FMO DATABASE

FMODB ID: KV3M3

Calculation Name: 1R4A-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester | magnesium ion

Ligand 3-letter code: GNP | MG

Ligand of Interest (LOI):

PDB ID: 1R4A

Chain ID: A

ChEMBL ID:

UniProt ID: P61212

Base Structure: X-ray

Registration Date: 2025-10-05

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1741089.309093
FMO2-HF: Nuclear repulsion	1674832.164694
FMO2-HF: Total energy	-66257.144399
FMO2-MP2: Total energy	-66447.879037

3D Structure

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:16:ARG)

Summations of interaction energy for fragment #1(A:16:ARG)

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.
-74.874	-72.297	1.736	-1.167	-3.144	-0.012

Interaction energy analysis for fragmet #1(A:16:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.742 / q_NPA : 1.860

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	18	MET	0	-0.007	0.021	2.942	-9.929	-7.822	1.739	-1.119	-2.726	-0.012
4	A	19	ARG	1	0.888	0.955	4.722	62.133	62.249	-0.001	-0.011	-0.104	0.000
46	A	61	LEU	0	-0.014	-0.001	3.753	-3.786	-3.618	0.000	-0.028	-0.140	0.000
47	A	62	LYS	1	0.946	0.987	4.790	63.505	63.593	-0.001	-0.006	-0.080	0.000
71	A	86	ASP	-1	-0.837	-0.914	4.969	-89.583	-89.485	-0.001	-0.003	-0.094	0.000
5	A	20	ILE	0	-0.001	-0.004	7.946	1.094	1.094	0.000	0.000	0.000	0.000
6	A	21	LEU	0	-0.012	0.001	11.081	2.081	2.081	0.000	0.000	0.000	0.000
7	A	22	ILE	0	0.021	0.011	14.310	0.781	0.781	0.000	0.000	0.000	0.000
8	A	23	LEU	0	-0.023	-0.014	16.536	1.005	1.005	0.000	0.000	0.000	0.000
9	A	24	GLY	0	0.088	0.042	19.957	0.255	0.255	0.000	0.000	0.000	0.000
10	A	25	LEU	0	0.014	0.013	23.663	-0.092	-0.092	0.000	0.000	0.000	0.000
11	A	26	ASP	-1	-0.862	-0.923	26.805	-20.678	-20.678	0.000	0.000	0.000	0.000
12	A	27	GLY	0	0.053	0.022	28.851	0.452	0.452	0.000	0.000	0.000	0.000
13	A	28	ALA	0	-0.006	0.006	26.379	0.250	0.250	0.000	0.000	0.000	0.000
14	A	29	GLY	0	0.032	0.009	26.722	-0.141	-0.141	0.000	0.000	0.000	0.000
15	A	30	LYS	1	0.816	0.919	21.546	25.404	25.404	0.000	0.000	0.000	0.000
16	A	31	THR	0	0.027	-0.014	21.844	-0.648	-0.648	0.000	0.000	0.000	0.000
17	A	32	THR	0	-0.014	-0.012	23.122	-0.490	-0.490	0.000	0.000	0.000	0.000
18	A	33	ILE	0	-0.013	-0.006	19.430	-0.123	-0.123	0.000	0.000	0.000	0.000
19	A	34	LEU	0	-0.024	-0.016	16.795	-1.049	-1.049	0.000	0.000	0.000	0.000
20	A	35	TYR	0	-0.049	-0.048	18.731	-0.761	-0.761	0.000	0.000	0.000	0.000
21	A	36	ARG	1	0.832	0.936	21.260	24.206	24.206	0.000	0.000	0.000	0.000
22	A	37	LEU	0	0.004	0.007	15.563	-0.628	-0.628	0.000	0.000	0.000	0.000
23	A	38	GLN	0	-0.003	-0.002	13.689	-0.748	-0.748	0.000	0.000	0.000	0.000
24	A	39	VAL	0	-0.007	-0.002	16.838	0.656	0.656	0.000	0.000	0.000	0.000
25	A	40	GLY	0	-0.001	0.013	20.655	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	41	GLU	-1	-0.876	-0.967	23.783	-21.834	-21.834	0.000	0.000	0.000	0.000
27	A	42	VAL	0	0.021	0.014	25.818	0.793	0.793	0.000	0.000	0.000	0.000
28	A	43	VAL	0	-0.048	-0.006	27.725	-0.569	-0.569	0.000	0.000	0.000	0.000
29	A	44	THR	0	-0.027	-0.015	29.404	0.888	0.888	0.000	0.000	0.000	0.000
30	A	45	THR	0	-0.020	-0.007	27.698	-0.757	-0.757	0.000	0.000	0.000	0.000
31	A	46	ILE	0	0.016	0.006	29.578	0.946	0.946	0.000	0.000	0.000	0.000
32	A	47	PRO	0	-0.013	-0.015	29.316	-0.688	-0.688	0.000	0.000	0.000	0.000
33	A	48	THR	0	0.033	0.026	23.404	0.534	0.534	0.000	0.000	0.000	0.000
34	A	49	ILE	0	-0.043	-0.020	26.193	-0.363	-0.363	0.000	0.000	0.000	0.000
35	A	50	GLY	0	0.025	0.003	24.279	0.277	0.277	0.000	0.000	0.000	0.000
36	A	51	PHE	0	-0.044	-0.027	17.961	-0.339	-0.339	0.000	0.000	0.000	0.000
37	A	52	ASN	0	0.010	0.009	20.314	1.008	1.008	0.000	0.000	0.000	0.000
38	A	53	VAL	0	-0.029	-0.030	14.079	-1.329	-1.329	0.000	0.000	0.000	0.000
39	A	54	GLU	-1	-0.811	-0.874	15.753	-32.184	-32.184	0.000	0.000	0.000	0.000
40	A	55	THR	0	-0.055	-0.033	10.261	-4.377	-4.377	0.000	0.000	0.000	0.000
41	A	56	VAL	0	0.018	0.013	11.805	1.832	1.832	0.000	0.000	0.000	0.000
42	A	57	THR	0	-0.067	-0.048	9.436	-5.441	-5.441	0.000	0.000	0.000	0.000
43	A	58	TYR	0	0.032	-0.017	9.787	2.017	2.017	0.000	0.000	0.000	0.000
44	A	59	LYS	1	0.968	0.987	10.459	42.618	42.618	0.000	0.000	0.000	0.000
45	A	60	ASN	0	-0.070	-0.043	8.085	-8.186	-8.186	0.000	0.000	0.000	0.000
48	A	63	PHE	0	0.017	-0.002	5.768	-11.860	-11.860	0.000	0.000	0.000	0.000
49	A	64	GLN	0	0.009	0.016	8.414	4.693	4.693	0.000	0.000	0.000	0.000
50	A	65	VAL	0	0.010	0.000	10.383	-0.966	-0.966	0.000	0.000	0.000	0.000
51	A	66	TRP	0	0.003	-0.005	10.821	3.760	3.760	0.000	0.000	0.000	0.000
52	A	67	ASP	-1	-0.787	-0.864	15.422	-27.887	-27.887	0.000	0.000	0.000	0.000
53	A	68	LEU	0	0.015	0.015	16.655	0.793	0.793	0.000	0.000	0.000	0.000
54	A	69	GLY	0	0.061	0.021	20.343	0.785	0.785	0.000	0.000	0.000	0.000
55	A	70	GLY	0	-0.026	-0.015	24.029	-0.174	-0.174	0.000	0.000	0.000	0.000
56	A	71	GLN	0	0.025	0.022	25.796	0.227	0.227	0.000	0.000	0.000	0.000
57	A	72	THR	0	0.029	-0.010	28.216	-0.506	-0.506	0.000	0.000	0.000	0.000
58	A	73	SER	0	-0.004	0.003	29.296	-0.312	-0.312	0.000	0.000	0.000	0.000
59	A	74	ILE	0	-0.004	0.003	25.500	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	75	ARG	1	0.823	0.913	24.190	20.747	20.747	0.000	0.000	0.000	0.000
61	A	76	PRO	0	0.019	0.006	23.235	-0.980	-0.980	0.000	0.000	0.000	0.000
62	A	77	TYR	0	-0.011	0.000	22.003	-0.333	-0.333	0.000	0.000	0.000	0.000
63	A	78	TRP	0	0.028	-0.005	19.066	-1.370	-1.370	0.000	0.000	0.000	0.000
64	A	79	ARG	1	0.887	0.907	17.233	25.961	25.961	0.000	0.000	0.000	0.000
65	A	80	CYS	0	-0.067	-0.029	16.297	-0.887	-0.887	0.000	0.000	0.000	0.000
66	A	81	TYR	0	-0.018	-0.002	14.040	-0.795	-0.795	0.000	0.000	0.000	0.000
67	A	82	TYR	0	0.025	0.004	12.427	-2.720	-2.720	0.000	0.000	0.000	0.000
68	A	83	SER	0	0.016	0.019	10.505	-4.095	-4.095	0.000	0.000	0.000	0.000
69	A	84	ASN	0	-0.089	-0.054	5.120	-6.181	-6.181	0.000	0.000	0.000	0.000
70	A	85	THR	0	-0.011	-0.010	5.946	-6.720	-6.720	0.000	0.000	0.000	0.000
72	A	87	ALA	0	-0.037	-0.029	7.991	3.632	3.632	0.000	0.000	0.000	0.000
73	A	88	VAL	0	0.006	0.003	11.408	-0.061	-0.061	0.000	0.000	0.000	0.000
74	A	89	ILE	0	0.006	0.014	14.473	0.868	0.868	0.000	0.000	0.000	0.000
75	A	90	TYR	0	-0.042	-0.050	16.992	0.707	0.707	0.000	0.000	0.000	0.000
76	A	91	VAL	0	-0.009	0.000	20.493	0.812	0.812	0.000	0.000	0.000	0.000
77	A	92	VAL	0	0.008	-0.012	23.227	0.570	0.570	0.000	0.000	0.000	0.000
78	A	93	ASP	-1	-0.817	-0.898	26.850	-19.474	-19.474	0.000	0.000	0.000	0.000
79	A	94	SER	0	0.011	-0.017	29.997	0.232	0.232	0.000	0.000	0.000	0.000
80	A	95	CYS	0	-0.020	-0.003	31.878	0.626	0.626	0.000	0.000	0.000	0.000
81	A	96	ASP	-1	-0.820	-0.888	32.948	-17.740	-17.740	0.000	0.000	0.000	0.000
82	A	97	ARG	1	0.872	0.909	34.260	16.294	16.294	0.000	0.000	0.000	0.000
83	A	98	ASP	-1	-0.905	-0.930	36.569	-15.732	-15.732	0.000	0.000	0.000	0.000
84	A	99	ARG	1	0.760	0.841	31.905	18.859	18.859	0.000	0.000	0.000	0.000
85	A	100	ILE	0	0.039	0.027	30.775	-0.772	-0.772	0.000	0.000	0.000	0.000
86	A	101	GLY	0	0.023	0.009	30.939	-0.521	-0.521	0.000	0.000	0.000	0.000
87	A	102	ILE	0	0.014	0.008	29.583	-0.307	-0.307	0.000	0.000	0.000	0.000
88	A	103	SER	0	-0.002	-0.009	27.446	-0.811	-0.811	0.000	0.000	0.000	0.000
89	A	104	LYS	1	0.886	0.958	26.357	18.692	18.692	0.000	0.000	0.000	0.000
90	A	105	SER	0	-0.031	-0.015	26.739	-0.425	-0.425	0.000	0.000	0.000	0.000
91	A	106	GLU	-1	-0.834	-0.915	24.234	-22.793	-22.793	0.000	0.000	0.000	0.000
92	A	107	LEU	0	-0.034	-0.013	21.004	-1.053	-1.053	0.000	0.000	0.000	0.000
93	A	108	VAL	0	-0.010	-0.016	22.092	-0.953	-0.953	0.000	0.000	0.000	0.000
94	A	109	ALA	0	0.056	0.035	23.001	-0.632	-0.632	0.000	0.000	0.000	0.000
95	A	110	MET	0	-0.056	-0.019	18.155	-1.275	-1.275	0.000	0.000	0.000	0.000
96	A	111	LEU	0	-0.046	-0.021	18.086	-1.707	-1.707	0.000	0.000	0.000	0.000
97	A	112	GLU	-1	-0.917	-0.965	19.499	-23.498	-23.498	0.000	0.000	0.000	0.000
98	A	113	GLU	-1	-0.835	-0.879	16.744	-28.336	-28.336	0.000	0.000	0.000	0.000
99	A	114	GLU	-1	-0.845	-0.912	15.657	-32.294	-32.294	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.875	-0.946	11.787	-40.555	-40.555	0.000	0.000	0.000	0.000
101	A	116	LEU	0	0.012	0.018	11.139	-3.348	-3.348	0.000	0.000	0.000	0.000
102	A	117	ARG	1	0.757	0.880	13.210	29.578	29.578	0.000	0.000	0.000	0.000
103	A	118	LYS	1	0.905	0.939	10.400	38.067	38.067	0.000	0.000	0.000	0.000
104	A	119	ALA	0	0.014	0.041	10.846	-1.995	-1.995	0.000	0.000	0.000	0.000
105	A	120	ILE	0	-0.056	-0.028	11.285	3.591	3.591	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.010	-0.002	13.677	-0.530	-0.530	0.000	0.000	0.000	0.000
107	A	122	VAL	0	0.015	-0.001	14.968	0.863	0.863	0.000	0.000	0.000	0.000
108	A	123	VAL	0	-0.012	-0.002	17.835	0.176	0.176	0.000	0.000	0.000	0.000
109	A	124	PHE	0	0.052	0.007	18.103	0.340	0.340	0.000	0.000	0.000	0.000
110	A	125	ALA	0	0.019	0.003	23.027	0.548	0.548	0.000	0.000	0.000	0.000
111	A	126	ASN	0	0.048	0.014	25.538	0.243	0.243	0.000	0.000	0.000	0.000
112	A	127	LYS	1	0.831	0.912	27.415	20.727	20.727	0.000	0.000	0.000	0.000
113	A	128	GLN	0	-0.026	-0.035	29.247	0.879	0.879	0.000	0.000	0.000	0.000
114	A	129	ASP	-1	-0.841	-0.898	31.757	-19.288	-19.288	0.000	0.000	0.000	0.000
115	A	130	MET	0	-0.036	-0.014	33.726	0.597	0.597	0.000	0.000	0.000	0.000
116	A	131	GLU	-1	-0.910	-0.958	36.266	-15.033	-15.033	0.000	0.000	0.000	0.000
117	A	132	GLN	0	0.010	0.006	38.882	0.173	0.173	0.000	0.000	0.000	0.000
118	A	133	ALA	0	-0.008	0.004	33.548	-0.063	-0.063	0.000	0.000	0.000	0.000
119	A	134	MET	0	-0.063	0.000	30.602	0.258	0.258	0.000	0.000	0.000	0.000
120	A	135	THR	0	0.007	-0.047	33.141	-0.712	-0.712	0.000	0.000	0.000	0.000
121	A	136	PRO	0	0.040	-0.008	28.003	-0.075	-0.075	0.000	0.000	0.000	0.000
122	A	137	SER	0	0.022	0.021	29.710	-0.372	-0.372	0.000	0.000	0.000	0.000
123	A	138	GLU	-1	-0.814	-0.867	32.152	-17.147	-17.147	0.000	0.000	0.000	0.000
124	A	139	MET	0	0.018	0.007	26.092	0.057	0.057	0.000	0.000	0.000	0.000
125	A	140	ALA	0	-0.004	0.002	27.919	-0.318	-0.318	0.000	0.000	0.000	0.000
126	A	141	ASN	0	-0.029	-0.030	28.855	-0.189	-0.189	0.000	0.000	0.000	0.000
127	A	142	ALA	0	-0.006	0.012	31.989	0.111	0.111	0.000	0.000	0.000	0.000
128	A	143	LEU	0	0.001	-0.016	25.677	0.056	0.056	0.000	0.000	0.000	0.000
129	A	144	GLY	0	-0.010	0.001	28.081	-0.288	-0.288	0.000	0.000	0.000	0.000
130	A	145	LEU	0	0.007	0.005	23.630	-0.248	-0.248	0.000	0.000	0.000	0.000
131	A	146	PRO	0	-0.023	-0.022	26.102	-0.507	-0.507	0.000	0.000	0.000	0.000
132	A	147	ALA	0	-0.010	0.012	28.386	0.318	0.318	0.000	0.000	0.000	0.000
133	A	148	LEU	0	-0.057	-0.020	21.980	-0.193	-0.193	0.000	0.000	0.000	0.000
134	A	149	LYS	1	0.974	1.000	22.625	24.703	24.703	0.000	0.000	0.000	0.000
135	A	150	ASP	-1	-0.931	-0.985	19.649	-27.184	-27.184	0.000	0.000	0.000	0.000
136	A	151	ARG	1	0.806	0.909	14.821	32.191	32.191	0.000	0.000	0.000	0.000
137	A	152	LYS	1	0.932	0.975	11.668	44.521	44.521	0.000	0.000	0.000	0.000
138	A	153	TRP	0	0.007	-0.008	16.653	-1.487	-1.487	0.000	0.000	0.000	0.000
139	A	154	GLN	0	0.055	0.048	19.023	1.372	1.372	0.000	0.000	0.000	0.000
140	A	155	ILE	0	-0.069	-0.030	20.649	-0.548	-0.548	0.000	0.000	0.000	0.000
141	A	156	PHE	0	0.026	0.018	19.218	0.279	0.279	0.000	0.000	0.000	0.000
142	A	157	LYS	1	0.917	0.963	23.758	20.336	20.336	0.000	0.000	0.000	0.000
143	A	158	THR	0	0.013	0.004	22.778	-0.182	-0.182	0.000	0.000	0.000	0.000
144	A	159	SER	0	-0.042	-0.036	26.194	0.769	0.769	0.000	0.000	0.000	0.000
145	A	160	ALA	0	0.020	0.013	25.394	-0.417	-0.417	0.000	0.000	0.000	0.000
146	A	161	THR	0	0.003	0.001	26.352	-0.377	-0.377	0.000	0.000	0.000	0.000
147	A	162	LYS	1	0.888	0.937	29.430	18.653	18.653	0.000	0.000	0.000	0.000
148	A	163	GLY	0	-0.015	0.015	25.083	0.045	0.045	0.000	0.000	0.000	0.000
149	A	164	THR	0	0.005	-0.013	25.082	-0.306	-0.306	0.000	0.000	0.000	0.000
150	A	165	GLY	0	0.068	0.023	23.983	-0.048	-0.048	0.000	0.000	0.000	0.000
151	A	166	LEU	0	-0.025	-0.011	19.904	-0.833	-0.833	0.000	0.000	0.000	0.000
152	A	167	ASP	-1	-0.871	-0.933	17.898	-31.583	-31.583	0.000	0.000	0.000	0.000
153	A	168	GLU	-1	-0.890	-0.960	17.620	-27.457	-27.457	0.000	0.000	0.000	0.000
154	A	169	ALA	0	-0.009	-0.003	18.557	-0.803	-0.803	0.000	0.000	0.000	0.000
155	A	170	MET	0	-0.021	-0.014	12.205	-2.135	-2.135	0.000	0.000	0.000	0.000
156	A	171	GLU	-1	-0.844	-0.891	13.389	-40.405	-40.405	0.000	0.000	0.000	0.000
157	A	172	TRP	0	0.046	0.024	13.930	-2.538	-2.538	0.000	0.000	0.000	0.000
158	A	173	LEU	0	0.001	0.010	11.326	-1.502	-1.502	0.000	0.000	0.000	0.000
159	A	174	VAL	0	0.005	-0.011	8.280	-4.349	-4.349	0.000	0.000	0.000	0.000
160	A	175	GLU	-1	-0.954	-0.981	9.352	-41.708	-41.708	0.000	0.000	0.000	0.000
161	A	176	THR	0	-0.030	-0.020	11.273	-0.396	-0.396	0.000	0.000	0.000	0.000
162	A	177	LEU	0	-0.048	-0.037	5.906	-1.565	-1.565	0.000	0.000	0.000	0.000
163	A	178	LYS	1	0.885	0.950	6.492	48.323	48.323	0.000	0.000	0.000	0.000
164	A	179	SER	0	-0.088	-0.022	7.559	0.188	0.188	0.000	0.000	0.000	0.000
165	A	180	ARG	0	0.021	0.018	6.896	11.821	11.821	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:ARG)