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

tag_button

FMODB ID: GVQZ1

Calculation Name: 1MR3-F-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-3'-monophosphate-5'-diphosphate | glycerol | 1,3-propandiol | 1,2-ethanediol | magnesium ion | ethanol

Ligand 3-letter code: G3D | GOL | PDO | EDO | MG | EOH

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MR3

Chain ID: F

ChEMBL ID:

UniProt ID: P19146

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1973391.893052
FMO2-HF: Nuclear repulsion 1902533.530909
FMO2-HF: Total energy -70858.362144
FMO2-MP2: Total energy -71065.099122


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:5:ALA)


Summations of interaction energy for fragment #1(A:5:ALA)
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.
-46.879-45.10311.6-7.584-5.79-0.085
Interaction energy analysis for fragmet #1(A:5:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.800 / q_NPA : 0.889
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].
3A7LYS10.9990.9983.88738.68940.236-0.016-0.743-0.788-0.001
4A8LEU0-0.0010.0045.089-5.198-5.154-0.001-0.002-0.0400.000
34A38LYS10.9290.9752.48133.89734.9480.408-0.559-0.899-0.002
35A39LEU0-0.0060.0021.739-49.696-50.79811.210-6.248-3.860-0.082
36A40GLY00.007-0.0053.821-4.204-3.968-0.001-0.032-0.2030.000
5A9PHE00.0660.0255.4812.9832.9830.0000.0000.0000.000
6A10SER0-0.026-0.0186.7302.5402.5400.0000.0000.0000.000
7A11ASN0-0.072-0.0278.2322.5132.5130.0000.0000.0000.000
8A12LEU00.0380.03910.9940.9440.9440.0000.0000.0000.000
9A13PHE00.0620.0198.5760.5690.5690.0000.0000.0000.000
10A14GLY00.0030.01211.7881.3941.3940.0000.0000.0000.000
11A15ASN0-0.086-0.04911.732-2.733-2.7330.0000.0000.0000.000
12A16LYS10.8880.95914.30317.49717.4970.0000.0000.0000.000
13A17GLU-1-0.897-0.95814.861-17.349-17.3490.0000.0000.0000.000
14A18MET00.0130.03214.6660.4510.4510.0000.0000.0000.000
15A19ARG10.8000.88715.37013.36313.3630.0000.0000.0000.000
16A20ILE00.0050.00113.4181.0011.0010.0000.0000.0000.000
17A21LEU00.0050.01416.927-0.482-0.4820.0000.0000.0000.000
18A22MET0-0.032-0.00713.5970.2740.2740.0000.0000.0000.000
19A23VAL00.0300.00318.1060.0000.0000.0000.0000.0000.000
20A24GLY00.0630.02921.306-0.274-0.2740.0000.0000.0000.000
21A25LEU0-0.0110.01023.672-0.198-0.1980.0000.0000.0000.000
22A26ASP-1-0.795-0.86923.464-12.284-12.2840.0000.0000.0000.000
23A27GLY00.0230.00723.1800.2570.2570.0000.0000.0000.000
24A28ALA0-0.0080.00322.081-0.265-0.2650.0000.0000.0000.000
25A29GLY00.0350.01418.730-0.349-0.3490.0000.0000.0000.000
26A30LYS10.7630.86216.55213.62013.6200.0000.0000.0000.000
27A31THR00.031-0.00814.644-1.059-1.0590.0000.0000.0000.000
28A32THR0-0.030-0.01812.987-1.421-1.4210.0000.0000.0000.000
29A33VAL00.0260.01112.122-1.966-1.9660.0000.0000.0000.000
30A34LEU0-0.0160.00610.135-3.069-3.0690.0000.0000.0000.000
31A35TYR00.0190.0018.286-4.864-4.8640.0000.0000.0000.000
32A36LYS10.7780.8967.30321.88321.8830.0000.0000.0000.000
33A37LEU00.0160.0066.985-3.623-3.6230.0000.0000.0000.000
37A41GLU-1-0.949-0.9635.572-26.235-26.2350.0000.0000.0000.000
38A42VAL0-0.029-0.0148.2840.5770.5770.0000.0000.0000.000
39A43ILE00.0110.01510.8961.7531.7530.0000.0000.0000.000
40A44THR00.0070.00313.9980.8520.8520.0000.0000.0000.000
41A45THR0-0.031-0.02017.1480.5920.5920.0000.0000.0000.000
42A46ILE00.0220.00320.3360.1420.1420.0000.0000.0000.000
43A47PRO0-0.0150.01122.9030.4960.4960.0000.0000.0000.000
44A48THR0-0.041-0.03825.7800.6610.6610.0000.0000.0000.000
45A49ILE00.0350.02527.835-0.323-0.3230.0000.0000.0000.000
46A50GLY00.0150.00528.3190.2700.2700.0000.0000.0000.000
47A51PHE0-0.045-0.02124.721-0.129-0.1290.0000.0000.0000.000
48A52ASN00.019-0.00221.7800.0580.0580.0000.0000.0000.000
49A53VAL0-0.022-0.00918.9030.0560.0560.0000.0000.0000.000
50A54GLU-1-0.801-0.87514.897-20.324-20.3240.0000.0000.0000.000
51A55THR0-0.033-0.03513.8280.7300.7300.0000.0000.0000.000
52A56VAL0-0.0120.0107.664-1.286-1.2860.0000.0000.0000.000
53A57GLN00.0160.0039.7941.9471.9470.0000.0000.0000.000
54A58TYR0-0.010-0.0214.823-3.453-3.4530.0000.0000.0000.000
55A59LYS10.9230.9717.98634.28534.2850.0000.0000.0000.000
56A60ASN00.0270.02610.6470.3000.3000.0000.0000.0000.000
57A61ILE0-0.0020.01310.1801.3491.3490.0000.0000.0000.000
58A62SER00.0110.00411.356-1.320-1.3200.0000.0000.0000.000
59A63PHE00.0090.0059.8200.8790.8790.0000.0000.0000.000
60A64THR00.002-0.00113.746-0.144-0.1440.0000.0000.0000.000
61A65VAL00.001-0.00415.2150.3130.3130.0000.0000.0000.000
62A66TRP0-0.007-0.00418.0250.0050.0050.0000.0000.0000.000
63A67ASP-1-0.844-0.90321.363-14.273-14.2730.0000.0000.0000.000
64A68VAL0-0.043-0.01723.8900.3300.3300.0000.0000.0000.000
65A69GLY00.0790.02026.890-0.151-0.1510.0000.0000.0000.000
66A70GLY00.0320.00830.1460.1720.1720.0000.0000.0000.000
67A71GLN0-0.022-0.01233.7370.1410.1410.0000.0000.0000.000
68A72ASP-1-0.850-0.91129.591-10.697-10.6970.0000.0000.0000.000
69A73ARG10.8760.92932.8598.5478.5470.0000.0000.0000.000
70A74ILE00.0480.03930.635-0.065-0.0650.0000.0000.0000.000
71A75ARG10.8960.94930.5989.6669.6660.0000.0000.0000.000
72A76SER00.0620.01031.045-0.222-0.2220.0000.0000.0000.000
73A77LEU00.0220.01925.700-0.070-0.0700.0000.0000.0000.000
74A78TRP00.0150.01226.536-0.323-0.3230.0000.0000.0000.000
75A79ARG10.8580.87726.7809.1799.1790.0000.0000.0000.000
76A80HIS0-0.0040.00625.7770.2990.2990.0000.0000.0000.000
77A81TYR00.0450.01221.169-0.303-0.3030.0000.0000.0000.000
78A82TYR0-0.038-0.02123.667-0.196-0.1960.0000.0000.0000.000
79A83ARG10.9180.96925.59810.34110.3410.0000.0000.0000.000
80A84ASN0-0.0310.00120.6880.1960.1960.0000.0000.0000.000
81A85THR0-0.050-0.02620.950-0.862-0.8620.0000.0000.0000.000
82A86GLU-1-0.729-0.85119.802-15.007-15.0070.0000.0000.0000.000
83A87GLY0-0.006-0.01520.0080.3700.3700.0000.0000.0000.000
84A88VAL0-0.0150.00119.758-0.580-0.5800.0000.0000.0000.000
85A89ILE0-0.026-0.00915.422-0.086-0.0860.0000.0000.0000.000
86A90PHE00.0350.00419.6470.1240.1240.0000.0000.0000.000
87A91VAL0-0.039-0.02317.997-0.002-0.0020.0000.0000.0000.000
88A92ILE0-0.014-0.01521.2620.5740.5740.0000.0000.0000.000
89A93ASP-1-0.779-0.87823.328-12.961-12.9610.0000.0000.0000.000
90A94SER0-0.010-0.02424.3970.5350.5350.0000.0000.0000.000
91A95ASN00.000-0.01226.7850.7030.7030.0000.0000.0000.000
92A96ASP-1-0.801-0.86228.369-9.883-9.8830.0000.0000.0000.000
93A97ARG10.8140.86330.2309.7769.7760.0000.0000.0000.000
94A98SER0-0.109-0.05933.1810.3080.3080.0000.0000.0000.000
95A99ARG10.8090.85128.55010.98010.9800.0000.0000.0000.000
96A100ILE00.0150.01129.475-0.142-0.1420.0000.0000.0000.000
97A101GLY00.005-0.00131.750-0.016-0.0160.0000.0000.0000.000
98A102GLU-1-0.747-0.84531.451-10.098-10.0980.0000.0000.0000.000
99A103ALA00.007-0.00428.067-0.141-0.1410.0000.0000.0000.000
100A104ARG10.9050.96029.7458.7578.7570.0000.0000.0000.000
101A105GLU-1-0.917-0.96232.148-8.897-8.8970.0000.0000.0000.000
102A106VAL0-0.006-0.00228.0120.0210.0210.0000.0000.0000.000
103A107MET0-0.0260.00427.239-0.213-0.2130.0000.0000.0000.000
104A108GLN0-0.013-0.02229.3500.1170.1170.0000.0000.0000.000
105A109ARG10.8230.92632.1169.7169.7160.0000.0000.0000.000
106A110MET0-0.020-0.00824.878-0.008-0.0080.0000.0000.0000.000
107A111LEU0-0.009-0.00628.943-0.084-0.0840.0000.0000.0000.000
108A112ASN0-0.049-0.03030.9700.2870.2870.0000.0000.0000.000
109A113GLU-1-0.800-0.84630.385-9.592-9.5920.0000.0000.0000.000
110A114ASP-1-0.843-0.93331.631-9.472-9.4720.0000.0000.0000.000
111A115GLU-1-0.861-0.94029.611-10.259-10.2590.0000.0000.0000.000
112A116LEU0-0.0050.00725.300-0.466-0.4660.0000.0000.0000.000
113A117ARG10.8330.93128.2069.3819.3810.0000.0000.0000.000
114A118ASN0-0.003-0.00828.0650.2970.2970.0000.0000.0000.000
115A119ALA0-0.0200.02123.729-0.225-0.2250.0000.0000.0000.000
116A120VAL0-0.028-0.00321.8140.4580.4580.0000.0000.0000.000
117A121TRP00.023-0.01522.874-0.536-0.5360.0000.0000.0000.000
118A122LEU0-0.0280.00717.2500.2770.2770.0000.0000.0000.000
119A123VAL0-0.004-0.00821.116-0.270-0.2700.0000.0000.0000.000
120A124PHE00.0230.00014.812-0.296-0.2960.0000.0000.0000.000
121A125ALA00.0260.01620.6260.3460.3460.0000.0000.0000.000
122A126ASN00.0260.00718.387-0.754-0.7540.0000.0000.0000.000
123A127LYS10.8070.89920.70114.35414.3540.0000.0000.0000.000
124A128GLN0-0.058-0.04922.2090.7640.7640.0000.0000.0000.000
125A129ASP-1-0.844-0.90921.684-14.481-14.4810.0000.0000.0000.000
126A130LEU0-0.023-0.00223.8330.3500.3500.0000.0000.0000.000
127A131PRO0-0.0030.00126.8010.1380.1380.0000.0000.0000.000
128A132GLU-1-0.837-0.91629.955-10.494-10.4940.0000.0000.0000.000
129A133ALA00.0050.02027.9520.2690.2690.0000.0000.0000.000
130A134MET0-0.085-0.03129.5490.4890.4890.0000.0000.0000.000
131A135SER00.0660.01428.790-0.464-0.4640.0000.0000.0000.000
132A136ALA00.0650.01326.0930.0980.0980.0000.0000.0000.000
133A137ALA0-0.0040.01728.0210.0750.0750.0000.0000.0000.000
134A138GLU-1-0.824-0.90431.536-9.406-9.4060.0000.0000.0000.000
135A139ILE00.0010.00226.6440.1710.1710.0000.0000.0000.000
136A140THR0-0.012-0.02729.645-0.045-0.0450.0000.0000.0000.000
137A141GLU-1-0.945-0.96130.854-8.550-8.5500.0000.0000.0000.000
138A142LYS10.8980.94932.7069.2689.2680.0000.0000.0000.000
139A143LEU00.016-0.00227.4950.1390.1390.0000.0000.0000.000
140A144GLY00.0160.01932.0480.1100.1100.0000.0000.0000.000
141A145LEU00.0030.00027.8430.1300.1300.0000.0000.0000.000
142A146HIS00.0720.03031.9330.0100.0100.0000.0000.0000.000
143A147SER0-0.030-0.00534.7020.3580.3580.0000.0000.0000.000
144A148ILE0-0.0280.01029.7820.1730.1730.0000.0000.0000.000
145A149ARG10.8490.90533.8918.7588.7580.0000.0000.0000.000
146A150ASN0-0.022-0.02134.016-0.128-0.1280.0000.0000.0000.000
147A151ARG10.8630.93227.72310.90510.9050.0000.0000.0000.000
148A152PRO0-0.001-0.00526.1240.1080.1080.0000.0000.0000.000
149A153TRP00.0300.00625.551-0.442-0.4420.0000.0000.0000.000
150A154PHE00.0180.01521.0340.2420.2420.0000.0000.0000.000
151A155ILE0-0.036-0.01123.741-0.179-0.1790.0000.0000.0000.000
152A156GLN0-0.023-0.00918.3980.2720.2720.0000.0000.0000.000
153A157SER00.0140.00821.5370.1880.1880.0000.0000.0000.000
154A158THR0-0.013-0.01617.113-0.511-0.5110.0000.0000.0000.000
155A159CYS0-0.0310.00617.6100.5360.5360.0000.0000.0000.000
156A160ALA0-0.019-0.01114.656-1.249-1.2490.0000.0000.0000.000
157A161THR00.0390.01313.759-1.740-1.7400.0000.0000.0000.000
158A162SER00.011-0.04214.079-1.733-1.7330.0000.0000.0000.000
159A163GLY0-0.050-0.03912.355-2.043-2.0430.0000.0000.0000.000
160A164GLU-1-0.850-0.87413.183-17.844-17.8440.0000.0000.0000.000
161A165GLY00.0590.01916.1760.4560.4560.0000.0000.0000.000
162A166LEU0-0.031-0.02411.545-0.046-0.0460.0000.0000.0000.000
163A167TYR0-0.117-0.06910.588-2.326-2.3260.0000.0000.0000.000
164A168GLU-1-0.809-0.90712.914-19.979-19.9790.0000.0000.0000.000
165A169GLY00.0230.00916.6650.8370.8370.0000.0000.0000.000
166A170LEU0-0.008-0.01411.0780.3570.3570.0000.0000.0000.000
167A171GLU-1-0.878-0.92614.789-18.484-18.4840.0000.0000.0000.000
168A172TRP0-0.0070.00215.9890.5790.5790.0000.0000.0000.000
169A173LEU00.010-0.00315.5240.5600.5600.0000.0000.0000.000
170A174SER0-0.017-0.04314.8570.6450.6450.0000.0000.0000.000
171A175ASN0-0.035-0.00716.8730.4710.4710.0000.0000.0000.000
172A176ASN0-0.078-0.04120.1131.4281.4280.0000.0000.0000.000
173A177LEU0-0.057-0.01717.8910.6040.6040.0000.0000.0000.000
174A178LYS10.9390.97721.39211.25611.2560.0000.0000.0000.000
175A179ASN0-0.082-0.07019.643-0.099-0.0990.0000.0000.0000.000
176A180GLN0-0.091-0.04823.4220.7880.7880.0000.0000.0000.000
177A181SER-1-0.863-0.91124.234-12.162-12.1620.0000.0000.0000.000