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: V5111

Calculation Name: 3WOH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WOH

Chain ID: A

ChEMBL ID:

UniProt ID: K9M8L2

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptH
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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2639660.83297
FMO2-HF: Nuclear repulsion 2552982.968409
FMO2-HF: Total energy -86677.864561
FMO2-MP2: Total energy -86927.552147


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:5:GLY)


Summations of interaction energy for fragment #1(A:5:GLY)
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.
-1.4492.6060.557-2.158-2.4530
Interaction energy analysis for fragmet #1(A:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.015
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].
3A7LEU0-0.049-0.0223.486-1.1830.637-0.012-0.919-0.889-0.001
4A8SER0-0.066-0.0673.587-0.261-0.0810.002-0.050-0.1320.000
5A9GLY00.0110.0324.747-0.196-0.143-0.001-0.003-0.0490.000
6A10LYS10.8780.9686.729-0.287-0.2870.0000.0000.0000.000
7A11VAL00.0130.0199.3240.1940.1940.0000.0000.0000.000
8A12ALA0-0.005-0.00511.706-0.077-0.0770.0000.0000.0000.000
9A13LEU0-0.007-0.00413.3130.0000.0000.0000.0000.0000.000
10A14VAL00.0210.00815.302-0.025-0.0250.0000.0000.0000.000
11A15THR00.0160.01518.172-0.012-0.0120.0000.0000.0000.000
12A16GLY00.0340.00221.6150.0000.0000.0000.0000.0000.000
13A17GLY00.0300.01419.104-0.001-0.0010.0000.0000.0000.000
14A18SER0-0.036-0.01919.3800.0200.0200.0000.0000.0000.000
15A19ARG10.9100.92821.602-0.145-0.1450.0000.0000.0000.000
16A20GLY00.0440.03122.0250.0050.0050.0000.0000.0000.000
17A21LEU00.0650.01420.0560.0250.0250.0000.0000.0000.000
18A22GLY00.0730.04118.4850.0320.0320.0000.0000.0000.000
19A23ARG10.9640.99817.291-0.187-0.1870.0000.0000.0000.000
20A24ALA00.004-0.00315.6240.0560.0560.0000.0000.0000.000
21A25MET0-0.033-0.01413.9310.0730.0730.0000.0000.0000.000
22A26ALA00.0280.02212.7350.1180.1180.0000.0000.0000.000
23A27LEU00.011-0.00111.5010.1540.1540.0000.0000.0000.000
24A28ARG10.8070.9067.763-0.499-0.4990.0000.0000.0000.000
25A29LEU00.020-0.0088.0580.3590.3590.0000.0000.0000.000
26A30ALA00.0560.0267.4070.5440.5440.0000.0000.0000.000
27A31ARG10.8900.9535.5340.0920.0920.0000.0000.0000.000
28A32ASP-1-0.806-0.8733.5801.5102.3520.082-0.341-0.5820.001
29A33GLY00.0400.0252.7170.0161.0660.477-0.844-0.6830.000
30A34ALA0-0.035-0.0023.728-1.880-1.7700.009-0.001-0.1180.000
31A35ALA00.0170.0057.199-0.066-0.0660.0000.0000.0000.000
32A36VAL0-0.019-0.00310.271-0.111-0.1110.0000.0000.0000.000
33A37ALA0-0.0030.00212.874-0.061-0.0610.0000.0000.0000.000
34A38ILE0-0.029-0.03215.908-0.014-0.0140.0000.0000.0000.000
35A39VAL00.0250.01718.783-0.033-0.0330.0000.0000.0000.000
36A40TYR00.1670.22622.1770.0020.0020.0000.0000.0000.000
37A41VAL00.2630.20524.930-0.007-0.0070.0000.0000.0000.000
38A42SER0-0.514-0.50026.0480.0050.0050.0000.0000.0000.000
39A43ASP-1-0.849-0.93227.6180.1290.1290.0000.0000.0000.000
40A44ASP-1-0.787-0.90625.7960.1640.1640.0000.0000.0000.000
41A45SER0-0.030-0.00624.6160.0150.0150.0000.0000.0000.000
42A46SER00.0430.02423.4660.0050.0050.0000.0000.0000.000
43A47ALA00.0430.05721.0310.0220.0220.0000.0000.0000.000
44A48LYS10.9440.97019.715-0.200-0.2000.0000.0000.0000.000
45A49GLU-1-0.955-0.95820.0420.2010.2010.0000.0000.0000.000
46A50THR0-0.016-0.03315.9490.0150.0150.0000.0000.0000.000
47A51GLN0-0.060-0.04615.5120.0300.0300.0000.0000.0000.000
48A52GLY00.0440.02715.1640.0350.0350.0000.0000.0000.000
49A53GLU-1-0.944-0.95414.1650.2570.2570.0000.0000.0000.000
50A54ILE0-0.025-0.02010.0110.0290.0290.0000.0000.0000.000
51A55GLU-1-0.872-0.91610.7050.4060.4060.0000.0000.0000.000
52A56ARG10.8690.94012.558-0.244-0.2440.0000.0000.0000.000
53A57LEU0-0.096-0.0468.513-0.044-0.0440.0000.0000.0000.000
54A58GLY0-0.008-0.0088.3900.0350.0350.0000.0000.0000.000
55A59GLY0-0.0030.0027.7600.1650.1650.0000.0000.0000.000
56A60THR0-0.020-0.0268.660-0.206-0.2060.0000.0000.0000.000
57A61ALA00.0420.00811.0290.0910.0910.0000.0000.0000.000
58A62ARG10.9210.97313.863-0.379-0.3790.0000.0000.0000.000
59A63SER0-0.0030.01017.5240.0170.0170.0000.0000.0000.000
60A64TYR0-0.030-0.04118.607-0.004-0.0040.0000.0000.0000.000
61A65ARG10.9500.99723.328-0.125-0.1250.0000.0000.0000.000
62A66CYS0-0.0170.00026.158-0.008-0.0080.0000.0000.0000.000
63A67ASP-1-0.823-0.90027.9080.1070.1070.0000.0000.0000.000
64A68VAL0-0.061-0.04426.631-0.001-0.0010.0000.0000.0000.000
65A69SER00.0150.00529.186-0.004-0.0040.0000.0000.0000.000
66A70ASP-1-0.909-0.96432.6570.0860.0860.0000.0000.0000.000
67A71ALA0-0.006-0.00332.2730.0050.0050.0000.0000.0000.000
68A72GLU-1-0.855-0.86730.9840.0980.0980.0000.0000.0000.000
69A73GLN00.0520.03429.9860.0060.0060.0000.0000.0000.000
70A74VAL00.0390.00826.2930.0100.0100.0000.0000.0000.000
71A75THR0-0.066-0.12826.5680.0110.0110.0000.0000.0000.000
72A76ARG10.8930.95026.841-0.093-0.0930.0000.0000.0000.000
73A77CYS00.0360.02123.9580.0120.0120.0000.0000.0000.000
74A78VAL00.0480.02921.9490.0170.0170.0000.0000.0000.000
75A79LYS10.9260.96321.992-0.098-0.0980.0000.0000.0000.000
76A80ALA0-0.0050.01123.565-0.002-0.0020.0000.0000.0000.000
77A81VAL00.0150.01417.5540.0110.0110.0000.0000.0000.000
78A82THR0-0.081-0.05918.4980.0170.0170.0000.0000.0000.000
79A83ALA0-0.072-0.02919.5130.0000.0000.0000.0000.0000.000
80A84ASP-1-0.892-0.94518.6940.2280.2280.0000.0000.0000.000
81A85LEU0-0.063-0.03813.8470.0230.0230.0000.0000.0000.000
82A86GLY00.0480.04214.4590.0200.0200.0000.0000.0000.000
83A87PRO0-0.061-0.04316.1550.0010.0010.0000.0000.0000.000
84A88VAL00.0550.02815.3810.0260.0260.0000.0000.0000.000
85A89ASP-1-0.861-0.92812.6710.2390.2390.0000.0000.0000.000
86A90ILE00.0080.00510.558-0.033-0.0330.0000.0000.0000.000
87A91LEU0-0.026-0.00214.8110.0240.0240.0000.0000.0000.000
88A92VAL00.0100.01215.804-0.021-0.0210.0000.0000.0000.000
89A93ASN0-0.027-0.02818.7940.0060.0060.0000.0000.0000.000
90A94ASN00.021-0.01320.901-0.020-0.0200.0000.0000.0000.000
91A95ALA0-0.077-0.02422.985-0.009-0.0090.0000.0000.0000.000
92A96GLY00.0450.01325.880-0.008-0.0080.0000.0000.0000.000
93A97ILE0-0.057-0.01528.9160.0020.0020.0000.0000.0000.000
94A98ILE00.0210.00030.209-0.003-0.0030.0000.0000.0000.000
95A99ARG10.9210.95133.971-0.076-0.0760.0000.0000.0000.000
96A100ASP-1-0.856-0.90237.0530.0630.0630.0000.0000.0000.000
97A101GLY00.0360.01639.473-0.001-0.0010.0000.0000.0000.000
98A102LEU0-0.001-0.01443.0930.0000.0000.0000.0000.0000.000
99A103ALA00.032-0.00345.0030.0010.0010.0000.0000.0000.000
100A104ALA00.0060.00945.9050.0000.0000.0000.0000.0000.000
101A105SER0-0.107-0.05246.1140.0000.0000.0000.0000.0000.000
102A106ILE0-0.0260.00341.9870.0020.0020.0000.0000.0000.000
103A107LYS10.9950.99644.194-0.045-0.0450.0000.0000.0000.000
104A108ASP-1-0.853-0.92043.5980.0490.0490.0000.0000.0000.000
105A109GLU-1-0.966-0.97442.6090.0570.0570.0000.0000.0000.000
106A110ASP-1-0.854-0.95640.0550.0610.0610.0000.0000.0000.000
107A111TYR0-0.032-0.03338.9380.0050.0050.0000.0000.0000.000
108A112ASP-1-0.800-0.91738.7130.0620.0620.0000.0000.0000.000
109A113ALA0-0.046-0.01036.5940.0060.0060.0000.0000.0000.000
110A114VAL0-0.0620.00434.3710.0080.0080.0000.0000.0000.000
111A115MET00.0470.02633.7300.0080.0080.0000.0000.0000.000
112A116ASN0-0.017-0.02534.1200.0020.0020.0000.0000.0000.000
113A117THR0-0.058-0.06430.6830.0080.0080.0000.0000.0000.000
114A118ASN0-0.055-0.03329.3760.0160.0160.0000.0000.0000.000
115A119LEU0-0.0220.01029.4260.0040.0040.0000.0000.0000.000
116A120LYS10.9460.97630.571-0.074-0.0740.0000.0000.0000.000
117A121GLY00.0790.04128.6710.0020.0020.0000.0000.0000.000
118A122ALA00.0050.00926.0510.0080.0080.0000.0000.0000.000
119A123PHE0-0.004-0.00326.8680.0020.0020.0000.0000.0000.000
120A124LEU0-0.047-0.00529.047-0.002-0.0020.0000.0000.0000.000
121A125PHE00.028-0.00723.2400.0040.0040.0000.0000.0000.000
122A126ILE00.0060.00924.1540.0070.0070.0000.0000.0000.000
123A127LYS10.9370.97125.430-0.087-0.0870.0000.0000.0000.000
124A128ALA0-0.049-0.01925.039-0.004-0.0040.0000.0000.0000.000
125A129CYS0-0.040-0.01821.0890.0080.0080.0000.0000.0000.000
126A130TYR00.0400.02222.747-0.002-0.0020.0000.0000.0000.000
127A131PHE00.0440.00425.051-0.007-0.0070.0000.0000.0000.000
128A132GLY0-0.030-0.00621.921-0.007-0.0070.0000.0000.0000.000
129A133PHE00.0350.01017.452-0.009-0.0090.0000.0000.0000.000
130A134ILE00.0370.03521.240-0.014-0.0140.0000.0000.0000.000
131A135ARG10.8490.91623.447-0.085-0.0850.0000.0000.0000.000
132A136LYS10.8560.92216.334-0.190-0.1900.0000.0000.0000.000
133A137ARG10.8750.95819.586-0.043-0.0430.0000.0000.0000.000
134A138SER00.0620.04015.579-0.009-0.0090.0000.0000.0000.000
135A139GLY00.0570.01216.6920.0150.0150.0000.0000.0000.000
136A140SER0-0.078-0.04615.148-0.026-0.0260.0000.0000.0000.000
137A141ILE00.0310.00516.9860.0430.0430.0000.0000.0000.000
138A142ILE0-0.002-0.00715.880-0.020-0.0200.0000.0000.0000.000
139A143ASN0-0.004-0.02319.8740.0290.0290.0000.0000.0000.000
140A144ILE00.0050.00420.080-0.010-0.0100.0000.0000.0000.000
141A145SER0-0.033-0.03723.759-0.010-0.0100.0000.0000.0000.000
142A146SER00.0580.07326.573-0.002-0.0020.0000.0000.0000.000
143A147VAL00.0800.04327.898-0.005-0.0050.0000.0000.0000.000
144A148SER0-0.006-0.00230.206-0.006-0.0060.0000.0000.0000.000
145A149GLY0-0.018-0.02331.661-0.003-0.0030.0000.0000.0000.000
146A150VAL0-0.070-0.03229.799-0.002-0.0020.0000.0000.0000.000
147A151PHE0-0.009-0.01132.926-0.004-0.0040.0000.0000.0000.000
148A152GLY00.0110.02335.785-0.003-0.0030.0000.0000.0000.000
149A153SER0-0.006-0.03736.3530.0000.0000.0000.0000.0000.000
150A154ALA00.0270.01338.4230.0010.0010.0000.0000.0000.000
151A155GLY0-0.011-0.00440.6330.0010.0010.0000.0000.0000.000
152A156GLN00.0270.02234.3830.0010.0010.0000.0000.0000.000
153A157ALA00.0340.02337.8140.0030.0030.0000.0000.0000.000
154A158ASN00.0310.04138.5890.0010.0010.0000.0000.0000.000
155A159TYR00.0530.02829.4170.0070.0070.0000.0000.0000.000
156A160ALA00.018-0.00233.9520.0040.0040.0000.0000.0000.000
157A161SER0-0.013-0.03134.914-0.001-0.0010.0000.0000.0000.000
158A162ALA00.0280.02033.2570.0010.0010.0000.0000.0000.000
159A163LYS10.8540.94526.915-0.115-0.1150.0000.0000.0000.000
160A164ALA00.0310.02330.8470.0020.0020.0000.0000.0000.000
161A165GLY0-0.007-0.00433.027-0.002-0.0020.0000.0000.0000.000
162A166LEU00.0070.00426.2030.0000.0000.0000.0000.0000.000
163A167ILE0-0.0230.00128.6940.0030.0030.0000.0000.0000.000
164A168GLY0-0.010-0.00829.966-0.003-0.0030.0000.0000.0000.000
165A169LEU00.0050.00728.081-0.003-0.0030.0000.0000.0000.000
166A170THR00.0310.01125.1680.0040.0040.0000.0000.0000.000
167A171LYS10.9020.96327.302-0.046-0.0460.0000.0000.0000.000
168A172SER0-0.021-0.01329.663-0.006-0.0060.0000.0000.0000.000
169A173ILE00.0460.02525.359-0.002-0.0020.0000.0000.0000.000
170A174ALA0-0.0130.00125.695-0.002-0.0020.0000.0000.0000.000
171A175LYS10.9060.93426.665-0.033-0.0330.0000.0000.0000.000
172A176GLU-1-0.967-0.95829.1320.0550.0550.0000.0000.0000.000
173A177LEU0-0.024-0.01224.053-0.001-0.0010.0000.0000.0000.000
174A178ALA00.0250.02125.306-0.003-0.0030.0000.0000.0000.000
175A179GLU-1-0.915-0.95725.5190.0050.0050.0000.0000.0000.000
176A180ARG10.7900.90125.131-0.036-0.0360.0000.0000.0000.000
177A181ASN0-0.047-0.03618.8160.0000.0000.0000.0000.0000.000
178A182VAL0-0.059-0.01120.1610.0080.0080.0000.0000.0000.000
179A183ARG10.8650.94014.843-0.065-0.0650.0000.0000.0000.000
180A184CYS0-0.0590.00220.5980.0210.0210.0000.0000.0000.000
181A185ASN00.011-0.01020.126-0.030-0.0300.0000.0000.0000.000
182A186ALA00.0060.00622.5170.0170.0170.0000.0000.0000.000
183A187VAL00.0110.00319.308-0.009-0.0090.0000.0000.0000.000
184A188ALA00.1070.01222.7290.0050.0050.0000.0000.0000.000
185A189PRO0-0.085-0.04022.645-0.010-0.0100.0000.0000.0000.000
186A190GLY00.0330.01124.967-0.006-0.0060.0000.0000.0000.000
187A191LEU0-0.029-0.01427.8250.0070.0070.0000.0000.0000.000
188A192ILE0-0.043-0.01222.872-0.001-0.0010.0000.0000.0000.000
189A193ALA00.0160.04826.0200.0000.0000.0000.0000.0000.000
190A194THR0-0.070-0.11623.2160.0100.0100.0000.0000.0000.000
191A195ASP-1-0.879-0.88825.7790.1270.1270.0000.0000.0000.000
192A206ARG10.9620.96036.207-0.028-0.0280.0000.0000.0000.000
193A207LEU0-0.025-0.01931.4230.0000.0000.0000.0000.0000.000
194A208ASP-1-0.854-0.91134.7650.0220.0220.0000.0000.0000.000
195A209PRO0-0.045-0.01235.271-0.002-0.0020.0000.0000.0000.000
196A210VAL0-0.002-0.00630.1240.0010.0010.0000.0000.0000.000
197A211PRO00.0430.03031.693-0.002-0.0020.0000.0000.0000.000
198A212MET0-0.021-0.00725.1060.0000.0000.0000.0000.0000.000
199A213ARG10.9320.96930.549-0.015-0.0150.0000.0000.0000.000
200A214ARG10.7470.84922.628-0.044-0.0440.0000.0000.0000.000
201A215PHE00.0360.01827.5290.0010.0010.0000.0000.0000.000
202A216GLY00.0100.00124.114-0.006-0.0060.0000.0000.0000.000
203A217ARG10.8930.93617.794-0.084-0.0840.0000.0000.0000.000
204A218PRO00.0220.00319.0490.0050.0050.0000.0000.0000.000
205A219ASP-1-0.836-0.92514.7210.1740.1740.0000.0000.0000.000
206A220GLU-1-0.768-0.86615.2510.0760.0760.0000.0000.0000.000
207A221VAL00.0080.00317.383-0.006-0.0060.0000.0000.0000.000
208A222ALA0-0.023-0.01013.7780.0110.0110.0000.0000.0000.000
209A223GLY00.0030.00312.6240.0580.0580.0000.0000.0000.000
210A224LEU00.0010.01413.413-0.001-0.0010.0000.0000.0000.000
211A225VAL00.006-0.01414.141-0.012-0.0120.0000.0000.0000.000
212A226ALA00.0070.0029.6660.0160.0160.0000.0000.0000.000
213A227PHE00.0140.01011.424-0.017-0.0170.0000.0000.0000.000
214A228LEU0-0.021-0.00113.052-0.044-0.0440.0000.0000.0000.000
215A229ALA0-0.0070.03011.781-0.024-0.0240.0000.0000.0000.000
216A230GLY0-0.0060.01110.5820.0160.0160.0000.0000.0000.000
217A231ASP-1-0.872-0.95010.932-0.136-0.1360.0000.0000.0000.000
218A232GLU-1-0.933-0.96911.476-0.396-0.3960.0000.0000.0000.000
219A233SER0-0.045-0.04514.2290.0200.0200.0000.0000.0000.000
220A234SER0-0.020-0.01216.3960.0340.0340.0000.0000.0000.000
221A235TYR00.0210.01417.9240.0110.0110.0000.0000.0000.000
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223A237THR00.022-0.00821.1050.0210.0210.0000.0000.0000.000
224A238GLY00.0270.02023.645-0.008-0.0080.0000.0000.0000.000
225A239GLN0-0.035-0.01523.766-0.004-0.0040.0000.0000.0000.000
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227A241VAL0-0.0020.00721.442-0.010-0.0100.0000.0000.0000.000
228A242CYS00.0020.00523.5880.0160.0160.0000.0000.0000.000
229A243VAL0-0.019-0.00920.478-0.003-0.0030.0000.0000.0000.000
230A244ASP-1-0.740-0.88923.5870.0530.0530.0000.0000.0000.000
231A245GLY00.0090.00125.930-0.004-0.0040.0000.0000.0000.000
232A246GLY0-0.003-0.01227.491-0.007-0.0070.0000.0000.0000.000
233A247MET0-0.089-0.03929.7500.0000.0000.0000.0000.0000.000
234A248ALA0-0.034-0.02230.652-0.002-0.0020.0000.0000.0000.000
235A249MET0-0.050-0.00330.970-0.003-0.0030.0000.0000.0000.000