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: ML48Z

Calculation Name: 3REF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate | sulfate ion | magnesium ion

Ligand 3-letter code: GDP | SO4 | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3REF

Chain ID: A

ChEMBL ID:

UniProt ID: C4M4W4

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1806439.800425
FMO2-HF: Nuclear repulsion 1738838.203896
FMO2-HF: Total energy -67601.596529
FMO2-MP2: Total energy -67798.454862


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:12:GLY)


Summations of interaction energy for fragment #1(A:12:GLY)
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.
-257.466-252.55511.279-8.481-7.712-0.089
Interaction energy analysis for fragmet #1(A:12:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.931
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].
3A14ILE00.0360.0043.8313.9764.966-0.017-0.438-0.5350.000
9A20ALA0-0.031-0.0114.7974.5064.570-0.001-0.009-0.0540.000
10A21LEU00.0160.0033.536-17.237-16.7060.020-0.327-0.225-0.002
11A22LYS10.7900.9074.69937.01537.045-0.001-0.001-0.0290.000
82A93ASP-1-0.827-0.9102.199-117.928-117.0298.785-5.453-4.232-0.064
83A94VAL0-0.013-0.0145.1193.5303.577-0.001-0.002-0.0440.000
172A183ILE0-0.069-0.0452.634-6.608-5.6910.696-0.654-0.959-0.006
173A184PHE-1-0.880-0.9202.607-42.930-41.4971.798-1.597-1.634-0.017
4A15GLU-1-0.808-0.8787.176-33.462-33.4620.0000.0000.0000.000
5A16ASN0-0.022-0.01810.1433.0503.0500.0000.0000.0000.000
6A17GLY00.0140.01712.5550.3550.3550.0000.0000.0000.000
7A18LYS10.8320.91310.35220.58920.5890.0000.0000.0000.000
8A19LYS10.8840.9345.36830.09730.0970.0000.0000.0000.000
12A23ILE0-0.008-0.0076.836-1.806-1.8060.0000.0000.0000.000
13A24VAL00.0100.0099.7092.2252.2250.0000.0000.0000.000
14A25VAL0-0.0080.00412.7680.0890.0890.0000.0000.0000.000
15A26VAL00.0130.02316.2110.9310.9310.0000.0000.0000.000
16A27GLY00.1030.04018.7130.0750.0750.0000.0000.0000.000
17A28ASP-1-0.803-0.87322.199-11.814-11.8140.0000.0000.0000.000
18A29GLY00.007-0.00725.393-0.293-0.2930.0000.0000.0000.000
19A30ALA00.004-0.00727.7670.1250.1250.0000.0000.0000.000
20A31VAL0-0.0010.00923.7800.2490.2490.0000.0000.0000.000
21A32GLY00.0280.00725.3710.0550.0550.0000.0000.0000.000
22A33LYS10.8380.94019.99914.07914.0790.0000.0000.0000.000
23A34THR00.0550.01120.798-0.351-0.3510.0000.0000.0000.000
24A35CYS0-0.009-0.01822.604-0.021-0.0210.0000.0000.0000.000
25A36LEU00.0030.03718.0530.1880.1880.0000.0000.0000.000
26A37LEU00.0280.01515.782-0.263-0.2630.0000.0000.0000.000
27A38LEU0-0.0270.00619.454-0.061-0.0610.0000.0000.0000.000
28A39ALA0-0.002-0.00122.6720.0580.0580.0000.0000.0000.000
29A40PHE0-0.024-0.01414.5930.0690.0690.0000.0000.0000.000
30A41SER0-0.046-0.04118.3890.1370.1370.0000.0000.0000.000
31A42LYS10.9070.94319.85513.60013.6000.0000.0000.0000.000
32A43GLY00.0160.03123.1070.5110.5110.0000.0000.0000.000
33A44GLU-1-0.971-0.99524.863-9.981-9.9810.0000.0000.0000.000
34A45ILE0-0.010-0.01426.262-0.477-0.4770.0000.0000.0000.000
35A46PRO0-0.0010.00927.4180.3630.3630.0000.0000.0000.000
36A47THR0-0.003-0.00930.4410.1170.1170.0000.0000.0000.000
37A48ALA0-0.021-0.01831.4490.2380.2380.0000.0000.0000.000
38A49TYR0-0.0110.00030.445-0.061-0.0610.0000.0000.0000.000
39A50VAL0-0.0010.00527.006-0.267-0.2670.0000.0000.0000.000
40A51PRO0-0.012-0.00725.1790.2620.2620.0000.0000.0000.000
41A52THR0-0.055-0.04726.378-0.198-0.1980.0000.0000.0000.000
42A53VAL0-0.013-0.00620.746-0.317-0.3170.0000.0000.0000.000
43A54PHE0-0.065-0.03119.5920.5790.5790.0000.0000.0000.000
44A55GLU-1-0.910-0.95419.740-14.311-14.3110.0000.0000.0000.000
45A56ASN0-0.036-0.01414.4970.0310.0310.0000.0000.0000.000
46A57PHE0-0.031-0.01815.2640.3480.3480.0000.0000.0000.000
47A58SER00.0080.00912.791-1.005-1.0050.0000.0000.0000.000
48A59HIS00.0110.01113.1521.6951.6950.0000.0000.0000.000
49A60VAL0-0.037-0.01812.729-2.006-2.0060.0000.0000.0000.000
50A61MET00.0080.01812.0770.9020.9020.0000.0000.0000.000
51A62LYS10.9300.96312.86714.13314.1330.0000.0000.0000.000
52A63TYR0-0.010-0.03911.4410.8770.8770.0000.0000.0000.000
53A64LYS10.8040.9039.55928.28128.2810.0000.0000.0000.000
54A65ASN0-0.0070.00214.5551.6631.6630.0000.0000.0000.000
55A66GLU-1-0.854-0.90510.326-26.366-26.3660.0000.0000.0000.000
56A67GLU-1-0.885-0.93912.464-18.132-18.1320.0000.0000.0000.000
57A68PHE0-0.006-0.0046.617-1.528-1.5280.0000.0000.0000.000
58A69ILE0-0.028-0.0178.4852.9712.9710.0000.0000.0000.000
59A70LEU00.012-0.0038.091-4.388-4.3880.0000.0000.0000.000
60A71HIS0-0.033-0.0437.9334.8074.8070.0000.0000.0000.000
61A72LEU0-0.014-0.00210.167-1.627-1.6270.0000.0000.0000.000
62A73TRP00.0510.00711.2321.5431.5430.0000.0000.0000.000
63A74ASP-1-0.731-0.85514.635-15.211-15.2110.0000.0000.0000.000
64A75THR0-0.042-0.03917.2310.0970.0970.0000.0000.0000.000
65A76ALA00.016-0.00120.0020.5350.5350.0000.0000.0000.000
66A77GLY00.0180.00123.441-0.386-0.3860.0000.0000.0000.000
67A78GLN0-0.044-0.01626.0970.4250.4250.0000.0000.0000.000
68A79GLU-1-0.837-0.91927.704-10.893-10.8930.0000.0000.0000.000
69A80GLU-1-0.868-0.93626.682-11.107-11.1070.0000.0000.0000.000
70A81TYR00.0430.00723.228-0.660-0.6600.0000.0000.0000.000
71A82ASP-1-0.864-0.91823.353-12.654-12.6540.0000.0000.0000.000
72A83ARG10.8530.92524.54210.97710.9770.0000.0000.0000.000
73A84LEU00.0180.01121.495-0.344-0.3440.0000.0000.0000.000
74A85ARG10.7120.83119.17513.42413.4240.0000.0000.0000.000
75A86PRO00.008-0.00717.899-1.066-1.0660.0000.0000.0000.000
76A87LEU0-0.007-0.00216.745-1.045-1.0450.0000.0000.0000.000
77A88SER0-0.027-0.01014.952-0.958-0.9580.0000.0000.0000.000
78A89TYR0-0.022-0.03812.687-1.862-1.8620.0000.0000.0000.000
79A90ALA00.0240.04111.244-2.080-2.0800.0000.0000.0000.000
80A91ASP-1-0.908-0.9577.064-33.064-33.0640.0000.0000.0000.000
81A92SER0-0.024-0.0306.356-4.342-4.3420.0000.0000.0000.000
84A95VAL00.006-0.0038.3681.1671.1670.0000.0000.0000.000
85A96LEU0-0.015-0.00212.1060.9400.9400.0000.0000.0000.000
86A97LEU00.0190.00615.0620.8480.8480.0000.0000.0000.000
87A98CYS0-0.048-0.02018.0320.4390.4390.0000.0000.0000.000
88A99PHE00.0320.00720.7800.4020.4020.0000.0000.0000.000
89A100ALA0-0.026-0.01124.502-0.156-0.1560.0000.0000.0000.000
90A101VAL00.0330.01627.1150.2750.2750.0000.0000.0000.000
91A102ASN0-0.0170.00129.254-0.044-0.0440.0000.0000.0000.000
92A103ASN0-0.021-0.01630.2380.1140.1140.0000.0000.0000.000
93A104ARG10.8860.94430.1859.1829.1820.0000.0000.0000.000
94A105THR00.0270.01630.441-0.187-0.1870.0000.0000.0000.000
95A106SER0-0.008-0.01326.775-0.393-0.3930.0000.0000.0000.000
96A107PHE0-0.021-0.01025.850-0.593-0.5930.0000.0000.0000.000
97A108ASP-1-0.847-0.92926.239-10.553-10.5530.0000.0000.0000.000
98A109ASN0-0.045-0.04526.330-0.081-0.0810.0000.0000.0000.000
99A110ILE0-0.054-0.02020.856-0.523-0.5230.0000.0000.0000.000
100A111SER00.0110.00622.574-0.564-0.5640.0000.0000.0000.000
101A112THR0-0.069-0.03824.8000.0310.0310.0000.0000.0000.000
102A113LYS10.8960.96123.61512.77212.7720.0000.0000.0000.000
103A114TRP0-0.025-0.03920.061-0.510-0.5100.0000.0000.0000.000
104A115GLU-1-0.817-0.89618.036-16.562-16.5620.0000.0000.0000.000
105A116PRO00.0350.01018.734-0.715-0.7150.0000.0000.0000.000
106A117GLU-1-0.798-0.84619.696-15.269-15.2690.0000.0000.0000.000
107A118ILE0-0.011-0.01313.643-0.573-0.5730.0000.0000.0000.000
108A119LYS10.8670.93615.33215.04815.0480.0000.0000.0000.000
109A120HIS0-0.072-0.02317.0730.3930.3930.0000.0000.0000.000
110A121TYR0-0.048-0.03215.9850.1980.1980.0000.0000.0000.000
111A122ILE0-0.052-0.0309.227-0.907-0.9070.0000.0000.0000.000
112A123ASP-1-0.867-0.93211.510-21.987-21.9870.0000.0000.0000.000
113A124THR0-0.038-0.0128.0370.6710.6710.0000.0000.0000.000
114A125ALA0-0.056-0.0087.462-4.496-4.4960.0000.0000.0000.000
115A126LYS10.8900.9377.00940.33240.3320.0000.0000.0000.000
116A127THR00.0850.0429.607-0.061-0.0610.0000.0000.0000.000
117A128VAL00.0040.00612.0380.4020.4020.0000.0000.0000.000
118A129LEU0-0.0110.01014.6800.3900.3900.0000.0000.0000.000
119A130VAL0-0.003-0.02417.4800.1220.1220.0000.0000.0000.000
120A131GLY00.0590.03920.2040.3900.3900.0000.0000.0000.000
121A132LEU0-0.029-0.02621.5930.1380.1380.0000.0000.0000.000
122A133LYS10.8570.92724.98711.19411.1940.0000.0000.0000.000
123A134VAL00.0280.01827.1150.4180.4180.0000.0000.0000.000
124A135ASP-1-0.867-0.91429.092-10.272-10.2720.0000.0000.0000.000
125A136LEU0-0.052-0.03231.9050.3650.3650.0000.0000.0000.000
126A137ARG10.7470.85428.65210.87910.8790.0000.0000.0000.000
127A138LYS10.8890.93434.0348.1308.1300.0000.0000.0000.000
128A139ASP-1-0.873-0.92737.609-8.298-8.2980.0000.0000.0000.000
129A140GLY0-0.072-0.04739.7270.1450.1450.0000.0000.0000.000
130A141SER0-0.051-0.02237.2580.2270.2270.0000.0000.0000.000
131A142ASP-1-0.912-0.96436.492-8.753-8.7530.0000.0000.0000.000
132A143ASP-1-0.794-0.89633.360-9.313-9.3130.0000.0000.0000.000
133A144VAL0-0.042-0.00628.0070.0560.0560.0000.0000.0000.000
134A145THR0-0.003-0.03130.489-0.208-0.2080.0000.0000.0000.000
135A146LYS10.8710.91724.23612.42512.4250.0000.0000.0000.000
136A147GLN00.006-0.00227.040-0.331-0.3310.0000.0000.0000.000
137A148GLU-1-0.727-0.81728.038-10.161-10.1610.0000.0000.0000.000
138A149GLY00.0400.02024.795-0.279-0.2790.0000.0000.0000.000
139A150ASP-1-0.822-0.91623.378-13.406-13.4060.0000.0000.0000.000
140A151ASP-1-0.920-0.96223.809-11.300-11.3000.0000.0000.0000.000
141A152LEU0-0.082-0.04122.736-0.168-0.1680.0000.0000.0000.000
142A153CYS0-0.023-0.00119.163-0.720-0.7200.0000.0000.0000.000
143A154GLN0-0.0140.00020.048-0.879-0.8790.0000.0000.0000.000
144A155LYS10.8790.93122.26211.08911.0890.0000.0000.0000.000
145A156LEU0-0.010-0.00719.2930.0830.0830.0000.0000.0000.000
146A157GLY0-0.0090.01717.655-0.754-0.7540.0000.0000.0000.000
147A158CYS0-0.079-0.03415.274-0.939-0.9390.0000.0000.0000.000
148A159VAL0-0.002-0.02411.1350.3930.3930.0000.0000.0000.000
149A160ALA0-0.033-0.02214.4990.5370.5370.0000.0000.0000.000
150A161TYR0-0.056-0.03517.216-0.272-0.2720.0000.0000.0000.000
151A162ILE0-0.047-0.01116.3540.2380.2380.0000.0000.0000.000
152A163GLU-1-0.737-0.81520.668-11.426-11.4260.0000.0000.0000.000
153A164ALA00.006-0.00821.911-0.073-0.0730.0000.0000.0000.000
154A165SER0-0.046-0.06324.0400.4190.4190.0000.0000.0000.000
155A166SER00.022-0.00724.029-0.089-0.0890.0000.0000.0000.000
156A167VAL0-0.0010.00926.0700.1370.1370.0000.0000.0000.000
157A168ALA0-0.004-0.01629.8080.1050.1050.0000.0000.0000.000
158A169LYS10.8450.92625.99911.34311.3430.0000.0000.0000.000
159A170ILE00.0390.03225.761-0.146-0.1460.0000.0000.0000.000
160A171GLY00.0650.02622.275-0.236-0.2360.0000.0000.0000.000
161A172LEU0-0.043-0.01820.211-0.760-0.7600.0000.0000.0000.000
162A173ASN00.0180.00617.745-0.987-0.9870.0000.0000.0000.000
163A174GLU-1-0.808-0.89016.361-16.483-16.4830.0000.0000.0000.000
164A175VAL00.0040.00015.716-1.054-1.0540.0000.0000.0000.000
165A176PHE00.0140.01012.745-1.586-1.5860.0000.0000.0000.000
166A177GLU-1-0.907-0.96111.597-19.743-19.7430.0000.0000.0000.000
167A178LYS10.8790.92211.78715.68515.6850.0000.0000.0000.000
168A179SER00.006-0.0149.811-1.220-1.2200.0000.0000.0000.000
169A180VAL0-0.015-0.0037.351-4.440-4.4400.0000.0000.0000.000
170A181ASP-1-0.789-0.8867.287-27.196-27.1960.0000.0000.0000.000
171A182CYS0-0.120-0.0238.604-0.589-0.5890.0000.0000.0000.000