FMO DATABASE

FMODB ID: 2GL4R

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	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-840526.320514
FMO2-HF: Nuclear repulsion	793749.292971
FMO2-HF: Total energy	-46777.027543
FMO2-MP2: Total energy	-46916.778315

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:22:LYS)

Summations of interaction energy for fragment #1(A:22:LYS)

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.
267.094	268.863	0.099	-0.674	-1.193	-0.004

Interaction energy analysis for fragmet #1(A:22:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.826 / q_NPA : 1.893

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 ES EX CT+mix DI(MP2)

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].
3	A	24	LEU	0	-0.002	-0.003	3.332	-10.197	-8.469	0.100	-0.670	-1.158	-0.004
4	A	25	LYS	1	0.982	0.986	4.760	61.482	61.523	-0.001	-0.004	-0.035	0.000
5	A	26	VAL	0	0.076	0.045	8.140	2.118	2.118	0.000	0.000	0.000	0.000
6	A	27	ARG	1	0.847	0.924	10.070	50.100	50.100	0.000	0.000	0.000	0.000
7	A	28	THR	0	0.070	0.036	14.048	-0.152	-0.152	0.000	0.000	0.000	0.000
8	A	29	SER	0	-0.017	-0.012	17.645	1.716	1.716	0.000	0.000	0.000	0.000
9	A	30	ALA	0	0.052	0.025	17.786	-1.535	-1.535	0.000	0.000	0.000	0.000
10	A	31	SER	0	-0.010	0.005	18.772	0.021	0.021	0.000	0.000	0.000	0.000
11	A	32	PHE	0	0.017	-0.001	14.745	-0.932	-0.932	0.000	0.000	0.000	0.000
12	A	33	ARG	1	0.977	0.985	18.598	27.321	27.321	0.000	0.000	0.000	0.000
13	A	34	LEU	0	0.035	0.023	19.159	-1.605	-1.605	0.000	0.000	0.000	0.000
14	A	35	PRO	0	-0.039	-0.016	16.557	0.499	0.499	0.000	0.000	0.000	0.000
15	A	36	LYS	1	0.958	0.975	17.910	32.017	32.017	0.000	0.000	0.000	0.000
16	A	37	THR	0	0.047	0.015	19.620	-1.129	-1.129	0.000	0.000	0.000	0.000
17	A	38	LEU	0	0.036	0.022	21.410	1.132	1.132	0.000	0.000	0.000	0.000
18	A	39	LYS	1	0.936	0.964	23.846	21.277	21.277	0.000	0.000	0.000	0.000
19	A	40	LEU	0	0.027	0.021	27.260	0.539	0.539	0.000	0.000	0.000	0.000
20	A	41	ALA	0	0.022	0.018	29.047	0.410	0.410	0.000	0.000	0.000	0.000
21	A	42	ARG	1	0.933	0.954	32.740	16.630	16.630	0.000	0.000	0.000	0.000
22	A	43	SER	0	0.065	0.035	34.833	0.142	0.142	0.000	0.000	0.000	0.000
23	A	44	PRO	0	-0.051	-0.016	36.658	-0.183	-0.183	0.000	0.000	0.000	0.000
24	A	45	LYS	1	0.986	0.976	36.740	16.951	16.951	0.000	0.000	0.000	0.000
25	A	46	TYR	0	0.056	0.035	41.030	0.302	0.302	0.000	0.000	0.000	0.000
26	A	47	ALA	0	0.032	0.021	43.928	-0.249	-0.249	0.000	0.000	0.000	0.000
27	A	48	THR	0	0.006	-0.010	44.013	0.277	0.277	0.000	0.000	0.000	0.000
28	A	49	LYS	1	0.918	0.970	46.792	12.081	12.081	0.000	0.000	0.000	0.000
29	A	50	ALA	0	0.006	0.007	49.497	0.301	0.301	0.000	0.000	0.000	0.000
30	A	51	VAL	0	0.050	0.029	51.238	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	52	PRO	0	-0.023	-0.020	51.085	0.006	0.006	0.000	0.000	0.000	0.000
32	A	53	HIS	0	-0.058	-0.028	53.345	0.246	0.246	0.000	0.000	0.000	0.000
33	A	54	TYR	0	0.103	0.055	55.939	-0.116	-0.116	0.000	0.000	0.000	0.000
34	A	55	ASN	0	0.027	0.020	57.908	-0.244	-0.244	0.000	0.000	0.000	0.000
35	A	56	ARG	1	0.899	0.938	56.211	11.157	11.157	0.000	0.000	0.000	0.000
36	A	57	LEU	0	-0.023	-0.008	59.615	0.169	0.169	0.000	0.000	0.000	0.000
37	A	58	ASP	-1	-0.802	-0.910	61.911	-10.220	-10.220	0.000	0.000	0.000	0.000
38	A	59	SER	0	0.002	-0.032	63.763	0.039	0.039	0.000	0.000	0.000	0.000
39	A	60	TYR	0	0.073	0.021	65.982	0.010	0.010	0.000	0.000	0.000	0.000
40	A	61	LYS	1	0.806	0.914	62.981	10.142	10.142	0.000	0.000	0.000	0.000
41	A	62	VAL	0	-0.064	-0.027	63.696	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	63	ILE	0	-0.038	-0.016	66.329	0.013	0.013	0.000	0.000	0.000	0.000
43	A	64	GLU	-1	-0.900	-0.946	70.032	-9.022	-9.022	0.000	0.000	0.000	0.000
44	A	65	GLN	0	0.017	0.006	72.579	0.020	0.020	0.000	0.000	0.000	0.000
45	A	66	PRO	0	0.053	0.032	75.797	-0.099	-0.099	0.000	0.000	0.000	0.000
46	A	67	ILE	0	-0.101	-0.058	76.693	0.013	0.013	0.000	0.000	0.000	0.000
47	A	68	THR	0	0.131	0.039	80.138	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	69	SER	0	-0.052	-0.023	82.873	0.047	0.047	0.000	0.000	0.000	0.000
49	A	70	GLU	-1	-0.797	-0.900	84.420	-7.194	-7.194	0.000	0.000	0.000	0.000
50	A	71	THR	0	-0.033	-0.024	84.397	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	72	ALA	0	-0.111	-0.060	80.592	-0.080	-0.080	0.000	0.000	0.000	0.000
52	A	73	MET	0	0.043	0.044	81.674	-0.078	-0.078	0.000	0.000	0.000	0.000
53	A	74	LYS	1	1.011	1.014	84.637	7.265	7.265	0.000	0.000	0.000	0.000
54	A	75	LYS	1	0.895	0.950	77.909	8.126	8.126	0.000	0.000	0.000	0.000
55	A	76	VAL	0	-0.017	0.011	80.600	-0.111	-0.111	0.000	0.000	0.000	0.000
56	A	77	GLU	-1	-0.894	-0.947	81.937	-7.359	-7.359	0.000	0.000	0.000	0.000
57	A	78	ASP	-1	-0.866	-0.931	84.755	-7.395	-7.395	0.000	0.000	0.000	0.000
58	A	79	GLY	0	-0.082	-0.042	80.991	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	80	ASN	0	-0.005	0.005	77.482	-0.058	-0.058	0.000	0.000	0.000	0.000
60	A	81	THR	0	-0.155	-0.104	75.694	-0.185	-0.185	0.000	0.000	0.000	0.000
61	A	82	LEU	0	0.100	0.072	74.461	0.058	0.058	0.000	0.000	0.000	0.000
62	A	83	VAL	0	-0.047	-0.040	75.584	-0.156	-0.156	0.000	0.000	0.000	0.000
63	A	84	PHE	0	0.050	0.022	72.579	0.041	0.041	0.000	0.000	0.000	0.000
64	A	85	LYS	1	0.870	0.934	73.132	8.615	8.615	0.000	0.000	0.000	0.000
65	A	86	VAL	0	-0.042	-0.021	67.452	-0.045	-0.045	0.000	0.000	0.000	0.000
66	A	87	SER	0	0.091	0.058	65.399	0.039	0.039	0.000	0.000	0.000	0.000
67	A	88	LEU	0	-0.050	-0.045	64.906	-0.124	-0.124	0.000	0.000	0.000	0.000
68	A	89	LYS	1	0.920	0.947	60.063	10.277	10.277	0.000	0.000	0.000	0.000
69	A	90	ALA	0	0.089	0.080	60.919	-0.138	-0.138	0.000	0.000	0.000	0.000
70	A	91	ASN	0	-0.006	-0.018	57.212	0.169	0.169	0.000	0.000	0.000	0.000
71	A	92	LYS	1	0.959	0.977	61.566	9.869	9.869	0.000	0.000	0.000	0.000
72	A	93	TYR	0	0.048	0.022	57.408	0.100	0.100	0.000	0.000	0.000	0.000
73	A	94	GLN	0	0.039	0.026	57.951	0.142	0.142	0.000	0.000	0.000	0.000
74	A	95	ILE	0	0.033	0.017	62.124	0.088	0.088	0.000	0.000	0.000	0.000
75	A	96	LYS	1	0.884	0.948	63.201	9.821	9.821	0.000	0.000	0.000	0.000
76	A	97	LYS	1	0.936	0.978	59.083	10.643	10.643	0.000	0.000	0.000	0.000
77	A	98	ALA	0	0.016	0.008	64.290	0.074	0.074	0.000	0.000	0.000	0.000
78	A	99	VAL	0	-0.004	-0.009	66.632	0.100	0.100	0.000	0.000	0.000	0.000
79	A	100	LYS	1	0.891	0.953	65.280	9.568	9.568	0.000	0.000	0.000	0.000
80	A	101	GLU	-1	-0.880	-0.925	63.923	-9.952	-9.952	0.000	0.000	0.000	0.000
81	A	102	LEU	0	-0.047	-0.013	67.809	0.043	0.043	0.000	0.000	0.000	0.000
82	A	103	TYR	0	-0.027	-0.021	70.957	0.124	0.124	0.000	0.000	0.000	0.000
83	A	104	GLU	-1	-0.870	-0.916	70.071	-9.013	-9.013	0.000	0.000	0.000	0.000
84	A	105	VAL	0	-0.031	-0.002	71.447	0.079	0.079	0.000	0.000	0.000	0.000
85	A	106	ASP	-1	-0.850	-0.910	69.311	-9.342	-9.342	0.000	0.000	0.000	0.000
86	A	107	VAL	0	-0.034	-0.018	68.105	0.077	0.077	0.000	0.000	0.000	0.000
87	A	108	LEU	0	0.038	0.036	68.282	-0.191	-0.191	0.000	0.000	0.000	0.000
88	A	109	SER	0	-0.049	-0.050	67.896	-0.163	-0.163	0.000	0.000	0.000	0.000
89	A	110	VAL	0	0.028	0.025	66.511	0.108	0.108	0.000	0.000	0.000	0.000
90	A	111	ASN	0	-0.020	-0.028	67.604	-0.269	-0.269	0.000	0.000	0.000	0.000
91	A	112	THR	0	-0.025	-0.011	66.223	0.055	0.055	0.000	0.000	0.000	0.000
92	A	113	LEU	0	0.004	0.010	68.788	-0.046	-0.046	0.000	0.000	0.000	0.000
93	A	114	VAL	0	0.011	-0.008	66.977	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	115	ARG	1	0.907	0.962	70.212	8.677	8.677	0.000	0.000	0.000	0.000
95	A	116	PRO	0	0.069	0.023	72.881	-0.105	-0.105	0.000	0.000	0.000	0.000
96	A	117	ASN	0	0.019	0.020	74.795	-0.124	-0.124	0.000	0.000	0.000	0.000
97	A	118	GLY	0	0.070	0.049	70.939	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	119	THR	0	-0.030	-0.032	70.490	-0.068	-0.068	0.000	0.000	0.000	0.000
99	A	120	LYS	1	0.863	0.928	64.021	9.994	9.994	0.000	0.000	0.000	0.000
100	A	121	LYS	1	0.941	0.984	70.209	8.495	8.495	0.000	0.000	0.000	0.000
101	A	122	ALA	0	-0.020	-0.011	69.755	-0.139	-0.139	0.000	0.000	0.000	0.000
102	A	123	TYR	0	0.030	0.013	71.582	0.125	0.125	0.000	0.000	0.000	0.000
103	A	124	VAL	0	-0.025	-0.025	70.489	-0.172	-0.172	0.000	0.000	0.000	0.000
104	A	125	ARG	1	0.971	1.003	72.219	8.532	8.532	0.000	0.000	0.000	0.000
105	A	126	LEU	0	0.015	0.016	72.354	-0.198	-0.198	0.000	0.000	0.000	0.000
106	A	127	THR	0	-0.026	-0.048	71.049	0.061	0.061	0.000	0.000	0.000	0.000
107	A	128	ALA	0	0.005	-0.007	74.048	0.057	0.057	0.000	0.000	0.000	0.000
108	A	129	ASP	-1	-0.899	-0.929	75.315	-8.322	-8.322	0.000	0.000	0.000	0.000
109	A	130	PHE	0	-0.013	-0.014	73.432	0.058	0.058	0.000	0.000	0.000	0.000
110	A	131	ASP	-1	-0.783	-0.890	78.042	-7.722	-7.722	0.000	0.000	0.000	0.000
111	A	132	ALA	0	-0.043	-0.047	79.203	-0.039	-0.039	0.000	0.000	0.000	0.000
112	A	133	LEU	0	0.018	0.019	80.476	-0.036	-0.036	0.000	0.000	0.000	0.000
113	A	134	ASP	-1	-0.833	-0.918	83.275	-7.477	-7.477	0.000	0.000	0.000	0.000
114	A	135	ILE	0	-0.138	-0.068	76.636	-0.049	-0.049	0.000	0.000	0.000	0.000
115	A	136	ALA	0	-0.021	-0.009	80.468	-0.055	-0.055	0.000	0.000	0.000	0.000
116	A	137	ASN	0	0.016	0.011	81.861	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	138	ARG	1	0.891	0.945	76.321	8.218	8.218	0.000	0.000	0.000	0.000
118	A	139	ILE	0	-0.122	-0.060	76.833	-0.067	-0.067	0.000	0.000	0.000	0.000
119	A	140	GLY	0	0.006	0.004	80.551	-0.021	-0.021	0.000	0.000	0.000	0.000
120	A	141	TYR	0	-0.122	-0.061	79.011	0.040	0.040	0.000	0.000	0.000	0.000
121	A	142	ILE	-1	-0.841	-0.929	84.456	-7.472	-7.472	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:LYS)