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: 746LK

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 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1680009.691933
FMO2-HF: Nuclear repulsion 1603638.337275
FMO2-HF: Total energy -76371.354658
FMO2-MP2: Total energy -76600.80674


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
234.438235.254-0.004-0.505-0.3070
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.865 / q_NPA : 0.915
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].
3A4SER0-0.034-0.0283.837-5.979-5.163-0.004-0.505-0.3070.000
4A5LYS11.0361.0166.62734.09534.0950.0000.0000.0000.000
5A6ASN00.000-0.00110.268-1.269-1.2690.0000.0000.0000.000
6A7LEU00.0590.0419.2070.9490.9490.0000.0000.0000.000
7A8PRO00.0080.01711.380-0.581-0.5810.0000.0000.0000.000
8A9ILE00.0270.0039.699-1.984-1.9840.0000.0000.0000.000
9A10LEU0-0.006-0.0039.1112.0122.0120.0000.0000.0000.000
10A11LYS10.9360.9699.74216.49916.4990.0000.0000.0000.000
11A12ASN00.0390.01310.1183.0153.0150.0000.0000.0000.000
12A13HIS0-0.042-0.02011.626-0.988-0.9880.0000.0000.0000.000
13A14PHE00.006-0.00112.2081.0011.0010.0000.0000.0000.000
14A15ARG10.9810.9886.41029.80429.8040.0000.0000.0000.000
15A16LYS10.9730.99812.98915.44915.4490.0000.0000.0000.000
16A17HIS00.1280.05916.620-0.850-0.8500.0000.0000.0000.000
17A18TRP0-0.004-0.02014.6991.4131.4130.0000.0000.0000.000
18A19GLN00.002-0.00317.6950.7130.7130.0000.0000.0000.000
19A20GLU-1-0.883-0.92620.728-12.078-12.0780.0000.0000.0000.000
20A21ARG10.8520.92720.84913.78813.7880.0000.0000.0000.000
21A22VAL0-0.0120.00721.5370.0260.0260.0000.0000.0000.000
22A23LYS10.8930.94624.08910.22710.2270.0000.0000.0000.000
23A24VAL00.0370.02225.486-0.046-0.0460.0000.0000.0000.000
24A25HIS00.0300.02428.0010.5650.5650.0000.0000.0000.000
25A26PHE00.0860.02628.3800.2200.2200.0000.0000.0000.000
26A27ASP-1-0.815-0.89333.073-8.678-8.6780.0000.0000.0000.000
27A28GLN0-0.021-0.00733.0720.3070.3070.0000.0000.0000.000
28A29ALA00.0350.01736.1760.2240.2240.0000.0000.0000.000
29A30GLY00.1080.05039.0250.2330.2330.0000.0000.0000.000
30A31LYS10.8660.91736.3868.6258.6250.0000.0000.0000.000
31A32LYS10.9440.97240.3377.6527.6520.0000.0000.0000.000
32A33VAL00.0420.02041.9980.1760.1760.0000.0000.0000.000
33A34SER00.0400.02043.4550.1970.1970.0000.0000.0000.000
34A35ARG10.9060.94337.5158.0158.0150.0000.0000.0000.000
35A36ARG10.9120.96145.2656.5736.5730.0000.0000.0000.000
36A37HIS00.1010.06148.0520.1240.1240.0000.0000.0000.000
37A38ALA00.0390.02847.5530.1270.1270.0000.0000.0000.000
38A39ARG10.8860.94844.9946.7556.7550.0000.0000.0000.000
39A40ALA00.0660.04050.9930.1010.1010.0000.0000.0000.000
40A41SER00.016-0.00252.2570.1040.1040.0000.0000.0000.000
41A42LYS10.8350.91349.5116.3296.3290.0000.0000.0000.000
42A43ALA00.0370.00754.7550.0790.0790.0000.0000.0000.000
43A44ALA00.0820.04056.8920.0880.0880.0000.0000.0000.000
44A45LYS10.9130.96056.6145.5015.5010.0000.0000.0000.000
45A46ILE0-0.114-0.05656.7290.0400.0400.0000.0000.0000.000
46A47ALA00.0570.03559.9650.0710.0710.0000.0000.0000.000
47A48PRO00.0600.04661.934-0.061-0.0610.0000.0000.0000.000
48A49ARG10.8960.95158.4375.2355.2350.0000.0000.0000.000
49A50PRO00.0320.02057.060-0.058-0.0580.0000.0000.0000.000
50A51LEU0-0.066-0.04251.884-0.038-0.0380.0000.0000.0000.000
51A52ASP-1-0.942-0.94250.832-6.204-6.2040.0000.0000.0000.000
52A53LEU0-0.011-0.00553.6580.0810.0810.0000.0000.0000.000
53A54LEU00.0310.02654.160-0.154-0.1540.0000.0000.0000.000
54A55ARG10.8710.93250.6616.1046.1040.0000.0000.0000.000
55A56PRO0-0.0550.01352.7070.0340.0340.0000.0000.0000.000
56A57VAL00.0800.02552.456-0.173-0.1730.0000.0000.0000.000
57A58VAL0-0.027-0.01948.3390.0510.0510.0000.0000.0000.000
58A59ARG10.9360.96848.9026.1086.1080.0000.0000.0000.000
59A60ALA0-0.064-0.02243.693-0.035-0.0350.0000.0000.0000.000
60A61PRO00.0700.01842.7830.0430.0430.0000.0000.0000.000
61A62THR0-0.009-0.01739.285-0.215-0.2150.0000.0000.0000.000
62A63VAL00.0870.03341.0370.0850.0850.0000.0000.0000.000
63A64LYS10.9661.00933.9928.9188.9180.0000.0000.0000.000
64A65TYR00.001-0.01736.516-0.110-0.1100.0000.0000.0000.000
65A66ASN00.0530.05142.4700.0390.0390.0000.0000.0000.000
66A67ARG10.9970.99540.7177.5217.5210.0000.0000.0000.000
67A68LYS10.8880.96542.8947.1817.1810.0000.0000.0000.000
68A69VAL00.0390.01546.735-0.002-0.0020.0000.0000.0000.000
69A70ARG10.8760.92944.4196.7636.7630.0000.0000.0000.000
70A71ALA00.0960.05947.6080.1090.1090.0000.0000.0000.000
71A72GLY0-0.017-0.01247.690-0.173-0.1730.0000.0000.0000.000
72A73ARG10.9360.96747.6546.3706.3700.0000.0000.0000.000
73A74GLY00.050-0.01350.2650.0230.0230.0000.0000.0000.000
74A75PHE00.0780.02454.105-0.072-0.0720.0000.0000.0000.000
75A76THR0-0.0190.02055.7930.0910.0910.0000.0000.0000.000
76A77LEU00.012-0.01658.0210.0510.0510.0000.0000.0000.000
77A78ALA0-0.0020.01560.8690.0930.0930.0000.0000.0000.000
78A79GLU-1-0.749-0.89157.529-5.483-5.4830.0000.0000.0000.000
79A80ILE00.006-0.00559.7480.0460.0460.0000.0000.0000.000
80A81LYS10.9690.99063.4814.7144.7140.0000.0000.0000.000
81A82ALA00.0030.00165.4310.0780.0780.0000.0000.0000.000
82A83ALA0-0.0090.00164.9010.0510.0510.0000.0000.0000.000
83A84GLY00.0330.03666.9370.0330.0330.0000.0000.0000.000
84A85LEU0-0.026-0.00564.8110.0350.0350.0000.0000.0000.000
85A86THR00.0570.02366.880-0.062-0.0620.0000.0000.0000.000
86A87PRO00.0280.00061.777-0.043-0.0430.0000.0000.0000.000
87A88ALA0-0.001-0.00762.169-0.080-0.0800.0000.0000.0000.000
88A89TYR00.0530.02264.152-0.037-0.0370.0000.0000.0000.000
89A90ALA00.0720.03662.004-0.029-0.0290.0000.0000.0000.000
90A91ARG10.8940.94556.7015.3635.3630.0000.0000.0000.000
91A92THR0-0.081-0.04660.965-0.014-0.0140.0000.0000.0000.000
92A93ILE00.0330.03263.6720.0080.0080.0000.0000.0000.000
93A94GLY00.0440.03459.587-0.022-0.0220.0000.0000.0000.000
94A95ILE00.0140.02058.544-0.105-0.1050.0000.0000.0000.000
95A96ALA0-0.050-0.01253.978-0.016-0.0160.0000.0000.0000.000
96A97VAL00.0080.01256.108-0.003-0.0030.0000.0000.0000.000
97A98ASP-1-0.919-0.96751.739-6.162-6.1620.0000.0000.0000.000
98A99HIS00.0400.00853.9580.0550.0550.0000.0000.0000.000
99A100ARG10.9350.96849.3966.2376.2370.0000.0000.0000.000
100A101ARG10.7640.89651.7475.7405.7400.0000.0000.0000.000
101A102GLN00.0590.02453.5050.0880.0880.0000.0000.0000.000
102A103ASN0-0.046-0.03855.186-0.085-0.0850.0000.0000.0000.000
103A104ARG10.9860.98553.9915.7765.7760.0000.0000.0000.000
104A105ASN00.0330.00755.7130.0210.0210.0000.0000.0000.000
105A106GLN00.1150.06058.003-0.081-0.0810.0000.0000.0000.000
106A107GLU-1-0.837-0.91258.105-5.148-5.1480.0000.0000.0000.000
107A108ILE0-0.112-0.05653.632-0.082-0.0820.0000.0000.0000.000
108A109LEU0-0.040-0.01857.236-0.020-0.0200.0000.0000.0000.000
109A110ASP-1-0.787-0.88760.180-4.869-4.8690.0000.0000.0000.000
110A111LEU0-0.025-0.00755.826-0.008-0.0080.0000.0000.0000.000
111A112ASN0-0.074-0.04755.417-0.062-0.0620.0000.0000.0000.000
112A113ILE00.021-0.00659.3480.0310.0310.0000.0000.0000.000
113A114GLN00.0060.00162.7780.1020.1020.0000.0000.0000.000
114A115ARG10.8220.91254.5045.7115.7110.0000.0000.0000.000
115A116LEU0-0.044-0.02560.386-0.008-0.0080.0000.0000.0000.000
116A117LYS10.9520.99062.9444.7404.7400.0000.0000.0000.000
117A118GLU-1-0.867-0.93562.927-5.041-5.0410.0000.0000.0000.000
118A119TYR0-0.079-0.06060.530-0.022-0.0220.0000.0000.0000.000
119A120GLN0-0.050-0.05863.571-0.038-0.0380.0000.0000.0000.000
120A121SER0-0.0340.01466.9150.0560.0560.0000.0000.0000.000
121A122LYS10.8960.93662.1565.0835.0830.0000.0000.0000.000
122A123ILE0-0.061-0.00963.663-0.021-0.0210.0000.0000.0000.000
123A124ILE00.0690.03666.4720.0680.0680.0000.0000.0000.000
124A125VAL0-0.051-0.02868.112-0.067-0.0670.0000.0000.0000.000
125A126PHE00.0330.01667.1650.0750.0750.0000.0000.0000.000
126A127PRO00.001-0.00670.908-0.009-0.0090.0000.0000.0000.000
127A128ARG10.9550.96069.1514.5014.5010.0000.0000.0000.000
128A129LYS10.9620.98573.4803.9723.9720.0000.0000.0000.000
129A130GLY00.0680.03875.8970.0430.0430.0000.0000.0000.000
130A131LYS10.9000.96674.9994.1854.1850.0000.0000.0000.000
131A132ALA00.0810.03671.001-0.014-0.0140.0000.0000.0000.000
132A133PRO0-0.070-0.04172.9210.0110.0110.0000.0000.0000.000
133A134GLU-1-0.906-0.96366.102-4.839-4.8390.0000.0000.0000.000
134A135ALA0-0.005-0.00568.3120.0550.0550.0000.0000.0000.000
135A136GLU-1-0.916-0.94363.432-5.080-5.0800.0000.0000.0000.000
136A137GLN0-0.025-0.01259.318-0.027-0.0270.0000.0000.0000.000
137A138THR00.0390.02359.721-0.049-0.0490.0000.0000.0000.000
138A139LEU0-0.002-0.01355.074-0.082-0.0820.0000.0000.0000.000
139A140SER0-0.074-0.06352.506-0.089-0.0890.0000.0000.0000.000
140A141ALA00.0890.04054.9070.0540.0540.0000.0000.0000.000
141A142ALA0-0.031-0.02651.4250.0340.0340.0000.0000.0000.000
142A143ALA0-0.013-0.00553.501-0.024-0.0240.0000.0000.0000.000
143A144SER00.0280.02454.8860.0420.0420.0000.0000.0000.000
144A145PHE0-0.0100.00056.4940.0690.0690.0000.0000.0000.000
145A146PRO00.0720.05153.214-0.126-0.1260.0000.0000.0000.000
146A147ILE0-0.084-0.05250.0560.0510.0510.0000.0000.0000.000
147A148VAL00.0470.02551.202-0.144-0.1440.0000.0000.0000.000
148A149GLN0-0.036-0.02748.477-0.067-0.0670.0000.0000.0000.000
149A150PRO0-0.018-0.02352.2780.0460.0460.0000.0000.0000.000
150A151VAL00.0640.04154.448-0.100-0.1000.0000.0000.0000.000
151A152THR0-0.074-0.04153.9300.0110.0110.0000.0000.0000.000
152A153ASP-1-0.893-0.95056.458-5.546-5.5460.0000.0000.0000.000
153A154SER0-0.034-0.02857.8090.0920.0920.0000.0000.0000.000
154A155GLU-1-0.924-0.93158.495-5.370-5.3700.0000.0000.0000.000
155A156THR0-0.019-0.00659.618-0.006-0.0060.0000.0000.0000.000
156A157ARG10.9040.94358.7965.3515.3510.0000.0000.0000.000
157A158ALA00.0360.02863.479-0.009-0.0090.0000.0000.0000.000
158A159VAL0-0.032-0.02560.745-0.091-0.0910.0000.0000.0000.000
159A160GLU-1-0.934-0.96862.733-4.752-4.7520.0000.0000.0000.000
160A161ASP-1-0.946-0.96860.587-5.379-5.3790.0000.0000.0000.000
161A162ASN0-0.019-0.03361.7680.0090.0090.0000.0000.0000.000
162A163GLY00.0230.01860.8910.0280.0280.0000.0000.0000.000
163A164GLU-1-0.892-0.92258.159-5.390-5.3900.0000.0000.0000.000
164A165SER0-0.013-0.01154.860-0.147-0.1470.0000.0000.0000.000
165A166ALA00.0810.03652.181-0.063-0.0630.0000.0000.0000.000
166A167TYR00.0270.00446.225-0.141-0.1410.0000.0000.0000.000
167A168ARG10.9880.99150.7305.6665.6660.0000.0000.0000.000
168A169THR00.0700.03553.302-0.001-0.0010.0000.0000.0000.000
169A170LEU0-0.009-0.00947.810-0.041-0.0410.0000.0000.0000.000
170A171ARG10.8830.94244.7056.6626.6620.0000.0000.0000.000
171A172LEU00.0240.04449.850-0.065-0.0650.0000.0000.0000.000
172A173ALA00.0870.04851.292-0.020-0.0200.0000.0000.0000.000
173A174ARG10.9040.94242.4337.0117.0110.0000.0000.0000.000
174A175SER0-0.066-0.05248.327-0.114-0.1140.0000.0000.0000.000
175A176ASP-1-0.767-0.87450.336-5.739-5.7390.0000.0000.0000.000
176A177LYS10.9060.96145.7756.6026.6020.0000.0000.0000.000
177A178ARG10.8300.92143.3686.8156.8150.0000.0000.0000.000
178A179TYR00.028-0.01247.875-0.051-0.0510.0000.0000.0000.000
179A180LYS10.9621.00251.1986.0386.0380.0000.0000.0000.000
180A181GLY00.0510.04351.4710.0700.0700.0000.0000.0000.000
181A182ILE0-0.033-0.02351.0490.0460.0460.0000.0000.0000.000
182A183ARG10.8460.91053.3455.6785.6780.0000.0000.0000.000
183A184GLU-1-0.838-0.94754.918-5.603-5.6030.0000.0000.0000.000
184A185LYS10.7850.88054.0215.6485.6480.0000.0000.0000.000
185A186ARG10.8990.93853.8845.6955.6950.0000.0000.0000.000
186A187ALA00.0660.05358.9830.0480.0480.0000.0000.0000.000
187A188LYS10.9880.99657.8105.4035.4030.0000.0000.0000.000
188A189ASP-1-0.819-0.89458.494-5.375-5.3750.0000.0000.0000.000
189A190LYS10.9030.94261.4225.0705.0700.0000.0000.0000.000
190A191ALA0-0.022-0.00764.4590.0610.0610.0000.0000.0000.000
191A192GLU-1-0.865-0.92465.347-4.613-4.6130.0000.0000.0000.000
192A193ALA0-0.036-0.03965.340-0.040-0.0400.0000.0000.0000.000
193A194GLU-1-1.004-1.00565.894-4.612-4.6120.0000.0000.0000.000
194A195ALA0-0.018-0.02267.8980.0560.0560.0000.0000.0000.000
195A196GLU-1-0.820-0.89768.624-4.551-4.5510.0000.0000.0000.000
196A197LYS10.8530.93570.1384.5424.5420.0000.0000.0000.000
197A198LYS0-0.057-0.00269.2340.3900.3900.0000.0000.0000.000