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: KQLN3

Calculation Name: 1I4D-A-Xray549

Preferred Name:

Target Type:

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

Ligand 3-letter code: GDP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1I4D

Chain ID: A

ChEMBL ID:

UniProt ID: P53365

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1749422.28114
FMO2-HF: Nuclear repulsion 1674190.125079
FMO2-HF: Total energy -75232.156061
FMO2-MP2: Total energy -75453.557066


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:23:SER)


Summations of interaction energy for fragment #1(A:23: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.
-148.78-147.091-0.021-0.732-0.935-0.001
Interaction energy analysis for fragmet #1(A:23:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / 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].
3A25THR0-0.019-0.0273.8620.9182.446-0.019-0.723-0.786-0.001
122A144THR0-0.002-0.0114.548-3.567-3.504-0.001-0.008-0.0540.000
125A147GLU-1-0.995-0.9965.029-45.032-44.934-0.001-0.001-0.0950.000
4A26VAL0-0.062-0.0345.9441.9741.9740.0000.0000.0000.000
5A27ASP-1-0.724-0.8068.650-21.753-21.7530.0000.0000.0000.000
6A28LEU00.0370.01711.9581.4241.4240.0000.0000.0000.000
7A29GLU-1-0.871-0.94513.242-18.097-18.0970.0000.0000.0000.000
8A30LEU0-0.0200.00315.8561.1501.1500.0000.0000.0000.000
9A31GLU-1-0.739-0.84210.752-28.432-28.4320.0000.0000.0000.000
10A32LEU00.0220.01515.2620.7340.7340.0000.0000.0000.000
11A33GLN0-0.055-0.03817.7301.4411.4410.0000.0000.0000.000
12A34ILE0-0.0010.00916.5010.8800.8800.0000.0000.0000.000
13A35GLU-1-0.816-0.91317.058-17.133-17.1330.0000.0000.0000.000
14A36LEU0-0.0060.00219.3390.7600.7600.0000.0000.0000.000
15A37LEU0-0.0030.00822.5720.8270.8270.0000.0000.0000.000
16A38ARG10.7990.85116.50518.38118.3810.0000.0000.0000.000
17A39GLU-1-0.876-0.91423.142-11.808-11.8080.0000.0000.0000.000
18A40THR0-0.040-0.02224.7460.7100.7100.0000.0000.0000.000
19A41LYS10.8300.92326.31211.68911.6890.0000.0000.0000.000
20A42ARG10.9390.96121.38414.08214.0820.0000.0000.0000.000
21A43LYS10.8340.90827.35211.79811.7980.0000.0000.0000.000
22A44TYR00.012-0.00830.7310.4510.4510.0000.0000.0000.000
23A45GLU-1-0.862-0.95629.395-10.459-10.4590.0000.0000.0000.000
24A46SER0-0.028-0.00432.6790.3850.3850.0000.0000.0000.000
25A47VAL00.0290.00434.3880.2960.2960.0000.0000.0000.000
26A48LEU0-0.049-0.01335.6180.3010.3010.0000.0000.0000.000
27A49GLN0-0.019-0.00935.9490.3020.3020.0000.0000.0000.000
28A50LEU00.0100.00938.4650.2550.2550.0000.0000.0000.000
29A51GLY00.0360.02240.7100.2260.2260.0000.0000.0000.000
30A52ARG10.9420.97736.9208.5678.5670.0000.0000.0000.000
31A53ALA00.0110.00742.8050.1760.1760.0000.0000.0000.000
32A54LEU00.0070.00544.5800.1690.1690.0000.0000.0000.000
33A55THR0-0.025-0.02246.0060.1880.1880.0000.0000.0000.000
34A56ALA00.0070.00247.4170.1580.1580.0000.0000.0000.000
35A57HIS00.0130.00946.3600.2250.2250.0000.0000.0000.000
36A58LEU00.0190.00550.0540.1380.1380.0000.0000.0000.000
37A59TYR0-0.0010.00252.1430.1340.1340.0000.0000.0000.000
38A60SER00.015-0.00552.4790.1240.1240.0000.0000.0000.000
39A61LEU0-0.029-0.00253.7870.1120.1120.0000.0000.0000.000
40A62LEU0-0.0170.00856.1530.1140.1140.0000.0000.0000.000
41A63GLN00.0270.01156.8760.0480.0480.0000.0000.0000.000
42A64THR0-0.028-0.01858.4330.1060.1060.0000.0000.0000.000
43A65GLN0-0.025-0.02359.8670.0350.0350.0000.0000.0000.000
44A66HIS0-0.0060.00462.6650.0350.0350.0000.0000.0000.000
45A67ALA00.0260.01164.2120.0890.0890.0000.0000.0000.000
46A68LEU0-0.028-0.01064.6310.0780.0780.0000.0000.0000.000
47A69GLY00.0400.01866.7190.0720.0720.0000.0000.0000.000
48A70ASP-1-0.906-0.96168.542-4.580-4.5800.0000.0000.0000.000
49A71ALA0-0.041-0.01969.8220.0860.0860.0000.0000.0000.000
50A72PHE0-0.007-0.01467.9740.0650.0650.0000.0000.0000.000
51A73ALA00.0150.00772.6000.0680.0680.0000.0000.0000.000
52A74ASP-1-0.861-0.90574.554-4.129-4.1290.0000.0000.0000.000
53A75LEU00.007-0.00673.5910.0690.0690.0000.0000.0000.000
54A76SER0-0.053-0.03676.6040.0670.0670.0000.0000.0000.000
55A77GLN0-0.055-0.03178.3470.0670.0670.0000.0000.0000.000
56A78LYS10.7930.87279.1264.1604.1600.0000.0000.0000.000
57A79SER00.0010.01079.8790.0350.0350.0000.0000.0000.000
58A80PRO0-0.003-0.01581.821-0.023-0.0230.0000.0000.0000.000
59A81GLU-1-0.923-0.96483.884-3.746-3.7460.0000.0000.0000.000
60A82LEU0-0.0340.00478.129-0.024-0.0240.0000.0000.0000.000
61A83GLN0-0.032-0.00678.703-0.038-0.0380.0000.0000.0000.000
62A84GLU-1-0.913-0.93678.656-4.020-4.0200.0000.0000.0000.000
63A85GLU-1-0.851-0.93875.414-4.195-4.1950.0000.0000.0000.000
64A86PHE0-0.016-0.00273.562-0.097-0.0970.0000.0000.0000.000
65A87GLY00.0500.01573.643-0.069-0.0690.0000.0000.0000.000
66A88TYR0-0.043-0.01572.477-0.057-0.0570.0000.0000.0000.000
67A89ASN0-0.035-0.03969.500-0.141-0.1410.0000.0000.0000.000
68A90ALA0-0.014-0.00469.037-0.090-0.0900.0000.0000.0000.000
69A91GLU-1-0.821-0.90869.320-4.560-4.5600.0000.0000.0000.000
70A92THR0-0.0030.00366.789-0.095-0.0950.0000.0000.0000.000
71A93GLN0-0.0120.00463.794-0.193-0.1930.0000.0000.0000.000
72A94LYS10.8410.91064.4854.4404.4400.0000.0000.0000.000
73A95LEU0-0.042-0.00764.332-0.055-0.0550.0000.0000.0000.000
74A96LEU0-0.007-0.01260.671-0.094-0.0940.0000.0000.0000.000
75A97CYS0-0.049-0.00360.130-0.124-0.1240.0000.0000.0000.000
76A98LYS11.0211.01360.0774.7834.7830.0000.0000.0000.000
77A99ASN0-0.038-0.03959.637-0.092-0.0920.0000.0000.0000.000
78A100GLY00.0380.00756.474-0.121-0.1210.0000.0000.0000.000
79A101GLU-1-0.917-0.96855.573-5.483-5.4830.0000.0000.0000.000
80A102THR0-0.055-0.01955.611-0.104-0.1040.0000.0000.0000.000
81A103LEU0-0.020-0.00550.898-0.134-0.1340.0000.0000.0000.000
82A104LEU00.0200.01450.669-0.182-0.1820.0000.0000.0000.000
83A105GLY00.0170.01350.860-0.141-0.1410.0000.0000.0000.000
84A106ALA0-0.016-0.01050.369-0.142-0.1420.0000.0000.0000.000
85A107VAL0-0.008-0.01146.054-0.198-0.1980.0000.0000.0000.000
86A108ASN00.0180.00245.932-0.312-0.3120.0000.0000.0000.000
87A109PHE0-0.0150.00145.846-0.188-0.1880.0000.0000.0000.000
88A110PHE00.0290.02241.200-0.205-0.2050.0000.0000.0000.000
89A111VAL00.0110.00741.505-0.267-0.2670.0000.0000.0000.000
90A112SER0-0.013-0.00340.918-0.304-0.3040.0000.0000.0000.000
91A113SER0-0.017-0.02141.106-0.183-0.1830.0000.0000.0000.000
92A114ILE00.0130.00336.583-0.257-0.2570.0000.0000.0000.000
93A115ASN00.0200.00436.544-0.435-0.4350.0000.0000.0000.000
94A116THR0-0.031-0.01136.396-0.232-0.2320.0000.0000.0000.000
95A117LEU0-0.030-0.02033.968-0.233-0.2330.0000.0000.0000.000
96A118VAL00.0150.00031.562-0.356-0.3560.0000.0000.0000.000
97A119THR00.003-0.01231.569-0.471-0.4710.0000.0000.0000.000
98A120LYS10.9500.99133.1728.8138.8130.0000.0000.0000.000
99A121THR0-0.061-0.03432.321-0.193-0.1930.0000.0000.0000.000
100A122MET00.0320.01828.072-0.327-0.3270.0000.0000.0000.000
101A123GLU-1-0.811-0.90627.013-12.398-12.3980.0000.0000.0000.000
102A124ASP-1-0.843-0.90027.740-11.182-11.1820.0000.0000.0000.000
103A125THR00.0270.01124.763-0.360-0.3600.0000.0000.0000.000
104A126LEU00.005-0.00323.288-0.683-0.6830.0000.0000.0000.000
105A127MET0-0.0270.00923.452-0.510-0.5100.0000.0000.0000.000
106A128THR0-0.018-0.02522.823-0.488-0.4880.0000.0000.0000.000
107A129VAL0-0.010-0.02619.141-0.629-0.6290.0000.0000.0000.000
108A130LYS10.8880.97118.63812.68512.6850.0000.0000.0000.000
109A131GLN0-0.015-0.00218.393-0.582-0.5820.0000.0000.0000.000
110A132TYR0-0.014-0.03613.071-0.831-0.8310.0000.0000.0000.000
111A133GLU-1-0.839-0.88613.383-19.682-19.6820.0000.0000.0000.000
112A134ALA00.0140.01213.198-1.627-1.6270.0000.0000.0000.000
113A135ALA00.0330.00813.980-1.024-1.0240.0000.0000.0000.000
114A136ARG10.8620.9388.70627.55627.5560.0000.0000.0000.000
115A137LEU0-0.0060.0048.818-2.701-2.7010.0000.0000.0000.000
116A138GLU-1-0.862-0.9309.992-19.177-19.1770.0000.0000.0000.000
117A139TYR0-0.034-0.0179.631-0.779-0.7790.0000.0000.0000.000
118A140ASP-1-0.798-0.8845.501-44.687-44.6870.0000.0000.0000.000
119A141ALA0-0.0220.0136.148-3.215-3.2150.0000.0000.0000.000
120A142TYR00.0650.0298.4810.2120.2120.0000.0000.0000.000
121A143ARG10.8910.9485.78835.65635.6560.0000.0000.0000.000
123A145ASP-1-0.884-0.9406.085-22.469-22.4690.0000.0000.0000.000
124A146LEU0-0.107-0.0659.7731.8541.8540.0000.0000.0000.000
126A148GLU-1-0.984-0.9957.344-29.822-29.8220.0000.0000.0000.000
127A149LEU0-0.124-0.0519.7981.9841.9840.0000.0000.0000.000
128A150SER-1-0.978-0.97012.022-17.983-17.9830.0000.0000.0000.000
129A163GLU0-0.014-0.02721.3900.7710.7710.0000.0000.0000.000
130A164SER00.0580.01521.463-0.298-0.2980.0000.0000.0000.000
131A165ALA00.0470.04316.654-0.216-0.2160.0000.0000.0000.000
132A166GLN00.0540.03216.602-0.542-0.5420.0000.0000.0000.000
133A167ALA00.0150.00417.656-0.359-0.3590.0000.0000.0000.000
134A168THR00.0080.00516.457-0.188-0.1880.0000.0000.0000.000
135A169PHE00.0440.0299.772-0.286-0.2860.0000.0000.0000.000
136A170GLN0-0.095-0.05114.323-1.008-1.0080.0000.0000.0000.000
137A171ALA00.0540.02416.822-0.212-0.2120.0000.0000.0000.000
138A172HIS0-0.049-0.03913.302-0.061-0.0610.0000.0000.0000.000
139A173ARG10.8550.92512.94018.66718.6670.0000.0000.0000.000
140A174ASP-1-0.828-0.90914.145-15.462-15.4620.0000.0000.0000.000
141A175LYS10.8470.91417.10116.78916.7890.0000.0000.0000.000
142A176TYR0-0.029-0.04111.8640.1450.1450.0000.0000.0000.000
143A177GLU-1-0.869-0.93614.708-18.303-18.3030.0000.0000.0000.000
144A178LYS10.8100.90016.65813.39013.3900.0000.0000.0000.000
145A179LEU0-0.020-0.01918.0730.5300.5300.0000.0000.0000.000
146A180ARG10.8920.94014.28719.75019.7500.0000.0000.0000.000
147A181GLY00.0070.01317.9530.2840.2840.0000.0000.0000.000
148A182ASP-1-0.823-0.90921.354-12.391-12.3910.0000.0000.0000.000
149A183VAL0-0.0030.00219.5630.5370.5370.0000.0000.0000.000
150A184ALA00.0090.00720.8170.4080.4080.0000.0000.0000.000
151A185ILE0-0.032-0.00622.5440.5420.5420.0000.0000.0000.000
152A186LYS10.8450.90125.46511.84211.8420.0000.0000.0000.000
153A187LEU00.0120.00620.9660.4400.4400.0000.0000.0000.000
154A188LYS10.9140.97525.61311.31611.3160.0000.0000.0000.000
155A189PHE00.0860.02728.0520.2920.2920.0000.0000.0000.000
156A190LEU0-0.0230.01127.1150.4290.4290.0000.0000.0000.000
157A191GLU-1-0.837-0.91428.224-10.675-10.6750.0000.0000.0000.000
158A192GLU-1-0.940-0.96930.287-9.113-9.1130.0000.0000.0000.000
159A193ASN0-0.051-0.05133.4310.6020.6020.0000.0000.0000.000
160A194LYS10.8300.91529.36610.97910.9790.0000.0000.0000.000
161A195ILE00.0110.01233.0270.2630.2630.0000.0000.0000.000
162A196LYS10.9600.98436.0908.0158.0150.0000.0000.0000.000
163A197VAL0-0.032-0.01937.5800.2860.2860.0000.0000.0000.000
164A198MET00.0290.01135.6940.2540.2540.0000.0000.0000.000
165A199HIS00.0200.02338.8840.0700.0700.0000.0000.0000.000
166A200LYS10.9600.98241.2437.1997.1990.0000.0000.0000.000
167A201GLN0-0.010-0.01841.2700.2790.2790.0000.0000.0000.000
168A202LEU00.0170.00938.8080.1360.1360.0000.0000.0000.000
169A203LEU00.0270.02743.2800.1600.1600.0000.0000.0000.000
170A204LEU0-0.020-0.01346.4300.1780.1780.0000.0000.0000.000
171A205PHE00.0230.01645.2550.1480.1480.0000.0000.0000.000
172A206HIS00.0490.02446.9040.0160.0160.0000.0000.0000.000
173A207ASN0-0.055-0.03348.5350.2490.2490.0000.0000.0000.000
174A208ALA0-0.0050.00750.2990.1430.1430.0000.0000.0000.000
175A209VAL00.0090.00048.9400.1190.1190.0000.0000.0000.000
176A210SER0-0.001-0.01451.9040.1190.1190.0000.0000.0000.000
177A211ALA0-0.018-0.01254.1200.1340.1340.0000.0000.0000.000
178A212TYR0-0.0320.00154.9090.1050.1050.0000.0000.0000.000
179A213PHE00.0050.00853.7120.0520.0520.0000.0000.0000.000
180A214ALA0-0.028-0.01458.4260.1090.1090.0000.0000.0000.000
181A215GLY0-0.020-0.01760.1670.1020.1020.0000.0000.0000.000
182A216ASN00.0220.00659.1430.1520.1520.0000.0000.0000.000
183A217GLN00.0560.01962.3320.1140.1140.0000.0000.0000.000
184A218LYS10.8960.94763.9245.1105.1100.0000.0000.0000.000
185A219GLN0-0.043-0.02766.3150.0560.0560.0000.0000.0000.000
186A220LEU0-0.035-0.01164.3940.0410.0410.0000.0000.0000.000
187A221GLU-1-0.989-0.99567.631-4.789-4.7890.0000.0000.0000.000
188A222GLN-1-0.973-0.95469.465-4.351-4.3510.0000.0000.0000.000