FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: QY19Y

Calculation Name: 3WGO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WGO

Chain ID: A

ChEMBL ID:

UniProt ID: Q890V3

Base Structure: X-ray

Registration Date: 2023-06-21

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 323
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4622488.135203
FMO2-HF: Nuclear repulsion 4496531.548421
FMO2-HF: Total energy -125956.586782
FMO2-MP2: Total energy -126324.775974


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:4:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-51.66-48.1186.096-4.579-5.062-0.052
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.927 / q_NPA : 0.942
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].
3A6ARG10.8620.9433.80043.92745.526-0.010-0.598-0.9910.003
4A7ILE00.0390.0146.0152.3322.3320.0000.0000.0000.000
5A8GLY00.0180.0149.0320.3840.3840.0000.0000.0000.000
6A9ILE0-0.014-0.00312.6210.5050.5050.0000.0000.0000.000
7A10VAL00.0180.02215.1090.4940.4940.0000.0000.0000.000
8A11GLY00.0200.01318.6430.4780.4780.0000.0000.0000.000
9A12TYR0-0.046-0.07518.302-0.048-0.0480.0000.0000.0000.000
10A13GLY00.0200.01021.5170.4060.4060.0000.0000.0000.000
11A14ASN00.032-0.00622.190-0.485-0.4850.0000.0000.0000.000
12A15ILE00.0630.04919.093-0.266-0.2660.0000.0000.0000.000
13A16GLY00.0810.04217.928-0.560-0.5600.0000.0000.0000.000
14A17LYS10.9080.95917.16010.91010.9100.0000.0000.0000.000
15A18GLY00.0370.01617.576-0.390-0.3900.0000.0000.0000.000
16A19VAL0-0.008-0.00712.991-0.448-0.4480.0000.0000.0000.000
17A20GLU-1-0.863-0.90313.056-15.945-15.9450.0000.0000.0000.000
18A21LYS10.8280.91213.03912.27812.2780.0000.0000.0000.000
19A22ALA00.0550.03213.369-0.388-0.3880.0000.0000.0000.000
20A23ILE00.001-0.0047.530-0.573-0.5730.0000.0000.0000.000
21A24LYS10.9190.9638.58514.99614.9960.0000.0000.0000.000
22A25GLN0-0.056-0.01310.820-0.032-0.0320.0000.0000.0000.000
23A26ASN0-0.059-0.0387.2320.2680.2680.0000.0000.0000.000
24A27ASP-1-0.826-0.9116.284-24.632-24.6320.0000.0000.0000.000
25A28ASP-1-0.890-0.9243.044-35.268-34.2560.071-0.353-0.730-0.002
26A29MET0-0.063-0.0362.039-11.759-11.4236.035-3.606-2.766-0.053
27A30GLU-1-0.815-0.8803.598-34.050-33.6000.0020.000-0.4530.000
28A31LEU0-0.071-0.0255.515-0.073-0.111-0.001-0.0010.0400.000
29A32GLH0-0.059-0.0636.6141.1561.1560.0000.0000.0000.000
30A33ALA0-0.016-0.02510.1761.0341.0340.0000.0000.0000.000
31A34ILE0-0.0120.01313.879-0.233-0.2330.0000.0000.0000.000
32A35PHE00.0290.00514.8550.6530.6530.0000.0000.0000.000
33A36THR0-0.041-0.01919.4450.4830.4830.0000.0000.0000.000
34A37ARG10.9960.98023.04311.19711.1970.0000.0000.0000.000
35A38ARG10.9230.97626.1649.7639.7630.0000.0000.0000.000
36A39ASP-1-0.870-0.94027.378-9.566-9.5660.0000.0000.0000.000
37A40ILE00.005-0.00428.056-0.152-0.1520.0000.0000.0000.000
38A41ASN0-0.007-0.00229.136-0.098-0.0980.0000.0000.0000.000
39A42LYS10.8760.92926.12210.73710.7370.0000.0000.0000.000
40A43VAL00.0340.02128.5010.1770.1770.0000.0000.0000.000
41A44ASP-1-0.722-0.86126.168-10.718-10.7180.0000.0000.0000.000
42A45SER0-0.133-0.06421.922-0.118-0.1180.0000.0000.0000.000
43A46ASN0-0.082-0.05323.567-0.317-0.3170.0000.0000.0000.000
44A47ASN00.0160.02721.838-0.227-0.2270.0000.0000.0000.000
45A48SER0-0.014-0.01518.893-0.256-0.2560.0000.0000.0000.000
46A49LYS11.0011.00711.27319.85619.8560.0000.0000.0000.000
47A50LEU0-0.044-0.00916.800-0.361-0.3610.0000.0000.0000.000
48A51VAL00.0260.01717.2600.2970.2970.0000.0000.0000.000
49A52HIS00.0390.06420.107-0.195-0.1950.0000.0000.0000.000
50A53ILE00.026-0.00821.603-0.384-0.3840.0000.0000.0000.000
51A54SER0-0.034-0.06122.758-0.283-0.2830.0000.0000.0000.000
52A55ARG10.9570.97818.89314.38114.3810.0000.0000.0000.000
53A56LEU0-0.029-0.00117.594-0.612-0.6120.0000.0000.0000.000
54A57GLU-1-0.868-0.94517.932-15.048-15.0480.0000.0000.0000.000
55A58LEU0-0.010-0.00418.775-0.555-0.5550.0000.0000.0000.000
56A59TYR0-0.065-0.04212.787-0.373-0.3730.0000.0000.0000.000
57A60LYS10.9970.99513.68816.21616.2160.0000.0000.0000.000
58A61ASP-1-0.921-0.96012.040-21.964-21.9640.0000.0000.0000.000
59A62THR0-0.044-0.0099.690-2.651-2.6510.0000.0000.0000.000
60A63VAL0-0.055-0.0408.918-1.377-1.3770.0000.0000.0000.000
61A64ASP-1-0.836-0.9095.797-40.355-40.3550.0000.0000.0000.000
62A65VAL0-0.017-0.0189.1801.7641.7640.0000.0000.0000.000
63A66MET0-0.0150.02111.528-0.112-0.1120.0000.0000.0000.000
64A67ILE00.004-0.00611.4080.8000.8000.0000.0000.0000.000
65A68LEU0-0.016-0.01915.2270.4150.4150.0000.0000.0000.000
66A69CYS0-0.056-0.01817.4100.1860.1860.0000.0000.0000.000
67A70GLY0-0.037-0.01420.1170.4220.4220.0000.0000.0000.000
68A71GLY00.0170.00323.731-0.086-0.0860.0000.0000.0000.000
69A72SER00.0040.01426.2710.1820.1820.0000.0000.0000.000
70A73ALA00.0790.03527.829-0.263-0.2630.0000.0000.0000.000
71A74THR0-0.005-0.02429.186-0.083-0.0830.0000.0000.0000.000
72A75ASP-1-0.863-0.93428.303-9.661-9.6610.0000.0000.0000.000
73A76LEU0-0.055-0.02923.075-0.221-0.2210.0000.0000.0000.000
74A77VAL0-0.016-0.00626.925-0.287-0.2870.0000.0000.0000.000
75A78GLU-1-0.848-0.92829.484-9.573-9.5730.0000.0000.0000.000
76A79GLN0-0.074-0.04924.836-0.130-0.1300.0000.0000.0000.000
77A80GLY00.0210.01123.251-0.502-0.5020.0000.0000.0000.000
78A81PRO00.0440.01123.257-0.555-0.5550.0000.0000.0000.000
79A82MET00.0110.02224.435-0.162-0.1620.0000.0000.0000.000
80A83ILE0-0.023-0.00718.667-0.416-0.4160.0000.0000.0000.000
81A84ALA00.0610.03219.801-0.719-0.7190.0000.0000.0000.000
82A85SER0-0.076-0.05020.433-0.363-0.3630.0000.0000.0000.000
83A86GLN0-0.077-0.04919.335-0.287-0.2870.0000.0000.0000.000
84A87PHE0-0.024-0.01413.995-0.967-0.9670.0000.0000.0000.000
85A88ASN00.0550.04111.7642.5122.5120.0000.0000.0000.000
86A89THR0-0.0130.00715.114-0.233-0.2330.0000.0000.0000.000
87A90VAL00.0260.02114.0740.0900.0900.0000.0000.0000.000
88A91ASP-1-0.805-0.87317.082-12.487-12.4870.0000.0000.0000.000
89A92SER00.0490.00620.155-0.236-0.2360.0000.0000.0000.000
90A93PHE0-0.055-0.04022.4870.5170.5170.0000.0000.0000.000
91A94ASP-1-0.850-0.92825.734-9.860-9.8600.0000.0000.0000.000
92A95ASN00.0000.01328.1940.4120.4120.0000.0000.0000.000
93A96HIS00.0620.00229.9100.1220.1220.0000.0000.0000.000
94A97GLY00.0240.01832.429-0.021-0.0210.0000.0000.0000.000
95A98ARG10.9000.93832.7548.4438.4430.0000.0000.0000.000
96A99ILE00.0300.03028.472-0.140-0.1400.0000.0000.0000.000
97A100PRO0-0.015-0.00130.074-0.318-0.3180.0000.0000.0000.000
98A101GLN00.0830.04131.949-0.201-0.2010.0000.0000.0000.000
99A102HIS0-0.078-0.05124.3050.2010.2010.0000.0000.0000.000
100A103PHE00.009-0.00725.248-0.306-0.3060.0000.0000.0000.000
101A104GLU-1-0.926-0.94927.404-9.305-9.3050.0000.0000.0000.000
102A105ARG10.9250.97728.7409.9239.9230.0000.0000.0000.000
103A106MET0-0.031-0.01122.201-0.216-0.2160.0000.0000.0000.000
104A107ASP-1-0.834-0.89724.286-12.184-12.1840.0000.0000.0000.000
105A108GLU-1-0.957-0.97625.302-10.069-10.0690.0000.0000.0000.000
106A109ILE0-0.068-0.03323.389-0.185-0.1850.0000.0000.0000.000
107A110SER0-0.004-0.01420.541-0.327-0.3270.0000.0000.0000.000
108A111LYS10.9070.94721.55810.91610.9160.0000.0000.0000.000
109A112LYS10.8800.95423.61510.77610.7760.0000.0000.0000.000
110A113ALA0-0.015-0.00420.9840.0190.0190.0000.0000.0000.000
111A114GLY0-0.032-0.00120.041-0.652-0.6520.0000.0000.0000.000
112A115ASN0-0.033-0.01416.709-1.795-1.7950.0000.0000.0000.000
113A116ILE0-0.025-0.01614.7310.7910.7910.0000.0000.0000.000
114A117SER0-0.013-0.03416.888-0.586-0.5860.0000.0000.0000.000
115A118LEU0-0.054-0.00316.8850.5020.5020.0000.0000.0000.000
116A119ILE0-0.016-0.01319.540-0.099-0.0990.0000.0000.0000.000
117A120SER0-0.078-0.05222.4050.0910.0910.0000.0000.0000.000
118A121THR0-0.008-0.00318.0300.3510.3510.0000.0000.0000.000
119A122GLY00.0730.02320.9470.1380.1380.0000.0000.0000.000
120A123TRP0-0.005-0.00821.806-0.045-0.0450.0000.0000.0000.000
121A124ASP-1-0.810-0.87424.485-9.153-9.1530.0000.0000.0000.000
122A125PRO00.0360.02725.3560.2290.2290.0000.0000.0000.000
123A126GLY00.0250.00023.312-0.341-0.3410.0000.0000.0000.000
124A127LEU0-0.005-0.01420.6370.1920.1920.0000.0000.0000.000
125A128PHE0-0.014-0.01324.4320.2280.2280.0000.0000.0000.000
126A129SER00.0130.00026.6970.3140.3140.0000.0000.0000.000
127A130LEU00.0160.01622.3110.2600.2600.0000.0000.0000.000
128A131ASN0-0.014-0.01426.5960.3790.3790.0000.0000.0000.000
129A132ARG10.8180.90629.4609.3869.3860.0000.0000.0000.000
130A133LEU00.0460.03828.4670.2330.2330.0000.0000.0000.000
131A134LEU00.0140.00428.6130.2150.2150.0000.0000.0000.000
132A135GLY00.023-0.01731.3260.2190.2190.0000.0000.0000.000
133A136GLU-1-0.988-1.00734.507-7.974-7.9740.0000.0000.0000.000
134A137SER0-0.041-0.02333.4180.1560.1560.0000.0000.0000.000
135A138ILE0-0.040-0.01532.6090.1350.1350.0000.0000.0000.000
136A139LEU0-0.022-0.00136.2180.2390.2390.0000.0000.0000.000
137A140PRO00.0570.04839.3490.0920.0920.0000.0000.0000.000
138A141LYS10.8750.94040.7666.8366.8360.0000.0000.0000.000
139A142GLY00.0590.01142.3300.0400.0400.0000.0000.0000.000
140A143LYS10.7770.89442.0836.5366.5360.0000.0000.0000.000
141A144THR00.0590.03735.609-0.041-0.0410.0000.0000.0000.000
142A145HIS0-0.044-0.00838.0170.0330.0330.0000.0000.0000.000
143A146THR0-0.0050.01133.226-0.154-0.1540.0000.0000.0000.000
144A147PHE00.006-0.01735.0660.2230.2230.0000.0000.0000.000
145A148TRP00.004-0.00931.587-0.093-0.0930.0000.0000.0000.000
146A149GLY00.013-0.04033.3870.2080.2080.0000.0000.0000.000
147A150LYS10.9390.98034.7757.2787.2780.0000.0000.0000.000
148A151GLY00.0660.02232.940-0.191-0.1910.0000.0000.0000.000
149A152VAL0-0.0300.00632.4030.1970.1970.0000.0000.0000.000
150A153SER00.0530.01833.355-0.151-0.1510.0000.0000.0000.000
151A154LEU0-0.066-0.02228.861-0.081-0.0810.0000.0000.0000.000
152A155GLY00.1020.05133.5440.1480.1480.0000.0000.0000.000
153A156HIS00.0270.00135.5460.0550.0550.0000.0000.0000.000
154A157SER0-0.024-0.01635.6860.2190.2190.0000.0000.0000.000
155A158ASP-1-0.875-0.96334.940-8.081-8.0810.0000.0000.0000.000
156A159ALA0-0.054-0.02138.3190.1600.1600.0000.0000.0000.000
157A160ILE0-0.029-0.02541.0040.1580.1580.0000.0000.0000.000
158A161ARG10.9290.97336.2317.8387.8380.0000.0000.0000.000
159A162ARG10.8580.94939.7327.2307.2300.0000.0000.0000.000
160A163VAL0-0.048-0.00444.4120.0940.0940.0000.0000.0000.000
161A164GLN0-0.009-0.01747.4710.0180.0180.0000.0000.0000.000
162A165GLY00.0960.07050.0660.0650.0650.0000.0000.0000.000
163A166VAL0-0.061-0.02244.848-0.036-0.0360.0000.0000.0000.000
164A167LYS10.9881.00844.4786.2846.2840.0000.0000.0000.000
165A168ASN0-0.057-0.05339.254-0.303-0.3030.0000.0000.0000.000
166A169GLY00.0240.01740.4600.1750.1750.0000.0000.0000.000
167A170ILE0-0.061-0.01835.466-0.241-0.2410.0000.0000.0000.000
168A171GLN00.018-0.01937.8440.0030.0030.0000.0000.0000.000
169A172TYR0-0.076-0.05335.684-0.282-0.2820.0000.0000.0000.000
170A173ILE00.0560.02935.8240.2380.2380.0000.0000.0000.000
171A174ILE0-0.003-0.03237.538-0.186-0.1860.0000.0000.0000.000
172A175PRO0-0.0340.00437.0070.1610.1610.0000.0000.0000.000
173A176ILE00.0390.03140.1120.0690.0690.0000.0000.0000.000
174A177LYS10.8500.91242.6406.6006.6000.0000.0000.0000.000
175A178GLY00.0380.01743.865-0.023-0.0230.0000.0000.0000.000
176A179ALA00.0410.02343.7560.0240.0240.0000.0000.0000.000
177A180LEU0-0.031-0.01037.772-0.058-0.0580.0000.0000.0000.000
178A181ASP-1-0.797-0.90641.850-6.706-6.7060.0000.0000.0000.000
179A182LYS10.8840.95844.1045.9985.9980.0000.0000.0000.000
180A183ALA0-0.036-0.02740.9300.0150.0150.0000.0000.0000.000
181A184ARG10.8410.90036.5587.5117.5110.0000.0000.0000.000
182A185SER0-0.040-0.01741.8400.0290.0290.0000.0000.0000.000
183A186GLY00.0090.00443.9650.0520.0520.0000.0000.0000.000
184A187GLU-1-0.924-0.96744.860-5.861-5.8610.0000.0000.0000.000
185A188GLN0-0.046-0.01244.9510.0070.0070.0000.0000.0000.000
186A189CYS00.017-0.00546.0480.1370.1370.0000.0000.0000.000
187A190ASP-1-0.871-0.91746.018-6.502-6.5020.0000.0000.0000.000
188A191PHE0-0.004-0.00443.7700.0450.0450.0000.0000.0000.000
189A192THR00.002-0.00246.202-0.081-0.0810.0000.0000.0000.000
190A193THR00.030-0.01042.853-0.084-0.0840.0000.0000.0000.000
191A194ARG10.8590.92444.5365.8535.8530.0000.0000.0000.000
192A195GLU-1-0.877-0.93047.213-6.020-6.0200.0000.0000.0000.000
193A196LYS10.8490.93638.9277.2857.2850.0000.0000.0000.000
194A197HIS00.0200.02338.224-0.265-0.2650.0000.0000.0000.000
195A198GLU-1-0.937-0.94642.388-6.288-6.2880.0000.0000.0000.000
196A199MET0-0.0180.02339.842-0.245-0.2450.0000.0000.0000.000
197A200VAL0-0.0130.00142.1540.1850.1850.0000.0000.0000.000
198A201CYS0-0.055-0.03242.003-0.218-0.2180.0000.0000.0000.000
199A202TYR00.0250.00941.7140.1080.1080.0000.0000.0000.000
200A203VAL00.007-0.01242.844-0.166-0.1660.0000.0000.0000.000
201A204VAL00.0020.00843.3600.1150.1150.0000.0000.0000.000
202A205PRO0-0.037-0.02946.110-0.047-0.0470.0000.0000.0000.000
203A206GLU-1-0.985-0.96849.108-5.681-5.6810.0000.0000.0000.000
204A207GLU-1-0.858-0.92150.369-6.006-6.0060.0000.0000.0000.000
205A208ASN0-0.103-0.05952.6010.0420.0420.0000.0000.0000.000
206A209ALA00.033-0.00154.5320.0960.0960.0000.0000.0000.000
207A210ASP-1-0.930-0.98153.359-5.503-5.5030.0000.0000.0000.000
208A211LEU0-0.0500.01855.3550.0250.0250.0000.0000.0000.000
209A212LYS11.0771.00953.7505.3485.3480.0000.0000.0000.000
210A213LYS10.9030.93353.9224.9774.9770.0000.0000.0000.000
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