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: VQLR1

Calculation Name: 3FTD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FTD

Chain ID: A

ChEMBL ID:

UniProt ID: O67680

Base Structure: X-ray

Registration Date: 2023-09-23

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 239
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3101244.843173
FMO2-HF: Nuclear repulsion 3006647.774975
FMO2-HF: Total energy -94597.068198
FMO2-MP2: Total energy -94877.682899


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:7:SER)


Summations of interaction energy for fragment #1(A:7:SER)
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.
-3.658-0.0570000000000021.954-2.637-2.917-0.018
Interaction energy analysis for fragmet #1(A:7:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.006
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].
3A9GLY0-0.035-0.0303.8961.5262.560-0.012-0.524-0.4980.001
4A10GLN0-0.065-0.0263.5602.2352.9130.041-0.192-0.527-0.001
5A11HIS00.005-0.0026.1970.5530.5530.0000.0000.0000.000
6A12LEU0-0.089-0.0479.6860.1870.1870.0000.0000.0000.000
7A13LEU0-0.0090.0198.207-0.131-0.1310.0000.0000.0000.000
8A14VAL00.006-0.01611.5210.0150.0150.0000.0000.0000.000
9A15SER0-0.010-0.00313.2880.0420.0420.0000.0000.0000.000
10A16GLU-1-0.733-0.87410.9540.0400.0400.0000.0000.0000.000
11A17GLY00.0070.01714.940-0.013-0.0130.0000.0000.0000.000
12A18VAL0-0.012-0.01318.329-0.009-0.0090.0000.0000.0000.000
13A19LEU00.0040.00112.719-0.013-0.0130.0000.0000.0000.000
14A20LYS10.8650.93114.263-0.083-0.0830.0000.0000.0000.000
15A21LYS10.8270.90318.4870.0470.0470.0000.0000.0000.000
16A22ILE0-0.030-0.03218.792-0.002-0.0020.0000.0000.0000.000
17A23ALA00.0240.01018.024-0.008-0.0080.0000.0000.0000.000
18A24GLU-1-0.841-0.90320.158-0.024-0.0240.0000.0000.0000.000
19A25GLU-1-0.822-0.90423.348-0.073-0.0730.0000.0000.0000.000
20A26LEU0-0.028-0.00320.824-0.001-0.0010.0000.0000.0000.000
21A27ASN0-0.078-0.05124.8450.0080.0080.0000.0000.0000.000
22A28ILE0-0.010-0.00620.434-0.003-0.0030.0000.0000.0000.000
23A29GLU-1-0.795-0.87324.582-0.060-0.0600.0000.0000.0000.000
24A30GLU-1-0.812-0.90225.754-0.049-0.0490.0000.0000.0000.000
25A31GLY0-0.063-0.04426.808-0.007-0.0070.0000.0000.0000.000
26A32ASN0-0.049-0.03124.496-0.021-0.0210.0000.0000.0000.000
27A33THR00.0070.01323.426-0.006-0.0060.0000.0000.0000.000
28A34VAL0-0.010-0.00219.5410.0050.0050.0000.0000.0000.000
29A35VAL00.0060.00020.088-0.021-0.0210.0000.0000.0000.000
30A36GLU-1-0.757-0.87213.574-0.688-0.6880.0000.0000.0000.000
31A37VAL0-0.023-0.01317.573-0.035-0.0350.0000.0000.0000.000
32A38GLY0-0.042-0.02717.6140.0300.0300.0000.0000.0000.000
33A39GLY00.0370.01413.782-0.063-0.0630.0000.0000.0000.000
34A40GLY00.004-0.00310.7370.1440.1440.0000.0000.0000.000
35A41THR0-0.010-0.02310.597-0.130-0.1300.0000.0000.0000.000
36A42GLY00.0730.0336.9610.1160.1160.0000.0000.0000.000
37A43ASN0-0.024-0.0126.9930.3610.3610.0000.0000.0000.000
38A44LEU0-0.0280.0009.0670.2300.2300.0000.0000.0000.000
39A45THR00.050-0.01210.0620.0690.0690.0000.0000.0000.000
40A46LYS10.8210.9026.4470.0930.0930.0000.0000.0000.000
41A47VAL0-0.023-0.00410.5100.1250.1250.0000.0000.0000.000
42A48LEU0-0.012-0.00813.8150.0620.0620.0000.0000.0000.000
43A49LEU00.0260.01411.6750.0360.0360.0000.0000.0000.000
44A50GLN0-0.060-0.01414.1880.0430.0430.0000.0000.0000.000
45A51HIS0-0.030-0.00916.5280.0360.0360.0000.0000.0000.000
46A52PRO00.020-0.00119.934-0.010-0.0100.0000.0000.0000.000
47A53LEU0-0.0320.00817.712-0.005-0.0050.0000.0000.0000.000
48A54LYS10.9861.00321.4710.1140.1140.0000.0000.0000.000
49A55LYS10.8470.91019.6390.2550.2550.0000.0000.0000.000
50A56LEU0-0.006-0.00214.6750.0110.0110.0000.0000.0000.000
51A57TYR00.003-0.00817.063-0.032-0.0320.0000.0000.0000.000
52A58VAL00.000-0.00312.3980.0110.0110.0000.0000.0000.000
53A59ILE0-0.043-0.01515.521-0.030-0.0300.0000.0000.0000.000
54A60GLU-1-0.815-0.88911.092-1.218-1.2180.0000.0000.0000.000
55A61LEU00.0210.00714.5970.0130.0130.0000.0000.0000.000
56A62ASP-1-0.829-0.9129.114-1.851-1.8510.0000.0000.0000.000
57A63ARG10.9140.92510.8700.5200.5200.0000.0000.0000.000
58A64GLU-1-0.851-0.9045.256-3.256-3.2560.0000.0000.0000.000
59A65MET0-0.0220.0056.113-0.993-0.9930.0000.0000.0000.000
60A66VAL0-0.025-0.0237.535-0.025-0.0250.0000.0000.0000.000
61A67GLU-1-0.913-0.9548.133-0.900-0.9000.0000.0000.0000.000
62A68ASN0-0.028-0.0282.524-4.053-2.2271.926-1.920-1.832-0.018
63A69LEU0-0.019-0.0134.8990.6550.718-0.001-0.001-0.0600.000
64A70LYS10.9160.9677.5321.1721.1720.0000.0000.0000.000
65A71SER0-0.059-0.0235.3160.5630.5630.0000.0000.0000.000
66A72ILE0-0.049-0.0287.3470.3810.3810.0000.0000.0000.000
67A73GLY00.0230.0129.375-0.071-0.0710.0000.0000.0000.000
68A74ASP-1-0.838-0.89412.797-0.030-0.0300.0000.0000.0000.000
69A75GLU-1-0.914-0.96114.759-0.129-0.1290.0000.0000.0000.000
70A76ARG10.7360.83816.4840.0440.0440.0000.0000.0000.000
71A77LEU0-0.048-0.01511.114-0.033-0.0330.0000.0000.0000.000
72A78GLU-1-0.877-0.92915.741-0.290-0.2900.0000.0000.0000.000
73A79VAL0-0.005-0.00211.371-0.030-0.0300.0000.0000.0000.000
74A80ILE0-0.010-0.00414.6660.0240.0240.0000.0000.0000.000
75A81ASN0-0.057-0.02315.1070.0200.0200.0000.0000.0000.000
76A82GLU-1-0.852-0.93616.928-0.352-0.3520.0000.0000.0000.000
77A83ASP-1-0.762-0.83419.218-0.434-0.4340.0000.0000.0000.000
78A84ALA00.0650.02619.9770.0490.0490.0000.0000.0000.000
79A85SER0-0.130-0.10121.9180.0460.0460.0000.0000.0000.000
80A86LYS10.8000.88024.7210.3540.3540.0000.0000.0000.000
81A87PHE00.0340.03123.4340.0180.0180.0000.0000.0000.000
82A88PRO00.0220.02725.4350.0060.0060.0000.0000.0000.000
83A89PHE00.0610.02522.6330.0040.0040.0000.0000.0000.000
84A90CYS0-0.072-0.02426.2160.0050.0050.0000.0000.0000.000
85A91SER0-0.078-0.04126.6830.0080.0080.0000.0000.0000.000
86A92LEU00.0120.01621.9530.0010.0010.0000.0000.0000.000
87A93GLY00.0240.01025.7500.0070.0070.0000.0000.0000.000
88A94LYS10.8850.93528.3940.1210.1210.0000.0000.0000.000
89A95GLU-1-0.938-0.96929.900-0.101-0.1010.0000.0000.0000.000
90A96LEU0-0.035-0.00424.817-0.006-0.0060.0000.0000.0000.000
91A97LYS10.8110.90924.4120.1070.1070.0000.0000.0000.000
92A98VAL0-0.0060.00122.873-0.021-0.0210.0000.0000.0000.000
93A99VAL00.0240.00218.4760.0240.0240.0000.0000.0000.000
94A100GLY00.0670.02718.358-0.050-0.0500.0000.0000.0000.000
95A101ASN0-0.032-0.01915.7350.1250.1250.0000.0000.0000.000
96A102LEU0-0.0060.00117.787-0.066-0.0660.0000.0000.0000.000
97A103PRO00.0410.02617.3170.0430.0430.0000.0000.0000.000
98A104TYR00.0400.00020.0770.0290.0290.0000.0000.0000.000
99A105ASN0-0.027-0.00621.2480.0120.0120.0000.0000.0000.000
100A106VAL00.0260.00920.8130.0090.0090.0000.0000.0000.000
101A107ALA00.0040.01323.7120.0100.0100.0000.0000.0000.000
102A108SER00.007-0.01424.6640.0080.0080.0000.0000.0000.000
103A109LEU00.0070.00726.4730.0140.0140.0000.0000.0000.000
104A110ILE00.0550.03521.1590.0070.0070.0000.0000.0000.000
105A111ILE0-0.0040.01525.4350.0120.0120.0000.0000.0000.000
106A112GLU-1-0.773-0.85328.004-0.169-0.1690.0000.0000.0000.000
107A113ASN0-0.036-0.04025.5660.0340.0340.0000.0000.0000.000
108A114THR00.008-0.00526.5170.0010.0010.0000.0000.0000.000
109A115VAL0-0.025-0.00628.5770.0120.0120.0000.0000.0000.000
110A116TYR0-0.116-0.10631.5040.0170.0170.0000.0000.0000.000
111A117ASN00.0110.00329.0600.0070.0070.0000.0000.0000.000
112A118LYS10.9090.91731.3070.1170.1170.0000.0000.0000.000
113A119ASP-1-0.898-0.91933.395-0.111-0.1110.0000.0000.0000.000
114A121VAL00.0350.03327.882-0.006-0.0060.0000.0000.0000.000
115A122PRO00.0280.03129.8720.0040.0040.0000.0000.0000.000
116A123LEU0-0.010-0.01327.2630.0100.0100.0000.0000.0000.000
117A124ALA00.0130.01125.958-0.015-0.0150.0000.0000.0000.000
118A125VAL0-0.019-0.00523.2820.0190.0190.0000.0000.0000.000
119A126PHE00.0240.00722.363-0.026-0.0260.0000.0000.0000.000
120A127MET0-0.0260.01118.3920.0470.0470.0000.0000.0000.000
121A128VAL00.0120.00821.967-0.034-0.0340.0000.0000.0000.000
122A129GLN00.0550.00924.2980.0190.0190.0000.0000.0000.000
123A130LYS10.8700.92026.3160.0850.0850.0000.0000.0000.000
124A131GLU-1-0.816-0.88929.140-0.109-0.1090.0000.0000.0000.000
125A132VAL00.002-0.00228.0210.0050.0050.0000.0000.0000.000
126A133ALA00.0390.02628.6670.0040.0040.0000.0000.0000.000
127A134GLU-1-0.811-0.89330.558-0.072-0.0720.0000.0000.0000.000
128A135LYS10.8060.89233.8070.1140.1140.0000.0000.0000.000
129A136LEU0-0.027-0.00129.9230.0050.0050.0000.0000.0000.000
130A137GLN00.0490.03034.0070.0100.0100.0000.0000.0000.000
131A138GLY0-0.034-0.01135.6330.0060.0060.0000.0000.0000.000
132A139LYS10.8920.93437.7060.0710.0710.0000.0000.0000.000
133A140LYS10.8380.90037.2280.0710.0710.0000.0000.0000.000
134A141ASP-1-0.790-0.87737.488-0.092-0.0920.0000.0000.0000.000
135A142THR0-0.040-0.03138.233-0.001-0.0010.0000.0000.0000.000
136A143GLY00.014-0.00537.664-0.003-0.0030.0000.0000.0000.000
137A144TRP00.0390.00733.7110.0040.0040.0000.0000.0000.000
138A145LEU00.0270.02330.8730.0030.0030.0000.0000.0000.000
139A146SER0-0.005-0.01835.5000.0010.0010.0000.0000.0000.000
140A147VAL0-0.0180.00536.6330.0030.0030.0000.0000.0000.000
141A148PHE0-0.019-0.01234.1900.0020.0020.0000.0000.0000.000
142A149VAL00.0290.01032.5060.0010.0010.0000.0000.0000.000
143A150ARG10.9160.96235.4480.0950.0950.0000.0000.0000.000
144A151THR0-0.0230.01438.2340.0060.0060.0000.0000.0000.000
145A152PHE00.021-0.01136.3070.0040.0040.0000.0000.0000.000
146A153TYR0-0.003-0.00331.924-0.004-0.0040.0000.0000.0000.000
147A154ASP-1-0.820-0.87635.614-0.076-0.0760.0000.0000.0000.000
148A155VAL0-0.029-0.02731.955-0.006-0.0060.0000.0000.0000.000
149A156ASN0-0.029-0.01431.5780.0140.0140.0000.0000.0000.000
150A157TYR0-0.017-0.02730.711-0.014-0.0140.0000.0000.0000.000
151A158VAL0-0.0010.01426.7280.0090.0090.0000.0000.0000.000
152A159MET00.0200.00624.3230.0110.0110.0000.0000.0000.000
153A160THR0-0.026-0.00527.369-0.013-0.0130.0000.0000.0000.000
154A161VAL00.0200.00521.0940.0110.0110.0000.0000.0000.000
155A162PRO00.000-0.01224.150-0.014-0.0140.0000.0000.0000.000
156A163PRO00.0390.00322.3690.0010.0010.0000.0000.0000.000
157A164ARG10.9810.97620.659-0.021-0.0210.0000.0000.0000.000
158A165PHE0-0.0110.01319.0500.0250.0250.0000.0000.0000.000
159A166PHE0-0.013-0.00916.284-0.010-0.0100.0000.0000.0000.000
160A167VAL00.0030.01013.9010.0420.0420.0000.0000.0000.000
161A168PRO00.1100.04013.778-0.039-0.0390.0000.0000.0000.000
162A169PRO00.0020.01517.108-0.027-0.0270.0000.0000.0000.000
163A170PRO0-0.0020.02020.008-0.003-0.0030.0000.0000.0000.000
164A171LYS10.9000.92722.4570.1490.1490.0000.0000.0000.000
165A172VAL00.0110.01925.9180.0140.0140.0000.0000.0000.000
166A173GLN0-0.001-0.01125.621-0.009-0.0090.0000.0000.0000.000
167A174SER00.0140.02122.009-0.008-0.0080.0000.0000.0000.000
168A175ALA0-0.024-0.01725.0270.0230.0230.0000.0000.0000.000
169A176VAL00.0380.02622.805-0.023-0.0230.0000.0000.0000.000
170A177ILE0-0.044-0.02325.4950.0200.0200.0000.0000.0000.000
171A178LYS10.8780.92826.5330.0730.0730.0000.0000.0000.000
172A179LEU0-0.0400.00128.5120.0120.0120.0000.0000.0000.000
173A180VAL00.0490.01530.438-0.006-0.0060.0000.0000.0000.000
174A181LYS10.8320.91733.1120.1180.1180.0000.0000.0000.000
175A182ASN0-0.061-0.05435.2980.0070.0070.0000.0000.0000.000
176A183GLU-1-0.835-0.90738.783-0.107-0.1070.0000.0000.0000.000
177A184LYS10.7970.90439.3470.0910.0910.0000.0000.0000.000
178A185PHE00.0260.00443.6780.0040.0040.0000.0000.0000.000
179A186PRO00.0260.02944.125-0.005-0.0050.0000.0000.0000.000
180A187VAL0-0.042-0.02842.1240.0020.0020.0000.0000.0000.000
181A188LYS10.9040.95142.7620.0780.0780.0000.0000.0000.000
182A189ASP-1-0.802-0.89741.836-0.117-0.1170.0000.0000.0000.000
183A190LEU00.0420.01536.1520.0010.0010.0000.0000.0000.000
184A191LYS10.9420.97934.6360.1610.1610.0000.0000.0000.000
185A192ASN0-0.023-0.01139.594-0.002-0.0020.0000.0000.0000.000
186A193TYR00.0250.00440.6710.0030.0030.0000.0000.0000.000
187A194LYS10.8480.91834.0070.1690.1690.0000.0000.0000.000
188A195LYS10.8800.95640.1440.1060.1060.0000.0000.0000.000
189A196PHE00.0330.02842.7130.0020.0020.0000.0000.0000.000
190A197LEU00.0010.00640.1720.0020.0020.0000.0000.0000.000
191A198THR0-0.041-0.05638.3250.0010.0010.0000.0000.0000.000
192A199LYS10.9110.96841.1150.0820.0820.0000.0000.0000.000
193A200ILE0-0.0070.00244.7040.0030.0030.0000.0000.0000.000
194A201PHE00.0370.01141.2750.0030.0030.0000.0000.0000.000
195A202GLN0-0.044-0.01140.3550.0000.0000.0000.0000.0000.000
196A203ASN0-0.004-0.01844.0140.0070.0070.0000.0000.0000.000
197A204ARG10.8880.93741.4920.0880.0880.0000.0000.0000.000
198A205ARG11.0170.99845.1680.0660.0660.0000.0000.0000.000
199A206LYS10.8460.93548.0150.0730.0730.0000.0000.0000.000
200A207VAL0-0.0100.00550.458-0.002-0.0020.0000.0000.0000.000
201A208LEU00.0760.03949.609-0.002-0.0020.0000.0000.0000.000
202A209ARG10.8960.92252.9600.0450.0450.0000.0000.0000.000
203A210LYS10.8990.96153.9240.0540.0540.0000.0000.0000.000
204A211LYS10.7280.86246.8650.0760.0760.0000.0000.0000.000
205A212ILE00.0150.01549.688-0.004-0.0040.0000.0000.0000.000
206A213PRO00.0830.03853.6410.0020.0020.0000.0000.0000.000
207A214GLU-1-0.822-0.92257.443-0.046-0.0460.0000.0000.0000.000
208A215GLU-1-0.929-0.94859.386-0.047-0.0470.0000.0000.0000.000
209A216LEU00.1060.04755.6880.0000.0000.0000.0000.0000.000
210A217LEU0-0.086-0.03253.566-0.001-0.0010.0000.0000.0000.000
211A218LYS10.8570.90357.0510.0440.0440.0000.0000.0000.000
212A219GLU-1-0.887-0.93259.222-0.049-0.0490.0000.0000.0000.000
213A220ALA0-0.011-0.00654.7110.0000.0000.0000.0000.0000.000
214A221GLY00.0140.01456.3380.0000.0000.0000.0000.0000.000
215A222ILE0-0.065-0.02952.4430.0000.0000.0000.0000.0000.000
216A223ASN00.0280.00556.2970.0010.0010.0000.0000.0000.000
217A224PRO00.0400.01255.936-0.002-0.0020.0000.0000.0000.000
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