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

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FMODB ID: N6LZQ

Calculation Name: 6WOO-A-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: A

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 206
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2356348.422665
FMO2-HF: Nuclear repulsion 2277972.215703
FMO2-HF: Total energy -78376.206961
FMO2-MP2: Total energy -78610.511215


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
8.08911.1260.581-1.713-1.905-0.009
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.925
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].
3A4PRO0-0.039-0.0312.902-9.424-6.5470.582-1.704-1.756-0.009
4A5ALA0-0.031-0.0084.3504.2834.443-0.001-0.009-0.1490.000
5A6THR00.0680.0485.9532.8752.8750.0000.0000.0000.000
6A7PHE0-0.090-0.0578.6611.7071.7070.0000.0000.0000.000
7A8ASP-1-0.816-0.9258.247-29.573-29.5730.0000.0000.0000.000
8A9LEU0-0.048-0.01110.7601.4401.4400.0000.0000.0000.000
9A10THR00.0310.02014.3890.7300.7300.0000.0000.0000.000
10A11PRO00.0500.01516.9070.3970.3970.0000.0000.0000.000
11A12GLU-1-0.860-0.93420.287-13.931-13.9310.0000.0000.0000.000
12A13ASP-1-0.790-0.87718.044-15.538-15.5380.0000.0000.0000.000
13A14ALA00.0080.00119.1780.3880.3880.0000.0000.0000.000
14A15GLN0-0.062-0.04120.8740.8720.8720.0000.0000.0000.000
15A16LEU00.0070.01023.4460.5090.5090.0000.0000.0000.000
16A17LEU0-0.021-0.01919.5090.3830.3830.0000.0000.0000.000
17A18LEU0-0.017-0.01122.9950.3820.3820.0000.0000.0000.000
18A19ALA00.0180.03126.1260.4250.4250.0000.0000.0000.000
19A20ALA0-0.041-0.02127.0410.3870.3870.0000.0000.0000.000
20A21ASN0-0.007-0.01929.066-0.033-0.0330.0000.0000.0000.000
21A22THR0-0.030-0.03123.3300.1980.1980.0000.0000.0000.000
22A23HIS00.0510.00021.5490.1100.1100.0000.0000.0000.000
23A24LEU0-0.037-0.00226.1700.0890.0890.0000.0000.0000.000
24A25GLY00.028-0.01529.5290.4180.4180.0000.0000.0000.000
25A26ALA0-0.054-0.02727.4970.1730.1730.0000.0000.0000.000
26A27ARG10.8500.93429.3999.4829.4820.0000.0000.0000.000
27A28ASN0-0.0040.00831.546-0.208-0.2080.0000.0000.0000.000
28A29VAL0-0.0130.00634.0610.0090.0090.0000.0000.0000.000
29A30GLN00.034-0.00228.270-0.260-0.2600.0000.0000.0000.000
30A31VAL00.0280.02227.8680.2790.2790.0000.0000.0000.000
31A32HIS00.008-0.01028.081-0.462-0.4620.0000.0000.0000.000
32A33GLN0-0.0040.00122.862-0.452-0.4520.0000.0000.0000.000
33A34GLU-1-0.842-0.93423.364-12.758-12.7580.0000.0000.0000.000
34A35PRO0-0.0030.01318.4900.0240.0240.0000.0000.0000.000
35A36TYR0-0.051-0.03016.812-1.109-1.1090.0000.0000.0000.000
36A37VAL00.0460.02020.9800.2200.2200.0000.0000.0000.000
37A38PHE0-0.074-0.05319.976-0.629-0.6290.0000.0000.0000.000
38A39ASN00.001-0.00423.9440.4050.4050.0000.0000.0000.000
39A40ALA00.0250.02727.5300.0080.0080.0000.0000.0000.000
40A41ARG10.9090.95930.5368.7448.7440.0000.0000.0000.000
41A42PRO00.0310.00432.9170.1470.1470.0000.0000.0000.000
42A43ASP-1-0.924-0.97536.481-7.815-7.8150.0000.0000.0000.000
43A44GLY00.0070.02736.990-0.016-0.0160.0000.0000.0000.000
44A45VAL0-0.033-0.02033.1290.0240.0240.0000.0000.0000.000
45A46HIS00.0560.02628.2060.1090.1090.0000.0000.0000.000
46A47VAL0-0.0240.00225.0760.0120.0120.0000.0000.0000.000
47A48ILE00.0010.01321.525-0.158-0.1580.0000.0000.0000.000
48A49ASN0-0.046-0.02017.425-0.653-0.6530.0000.0000.0000.000
49A50VAL00.0590.02118.852-0.567-0.5670.0000.0000.0000.000
50A51GLY00.0580.03415.193-0.487-0.4870.0000.0000.0000.000
51A52LYS10.9110.94814.29215.34515.3450.0000.0000.0000.000
52A53THR0-0.009-0.03014.942-0.878-0.8780.0000.0000.0000.000
53A54TRP00.0200.02211.246-0.759-0.7590.0000.0000.0000.000
54A55GLU-1-0.910-0.9568.967-29.458-29.4580.0000.0000.0000.000
55A56LYS10.8210.90411.36916.96016.9600.0000.0000.0000.000
56A57LEU0-0.0090.01813.6690.1190.1190.0000.0000.0000.000
57A58VAL00.0470.0209.500-0.435-0.4350.0000.0000.0000.000
58A59LEU0-0.083-0.0409.171-1.358-1.3580.0000.0000.0000.000
59A60ALA00.0360.01011.2060.0130.0130.0000.0000.0000.000
60A61ALA00.0310.01313.8920.5010.5010.0000.0000.0000.000
61A62ARG10.8910.9415.53440.23840.2380.0000.0000.0000.000
62A63ILE0-0.016-0.00112.0240.0020.0020.0000.0000.0000.000
63A64ILE00.0240.00114.1390.8810.8810.0000.0000.0000.000
64A65ALA0-0.006-0.00514.1010.6360.6360.0000.0000.0000.000
65A66ALA0-0.049-0.00613.118-0.160-0.1600.0000.0000.0000.000
66A67ILE0-0.043-0.01615.0840.5920.5920.0000.0000.0000.000
67A68PRO0-0.053-0.02118.8790.3530.3530.0000.0000.0000.000
68A69ASN0-0.055-0.05020.3520.3070.3070.0000.0000.0000.000
69A70PRO00.0020.01223.047-0.152-0.1520.0000.0000.0000.000
70A71GLU-1-0.915-0.95824.083-10.899-10.8990.0000.0000.0000.000
71A72ASP-1-0.765-0.84024.193-11.764-11.7640.0000.0000.0000.000
72A73VAL0-0.022-0.01421.373-0.278-0.2780.0000.0000.0000.000
73A74VAL00.0120.00324.2780.4520.4520.0000.0000.0000.000
74A75ALA0-0.0070.00726.327-0.299-0.2990.0000.0000.0000.000
75A76ILE0-0.044-0.02527.5170.5230.5230.0000.0000.0000.000
76A77SER0-0.013-0.03929.223-0.214-0.2140.0000.0000.0000.000
77A78SER0-0.041-0.02731.9020.3440.3440.0000.0000.0000.000
78A79ARG10.7860.86630.57810.00910.0090.0000.0000.0000.000
79A80THR00.0710.02234.722-0.279-0.2790.0000.0000.0000.000
80A81TYR0-0.057-0.04433.326-0.080-0.0800.0000.0000.0000.000
81A82GLY00.0780.04631.121-0.239-0.2390.0000.0000.0000.000
82A83GLN0-0.0060.01731.668-0.100-0.1000.0000.0000.0000.000
83A84ARG10.8500.89633.6049.0029.0020.0000.0000.0000.000
84A85ALA00.0030.01628.771-0.126-0.1260.0000.0000.0000.000
85A86VAL00.0480.02228.040-0.305-0.3050.0000.0000.0000.000
86A87LEU00.0080.01129.537-0.102-0.1020.0000.0000.0000.000
87A88LYS10.8410.92929.87010.13210.1320.0000.0000.0000.000
88A89PHE00.0000.00121.714-0.109-0.1090.0000.0000.0000.000
89A90ALA00.0070.00726.781-0.235-0.2350.0000.0000.0000.000
90A91ALA0-0.038-0.02028.8190.0240.0240.0000.0000.0000.000
91A92HIS0-0.037-0.02326.5320.4980.4980.0000.0000.0000.000
92A93THR0-0.012-0.01822.728-0.429-0.4290.0000.0000.0000.000
93A94GLY00.0120.01225.085-0.191-0.1910.0000.0000.0000.000
94A95ALA00.0480.03824.877-0.132-0.1320.0000.0000.0000.000
95A96THR00.0250.01126.9400.3700.3700.0000.0000.0000.000
96A97PRO0-0.017-0.01129.889-0.121-0.1210.0000.0000.0000.000
97A98ILE0-0.021-0.01831.4530.3360.3360.0000.0000.0000.000
98A99ALA00.0050.01333.499-0.067-0.0670.0000.0000.0000.000
99A100GLY0-0.014-0.00434.7560.2720.2720.0000.0000.0000.000
100A101ARG10.9350.94736.9917.3887.3880.0000.0000.0000.000
101A102PHE00.0310.01032.1410.0850.0850.0000.0000.0000.000
102A103THR0-0.034-0.01236.7630.0850.0850.0000.0000.0000.000
103A104PRO0-0.0220.00337.807-0.121-0.1210.0000.0000.0000.000
104A105GLY0-0.049-0.02237.8340.2470.2470.0000.0000.0000.000
105A106SER0-0.030-0.02834.5710.1140.1140.0000.0000.0000.000
106A107PHE00.009-0.00930.031-0.156-0.1560.0000.0000.0000.000
107A108THR00.0160.01433.4660.0540.0540.0000.0000.0000.000
108A109ASN0-0.030-0.03436.2020.1270.1270.0000.0000.0000.000
109A110TYR00.0720.02737.5490.0480.0480.0000.0000.0000.000
110A111ILE0-0.0110.01338.9450.0630.0630.0000.0000.0000.000
111A112THR0-0.048-0.00739.9760.1910.1910.0000.0000.0000.000
112A113ARG10.9840.97040.4786.7516.7510.0000.0000.0000.000
113A114SER0-0.008-0.00138.505-0.168-0.1680.0000.0000.0000.000
114A115PHE00.0040.03334.595-0.167-0.1670.0000.0000.0000.000
115A116LYS10.8430.90931.7239.0339.0330.0000.0000.0000.000
116A117GLU-1-0.894-0.95130.180-9.654-9.6540.0000.0000.0000.000
117A118PRO0-0.033-0.00126.047-0.263-0.2630.0000.0000.0000.000
118A119ARG10.8440.88622.13513.09713.0970.0000.0000.0000.000
119A120LEU0-0.030-0.00718.615-0.729-0.7290.0000.0000.0000.000
120A121VAL00.0170.01822.4550.5250.5250.0000.0000.0000.000
121A122ILE0-0.024-0.00620.668-0.585-0.5850.0000.0000.0000.000
122A123VAL00.0130.00224.0090.5990.5990.0000.0000.0000.000
123A124THR0-0.005-0.00725.626-0.326-0.3260.0000.0000.0000.000
124A125ASP-1-0.769-0.87027.734-9.883-9.8830.0000.0000.0000.000
125A126PRO00.0480.02126.9100.2300.2300.0000.0000.0000.000
126A127ARG10.8910.94329.1169.5039.5030.0000.0000.0000.000
127A128LEU0-0.063-0.03632.6310.3020.3020.0000.0000.0000.000
128A129ASP-1-0.740-0.85630.677-9.686-9.6860.0000.0000.0000.000
129A130ALA00.0190.01431.787-0.167-0.1670.0000.0000.0000.000
130A131GLN0-0.054-0.03632.694-0.011-0.0110.0000.0000.0000.000
131A132ALA00.0000.00530.263-0.012-0.0120.0000.0000.0000.000
132A133ILE00.0380.03227.064-0.156-0.1560.0000.0000.0000.000
133A134LYS10.8980.96629.5039.3519.3510.0000.0000.0000.000
134A135GLU-1-0.727-0.85532.580-8.781-8.7810.0000.0000.0000.000
135A136ALA00.0620.02927.3620.0720.0720.0000.0000.0000.000
136A137SER0-0.086-0.06028.777-0.085-0.0850.0000.0000.0000.000
137A138TYR0-0.061-0.03429.8020.0560.0560.0000.0000.0000.000
138A139VAL0-0.020-0.00729.6340.2030.2030.0000.0000.0000.000
139A140ASN0-0.045-0.01525.5690.0780.0780.0000.0000.0000.000
140A141ILE00.0270.02624.675-0.403-0.4030.0000.0000.0000.000
141A142PRO0-0.018-0.00520.0170.1570.1570.0000.0000.0000.000
142A143VAL0-0.029-0.02121.9230.3740.3740.0000.0000.0000.000
143A144ILE00.0180.02117.315-0.370-0.3700.0000.0000.0000.000
144A145ALA00.0160.00520.8390.6830.6830.0000.0000.0000.000
145A146LEU0-0.0210.00021.820-0.569-0.5690.0000.0000.0000.000
146A147THR00.0370.02723.1470.4630.4630.0000.0000.0000.000
147A148ASP-1-0.798-0.89024.758-10.705-10.7050.0000.0000.0000.000
148A149LEU00.000-0.01024.207-0.309-0.3090.0000.0000.0000.000
149A150ASP-1-0.884-0.94826.970-9.674-9.6740.0000.0000.0000.000
150A151SER0-0.049-0.01826.9770.3190.3190.0000.0000.0000.000
151A152PRO0-0.011-0.00427.955-0.151-0.1510.0000.0000.0000.000
152A153SER00.0510.00724.226-0.396-0.3960.0000.0000.0000.000
153A154GLU-1-0.937-0.96225.476-10.933-10.9330.0000.0000.0000.000
154A155PHE0-0.032-0.03426.4070.2300.2300.0000.0000.0000.000
155A156VAL0-0.010-0.00122.309-0.076-0.0760.0000.0000.0000.000
156A157ASP-1-0.767-0.86018.799-15.956-15.9560.0000.0000.0000.000
157A158VAL0-0.057-0.04914.740-0.097-0.0970.0000.0000.0000.000
158A159ALA00.0100.00817.6450.2220.2220.0000.0000.0000.000
159A160ILE0-0.005-0.00217.299-0.986-0.9860.0000.0000.0000.000
160A161PRO0-0.0220.01018.5000.7120.7120.0000.0000.0000.000
161A162CYS0-0.050-0.01321.530-0.240-0.2400.0000.0000.0000.000
162A163ASN00.0190.01624.2760.5010.5010.0000.0000.0000.000
163A164ASN00.004-0.00627.3440.2300.2300.0000.0000.0000.000
164A165ARG10.9160.95430.4399.4219.4210.0000.0000.0000.000
165A166GLY00.0280.01432.5360.2230.2230.0000.0000.0000.000
166A167LYS10.8840.94732.6878.9438.9430.0000.0000.0000.000
167A168HIS00.0120.01030.763-0.278-0.2780.0000.0000.0000.000
168A169SER00.0080.00427.092-0.454-0.4540.0000.0000.0000.000
169A170ILE00.0230.02026.524-0.304-0.3040.0000.0000.0000.000
170A171GLY00.0280.00927.041-0.292-0.2920.0000.0000.0000.000
171A172LEU00.0100.00724.078-0.196-0.1960.0000.0000.0000.000
172A173ILE00.0180.00720.972-0.526-0.5260.0000.0000.0000.000
173A174TRP00.006-0.01222.180-0.653-0.6530.0000.0000.0000.000
174A175TYR0-0.034-0.01423.886-0.372-0.3720.0000.0000.0000.000
175A176LEU00.000-0.01019.704-0.329-0.3290.0000.0000.0000.000
176A177LEU00.0020.00517.771-0.783-0.7830.0000.0000.0000.000
177A178ALA0-0.004-0.00919.627-0.430-0.4300.0000.0000.0000.000
178A179ARG10.7230.84917.52715.99315.9930.0000.0000.0000.000
179A180GLU-1-0.766-0.88415.098-19.485-19.4850.0000.0000.0000.000
180A181VAL0-0.027-0.01716.166-1.045-1.0450.0000.0000.0000.000
181A182LEU0-0.016-0.00817.744-0.174-0.1740.0000.0000.0000.000
182A183ARG10.8450.94316.26817.90617.9060.0000.0000.0000.000
183A184LEU0-0.052-0.01911.057-0.820-0.8200.0000.0000.0000.000
184A185ARG10.9280.95815.23416.41616.4160.0000.0000.0000.000
185A186GLY00.0420.03317.5230.9180.9180.0000.0000.0000.000
186A187ALA0-0.037-0.02320.6000.0370.0370.0000.0000.0000.000
187A188LEU0-0.050-0.01220.2010.4620.4620.0000.0000.0000.000
188A189VAL00.019-0.00119.234-0.903-0.9030.0000.0000.0000.000
189A190ASP-1-0.915-0.94718.356-15.228-15.2280.0000.0000.0000.000
190A191ARG10.8930.9449.33827.58927.5890.0000.0000.0000.000
191A192THR00.003-0.00916.3820.2110.2110.0000.0000.0000.000
192A193GLN00.0760.03418.4710.1050.1050.0000.0000.0000.000
193A194PRO00.0040.00020.991-0.309-0.3090.0000.0000.0000.000
194A195TRP00.0590.02222.046-0.034-0.0340.0000.0000.0000.000
195A196SER00.0030.01624.5840.1020.1020.0000.0000.0000.000
196A197ILE0-0.025-0.00827.4050.5740.5740.0000.0000.0000.000
197A198MET00.021-0.00628.640-0.329-0.3290.0000.0000.0000.000
198A199PRO00.0580.02426.9820.1170.1170.0000.0000.0000.000
199A200ASP-1-0.885-0.93729.333-9.505-9.5050.0000.0000.0000.000
200A201LEU0-0.040-0.02431.7360.2680.2680.0000.0000.0000.000
201A202TYR00.0470.03326.1620.2200.2200.0000.0000.0000.000
202A203PHE0-0.016-0.00229.5130.0950.0950.0000.0000.0000.000
203A204TYR00.0040.00533.3650.1790.1790.0000.0000.0000.000
204A205ARG10.9150.97836.1927.5257.5250.0000.0000.0000.000
205A206ASN00.008-0.00739.4410.0070.0070.0000.0000.0000.000
206A207PRO-1-0.884-0.93442.527-6.947-6.9470.0000.0000.0000.000