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: YNYN2

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2296498.923774
FMO2-HF: Nuclear repulsion 2218469.046959
FMO2-HF: Total energy -78029.876815
FMO2-MP2: Total energy -78256.919774


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.
-22.708-24.08212.313-5.225-5.7140.049
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 : 0.051 / q_NPA : 0.013
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].
3A11LYS10.8980.9513.786-1.3370.075-0.004-0.631-0.7770.002
4A12GLU-1-0.867-0.9296.2070.1210.1210.0000.0000.0000.000
5A13GLU-1-0.793-0.9148.350-1.137-1.1370.0000.0000.0000.000
6A14ASP-1-0.813-0.8658.733-0.006-0.0060.0000.0000.0000.000
7A15VAL00.0160.0107.3620.3160.3160.0000.0000.0000.000
8A16LEU00.0200.01310.1390.0320.0320.0000.0000.0000.000
9A17LYS10.8130.89212.3040.0650.0650.0000.0000.0000.000
10A18PHE00.016-0.0198.725-0.021-0.0210.0000.0000.0000.000
11A19LEU0-0.0060.00814.064-0.023-0.0230.0000.0000.0000.000
12A20ALA00.003-0.00515.814-0.038-0.0380.0000.0000.0000.000
13A21ALA0-0.022-0.00517.501-0.041-0.0410.0000.0000.0000.000
14A22GLY00.0170.00818.6890.0020.0020.0000.0000.0000.000
15A23THR0-0.019-0.01013.881-0.062-0.0620.0000.0000.0000.000
16A24HIS00.0550.01815.2630.1640.1640.0000.0000.0000.000
17A25LEU0-0.073-0.02416.816-0.018-0.0180.0000.0000.0000.000
18A26GLY00.0690.03620.6690.0110.0110.0000.0000.0000.000
19A27GLY00.0230.00922.098-0.072-0.0720.0000.0000.0000.000
20A28THR00.006-0.00825.4130.0340.0340.0000.0000.0000.000
21A29ASN0-0.0190.00227.609-0.019-0.0190.0000.0000.0000.000
22A30LEU0-0.010-0.01121.8990.0490.0490.0000.0000.0000.000
23A31ASP-1-0.806-0.89924.0240.6170.6170.0000.0000.0000.000
24A32PHE00.0580.00923.8930.0670.0670.0000.0000.0000.000
25A33GLN0-0.0150.00421.9760.0100.0100.0000.0000.0000.000
26A34MET0-0.011-0.00118.0290.1640.1640.0000.0000.0000.000
27A35GLU-1-0.938-0.95719.3610.8350.8350.0000.0000.0000.000
28A36GLN0-0.048-0.03316.8920.1350.1350.0000.0000.0000.000
29A37TYR0-0.038-0.03714.1810.3350.3350.0000.0000.0000.000
30A38ILE00.0020.02315.7410.0960.0960.0000.0000.0000.000
31A39TYR0-0.036-0.02814.6950.0840.0840.0000.0000.0000.000
32A40LYS10.9360.97016.709-0.909-0.9090.0000.0000.0000.000
33A41ARG10.8880.94220.088-0.481-0.4810.0000.0000.0000.000
34A42LYS10.9430.98121.847-0.517-0.5170.0000.0000.0000.000
35A43SER00.0390.00925.181-0.001-0.0010.0000.0000.0000.000
36A44ASP-1-0.876-0.93826.9630.4400.4400.0000.0000.0000.000
37A45GLY00.0430.02428.261-0.012-0.0120.0000.0000.0000.000
38A46ILE0-0.073-0.02022.8990.0310.0310.0000.0000.0000.000
39A47TYR00.0230.00521.8130.0010.0010.0000.0000.0000.000
40A48ILE0-0.061-0.03216.5150.0080.0080.0000.0000.0000.000
41A49ILE00.0530.01614.9570.0670.0670.0000.0000.0000.000
42A50ASN0-0.054-0.03711.2050.3690.3690.0000.0000.0000.000
43A51LEU00.0650.0169.9400.2960.2960.0000.0000.0000.000
44A52LYS10.9520.9925.592-4.004-4.0040.0000.0000.0000.000
45A53ARG10.8600.9067.642-2.564-2.5640.0000.0000.0000.000
46A54THR0-0.019-0.02310.0740.0060.0060.0000.0000.0000.000
47A55TRP00.019-0.0101.775-11.508-15.47311.365-3.888-3.5120.041
48A56GLU-1-0.834-0.8905.6096.0816.0810.0000.0000.0000.000
49A57LYS10.9170.9616.537-2.738-2.7380.0000.0000.0000.000
50A58LEU0-0.0040.0087.909-0.522-0.5220.0000.0000.0000.000
51A59LEU00.002-0.0012.588-2.189-1.0100.952-0.706-1.4250.006
52A60LEU0-0.041-0.0197.040-0.767-0.7670.0000.0000.0000.000
53A61ALA00.0380.01110.097-0.413-0.4130.0000.0000.0000.000
54A62ALA00.008-0.0048.793-0.244-0.2440.0000.0000.0000.000
55A63ARG10.9600.9716.629-1.804-1.8040.0000.0000.0000.000
56A64ALA0-0.013-0.00211.163-0.144-0.1440.0000.0000.0000.000
57A65ILE00.005-0.00714.179-0.096-0.0960.0000.0000.0000.000
58A66VAL0-0.072-0.03812.167-0.085-0.0850.0000.0000.0000.000
59A67ALA0-0.040-0.00914.842-0.073-0.0730.0000.0000.0000.000
60A68ILE0-0.056-0.00916.9020.0000.0000.0000.0000.0000.000
61A69GLU-1-0.816-0.88819.9290.0370.0370.0000.0000.0000.000
62A70ASN0-0.017-0.02022.120-0.054-0.0540.0000.0000.0000.000
63A71PRO0-0.029-0.01520.2970.0320.0320.0000.0000.0000.000
64A72ALA00.0590.04121.9060.0370.0370.0000.0000.0000.000
65A73ASP-1-0.757-0.83823.9120.1060.1060.0000.0000.0000.000
66A74VAL0-0.009-0.00419.0720.0440.0440.0000.0000.0000.000
67A75SER00.0160.00822.388-0.026-0.0260.0000.0000.0000.000
68A76VAL0-0.035-0.01820.0220.0520.0520.0000.0000.0000.000
69A77ILE00.001-0.00122.846-0.036-0.0360.0000.0000.0000.000
70A78SER0-0.025-0.02323.9820.0620.0620.0000.0000.0000.000
71A79SER0-0.004-0.01526.264-0.035-0.0350.0000.0000.0000.000
72A80ARG10.7890.86024.656-0.479-0.4790.0000.0000.0000.000
73A81ASN00.0760.03028.1250.0270.0270.0000.0000.0000.000
74A82THR0-0.052-0.02524.811-0.005-0.0050.0000.0000.0000.000
75A83GLY00.0780.03823.7960.0140.0140.0000.0000.0000.000
76A84GLN0-0.065-0.01824.314-0.024-0.0240.0000.0000.0000.000
77A85ARG10.8490.91625.042-0.114-0.1140.0000.0000.0000.000
78A86ALA00.0100.01020.676-0.024-0.0240.0000.0000.0000.000
79A87VAL00.0570.02521.163-0.013-0.0130.0000.0000.0000.000
80A88LEU00.0170.01222.681-0.026-0.0260.0000.0000.0000.000
81A89LYS10.8890.94821.146-0.031-0.0310.0000.0000.0000.000
82A90PHE00.0440.01314.929-0.039-0.0390.0000.0000.0000.000
83A91ALA00.0240.03219.643-0.035-0.0350.0000.0000.0000.000
84A92ALA0-0.032-0.01622.294-0.033-0.0330.0000.0000.0000.000
85A93ALA0-0.055-0.01217.952-0.035-0.0350.0000.0000.0000.000
86A94THR0-0.036-0.04216.260-0.042-0.0420.0000.0000.0000.000
87A95GLY00.0510.02318.944-0.022-0.0220.0000.0000.0000.000
88A96ALA0-0.0170.01420.2960.0090.0090.0000.0000.0000.000
89A97THR00.030-0.01222.342-0.023-0.0230.0000.0000.0000.000
90A98PRO0-0.054-0.02525.2970.0350.0350.0000.0000.0000.000
91A99ILE0-0.004-0.01026.187-0.015-0.0150.0000.0000.0000.000
92A100ALA0-0.007-0.00427.8990.0290.0290.0000.0000.0000.000
93A101GLY0-0.021-0.00928.960-0.020-0.0200.0000.0000.0000.000
94A102ARG10.8980.92431.655-0.144-0.1440.0000.0000.0000.000
95A103PHE00.0520.02930.684-0.013-0.0130.0000.0000.0000.000
96A104THR0-0.0040.00433.2630.0020.0020.0000.0000.0000.000
97A105PRO0-0.0070.00735.9020.0030.0030.0000.0000.0000.000
98A106GLY00.0380.01736.450-0.014-0.0140.0000.0000.0000.000
99A107THR0-0.068-0.04033.064-0.011-0.0110.0000.0000.0000.000
100A108PHE00.010-0.01028.091-0.006-0.0060.0000.0000.0000.000
101A109THR0-0.028-0.03233.309-0.001-0.0010.0000.0000.0000.000
102A110ASN0-0.036-0.01436.407-0.007-0.0070.0000.0000.0000.000
103A111GLN0-0.0130.00734.368-0.011-0.0110.0000.0000.0000.000
104A112ILE00.0110.00638.4900.0000.0000.0000.0000.0000.000
105A113GLN00.0320.01637.623-0.001-0.0010.0000.0000.0000.000
106A114ALA00.0220.02036.9100.0110.0110.0000.0000.0000.000
107A115ALA0-0.022-0.01535.6750.0060.0060.0000.0000.0000.000
108A116PHE0-0.035-0.03832.4820.0020.0020.0000.0000.0000.000
109A117ARG10.8850.94731.342-0.163-0.1630.0000.0000.0000.000
110A118GLU-1-0.901-0.92629.1820.0930.0930.0000.0000.0000.000
111A119PRO0-0.082-0.04625.8150.0000.0000.0000.0000.0000.000
112A120ARG10.7980.84624.177-0.107-0.1070.0000.0000.0000.000
113A121LEU0-0.041-0.00817.7530.0330.0330.0000.0000.0000.000
114A122LEU0-0.0190.00522.225-0.034-0.0340.0000.0000.0000.000
115A123VAL0-0.001-0.00317.7160.0710.0710.0000.0000.0000.000
116A124VAL0-0.005-0.00420.641-0.061-0.0610.0000.0000.0000.000
117A125THR00.008-0.01320.7440.0850.0850.0000.0000.0000.000
118A126ASP-1-0.821-0.92022.2430.5520.5520.0000.0000.0000.000
119A127PRO00.0540.02722.476-0.053-0.0530.0000.0000.0000.000
120A128ARG10.7840.89225.415-0.499-0.4990.0000.0000.0000.000
121A129ALA0-0.046-0.02627.847-0.033-0.0330.0000.0000.0000.000
122A130ASP-1-0.740-0.85025.4970.3660.3660.0000.0000.0000.000
123A131HIS00.0380.01328.1030.0110.0110.0000.0000.0000.000
124A132GLN0-0.014-0.00129.7260.0030.0030.0000.0000.0000.000
125A133PRO00.0100.00528.034-0.005-0.0050.0000.0000.0000.000
126A134LEU00.0140.00923.7740.0040.0040.0000.0000.0000.000
127A135THR0-0.020-0.01127.7210.0030.0030.0000.0000.0000.000
128A136GLU-1-0.705-0.82431.0880.2040.2040.0000.0000.0000.000
129A137ALA00.0130.00427.121-0.014-0.0140.0000.0000.0000.000
130A138SER0-0.063-0.04628.808-0.008-0.0080.0000.0000.0000.000
131A139TYR0-0.040-0.02929.798-0.016-0.0160.0000.0000.0000.000
132A140VAL0-0.040-0.01330.660-0.019-0.0190.0000.0000.0000.000
133A141ASN0-0.071-0.02729.1030.0000.0000.0000.0000.0000.000
134A142LEU0-0.0120.02425.1810.0020.0020.0000.0000.0000.000
135A143PRO00.0250.01121.8040.0270.0270.0000.0000.0000.000
136A144THR0-0.016-0.03421.9400.0020.0020.0000.0000.0000.000
137A145ILE00.0050.00515.6810.0980.0980.0000.0000.0000.000
138A146ALA00.0230.00618.024-0.094-0.0940.0000.0000.0000.000
139A147LEU0-0.0200.01416.2350.1590.1590.0000.0000.0000.000
140A148CYS0-0.062-0.03017.730-0.129-0.1290.0000.0000.0000.000
141A149ASN00.0650.01918.7250.1440.1440.0000.0000.0000.000
142A150THR00.000-0.00820.5150.0080.0080.0000.0000.0000.000
143A151ASP-1-0.824-0.88922.2710.5460.5460.0000.0000.0000.000
144A152SER0-0.028-0.01922.316-0.050-0.0500.0000.0000.0000.000
145A153PRO0-0.0070.01023.8620.0400.0400.0000.0000.0000.000
146A154LEU00.021-0.01219.7680.0040.0040.0000.0000.0000.000
147A155ARG10.9120.96823.600-0.399-0.3990.0000.0000.0000.000
148A156TYR00.0380.01625.666-0.028-0.0280.0000.0000.0000.000
149A157VAL0-0.0120.00019.586-0.014-0.0140.0000.0000.0000.000
150A158ASP-1-0.807-0.87220.2040.6190.6190.0000.0000.0000.000
151A159ILE0-0.075-0.04714.0680.1380.1380.0000.0000.0000.000
152A160ALA00.0300.00316.770-0.018-0.0180.0000.0000.0000.000
153A161ILE00.003-0.00512.0390.2630.2630.0000.0000.0000.000
154A162PRO0-0.0140.02212.745-0.187-0.1870.0000.0000.0000.000
155A163CYS0-0.033-0.02514.1980.1900.1900.0000.0000.0000.000
156A164ASN00.0520.03016.479-0.160-0.1600.0000.0000.0000.000
157A165ASN00.0070.01819.689-0.076-0.0760.0000.0000.0000.000
158A166LYS10.9830.99220.999-0.497-0.4970.0000.0000.0000.000
159A167GLY00.0220.01322.937-0.058-0.0580.0000.0000.0000.000
160A168ALA00.008-0.01522.4670.0330.0330.0000.0000.0000.000
161A169HIS00.0240.00921.4580.0150.0150.0000.0000.0000.000
162A170SER00.0250.02617.7090.0370.0370.0000.0000.0000.000
163A171VAL00.0120.01017.9210.0550.0550.0000.0000.0000.000
164A172GLY00.0130.00218.9890.0050.0050.0000.0000.0000.000
165A173LEU0-0.025-0.00914.118-0.038-0.0380.0000.0000.0000.000
166A174MET0-0.018-0.00612.3430.0680.0680.0000.0000.0000.000
167A175TRP00.009-0.00714.0960.0470.0470.0000.0000.0000.000
168A176TRP0-0.042-0.02912.382-0.043-0.0430.0000.0000.0000.000
169A177MET0-0.004-0.0019.2520.0600.0600.0000.0000.0000.000
170A178LEU00.0080.00910.398-0.050-0.0500.0000.0000.0000.000
171A179ALA0-0.006-0.00411.928-0.119-0.1190.0000.0000.0000.000
172A180ARG10.7490.8537.3880.1450.1450.0000.0000.0000.000
173A181GLU-1-0.756-0.8796.022-1.759-1.7590.0000.0000.0000.000
174A182VAL00.0000.0088.734-0.206-0.2060.0000.0000.0000.000
175A183LEU00.002-0.00111.768-0.119-0.1190.0000.0000.0000.000
176A184ARG10.8110.9027.0521.5841.5840.0000.0000.0000.000
177A185MET0-0.103-0.0416.016-0.179-0.1790.0000.0000.0000.000
178A186ARG10.8840.9309.9360.1400.1400.0000.0000.0000.000
179A187GLY0-0.0160.00912.2730.0200.0200.0000.0000.0000.000
180A188THR0-0.035-0.01713.6180.0540.0540.0000.0000.0000.000
181A189ILE0-0.018-0.00412.0200.0670.0670.0000.0000.0000.000
182A190SER00.0300.00212.026-0.171-0.1710.0000.0000.0000.000
183A191ARG10.8890.9406.1942.3762.3760.0000.0000.0000.000
184A192GLU-1-0.868-0.9027.028-3.059-3.0590.0000.0000.0000.000
185A193HIS0-0.023-0.0269.289-0.016-0.0160.0000.0000.0000.000
186A194PRO0-0.030-0.02811.757-0.021-0.0210.0000.0000.0000.000
187A195TRP0-0.0100.00213.0020.0140.0140.0000.0000.0000.000
188A196GLU-1-0.798-0.91114.617-0.401-0.4010.0000.0000.0000.000
189A197VAL0-0.053-0.00317.5140.0770.0770.0000.0000.0000.000
190A198MET00.0500.03617.160-0.013-0.0130.0000.0000.0000.000
191A199PRO00.000-0.01916.0350.0360.0360.0000.0000.0000.000
192A200ASP-1-0.828-0.91918.4510.0640.0640.0000.0000.0000.000
193A201LEU0-0.0090.00221.5180.0130.0130.0000.0000.0000.000
194A202TYR00.0180.00117.497-0.022-0.0220.0000.0000.0000.000
195A203PHE0-0.0290.00119.4130.0320.0320.0000.0000.0000.000
196A204TYR00.0190.00923.893-0.034-0.0340.0000.0000.0000.000
197A205ARG10.9540.98627.051-0.103-0.1030.0000.0000.0000.000