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: YV8Y2

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 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 239
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3096346.441578
FMO2-HF: Nuclear repulsion 3001749.772448
FMO2-HF: Total energy -94596.66913
FMO2-MP2: Total energy -94877.281008


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.
-8.518-3.2160.206-3.018-2.491-0.002
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 : 0.042 / q_NPA : 0.023
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].
3A9GLY0-0.049-0.0363.812-2.0430.690-0.022-1.612-1.0990.010
4A10GLN00.0070.0163.065-2.279-1.1760.088-0.604-0.587-0.005
5A11HIS00.0110.0136.3260.7190.7190.0000.0000.0000.000
6A12LEU0-0.065-0.0379.9370.4200.4200.0000.0000.0000.000
7A13LEU0-0.0130.0118.140-0.144-0.1440.0000.0000.0000.000
8A14VAL00.000-0.01111.7320.1120.1120.0000.0000.0000.000
9A15SER0-0.002-0.00413.4920.0640.0640.0000.0000.0000.000
10A16GLU-1-0.764-0.90111.1900.0330.0330.0000.0000.0000.000
11A17GLY0-0.0040.01114.8990.0190.0190.0000.0000.0000.000
12A18VAL0-0.017-0.01818.0380.0050.0050.0000.0000.0000.000
13A19LEU00.0030.00412.453-0.005-0.0050.0000.0000.0000.000
14A20LYS10.8880.93914.214-0.155-0.1550.0000.0000.0000.000
15A21LYS10.8290.91418.3340.0640.0640.0000.0000.0000.000
16A22ILE0-0.022-0.02918.5700.0000.0000.0000.0000.0000.000
17A23ALA00.0210.00517.9060.0010.0010.0000.0000.0000.000
18A24GLU-1-0.837-0.90320.0300.0000.0000.0000.0000.0000.000
19A25GLU-1-0.853-0.91923.170-0.070-0.0700.0000.0000.0000.000
20A26LEU0-0.030-0.00420.661-0.004-0.0040.0000.0000.0000.000
21A27ASN0-0.080-0.03224.6190.0090.0090.0000.0000.0000.000
22A28ILE0-0.013-0.00620.350-0.001-0.0010.0000.0000.0000.000
23A29GLU-1-0.858-0.94324.5140.0150.0150.0000.0000.0000.000
24A30GLU-1-0.866-0.94726.1310.0930.0930.0000.0000.0000.000
25A31GLY0-0.023-0.00726.536-0.013-0.0130.0000.0000.0000.000
26A32ASN0-0.0220.00424.817-0.023-0.0230.0000.0000.0000.000
27A33THR00.0140.01523.4350.0130.0130.0000.0000.0000.000
28A34VAL0-0.005-0.00219.703-0.011-0.0110.0000.0000.0000.000
29A35VAL00.0120.00220.182-0.006-0.0060.0000.0000.0000.000
30A36GLU-1-0.782-0.89513.611-0.515-0.5150.0000.0000.0000.000
31A37VAL0-0.024-0.02217.475-0.036-0.0360.0000.0000.0000.000
32A38GLY0-0.044-0.02917.4280.0050.0050.0000.0000.0000.000
33A39GLY00.0280.00614.171-0.077-0.0770.0000.0000.0000.000
34A40GLY0-0.036-0.02910.6840.1060.1060.0000.0000.0000.000
35A41THR00.0290.00310.805-0.029-0.0290.0000.0000.0000.000
36A42GLY00.0690.0406.9780.1380.1380.0000.0000.0000.000
37A43ASN0-0.021-0.0266.6830.7230.7230.0000.0000.0000.000
38A44LEU0-0.0020.0148.6980.2460.2460.0000.0000.0000.000
39A45THR00.0470.00610.1230.1300.1300.0000.0000.0000.000
40A46LYS10.8750.9355.527-0.616-0.6160.0000.0000.0000.000
41A47VAL0-0.021-0.00610.4780.0960.0960.0000.0000.0000.000
42A48LEU0-0.002-0.00813.5380.0480.0480.0000.0000.0000.000
43A49LEU0-0.0080.00811.8370.0170.0170.0000.0000.0000.000
44A50GLN0-0.055-0.01514.3260.0350.0350.0000.0000.0000.000
45A51HIS0-0.037-0.01516.657-0.014-0.0140.0000.0000.0000.000
46A52PRO00.0230.01019.8030.0090.0090.0000.0000.0000.000
47A53LEU0-0.0200.00417.843-0.016-0.0160.0000.0000.0000.000
48A54LYS10.9830.99421.8360.0090.0090.0000.0000.0000.000
49A55LYS10.8520.91020.1390.0540.0540.0000.0000.0000.000
50A56LEU0-0.005-0.00114.773-0.011-0.0110.0000.0000.0000.000
51A57TYR00.004-0.00217.4070.0040.0040.0000.0000.0000.000
52A58VAL00.0220.01412.622-0.014-0.0140.0000.0000.0000.000
53A59ILE0-0.058-0.02415.797-0.007-0.0070.0000.0000.0000.000
54A60GLU-1-0.830-0.91011.642-1.289-1.2890.0000.0000.0000.000
55A61LEU00.0210.01115.1710.0450.0450.0000.0000.0000.000
56A62ASP-1-0.854-0.93210.317-2.001-2.0010.0000.0000.0000.000
57A63ARG10.9300.92711.7480.5220.5220.0000.0000.0000.000
58A64GLU-1-0.903-0.9326.409-3.334-3.3340.0000.0000.0000.000
59A65MET0-0.028-0.0017.177-0.673-0.6730.0000.0000.0000.000
60A66VAL0-0.042-0.0318.0800.1840.1840.0000.0000.0000.000
61A67GLU-1-0.929-0.9588.243-0.288-0.2880.0000.0000.0000.000
62A68ASN0-0.030-0.0323.143-2.810-1.3440.140-0.802-0.805-0.007
63A69LEU0-0.016-0.0025.5050.8730.8730.0000.0000.0000.000
64A70LYS10.9200.9717.8930.7100.7100.0000.0000.0000.000
65A71SER0-0.057-0.0265.6210.6090.6090.0000.0000.0000.000
66A72ILE0-0.077-0.0447.4760.4560.4560.0000.0000.0000.000
67A73GLY00.0130.0079.465-0.157-0.1570.0000.0000.0000.000
68A74ASP-1-0.826-0.90012.8720.1980.1980.0000.0000.0000.000
69A75GLU-1-0.880-0.93614.9090.1400.1400.0000.0000.0000.000
70A76ARG10.7130.82716.679-0.267-0.2670.0000.0000.0000.000
71A77LEU0-0.042-0.00511.239-0.069-0.0690.0000.0000.0000.000
72A78GLU-1-0.873-0.92415.842-0.097-0.0970.0000.0000.0000.000
73A79VAL0-0.024-0.01311.811-0.041-0.0410.0000.0000.0000.000
74A80ILE0-0.004-0.00415.2370.0310.0310.0000.0000.0000.000
75A81ASN0-0.061-0.02815.760-0.011-0.0110.0000.0000.0000.000
76A82GLU-1-0.877-0.94717.508-0.331-0.3310.0000.0000.0000.000
77A83ASP-1-0.766-0.84019.361-0.482-0.4820.0000.0000.0000.000
78A84ALA00.0740.02320.2820.0500.0500.0000.0000.0000.000
79A85SER0-0.129-0.09722.1950.0470.0470.0000.0000.0000.000
80A86LYS10.8230.88525.0040.3930.3930.0000.0000.0000.000
81A87PHE00.0360.03623.6910.0190.0190.0000.0000.0000.000
82A88PRO00.0200.03125.7960.0070.0070.0000.0000.0000.000
83A89PHE00.0780.03323.0740.0110.0110.0000.0000.0000.000
84A90CYS0-0.063-0.00626.8300.0160.0160.0000.0000.0000.000
85A91SER0-0.094-0.04927.3830.0130.0130.0000.0000.0000.000
86A92LEU0-0.0020.00822.4940.0060.0060.0000.0000.0000.000
87A93GLY00.0210.00026.3600.0180.0180.0000.0000.0000.000
88A94LYS10.9180.94828.8340.0600.0600.0000.0000.0000.000
89A95GLU-1-0.921-0.96230.050-0.049-0.0490.0000.0000.0000.000
90A96LEU0-0.042-0.00225.1430.0050.0050.0000.0000.0000.000
91A97LYS10.8300.92524.4100.0360.0360.0000.0000.0000.000
92A98VAL00.0030.00622.837-0.013-0.0130.0000.0000.0000.000
93A99VAL00.0370.01418.4710.0130.0130.0000.0000.0000.000
94A100GLY00.0650.03718.244-0.042-0.0420.0000.0000.0000.000
95A101ASN00.0010.00316.0910.1180.1180.0000.0000.0000.000
96A102LEU0-0.009-0.00218.128-0.082-0.0820.0000.0000.0000.000
97A103PRO00.0480.02917.8490.0250.0250.0000.0000.0000.000
98A104TYR00.050-0.00120.4870.0650.0650.0000.0000.0000.000
99A105ASN0-0.047-0.01922.2190.0160.0160.0000.0000.0000.000
100A106VAL00.0430.02121.3210.0190.0190.0000.0000.0000.000
101A107ALA00.0040.02124.3460.0230.0230.0000.0000.0000.000
102A108SER00.004-0.02025.2130.0190.0190.0000.0000.0000.000
103A109LEU00.0030.00826.8150.0200.0200.0000.0000.0000.000
104A110ILE00.0730.03921.4470.0180.0180.0000.0000.0000.000
105A111ILE0-0.0100.00725.7730.0240.0240.0000.0000.0000.000
106A112GLU-1-0.767-0.84728.251-0.190-0.1900.0000.0000.0000.000
107A113ASN0-0.035-0.03925.9940.0380.0380.0000.0000.0000.000
108A114THR00.011-0.00426.8820.0100.0100.0000.0000.0000.000
109A115VAL0-0.026-0.00328.8810.0160.0160.0000.0000.0000.000
110A116TYR0-0.111-0.09431.8930.0200.0200.0000.0000.0000.000
111A117ASN0-0.021-0.01829.6240.0170.0170.0000.0000.0000.000
112A118LYS10.9210.93131.6800.1090.1090.0000.0000.0000.000
113A119ASP-1-0.940-0.95333.489-0.090-0.0900.0000.0000.0000.000
114A121VAL00.0130.01727.951-0.004-0.0040.0000.0000.0000.000
115A122PRO00.0270.02829.970-0.004-0.0040.0000.0000.0000.000
116A123LEU00.000-0.00627.1140.0040.0040.0000.0000.0000.000
117A124ALA00.0110.00925.879-0.009-0.0090.0000.0000.0000.000
118A125VAL0-0.0160.00523.0600.0110.0110.0000.0000.0000.000
119A126PHE00.0360.01222.600-0.026-0.0260.0000.0000.0000.000
120A127MET0-0.0410.00518.3980.0420.0420.0000.0000.0000.000
121A128VAL00.0080.00622.284-0.040-0.0400.0000.0000.0000.000
122A129GLN00.0500.00524.666-0.002-0.0020.0000.0000.0000.000
123A130LYS10.8890.93726.5660.1900.1900.0000.0000.0000.000
124A131GLU-1-0.815-0.89329.287-0.177-0.1770.0000.0000.0000.000
125A132VAL0-0.005-0.00528.4190.0120.0120.0000.0000.0000.000
126A133ALA00.0310.01728.7220.0130.0130.0000.0000.0000.000
127A134GLU-1-0.838-0.92330.671-0.139-0.1390.0000.0000.0000.000
128A135LYS10.8040.88434.0810.1870.1870.0000.0000.0000.000
129A136LEU0-0.028-0.00130.2370.0120.0120.0000.0000.0000.000
130A137GLN00.0300.01634.2890.0190.0190.0000.0000.0000.000
131A138GLY0-0.019-0.00935.7440.0100.0100.0000.0000.0000.000
132A139LYS10.8810.94837.8920.1000.1000.0000.0000.0000.000
133A140LYS10.8410.89837.0090.1310.1310.0000.0000.0000.000
134A141ASP-1-0.767-0.85537.534-0.155-0.1550.0000.0000.0000.000
135A142THR0-0.037-0.02638.5320.0030.0030.0000.0000.0000.000
136A143GLY00.0230.00537.928-0.007-0.0070.0000.0000.0000.000
137A144TRP00.0320.00734.3860.0070.0070.0000.0000.0000.000
138A145LEU00.0140.01731.0350.0050.0050.0000.0000.0000.000
139A146SER0-0.011-0.02135.6780.0060.0060.0000.0000.0000.000
140A147VAL0-0.0120.00136.6910.0050.0050.0000.0000.0000.000
141A148PHE0-0.007-0.00834.4670.0060.0060.0000.0000.0000.000
142A149VAL00.0220.00132.7230.0040.0040.0000.0000.0000.000
143A150ARG10.9320.97035.5790.1270.1270.0000.0000.0000.000
144A151THR0-0.0280.01438.1200.0070.0070.0000.0000.0000.000
145A152PHE00.007-0.01636.5100.0070.0070.0000.0000.0000.000
146A153TYR00.0030.00531.906-0.002-0.0020.0000.0000.0000.000
147A154ASP-1-0.821-0.87935.730-0.083-0.0830.0000.0000.0000.000
148A155VAL0-0.029-0.02432.085-0.007-0.0070.0000.0000.0000.000
149A156ASN0-0.043-0.01531.5570.0140.0140.0000.0000.0000.000
150A157TYR00.001-0.01130.759-0.021-0.0210.0000.0000.0000.000
151A158VAL00.0070.01526.4910.0100.0100.0000.0000.0000.000
152A159MET00.0230.01023.9150.0130.0130.0000.0000.0000.000
153A160THR0-0.047-0.02427.220-0.015-0.0150.0000.0000.0000.000
154A161VAL00.0170.00221.1880.0120.0120.0000.0000.0000.000
155A162PRO0-0.013-0.01424.447-0.025-0.0250.0000.0000.0000.000
156A163PRO00.0680.01322.602-0.008-0.0080.0000.0000.0000.000
157A164ARG10.9870.97920.8250.1330.1330.0000.0000.0000.000
158A165PHE0-0.0240.00819.1010.0060.0060.0000.0000.0000.000
159A166PHE0-0.021-0.01216.462-0.008-0.0080.0000.0000.0000.000
160A167VAL0-0.0100.02713.9730.0660.0660.0000.0000.0000.000
161A168PRO00.1000.01913.950-0.122-0.1220.0000.0000.0000.000
162A169PRO0-0.0060.00017.0500.0020.0020.0000.0000.0000.000
163A170PRO0-0.0180.01720.208-0.008-0.0080.0000.0000.0000.000
164A171LYS10.9590.95922.3950.4140.4140.0000.0000.0000.000
165A172VAL00.0060.01325.7270.0320.0320.0000.0000.0000.000
166A173GLN00.0180.01125.513-0.013-0.0130.0000.0000.0000.000
167A174SER00.0150.01422.373-0.003-0.0030.0000.0000.0000.000
168A175ALA0-0.019-0.01425.2500.0280.0280.0000.0000.0000.000
169A176VAL00.0480.03322.594-0.028-0.0280.0000.0000.0000.000
170A177ILE0-0.041-0.02125.3080.0240.0240.0000.0000.0000.000
171A178LYS10.8800.92426.5700.0630.0630.0000.0000.0000.000
172A179LEU0-0.045-0.01728.4760.0070.0070.0000.0000.0000.000
173A180VAL00.0440.01430.3780.0010.0010.0000.0000.0000.000
174A181LYS10.8460.93733.0300.0940.0940.0000.0000.0000.000
175A182ASN0-0.068-0.06335.1040.0100.0100.0000.0000.0000.000
176A183GLU-1-0.842-0.91038.750-0.098-0.0980.0000.0000.0000.000
177A184LYS10.8030.91239.1630.0980.0980.0000.0000.0000.000
178A185PHE00.018-0.00543.5600.0040.0040.0000.0000.0000.000
179A186PRO00.0100.02743.967-0.005-0.0050.0000.0000.0000.000
180A187VAL0-0.042-0.03142.4990.0010.0010.0000.0000.0000.000
181A188LYS10.9911.00042.8710.0750.0750.0000.0000.0000.000
182A189ASP-1-0.808-0.90742.508-0.117-0.1170.0000.0000.0000.000
183A190LEU00.0450.01336.754-0.003-0.0030.0000.0000.0000.000
184A191LYS10.9550.98035.2300.1620.1620.0000.0000.0000.000
185A192ASN0-0.040-0.01340.096-0.008-0.0080.0000.0000.0000.000
186A193TYR00.0250.00540.8170.0010.0010.0000.0000.0000.000
187A194LYS10.8490.91534.5760.1960.1960.0000.0000.0000.000
188A195LYS10.8680.94840.3560.1140.1140.0000.0000.0000.000
189A196PHE00.0230.02042.889-0.001-0.0010.0000.0000.0000.000
190A197LEU00.0060.00440.4490.0000.0000.0000.0000.0000.000
191A198THR0-0.027-0.04538.807-0.001-0.0010.0000.0000.0000.000
192A199LYS10.9741.00141.5450.1070.1070.0000.0000.0000.000
193A200ILE0-0.0030.00845.0780.0010.0010.0000.0000.0000.000
194A201PHE00.0380.01241.7570.0010.0010.0000.0000.0000.000
195A202GLN0-0.063-0.01640.838-0.006-0.0060.0000.0000.0000.000
196A203ASN0-0.021-0.02444.5000.0070.0070.0000.0000.0000.000
197A204ARG10.9190.94142.2430.1410.1410.0000.0000.0000.000
198A205ARG10.9910.99245.7500.1120.1120.0000.0000.0000.000
199A206LYS10.8790.95748.5580.1050.1050.0000.0000.0000.000
200A207VAL0-0.0130.00451.057-0.002-0.0020.0000.0000.0000.000
201A208LEU00.0940.02949.788-0.002-0.0020.0000.0000.0000.000
202A209ARG10.9040.93853.3570.0690.0690.0000.0000.0000.000
203A210LYS10.8610.93254.3540.0840.0840.0000.0000.0000.000
204A211LYS10.7010.83847.3830.1090.1090.0000.0000.0000.000
205A212ILE00.0000.01050.492-0.003-0.0030.0000.0000.0000.000
206A213PRO00.0670.03554.4830.0010.0010.0000.0000.0000.000
207A214GLU-1-0.814-0.91458.192-0.062-0.0620.0000.0000.0000.000
208A215GLU-1-0.936-0.95960.084-0.059-0.0590.0000.0000.0000.000
209A216LEU00.0860.03855.9680.0000.0000.0000.0000.0000.000
210A217LEU0-0.068-0.02554.0010.0000.0000.0000.0000.0000.000
211A218LYS10.8470.90157.3880.0590.0590.0000.0000.0000.000
212A219GLU-1-0.895-0.93059.465-0.057-0.0570.0000.0000.0000.000
213A220ALA0-0.023-0.00654.8940.0010.0010.0000.0000.0000.000
214A221GLY0-0.003-0.00256.3680.0000.0000.0000.0000.0000.000
215A222ILE0-0.052-0.02552.633-0.001-0.0010.0000.0000.0000.000
216A223ASN00.0270.00656.5100.0010.0010.0000.0000.0000.000
217A224PRO00.0620.02556.311-0.004-0.0040.0000.0000.0000.000
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