FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 5556Z

Calculation Name: 2QOR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-monophosphate | pyrophosphate 2-

Ligand 3-letter code: 5GP | POP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2QOR

Chain ID: A

ChEMBL ID:

UniProt ID: A5K709

Base Structure: X-ray

Registration Date: 2025-10-05

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
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2328654.923036
FMO2-HF: Nuclear repulsion 2249194.425926
FMO2-HF: Total energy -79460.49711
FMO2-MP2: Total energy -79692.092755


3D Structure Molmil
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.
0.968999999999982.207-0.002-0.528-0.708-0.001
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 : 0.853 / q_NPA : 0.913
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].
3A3ARG10.9710.9903.80533.11234.350-0.002-0.528-0.708-0.001
4A4ILE00.0280.0216.5750.3940.3940.0000.0000.0000.000
5A5PRO00.0370.0428.6700.6650.6650.0000.0000.0000.000
6A6PRO00.0140.00811.1281.6251.6250.0000.0000.0000.000
7A7LEU00.0140.03514.5680.3450.3450.0000.0000.0000.000
8A8VAL0-0.033-0.01917.6570.5620.5620.0000.0000.0000.000
9A9VAL00.0050.00620.3440.3850.3850.0000.0000.0000.000
10A10CYS00.0100.02323.8730.3120.3120.0000.0000.0000.000
11A11GLY00.0520.02426.7930.0850.0850.0000.0000.0000.000
12A12PRO00.0260.03330.3790.0280.0280.0000.0000.0000.000
13A13SER0-0.006-0.01333.976-0.070-0.0700.0000.0000.0000.000
14A14GLY00.012-0.00136.0040.2140.2140.0000.0000.0000.000
15A15VAL0-0.0190.00132.1180.1880.1880.0000.0000.0000.000
16A16GLY00.0190.01033.780-0.092-0.0920.0000.0000.0000.000
17A17LYS10.8850.96028.54310.18210.1820.0000.0000.0000.000
18A18GLY00.1050.05729.027-0.240-0.2400.0000.0000.0000.000
19A19THR0-0.072-0.04130.263-0.070-0.0700.0000.0000.0000.000
20A20LEU00.0070.00727.960-0.043-0.0430.0000.0000.0000.000
21A21ILE00.0280.01924.722-0.205-0.2050.0000.0000.0000.000
22A22LYS10.9130.94926.2629.7659.7650.0000.0000.0000.000
23A23LYS10.8830.97428.7409.7179.7170.0000.0000.0000.000
24A24VAL00.0360.02421.869-0.011-0.0110.0000.0000.0000.000
25A25LEU0-0.012-0.01922.848-0.272-0.2720.0000.0000.0000.000
26A26SER0-0.050-0.02925.1260.2170.2170.0000.0000.0000.000
27A27GLU-1-0.813-0.84324.577-11.425-11.4250.0000.0000.0000.000
28A28PHE0-0.013-0.00520.466-0.203-0.2030.0000.0000.0000.000
29A29PRO00.0300.02421.257-0.675-0.6750.0000.0000.0000.000
30A30SER0-0.065-0.06720.260-0.192-0.1920.0000.0000.0000.000
31A31ARG10.7420.86517.00513.99113.9910.0000.0000.0000.000
32A32PHE00.0290.01016.419-1.116-1.1160.0000.0000.0000.000
33A33ARG10.8350.91318.35515.20515.2050.0000.0000.0000.000
34A34PHE0-0.044-0.01819.828-0.474-0.4740.0000.0000.0000.000
35A35SER00.0240.00620.955-0.155-0.1550.0000.0000.0000.000
36A36ILE0-0.040-0.01222.8120.4210.4210.0000.0000.0000.000
37A37SER00.0070.00926.228-0.159-0.1590.0000.0000.0000.000
38A38CYS0-0.034-0.00127.2910.5030.5030.0000.0000.0000.000
39A39THR0-0.018-0.03130.0270.0220.0220.0000.0000.0000.000
40A40THR0-0.0110.00333.2880.0600.0600.0000.0000.0000.000
41A41ARG10.7510.87334.7249.2329.2320.0000.0000.0000.000
42A42ASN00.012-0.00438.594-0.123-0.1230.0000.0000.0000.000
43A43LYS10.8980.97138.2518.0258.0250.0000.0000.0000.000
44A44ARG10.7620.84939.3988.0428.0420.0000.0000.0000.000
45A45GLU-1-0.921-0.96940.581-7.113-7.1130.0000.0000.0000.000
46A46LYS10.9270.94740.0737.3077.3070.0000.0000.0000.000
47A47GLU-1-0.738-0.80335.962-8.958-8.9580.0000.0000.0000.000
48A48THR0-0.022-0.02834.5540.3320.3320.0000.0000.0000.000
49A49ASN00.0130.00033.785-0.469-0.4690.0000.0000.0000.000
50A50GLY00.0150.00630.4320.1040.1040.0000.0000.0000.000
51A51VAL0-0.042-0.01229.624-0.179-0.1790.0000.0000.0000.000
52A52ASP-1-0.833-0.91629.168-9.945-9.9450.0000.0000.0000.000
53A53TYR00.002-0.01529.956-0.144-0.1440.0000.0000.0000.000
54A54TYR0-0.026-0.02226.0310.5000.5000.0000.0000.0000.000
55A55PHE0-0.024-0.02931.6770.0000.0000.0000.0000.0000.000
56A56VAL0-0.013-0.00133.3930.0480.0480.0000.0000.0000.000
57A57ASP-1-0.758-0.87036.188-8.039-8.0390.0000.0000.0000.000
58A58LYS10.9490.93537.0597.7677.7670.0000.0000.0000.000
59A59ASP-1-0.859-0.91437.320-8.021-8.0210.0000.0000.0000.000
60A60ASP-1-0.877-0.94535.370-8.905-8.9050.0000.0000.0000.000
61A61PHE0-0.085-0.03830.069-0.305-0.3050.0000.0000.0000.000
62A62GLU-1-0.855-0.92932.507-8.938-8.9380.0000.0000.0000.000
63A63ARG10.8730.92333.4898.1198.1190.0000.0000.0000.000
64A64LYS10.9540.97929.3899.7999.7990.0000.0000.0000.000
65A65LEU0-0.027-0.00728.390-0.422-0.4220.0000.0000.0000.000
66A66LYS10.8030.89728.8538.5578.5570.0000.0000.0000.000
67A67GLU-1-0.937-0.96229.315-10.239-10.2390.0000.0000.0000.000
68A68GLY00.0010.00925.678-0.414-0.4140.0000.0000.0000.000
69A69GLN0-0.030-0.01823.958-0.958-0.9580.0000.0000.0000.000
70A70PHE0-0.032-0.02123.522-0.450-0.4500.0000.0000.0000.000
71A71LEU0-0.043-0.01917.446-0.304-0.3040.0000.0000.0000.000
72A72GLU-1-0.831-0.89721.188-12.943-12.9430.0000.0000.0000.000
73A73PHE0-0.001-0.01623.9940.3270.3270.0000.0000.0000.000
74A74ASP-1-0.721-0.81827.773-10.093-10.0930.0000.0000.0000.000
75A75LYS10.8640.93130.8148.6048.6040.0000.0000.0000.000
76A76TYR00.0290.01933.4220.1500.1500.0000.0000.0000.000
77A77ALA0-0.018-0.02735.4380.1200.1200.0000.0000.0000.000
78A78ASN0-0.063-0.05239.0220.1490.1490.0000.0000.0000.000
79A79ASN0-0.0260.00337.1570.1310.1310.0000.0000.0000.000
80A80PHE00.0230.01233.206-0.056-0.0560.0000.0000.0000.000
81A81TYR0-0.009-0.00730.0460.1560.1560.0000.0000.0000.000
82A82GLY00.0670.03027.1280.0020.0020.0000.0000.0000.000
83A83THR0-0.027-0.00921.0050.1100.1100.0000.0000.0000.000
84A84LEU0-0.013-0.01223.316-0.131-0.1310.0000.0000.0000.000
85A85LYS10.8880.93719.07714.42714.4270.0000.0000.0000.000
86A86SER00.0840.04018.776-0.685-0.6850.0000.0000.0000.000
87A87GLU-1-0.780-0.84420.074-13.549-13.5490.0000.0000.0000.000
88A88TYR00.015-0.00411.621-0.710-0.7100.0000.0000.0000.000
89A89ASP-1-0.906-0.96215.157-20.043-20.0430.0000.0000.0000.000
90A90LEU0-0.019-0.01115.793-0.620-0.6200.0000.0000.0000.000
91A91ALA0-0.010-0.00116.195-0.101-0.1010.0000.0000.0000.000
92A92VAL0-0.032-0.02110.505-1.241-1.2410.0000.0000.0000.000
93A93GLY0-0.031-0.01412.584-1.215-1.2150.0000.0000.0000.000
94A94GLU-1-0.894-0.96014.987-15.008-15.0080.0000.0000.0000.000
95A95GLY0-0.044-0.01411.8000.2520.2520.0000.0000.0000.000
96A96LYS10.8000.91712.27514.82714.8270.0000.0000.0000.000
97A97ILE0-0.024-0.00313.107-1.330-1.3300.0000.0000.0000.000
98A98CYS0-0.0100.00614.5541.4401.4400.0000.0000.0000.000
99A99LEU0-0.0060.00116.765-0.173-0.1730.0000.0000.0000.000
100A100PHE00.038-0.00117.0800.4830.4830.0000.0000.0000.000
101A101GLU-1-0.885-0.95922.028-10.556-10.5560.0000.0000.0000.000
102A102MET0-0.046-0.00522.141-0.026-0.0260.0000.0000.0000.000
103A103ASN0-0.011-0.01726.689-0.216-0.2160.0000.0000.0000.000
104A104ILE00.0690.01827.140-0.428-0.4280.0000.0000.0000.000
105A105ASN0-0.039-0.04127.213-0.334-0.3340.0000.0000.0000.000
106A106GLY00.0600.04825.656-0.251-0.2510.0000.0000.0000.000
107A107VAL0-0.031-0.02922.435-0.653-0.6530.0000.0000.0000.000
108A108LYS10.8240.92122.15710.26410.2640.0000.0000.0000.000
109A109GLN00.0480.00222.434-0.593-0.5930.0000.0000.0000.000
110A110LEU0-0.025-0.02518.116-0.660-0.6600.0000.0000.0000.000
111A111LYS10.8240.92917.97414.48814.4880.0000.0000.0000.000
112A112GLU-1-0.944-0.95618.206-13.827-13.8270.0000.0000.0000.000
113A113SER0-0.040-0.00917.025-0.422-0.4220.0000.0000.0000.000
114A114LYS10.9350.95214.56515.59615.5960.0000.0000.0000.000
115A115HIS00.0050.00113.221-0.117-0.1170.0000.0000.0000.000
116A116ILE0-0.018-0.01512.054-1.476-1.4760.0000.0000.0000.000
117A117GLN0-0.038-0.0187.8501.6941.6940.0000.0000.0000.000
118A118ASP-1-0.858-0.92510.132-24.151-24.1510.0000.0000.0000.000
119A119GLY0-0.024-0.02411.858-0.574-0.5740.0000.0000.0000.000
120A120ILE0-0.0160.00613.4410.7250.7250.0000.0000.0000.000
121A121TYR00.0340.01016.5250.5450.5450.0000.0000.0000.000
122A122ILE00.004-0.00420.0690.3750.3750.0000.0000.0000.000
123A123PHE0-0.001-0.00123.0820.3170.3170.0000.0000.0000.000
124A124VAL0-0.011-0.01626.7580.2010.2010.0000.0000.0000.000
125A125LYS10.9780.97729.4899.6069.6060.0000.0000.0000.000
126A126PRO0-0.0040.00032.881-0.019-0.0190.0000.0000.0000.000
127A127PRO00.0200.01436.357-0.034-0.0340.0000.0000.0000.000
128A128SER00.0260.00338.5360.1090.1090.0000.0000.0000.000
129A129ILE00.0560.01938.752-0.080-0.0800.0000.0000.0000.000
130A130ASP-1-0.894-0.94441.551-6.728-6.7280.0000.0000.0000.000
131A131ILE00.0630.03241.1500.0260.0260.0000.0000.0000.000
132A132LEU0-0.021-0.00237.063-0.007-0.0070.0000.0000.0000.000
133A133LEU00.016-0.00640.9620.0060.0060.0000.0000.0000.000
134A134GLY00.0210.00943.9790.1320.1320.0000.0000.0000.000
135A135ARG10.8820.93337.9338.1038.1030.0000.0000.0000.000
136A136LEU0-0.042-0.02039.704-0.026-0.0260.0000.0000.0000.000
137A137LYS10.9660.97243.1036.6376.6370.0000.0000.0000.000
138A138ASN0-0.028-0.00945.0470.2050.2050.0000.0000.0000.000
139A139ARG10.8200.91937.5258.0608.0600.0000.0000.0000.000
140A140ASN00.013-0.00345.4670.0750.0750.0000.0000.0000.000
141A141THR0-0.0050.00145.9550.0720.0720.0000.0000.0000.000
142A142GLU-1-0.795-0.85741.221-7.922-7.9220.0000.0000.0000.000
143A143LYS10.9790.97845.9926.5066.5060.0000.0000.0000.000
144A144PRO00.0480.00747.049-0.144-0.1440.0000.0000.0000.000
145A145GLU-1-0.811-0.87946.379-6.940-6.9400.0000.0000.0000.000
146A146GLU-1-0.805-0.89143.102-7.501-7.5010.0000.0000.0000.000
147A147ILE0-0.023-0.01342.656-0.222-0.2220.0000.0000.0000.000
148A148ASN0-0.003-0.01643.631-0.149-0.1490.0000.0000.0000.000
149A149LYS10.8400.91641.1457.1697.1690.0000.0000.0000.000
150A150ARG10.8640.92536.8568.1168.1160.0000.0000.0000.000
151A151MET0-0.028-0.00539.401-0.105-0.1050.0000.0000.0000.000
152A152GLN00.0250.02641.468-0.116-0.1160.0000.0000.0000.000
153A153GLU-1-0.842-0.92136.183-8.982-8.9820.0000.0000.0000.000
154A154LEU0-0.0120.00036.633-0.182-0.1820.0000.0000.0000.000
155A155THR0-0.040-0.02737.200-0.051-0.0510.0000.0000.0000.000
156A156ARG10.8410.91733.3179.2589.2580.0000.0000.0000.000
157A157GLU-1-0.875-0.97432.425-9.783-9.7830.0000.0000.0000.000
158A158MET0-0.069-0.05332.696-0.343-0.3430.0000.0000.0000.000
159A159ASP-1-0.852-0.90535.080-8.718-8.7180.0000.0000.0000.000
160A160GLU-1-0.740-0.86230.792-10.056-10.0560.0000.0000.0000.000
161A161ALA0-0.013-0.00429.119-0.400-0.4000.0000.0000.0000.000
162A162ASP-1-0.919-0.97328.013-10.222-10.2220.0000.0000.0000.000
163A163LYS10.8190.92128.3838.9048.9040.0000.0000.0000.000
164A164VAL0-0.016-0.00124.538-0.260-0.2600.0000.0000.0000.000
165A165GLY00.0020.01523.063-0.597-0.5970.0000.0000.0000.000
166A166PHE0-0.036-0.03821.752-0.754-0.7540.0000.0000.0000.000
167A167ASN00.0230.01416.8260.3010.3010.0000.0000.0000.000
168A168TYR0-0.044-0.04320.6360.0970.0970.0000.0000.0000.000
169A169PHE0-0.010-0.01123.5360.1130.1130.0000.0000.0000.000
170A170ILE00.0110.02326.8410.1630.1630.0000.0000.0000.000
171A171VAL0-0.012-0.00928.8960.1420.1420.0000.0000.0000.000
172A172ASN0-0.022-0.03232.241-0.001-0.0010.0000.0000.0000.000
173A173ASP-1-0.853-0.90633.820-8.386-8.3860.0000.0000.0000.000
174A174ASP-1-0.807-0.90936.059-8.092-8.0920.0000.0000.0000.000
175A175LEU0-0.0200.00233.315-0.293-0.2930.0000.0000.0000.000
176A176ALA0-0.030-0.01132.910-0.323-0.3230.0000.0000.0000.000
177A177ARG10.8060.86631.6128.9928.9920.0000.0000.0000.000
178A178THR00.013-0.01529.971-0.266-0.2660.0000.0000.0000.000
179A179TYR0-0.048-0.06925.869-0.354-0.3540.0000.0000.0000.000
180A180ALA0-0.010-0.00127.746-0.394-0.3940.0000.0000.0000.000
181A181GLU-1-0.733-0.83127.187-10.611-10.6110.0000.0000.0000.000
182A182LEU0-0.023-0.01123.500-0.439-0.4390.0000.0000.0000.000
183A183ARG10.8470.89223.21710.74010.7400.0000.0000.0000.000
184A184GLU-1-0.931-0.95822.368-11.391-11.3910.0000.0000.0000.000
185A185TYR00.0050.00819.545-0.669-0.6690.0000.0000.0000.000
186A186LEU0-0.025-0.01418.836-0.817-0.8170.0000.0000.0000.000
187A187LEU0-0.026-0.02517.606-0.850-0.8500.0000.0000.0000.000
188A188GLY0-0.0200.00017.622-0.506-0.5060.0000.0000.0000.000
189A189SER0-0.050-0.03115.752-0.574-0.5740.0000.0000.0000.000
190A190TYR0-0.078-0.05712.285-0.819-0.8190.0000.0000.0000.000
191A191PRO00.0330.02111.3090.6750.6750.0000.0000.0000.000
192A192GLN0-0.002-0.0158.3641.6161.6160.0000.0000.0000.000
193A193LEU0-0.052-0.00613.1730.4730.4730.0000.0000.0000.000
194A194ARG10.9800.98016.57714.09714.0970.0000.0000.0000.000
195A195GLY00.0510.02720.005-0.264-0.2640.0000.0000.0000.000
196A196GLY-1-0.813-0.88022.205-13.737-13.7370.0000.0000.0000.000