0.00515.8350.0660.0660.0000.0000.0000.000
160A207GLU-1-0.887-0.92117.9260.3550.3550.0000.0000.0000.000
161A208LEU0-0.083-0.03315.542-0.033-0.0330.0000.0000.0000.000
162A209PRO00.0220.01114.3060.1530.1530.0000.0000.0000.000
163A210GLY00.000-0.01411.500-0.080-0.0800.0000.0000.0000.000
164A211VAL0-0.066-0.01511.5150.0690.0690.0000.0000.0000.000
165A212ALA00.0050.0129.266-0.016-0.0160.0000.0000.0000.000
166A213SER0-0.061-0.0474.3460.2290.239-0.001-0.0100.0010.000
167A214ALA00.013-0.0043.8582.2252.6500.005-0.079-0.3510.000
168A215VAL0-0.018-0.0035.686-0.447-0.4470.0000.0000.0000.000
169A216ALA0-0.0040.0098.617-0.144-0.1440.0000.0000.0000.000
170A217VAL00.008-0.01510.5970.0780.0780.0000.0000.0000.000
171A218GLU-1-0.795-0.83713.835-0.075-0.0750.0000.0000.0000.000
172A219SER0-0.020-0.03616.8050.0430.0430.0000.0000.0000.000
173A220ILE0-0.096-0.04014.3320.0340.0340.0000.0000.0000.000
174A221HIS0-0.074-0.08017.6120.0360.0360.0000.0000.0000.000
175A222ALA0-0.0070.00319.9080.0170.0170.0000.0000.0000.000
176A223GLY00.0830.03320.290-0.012-0.0120.0000.0000.0000.000
177A224TRP0-0.005-0.01022.193-0.013-0.0130.0000.0000.0000.000
178A225ASP-1-0.868-0.93024.3220.0030.0030.0000.0000.0000.000
179A226ALA00.025-0.00626.244-0.003-0.0030.0000.0000.0000.000
180A227ALA0-0.044-0.01127.9750.0000.0000.0000.0000.0000.000
181A228ALA0-0.067-0.03331.153-0.004-0.0040.0000.0000.0000.000
182A229GLY00.0030.01130.386-0.005-0.0050.0000.0000.0000.000
183A230GLN0-0.061-0.02729.952-0.008-0.0080.0000.0000.0000.000
184A231TYR00.0470.00623.8860.0000.0000.0000.0000.0000.000
185A232ARG10.9020.96126.0150.0220.0220.0000.0000.0000.000
186A233GLU-1-0.879-0.93524.328-0.089-0.0890.0000.0000.0000.000
187A234VAL0-0.032-0.01320.4380.0120.0120.0000.0000.0000.000
188A235PRO00.0070.00323.830-0.006-0.0060.0000.0000.0000.000
189A236GLN00.0150.01124.853-0.007-0.0070.0000.0000.0000.000
190A237ASP-1-0.906-0.95625.2430.0430.0430.0000.0000.0000.000
191A238ASP-1-0.823-0.91222.6480.0520.0520.0000.0000.0000.000
192A239ARG10.7740.87420.1430.0610.0610.0000.0000.0000.000
193A240ASP-1-0.937-0.97421.1930.0610.0610.0000.0000.0000.000
194A241TRP0-0.055-0.02719.6410.0260.0260.0000.0000.0000.000
195A242LEU00.002-0.00716.7940.0350.0350.0000.0000.0000.000
196A243LYS10.8710.94217.915-0.070-0.0700.0000.0000.0000.000
197A244GLY00.0100.00518.1440.0270.0270.0000.0000.0000.000
198A245HIS00.0300.01316.5850.0720.0720.0000.0000.0000.000
199A246LEU00.002-0.00912.4760.0840.0840.0000.0000.0000.000
200A247ASP-1-0.819-0.88013.5720.2230.2230.0000.0000.0000.000
201A248ALA0-0.024-0.00115.2320.0410.0410.0000.0000.0000.000
202A249LEU00.009-0.01210.3990.0800.0800.0000.0000.0000.000
203A250ARG10.9030.92710.6510.0230.0230.0000.0000.0000.000
204A251ALA0-0.056-0.01411.6210.0470.0470.0000.0000.0000.000
205A252GLN0-0.092-0.03810.8210.0870.0870.0000.0000.0000.000
206A253GLY0-0.012-0.0038.5680.2310.2310.0000.0000.0000.000
207A254MET0-0.0510.0006.5001.0611.0610.0000.0000.0000.000
208A255PRO0-0.007-0.0062.258-1.718-1.4522.111-1.226-1.150-0.004
209A256ILE00.0130.0064.5670.0330.103-0.001-0.018-0.0510.000
210A257VAL0-0.009-0.0016.012-0.382-0.3820.0000.0000.0000.000
211A258ALA0-0.028-0.0028.4400.1760.1760.0000.0000.0000.000
212A259ILE00.0180.00712.113-0.108-0.1080.0000.0000.0000.000
213A260ASP-1-0.677-0.82214.443-0.112-0.1120.0000.0000.0000.000
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