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: 6488Z

Calculation Name: 3M1I-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: GTP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3M1I

Chain ID: A

ChEMBL ID:

UniProt ID: P32835

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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2342659.780341
FMO2-HF: Nuclear repulsion 2259966.692135
FMO2-HF: Total energy -82693.088206
FMO2-MP2: Total energy -82935.943347


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:10:VAL)


Summations of interaction energy for fragment #1(A:10:VAL)
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.
-38.283-30.613.08-4.475-6.278-0.046
Interaction energy analysis for fragmet #1(A:10:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.927
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].
3A12THR00.0310.0063.8520.7601.933-0.009-0.447-0.7160.000
50A59GLY00.0230.0234.438-3.985-3.881-0.001-0.009-0.0940.000
51A60GLU-1-0.892-0.9172.325-52.414-49.2721.696-2.011-2.828-0.020
52A61ILE0-0.037-0.0232.465-13.752-10.8461.393-1.973-2.326-0.026
53A62LYS10.8770.9493.70141.11241.4600.001-0.035-0.3140.000
4A13PHE0-0.013-0.0086.0792.2572.2570.0000.0000.0000.000
5A14LYS10.8150.9229.66618.12918.1290.0000.0000.0000.000
6A15LEU00.008-0.01012.6950.9090.9090.0000.0000.0000.000
7A16VAL00.0000.00414.8860.3750.3750.0000.0000.0000.000
8A17LEU0-0.0160.00218.5030.2590.2590.0000.0000.0000.000
9A18VAL00.0200.02820.4840.4340.4340.0000.0000.0000.000
10A19GLY00.0700.02724.190-0.018-0.0180.0000.0000.0000.000
11A20ASP-1-0.790-0.86927.621-9.544-9.5440.0000.0000.0000.000
12A21GLY00.0080.01329.394-0.314-0.3140.0000.0000.0000.000
13A22GLY00.0230.01430.6600.1900.1900.0000.0000.0000.000
14A23THR0-0.078-0.05028.081-0.078-0.0780.0000.0000.0000.000
15A24GLY00.0410.02027.039-0.080-0.0800.0000.0000.0000.000
16A25LYS10.7910.91122.92311.61811.6180.0000.0000.0000.000
17A26THR00.1030.01721.890-0.272-0.2720.0000.0000.0000.000
18A27THR0-0.051-0.01122.015-0.383-0.3830.0000.0000.0000.000
19A28PHE0-0.019-0.01318.620-0.225-0.2250.0000.0000.0000.000
20A29VAL00.0120.00116.444-0.592-0.5920.0000.0000.0000.000
21A30LYS10.9140.94917.64211.66011.6600.0000.0000.0000.000
22A31ARG10.8090.92119.11211.76611.7660.0000.0000.0000.000
23A32HIS10.8040.88614.88616.91316.9130.0000.0000.0000.000
24A33LEU0-0.0070.01013.818-0.948-0.9480.0000.0000.0000.000
25A34THR0-0.002-0.03415.795-0.337-0.3370.0000.0000.0000.000
26A35GLY00.0320.03918.6470.3700.3700.0000.0000.0000.000
27A36GLU-1-0.804-0.86420.571-12.082-12.0820.0000.0000.0000.000
28A37PHE00.004-0.02423.518-0.176-0.1760.0000.0000.0000.000
29A38GLU-1-0.807-0.87925.861-9.927-9.9270.0000.0000.0000.000
30A39LYS10.8300.89027.6999.1499.1490.0000.0000.0000.000
31A40LYS10.8310.90630.49110.05010.0500.0000.0000.0000.000
32A41TYR0-0.009-0.01829.621-0.434-0.4340.0000.0000.0000.000
33A42ILE00.0380.01829.1100.3190.3190.0000.0000.0000.000
34A43ALA0-0.078-0.03828.628-0.312-0.3120.0000.0000.0000.000
35A44THR00.0790.03923.5120.3120.3120.0000.0000.0000.000
36A45ILE0-0.039-0.02626.4930.3820.3820.0000.0000.0000.000
37A46GLY00.002-0.00125.941-0.314-0.3140.0000.0000.0000.000
38A47VAL0-0.061-0.03719.919-0.058-0.0580.0000.0000.0000.000
39A48GLU-1-0.869-0.90619.863-13.321-13.3210.0000.0000.0000.000
40A49VAL0-0.042-0.03214.161-0.321-0.3210.0000.0000.0000.000
41A50HIS0-0.004-0.01114.511-0.816-0.8160.0000.0000.0000.000
42A51PRO0-0.0260.0019.290-0.791-0.7910.0000.0000.0000.000
43A52LEU00.001-0.0049.6561.0761.0760.0000.0000.0000.000
44A53SER0-0.011-0.0295.058-1.263-1.2630.0000.0000.0000.000
45A54PHE0-0.024-0.0146.7323.8863.8860.0000.0000.0000.000
46A55TYR00.0770.0346.383-4.149-4.1490.0000.0000.0000.000
47A56THR0-0.032-0.0387.0323.6873.6870.0000.0000.0000.000
48A57ASN00.0350.0098.362-2.235-2.2350.0000.0000.0000.000
49A58PHE0-0.030-0.0107.5821.1281.1280.0000.0000.0000.000
54A63PHE0-0.017-0.0155.4561.1181.1180.0000.0000.0000.000
55A64ASP-1-0.805-0.9039.047-29.580-29.5800.0000.0000.0000.000
56A65VAL0-0.040-0.03311.0091.1821.1820.0000.0000.0000.000
57A66TRP00.0550.01714.3371.3221.3220.0000.0000.0000.000
58A67ASP-1-0.781-0.88817.449-13.021-13.0210.0000.0000.0000.000
59A68THR00.002-0.02120.2470.5100.5100.0000.0000.0000.000
60A69ALA00.0150.01223.5330.2970.2970.0000.0000.0000.000
61A70GLY0-0.012-0.00627.0770.1020.1020.0000.0000.0000.000
62A71LEU0-0.056-0.03629.1510.3770.3770.0000.0000.0000.000
63A72GLU-1-0.814-0.88532.078-8.774-8.7740.0000.0000.0000.000
64A73LYS10.9250.95733.7138.2958.2950.0000.0000.0000.000
65A74PHE00.0320.00430.4440.1310.1310.0000.0000.0000.000
66A75GLY00.0320.02329.269-0.331-0.3310.0000.0000.0000.000
67A76GLY00.0260.01128.140-0.371-0.3710.0000.0000.0000.000
68A77LEU00.012-0.01025.0720.2860.2860.0000.0000.0000.000
69A78ARG10.8330.90827.5789.5369.5360.0000.0000.0000.000
70A79ASP-1-0.849-0.93225.634-11.341-11.3410.0000.0000.0000.000
71A80GLY00.0500.02525.089-0.442-0.4420.0000.0000.0000.000
72A81TYR0-0.033-0.01721.610-0.435-0.4350.0000.0000.0000.000
73A82TYR0-0.0080.00020.430-0.922-0.9220.0000.0000.0000.000
74A83ILE00.0820.04720.484-0.624-0.6240.0000.0000.0000.000
75A84ASN0-0.009-0.00616.711-0.140-0.1400.0000.0000.0000.000
76A85ALA0-0.005-0.00416.019-1.370-1.3700.0000.0000.0000.000
77A86GLN00.0450.03010.6420.3430.3430.0000.0000.0000.000
78A87CYS0-0.045-0.00113.918-0.095-0.0950.0000.0000.0000.000
79A88ALA00.0370.01916.2620.1460.1460.0000.0000.0000.000
80A89ILE0-0.003-0.00217.1900.1580.1580.0000.0000.0000.000
81A90ILE00.0060.00520.6390.2970.2970.0000.0000.0000.000
82A91MET0-0.0090.00522.7930.2380.2380.0000.0000.0000.000
83A92PHE0-0.007-0.02626.0390.4280.4280.0000.0000.0000.000
84A93ASP-1-0.728-0.82829.387-9.450-9.4500.0000.0000.0000.000
85A94VAL0-0.026-0.00931.5580.3410.3410.0000.0000.0000.000
86A95THR0-0.022-0.03734.1110.3880.3880.0000.0000.0000.000
87A96SER00.0280.01435.3790.3480.3480.0000.0000.0000.000
88A97ARG10.9320.95036.0227.2527.2520.0000.0000.0000.000
89A98ILE0-0.0040.00636.924-0.050-0.0500.0000.0000.0000.000
90A99THR00.0550.02632.206-0.195-0.1950.0000.0000.0000.000
91A100TYR00.0130.00932.288-0.261-0.2610.0000.0000.0000.000
92A101LYS10.9360.96134.0937.5607.5600.0000.0000.0000.000
93A102ASN00.020-0.00133.1440.2050.2050.0000.0000.0000.000
94A103VAL0-0.0060.01929.244-0.238-0.2380.0000.0000.0000.000
95A104PRO0-0.038-0.02930.503-0.270-0.2700.0000.0000.0000.000
96A105ASN0-0.027-0.00432.4630.0050.0050.0000.0000.0000.000
97A106TRP00.0360.00027.449-0.206-0.2060.0000.0000.0000.000
98A107HIS00.0210.00526.3690.0080.0080.0000.0000.0000.000
99A108ARG10.7530.84328.1739.1689.1680.0000.0000.0000.000
100A109ASP-1-0.785-0.87329.353-9.920-9.9200.0000.0000.0000.000
101A110LEU00.0180.01821.812-0.223-0.2230.0000.0000.0000.000
102A111VAL0-0.012-0.01925.083-0.269-0.2690.0000.0000.0000.000
103A112ARG10.8940.95526.5329.7099.7090.0000.0000.0000.000
104A113VAL0-0.0140.01423.2090.0850.0850.0000.0000.0000.000
105A114CYS0-0.053-0.02120.436-0.443-0.4430.0000.0000.0000.000
106A115GLU-1-0.922-0.96022.915-12.135-12.1350.0000.0000.0000.000
107A116ASN0-0.055-0.03121.8410.3610.3610.0000.0000.0000.000
108A117ILE00.0040.01818.084-0.809-0.8090.0000.0000.0000.000
109A118PRO0-0.0220.00315.6320.8840.8840.0000.0000.0000.000
110A119ILE00.024-0.00718.274-0.365-0.3650.0000.0000.0000.000
111A120VAL0-0.028-0.01118.7670.4070.4070.0000.0000.0000.000
112A121LEU0-0.051-0.01321.5330.1390.1390.0000.0000.0000.000
113A122CYS00.008-0.00622.049-0.077-0.0770.0000.0000.0000.000
114A123GLY00.0380.02725.3850.2310.2310.0000.0000.0000.000
115A124ASN00.019-0.01326.773-0.015-0.0150.0000.0000.0000.000
116A125LYS10.8650.90628.5349.9929.9920.0000.0000.0000.000
117A126VAL0-0.060-0.03429.7280.3700.3700.0000.0000.0000.000
118A127ASP-1-0.793-0.85731.097-9.565-9.5650.0000.0000.0000.000
119A128VAL0-0.0040.00533.3010.3110.3110.0000.0000.0000.000
120A129LYS11.0201.00236.1347.0917.0910.0000.0000.0000.000
121A130GLU-1-0.863-0.91939.428-7.160-7.1600.0000.0000.0000.000
122A131ARG10.8180.87232.5419.1739.1730.0000.0000.0000.000
123A132LYS10.8120.89938.3317.6257.6250.0000.0000.0000.000
124A133VAL0-0.036-0.01034.8210.2080.2080.0000.0000.0000.000
125A134LYS10.9620.98136.0607.4777.4770.0000.0000.0000.000
126A135ALA00.1150.04035.1160.0180.0180.0000.0000.0000.000
127A136LYS10.9710.98635.8506.9986.9980.0000.0000.0000.000
128A137THR0-0.036-0.00937.3400.1650.1650.0000.0000.0000.000
129A138ILE0-0.043-0.00731.214-0.013-0.0130.0000.0000.0000.000
130A139THR0-0.051-0.03833.699-0.079-0.0790.0000.0000.0000.000
131A140PHE00.0110.01329.549-0.009-0.0090.0000.0000.0000.000
132A141HIS00.0750.02827.6450.0930.0930.0000.0000.0000.000
133A142ARG10.9490.98129.0738.7298.7290.0000.0000.0000.000
134A143LYS10.9560.97331.3638.3018.3010.0000.0000.0000.000
135A144LYS10.9070.96028.4809.8349.8340.0000.0000.0000.000
136A145ASN0-0.0060.01125.600-0.247-0.2470.0000.0000.0000.000
137A146LEU0-0.0120.01423.823-0.407-0.4070.0000.0000.0000.000
138A147GLN00.0240.02221.3620.9160.9160.0000.0000.0000.000
139A148TYR0-0.064-0.09223.6840.0900.0900.0000.0000.0000.000
140A149TYR00.010-0.00120.214-0.252-0.2520.0000.0000.0000.000
141A150ASP-1-0.746-0.80025.494-9.659-9.6590.0000.0000.0000.000
142A151ILE0-0.003-0.00823.108-0.232-0.2320.0000.0000.0000.000
143A152SER0-0.063-0.06226.0450.3900.3900.0000.0000.0000.000
144A153ALA00.0080.01024.488-0.230-0.2300.0000.0000.0000.000
145A154LYS10.8870.96025.4928.9648.9640.0000.0000.0000.000
146A155SER00.048-0.00328.085-0.076-0.0760.0000.0000.0000.000
147A156ASN00.0320.01722.731-0.436-0.4360.0000.0000.0000.000
148A157TYR00.0110.01723.718-0.438-0.4380.0000.0000.0000.000
149A158ASN0-0.020-0.03223.019-0.231-0.2310.0000.0000.0000.000
150A159PHE00.0340.02218.789-0.480-0.4800.0000.0000.0000.000
151A160GLU-1-0.764-0.90116.832-14.878-14.8780.0000.0000.0000.000
152A161LYS10.8760.95316.57611.82411.8240.0000.0000.0000.000
153A162PRO0-0.029-0.02417.896-0.371-0.3710.0000.0000.0000.000
154A163PHE00.0490.02512.829-0.223-0.2230.0000.0000.0000.000
155A164LEU00.0140.02113.162-1.141-1.1410.0000.0000.0000.000
156A165TRP0-0.026-0.01914.462-0.407-0.4070.0000.0000.0000.000
157A166LEU0-0.004-0.01013.923-0.120-0.1200.0000.0000.0000.000
158A167ALA00.0470.02810.246-0.777-0.7770.0000.0000.0000.000
159A168ARG10.7820.88911.28616.28416.2840.0000.0000.0000.000
160A169LYS10.8520.94113.83115.90315.9030.0000.0000.0000.000
161A170LEU0-0.016-0.01310.2960.3770.3770.0000.0000.0000.000
162A171ALA0-0.012-0.0048.796-1.437-1.4370.0000.0000.0000.000
163A172GLY0-0.0120.00610.2610.3820.3820.0000.0000.0000.000
164A173ASN00.0250.01612.8031.8991.8990.0000.0000.0000.000
165A174PRO0-0.002-0.01614.270-0.491-0.4910.0000.0000.0000.000
166A175GLN00.001-0.00815.4770.1810.1810.0000.0000.0000.000
167A176LEU0-0.0130.0218.900-0.102-0.1020.0000.0000.0000.000
168A177GLU-1-0.821-0.91913.031-15.378-15.3780.0000.0000.0000.000
169A178PHE0-0.029-0.02410.749-1.461-1.4610.0000.0000.0000.000
170A179VAL0-0.020-0.01010.1691.3841.3840.0000.0000.0000.000
171A180ALA00.0010.00512.109-0.727-0.7270.0000.0000.0000.000
172A181SER00.0140.01210.384-0.835-0.8350.0000.0000.0000.000
173A182PRO0-0.032-0.0299.6951.4191.4190.0000.0000.0000.000
174A183ALA00.0080.01412.589-0.168-0.1680.0000.0000.0000.000
175A184LEU0-0.016-0.01213.0660.4550.4550.0000.0000.0000.000
176A185ALA00.0020.00616.9360.4740.4740.0000.0000.0000.000
177A186PRO0-0.017-0.00120.445-0.407-0.4070.0000.0000.0000.000
178A187PRO00.0000.00521.5720.2270.2270.0000.0000.0000.000
179A188GLU-1-0.891-0.96824.515-10.963-10.9630.0000.0000.0000.000
180A189VAL0-0.075-0.02825.0960.2720.2720.0000.0000.0000.000
181A190GLN00.0350.00426.9960.0090.0090.0000.0000.0000.000
182A191VAL0-0.0200.00630.4470.1100.1100.0000.0000.0000.000
183A192ASP-1-0.872-0.95634.092-7.949-7.9490.0000.0000.0000.000
184A193GLU-1-0.838-0.90136.894-7.405-7.4050.0000.0000.0000.000
185A194GLN0-0.035-0.01929.8840.1790.1790.0000.0000.0000.000
186A195LEU0-0.008-0.01033.622-0.050-0.0500.0000.0000.0000.000
187A196MET0-0.014-0.01635.4130.1390.1390.0000.0000.0000.000
188A197GLN0-0.099-0.06338.3200.0130.0130.0000.0000.0000.000
189A198GLN0-0.052-0.02933.233-0.186-0.1860.0000.0000.0000.000
190A199TYR0-0.027-0.00231.072-0.232-0.2320.0000.0000.0000.000
191A200GLN00.0080.01835.089-0.122-0.1220.0000.0000.0000.000
192A201GLN00.0190.00338.4830.0260.0260.0000.0000.0000.000
193A202GLU-1-0.973-0.98531.042-9.613-9.6130.0000.0000.0000.000
194A203MET00.0290.00835.194-0.106-0.1060.0000.0000.0000.000
195A204GLU-1-0.906-0.92836.799-7.092-7.0920.0000.0000.0000.000
196A205GLN0-0.033-0.02235.3160.2310.2310.0000.0000.0000.000
197A206ALA0-0.034-0.02234.079-0.019-0.0190.0000.0000.0000.000
198A207THR0-0.071-0.05035.9710.0350.0350.0000.0000.0000.000
199A208ALA0-0.025-0.00138.6210.1370.1370.0000.0000.0000.000
200A209LEU0-0.054-0.01534.6480.1240.1240.0000.0000.0000.000
201A210PRO0-0.027-0.01737.410-0.112-0.1120.0000.0000.0000.000
202A211LEU00.0370.02932.758-0.233-0.2330.0000.0000.0000.000
203A212PRO0-0.093-0.05231.3870.1740.1740.0000.0000.0000.000
204A213ASP-1-0.842-0.92432.426-9.280-9.2800.0000.0000.0000.000
205A214GLU-1-0.876-0.93335.232-8.227-8.2270.0000.0000.0000.000
206A215ASP-1-0.902-0.95237.279-7.189-7.1890.0000.0000.0000.000
207A216ASP-1-1.079-1.02834.988-8.508-8.5080.0000.0000.0000.000
208A217ALA-1-0.971-0.97633.881-8.648-8.6480.0000.0000.0000.000