Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4L3QN

Calculation Name: 3BCH-A-Xray372

Preferred Name: 40S ribosomal protein SA

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3BCH

Chain ID: A

ChEMBL ID: CHEMBL6119

UniProt ID: P08865

Base Structure: X-ray

Registration Date: 2023-09-26

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287132.726512
FMO2-HF: Nuclear repulsion 2209103.536942
FMO2-HF: Total energy -78029.18957
FMO2-MP2: Total energy -78256.203251


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:9:GLN)


Summations of interaction energy for fragment #1(A:9:GLN)
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.
-17.599-13.2484.032-3.482-4.9010.036
Interaction energy analysis for fragmet #1(A:9:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.009
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].
3A11LYS10.9800.9923.532-0.0261.6730.003-0.789-0.9130.001
4A12GLU-1-0.872-0.9345.9400.1860.1860.0000.0000.0000.000
5A13GLU-1-0.861-0.9538.362-0.839-0.8390.0000.0000.0000.000
6A14ASP-1-0.865-0.9238.247-0.050-0.0500.0000.0000.0000.000
7A15VAL0-0.020-0.0127.4710.3150.3150.0000.0000.0000.000
8A16LEU00.0180.00610.2070.0510.0510.0000.0000.0000.000
9A17LYS10.9260.97513.2340.1270.1270.0000.0000.0000.000
10A18PHE00.030-0.0079.2900.0070.0070.0000.0000.0000.000
11A19LEU0-0.032-0.00414.276-0.014-0.0140.0000.0000.0000.000
12A20ALA0-0.010-0.00416.095-0.028-0.0280.0000.0000.0000.000
13A21ALA0-0.025-0.00517.971-0.032-0.0320.0000.0000.0000.000
14A22GLY00.0090.00718.804-0.003-0.0030.0000.0000.0000.000
15A23THR00.000-0.02314.553-0.009-0.0090.0000.0000.0000.000
16A24HIS00.0460.01415.3300.1270.1270.0000.0000.0000.000
17A25LEU0-0.061-0.01216.886-0.003-0.0030.0000.0000.0000.000
18A26GLY00.0760.03620.6860.0050.0050.0000.0000.0000.000
19A27GLY0-0.001-0.00222.052-0.064-0.0640.0000.0000.0000.000
20A28THR0-0.001-0.01025.4940.0310.0310.0000.0000.0000.000
21A29ASN00.0080.00527.823-0.009-0.0090.0000.0000.0000.000
22A30LEU0-0.009-0.01222.0090.0400.0400.0000.0000.0000.000
23A31ASP-1-0.846-0.92123.9400.5480.5480.0000.0000.0000.000
24A32PHE00.0540.00823.9790.0620.0620.0000.0000.0000.000
25A33GLN00.0070.01421.7030.0240.0240.0000.0000.0000.000
26A34MET0-0.035-0.01918.0520.1450.1450.0000.0000.0000.000
27A35GLU-1-0.937-0.95819.3370.8070.8070.0000.0000.0000.000
28A36GLN0-0.049-0.02516.6590.1280.1280.0000.0000.0000.000
29A37TYR0-0.030-0.03613.7140.3290.3290.0000.0000.0000.000
30A38ILE0-0.0300.00315.4430.1070.1070.0000.0000.0000.000
31A39TYR0-0.080-0.04213.9430.0190.0190.0000.0000.0000.000
32A40LYS10.9790.98117.120-0.806-0.8060.0000.0000.0000.000
33A41ARG10.8940.95720.399-0.455-0.4550.0000.0000.0000.000
34A42LYS10.9200.97021.128-0.554-0.5540.0000.0000.0000.000
35A43SER00.0410.01025.2350.0000.0000.0000.0000.0000.000
36A44ASP-1-0.857-0.92727.1080.4100.4100.0000.0000.0000.000
37A45GLY00.0190.00628.456-0.008-0.0080.0000.0000.0000.000
38A46ILE0-0.0390.00323.2190.0300.0300.0000.0000.0000.000
39A47TYR00.011-0.00321.7610.0080.0080.0000.0000.0000.000
40A48ILE0-0.058-0.03316.7470.0000.0000.0000.0000.0000.000
41A49ILE00.0430.01714.5290.0600.0600.0000.0000.0000.000
42A50ASN0-0.020-0.02311.0500.3370.3370.0000.0000.0000.000
43A51LEU00.0630.01510.0970.2360.2360.0000.0000.0000.000
44A52LYS10.9560.9906.178-2.965-2.9650.0000.0000.0000.000
45A53ARG10.8030.8817.351-2.726-2.7260.0000.0000.0000.000
46A54THR0-0.003-0.0179.7220.0900.0900.0000.0000.0000.000
47A55TRP0-0.001-0.0052.110-9.258-7.9123.151-1.971-2.5260.029
48A56GLU-1-0.801-0.8715.4155.8355.8350.0000.0000.0000.000
49A57LYS10.9240.9686.387-2.867-2.8670.0000.0000.0000.000
50A58LEU00.0190.0158.221-0.507-0.5070.0000.0000.0000.000
51A59LEU0-0.0050.0042.808-2.575-1.2690.878-0.722-1.4620.006
52A60LEU0-0.046-0.0236.908-0.755-0.7550.0000.0000.0000.000
53A61ALA00.0280.0069.540-0.373-0.3730.0000.0000.0000.000
54A62ALA00.0120.0068.765-0.210-0.2100.0000.0000.0000.000
55A63ARG10.9610.9695.559-1.172-1.1720.0000.0000.0000.000
56A64ALA00.0010.00210.670-0.111-0.1110.0000.0000.0000.000
57A65ILE0-0.008-0.00613.796-0.068-0.0680.0000.0000.0000.000
58A66VAL0-0.072-0.04111.798-0.065-0.0650.0000.0000.0000.000
59A67ALA0-0.032-0.01014.599-0.053-0.0530.0000.0000.0000.000
60A68ILE0-0.055-0.00316.4770.0090.0090.0000.0000.0000.000
61A69GLU-1-0.843-0.91519.609-0.060-0.0600.0000.0000.0000.000
62A70ASN00.0140.01021.551-0.044-0.0440.0000.0000.0000.000
63A71PRO0-0.021-0.01320.7420.0290.0290.0000.0000.0000.000
64A72ALA00.0490.03021.8110.0320.0320.0000.0000.0000.000
65A73ASP-1-0.836-0.90523.9870.0550.0550.0000.0000.0000.000
66A74VAL0-0.040-0.01618.8160.0410.0410.0000.0000.0000.000
67A75SER00.0260.00922.022-0.025-0.0250.0000.0000.0000.000
68A76VAL0-0.053-0.01719.9410.0470.0470.0000.0000.0000.000
69A77ILE00.0350.01522.934-0.030-0.0300.0000.0000.0000.000
70A78SER0-0.034-0.02824.2830.0540.0540.0000.0000.0000.000
71A79SER0-0.0060.00926.667-0.031-0.0310.0000.0000.0000.000
72A80ARG10.8080.88924.882-0.393-0.3930.0000.0000.0000.000
73A81ASN00.0730.02928.6470.0200.0200.0000.0000.0000.000
74A82THR0-0.064-0.03725.144-0.007-0.0070.0000.0000.0000.000
75A83GLY00.0600.02924.3100.0070.0070.0000.0000.0000.000
76A84GLN0-0.051-0.01224.850-0.023-0.0230.0000.0000.0000.000
77A85ARG10.8810.94525.877-0.075-0.0750.0000.0000.0000.000
78A86ALA00.0110.00321.317-0.025-0.0250.0000.0000.0000.000
79A87VAL00.0380.02021.953-0.019-0.0190.0000.0000.0000.000
80A88LEU00.0220.01123.229-0.025-0.0250.0000.0000.0000.000
81A89LYS10.8710.94322.2940.0020.0020.0000.0000.0000.000
82A90PHE00.0610.02215.264-0.034-0.0340.0000.0000.0000.000
83A91ALA00.0210.01620.144-0.035-0.0350.0000.0000.0000.000
84A92ALA0-0.036-0.01022.650-0.028-0.0280.0000.0000.0000.000
85A93ALA0-0.056-0.02418.938-0.031-0.0310.0000.0000.0000.000
86A94THR0-0.044-0.02316.756-0.043-0.0430.0000.0000.0000.000
87A95GLY00.0590.03419.328-0.027-0.0270.0000.0000.0000.000
88A96ALA0-0.0100.01920.4410.0100.0100.0000.0000.0000.000
89A97THR00.007-0.02522.464-0.018-0.0180.0000.0000.0000.000
90A98PRO0-0.051-0.01725.3910.0320.0320.0000.0000.0000.000
91A99ILE00.004-0.00326.383-0.012-0.0120.0000.0000.0000.000
92A100ALA0-0.026-0.01528.3020.0250.0250.0000.0000.0000.000
93A101GLY0-0.019-0.01429.514-0.017-0.0170.0000.0000.0000.000
94A102ARG10.9180.94432.029-0.117-0.1170.0000.0000.0000.000
95A103PHE00.0690.04830.622-0.006-0.0060.0000.0000.0000.000
96A104THR0-0.040-0.03133.6480.0050.0050.0000.0000.0000.000
97A105PRO00.0130.01836.0370.0010.0010.0000.0000.0000.000
98A106GLY00.013-0.00436.302-0.011-0.0110.0000.0000.0000.000
99A107THR0-0.080-0.05532.673-0.011-0.0110.0000.0000.0000.000
100A108PHE00.0200.00327.989-0.004-0.0040.0000.0000.0000.000
101A109THR00.009-0.01533.154-0.009-0.0090.0000.0000.0000.000
102A110ASN0-0.025-0.00436.012-0.003-0.0030.0000.0000.0000.000
103A111GLN0-0.070-0.02834.026-0.004-0.0040.0000.0000.0000.000
104A112ILE00.0170.01738.0560.0000.0000.0000.0000.0000.000
105A113GLN00.002-0.01137.2730.0020.0020.0000.0000.0000.000
106A114ALA00.0240.02036.7020.0080.0080.0000.0000.0000.000
107A115ALA0-0.040-0.02034.9740.0060.0060.0000.0000.0000.000
108A116PHE0-0.021-0.03231.538-0.001-0.0010.0000.0000.0000.000
109A117ARG10.9641.00030.697-0.128-0.1280.0000.0000.0000.000
110A118GLU-1-0.915-0.93228.4280.0410.0410.0000.0000.0000.000
111A119PRO0-0.076-0.04625.2490.0030.0030.0000.0000.0000.000
112A120ARG10.9130.93722.775-0.044-0.0440.0000.0000.0000.000
113A121LEU0-0.037-0.01617.2940.0310.0310.0000.0000.0000.000
114A122LEU0-0.0100.01122.043-0.028-0.0280.0000.0000.0000.000
115A123VAL0-0.010-0.00317.6650.0620.0620.0000.0000.0000.000
116A124VAL00.013-0.00220.528-0.052-0.0520.0000.0000.0000.000
117A125THR00.004-0.02020.8180.0710.0710.0000.0000.0000.000
118A126ASP-1-0.842-0.94521.9870.4820.4820.0000.0000.0000.000
119A127PRO00.0430.02322.511-0.046-0.0460.0000.0000.0000.000
120A128ARG10.8640.94825.319-0.441-0.4410.0000.0000.0000.000
121A129ALA0-0.024-0.02427.960-0.029-0.0290.0000.0000.0000.000
122A130ASP-1-0.788-0.89525.9610.2970.2970.0000.0000.0000.000
123A131HIS00.0480.01828.1690.0070.0070.0000.0000.0000.000
124A132GLN0-0.045-0.01929.8650.0030.0030.0000.0000.0000.000
125A133PRO00.0240.01227.829-0.005-0.0050.0000.0000.0000.000
126A134LEU00.0150.01823.6930.0020.0020.0000.0000.0000.000
127A135THR0-0.006-0.00727.7290.0070.0070.0000.0000.0000.000
128A136GLU-1-0.741-0.83630.9360.1640.1640.0000.0000.0000.000
129A137ALA00.0250.00126.662-0.013-0.0130.0000.0000.0000.000
130A138SER0-0.061-0.04028.730-0.006-0.0060.0000.0000.0000.000
131A139TYR0-0.039-0.02429.535-0.008-0.0080.0000.0000.0000.000
132A140VAL0-0.050-0.01829.943-0.014-0.0140.0000.0000.0000.000
133A141ASN0-0.057-0.01528.4310.0010.0010.0000.0000.0000.000
134A142LEU0-0.0290.01124.496-0.005-0.0050.0000.0000.0000.000
135A143PRO00.0230.01321.1230.0280.0280.0000.0000.0000.000
136A144THR0-0.006-0.02921.5690.0000.0000.0000.0000.0000.000
137A145ILE0-0.005-0.00415.1790.0830.0830.0000.0000.0000.000
138A146ALA00.0290.01518.073-0.084-0.0840.0000.0000.0000.000
139A147LEU0-0.0250.00416.1430.1460.1460.0000.0000.0000.000
140A148CYS0-0.048-0.02217.651-0.115-0.1150.0000.0000.0000.000
141A149ASN00.0760.04418.5950.1530.1530.0000.0000.0000.000
142A150THR00.016-0.02020.4370.0100.0100.0000.0000.0000.000
143A151ASP-1-0.910-0.94022.3040.5000.5000.0000.0000.0000.000
144A152SER0-0.033-0.01922.356-0.050-0.0500.0000.0000.0000.000
145A153PRO00.0110.01624.3960.0230.0230.0000.0000.0000.000
146A154LEU00.042-0.01419.8270.0130.0130.0000.0000.0000.000
147A155ARG10.9310.98523.690-0.361-0.3610.0000.0000.0000.000
148A156TYR00.0230.00526.033-0.012-0.0120.0000.0000.0000.000
149A157VAL0-0.0350.00219.520-0.013-0.0130.0000.0000.0000.000
150A158ASP-1-0.812-0.88120.2010.4980.4980.0000.0000.0000.000
151A159ILE0-0.065-0.03413.7590.1250.1250.0000.0000.0000.000
152A160ALA00.019-0.00416.457-0.052-0.0520.0000.0000.0000.000
153A161ILE0-0.008-0.01811.9980.2430.2430.0000.0000.0000.000
154A162PRO0-0.0140.02012.599-0.173-0.1730.0000.0000.0000.000
155A163CYS0-0.028-0.01714.2600.1540.1540.0000.0000.0000.000
156A164ASN00.0390.04316.647-0.137-0.1370.0000.0000.0000.000
157A165ASN00.0310.03619.644-0.030-0.0300.0000.0000.0000.000
158A166LYS11.0021.01221.244-0.423-0.4230.0000.0000.0000.000
159A167GLY00.003-0.00923.571-0.052-0.0520.0000.0000.0000.000
160A168ALA00.0380.00023.0480.0260.0260.0000.0000.0000.000
161A169HIS00.0240.01521.7580.0150.0150.0000.0000.0000.000
162A170SER00.0170.00218.5610.0300.0300.0000.0000.0000.000
163A171VAL00.0320.01918.3170.0480.0480.0000.0000.0000.000
164A172GLY00.005-0.00519.4400.0030.0030.0000.0000.0000.000
165A173LEU0-0.030-0.01214.800-0.045-0.0450.0000.0000.0000.000
166A174MET0-0.0030.00612.5040.0380.0380.0000.0000.0000.000
167A175TRP00.0220.00214.7090.0320.0320.0000.0000.0000.000
168A176TRP0-0.027-0.02213.389-0.053-0.0530.0000.0000.0000.000
169A177MET0-0.005-0.01710.2920.0210.0210.0000.0000.0000.000
170A178LEU0-0.0040.00511.183-0.043-0.0430.0000.0000.0000.000
171A179ALA00.0070.00512.276-0.121-0.1210.0000.0000.0000.000
172A180ARG10.7670.8918.7870.0970.0970.0000.0000.0000.000
173A181GLU-1-0.822-0.9376.343-1.279-1.2790.0000.0000.0000.000
174A182VAL00.0160.0179.378-0.242-0.2420.0000.0000.0000.000
175A183LEU00.001-0.00612.039-0.128-0.1280.0000.0000.0000.000
176A184ARG10.8500.9327.8961.3541.3540.0000.0000.0000.000
177A185MET0-0.125-0.0536.143-0.164-0.1640.0000.0000.0000.000
178A186ARG10.8910.92810.0730.2410.2410.0000.0000.0000.000
179A187GLY0-0.042-0.00112.6950.0240.0240.0000.0000.0000.000
180A188THR0-0.034-0.00914.0910.0640.0640.0000.0000.0000.000
181A189ILE00.0010.00312.7630.0550.0550.0000.0000.0000.000
182A190SER00.0470.02513.099-0.207-0.2070.0000.0000.0000.000
183A191ARG10.9880.9786.6442.4612.4610.0000.0000.0000.000
184A192GLU-1-0.966-0.9748.031-2.978-2.9780.0000.0000.0000.000
185A193HIS0-0.030-0.01610.298-0.020-0.0200.0000.0000.0000.000
186A194PRO0-0.032-0.03312.928-0.009-0.0090.0000.0000.0000.000
187A195TRP00.0110.00613.8910.0320.0320.0000.0000.0000.000
188A196GLU-1-0.860-0.93715.787-0.425-0.4250.0000.0000.0000.000
189A197VAL0-0.037-0.00118.6590.0670.0670.0000.0000.0000.000
190A198MET00.0490.02618.481-0.013-0.0130.0000.0000.0000.000
191A199PRO0-0.013-0.02217.1870.0300.0300.0000.0000.0000.000
192A200ASP-1-0.843-0.91819.7930.0250.0250.0000.0000.0000.000
193A201LEU0-0.022-0.01422.7830.0140.0140.0000.0000.0000.000
194A202TYR0-0.016-0.01919.0790.0070.0070.0000.0000.0000.000
195A203PHE0-0.0050.01020.2120.0350.0350.0000.0000.0000.000
196A204TYR00.0060.00824.703-0.033-0.0330.0000.0000.0000.000
197A205ARG10.9760.99127.839-0.060-0.0600.0000.0000.0000.000