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: N8MLQ

Calculation Name: 7MPP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-monophosphate

Ligand 3-letter code: 5GP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7MPP

Chain ID: A

ChEMBL ID:

UniProt ID:

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 206
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2448604.396566
FMO2-HF: Nuclear repulsion 2366695.433547
FMO2-HF: Total energy -81908.963018
FMO2-MP2: Total energy -82147.849083


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-146.752-144.43411.621-7.52-6.42-0.086
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.784 / q_NPA : 0.874
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].
3A3GLU-1-0.845-0.9083.857-30.107-28.662-0.015-0.579-0.8510.001
4A4ILE0-0.030-0.0173.8591.1361.321-0.001-0.035-0.1490.000
146A146ARG10.9210.9384.28847.96648.134-0.001-0.013-0.1540.000
150A150GLU-1-0.815-0.9041.799-113.098-112.56511.639-6.893-5.280-0.087
151A151TYR0-0.050-0.0105.1320.2620.249-0.0010.0000.0140.000
5A5ARG10.7780.8427.37225.02425.0240.0000.0000.0000.000
6A6VAL0-0.003-0.0019.3710.7970.7970.0000.0000.0000.000
7A7HIS0-0.031-0.02912.0251.7071.7070.0000.0000.0000.000
8A8GLN0-0.009-0.02015.8560.4820.4820.0000.0000.0000.000
9A9GLY00.0000.01218.9780.6390.6390.0000.0000.0000.000
10A10ASP-1-0.765-0.90021.002-13.399-13.3990.0000.0000.0000.000
11A11LEU00.0090.01917.064-0.677-0.6770.0000.0000.0000.000
12A12PRO0-0.0130.00418.5440.8990.8990.0000.0000.0000.000
13A13ASN0-0.027-0.01920.9920.3320.3320.0000.0000.0000.000
14A14LEU00.002-0.01121.292-0.434-0.4340.0000.0000.0000.000
15A15ASP-1-0.909-0.95221.119-13.304-13.3040.0000.0000.0000.000
16A16ASN0-0.027-0.01215.6690.7470.7470.0000.0000.0000.000
17A17TYR0-0.034-0.06114.878-0.327-0.3270.0000.0000.0000.000
18A18ARG10.8480.93721.04513.30213.3020.0000.0000.0000.000
19A19ILE0-0.0040.00619.4930.0500.0500.0000.0000.0000.000
20A20ASP-1-0.832-0.91323.676-11.880-11.8800.0000.0000.0000.000
21A21ALA0-0.047-0.02322.3360.3080.3080.0000.0000.0000.000
22A22VAL0-0.0020.01018.361-0.678-0.6780.0000.0000.0000.000
23A23ALA0-0.0300.00415.3210.5320.5320.0000.0000.0000.000
24A24VAL0-0.023-0.03316.985-0.361-0.3610.0000.0000.0000.000
25A25ASP-1-0.866-0.93714.616-19.659-19.6590.0000.0000.0000.000
26A26THR0-0.065-0.05216.9990.1470.1470.0000.0000.0000.000
27A27GLU-1-0.821-0.89114.605-20.446-20.4460.0000.0000.0000.000
28A28THR0-0.020-0.04217.8100.4530.4530.0000.0000.0000.000
29A29LEU0-0.016-0.01820.650-0.348-0.3480.0000.0000.0000.000
30A30GLY0-0.0100.00023.1540.3340.3340.0000.0000.0000.000
31A31LEU00.0330.01723.314-0.162-0.1620.0000.0000.0000.000
32A32GLN00.0310.01726.1180.2330.2330.0000.0000.0000.000
33A33PRO00.0540.02127.3700.0860.0860.0000.0000.0000.000
34A34HIS0-0.053-0.02928.912-0.121-0.1210.0000.0000.0000.000
35A35ARG10.7500.85328.73510.89110.8910.0000.0000.0000.000
36A36ASP-1-0.817-0.87425.537-11.563-11.5630.0000.0000.0000.000
37A37ARG10.8040.88922.14013.66713.6670.0000.0000.0000.000
38A38LEU00.0880.04720.894-0.449-0.4490.0000.0000.0000.000
39A39CYS0-0.146-0.05319.4440.5910.5910.0000.0000.0000.000
40A40VAL0-0.005-0.00413.874-0.414-0.4140.0000.0000.0000.000
41A41VAL00.0310.02316.9720.8400.8400.0000.0000.0000.000
42A42GLN0-0.044-0.03012.011-0.363-0.3630.0000.0000.0000.000
43A43LEU00.005-0.00613.7171.4871.4870.0000.0000.0000.000
44A44SER00.011-0.01811.967-1.887-1.8870.0000.0000.0000.000
45A45SER00.032-0.00513.8521.8031.8030.0000.0000.0000.000
46A46GLY00.0160.01914.5091.1811.1810.0000.0000.0000.000
47A47ASP-1-0.842-0.88913.531-23.794-23.7940.0000.0000.0000.000
48A48GLY0-0.025-0.00710.389-0.755-0.7550.0000.0000.0000.000
49A49THR0-0.074-0.0518.732-4.392-4.3920.0000.0000.0000.000
50A50ALA00.0140.0098.5501.9431.9430.0000.0000.0000.000
51A51ASP-1-0.791-0.82210.434-22.740-22.7400.0000.0000.0000.000
52A52VAL00.003-0.0089.5960.3730.3730.0000.0000.0000.000
53A53ILE00.0010.01012.7750.0780.0780.0000.0000.0000.000
54A54GLN00.0260.01415.307-0.506-0.5060.0000.0000.0000.000
55A55ILE0-0.0010.01017.6530.8750.8750.0000.0000.0000.000
56A56ALA00.0520.03321.2900.0490.0490.0000.0000.0000.000
57A57LYS10.9740.96824.07010.85410.8540.0000.0000.0000.000
58A58GLY0-0.021-0.01426.7840.2830.2830.0000.0000.0000.000
59A59GLN0-0.064-0.03323.3950.1180.1180.0000.0000.0000.000
60A60LYS10.9220.94827.94310.09710.0970.0000.0000.0000.000
61A61SER0-0.0070.00128.5580.1060.1060.0000.0000.0000.000
62A62ALA00.0800.04323.374-0.265-0.2650.0000.0000.0000.000
63A63PRO0-0.0030.00525.486-0.029-0.0290.0000.0000.0000.000
64A64ASN0-0.045-0.03523.3010.6860.6860.0000.0000.0000.000
65A65LEU00.0560.02520.2240.0560.0560.0000.0000.0000.000
66A66VAL00.015-0.00823.0680.1730.1730.0000.0000.0000.000
67A67ARG10.9250.97826.63111.10911.1090.0000.0000.0000.000
68A68LEU00.0470.03121.0760.2300.2300.0000.0000.0000.000
69A69LEU0-0.021-0.01122.7680.1800.1800.0000.0000.0000.000
70A70SER0-0.034-0.04225.9820.3330.3330.0000.0000.0000.000
71A71ASP-1-0.913-0.95027.709-10.467-10.4670.0000.0000.0000.000
72A72ARG10.9290.94828.6858.9428.9420.0000.0000.0000.000
73A73ASP-1-0.908-0.95130.390-9.714-9.7140.0000.0000.0000.000
74A74ILE0-0.0500.00023.782-0.312-0.3120.0000.0000.0000.000
75A75THR0-0.029-0.02024.8130.1940.1940.0000.0000.0000.000
76A76LYS10.7790.90322.41811.37011.3700.0000.0000.0000.000
77A77ILE0-0.027-0.01219.2390.5990.5990.0000.0000.0000.000
78A78PHE00.0830.04519.359-0.723-0.7230.0000.0000.0000.000
79A79HIS00.006-0.00918.3550.3900.3900.0000.0000.0000.000
80A80PHE00.016-0.03920.1620.0680.0680.0000.0000.0000.000
81A81GLY00.1000.03022.9690.0570.0570.0000.0000.0000.000
82A82ARG10.7660.85023.83510.38510.3850.0000.0000.0000.000
83A83PHE0-0.0230.00221.5040.5620.5620.0000.0000.0000.000
84A84ASP-1-0.779-0.88720.139-14.978-14.9780.0000.0000.0000.000
85A85LEU00.002-0.01023.1990.2170.2170.0000.0000.0000.000
86A86ALA00.0320.02126.4010.3600.3600.0000.0000.0000.000
87A87ILE00.0050.00322.9960.3320.3320.0000.0000.0000.000
88A88LEU00.0130.01121.7130.1360.1360.0000.0000.0000.000
89A89ALA00.0130.01125.6980.2510.2510.0000.0000.0000.000
90A90HIS0-0.048-0.01429.0660.4460.4460.0000.0000.0000.000
91A91THR0-0.079-0.04025.7030.2060.2060.0000.0000.0000.000
92A92PHE0-0.031-0.03723.5170.2670.2670.0000.0000.0000.000
93A93GLY0-0.0120.01029.3280.2080.2080.0000.0000.0000.000
94A94VAL0-0.034-0.01929.5080.2980.2980.0000.0000.0000.000
95A95MET0-0.0130.00629.123-0.507-0.5070.0000.0000.0000.000
96A96PRO0-0.031-0.00825.8820.1910.1910.0000.0000.0000.000
97A97ASP-1-0.889-0.96028.946-9.824-9.8240.0000.0000.0000.000
98A98VAL0-0.0320.00428.5680.1270.1270.0000.0000.0000.000
99A99VAL0-0.007-0.00626.067-0.522-0.5220.0000.0000.0000.000
100A100PHE00.0250.00623.3210.3120.3120.0000.0000.0000.000
101A101CYS-1-0.885-0.81523.380-13.632-13.6320.0000.0000.0000.000
102A102THR00.045-0.01419.5370.3190.3190.0000.0000.0000.000
103A103LYS10.8760.92122.54813.40013.4000.0000.0000.0000.000
104A104ILE00.030-0.02424.3330.4360.4360.0000.0000.0000.000
105A105ALA00.0310.01824.9370.3500.3500.0000.0000.0000.000
106A106SER0-0.013-0.00223.8900.1310.1310.0000.0000.0000.000
107A107LYS10.9020.94925.97810.85510.8550.0000.0000.0000.000
108A108LEU00.0160.02529.2370.4150.4150.0000.0000.0000.000
109A109THR0-0.038-0.03727.5960.1600.1600.0000.0000.0000.000
110A110ARG10.7720.86823.81513.25413.2540.0000.0000.0000.000
111A111THR0-0.007-0.01928.447-0.033-0.0330.0000.0000.0000.000
112A112TYR0-0.050-0.03426.2120.4540.4540.0000.0000.0000.000
113A113THR0-0.007-0.00826.443-0.029-0.0290.0000.0000.0000.000
114A114ASP-1-0.845-0.90929.709-9.980-9.9800.0000.0000.0000.000
115A115ARG10.7960.88024.52212.04812.0480.0000.0000.0000.000
116A116HIS00.0210.04024.374-0.791-0.7910.0000.0000.0000.000
117A117GLY00.012-0.00221.168-0.062-0.0620.0000.0000.0000.000
118A118LEU00.0470.02414.4850.1690.1690.0000.0000.0000.000
119A119LYS10.9110.95914.47519.83919.8390.0000.0000.0000.000
120A120GLU-1-0.849-0.90316.726-13.812-13.8120.0000.0000.0000.000
121A121ILE0-0.0140.00418.7590.1070.1070.0000.0000.0000.000
122A122CYS00.0060.00514.057-0.112-0.1120.0000.0000.0000.000
123A123GLY00.0050.01416.203-0.434-0.4340.0000.0000.0000.000
124A124GLU-1-0.807-0.87517.300-12.668-12.6680.0000.0000.0000.000
125A125LEU0-0.037-0.01819.5310.4150.4150.0000.0000.0000.000
126A126LEU0-0.044-0.01914.720-0.095-0.0950.0000.0000.0000.000
127A127ASN0-0.036-0.00115.520-0.766-0.7660.0000.0000.0000.000
128A128VAL0-0.0100.00210.389-1.438-1.4380.0000.0000.0000.000
129A129ASN0-0.021-0.02410.8412.8232.8230.0000.0000.0000.000
130A130ILE00.0590.03710.215-2.649-2.6490.0000.0000.0000.000
131A131SER0-0.027-0.01810.1463.0613.0610.0000.0000.0000.000
132A132LYS10.8820.92211.52520.68220.6820.0000.0000.0000.000
133A133GLN0-0.028-0.00312.498-0.360-0.3600.0000.0000.0000.000
134A134GLN00.031-0.00210.1781.9221.9220.0000.0000.0000.000
135A135GLN00.0230.04513.3390.1850.1850.0000.0000.0000.000
136A136SER0-0.035-0.01315.8541.2041.2040.0000.0000.0000.000
137A137SER0-0.026-0.01715.2160.0010.0010.0000.0000.0000.000
138A138ASP-1-0.845-0.93717.477-14.494-14.4940.0000.0000.0000.000
139A139TRP00.0150.00311.871-1.627-1.6270.0000.0000.0000.000
140A140ALA0-0.045-0.02918.106-0.009-0.0090.0000.0000.0000.000
141A141ALA00.0120.00917.7810.5430.5430.0000.0000.0000.000
142A142GLU-1-0.952-0.96818.983-14.501-14.5010.0000.0000.0000.000
143A143THR0-0.022-0.00314.610-0.554-0.5540.0000.0000.0000.000
144A144LEU00.0060.02012.504-0.068-0.0680.0000.0000.0000.000
145A145SER00.005-0.01711.211-1.768-1.7680.0000.0000.0000.000
147A147ALA00.0000.0006.407-4.593-4.5930.0000.0000.0000.000
148A148GLN00.0250.0267.632-1.714-1.7140.0000.0000.0000.000
149A149ILE00.0530.0276.768-0.291-0.2910.0000.0000.0000.000
152A152ALA00.0760.0368.2690.8350.8350.0000.0000.0000.000
153A153ALA00.0250.0095.9651.7141.7140.0000.0000.0000.000
154A154SER0-0.099-0.0675.9810.4760.4760.0000.0000.0000.000
155A155ASP-1-0.786-0.8938.084-21.311-21.3110.0000.0000.0000.000
156A156VAL0-0.016-0.01210.8501.8621.8620.0000.0000.0000.000
157A157LEU0-0.045-0.0196.2140.6720.6720.0000.0000.0000.000
158A158TYR0-0.029-0.0217.3700.3370.3370.0000.0000.0000.000
159A159LEU00.0010.00513.2511.5021.5020.0000.0000.0000.000
160A160HIS00.0300.01516.4420.4050.4050.0000.0000.0000.000
161A161ARG11.0091.00312.75922.30622.3060.0000.0000.0000.000
162A162LEU0-0.035-0.01416.4770.6750.6750.0000.0000.0000.000
163A163LYS10.8830.93419.41913.68913.6890.0000.0000.0000.000
164A164ASP-1-0.877-0.93720.969-14.173-14.1730.0000.0000.0000.000
165A165ILE00.0010.00220.3580.6380.6380.0000.0000.0000.000
166A166PHE0-0.031-0.03721.4140.5640.5640.0000.0000.0000.000
167A167GLU-1-0.834-0.91125.503-11.554-11.5540.0000.0000.0000.000
168A168GLU-1-0.930-0.95426.290-11.654-11.6540.0000.0000.0000.000
169A169ARG10.8570.91725.49612.42112.4210.0000.0000.0000.000
170A170LEU0-0.020-0.01828.6050.4100.4100.0000.0000.0000.000
171A171LYS10.8410.91431.4709.7639.7630.0000.0000.0000.000
172A172ARG10.7800.86430.88410.25910.2590.0000.0000.0000.000
173A173GLU-1-0.832-0.89432.960-9.375-9.3750.0000.0000.0000.000
174A174GLU-1-0.949-0.96235.654-7.727-7.7270.0000.0000.0000.000
175A175ARG10.8670.92333.4249.3449.3440.0000.0000.0000.000
176A176GLU-1-0.804-0.88832.613-9.525-9.5250.0000.0000.0000.000
177A177SER0-0.012-0.00633.985-0.171-0.1710.0000.0000.0000.000
178A178VAL00.0490.02535.1260.0130.0130.0000.0000.0000.000
179A179ALA00.0490.02530.320-0.073-0.0730.0000.0000.0000.000
180A180LYS10.9460.98431.8748.7268.7260.0000.0000.0000.000
181A181ALA0-0.003-0.00133.294-0.017-0.0170.0000.0000.0000.000
182A182CYS0-0.043-0.02831.9730.0540.0540.0000.0000.0000.000
183A183PHE0-0.026-0.02227.308-0.139-0.1390.0000.0000.0000.000
184A184GLN00.031-0.00430.836-0.074-0.0740.0000.0000.0000.000
185A185PHE00.0220.01933.8830.1430.1430.0000.0000.0000.000
186A186LEU0-0.0210.00426.6180.0430.0430.0000.0000.0000.000
187A187PRO00.0540.02230.333-0.048-0.0480.0000.0000.0000.000
188A188MET0-0.0050.01331.6970.1070.1070.0000.0000.0000.000
189A189ARG10.7790.85932.0629.2829.2820.0000.0000.0000.000
190A190ALA00.0480.02729.3880.0380.0380.0000.0000.0000.000
191A191ASN0-0.013-0.02331.248-0.008-0.0080.0000.0000.0000.000
192A192LEU0-0.002-0.00634.3310.1560.1560.0000.0000.0000.000
193A193ASP-1-0.773-0.83731.063-9.825-9.8250.0000.0000.0000.000
194A194LEU0-0.057-0.01530.3950.0780.0780.0000.0000.0000.000
195A195LEU0-0.025-0.01134.0300.1830.1830.0000.0000.0000.000
196A196GLY00.0040.01536.6030.2430.2430.0000.0000.0000.000
197A197TRP0-0.008-0.01337.5790.1290.1290.0000.0000.0000.000
198A198SER0-0.057-0.04632.9660.0290.0290.0000.0000.0000.000
199A199GLU-1-0.907-0.92534.080-9.612-9.6120.0000.0000.0000.000
200A200ILE0-0.027-0.00136.2940.1620.1620.0000.0000.0000.000
201A201ASP-1-0.861-0.93337.592-8.513-8.5130.0000.0000.0000.000
202A202ILE0-0.040-0.02238.5070.1810.1810.0000.0000.0000.000
203A203PHE0-0.060-0.03737.3950.1780.1780.0000.0000.0000.000
204A204ALA0-0.0090.01841.2320.1000.1000.0000.0000.0000.000
205A205HIS0-0.058-0.03042.9520.0500.0500.0000.0000.0000.000
206A206SER-1-0.944-0.96644.080-7.165-7.1650.0000.0000.0000.000