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: N9NRQ

Calculation Name: 2YMO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YMO

Chain ID: A

ChEMBL ID:

UniProt ID: C6KSX0

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2656916.158299
FMO2-HF: Nuclear repulsion 2563179.931539
FMO2-HF: Total energy -93736.226759
FMO2-MP2: Total energy -94001.677981


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:29:LEU)


Summations of interaction energy for fragment #1(A:29:LEU)
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.
-11.779-3.5567.555-4.398-11.379-0.021
Interaction energy analysis for fragmet #1(A:29:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / 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].
3A31CYS0-0.0650.0013.7510.7812.600-0.036-0.754-1.0290.002
4A32ASP-1-0.743-0.8846.5020.5410.5410.0000.0000.0000.000
5A33PHE00.017-0.0049.5830.0870.0870.0000.0000.0000.000
6A34ASN0-0.021-0.00312.594-0.119-0.1190.0000.0000.0000.000
7A35ASP-1-0.903-0.96913.1370.5320.5320.0000.0000.0000.000
8A36VAL0-0.061-0.0178.9040.0360.0360.0000.0000.0000.000
9A37TYR0-0.044-0.0296.813-0.421-0.4210.0000.0000.0000.000
10A38LYS10.8530.92812.681-0.658-0.6580.0000.0000.0000.000
11A39LEU00.0420.01115.229-0.031-0.0310.0000.0000.0000.000
12A40GLU-1-0.855-0.88818.0950.4170.4170.0000.0000.0000.000
13A41PHE0-0.048-0.04321.2700.0080.0080.0000.0000.0000.000
14A42HIS00.0130.01921.651-0.018-0.0180.0000.0000.0000.000
15A43PRO0-0.010-0.01926.399-0.015-0.0150.0000.0000.0000.000
16A44ASN0-0.037-0.02430.1730.0050.0050.0000.0000.0000.000
17A45GLN00.022-0.00424.1030.0140.0140.0000.0000.0000.000
18A46GLN00.0360.02029.155-0.007-0.0070.0000.0000.0000.000
19A47THR0-0.002-0.00126.496-0.010-0.0100.0000.0000.0000.000
20A48SER0-0.0110.01922.6690.0080.0080.0000.0000.0000.000
21A49VAL00.003-0.00819.0850.0070.0070.0000.0000.0000.000
22A50THR00.0090.00217.174-0.004-0.0040.0000.0000.0000.000
23A51LYS10.8360.92113.532-0.646-0.6460.0000.0000.0000.000
24A52LEU00.0280.01312.328-0.059-0.0590.0000.0000.0000.000
25A54ASN0-0.010-0.0237.323-0.081-0.0810.0000.0000.0000.000
26A55LEU0-0.009-0.0062.239-1.044-0.1322.916-1.040-2.788-0.001
27A56THR00.016-0.0083.174-0.586-0.0710.053-0.155-0.4120.000
28A57PRO0-0.0170.0112.427-2.688-1.1421.277-0.735-2.087-0.001
29A58ASN0-0.032-0.0243.0942.2611.6040.1020.767-0.2120.000
30A59VAL00.0280.0006.392-0.130-0.1300.0000.0000.0000.000
31A60LEU0-0.059-0.0288.682-0.094-0.0940.0000.0000.0000.000
32A61GLU-1-0.828-0.8952.673-9.291-6.8060.668-1.283-1.870-0.016
33A62LYS10.8920.9554.9931.3021.3020.0000.0000.0000.000
34A63VAL00.0420.0292.223-2.986-1.6342.570-1.161-2.762-0.005
35A64THR0-0.049-0.0043.5900.4280.7340.006-0.027-0.2850.000
36A65ILE00.0060.0055.7870.4430.388-0.001-0.0100.0660.000
37A66LYS10.9230.9768.494-0.927-0.9270.0000.0000.0000.000
38A67CYS0-0.083-0.01311.0960.0890.0890.0000.0000.0000.000
39A68GLY00.0730.04714.130-0.071-0.0710.0000.0000.0000.000
40A69SER0-0.076-0.07416.8350.0110.0110.0000.0000.0000.000
41A70ASP-1-0.797-0.87019.4270.1920.1920.0000.0000.0000.000
42A71LYS10.8310.90721.713-0.229-0.2290.0000.0000.0000.000
43A72LEU0-0.0090.01217.743-0.005-0.0050.0000.0000.0000.000
44A73ASN00.0300.01720.685-0.017-0.0170.0000.0000.0000.000
45A74TYR0-0.027-0.02216.428-0.009-0.0090.0000.0000.0000.000
46A75ASN00.0300.02019.216-0.015-0.0150.0000.0000.0000.000
47A76LEU00.014-0.00212.7250.0440.0440.0000.0000.0000.000
48A77TYR0-0.0550.00416.667-0.040-0.0400.0000.0000.0000.000
49A78PRO00.1160.03215.3350.0350.0350.0000.0000.0000.000
50A79PRO00.021-0.00616.266-0.006-0.0060.0000.0000.0000.000
51A80THR00.0320.00714.3960.0090.0090.0000.0000.0000.000
52A81CYS0-0.195-0.07110.824-0.095-0.0950.0000.0000.0000.000
53A82PHE00.0190.0179.734-0.010-0.0100.0000.0000.0000.000
54A83GLU-1-0.948-0.96712.316-0.233-0.2330.0000.0000.0000.000
55A117ILE0-0.035-0.03715.3690.0150.0150.0000.0000.0000.000
56A118ASN0-0.0110.00215.310-0.051-0.0510.0000.0000.0000.000
57A119GLU-1-0.914-0.97210.7710.1410.1410.0000.0000.0000.000
58A120VAL00.0030.01410.099-0.060-0.0600.0000.0000.0000.000
59A121SER0-0.045-0.0666.791-0.082-0.0820.0000.0000.0000.000
60A122PHE00.0580.0407.4640.0860.0860.0000.0000.0000.000
61A123ARG10.8770.9177.0330.9310.9310.0000.0000.0000.000
62A124ILE00.0400.0385.1080.2160.2160.0000.0000.0000.000
63A125PRO00.0630.0389.291-0.116-0.1160.0000.0000.0000.000
64A126PRO00.002-0.01612.243-0.047-0.0470.0000.0000.0000.000
65A127ASN0-0.032-0.01912.3110.1240.1240.0000.0000.0000.000
66A128MET00.0200.00015.557-0.021-0.0210.0000.0000.0000.000
67A129MET0-0.0130.01117.5100.0200.0200.0000.0000.0000.000
68A130PRO00.000-0.00115.729-0.023-0.0230.0000.0000.0000.000
69A131GLU-1-0.889-0.92613.782-0.235-0.2350.0000.0000.0000.000
70A132LYS10.8920.92914.4100.0630.0630.0000.0000.0000.000
71A133PRO0-0.009-0.00211.036-0.033-0.0330.0000.0000.0000.000
72A134ILE00.0400.04010.6370.0280.0280.0000.0000.0000.000
73A135TYR0-0.059-0.06510.6000.0270.0270.0000.0000.0000.000
74A137PHE0-0.003-0.01013.2490.0920.0920.0000.0000.0000.000
75A139GLU-1-0.797-0.89815.4780.2080.2080.0000.0000.0000.000
76A140ASN0-0.003-0.01919.074-0.042-0.0420.0000.0000.0000.000
77A141LYS10.9460.96621.293-0.148-0.1480.0000.0000.0000.000
78A142LYS10.9761.00625.001-0.204-0.2040.0000.0000.0000.000
79A158ASP-1-0.948-0.96629.1760.1180.1180.0000.0000.0000.000
80A159ILE0-0.056-0.02626.7670.0070.0070.0000.0000.0000.000
81A160ILE0-0.035-0.03020.6430.0020.0020.0000.0000.0000.000
82A161ASN0-0.0150.01719.747-0.013-0.0130.0000.0000.0000.000
83A162ARG10.8730.91517.732-0.242-0.2420.0000.0000.0000.000
84A163GLY00.0330.01713.5630.0460.0460.0000.0000.0000.000
85A164ILE0-0.052-0.02813.263-0.081-0.0810.0000.0000.0000.000
86A165VAL00.022-0.0057.4090.1480.1480.0000.0000.0000.000
87A166GLU-1-0.817-0.8728.9640.1090.1090.0000.0000.0000.000
88A167ILE0-0.015-0.0125.0380.1460.1460.0000.0000.0000.000
89A168ILE00.0110.0007.012-0.064-0.0640.0000.0000.0000.000
90A169ILE00.0150.0077.289-0.227-0.2270.0000.0000.0000.000
91A170PRO0-0.0390.0047.1450.1040.1040.0000.0000.0000.000
92A171SER00.0170.0009.7380.0460.0460.0000.0000.0000.000
93A172LEU0-0.061-0.03613.223-0.045-0.0450.0000.0000.0000.000
94A173ASN00.001-0.01015.1510.0710.0710.0000.0000.0000.000
95A174GLU-1-0.924-0.96218.018-0.305-0.3050.0000.0000.0000.000
96A175LYS10.9050.93918.6510.2300.2300.0000.0000.0000.000
97A176VAL0-0.0100.00416.599-0.013-0.0130.0000.0000.0000.000
98A177LYS10.8420.92619.1790.4080.4080.0000.0000.0000.000
99A178GLY00.025-0.00121.227-0.022-0.0220.0000.0000.0000.000
100A179CYS0-0.123-0.03123.5660.0150.0150.0000.0000.0000.000
101A180ASP-1-0.682-0.78424.832-0.268-0.2680.0000.0000.0000.000
102A181PHE0-0.041-0.04526.0470.0170.0170.0000.0000.0000.000
103A182THR0-0.074-0.05626.8060.0120.0120.0000.0000.0000.000
104A183THR00.002-0.00227.5780.0120.0120.0000.0000.0000.000
105A184SER00.0030.01029.346-0.009-0.0090.0000.0000.0000.000
106A185GLU-1-0.941-0.96429.298-0.164-0.1640.0000.0000.0000.000
107A186SER0-0.024-0.02823.984-0.015-0.0150.0000.0000.0000.000
108A187THR00.0430.00820.4800.0030.0030.0000.0000.0000.000
109A188ILE0-0.053-0.00518.219-0.017-0.0170.0000.0000.0000.000
110A189PHE0-0.001-0.00319.632-0.026-0.0260.0000.0000.0000.000
111A190SER0-0.028-0.01422.5000.0180.0180.0000.0000.0000.000
112A191LYS10.8820.94124.7300.2310.2310.0000.0000.0000.000
113A192GLY00.0390.02326.875-0.017-0.0170.0000.0000.0000.000
114A193TYR0-0.025-0.01129.1590.0070.0070.0000.0000.0000.000
115A194SER0-0.020-0.04031.995-0.001-0.0010.0000.0000.0000.000
116A195ILE00.0560.00434.4500.0010.0010.0000.0000.0000.000
117A196ASN00.023-0.00636.0840.0010.0010.0000.0000.0000.000
118A197GLU-1-0.842-0.88735.745-0.141-0.1410.0000.0000.0000.000
119A198ILE00.0320.02133.0220.0030.0030.0000.0000.0000.000
120A199SER0-0.0130.01536.5240.0040.0040.0000.0000.0000.000
121A200ASN00.026-0.01339.7590.0000.0000.0000.0000.0000.000
122A201LYS10.8040.93339.7100.1190.1190.0000.0000.0000.000
123A202SER0-0.025-0.02744.5070.0020.0020.0000.0000.0000.000
124A203SER00.0640.00647.158-0.002-0.0020.0000.0000.0000.000
125A204ASN00.0100.01048.3700.0010.0010.0000.0000.0000.000
126A205ASN00.0210.04543.245-0.005-0.0050.0000.0000.0000.000
127A206GLN00.032-0.00543.155-0.002-0.0020.0000.0000.0000.000
128A207GLN0-0.049-0.01841.4580.0000.0000.0000.0000.0000.000
129A208ASP-1-0.857-0.92936.297-0.131-0.1310.0000.0000.0000.000
130A209ILE0-0.054-0.01633.3520.0030.0030.0000.0000.0000.000
131A210VAL00.0130.00933.017-0.008-0.0080.0000.0000.0000.000
132A212THR00.0250.00029.290-0.009-0.0090.0000.0000.0000.000
133A213VAL0-0.0060.00223.2400.0040.0040.0000.0000.0000.000
134A214LYS10.8560.92826.7040.2220.2220.0000.0000.0000.000
135A215ALA00.0100.00721.572-0.010-0.0100.0000.0000.0000.000
136A216HIS10.8510.91619.7520.3770.3770.0000.0000.0000.000
137A217ALA00.0420.00718.814-0.035-0.0350.0000.0000.0000.000
138A218ASN00.005-0.01314.167-0.035-0.0350.0000.0000.0000.000
139A219ASP-1-0.809-0.87415.255-0.450-0.4500.0000.0000.0000.000
140A220LEU0-0.027-0.00612.571-0.032-0.0320.0000.0000.0000.000
141A221ILE0-0.014-0.01715.9300.0630.0630.0000.0000.0000.000
142A222GLY00.038-0.00717.764-0.050-0.0500.0000.0000.0000.000
143A223PHE0-0.048-0.03019.8700.0310.0310.0000.0000.0000.000
144A224LYS10.9520.97921.8880.2380.2380.0000.0000.0000.000
145A225CYS0-0.0490.00823.9850.0100.0100.0000.0000.0000.000
146A226PRO00.0660.02426.917-0.007-0.0070.0000.0000.0000.000
147A227SER00.0230.01327.6940.0020.0020.0000.0000.0000.000
148A228ASN0-0.017-0.02228.7590.0050.0050.0000.0000.0000.000
149A229TYR0-0.0120.00130.4460.0090.0090.0000.0000.0000.000
150A230SER00.0380.03629.887-0.010-0.0100.0000.0000.0000.000
151A231VAL0-0.004-0.02325.3500.0000.0000.0000.0000.0000.000
152A232GLU-1-0.972-0.95228.535-0.145-0.1450.0000.0000.0000.000
153A233PRO00.034-0.01526.412-0.001-0.0010.0000.0000.0000.000
154A234HIS00.0550.01424.963-0.007-0.0070.0000.0000.0000.000
155A235ASP-1-0.857-0.92022.638-0.255-0.2550.0000.0000.0000.000
156A236CYS0-0.0160.02022.796-0.021-0.0210.0000.0000.0000.000
157A237PHE00.000-0.02419.057-0.032-0.0320.0000.0000.0000.000
158A238VAL0-0.0100.01218.917-0.024-0.0240.0000.0000.0000.000
159A239SER0-0.034-0.03121.2700.0260.0260.0000.0000.0000.000
160A240ALA00.002-0.00424.693-0.015-0.0150.0000.0000.0000.000
161A241PHE00.0120.00926.7500.0130.0130.0000.0000.0000.000
162A242ASN0-0.053-0.03129.931-0.002-0.0020.0000.0000.0000.000
163A243LEU00.0180.00031.9660.0070.0070.0000.0000.0000.000
164A244SER0-0.039-0.00833.9900.0060.0060.0000.0000.0000.000
165A245GLY00.0380.01935.0270.0050.0050.0000.0000.0000.000
166A246LYS10.9420.96732.8740.1380.1380.0000.0000.0000.000
167A247ASN00.0170.00128.334-0.012-0.0120.0000.0000.0000.000
168A248GLU-1-0.836-0.92228.209-0.151-0.1510.0000.0000.0000.000
169A249ASN0-0.0070.00322.780-0.022-0.0220.0000.0000.0000.000
170A250LEU00.0640.04022.1990.0110.0110.0000.0000.0000.000
171A251GLU-1-0.845-0.96418.784-0.304-0.3040.0000.0000.0000.000
172A252ASN0-0.054-0.01421.4010.0020.0020.0000.0000.0000.000
173A253LYS10.7520.87124.2770.1840.1840.0000.0000.0000.000
174A254LEU00.016-0.01921.0830.0000.0000.0000.0000.0000.000
175A255LYS10.9181.01917.1960.2410.2410.0000.0000.0000.000
176A256LEU0-0.048-0.01816.685-0.046-0.0460.0000.0000.0000.000
177A257THR00.0030.00311.744-0.066-0.0660.0000.0000.0000.000
178A258ASN0-0.014-0.0287.0920.0520.0520.0000.0000.0000.000
179A259ILE00.0120.00911.0930.0120.0120.0000.0000.0000.000
180A260ILE0-0.065-0.02511.125-0.042-0.0420.0000.0000.0000.000
181A261MET0-0.023-0.00715.0600.0340.0340.0000.0000.0000.000
182A262ASP-1-0.800-0.89117.298-0.377-0.3770.0000.0000.0000.000
183A263HIS00.007-0.02219.0580.0170.0170.0000.0000.0000.000
184A264TYR0-0.0430.00919.1830.0390.0390.0000.0000.0000.000
185A265ASN0-0.067-0.05819.0600.0360.0360.0000.0000.0000.000
186A266ASN0-0.037-0.01423.049-0.007-0.0070.0000.0000.0000.000
187A267THR0-0.060-0.02818.8770.0080.0080.0000.0000.0000.000
188A268PHE00.0170.02018.784-0.025-0.0250.0000.0000.0000.000
189A269TYR00.028-0.01414.693-0.004-0.0040.0000.0000.0000.000
190A270SER00.0190.01714.5050.0000.0000.0000.0000.0000.000
191A271ARG10.9140.96410.3011.0011.0010.0000.0000.0000.000
192A272LEU0-0.017-0.00314.7760.0270.0270.0000.0000.0000.000
193A273PRO00.0480.02415.848-0.060-0.0600.0000.0000.0000.000
194A274SER00.0550.02614.7840.0170.0170.0000.0000.0000.000
195A275LEU0-0.038-0.01616.6100.0410.0410.0000.0000.0000.000
196A276ILE0-0.037-0.00320.096-0.010-0.0100.0000.0000.0000.000
197A277SER00.0370.00322.8570.0090.0090.0000.0000.0000.000
198A278ASP-1-0.874-0.93126.049-0.152-0.1520.0000.0000.0000.000
199A279ASN0-0.046-0.03027.224-0.024-0.0240.0000.0000.0000.000
200A280TRP00.0230.01425.8970.0140.0140.0000.0000.0000.000
201A281LYS10.8540.91127.7760.1530.1530.0000.0000.0000.000
202A282PHE0-0.027-0.00522.3320.0070.0070.0000.0000.0000.000
203A283PHE00.0360.00027.987-0.007-0.0070.0000.0000.0000.000
204A285VAL00.0190.00028.1690.0030.0030.0000.0000.0000.000
205A287SER0-0.042-0.03130.7720.0130.0130.0000.0000.0000.000
206A288LYS10.9410.95533.8190.1160.1160.0000.0000.0000.000
207A289ASP-1-0.904-0.94536.377-0.105-0.1050.0000.0000.0000.000
208A290ASN0-0.071-0.05640.0620.0030.0030.0000.0000.0000.000
209A291GLU-1-0.851-0.88037.495-0.111-0.1110.0000.0000.0000.000
210A292LYS10.8340.92437.8500.1160.1160.0000.0000.0000.000
211A293LYS10.9240.97335.2630.1220.1220.0000.0000.0000.000
212A294LEU0-0.016-0.00931.2330.0010.0010.0000.0000.0000.000
213A295VAL00.0280.01431.203-0.008-0.0080.0000.0000.0000.000
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