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: 7G51K

Calculation Name: 2FPN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FPN

Chain ID: A

ChEMBL ID:

UniProt ID: O32277

Base Structure: X-ray

Registration Date: 2023-06-19

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2203357.512709
FMO2-HF: Nuclear repulsion 2115162.015255
FMO2-HF: Total energy -88195.497455
FMO2-MP2: Total energy -88450.882788


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:1:LEU)


Summations of interaction energy for fragment #1(A:1: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.
-5.637-0.6290.295-2.507-2.794-0.008
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.024
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].
3A3PRO00.0380.0033.736-2.012-0.118-0.006-0.975-0.9120.004
4A4LEU00.0060.0126.6000.3240.3240.0000.0000.0000.000
5A5ALA00.0010.0103.4870.0440.3480.012-0.099-0.2160.000
6A6GLN0-0.028-0.0173.3900.7921.8130.023-0.377-0.6670.000
7A7MET0-0.061-0.0335.7450.5310.5310.0000.0000.0000.000
8A8ALA00.0190.0218.7540.2160.2160.0000.0000.0000.000
9A9GLU-1-0.867-0.9445.802-0.946-0.9460.0000.0000.0000.000
10A10GLY0-0.088-0.0449.1370.1850.1850.0000.0000.0000.000
11A11MET0-0.037-0.02510.8280.0910.0910.0000.0000.0000.000
12A12GLU-1-0.882-0.93711.792-0.424-0.4240.0000.0000.0000.000
13A13ARG10.9150.9667.8740.4300.4300.0000.0000.0000.000
14A14GLN0-0.112-0.03514.7470.0520.0520.0000.0000.0000.000
15A15ASP-1-0.927-0.97116.966-0.122-0.1220.0000.0000.0000.000
16A16VAL0-0.096-0.04916.8330.0110.0110.0000.0000.0000.000
17A17SER0-0.0110.00617.134-0.035-0.0350.0000.0000.0000.000
18A18ILE0-0.028-0.00813.251-0.011-0.0110.0000.0000.0000.000
19A19ASP-1-0.842-0.90917.740-0.213-0.2130.0000.0000.0000.000
20A20LYS10.8770.92118.8580.3070.3070.0000.0000.0000.000
21A21TRP0-0.0250.00114.125-0.067-0.0670.0000.0000.0000.000
22A22THR0-0.004-0.03016.1710.0590.0590.0000.0000.0000.000
23A23LEU0-0.0380.00211.468-0.068-0.0680.0000.0000.0000.000
24A24HIS00.0220.01215.2460.0510.0510.0000.0000.0000.000
25A25ALA00.0420.03416.253-0.029-0.0290.0000.0000.0000.000
26A26LYS10.9340.95718.1040.1920.1920.0000.0000.0000.000
27A27GLN0-0.033-0.01721.3360.0000.0000.0000.0000.0000.000
28A28ASN0-0.032-0.03223.4480.0020.0020.0000.0000.0000.000
29A29LEU00.0290.01026.8150.0040.0040.0000.0000.0000.000
30A30SER0-0.035-0.02729.4750.0030.0030.0000.0000.0000.000
31A31LEU0-0.0120.00331.4880.0030.0030.0000.0000.0000.000
32A32THR0-0.008-0.02635.2610.0010.0010.0000.0000.0000.000
33A33GLU-1-0.770-0.88237.951-0.066-0.0660.0000.0000.0000.000
34A34LYS10.9810.97639.2470.0450.0450.0000.0000.0000.000
35A35GLU-1-0.805-0.88935.789-0.064-0.0640.0000.0000.0000.000
36A36PHE00.0060.00433.281-0.003-0.0030.0000.0000.0000.000
37A37TYR00.036-0.00434.993-0.005-0.0050.0000.0000.0000.000
38A38GLN00.0190.02436.069-0.002-0.0020.0000.0000.0000.000
39A39LYS10.9610.98926.6390.1120.1120.0000.0000.0000.000
40A40VAL00.0150.00531.928-0.004-0.0040.0000.0000.0000.000
41A41GLN0-0.037-0.01033.241-0.002-0.0020.0000.0000.0000.000
42A42ARG10.9280.95131.4720.0750.0750.0000.0000.0000.000
43A43LEU00.0060.01326.999-0.002-0.0020.0000.0000.0000.000
44A44LYS10.9150.97129.7760.0820.0820.0000.0000.0000.000
45A45GLN0-0.048-0.01532.4350.0030.0030.0000.0000.0000.000
46A46GLU-1-0.911-0.95526.275-0.092-0.0920.0000.0000.0000.000
47A47TYR0-0.042-0.03123.656-0.008-0.0080.0000.0000.0000.000
48A48ARG10.9150.93627.9170.0840.0840.0000.0000.0000.000
49A49GLN00.0100.02224.0310.0160.0160.0000.0000.0000.000
50A50TYR0-0.054-0.02122.982-0.006-0.0060.0000.0000.0000.000
51A51ASP-1-0.876-0.91729.382-0.098-0.0980.0000.0000.0000.000
52A52TRP0-0.036-0.04928.529-0.006-0.0060.0000.0000.0000.000
53A53VAL00.0200.02233.6770.0070.0070.0000.0000.0000.000
54A54ILE0-0.052-0.03634.733-0.004-0.0040.0000.0000.0000.000
55A55ALA00.0120.00936.2480.0030.0030.0000.0000.0000.000
56A56ARG10.8580.90537.5010.0640.0640.0000.0000.0000.000
57A57GLU-1-0.749-0.85336.906-0.096-0.0960.0000.0000.0000.000
58A58ASP-1-0.835-0.89439.994-0.066-0.0660.0000.0000.0000.000
59A59LYS10.7940.88741.8560.0610.0610.0000.0000.0000.000
60A60MET0-0.030-0.02434.910-0.002-0.0020.0000.0000.0000.000
61A61ILE0-0.015-0.00536.6900.0030.0030.0000.0000.0000.000
62A62LYS10.8440.90932.1490.1060.1060.0000.0000.0000.000
63A63ALA0-0.0200.00032.3140.0050.0050.0000.0000.0000.000
64A64ILE0-0.008-0.02229.295-0.008-0.0080.0000.0000.0000.000
65A65GLY00.0250.02128.9310.0080.0080.0000.0000.0000.000
66A66THR00.017-0.00527.366-0.018-0.0180.0000.0000.0000.000
67A67TYR00.0550.02723.4090.0170.0170.0000.0000.0000.000
68A68THR0-0.032-0.00124.740-0.013-0.0130.0000.0000.0000.000
69A69ASP-1-0.799-0.87621.788-0.178-0.1780.0000.0000.0000.000
70A70LYS10.9750.95423.0580.1060.1060.0000.0000.0000.000
71A71LYS10.9250.98421.6270.1390.1390.0000.0000.0000.000
72A72ASN0-0.056-0.05718.4360.0010.0010.0000.0000.0000.000
73A73ARG10.8010.92116.9560.2310.2310.0000.0000.0000.000
74A74THR00.0000.03018.194-0.033-0.0330.0000.0000.0000.000
75A75SER0-0.011-0.01720.2140.0390.0390.0000.0000.0000.000
76A76PHE00.0280.00917.872-0.021-0.0210.0000.0000.0000.000
77A77ARG10.7740.86022.4830.2350.2350.0000.0000.0000.000
78A78LEU00.0020.01223.157-0.014-0.0140.0000.0000.0000.000
79A79GLN0-0.0040.00425.2470.0100.0100.0000.0000.0000.000
80A80LEU0-0.0140.00327.112-0.004-0.0040.0000.0000.0000.000
81A81VAL0-0.018-0.00829.6770.0070.0070.0000.0000.0000.000
82A82THR00.0320.01931.720-0.001-0.0010.0000.0000.0000.000
83A83THR0-0.015-0.00934.4700.0010.0010.0000.0000.0000.000
84A84LEU00.0270.01237.1010.0020.0020.0000.0000.0000.000
85A85LYS10.9490.97440.3450.0570.0570.0000.0000.0000.000
86A86LYS10.8940.92836.6500.0770.0770.0000.0000.0000.000
87A87HIS00.0220.02441.707-0.002-0.0020.0000.0000.0000.000
88A88ASN0-0.004-0.00937.4460.0000.0000.0000.0000.0000.000
89A89PRO00.0170.03736.791-0.002-0.0020.0000.0000.0000.000
90A90THR00.0290.02332.8030.0000.0000.0000.0000.0000.000
91A91SER0-0.020-0.03631.6390.0010.0010.0000.0000.0000.000
92A92TYR0-0.001-0.00826.174-0.004-0.0040.0000.0000.0000.000
93A93LEU0-0.0020.01024.4950.0090.0090.0000.0000.0000.000
94A94LEU0-0.029-0.01421.549-0.006-0.0060.0000.0000.0000.000
95A95TYR0-0.046-0.04117.2760.0280.0280.0000.0000.0000.000
96A96GLU-1-0.809-0.89519.200-0.282-0.2820.0000.0000.0000.000
97A97GLN00.0440.01415.050-0.018-0.0180.0000.0000.0000.000
98A98MET0-0.0310.00017.786-0.035-0.0350.0000.0000.0000.000
99A99SER00.016-0.03017.3750.0230.0230.0000.0000.0000.000
100A100LEU0-0.014-0.00618.882-0.021-0.0210.0000.0000.0000.000
101A101GLU-1-0.802-0.88218.876-0.201-0.2010.0000.0000.0000.000
102A102THR00.0290.02914.343-0.033-0.0330.0000.0000.0000.000
103A103PRO0-0.049-0.02011.4440.0640.0640.0000.0000.0000.000
104A104ASP-1-0.890-0.94913.099-0.281-0.2810.0000.0000.0000.000
105A105SER0-0.003-0.0428.263-0.074-0.0740.0000.0000.0000.000
106A106TRP00.0660.0196.894-0.072-0.0720.0000.0000.0000.000
107A107ASN00.0410.0202.808-4.297-2.6530.267-1.050-0.861-0.012
108A108ASP-1-0.824-0.8765.874-0.354-0.3540.0000.0000.0000.000
109A109THR0-0.021-0.0109.1910.0600.0600.0000.0000.0000.000
110A110TYR00.012-0.0026.5970.0410.0410.0000.0000.0000.000
111A111GLU-1-0.875-0.9414.633-0.572-0.427-0.001-0.006-0.1380.000
112A112GLN0-0.046-0.0248.5050.1780.1780.0000.0000.0000.000
113A113PHE00.0210.02911.9230.0760.0760.0000.0000.0000.000
114A114GLU-1-0.882-0.9618.400-0.422-0.4220.0000.0000.0000.000
115A115ARG10.8580.9208.6670.3840.3840.0000.0000.0000.000
116A116GLU-1-0.840-0.90713.361-0.270-0.2700.0000.0000.0000.000
117A117THR0-0.010-0.00214.7920.0420.0420.0000.0000.0000.000
118A118LEU0-0.019-0.00313.5100.0320.0320.0000.0000.0000.000
119A119GLY0-0.0130.00317.5280.0250.0250.0000.0000.0000.000
120A120ILE0-0.065-0.01819.6970.0180.0180.0000.0000.0000.000
121A121PHE0-0.093-0.07118.7190.0150.0150.0000.0000.0000.000
122A122GLN0-0.047-0.01221.1550.0170.0170.0000.0000.0000.000
123A123GLU-1-0.870-0.92320.185-0.111-0.1110.0000.0000.0000.000
124A124LYS10.8840.95110.5610.2480.2480.0000.0000.0000.000
125A125VAL0-0.013-0.00316.0740.0100.0100.0000.0000.0000.000
126A126VAL0-0.010-0.01014.742-0.030-0.0300.0000.0000.0000.000
127A127ILE0-0.0170.00211.0560.0230.0230.0000.0000.0000.000
128A128PHE0-0.064-0.03413.066-0.041-0.0410.0000.0000.0000.000
129A129THR00.0570.01410.654-0.038-0.0380.0000.0000.0000.000
130A130CYS0-0.067-0.03013.5570.0390.0390.0000.0000.0000.000
131A131LEU00.0580.03511.574-0.003-0.0030.0000.0000.0000.000
132A132ASN0-0.070-0.04715.8810.0520.0520.0000.0000.0000.000
133A133GLY00.0760.03118.688-0.024-0.0240.0000.0000.0000.000
134A134HIS0-0.060-0.02919.9120.0260.0260.0000.0000.0000.000
135A135LEU00.005-0.01221.608-0.008-0.0080.0000.0000.0000.000
136A136ASP-1-0.818-0.92123.759-0.103-0.1030.0000.0000.0000.000
137A137ASP-1-0.944-0.96425.440-0.099-0.0990.0000.0000.0000.000
138A138ASN00.0240.01228.4060.0160.0160.0000.0000.0000.000
139A139MET00.000-0.00730.2620.0050.0050.0000.0000.0000.000
140A140ASN00.007-0.01132.7970.0040.0040.0000.0000.0000.000
141A141ILE00.0140.02126.4320.0080.0080.0000.0000.0000.000
142A142VAL00.000-0.00529.1080.0050.0050.0000.0000.0000.000
143A143LEU0-0.034-0.01831.0790.0060.0060.0000.0000.0000.000
144A144GLN00.0530.01631.4640.0040.0040.0000.0000.0000.000
145A145LYS10.9721.01027.4680.0410.0410.0000.0000.0000.000
146A146LYS10.9290.95331.3690.0460.0460.0000.0000.0000.000
147A147ALA00.0440.02834.1930.0040.0040.0000.0000.0000.000
148A148ASN0-0.005-0.00732.7650.0070.0070.0000.0000.0000.000
149A149GLN00.0080.01330.8070.0010.0010.0000.0000.0000.000
150A150LEU00.0370.01934.4670.0020.0020.0000.0000.0000.000
151A151LEU0-0.0110.00336.7370.0020.0020.0000.0000.0000.000
152A152ASN0-0.085-0.05634.5440.0060.0060.0000.0000.0000.000
153A153GLU-1-0.989-0.98437.362-0.014-0.0140.0000.0000.0000.000
154A154PHE0-0.038-0.01538.9620.0010.0010.0000.0000.0000.000
155A155GLN00.015-0.00740.2230.0040.0040.0000.0000.0000.000
156A156ALA0-0.037-0.03340.6580.0000.0000.0000.0000.0000.000
157A157ARG10.9510.96742.693-0.006-0.0060.0000.0000.0000.000
158A158SER0-0.149-0.07743.7560.0010.0010.0000.0000.0000.000
159A159VAL00.041-0.01138.8160.0000.0000.0000.0000.0000.000
160A160GLU-1-0.779-0.88641.555-0.006-0.0060.0000.0000.0000.000
161A161HIS00.0240.03038.912-0.002-0.0020.0000.0000.0000.000
162A162VAL0-0.0230.00039.6220.0000.0000.0000.0000.0000.000
163A163VAL0-0.019-0.00735.430-0.001-0.0010.0000.0000.0000.000
164A164GLU-1-0.913-0.95038.771-0.027-0.0270.0000.0000.0000.000
165A165PRO0-0.034-0.02438.197-0.002-0.0020.0000.0000.0000.000
166A166ASN00.0300.01336.828-0.005-0.0050.0000.0000.0000.000
167A167PHE00.003-0.01238.5700.0000.0000.0000.0000.0000.000
168A168VAL00.0690.03036.6670.0000.0000.0000.0000.0000.000
169A169SER00.0130.00739.4580.0000.0000.0000.0000.0000.000
170A170ILE0-0.031-0.01838.3620.0010.0010.0000.0000.0000.000
171A171SER00.010-0.00242.297-0.001-0.0010.0000.0000.0000.000
172A172ALA0-0.0130.01343.0390.0010.0010.0000.0000.0000.000
173A173PHE00.031-0.01044.7520.0000.0000.0000.0000.0000.000
174A174THR00.0590.06944.4110.0010.0010.0000.0000.0000.000
175A175ASP-1-0.952-0.97846.8460.0060.0060.0000.0000.0000.000
176A176GLU-1-0.909-0.97145.7130.0020.0020.0000.0000.0000.000
177A177TRP0-0.061-0.02446.784-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.910-0.94352.5100.0010.0010.0000.0000.0000.000
179A179GLU-1-0.928-0.96454.197-0.004-0.0040.0000.0000.0000.000
180A180TYR0-0.054-0.05253.3920.0000.0000.0000.0000.0000.000
181A181ILE00.0030.00753.4930.0000.0000.0000.0000.0000.000
182A182MET0-0.0010.00153.7950.0000.0000.0000.0000.0000.000
183A183THR0-0.0020.00054.7180.0000.0000.0000.0000.0000.000
184A184SER00.0470.02953.6270.0000.0000.0000.0000.0000.000
185A185LYS10.9430.96648.1970.0010.0010.0000.0000.0000.000
186A186HIS10.7860.87447.0590.0040.0040.0000.0000.0000.000
187A187LYS10.8610.94550.142-0.003-0.0030.0000.0000.0000.000
188A188MET0-0.0510.00347.9540.0010.0010.0000.0000.0000.000
189A189ASN0-0.028-0.03648.7870.0000.0000.0000.0000.0000.000
190A190LEU00.1140.07243.8350.0000.0000.0000.0000.0000.000
191A191GLN00.0170.00845.7030.0000.0000.0000.0000.0000.000
192A192ILE0-0.0120.01440.030-0.001-0.0010.0000.0000.0000.000
193A193ALA0-0.005-0.02042.4070.0000.0000.0000.0000.0000.000
194A194LEU0-0.0150.00537.589-0.001-0.0010.0000.0000.0000.000
195A195ARG10.9030.94940.6190.0330.0330.0000.0000.0000.000
196A196SER00.0070.01836.938-0.001-0.0010.0000.0000.0000.000
197A197ALA00.0170.00638.5770.0030.0030.0000.0000.0000.000
198A198GLY00.0070.00438.227-0.003-0.0030.0000.0000.0000.000
199A199MET00.004-0.01137.624-0.001-0.0010.0000.0000.0000.000
200A200GLY00.0660.04035.2120.0030.0030.0000.0000.0000.000
201A201GLY0-0.019-0.01536.2320.0030.0030.0000.0000.0000.000
202A202LYS10.8800.92938.6130.0540.0540.0000.0000.0000.000
203A203HIS0-0.0050.01434.7700.0050.0050.0000.0000.0000.000
204A204THR0-0.0200.00140.1220.0020.0020.0000.0000.0000.000
205A205VAL00.0250.00140.312-0.001-0.0010.0000.0000.0000.000
206A206THR0-0.077-0.03742.8830.0010.0010.0000.0000.0000.000
207A207VAL00.0390.01643.6440.0000.0000.0000.0000.0000.000
208A208GLY0-0.0190.00446.3260.0000.0000.0000.0000.0000.000
209A209THR00.0260.04249.0790.0000.0000.0000.0000.0000.000
210A210PRO0-0.021-0.01851.6370.0000.0000.0000.0000.0000.000
211A211ILE00.007-0.02150.6290.0000.0000.0000.0000.0000.000
212A212VAL00.0060.00948.2550.0000.0000.0000.0000.0000.000
213A213THR0-0.021-0.00651.3580.0000.0000.0000.0000.0000.000
214A214THR0-0.010-0.00253.938-0.001-0.0010.0000.0000.0000.000