FMODB

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

Last updated: 2025-10-14

All entries: 75777

Number of unique PDB entries: 32023

tag_button

FMODB ID: N6LYQ

Calculation Name: 6WOO-q-Other547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate | n-carboxy-l-threonine | zinc ion

Ligand 3-letter code: GDP | U6A | ZN

Ligand of Interest (LOI):

PDB ID: 6WOO

Chain ID: q

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2408205.812997
FMO2-HF: Nuclear repulsion 2322002.025706
FMO2-HF: Total energy -86203.787291
FMO2-MP2: Total energy -86452.433419


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
128.096130.8740.948-1.344-2.38-0.013
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.888 / q_NPA : 0.930
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].
3A3LYS11.0011.0093.88242.51743.533-0.009-0.381-0.6250.000
4A4ILE00.0330.0232.151-11.392-10.1740.951-0.843-1.326-0.012
5A5THR00.0450.0183.0105.4995.9500.007-0.114-0.343-0.001
6A6SER00.016-0.0074.9838.4178.510-0.001-0.006-0.0860.000
7A7SER0-0.035-0.0066.8264.8614.8610.0000.0000.0000.000
8A8GLN00.0610.0298.2110.3570.3570.0000.0000.0000.000
9A9VAL0-0.020-0.0138.3822.3392.3390.0000.0000.0000.000
10A10ARG10.8450.91510.70422.99122.9910.0000.0000.0000.000
11A11GLU-1-0.848-0.91812.733-20.387-20.3870.0000.0000.0000.000
12A12HIS00.0200.00313.0001.1671.1670.0000.0000.0000.000
13A13VAL00.0370.01214.7511.1951.1950.0000.0000.0000.000
14A14LYS10.9180.96116.78715.68415.6840.0000.0000.0000.000
15A15GLU-1-0.948-0.98618.181-15.075-15.0750.0000.0000.0000.000
16A16LEU00.0000.03018.5060.6360.6360.0000.0000.0000.000
17A17LEU00.0250.01920.3730.9360.9360.0000.0000.0000.000
18A18LYS10.8630.93322.96212.64212.6420.0000.0000.0000.000
19A19TYR00.0770.05023.0590.5990.5990.0000.0000.0000.000
20A20SER00.005-0.02526.3350.2430.2430.0000.0000.0000.000
21A21ASN0-0.043-0.02028.9070.5620.5620.0000.0000.0000.000
22A22GLU-1-0.859-0.93522.103-13.769-13.7690.0000.0000.0000.000
23A23THR0-0.007-0.04224.1960.1840.1840.0000.0000.0000.000
24A24LYS10.8530.92826.2979.9159.9150.0000.0000.0000.000
25A25LYS10.8750.94226.63111.85611.8560.0000.0000.0000.000
26A26ARG10.9000.96729.9289.9259.9250.0000.0000.0000.000
27A27ASN0-0.012-0.01331.880-0.302-0.3020.0000.0000.0000.000
28A28PHE00.0290.01032.1930.1260.1260.0000.0000.0000.000
29A29LEU00.0160.01627.711-0.241-0.2410.0000.0000.0000.000
30A30GLU-1-0.789-0.88525.025-11.903-11.9030.0000.0000.0000.000
31A31THR0-0.045-0.03524.096-0.491-0.4910.0000.0000.0000.000
32A32VAL0-0.039-0.00818.0260.0500.0500.0000.0000.0000.000
33A33GLU-1-0.966-0.98020.303-14.317-14.3170.0000.0000.0000.000
34A34LEU00.0460.03113.606-0.644-0.6440.0000.0000.0000.000
35A35GLN0-0.004-0.00518.1950.6660.6660.0000.0000.0000.000
36A36VAL0-0.006-0.01316.142-0.625-0.6250.0000.0000.0000.000
37A37GLY00.0430.03114.8340.5500.5500.0000.0000.0000.000
38A38LEU0-0.045-0.02014.273-0.968-0.9680.0000.0000.0000.000
39A39LYS11.0321.01516.42715.50115.5010.0000.0000.0000.000
40A40ASN0-0.053-0.02318.7610.6920.6920.0000.0000.0000.000
41A41TYR00.043-0.00118.9620.0110.0110.0000.0000.0000.000
42A42ASP-1-0.788-0.87123.336-11.779-11.7790.0000.0000.0000.000
43A43PRO0-0.017-0.03726.582-0.075-0.0750.0000.0000.0000.000
44A44GLN0-0.065-0.03526.4220.3040.3040.0000.0000.0000.000
45A45ARG10.9450.96629.4878.7788.7780.0000.0000.0000.000
46A46ASP-1-0.896-0.94830.532-9.718-9.7180.0000.0000.0000.000
47A47LYS10.8530.93232.0608.6948.6940.0000.0000.0000.000
48A48ARG11.0171.01223.41612.78812.7880.0000.0000.0000.000
49A49PHE00.0360.00427.045-0.004-0.0040.0000.0000.0000.000
50A50SER0-0.032-0.01627.4690.2760.2760.0000.0000.0000.000
51A51GLY00.0300.03926.9900.3210.3210.0000.0000.0000.000
52A52SER0-0.065-0.02725.847-0.292-0.2920.0000.0000.0000.000
53A53LEU00.0170.02222.0450.4500.4500.0000.0000.0000.000
54A54LYS10.8890.93323.91611.07511.0750.0000.0000.0000.000
55A55LEU00.0350.00919.412-0.424-0.4240.0000.0000.0000.000
56A56PRO00.0370.01722.2850.3700.3700.0000.0000.0000.000
57A57ASN0-0.0060.00320.325-0.130-0.1300.0000.0000.0000.000
58A58CYS00.0120.02223.2530.1340.1340.0000.0000.0000.000
59A59PRO0-0.0120.00422.995-0.240-0.2400.0000.0000.0000.000
60A60ARG10.9820.99024.27010.32810.3280.0000.0000.0000.000
61A61PRO00.0140.01727.0320.2080.2080.0000.0000.0000.000
62A62ASN0-0.100-0.06629.4550.5830.5830.0000.0000.0000.000
63A63MET00.0260.02132.539-0.034-0.0340.0000.0000.0000.000
64A64SER0-0.049-0.02435.3200.2130.2130.0000.0000.0000.000
65A65ILE00.0370.01637.049-0.188-0.1880.0000.0000.0000.000
66A66CYS0-0.0140.00639.7820.2240.2240.0000.0000.0000.000
67A67ILE00.0310.01041.989-0.164-0.1640.0000.0000.0000.000
68A68PHE0-0.059-0.03442.7230.0600.0600.0000.0000.0000.000
69A69GLY0-0.013-0.00245.2260.1200.1200.0000.0000.0000.000
70A70ASP-1-0.827-0.93346.526-6.327-6.3270.0000.0000.0000.000
71A71ALA0-0.047-0.03850.139-0.022-0.0220.0000.0000.0000.000
72A72PHE0-0.0010.00648.7250.0700.0700.0000.0000.0000.000
73A73ASP-1-0.756-0.88843.567-7.428-7.4280.0000.0000.0000.000
74A74VAL00.0010.00346.889-0.053-0.0530.0000.0000.0000.000
75A75ASP-1-0.883-0.95849.297-6.037-6.0370.0000.0000.0000.000
76A76ARG10.8420.93344.2677.0347.0340.0000.0000.0000.000
77A77ALA00.004-0.01143.781-0.099-0.0990.0000.0000.0000.000
78A78LYS10.9280.97945.3745.9865.9860.0000.0000.0000.000
79A79SER0-0.032-0.01045.9790.1360.1360.0000.0000.0000.000
80A80CYS-1-0.885-0.89440.966-7.965-7.9650.0000.0000.0000.000
81A81GLY0-0.057-0.06242.2070.1680.1680.0000.0000.0000.000
82A82VAL0-0.108-0.06042.529-0.060-0.0600.0000.0000.0000.000
83A83ASP-1-0.877-0.94744.789-6.888-6.8880.0000.0000.0000.000
84A84ALA0-0.018-0.01447.739-0.045-0.0450.0000.0000.0000.000
85A85MET0-0.057-0.02748.1500.1400.1400.0000.0000.0000.000
86A86SER00.0680.05050.653-0.026-0.0260.0000.0000.0000.000
87A87VAL00.006-0.00752.827-0.051-0.0510.0000.0000.0000.000
88A88ASP-1-0.902-0.94453.848-5.510-5.5100.0000.0000.0000.000
89A89ASP-1-0.853-0.92652.940-5.799-5.7990.0000.0000.0000.000
90A90LEU00.002-0.01349.484-0.006-0.0060.0000.0000.0000.000
91A91LYS10.9640.97851.9195.7745.7740.0000.0000.0000.000
92A92LYS10.9030.94555.0335.5525.5520.0000.0000.0000.000
93A93LEU0-0.0100.00948.2750.0100.0100.0000.0000.0000.000
94A94ASN0-0.014-0.03848.727-0.126-0.1260.0000.0000.0000.000
95A95LYS10.9731.01451.6025.4565.4560.0000.0000.0000.000
96A96ASN00.0260.01053.881-0.021-0.0210.0000.0000.0000.000
97A97LYS11.0331.00151.4795.9345.9340.0000.0000.0000.000
98A98LYS10.9370.95749.5055.9145.9140.0000.0000.0000.000
99A99LEU00.0430.03748.370-0.158-0.1580.0000.0000.0000.000
100A100ILE00.0820.05044.411-0.139-0.1390.0000.0000.0000.000
101A101LYS10.8630.92744.1616.5966.5960.0000.0000.0000.000
102A102LYS10.8970.94343.2916.6326.6320.0000.0000.0000.000
103A103LEU00.0690.05342.645-0.139-0.1390.0000.0000.0000.000
104A104SER00.0500.01240.098-0.163-0.1630.0000.0000.0000.000
105A105LYS10.8970.95738.8567.6217.6210.0000.0000.0000.000
106A106LYS10.9290.96538.1867.2857.2850.0000.0000.0000.000
107A107TYR00.0340.01638.265-0.205-0.2050.0000.0000.0000.000
108A108ASN00.002-0.02533.4500.1590.1590.0000.0000.0000.000
109A109ALA0-0.0060.01634.889-0.247-0.2470.0000.0000.0000.000
110A110PHE0-0.028-0.01636.4910.2160.2160.0000.0000.0000.000
111A111ILE00.0270.02438.363-0.227-0.2270.0000.0000.0000.000
112A112ALA0-0.011-0.01440.9710.1910.1910.0000.0000.0000.000
113A113SER00.0930.02443.1830.0010.0010.0000.0000.0000.000
114A114GLU-1-0.813-0.92442.258-7.398-7.3980.0000.0000.0000.000
115A115VAL0-0.028-0.00845.7190.1020.1020.0000.0000.0000.000
116A116LEU0-0.058-0.03547.1430.1220.1220.0000.0000.0000.000
117A117ILE0-0.033-0.00242.351-0.065-0.0650.0000.0000.0000.000
118A118LYS10.9670.98745.4596.0876.0870.0000.0000.0000.000
119A119GLN00.000-0.01348.8170.1030.1030.0000.0000.0000.000
120A120VAL00.0140.02743.4080.0530.0530.0000.0000.0000.000
121A121PRO0-0.006-0.00345.086-0.036-0.0360.0000.0000.0000.000
122A122ARG10.9190.96446.2346.2466.2460.0000.0000.0000.000
123A123LEU0-0.024-0.01948.9670.0660.0660.0000.0000.0000.000
124A124LEU00.0680.03641.993-0.034-0.0340.0000.0000.0000.000
125A125GLY00.0430.02442.783-0.110-0.1100.0000.0000.0000.000
126A126PRO00.021-0.01542.288-0.190-0.1900.0000.0000.0000.000
127A127GLN0-0.023-0.00443.939-0.064-0.0640.0000.0000.0000.000
128A128LEU0-0.024-0.00239.422-0.061-0.0610.0000.0000.0000.000
129A129SER00.0060.00439.068-0.100-0.1000.0000.0000.0000.000
130A130LYS10.8920.93932.3639.5019.5010.0000.0000.0000.000
131A131ALA00.0170.00934.133-0.254-0.2540.0000.0000.0000.000
132A132GLY00.0350.02932.224-0.106-0.1060.0000.0000.0000.000
133A133LYS10.8110.91433.1569.0389.0380.0000.0000.0000.000
134A134PHE00.0090.00035.9290.2840.2840.0000.0000.0000.000
135A135PRO00.0120.01736.462-0.208-0.2080.0000.0000.0000.000
136A136THR00.000-0.00433.886-0.180-0.1800.0000.0000.0000.000
137A137PRO0-0.037-0.00936.5510.1270.1270.0000.0000.0000.000
138A138VAL0-0.004-0.01137.975-0.252-0.2520.0000.0000.0000.000
139A139SER00.018-0.00240.4750.1450.1450.0000.0000.0000.000
140A140HIS0-0.0050.01443.749-0.147-0.1470.0000.0000.0000.000
141A141ASN0-0.025-0.01246.712-0.012-0.0120.0000.0000.0000.000
142A142ASP-1-0.789-0.85640.792-7.666-7.6660.0000.0000.0000.000
143A143ASP-1-0.854-0.93238.026-8.126-8.1260.0000.0000.0000.000
144A144LEU0-0.089-0.03140.5210.0100.0100.0000.0000.0000.000
145A145TYR00.013-0.02837.796-0.131-0.1310.0000.0000.0000.000
146A146GLY00.0530.04034.473-0.252-0.2520.0000.0000.0000.000
147A147LYS10.8750.93333.5417.5507.5500.0000.0000.0000.000
148A148VAL0-0.054-0.01632.666-0.191-0.1910.0000.0000.0000.000
149A149THR00.010-0.00127.770-0.305-0.3050.0000.0000.0000.000
150A150ASP-1-0.772-0.86229.404-9.741-9.7410.0000.0000.0000.000
151A151VAL0-0.033-0.02530.269-0.242-0.2420.0000.0000.0000.000
152A152ARG10.8400.90030.2488.9828.9820.0000.0000.0000.000
153A153SER00.0630.00625.388-0.397-0.3970.0000.0000.0000.000
154A154THR0-0.067-0.00525.788-0.479-0.4790.0000.0000.0000.000
155A155ILE00.0180.02122.9710.5590.5590.0000.0000.0000.000
156A156LYS10.8420.89726.99210.14510.1450.0000.0000.0000.000
157A157PHE00.0930.04721.323-0.145-0.1450.0000.0000.0000.000
158A158GLN0-0.018-0.02126.3850.1240.1240.0000.0000.0000.000
159A159LEU00.0220.03723.4710.1140.1140.0000.0000.0000.000
160A160LYS10.9790.98527.4769.0859.0850.0000.0000.0000.000
161A161LYS10.9030.92231.0028.8958.8950.0000.0000.0000.000
162A162VAL00.0290.02127.8040.1520.1520.0000.0000.0000.000
163A163LEU0-0.0140.01123.6360.0020.0020.0000.0000.0000.000
164A164CYS0-0.019-0.00623.519-0.550-0.5500.0000.0000.0000.000
165A165LEU0-0.009-0.01822.7930.5260.5260.0000.0000.0000.000
166A166ALA00.0000.00821.018-0.547-0.5470.0000.0000.0000.000
167A167VAL0-0.049-0.01419.5690.7490.7490.0000.0000.0000.000
168A168ALA00.003-0.00319.731-0.643-0.6430.0000.0000.0000.000
169A169VAL0-0.048-0.02915.885-0.080-0.0800.0000.0000.0000.000
170A170GLY00.0830.04619.199-0.395-0.3950.0000.0000.0000.000
171A171ASN0-0.010-0.02721.7860.1290.1290.0000.0000.0000.000
172A172VAL00.0070.00422.943-0.329-0.3290.0000.0000.0000.000
173A173GLU-1-0.887-0.94924.019-11.305-11.3050.0000.0000.0000.000
174A174MET0-0.069-0.01322.5290.5400.5400.0000.0000.0000.000
175A175GLU-1-0.838-0.93121.177-13.755-13.7550.0000.0000.0000.000
176A176GLU-1-0.882-0.96017.958-15.577-15.5770.0000.0000.0000.000
177A177ASP-1-0.904-0.94714.210-22.311-22.3110.0000.0000.0000.000
178A178VAL0-0.045-0.00515.440-1.093-1.0930.0000.0000.0000.000
179A179LEU00.0060.01516.825-0.550-0.5500.0000.0000.0000.000
180A180VAL00.017-0.00410.613-0.863-0.8630.0000.0000.0000.000
181A181ASN0-0.020-0.00111.639-3.015-3.0150.0000.0000.0000.000
182A182GLN00.001-0.00913.554-0.428-0.4280.0000.0000.0000.000
183A183ILE00.0250.02011.1280.4200.4200.0000.0000.0000.000
184A184LEU00.001-0.0067.417-0.895-0.8950.0000.0000.0000.000
185A185MET0-0.0280.00611.3770.6720.6720.0000.0000.0000.000
186A186SER00.0180.00414.9121.0991.0990.0000.0000.0000.000
187A187VAL00.0060.00310.9180.8380.8380.0000.0000.0000.000
188A188ASN00.007-0.00612.9770.3170.3170.0000.0000.0000.000
189A189PHE0-0.040-0.02715.1681.0711.0710.0000.0000.0000.000
190A190PHE00.0090.01616.5801.0241.0240.0000.0000.0000.000
191A191VAL0-0.073-0.03814.5580.6780.6780.0000.0000.0000.000
192A192SER00.0710.04917.6050.0260.0260.0000.0000.0000.000
193A193LEU0-0.092-0.04120.5470.7720.7720.0000.0000.0000.000
194A194LEU0-0.093-0.04818.6980.5840.5840.0000.0000.0000.000
195A195LYS00.1000.07319.960-0.419-0.4190.0000.0000.0000.000
196A196LYS10.8510.89816.02515.67315.6730.0000.0000.0000.000
197A197ASN00.0680.02011.589-0.985-0.9850.0000.0000.0000.000
198A198TRP0-0.037-0.00512.6030.0400.0400.0000.0000.0000.000
199A199GLN00.0510.0069.2080.8190.8190.0000.0000.0000.000
200A200ASN0-0.043-0.0246.941-2.695-2.6950.0000.0000.0000.000
201A201VAL0-0.023-0.0015.633-5.681-5.6810.0000.0000.0000.000
202A202GLY00.0690.0348.2172.9642.9640.0000.0000.0000.000
203A203SER0-0.053-0.03911.487-0.008-0.0080.0000.0000.0000.000
204A204LEU00.0020.0097.6020.8430.8430.0000.0000.0000.000
205A205VAL00.0420.00912.0960.7430.7430.0000.0000.0000.000
206A206VAL00.0080.00814.286-0.275-0.2750.0000.0000.0000.000
207A207LYS10.9070.97016.85313.76813.7680.0000.0000.0000.000
208A208SER00.0720.03720.2420.2690.2690.0000.0000.0000.000
209A209SER0-0.073-0.03722.4940.8480.8480.0000.0000.0000.000
210A210MET0-0.037-0.01624.6110.4400.4400.0000.0000.0000.000
211A211GLY00.000-0.01221.707-0.582-0.5820.0000.0000.0000.000
212A212PRO00.0050.02220.4940.4030.4030.0000.0000.0000.000
213A213ALA0-0.039-0.01720.633-0.442-0.4420.0000.0000.0000.000
214A214PHE00.0510.02515.683-0.243-0.2430.0000.0000.0000.000
215A215ARG10.8910.93016.15814.44814.4480.0000.0000.0000.000
216A216LEU00.0100.0109.976-0.979-0.9790.0000.0000.0000.000
217A217TYR-1-0.944-0.9475.466-23.581-23.5810.0000.0000.0000.000