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: 97Q82

Calculation Name: 4LPS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate | malonate ion | phosphate ion | nickel (ii) ion

Ligand 3-letter code: GDP | MLI | PO4 | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LPS

Chain ID: A

ChEMBL ID:

UniProt ID: O25560

Base Structure: X-ray

Registration Date: 2025-10-04

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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2653961.909024
FMO2-HF: Nuclear repulsion 2567172.895051
FMO2-HF: Total energy -86789.013973
FMO2-MP2: Total energy -87034.992927


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:28:SER)


Summations of interaction energy for fragment #1(A:28: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.
-168.102-163.15813.483-10.128-8.298-0.105
Interaction energy analysis for fragmet #1(A:28:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.871 / q_NPA : 0.920
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].
3A30ASN00.026-0.0023.85811.52412.927-0.006-0.533-0.8650.000
4A31ASP-1-0.770-0.8971.917-106.897-104.46813.147-9.171-6.405-0.101
5A32ILE0-0.008-0.0022.5446.1577.2250.343-0.420-0.990-0.004
6A33LYS10.8840.9465.18430.10830.152-0.001-0.004-0.0380.000
7A34ALA0-0.004-0.0076.7494.2134.2130.0000.0000.0000.000
8A35ALA0-0.019-0.0067.2613.6803.6800.0000.0000.0000.000
9A36GLU-1-0.878-0.9479.005-25.439-25.4390.0000.0000.0000.000
10A37MET0-0.041-0.01810.9402.7492.7490.0000.0000.0000.000
11A38LYS10.9450.98311.74323.48723.4870.0000.0000.0000.000
12A39GLU-1-0.950-0.97812.651-19.738-19.7380.0000.0000.0000.000
13A40ARG10.7740.85915.18318.33418.3340.0000.0000.0000.000
14A41TYR0-0.031-0.03213.6901.4431.4430.0000.0000.0000.000
15A42LEU0-0.0010.00116.4070.9460.9460.0000.0000.0000.000
16A43LYS10.8880.95217.84317.18217.1820.0000.0000.0000.000
17A44GLU-1-0.847-0.91220.990-12.569-12.5690.0000.0000.0000.000
18A45GLY0-0.0080.01122.5540.4810.4810.0000.0000.0000.000
19A46LEU0-0.071-0.03120.7610.2860.2860.0000.0000.0000.000
20A47TYR0-0.046-0.04720.797-0.519-0.5190.0000.0000.0000.000
21A48VAL0-0.0020.00116.8250.3160.3160.0000.0000.0000.000
22A49LEU00.0070.00818.523-0.441-0.4410.0000.0000.0000.000
23A50ASN00.021-0.00314.2830.8260.8260.0000.0000.0000.000
24A51PHE00.0280.00517.7500.1170.1170.0000.0000.0000.000
25A52MET00.0020.01015.127-0.485-0.4850.0000.0000.0000.000
26A53SER00.018-0.02119.5890.5520.5520.0000.0000.0000.000
27A54SER00.0330.00521.797-0.630-0.6300.0000.0000.0000.000
28A55PRO00.0160.00923.9300.1090.1090.0000.0000.0000.000
29A56GLY00.0130.01926.1130.3020.3020.0000.0000.0000.000
30A57SER0-0.025-0.03526.3950.3350.3350.0000.0000.0000.000
31A58GLY00.0100.00028.4020.1360.1360.0000.0000.0000.000
32A59LYS10.8450.92521.99013.57813.5780.0000.0000.0000.000
33A60THR00.0610.03226.9000.2400.2400.0000.0000.0000.000
34A61THR0-0.041-0.02228.7170.1620.1620.0000.0000.0000.000
35A62MET0-0.0100.01225.4740.2680.2680.0000.0000.0000.000
36A63LEU00.0080.01125.1460.1340.1340.0000.0000.0000.000
37A64GLU-1-0.788-0.89029.671-9.227-9.2270.0000.0000.0000.000
38A65ASN0-0.035-0.03133.2210.1880.1880.0000.0000.0000.000
39A66LEU00.0240.01028.5640.1850.1850.0000.0000.0000.000
40A67ALA00.0090.01432.4910.0750.0750.0000.0000.0000.000
41A68ASP-1-0.853-0.90833.810-8.263-8.2630.0000.0000.0000.000
42A69PHE0-0.029-0.00834.5340.2330.2330.0000.0000.0000.000
43A70LYS10.8420.90435.1018.4248.4240.0000.0000.0000.000
44A71ASP-1-0.809-0.88635.453-8.983-8.9830.0000.0000.0000.000
45A72PHE0-0.015-0.00827.018-0.242-0.2420.0000.0000.0000.000
46A73LYS10.9350.96930.6689.6459.6450.0000.0000.0000.000
47A74PHE0-0.027-0.02026.505-0.395-0.3950.0000.0000.0000.000
48A75CYS0-0.0070.02025.0750.1800.1800.0000.0000.0000.000
49A76VAL0-0.006-0.01724.123-0.382-0.3820.0000.0000.0000.000
50A77VAL00.0060.00319.0290.2280.2280.0000.0000.0000.000
51A78GLU0-0.018-0.05821.388-0.388-0.3880.0000.0000.0000.000
52A79GLY00.0230.00719.652-0.333-0.3330.0000.0000.0000.000
53A80ASP-1-0.867-0.90720.644-12.623-12.6230.0000.0000.0000.000
54A81LEU00.0100.03321.002-0.264-0.2640.0000.0000.0000.000
55A82GLN00.028-0.01023.154-0.208-0.2080.0000.0000.0000.000
56A83THR0-0.063-0.03526.5260.3650.3650.0000.0000.0000.000
57A84ASN00.0950.04127.568-0.382-0.3820.0000.0000.0000.000
58A85ARG10.9731.00029.5099.7829.7820.0000.0000.0000.000
59A86ASP-1-0.774-0.88327.258-10.764-10.7640.0000.0000.0000.000
60A87ALA00.0260.01127.2420.0970.0970.0000.0000.0000.000
61A88ASP-1-0.830-0.91329.062-9.527-9.5270.0000.0000.0000.000
62A89ARG10.6960.83431.04310.29410.2940.0000.0000.0000.000
63A90LEU00.0090.00928.0490.2600.2600.0000.0000.0000.000
64A91ARG10.8220.88929.10510.69310.6930.0000.0000.0000.000
65A92LYS10.8900.95133.6918.2178.2170.0000.0000.0000.000
66A93LYS10.7830.88434.6188.9398.9390.0000.0000.0000.000
67A94GLY0-0.0060.00635.8910.0480.0480.0000.0000.0000.000
68A95VAL0-0.016-0.00129.352-0.083-0.0830.0000.0000.0000.000
69A96SER00.0100.00429.2310.0530.0530.0000.0000.0000.000
70A97ALA00.0130.01927.067-0.471-0.4710.0000.0000.0000.000
71A98HIS10.8030.86924.70812.16412.1640.0000.0000.0000.000
72A99GLN0-0.053-0.03423.9260.0790.0790.0000.0000.0000.000
73A100ILE00.0080.01217.737-0.048-0.0480.0000.0000.0000.000
74A101THR0-0.053-0.02621.6470.3480.3480.0000.0000.0000.000
75A102THR0-0.019-0.04417.7320.1820.1820.0000.0000.0000.000
76A103GLY00.0140.01819.957-0.442-0.4420.0000.0000.0000.000
77A104GLU-1-0.970-1.00420.700-13.286-13.2860.0000.0000.0000.000
78A105ALA0-0.044-0.00715.592-0.265-0.2650.0000.0000.0000.000
79A106CYS-1-0.704-0.75615.925-19.430-19.4300.0000.0000.0000.000
80A107HIS10.7100.78611.60324.03824.0380.0000.0000.0000.000
81A108LEU00.0470.03114.4860.0680.0680.0000.0000.0000.000
82A109GLU-1-0.868-0.9329.953-30.874-30.8740.0000.0000.0000.000
83A110ALA00.0420.0218.7932.2672.2670.0000.0000.0000.000
84A111SER0-0.027-0.03110.7360.7210.7210.0000.0000.0000.000
85A112MET0-0.059-0.00912.3281.7861.7860.0000.0000.0000.000
86A113ILE00.0170.01014.0061.5071.5070.0000.0000.0000.000
87A114GLU-1-0.833-0.90514.943-19.792-19.7920.0000.0000.0000.000
88A115GLY00.0580.02816.7760.8880.8880.0000.0000.0000.000
89A116ALA0-0.014-0.01319.6110.8750.8750.0000.0000.0000.000
90A117PHE0-0.017-0.01518.7070.6190.6190.0000.0000.0000.000
91A118ASP-1-0.797-0.88220.266-15.071-15.0710.0000.0000.0000.000
92A119LEU0-0.018-0.00822.5070.6720.6720.0000.0000.0000.000
93A120LEU0-0.004-0.00622.9030.5330.5330.0000.0000.0000.000
94A121LYS10.8620.92623.41913.32013.3200.0000.0000.0000.000
95A122ASP-1-0.915-0.95225.728-11.445-11.4450.0000.0000.0000.000
96A123GLU-1-0.897-0.92328.457-10.578-10.5780.0000.0000.0000.000
97A124GLY00.0030.00629.5020.3390.3390.0000.0000.0000.000
98A125ALA0-0.011-0.01227.7300.2540.2540.0000.0000.0000.000
99A126LEU0-0.0040.00322.5160.0310.0310.0000.0000.0000.000
100A127GLU-1-0.910-0.95626.336-10.067-10.0670.0000.0000.0000.000
101A128LYS10.8250.91929.1699.9389.9380.0000.0000.0000.000
102A129SER0-0.059-0.02626.4030.2110.2110.0000.0000.0000.000
103A130ASP-1-0.845-0.91126.893-10.716-10.7160.0000.0000.0000.000
104A131PHE0-0.004-0.01524.094-0.485-0.4850.0000.0000.0000.000
105A132LEU00.0210.01418.7960.2840.2840.0000.0000.0000.000
106A133ILE0-0.019-0.01121.097-0.590-0.5900.0000.0000.0000.000
107A134ILE00.0200.00616.0640.0930.0930.0000.0000.0000.000
108A135GLU-1-0.757-0.83119.775-12.460-12.4600.0000.0000.0000.000
109A136ASN00.015-0.01714.349-0.037-0.0370.0000.0000.0000.000
110A137VAL00.0260.01818.0230.8830.8830.0000.0000.0000.000
111A138GLY0-0.053-0.02419.492-0.248-0.2480.0000.0000.0000.000
112A139ASN0-0.014-0.04517.2910.6310.6310.0000.0000.0000.000
113A140LEU00.0080.01218.581-0.673-0.6730.0000.0000.0000.000
114A141VAL00.0300.00615.627-0.207-0.2070.0000.0000.0000.000
115A142CYS0-0.026-0.02613.525-0.683-0.6830.0000.0000.0000.000
116A143PRO00.007-0.00112.161-2.143-2.1430.0000.0000.0000.000
117A144SER0-0.032-0.02612.168-1.231-1.2310.0000.0000.0000.000
118A145SER0-0.0060.0098.3830.4860.4860.0000.0000.0000.000
119A146TYR0-0.074-0.0437.369-4.255-4.2550.0000.0000.0000.000
120A147ASN00.0470.0426.8576.0896.0890.0000.0000.0000.000
121A148LEU00.0230.0088.630-1.675-1.6750.0000.0000.0000.000
122A149GLY00.0250.02010.3111.4011.4010.0000.0000.0000.000
123A150ALA0-0.064-0.03111.3481.4871.4870.0000.0000.0000.000
124A151ALA0-0.0170.01014.388-0.713-0.7130.0000.0000.0000.000
125A152MET0-0.021-0.01117.1520.5900.5900.0000.0000.0000.000
126A153ASN00.0030.00413.989-0.926-0.9260.0000.0000.0000.000
127A154ILE0-0.020-0.00417.3300.5530.5530.0000.0000.0000.000
128A155VAL00.0260.01619.155-0.092-0.0920.0000.0000.0000.000
129A156LEU0-0.044-0.02221.6510.6450.6450.0000.0000.0000.000
130A157LEU0-0.004-0.00324.549-0.340-0.3400.0000.0000.0000.000
131A158SER0-0.047-0.05726.9040.4840.4840.0000.0000.0000.000
132A159VAL00.0270.01330.284-0.016-0.0160.0000.0000.0000.000
133A160PRO0-0.042-0.03433.1170.0350.0350.0000.0000.0000.000
134A161GLU-1-0.767-0.79426.810-11.597-11.5970.0000.0000.0000.000
135A162GLY0-0.0010.00430.745-0.104-0.1040.0000.0000.0000.000
136A163ASP-1-0.813-0.91230.472-9.507-9.5070.0000.0000.0000.000
137A164ASP-1-0.764-0.87630.391-10.559-10.5590.0000.0000.0000.000
138A165LYS10.7940.88225.93210.26110.2610.0000.0000.0000.000
139A166VAL00.0170.01424.119-0.516-0.5160.0000.0000.0000.000
140A167LEU0-0.001-0.00923.291-0.602-0.6020.0000.0000.0000.000
141A168LYS10.8330.91724.03810.53710.5370.0000.0000.0000.000
142A169TYR0-0.0090.00220.168-0.003-0.0030.0000.0000.0000.000
143A170PRO00.0520.02719.051-0.477-0.4770.0000.0000.0000.000
144A171THR00.0450.00313.0340.4170.4170.0000.0000.0000.000
145A172MET00.0020.01515.425-0.895-0.8950.0000.0000.0000.000
146A173PHE00.005-0.00817.1530.0510.0510.0000.0000.0000.000
147A174MET0-0.019-0.00416.2930.4150.4150.0000.0000.0000.000
148A175CYS0-0.058-0.01813.354-0.147-0.1470.0000.0000.0000.000
149A176ALA0-0.0210.00415.150-0.155-0.1550.0000.0000.0000.000
150A177ASP-1-0.730-0.82717.137-18.216-18.2160.0000.0000.0000.000
151A178ALA0-0.013-0.01319.8740.7940.7940.0000.0000.0000.000
152A179VAL00.0100.00622.279-0.477-0.4770.0000.0000.0000.000
153A180ILE0-0.009-0.01224.6610.5320.5320.0000.0000.0000.000
154A181ILE00.0280.01927.479-0.134-0.1340.0000.0000.0000.000
155A182SER00.002-0.01129.4960.3800.3800.0000.0000.0000.000
156A183LYS10.8450.91431.2739.9349.9340.0000.0000.0000.000
157A184ALA00.0630.02534.7100.1690.1690.0000.0000.0000.000
158A185ASP-1-0.800-0.86836.182-8.163-8.1630.0000.0000.0000.000
159A186MET0-0.048-0.02537.2170.2830.2830.0000.0000.0000.000
160A187VAL0-0.017-0.01036.6400.0170.0170.0000.0000.0000.000
161A188GLU-1-0.934-0.95738.846-6.967-6.9670.0000.0000.0000.000
162A189VAL00.0120.00241.0190.0360.0360.0000.0000.0000.000
163A190PHE0-0.007-0.01037.175-0.011-0.0110.0000.0000.0000.000
164A191ASN0-0.072-0.02839.0400.0230.0230.0000.0000.0000.000
165A192PHE0-0.0160.00831.254-0.090-0.0900.0000.0000.0000.000
166A193ARG10.8770.91335.1438.8498.8490.0000.0000.0000.000
167A194VAL00.032-0.00633.651-0.269-0.2690.0000.0000.0000.000
168A195SER0-0.032-0.00333.348-0.218-0.2180.0000.0000.0000.000
169A196GLN00.0230.03031.0120.1610.1610.0000.0000.0000.000
170A197VAL00.0410.01228.132-0.324-0.3240.0000.0000.0000.000
171A198LYS10.9250.97128.63610.04010.0400.0000.0000.0000.000
172A199GLU-1-0.858-0.95429.706-9.305-9.3050.0000.0000.0000.000
173A200ASP-1-0.816-0.88626.920-10.889-10.8890.0000.0000.0000.000
174A201MET00.0150.01522.270-0.512-0.5120.0000.0000.0000.000
175A202GLN0-0.055-0.02925.485-0.286-0.2860.0000.0000.0000.000
176A203LYS10.7980.88326.47310.71210.7120.0000.0000.0000.000
177A204LEU0-0.049-0.01521.010-0.276-0.2760.0000.0000.0000.000
178A205LYS10.8380.92317.02816.76616.7660.0000.0000.0000.000
179A206PRO0-0.0050.00422.5370.2950.2950.0000.0000.0000.000
180A207GLU-1-0.891-0.95220.831-14.054-14.0540.0000.0000.0000.000
181A208ALA0-0.0070.00422.4170.0240.0240.0000.0000.0000.000
182A209PRO0-0.059-0.01724.1910.5520.5520.0000.0000.0000.000
183A210ILE0-0.006-0.02026.120-0.317-0.3170.0000.0000.0000.000
184A211PHE0-0.0100.00327.1690.4290.4290.0000.0000.0000.000
185A212LEU0-0.0110.00130.647-0.131-0.1310.0000.0000.0000.000
186A213MET00.0200.00429.6360.0330.0330.0000.0000.0000.000
187A214SER0-0.044-0.05433.5750.0280.0280.0000.0000.0000.000
188A215SER00.0220.02235.3800.0580.0580.0000.0000.0000.000
189A216LYS10.8430.90436.7637.9677.9670.0000.0000.0000.000
190A217ASP-1-0.845-0.92138.295-7.967-7.9670.0000.0000.0000.000
191A218PRO00.0290.00437.700-0.256-0.2560.0000.0000.0000.000
192A219LYS10.8710.93237.8398.0458.0450.0000.0000.0000.000
193A220SER00.0330.01234.560-0.280-0.2800.0000.0000.0000.000
194A221LEU0-0.045-0.02632.157-0.355-0.3550.0000.0000.0000.000
195A222GLU-1-0.923-0.95733.326-8.374-8.3740.0000.0000.0000.000
196A223ASP-1-0.842-0.90534.509-8.763-8.7630.0000.0000.0000.000
197A224PHE00.003-0.00225.236-0.284-0.2840.0000.0000.0000.000
198A225LYS10.8330.90229.7368.6628.6620.0000.0000.0000.000
199A226ASN00.005-0.00830.907-0.201-0.2010.0000.0000.0000.000
200A227PHE00.0150.00725.086-0.108-0.1080.0000.0000.0000.000
201A228LEU00.0170.00624.670-0.377-0.3770.0000.0000.0000.000
202A229LEU0-0.043-0.02126.982-0.279-0.2790.0000.0000.0000.000
203A230GLU-1-0.863-0.90529.230-10.121-10.1210.0000.0000.0000.000
204A231LYS10.8110.89223.64411.90111.9010.0000.0000.0000.000
205A232LYS10.8360.92024.33011.69411.6940.0000.0000.0000.000
206A233ARG10.7940.88725.4989.8279.8270.0000.0000.0000.000
207A234GLU-1-0.831-0.90925.632-11.798-11.7980.0000.0000.0000.000
208A235ASN0-0.0190.00420.821-0.636-0.6360.0000.0000.0000.000
209A236TYR0-0.028-0.01518.797-0.289-0.2890.0000.0000.0000.000
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