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: R4848

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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2315347.832155
FMO2-HF: Nuclear repulsion 2232877.531095
FMO2-HF: Total energy -82470.301059
FMO2-MP2: Total energy -82718.164291


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
468.569470.2560.188-0.614-1.261-0.003
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.943 / q_NPA : 0.960
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].
3A4TYR0-0.001-0.0173.8377.8908.684-0.003-0.286-0.505-0.001
4A5LYS10.9330.9644.26239.46739.594-0.001-0.025-0.1010.000
5A6TYR00.0880.0552.554-0.842-0.0760.192-0.303-0.655-0.002
6A7LEU0-0.025-0.0257.2006.1316.1310.0000.0000.0000.000
7A8GLU-1-0.945-0.9819.140-25.671-25.6710.0000.0000.0000.000
8A9GLU-1-0.771-0.8689.978-22.579-22.5790.0000.0000.0000.000
9A10LEU00.0260.03311.2272.1162.1160.0000.0000.0000.000
10A11GLN0-0.070-0.04613.0743.3043.3040.0000.0000.0000.000
11A12ARG10.8350.89712.84523.91823.9180.0000.0000.0000.000
12A13LYS11.0241.03016.16219.68819.6880.0000.0000.0000.000
13A14LYS10.8400.91718.16815.12715.1270.0000.0000.0000.000
14A15GLN0-0.008-0.00520.7030.6180.6180.0000.0000.0000.000
15A16SER00.0330.01319.1970.2620.2620.0000.0000.0000.000
16A17ASP-1-0.796-0.90121.554-12.944-12.9440.0000.0000.0000.000
17A18VAL00.0500.02317.3100.2590.2590.0000.0000.0000.000
18A19LEU0-0.032-0.02316.712-0.060-0.0600.0000.0000.0000.000
19A20ARG10.9100.96020.60412.40112.4010.0000.0000.0000.000
20A21PHE00.0460.03722.2770.5360.5360.0000.0000.0000.000
21A22LEU00.009-0.00817.9180.2250.2250.0000.0000.0000.000
22A23GLN0-0.061-0.02922.1480.4110.4110.0000.0000.0000.000
23A24ARG11.0241.01124.00611.24911.2490.0000.0000.0000.000
24A25VAL00.0750.04824.6560.4070.4070.0000.0000.0000.000
25A26ARG10.9560.97317.64316.58416.5840.0000.0000.0000.000
26A27VAL0-0.098-0.04125.4030.2850.2850.0000.0000.0000.000
27A28TRP00.0650.03928.3990.2540.2540.0000.0000.0000.000
28A29GLU-1-0.744-0.86624.298-12.741-12.7410.0000.0000.0000.000
29A30TYR0-0.075-0.06322.5240.0450.0450.0000.0000.0000.000
30A31ARG10.8850.95429.2229.8229.8220.0000.0000.0000.000
31A32GLN00.0650.04532.3860.4470.4470.0000.0000.0000.000
32A33LYS10.8650.94026.29511.84411.8440.0000.0000.0000.000
33A34ASN00.0740.02432.2610.2320.2320.0000.0000.0000.000
34A35VAL0-0.0290.00232.230-0.352-0.3520.0000.0000.0000.000
35A36ILE0-0.015-0.01630.907-0.289-0.2890.0000.0000.0000.000
36A37HIS0-0.013-0.01227.670-0.102-0.1020.0000.0000.0000.000
37A38ARG10.9800.99124.22311.73911.7390.0000.0000.0000.000
38A39ALA00.0120.01322.1010.0510.0510.0000.0000.0000.000
39A40SER00.0350.01022.232-0.097-0.0970.0000.0000.0000.000
40A41ARG10.9910.98916.29216.46716.4670.0000.0000.0000.000
41A42PRO0-0.0190.00915.3060.4340.4340.0000.0000.0000.000
42A43THR00.0350.00016.237-0.724-0.7240.0000.0000.0000.000
43A44ARG10.8620.93614.59617.78617.7860.0000.0000.0000.000
44A45PRO00.0550.02611.014-0.014-0.0140.0000.0000.0000.000
45A46ASP-1-0.730-0.8339.210-28.643-28.6430.0000.0000.0000.000
46A47LYS10.9170.96810.69218.64018.6400.0000.0000.0000.000
47A48ALA00.010-0.00514.2041.0381.0380.0000.0000.0000.000
48A49ARG10.9330.9808.65029.47329.4730.0000.0000.0000.000
49A50ARG10.8370.89411.21325.77225.7720.0000.0000.0000.000
50A51LEU0-0.110-0.05013.7571.1521.1520.0000.0000.0000.000
51A52GLY00.0420.02016.0841.0491.0490.0000.0000.0000.000
52A53TYR00.002-0.00814.9220.2030.2030.0000.0000.0000.000
53A54LYS10.9290.95913.02218.99218.9920.0000.0000.0000.000
54A55ALA0-0.011-0.00314.8400.7630.7630.0000.0000.0000.000
55A56LYS10.8950.95916.58414.05714.0570.0000.0000.0000.000
56A57GLN00.0990.04419.771-0.255-0.2550.0000.0000.0000.000
57A58GLY00.0500.02123.5320.0110.0110.0000.0000.0000.000
58A59PHE0-0.037-0.01320.2520.1020.1020.0000.0000.0000.000
59A60VAL0-0.011-0.00522.317-0.046-0.0460.0000.0000.0000.000
60A61ILE0-0.013-0.00918.897-0.379-0.3790.0000.0000.0000.000
61A62TYR00.0290.00722.7500.3550.3550.0000.0000.0000.000
62A63ARG10.7970.90021.36513.36513.3650.0000.0000.0000.000
63A64VAL0-0.011-0.00826.4130.4660.4660.0000.0000.0000.000
64A65ARG10.8710.96328.7899.1189.1180.0000.0000.0000.000
65A66VAL0-0.059-0.04031.2540.3450.3450.0000.0000.0000.000
66A67ARG10.9980.99833.5538.0458.0450.0000.0000.0000.000
67A68ARG10.8460.92230.7919.8119.8110.0000.0000.0000.000
68A69GLY00.0420.02536.0830.2000.2000.0000.0000.0000.000
69A70ASN0-0.007-0.00238.658-0.329-0.3290.0000.0000.0000.000
70A71ARG10.9090.95841.3027.1627.1620.0000.0000.0000.000
71A72LYS11.0041.01342.8946.4976.4970.0000.0000.0000.000
72A73ARG10.8790.94646.4506.3236.3230.0000.0000.0000.000
73A74PRO0-0.033-0.04348.0740.0560.0560.0000.0000.0000.000
74A75VAL00.0150.02750.4780.0220.0220.0000.0000.0000.000
75A76SER00.0880.04954.157-0.007-0.0070.0000.0000.0000.000
76A77LYS11.0050.99156.4525.2915.2910.0000.0000.0000.000
77A78GLY0-0.0270.00355.0200.0110.0110.0000.0000.0000.000
78A79ALA00.0180.01556.0220.0010.0010.0000.0000.0000.000
79A80THR0-0.084-0.08054.676-0.060-0.0600.0000.0000.0000.000
80A81TYR00.0390.03256.919-0.001-0.0010.0000.0000.0000.000
81A82GLY00.0170.00558.783-0.058-0.0580.0000.0000.0000.000
82A83LYS10.9960.99958.5455.2655.2650.0000.0000.0000.000
83A84PRO00.1270.05757.812-0.133-0.1330.0000.0000.0000.000
84A85THR00.0160.01953.291-0.056-0.0560.0000.0000.0000.000
85A86ASN0-0.069-0.04153.135-0.249-0.2490.0000.0000.0000.000
86A87GLN00.0660.03354.167-0.008-0.0080.0000.0000.0000.000
87A88GLY00.0120.03151.345-0.044-0.0440.0000.0000.0000.000
88A89VAL00.014-0.00850.468-0.082-0.0820.0000.0000.0000.000
89A90ASN00.0970.02847.785-0.178-0.1780.0000.0000.0000.000
90A91GLN00.0110.01145.375-0.123-0.1230.0000.0000.0000.000
91A92LEU00.0280.03844.764-0.136-0.1360.0000.0000.0000.000
92A93LYS10.8960.92739.4347.5857.5850.0000.0000.0000.000
93A94TYR0-0.017-0.00937.1810.1470.1470.0000.0000.0000.000
94A95GLN00.0700.02837.636-0.361-0.3610.0000.0000.0000.000
95A96ARG10.7740.89034.0858.7108.7100.0000.0000.0000.000
96A97SER00.0610.02830.3250.0730.0730.0000.0000.0000.000
97A98LEU00.0570.01631.587-0.031-0.0310.0000.0000.0000.000
98A99ARG10.8440.92923.88712.67312.6730.0000.0000.0000.000
99A100ALA00.0070.01629.017-0.088-0.0880.0000.0000.0000.000
100A101THR00.006-0.01231.2280.1870.1870.0000.0000.0000.000
101A102ALA0-0.0070.00028.9820.1650.1650.0000.0000.0000.000
102A103GLU-1-0.721-0.83026.401-11.658-11.6580.0000.0000.0000.000
103A104GLU-1-0.821-0.90829.535-8.549-8.5490.0000.0000.0000.000
104A105ARG10.9490.97833.2628.9698.9690.0000.0000.0000.000
105A106VAL0-0.003-0.00328.3180.1110.1110.0000.0000.0000.000
106A107GLY00.0120.00531.7400.0450.0450.0000.0000.0000.000
107A108ARG10.9090.93232.6428.3908.3900.0000.0000.0000.000
108A109ARG10.9210.97933.4849.3379.3370.0000.0000.0000.000
109A110ALA0-0.016-0.01331.4030.0930.0930.0000.0000.0000.000
110A111ALA00.0440.02232.699-0.233-0.2330.0000.0000.0000.000
111A112ASN00.0400.03531.9340.1390.1390.0000.0000.0000.000
112A113LEU0-0.064-0.03227.162-0.242-0.2420.0000.0000.0000.000
113A114ARG10.8410.92328.2639.9559.9550.0000.0000.0000.000
114A115VAL0-0.007-0.00326.344-0.478-0.4780.0000.0000.0000.000
115A116LEU00.0170.02920.8640.2170.2170.0000.0000.0000.000
116A117ASN00.027-0.00721.2660.4490.4490.0000.0000.0000.000
117A118SER0-0.041-0.04122.7020.1090.1090.0000.0000.0000.000
118A119TYR0-0.075-0.08018.048-0.606-0.6060.0000.0000.0000.000
119A120TRP00.0340.03121.4720.0540.0540.0000.0000.0000.000
120A121ILE0-0.025-0.01020.950-0.944-0.9440.0000.0000.0000.000
121A122ASN00.0530.01622.283-0.223-0.2230.0000.0000.0000.000
122A123GLN0-0.031-0.02525.1120.4340.4340.0000.0000.0000.000
123A124ASP-1-0.652-0.78928.774-9.975-9.9750.0000.0000.0000.000
124A125SER00.0590.03331.906-0.091-0.0910.0000.0000.0000.000
125A126THR0-0.004-0.01435.0680.1640.1640.0000.0000.0000.000
126A127TYR0-0.019-0.02932.3410.1960.1960.0000.0000.0000.000
127A128LYS10.8790.94828.91210.35210.3520.0000.0000.0000.000
128A129TYR0-0.006-0.02026.3170.2000.2000.0000.0000.0000.000
129A130PHE0-0.036-0.03324.735-0.519-0.5190.0000.0000.0000.000
130A131GLU-1-0.685-0.79419.755-15.262-15.2620.0000.0000.0000.000
131A132VAL0-0.023-0.02322.499-0.335-0.3350.0000.0000.0000.000
132A133ILE0-0.0320.00319.266-0.032-0.0320.0000.0000.0000.000
133A134LEU0-0.005-0.01922.2690.3530.3530.0000.0000.0000.000
134A135VAL00.0130.00322.752-0.503-0.5030.0000.0000.0000.000
135A136ASP-1-0.791-0.88525.343-9.810-9.8100.0000.0000.0000.000
136A137PRO0-0.041-0.00528.271-0.160-0.1600.0000.0000.0000.000
137A138SER00.006-0.02430.3160.2130.2130.0000.0000.0000.000
138A139HIS00.0250.01126.164-0.178-0.1780.0000.0000.0000.000
139A140LYS11.0230.99028.6378.8938.8930.0000.0000.0000.000
140A141ALA00.0620.03523.775-0.059-0.0590.0000.0000.0000.000
141A142ILE0-0.082-0.03323.519-0.592-0.5920.0000.0000.0000.000
142A143ARG10.9180.94525.5369.2989.2980.0000.0000.0000.000
143A144ARG10.9911.02827.24210.28410.2840.0000.0000.0000.000
144A145ASP-1-0.790-0.90421.940-13.392-13.3920.0000.0000.0000.000
145A146ALA00.0790.03124.162-0.224-0.2240.0000.0000.0000.000
146A147LYS10.9590.97617.03716.61516.6150.0000.0000.0000.000
147A148TYR0-0.042-0.04117.640-0.772-0.7720.0000.0000.0000.000
148A149ASN00.0600.04123.4050.4180.4180.0000.0000.0000.000
149A150TRP00.0240.02322.9120.5900.5900.0000.0000.0000.000
150A151ILE0-0.052-0.03025.4730.3940.3940.0000.0000.0000.000
151A152CYS00.017-0.01227.8700.3240.3240.0000.0000.0000.000
152A153ASN00.0290.04430.7290.5330.5330.0000.0000.0000.000
153A154PRO00.0800.04233.331-0.164-0.1640.0000.0000.0000.000
154A155VAL00.0480.02033.5540.0170.0170.0000.0000.0000.000
155A156HIS0-0.021-0.00329.913-0.198-0.1980.0000.0000.0000.000
156A157LYS10.9981.00431.8237.8117.8110.0000.0000.0000.000
157A158HIS00.0180.00133.5850.2420.2420.0000.0000.0000.000
158A159ARG10.8530.93125.91611.52311.5230.0000.0000.0000.000
159A160GLU-1-0.803-0.90430.154-9.663-9.6630.0000.0000.0000.000
160A161ALA00.0160.01731.6420.0840.0840.0000.0000.0000.000
161A162ARG10.8660.92534.6718.9358.9350.0000.0000.0000.000
162A163GLY0-0.0100.00032.4960.0630.0630.0000.0000.0000.000
163A164LEU0-0.010-0.01430.745-0.041-0.0410.0000.0000.0000.000
164A165THR0-0.021-0.01826.945-0.284-0.2840.0000.0000.0000.000
165A166ALA00.0180.00324.1120.2330.2330.0000.0000.0000.000
166A167THR00.0200.00426.1680.1780.1780.0000.0000.0000.000
167A168GLY00.0040.03128.1860.3710.3710.0000.0000.0000.000
168A169LYS10.9830.98728.09411.14211.1420.0000.0000.0000.000
169A170LYS11.0051.00728.02210.77410.7740.0000.0000.0000.000
170A171SER0-0.049-0.04530.7520.2430.2430.0000.0000.0000.000
171A172ARG10.8550.93233.5379.3779.3770.0000.0000.0000.000
172A173GLY00.0300.03334.2120.2490.2490.0000.0000.0000.000
173A174ILE0-0.067-0.03132.3320.1140.1140.0000.0000.0000.000
174A175ASN0-0.037-0.02028.727-0.345-0.3450.0000.0000.0000.000
175A176LYS10.9940.98730.18310.53710.5370.0000.0000.0000.000
176A177GLY00.0710.03433.555-0.196-0.1960.0000.0000.0000.000
177A178HIS00.1150.04636.055-0.063-0.0630.0000.0000.0000.000
178A179LYS10.9130.97034.6458.9568.9560.0000.0000.0000.000
179A180PHE0-0.089-0.04332.688-0.100-0.1000.0000.0000.0000.000
180A181HIS00.1240.07037.6250.0380.0380.0000.0000.0000.000
181A182ASN00.0440.01541.0630.0040.0040.0000.0000.0000.000
182A183THR0-0.111-0.07137.7530.1300.1300.0000.0000.0000.000
183A184GLN00.0940.05336.8690.0260.0260.0000.0000.0000.000
184A185ALA00.0240.01336.429-0.211-0.2110.0000.0000.0000.000
185A186GLY0-0.005-0.02038.490-0.088-0.0880.0000.0000.0000.000
186A187ARG10.9600.98539.5527.4987.4980.0000.0000.0000.000
187A188ARG10.9480.97442.0797.3727.3720.0000.0000.0000.000
188A189LYS10.9941.01541.6617.6617.6610.0000.0000.0000.000
189A190THR0-0.023-0.02142.3000.1080.1080.0000.0000.0000.000
190A191TRP00.0460.03444.9850.0490.0490.0000.0000.0000.000
191A192LYS11.0010.99347.6456.4136.4130.0000.0000.0000.000
192A193ARG10.9410.98244.3357.0547.0540.0000.0000.0000.000
193A194GLN0-0.023-0.02347.191-0.045-0.0450.0000.0000.0000.000
194A195ASN0-0.0030.00050.851-0.027-0.0270.0000.0000.0000.000
195A196THR0-0.043-0.02152.5570.0960.0960.0000.0000.0000.000
196A197LEU00.0390.02654.706-0.048-0.0480.0000.0000.0000.000
197A198SER0-0.041-0.02854.9910.0510.0510.0000.0000.0000.000
198A199LEU00.0030.00757.2110.0630.0630.0000.0000.0000.000
199A200TRP00.0280.02355.186-0.057-0.0570.0000.0000.0000.000
200A201ARG10.9080.94861.4585.0345.0340.0000.0000.0000.000
201A202TYR00.0570.03264.3080.0470.0470.0000.0000.0000.000
202A203ARG00.0490.02863.896-0.128-0.1280.0000.0000.0000.000