FMO DATABASE

FMODB ID: 8KNVY

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	-731873.992989
FMO2-HF: Nuclear repulsion	685429.840758
FMO2-HF: Total energy	-46444.152231
FMO2-MP2: Total energy	-46582.614506

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: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.
294.298	295.845	0.013	-0.726	-0.833	-0.001

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 : 0.908 / q_NPA : 0.942

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	4	ARG	1	0.986	0.997	3.429	36.453	37.873	0.015	-0.709	-0.726	-0.001
4	A	5	VAL	0	0.001	0.001	5.334	4.530	4.579	-0.001	-0.006	-0.041	0.000
29	A	30	LEU	0	-0.023	-0.014	4.595	2.309	2.387	-0.001	-0.011	-0.066	0.000
5	A	6	THR	0	0.077	0.046	8.753	0.137	0.137	0.000	0.000	0.000	0.000
6	A	7	PHE	0	0.020	0.013	12.228	0.211	0.211	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.859	0.913	15.268	18.768	18.768	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.939	0.961	18.252	14.340	14.340	0.000	0.000	0.000	0.000
9	A	10	ARG	1	1.023	1.026	20.723	13.631	13.631	0.000	0.000	0.000	0.000
10	A	11	ASN	0	0.057	0.043	21.553	0.314	0.314	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.026	0.009	18.429	-0.804	-0.804	0.000	0.000	0.000	0.000
12	A	13	TYR	0	0.084	0.057	17.973	-1.020	-1.020	0.000	0.000	0.000	0.000
13	A	14	ASN	0	0.016	0.018	16.173	-0.899	-0.899	0.000	0.000	0.000	0.000
14	A	15	THR	0	0.046	0.025	18.990	0.375	0.375	0.000	0.000	0.000	0.000
15	A	16	LYS	1	1.005	0.983	21.692	11.568	11.568	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.120	-0.081	23.560	0.596	0.596	0.000	0.000	0.000	0.000
17	A	18	ASN	0	-0.027	-0.016	19.436	0.168	0.168	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.998	1.011	18.049	14.441	14.441	0.000	0.000	0.000	0.000
19	A	20	ILE	0	0.019	0.015	12.407	0.548	0.548	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.954	0.986	13.308	18.414	18.414	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.027	0.007	7.208	1.135	1.135	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.003	-0.005	10.539	0.754	0.754	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.981	1.000	7.784	28.527	28.527	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.061	-0.038	11.350	2.373	2.373	0.000	0.000	0.000	0.000
25	A	26	PRO	0	0.059	0.019	13.487	-1.067	-1.067	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.052	0.043	14.910	0.734	0.734	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.030	0.023	11.539	-0.075	-0.075	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.019	0.011	8.766	-3.225	-3.225	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.972	0.977	8.642	20.393	20.393	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.016	-0.002	11.427	0.372	0.372	0.000	0.000	0.000	0.000
32	A	33	GLN	0	-0.018	-0.009	12.980	1.672	1.672	0.000	0.000	0.000	0.000
33	A	34	HIS	0	0.048	0.022	16.169	-0.960	-0.960	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.019	-0.008	17.260	0.847	0.847	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.982	0.986	19.972	12.577	12.577	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.950	0.970	23.752	11.045	11.045	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.088	0.047	22.364	0.383	0.383	0.000	0.000	0.000	0.000
38	A	39	ALA	0	-0.038	-0.011	26.435	0.158	0.158	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.005	0.003	30.235	-0.072	-0.072	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.909	0.940	32.153	8.793	8.793	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.016	0.015	34.685	0.049	0.049	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.957	0.977	36.131	8.543	8.543	0.000	0.000	0.000	0.000
43	A	44	CYS	-1	-0.919	-0.738	40.886	-6.797	-6.797	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.027	-0.014	44.369	-0.078	-0.078	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.760	-0.899	46.976	-6.199	-6.199	0.000	0.000	0.000	0.000
46	A	47	THR	0	0.078	-0.010	45.830	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.053	0.019	42.426	-0.088	-0.088	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.019	0.000	40.694	-0.274	-0.274	0.000	0.000	0.000	0.000
49	A	50	PRO	0	-0.017	-0.014	37.057	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.020	0.014	39.053	0.048	0.048	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.018	-0.016	39.390	-0.199	-0.199	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.012	0.009	39.801	0.178	0.178	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.037	-0.001	38.878	-0.060	-0.060	0.000	0.000	0.000	0.000
54	A	55	SER	0	0.008	-0.002	34.952	-0.272	-0.272	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.027	-0.025	30.717	0.106	0.106	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.031	0.002	31.556	0.147	0.147	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.897	0.941	28.821	10.629	10.629	0.000	0.000	0.000	0.000
58	A	59	PRO	0	0.060	0.032	32.822	0.033	0.033	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.961	0.962	34.575	8.411	8.411	0.000	0.000	0.000	0.000
60	A	61	GLN	0	-0.005	-0.001	29.994	0.154	0.154	0.000	0.000	0.000	0.000
61	A	62	TYR	0	0.086	0.041	34.056	0.101	0.101	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.027	-0.016	37.036	0.236	0.236	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.005	0.007	37.478	0.151	0.151	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.015	0.019	36.031	-0.132	-0.132	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.048	0.017	39.340	0.234	0.234	0.000	0.000	0.000	0.000
66	A	67	ARG	1	1.031	1.003	41.685	6.317	6.317	0.000	0.000	0.000	0.000
67	A	68	THR	0	0.041	0.036	42.953	-0.034	-0.034	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.988	0.997	36.629	8.466	8.466	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.841	0.941	39.330	7.467	7.467	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.022	-0.034	41.647	0.078	0.078	0.000	0.000	0.000	0.000
71	A	72	VAL	0	0.000	0.019	43.887	-0.083	-0.083	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.035	0.014	46.220	0.028	0.028	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.971	0.989	46.572	6.781	6.781	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.067	0.022	51.431	-0.075	-0.075	0.000	0.000	0.000	0.000
75	A	76	TYR	0	0.046	0.027	50.635	0.004	0.004	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.026	0.009	48.243	-0.133	-0.133	0.000	0.000	0.000	0.000
77	A	78	GLY	0	-0.009	-0.010	44.523	-0.129	-0.129	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.074	-0.027	45.162	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.981	0.991	46.031	6.440	6.440	0.000	0.000	0.000	0.000
80	A	81	SER	0	-0.011	-0.125	44.893	0.019	0.019	0.000	0.000	0.000	0.000
81	A	82	ALA	0	-0.066	-0.040	46.650	0.046	0.046	0.000	0.000	0.000	0.000
82	A	83	ASN	0	0.042	0.028	47.942	0.227	0.227	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.084	0.046	49.249	0.136	0.136	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.043	-0.023	50.381	0.117	0.117	0.000	0.000	0.000	0.000
85	A	86	LYS	1	1.003	0.995	52.881	6.071	6.071	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.806	-0.877	53.805	-5.821	-5.821	0.000	0.000	0.000	0.000
87	A	88	ARG	1	0.834	0.888	52.874	6.118	6.118	0.000	0.000	0.000	0.000
88	A	89	ILE	0	-0.022	-0.003	56.352	0.068	0.068	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.012	0.007	58.786	0.095	0.095	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.830	0.885	55.893	5.761	5.761	0.000	0.000	0.000	0.000
91	A	92	ALA	0	0.005	0.011	60.890	0.059	0.059	0.000	0.000	0.000	0.000
92	A	93	PHE	0	0.048	0.019	62.561	0.058	0.058	0.000	0.000	0.000	0.000
93	A	94	LEU	0	0.037	0.013	63.633	0.080	0.080	0.000	0.000	0.000	0.000
94	A	95	ILE	0	-0.031	-0.013	64.061	0.079	0.079	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.973	-1.004	65.899	-4.804	-4.804	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.837	-0.914	68.843	-4.472	-4.472	0.000	0.000	0.000	0.000
97	A	98	GLN	0	-0.027	-0.017	69.430	0.119	0.119	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.878	0.947	67.236	4.863	4.863	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.022	0.019	72.519	0.067	0.067	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.029	0.012	74.448	0.070	0.070	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.897	0.935	72.515	4.470	4.470	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.907	0.979	73.992	4.376	4.376	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.112	0.064	78.649	0.051	0.051	0.000	0.000	0.000	0.000
104	A	105	ILE	0	0.009	0.007	77.927	0.052	0.052	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.904	0.963	78.014	4.201	4.201	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.850	-0.933	81.381	-3.946	-3.946	0.000	0.000	0.000	0.000
107	A	108	GLN	0	0.018	0.005	84.548	0.055	0.055	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.021	-0.029	84.061	0.046	0.046	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.988	-1.003	84.522	-3.793	-3.793	0.000	0.000	0.000	0.000
110	A	111	ALA	0	-0.032	-0.011	87.877	0.050	0.050	0.000	0.000	0.000	0.000
111	A	112	ALA	0	0.024	0.023	89.502	0.046	0.046	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.998	0.995	84.998	3.852	3.852	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.874	0.931	88.996	3.691	3.691	0.000	0.000	0.000	0.000
114	A	115	ALA	0	-0.003	0.015	93.692	0.043	0.043	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.864	-0.943	91.757	-3.541	-3.541	0.000	0.000	0.000	0.000
116	A	117	LYS	1	0.903	0.945	90.422	3.611	3.611	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.898	0.946	96.852	3.382	3.382	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.835	-0.905	99.197	-3.228	-3.228	0.000	0.000	0.000	0.000
119	A	120	ALA	0	-0.010	-0.011	98.921	0.028	0.028	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.847	0.923	98.080	3.320	3.320	0.000	0.000	0.000	0.000
121	A	122	LYS	0	-0.051	-0.001	102.305	0.134	0.134	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)