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

tag_button

FMODB ID: Y7V22

Calculation Name: 5IT7-A-Other547

Preferred Name:

Target Type:

Ligand Name: phosphomethylphosphonic acid guanylate ester | (2s)-1-amino-n,n,n-trimethyl-1-oxobutan-2-aminium

Ligand 3-letter code: GCP | 6EM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5IT7

Chain ID: A

ChEMBL ID:

UniProt ID: P38665

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1686578.96866
FMO2-HF: Nuclear repulsion 1617136.913991
FMO2-HF: Total energy -69442.054669
FMO2-MP2: Total energy -69651.535172


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:3:ILE)


Summations of interaction energy for fragment #1(A:3:ILE)
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.
258.47261.8850.354-1.553-2.215-0.014
Interaction energy analysis for fragmet #1(A:3:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.906
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].
3A5HIS0-0.0080.0002.791-1.2732.0730.355-1.549-2.151-0.014
4A6THR00.0870.0495.2533.7433.812-0.001-0.004-0.0640.000
5A7SER0-0.051-0.0288.0422.5732.5730.0000.0000.0000.000
6A8LYS10.9310.9549.04916.96716.9670.0000.0000.0000.000
7A9GLN00.0860.0355.9605.2825.2820.0000.0000.0000.000
8A10HIS00.0210.0119.9872.4842.4840.0000.0000.0000.000
9A11LYS10.9010.97412.77620.66620.6660.0000.0000.0000.000
10A12ARG10.9960.98815.25614.99014.9900.0000.0000.0000.000
11A13SER00.0570.00918.594-0.181-0.1810.0000.0000.0000.000
12A14SER0-0.0070.01320.8940.1270.1270.0000.0000.0000.000
13A15HIS0-0.035-0.02022.7510.9870.9870.0000.0000.0000.000
14A16ARG10.8230.90925.4639.4159.4150.0000.0000.0000.000
15A17THR00.0740.03125.0640.0710.0710.0000.0000.0000.000
16A18ALA00.0520.03327.5580.2010.2010.0000.0000.0000.000
17A19PRO0-0.0220.00430.552-0.115-0.1150.0000.0000.0000.000
18A20LYS10.9360.96129.63910.26210.2620.0000.0000.0000.000
19A21SER0-0.082-0.05733.0170.2100.2100.0000.0000.0000.000
20A22ASP-1-0.777-0.88536.688-8.473-8.4730.0000.0000.0000.000
21A23ASN0-0.073-0.03338.3910.1510.1510.0000.0000.0000.000
22A24VAL00.1270.06240.397-0.124-0.1240.0000.0000.0000.000
23A25TYR00.0830.03941.657-0.132-0.1320.0000.0000.0000.000
24A26LEU0-0.038-0.01637.729-0.030-0.0300.0000.0000.0000.000
25A27LYS10.9930.98934.8048.6038.6030.0000.0000.0000.000
26A28LEU0-0.009-0.00438.389-0.168-0.1680.0000.0000.0000.000
27A29LEU00.0270.01640.641-0.059-0.0590.0000.0000.0000.000
28A30VAL0-0.005-0.01634.509-0.100-0.1000.0000.0000.0000.000
29A31LYS10.9390.97836.2377.7357.7350.0000.0000.0000.000
30A32LEU00.0380.03137.302-0.091-0.0910.0000.0000.0000.000
31A33TYR00.033-0.02537.100-0.086-0.0860.0000.0000.0000.000
32A34ALA0-0.031-0.02532.944-0.168-0.1680.0000.0000.0000.000
33A35PHE0-0.028-0.01033.734-0.246-0.2460.0000.0000.0000.000
34A36LEU00.0660.03435.820-0.103-0.1030.0000.0000.0000.000
35A37ALA0-0.029-0.00732.962-0.031-0.0310.0000.0000.0000.000
36A38ARG10.9350.97730.3829.1639.1630.0000.0000.0000.000
37A39ARG10.9630.98132.7267.9697.9690.0000.0000.0000.000
38A40THR0-0.051-0.03935.8870.1510.1510.0000.0000.0000.000
39A41ASP-1-0.812-0.89532.201-9.129-9.1290.0000.0000.0000.000
40A42ALA00.0270.02634.9990.0330.0330.0000.0000.0000.000
41A43PRO00.020-0.00634.357-0.159-0.1590.0000.0000.0000.000
42A44PHE00.0520.03935.363-0.149-0.1490.0000.0000.0000.000
43A45ASN00.013-0.01136.5640.0160.0160.0000.0000.0000.000
44A46LYS10.8580.92130.3529.2209.2200.0000.0000.0000.000
45A47VAL0-0.056-0.00832.619-0.318-0.3180.0000.0000.0000.000
46A48ILE00.0380.02335.005-0.120-0.1200.0000.0000.0000.000
47A49LEU00.0330.03430.725-0.033-0.0330.0000.0000.0000.000
48A50LYS10.9290.96028.46910.03310.0330.0000.0000.0000.000
49A51SER0-0.087-0.05632.8360.0470.0470.0000.0000.0000.000
50A52LEU00.0450.01636.1270.1360.1360.0000.0000.0000.000
51A53PHE00.0270.01730.3420.1040.1040.0000.0000.0000.000
52A54LEU0-0.0480.00533.036-0.144-0.1440.0000.0000.0000.000
53A55SER00.0220.00334.9880.2100.2100.0000.0000.0000.000
54A56LYS11.0371.00336.5737.1017.1010.0000.0000.0000.000
55A57ILE00.0050.00537.2520.1160.1160.0000.0000.0000.000
56A58ASN0-0.036-0.02734.0420.0230.0230.0000.0000.0000.000
57A59ARG10.8930.95837.4647.8867.8860.0000.0000.0000.000
58A60PRO0-0.0160.00440.1810.1360.1360.0000.0000.0000.000
59A61PRO00.0090.00643.336-0.034-0.0340.0000.0000.0000.000
60A62VAL0-0.018-0.00645.281-0.018-0.0180.0000.0000.0000.000
61A63SER0-0.029-0.01147.8790.0240.0240.0000.0000.0000.000
62A64VAL00.0680.02851.501-0.056-0.0560.0000.0000.0000.000
63A65SER00.031-0.01053.939-0.012-0.0120.0000.0000.0000.000
64A66ARG10.8970.96346.2896.6656.6650.0000.0000.0000.000
65A67ILE00.0090.00350.038-0.053-0.0530.0000.0000.0000.000
66A68SER00.0310.00551.7370.0510.0510.0000.0000.0000.000
67A69ARG10.9390.96351.1936.0106.0100.0000.0000.0000.000
68A70ALA0-0.008-0.00848.915-0.001-0.0010.0000.0000.0000.000
69A71LEU0-0.034-0.00350.526-0.033-0.0330.0000.0000.0000.000
70A72LYS10.9210.95453.5655.4845.4840.0000.0000.0000.000
71A73GLN0-0.044-0.00847.337-0.035-0.0350.0000.0000.0000.000
72A74GLU-1-0.789-0.90152.574-5.616-5.6160.0000.0000.0000.000
73A75GLY00.0190.03151.673-0.133-0.1330.0000.0000.0000.000
74A76ALA0-0.091-0.06550.326-0.121-0.1210.0000.0000.0000.000
75A77ALA00.0370.02252.099-0.035-0.0350.0000.0000.0000.000
76A78GLN00.0210.01054.4240.0210.0210.0000.0000.0000.000
77A79LYS10.8470.94847.8936.3086.3080.0000.0000.0000.000
78A80THR00.0080.00848.7410.0360.0360.0000.0000.0000.000
79A81ILE00.0090.00847.897-0.187-0.1870.0000.0000.0000.000
80A82VAL0-0.012-0.00243.0470.0110.0110.0000.0000.0000.000
81A83VAL0-0.008-0.00544.368-0.134-0.1340.0000.0000.0000.000
82A84VAL00.0190.00539.4260.0250.0250.0000.0000.0000.000
83A85GLY0-0.011-0.03241.288-0.208-0.2080.0000.0000.0000.000
84A86THR0-0.053-0.01343.7960.0570.0570.0000.0000.0000.000
85A87VAL00.0570.03047.410-0.055-0.0550.0000.0000.0000.000
86A88THR0-0.023-0.03250.0670.0180.0180.0000.0000.0000.000
87A89ASP-1-0.816-0.91052.569-5.411-5.4110.0000.0000.0000.000
88A90ASP-1-0.809-0.86454.995-5.835-5.8350.0000.0000.0000.000
89A91ASN0-0.001-0.01057.113-0.013-0.0130.0000.0000.0000.000
90A92ARG10.8770.91453.4715.7945.7940.0000.0000.0000.000
91A93ILE0-0.0330.00057.631-0.001-0.0010.0000.0000.0000.000
92A94PHE00.0460.02460.658-0.007-0.0070.0000.0000.0000.000
93A95GLU-1-0.850-0.93263.261-4.949-4.9490.0000.0000.0000.000
94A96PHE0-0.074-0.04855.215-0.117-0.1170.0000.0000.0000.000
95A97PRO00.0090.00957.4980.0650.0650.0000.0000.0000.000
96A98LYS10.9900.99858.7964.8974.8970.0000.0000.0000.000
97A99THR0-0.010-0.00855.069-0.064-0.0640.0000.0000.0000.000
98A100THR0-0.007-0.00352.4610.0260.0260.0000.0000.0000.000
99A101VAL0-0.037-0.02550.330-0.109-0.1090.0000.0000.0000.000
100A102ALA00.0420.02547.4410.0400.0400.0000.0000.0000.000
101A103ALA0-0.027-0.01546.811-0.109-0.1090.0000.0000.0000.000
102A104LEU0-0.050-0.02041.160-0.024-0.0240.0000.0000.0000.000
103A105ARG10.9190.95544.3986.9296.9290.0000.0000.0000.000
104A106PHE00.0510.03348.769-0.035-0.0350.0000.0000.0000.000
105A107THR0-0.003-0.00552.0850.0120.0120.0000.0000.0000.000
106A108ALA00.0660.02554.4500.0150.0150.0000.0000.0000.000
107A109GLY00.0700.04658.0500.0670.0670.0000.0000.0000.000
108A110ALA0-0.006-0.01254.4380.0380.0380.0000.0000.0000.000
109A111LYS10.9580.97853.9995.8045.8040.0000.0000.0000.000
110A112ALA00.0480.03257.3540.0390.0390.0000.0000.0000.000
111A113LYS10.8690.94158.8965.3035.3030.0000.0000.0000.000
112A114ILE0-0.046-0.02854.2150.0180.0180.0000.0000.0000.000
113A115LEU0-0.014-0.01058.6330.0280.0280.0000.0000.0000.000
114A116LYS10.9860.99961.1574.8384.8380.0000.0000.0000.000
115A117ALA0-0.0300.00061.1760.0750.0750.0000.0000.0000.000
116A118GLY00.0420.02463.3170.0310.0310.0000.0000.0000.000
117A119GLY0-0.017-0.01459.152-0.029-0.0290.0000.0000.0000.000
118A120GLU-1-0.760-0.84855.922-5.587-5.5870.0000.0000.0000.000
119A121ALA0-0.041-0.01654.230-0.107-0.1070.0000.0000.0000.000
120A122ILE0-0.0110.00749.677-0.002-0.0020.0000.0000.0000.000
121A123THR0-0.026-0.04048.252-0.037-0.0370.0000.0000.0000.000
122A124LEU00.015-0.01942.277-0.020-0.0200.0000.0000.0000.000
123A125ASP-1-0.817-0.87044.928-6.669-6.6690.0000.0000.0000.000
124A126GLN00.0660.02146.1900.0900.0900.0000.0000.0000.000
125A127LEU0-0.034-0.01344.4690.0530.0530.0000.0000.0000.000
126A128ALA0-0.027-0.01643.617-0.001-0.0010.0000.0000.0000.000
127A129VAL00.0070.00145.183-0.033-0.0330.0000.0000.0000.000
128A130ARG10.8430.89948.2845.8985.8980.0000.0000.0000.000
129A131ALA0-0.017-0.00446.1200.0480.0480.0000.0000.0000.000
130A132PRO00.0300.03143.630-0.200-0.2000.0000.0000.0000.000
131A133LYS10.9320.95640.1287.1127.1120.0000.0000.0000.000
132A134GLY0-0.023-0.01741.464-0.131-0.1310.0000.0000.0000.000
133A135GLN00.0690.02543.472-0.102-0.1020.0000.0000.0000.000
134A136ASN00.0500.01546.4190.0340.0340.0000.0000.0000.000
135A137THR0-0.0190.01043.7340.0750.0750.0000.0000.0000.000
136A138LEU00.0610.02245.377-0.057-0.0570.0000.0000.0000.000
137A139ILE0-0.021-0.00639.6270.0190.0190.0000.0000.0000.000
138A140VAL00.0190.01943.375-0.019-0.0190.0000.0000.0000.000
139A141ARG10.9420.95635.4268.1838.1830.0000.0000.0000.000
140A142GLY00.0610.03642.6030.1320.1320.0000.0000.0000.000
141A143PRO0-0.013-0.01341.961-0.215-0.2150.0000.0000.0000.000
142A144ARG10.8960.93434.7568.6458.6450.0000.0000.0000.000
143A145ALA00.0170.00539.293-0.088-0.0880.0000.0000.0000.000
144A146SER0-0.0150.00540.5790.0870.0870.0000.0000.0000.000
145A147ARG10.9400.96537.8538.1448.1440.0000.0000.0000.000
146A148GLU-1-0.764-0.87743.460-6.819-6.8190.0000.0000.0000.000
147A149ALA00.0000.00839.928-0.041-0.0410.0000.0000.0000.000
148A150ALA0-0.034-0.01539.309-0.122-0.1220.0000.0000.0000.000
149A151ARG10.9080.93940.3046.5836.5830.0000.0000.0000.000
150A152HIS0-0.013-0.02041.2400.0490.0490.0000.0000.0000.000
151A153PHE0-0.056-0.03035.594-0.159-0.1590.0000.0000.0000.000
152A154GLY00.0580.03136.2230.0550.0550.0000.0000.0000.000
153A155PHE0-0.001-0.00536.9380.1290.1290.0000.0000.0000.000
154A156GLY00.0530.03239.051-0.210-0.2100.0000.0000.0000.000
155A157PRO00.0590.03940.6000.1200.1200.0000.0000.0000.000
156A158HIS00.007-0.01740.468-0.377-0.3770.0000.0000.0000.000
157A159LYS10.8490.91737.0468.5118.5110.0000.0000.0000.000
158A160GLY00.0390.03441.824-0.006-0.0060.0000.0000.0000.000
159A161LYS10.8310.92438.6078.0908.0900.0000.0000.0000.000
160A162ALA0-0.018-0.01344.2500.1440.1440.0000.0000.0000.000
161A163PRO00.0200.03644.286-0.200-0.2000.0000.0000.0000.000
162A164ARG10.9100.94138.0098.1738.1730.0000.0000.0000.000
163A165ILE00.0420.02145.728-0.003-0.0030.0000.0000.0000.000
164A166GLN00.0290.01948.9330.1090.1090.0000.0000.0000.000
165A167SER00.0130.00751.2810.1440.1440.0000.0000.0000.000
166A168THR00.0840.01453.981-0.065-0.0650.0000.0000.0000.000
167A169GLY00.0080.02755.931-0.036-0.0360.0000.0000.0000.000
168A170ARG10.9830.99057.1295.0215.0210.0000.0000.0000.000
169A171LYS10.9320.95958.7875.4405.4400.0000.0000.0000.000
170A172PHE00.0650.04254.012-0.014-0.0140.0000.0000.0000.000
171A173GLU-1-0.856-0.93348.414-6.716-6.7160.0000.0000.0000.000
172A174ARG10.8730.93452.7345.8905.8900.0000.0000.0000.000
173A175ALA00.0340.00654.8470.1070.1070.0000.0000.0000.000
174A176ARG11.0060.99448.7166.4216.4210.0000.0000.0000.000
175A177GLY00.0690.05450.580-0.114-0.1140.0000.0000.0000.000
176A178ARG10.8390.92248.4696.4316.4310.0000.0000.0000.000
177A179ARG10.8680.92552.9795.6305.6300.0000.0000.0000.000
178A180ARG11.0671.03654.6975.7415.7410.0000.0000.0000.000
179A181SER00.0390.02956.942-0.024-0.0240.0000.0000.0000.000
180A182ARG10.8880.93756.7285.3915.3910.0000.0000.0000.000
181A183ALA00.0940.05054.250-0.128-0.1280.0000.0000.0000.000
182A184PHE00.0360.02947.9810.0080.0080.0000.0000.0000.000
183A185LYS10.8580.92650.7446.3506.3500.0000.0000.0000.000
184A186VAL-1-0.805-0.88745.411-6.959-6.9590.0000.0000.0000.000