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: 5N3RZ

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2288459.629026
FMO2-HF: Nuclear repulsion 2210429.844565
FMO2-HF: Total energy -78029.78446
FMO2-MP2: Total energy -78256.811346


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.
-20.799-20.88611.161-5.127-5.9480.044
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 : 0.046 / 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].
3A11LYS10.9630.9903.494-1.0890.6270.004-0.812-0.9090.001
4A12GLU-1-0.875-0.9375.9100.2090.2090.0000.0000.0000.000
5A13GLU-1-0.808-0.9308.335-0.950-0.9500.0000.0000.0000.000
6A14ASP-1-0.835-0.8778.3800.0520.0520.0000.0000.0000.000
7A15VAL00.0030.0047.4130.3040.3040.0000.0000.0000.000
8A16LEU00.0160.00710.1600.0450.0450.0000.0000.0000.000
9A17LYS10.8300.90812.4410.0920.0920.0000.0000.0000.000
10A18PHE00.022-0.0159.0560.0030.0030.0000.0000.0000.000
11A19LEU0-0.0220.00014.229-0.023-0.0230.0000.0000.0000.000
12A20ALA0-0.005-0.00416.045-0.031-0.0310.0000.0000.0000.000
13A21ALA0-0.024-0.00417.828-0.037-0.0370.0000.0000.0000.000
14A22GLY00.0140.00818.753-0.005-0.0050.0000.0000.0000.000
15A23THR00.002-0.01814.285-0.007-0.0070.0000.0000.0000.000
16A24HIS00.0390.00815.2200.1430.1430.0000.0000.0000.000
17A25LEU0-0.064-0.01016.833-0.010-0.0100.0000.0000.0000.000
18A26GLY00.0800.04020.6320.0080.0080.0000.0000.0000.000
19A27GLY00.001-0.00122.145-0.066-0.0660.0000.0000.0000.000
20A28THR00.017-0.00225.6230.0330.0330.0000.0000.0000.000
21A29ASN0-0.0090.00227.907-0.013-0.0130.0000.0000.0000.000
22A30LEU0-0.001-0.01022.0560.0420.0420.0000.0000.0000.000
23A31ASP-1-0.828-0.90824.0160.5820.5820.0000.0000.0000.000
24A32PHE00.0610.01024.0060.0630.0630.0000.0000.0000.000
25A33GLN0-0.0020.00921.8260.0160.0160.0000.0000.0000.000
26A34MET0-0.035-0.01617.9940.1540.1540.0000.0000.0000.000
27A35GLU-1-0.935-0.95919.4070.8150.8150.0000.0000.0000.000
28A36GLN0-0.060-0.03616.8540.1300.1300.0000.0000.0000.000
29A37TYR0-0.034-0.03813.9880.3320.3320.0000.0000.0000.000
30A38ILE0-0.0240.00915.5310.1160.1160.0000.0000.0000.000
31A39TYR0-0.064-0.03815.0780.0330.0330.0000.0000.0000.000
32A40LYS10.9690.97917.081-0.860-0.8600.0000.0000.0000.000
33A41ARG10.8880.95520.361-0.467-0.4670.0000.0000.0000.000
34A42LYS10.9470.98321.536-0.531-0.5310.0000.0000.0000.000
35A43SER00.0620.02125.193-0.002-0.0020.0000.0000.0000.000
36A44ASP-1-0.904-0.94827.0140.4280.4280.0000.0000.0000.000
37A45GLY00.0240.00928.395-0.009-0.0090.0000.0000.0000.000
38A46ILE0-0.050-0.01123.1870.0300.0300.0000.0000.0000.000
39A47TYR00.014-0.00621.9180.0050.0050.0000.0000.0000.000
40A48ILE0-0.060-0.03316.7600.0060.0060.0000.0000.0000.000
41A49ILE00.0430.01214.7200.0590.0590.0000.0000.0000.000
42A50ASN0-0.027-0.02611.1780.3520.3520.0000.0000.0000.000
43A51LEU00.0680.02310.0800.2470.2470.0000.0000.0000.000
44A52LYS10.9520.9886.168-3.419-3.4190.0000.0000.0000.000
45A53ARG10.8220.8877.453-2.585-2.5850.0000.0000.0000.000
46A54THR0-0.013-0.0239.6950.1010.1010.0000.0000.0000.000
47A55TRP00.004-0.0171.811-11.049-14.10910.186-3.591-3.5350.038
48A56GLU-1-0.809-0.8715.4565.8925.8920.0000.0000.0000.000
49A57LYS10.9300.9716.412-2.772-2.7720.0000.0000.0000.000
50A58LEU00.0120.0157.987-0.526-0.5260.0000.0000.0000.000
51A59LEU00.0040.0042.661-2.490-1.2330.971-0.724-1.5040.005
52A60LEU0-0.043-0.0216.769-0.781-0.7810.0000.0000.0000.000
53A61ALA00.0290.0049.660-0.392-0.3920.0000.0000.0000.000
54A62ALA00.0130.0038.557-0.224-0.2240.0000.0000.0000.000
55A63ARG10.9590.9705.979-1.361-1.3610.0000.0000.0000.000
56A64ALA0-0.0020.00310.770-0.122-0.1220.0000.0000.0000.000
57A65ILE0-0.006-0.00813.751-0.074-0.0740.0000.0000.0000.000
58A66VAL0-0.069-0.03911.891-0.071-0.0710.0000.0000.0000.000
59A67ALA0-0.038-0.01114.574-0.057-0.0570.0000.0000.0000.000
60A68ILE0-0.056-0.00716.6190.0060.0060.0000.0000.0000.000
61A69GLU-1-0.809-0.88519.655-0.025-0.0250.0000.0000.0000.000
62A70ASN0-0.001-0.01321.603-0.053-0.0530.0000.0000.0000.000
63A71PRO0-0.031-0.01520.3440.0300.0300.0000.0000.0000.000
64A72ALA00.0420.03021.6400.0340.0340.0000.0000.0000.000
65A73ASP-1-0.769-0.86023.4990.0610.0610.0000.0000.0000.000
66A74VAL0-0.012-0.00318.6160.0420.0420.0000.0000.0000.000
67A75SER00.0210.01021.854-0.027-0.0270.0000.0000.0000.000
68A76VAL0-0.059-0.01919.6650.0500.0500.0000.0000.0000.000
69A77ILE00.0220.00722.595-0.033-0.0330.0000.0000.0000.000
70A78SER0-0.035-0.01823.8860.0570.0570.0000.0000.0000.000
71A79SER0-0.005-0.00426.247-0.033-0.0330.0000.0000.0000.000
72A80ARG10.8020.87324.736-0.430-0.4300.0000.0000.0000.000
73A81ASN00.0740.02828.3460.0210.0210.0000.0000.0000.000
74A82THR0-0.047-0.02625.057-0.006-0.0060.0000.0000.0000.000
75A83GLY00.0600.02723.9350.0090.0090.0000.0000.0000.000
76A84GLN0-0.042-0.00524.304-0.022-0.0220.0000.0000.0000.000
77A85ARG10.8630.93225.332-0.089-0.0890.0000.0000.0000.000
78A86ALA00.0140.00620.767-0.025-0.0250.0000.0000.0000.000
79A87VAL00.0430.02221.376-0.019-0.0190.0000.0000.0000.000
80A88LEU00.0190.01022.712-0.026-0.0260.0000.0000.0000.000
81A89LYS10.8920.95221.506-0.003-0.0030.0000.0000.0000.000
82A90PHE00.0470.01114.880-0.038-0.0380.0000.0000.0000.000
83A91ALA00.0180.02419.658-0.036-0.0360.0000.0000.0000.000
84A92ALA0-0.035-0.01122.195-0.030-0.0300.0000.0000.0000.000
85A93ALA0-0.053-0.01918.357-0.031-0.0310.0000.0000.0000.000
86A94THR0-0.025-0.02916.229-0.043-0.0430.0000.0000.0000.000
87A95GLY00.0390.02418.924-0.027-0.0270.0000.0000.0000.000
88A96ALA0-0.0130.01720.0970.0110.0110.0000.0000.0000.000
89A97THR00.015-0.01722.149-0.019-0.0190.0000.0000.0000.000
90A98PRO0-0.053-0.02024.9870.0330.0330.0000.0000.0000.000
91A99ILE00.001-0.00725.989-0.014-0.0140.0000.0000.0000.000
92A100ALA0-0.021-0.01327.8270.0270.0270.0000.0000.0000.000
93A101GLY0-0.017-0.01229.051-0.018-0.0180.0000.0000.0000.000
94A102ARG10.9240.94931.618-0.125-0.1250.0000.0000.0000.000
95A103PHE00.0650.04330.202-0.006-0.0060.0000.0000.0000.000
96A104THR0-0.035-0.03033.3250.0040.0040.0000.0000.0000.000
97A105PRO00.0130.01535.7970.0010.0010.0000.0000.0000.000
98A106GLY00.0250.00736.130-0.012-0.0120.0000.0000.0000.000
99A107THR0-0.084-0.05032.417-0.011-0.0110.0000.0000.0000.000
100A108PHE00.007-0.00927.736-0.004-0.0040.0000.0000.0000.000
101A109THR0-0.014-0.03933.044-0.008-0.0080.0000.0000.0000.000
102A110ASN0-0.050-0.01135.950-0.005-0.0050.0000.0000.0000.000
103A111GLN00.0070.02634.356-0.007-0.0070.0000.0000.0000.000
104A112ILE00.0110.01038.0120.0000.0000.0000.0000.0000.000
105A113GLN00.0160.00137.1920.0040.0040.0000.0000.0000.000
106A114ALA00.0250.01936.7390.0090.0090.0000.0000.0000.000
107A115ALA0-0.042-0.02435.0860.0070.0070.0000.0000.0000.000
108A116PHE0-0.023-0.03131.645-0.001-0.0010.0000.0000.0000.000
109A117ARG10.9110.95830.619-0.141-0.1410.0000.0000.0000.000
110A118GLU-1-0.905-0.92928.3860.0590.0590.0000.0000.0000.000
111A119PRO0-0.083-0.05225.0770.0010.0010.0000.0000.0000.000
112A120ARG10.8090.87123.246-0.055-0.0550.0000.0000.0000.000
113A121LEU0-0.044-0.01217.2640.0330.0330.0000.0000.0000.000
114A122LEU0-0.0090.01122.000-0.030-0.0300.0000.0000.0000.000
115A123VAL0-0.006-0.00617.3860.0640.0640.0000.0000.0000.000
116A124VAL00.006-0.00620.289-0.055-0.0550.0000.0000.0000.000
117A125THR00.003-0.01920.6680.0770.0770.0000.0000.0000.000
118A126ASP-1-0.814-0.91821.8120.5100.5100.0000.0000.0000.000
119A127PRO00.0390.02022.336-0.048-0.0480.0000.0000.0000.000
120A128ARG10.7930.90725.221-0.470-0.4700.0000.0000.0000.000
121A129ALA0-0.025-0.02327.823-0.031-0.0310.0000.0000.0000.000
122A130ASP-1-0.775-0.88125.5060.3270.3270.0000.0000.0000.000
123A131HIS00.0470.01928.0630.0080.0080.0000.0000.0000.000
124A132GLN0-0.038-0.01429.7750.0020.0020.0000.0000.0000.000
125A133PRO00.0270.01127.712-0.005-0.0050.0000.0000.0000.000
126A134LEU00.0150.01923.6430.0020.0020.0000.0000.0000.000
127A135THR0-0.020-0.01527.6700.0060.0060.0000.0000.0000.000
128A136GLU-1-0.723-0.82530.9030.1770.1770.0000.0000.0000.000
129A137ALA00.018-0.00226.639-0.014-0.0140.0000.0000.0000.000
130A138SER0-0.059-0.03628.765-0.006-0.0060.0000.0000.0000.000
131A139TYR0-0.036-0.02229.577-0.015-0.0150.0000.0000.0000.000
132A140VAL0-0.045-0.01629.992-0.015-0.0150.0000.0000.0000.000
133A141ASN0-0.067-0.02228.5540.0020.0020.0000.0000.0000.000
134A142LEU0-0.0180.01524.503-0.004-0.0040.0000.0000.0000.000
135A143PRO00.0170.01021.2020.0280.0280.0000.0000.0000.000
136A144THR0-0.016-0.03321.5310.0030.0030.0000.0000.0000.000
137A145ILE00.001-0.00115.1010.0900.0900.0000.0000.0000.000
138A146ALA00.0370.02018.014-0.087-0.0870.0000.0000.0000.000
139A147LEU0-0.0160.01215.8580.1550.1550.0000.0000.0000.000
140A148CYS0-0.061-0.03017.537-0.126-0.1260.0000.0000.0000.000
141A149ASN00.0660.02318.4910.1530.1530.0000.0000.0000.000
142A150THR00.013-0.01120.5400.0100.0100.0000.0000.0000.000
143A151ASP-1-0.831-0.89522.2350.5130.5130.0000.0000.0000.000
144A152SER0-0.037-0.01522.290-0.047-0.0470.0000.0000.0000.000
145A153PRO00.0140.01824.3630.0230.0230.0000.0000.0000.000
146A154LEU00.036-0.01519.9090.0170.0170.0000.0000.0000.000
147A155ARG10.9250.98223.697-0.373-0.3730.0000.0000.0000.000
148A156TYR00.0270.00426.039-0.012-0.0120.0000.0000.0000.000
149A157VAL0-0.0240.00119.520-0.013-0.0130.0000.0000.0000.000
150A158ASP-1-0.806-0.87320.2090.5250.5250.0000.0000.0000.000
151A159ILE0-0.070-0.03813.8230.1280.1280.0000.0000.0000.000
152A160ALA00.017-0.00216.492-0.050-0.0500.0000.0000.0000.000
153A161ILE0-0.001-0.01511.8110.2580.2580.0000.0000.0000.000
154A162PRO0-0.0090.02812.567-0.181-0.1810.0000.0000.0000.000
155A163CYS0-0.030-0.02214.1280.1720.1720.0000.0000.0000.000
156A164ASN00.0290.03216.483-0.151-0.1510.0000.0000.0000.000
157A165ASN00.0330.03419.420-0.034-0.0340.0000.0000.0000.000
158A166LYS10.9900.99721.043-0.451-0.4510.0000.0000.0000.000
159A167GLY0-0.002-0.01123.346-0.053-0.0530.0000.0000.0000.000
160A168ALA00.031-0.00422.7800.0290.0290.0000.0000.0000.000
161A169HIS00.0230.01221.5060.0170.0170.0000.0000.0000.000
162A170SER00.0230.01218.2580.0350.0350.0000.0000.0000.000
163A171VAL00.0220.01418.0360.0540.0540.0000.0000.0000.000
164A172GLY00.007-0.00119.1620.0060.0060.0000.0000.0000.000
165A173LEU0-0.029-0.01314.578-0.042-0.0420.0000.0000.0000.000
166A174MET00.0000.00512.3440.0570.0570.0000.0000.0000.000
167A175TRP00.009-0.00214.2090.0390.0390.0000.0000.0000.000
168A176TRP0-0.028-0.01912.775-0.046-0.0460.0000.0000.0000.000
169A177MET0-0.015-0.0129.6050.0540.0540.0000.0000.0000.000
170A178LEU00.0020.00610.551-0.052-0.0520.0000.0000.0000.000
171A179ALA0-0.003-0.00311.788-0.131-0.1310.0000.0000.0000.000
172A180ARG10.7510.8527.6460.1220.1220.0000.0000.0000.000
173A181GLU-1-0.773-0.8916.200-1.715-1.7150.0000.0000.0000.000
174A182VAL00.0080.0148.857-0.241-0.2410.0000.0000.0000.000
175A183LEU00.006-0.00511.689-0.127-0.1270.0000.0000.0000.000
176A184ARG10.8290.9187.5681.4781.4780.0000.0000.0000.000
177A185MET0-0.109-0.0505.775-0.153-0.1530.0000.0000.0000.000
178A186ARG10.8880.9339.9340.2410.2410.0000.0000.0000.000
179A187GLY0-0.0320.00312.4900.0280.0280.0000.0000.0000.000
180A188THR0-0.037-0.01313.8900.0620.0620.0000.0000.0000.000
181A189ILE0-0.010-0.00112.3050.0580.0580.0000.0000.0000.000
182A190SER00.0250.01712.595-0.168-0.1680.0000.0000.0000.000
183A191ARG10.9220.9536.3862.4432.4430.0000.0000.0000.000
184A192GLU-1-0.899-0.9377.687-2.795-2.7950.0000.0000.0000.000
185A193HIS0-0.028-0.0279.980-0.029-0.0290.0000.0000.0000.000
186A194PRO0-0.033-0.03312.520-0.022-0.0220.0000.0000.0000.000
187A195TRP0-0.019-0.00413.4260.0370.0370.0000.0000.0000.000
188A196GLU-1-0.807-0.91315.133-0.421-0.4210.0000.0000.0000.000
189A197VAL0-0.051-0.00517.8990.0720.0720.0000.0000.0000.000
190A198MET00.0430.02917.721-0.016-0.0160.0000.0000.0000.000
191A199PRO00.009-0.01316.5630.0320.0320.0000.0000.0000.000
192A200ASP-1-0.836-0.91419.0390.0420.0420.0000.0000.0000.000
193A201LEU0-0.033-0.01622.0350.0130.0130.0000.0000.0000.000
194A202TYR00.002-0.01417.803-0.017-0.0170.0000.0000.0000.000
195A203PHE0-0.0150.00119.8240.0360.0360.0000.0000.0000.000
196A204TYR00.0100.01424.218-0.033-0.0330.0000.0000.0000.000
197A205ARG10.9740.98927.434-0.071-0.0710.0000.0000.0000.000