FMO DATABASE

FMODB ID: 46LGN

Calculation Name: 3NKV-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester | adenosine monophosphate | barium ion | magnesium ion

Ligand 3-letter code: GNP | AMP | BA | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3NKV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H0U4

Base Structure: X-ray

Registration Date: 2025-10-04

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	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1819395.783375
FMO2-HF: Nuclear repulsion	1752218.958654
FMO2-HF: Total energy	-67176.824721
FMO2-MP2: Total energy	-67374.237556

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:4:GLU)

Summations of interaction energy for fragment #1(A:4:GLU)

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.
-28.147	-25.621	0.009	-0.894	-1.642	0

Interaction energy analysis for fragmet #1(A:4:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.034

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	6	ASP	-1	-0.801	-0.884	3.807	-7.353	-5.453	-0.010	-0.690	-1.200	0.001
53	A	56	THR	0	0.007	-0.001	2.976	-2.720	-2.094	0.019	-0.204	-0.442	-0.001
4	A	7	TYR	0	-0.026	-0.014	6.091	1.895	1.895	0.000	0.000	0.000	0.000
5	A	8	LEU	0	-0.060	-0.032	7.698	0.555	0.555	0.000	0.000	0.000	0.000
6	A	9	PHE	0	0.000	-0.003	9.365	-0.240	-0.240	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.898	0.956	13.030	-3.289	-3.289	0.000	0.000	0.000	0.000
8	A	11	LEU	0	0.024	0.006	15.803	-0.242	-0.242	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.007	0.008	18.742	0.122	0.122	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.014	0.021	22.256	-0.122	-0.122	0.000	0.000	0.000	0.000
11	A	14	ILE	0	0.016	0.026	25.073	0.053	0.053	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.078	0.033	28.492	-0.068	-0.068	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.768	-0.872	32.043	0.216	0.216	0.000	0.000	0.000	0.000
14	A	17	SER	0	-0.059	-0.049	33.907	0.007	0.007	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.043	0.025	34.930	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	19	VAL	0	0.008	0.010	31.355	-0.035	-0.035	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.015	0.010	30.896	-0.042	-0.042	0.000	0.000	0.000	0.000
18	A	21	LYS	1	0.818	0.926	27.350	-0.331	-0.331	0.000	0.000	0.000	0.000
19	A	22	SER	0	0.045	-0.003	25.935	-0.040	-0.040	0.000	0.000	0.000	0.000
20	A	23	CYS	0	-0.049	-0.020	25.606	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	24	LEU	0	0.015	0.013	24.253	-0.074	-0.074	0.000	0.000	0.000	0.000
22	A	25	LEU	0	0.004	0.003	19.410	-0.090	-0.090	0.000	0.000	0.000	0.000
23	A	26	LEU	0	-0.032	-0.013	21.013	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.806	0.896	22.079	0.435	0.435	0.000	0.000	0.000	0.000
25	A	28	PHE	0	0.001	0.000	14.853	-0.123	-0.123	0.000	0.000	0.000	0.000
26	A	29	ALA	0	-0.042	-0.020	16.881	-0.176	-0.176	0.000	0.000	0.000	0.000
27	A	30	ASP	-1	-0.839	-0.912	17.451	0.198	0.198	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.876	-0.906	20.215	-0.785	-0.785	0.000	0.000	0.000	0.000
29	A	32	THR	0	-0.037	-0.017	21.767	0.044	0.044	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.030	-0.054	25.122	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.006	-0.007	28.235	0.004	0.004	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.768	-0.849	31.722	-0.151	-0.151	0.000	0.000	0.000	0.000
33	A	36	SER	0	-0.068	-0.029	34.374	0.019	0.019	0.000	0.000	0.000	0.000
34	A	37	TYR	0	-0.001	0.004	34.317	0.008	0.008	0.000	0.000	0.000	0.000
35	A	38	ILE	0	0.016	0.000	33.290	0.013	0.013	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.066	-0.030	32.944	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	40	THR	0	0.049	0.026	27.575	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	41	ILE	0	-0.045	-0.025	30.074	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	42	GLY	0	0.014	0.012	29.579	0.060	0.060	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.046	-0.037	24.247	-0.049	-0.049	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.861	-0.906	24.246	0.753	0.753	0.000	0.000	0.000	0.000
42	A	45	PHE	0	-0.064	-0.051	14.698	0.110	0.110	0.000	0.000	0.000	0.000
43	A	46	LYS	1	0.853	0.921	17.812	-0.540	-0.540	0.000	0.000	0.000	0.000
44	A	47	ILE	0	-0.018	-0.010	10.978	0.309	0.309	0.000	0.000	0.000	0.000
45	A	48	ARG	1	0.815	0.872	12.557	1.288	1.288	0.000	0.000	0.000	0.000
46	A	49	THR	0	-0.028	0.000	5.898	0.976	0.976	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.012	-0.006	8.975	0.024	0.024	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.816	-0.898	6.440	-14.209	-14.209	0.000	0.000	0.000	0.000
49	A	52	LEU	0	-0.031	-0.024	9.098	1.116	1.116	0.000	0.000	0.000	0.000
50	A	53	ASP	-1	-0.850	-0.925	11.522	-2.745	-2.745	0.000	0.000	0.000	0.000
51	A	54	GLY	0	-0.019	0.004	9.712	0.284	0.284	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.851	0.938	7.277	5.388	5.388	0.000	0.000	0.000	0.000
54	A	57	ILE	0	-0.027	-0.020	5.583	2.316	2.316	0.000	0.000	0.000	0.000
55	A	58	LYS	1	0.885	0.951	5.870	-13.298	-13.298	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.020	0.012	9.137	0.511	0.511	0.000	0.000	0.000	0.000
57	A	60	GLN	0	0.000	-0.008	11.764	0.272	0.272	0.000	0.000	0.000	0.000
58	A	61	ILE	0	0.012	0.004	14.263	-0.192	-0.192	0.000	0.000	0.000	0.000
59	A	62	TRP	0	0.024	0.010	16.201	0.139	0.139	0.000	0.000	0.000	0.000
60	A	63	ASP	-1	-0.787	-0.884	21.172	0.262	0.262	0.000	0.000	0.000	0.000
61	A	64	THR	0	-0.002	-0.025	24.563	0.056	0.056	0.000	0.000	0.000	0.000
62	A	65	ALA	0	0.015	0.008	27.596	-0.081	-0.081	0.000	0.000	0.000	0.000
63	A	66	GLY	0	0.034	0.013	31.049	0.003	0.003	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.005	-0.010	33.528	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	68	GLU	-1	-0.772	-0.889	35.569	0.366	0.366	0.000	0.000	0.000	0.000
66	A	69	ARG	1	0.891	0.942	36.848	-0.367	-0.367	0.000	0.000	0.000	0.000
67	A	70	PHE	0	0.000	0.000	32.111	0.026	0.026	0.000	0.000	0.000	0.000
68	A	71	ARG	1	0.870	0.956	32.262	-0.249	-0.249	0.000	0.000	0.000	0.000
69	A	72	THR	0	0.071	0.038	31.865	0.043	0.043	0.000	0.000	0.000	0.000
70	A	73	ILE	0	0.005	0.023	28.845	0.049	0.049	0.000	0.000	0.000	0.000
71	A	74	THR	0	-0.058	-0.046	27.721	0.064	0.064	0.000	0.000	0.000	0.000
72	A	75	SER	0	-0.003	-0.016	27.027	0.070	0.070	0.000	0.000	0.000	0.000
73	A	76	SER	0	-0.002	-0.004	25.360	0.029	0.029	0.000	0.000	0.000	0.000
74	A	77	TYR	0	-0.040	-0.029	21.531	0.149	0.149	0.000	0.000	0.000	0.000
75	A	78	TYR	0	0.014	0.006	22.468	0.050	0.050	0.000	0.000	0.000	0.000
76	A	79	ARG	1	0.966	0.994	23.193	-0.926	-0.926	0.000	0.000	0.000	0.000
77	A	80	GLY	0	-0.019	-0.007	19.758	0.029	0.029	0.000	0.000	0.000	0.000
78	A	81	ALA	0	-0.033	-0.013	18.189	0.213	0.213	0.000	0.000	0.000	0.000
79	A	82	HIS	0	0.047	0.029	13.883	-0.099	-0.099	0.000	0.000	0.000	0.000
80	A	83	GLY	0	0.034	-0.005	18.555	-0.193	-0.193	0.000	0.000	0.000	0.000
81	A	84	ILE	0	-0.056	-0.027	20.835	0.105	0.105	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.001	-0.002	21.142	-0.093	-0.093	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.011	0.004	25.412	0.066	0.066	0.000	0.000	0.000	0.000
84	A	87	VAL	0	-0.044	-0.025	27.454	-0.068	-0.068	0.000	0.000	0.000	0.000
85	A	88	TYR	0	0.032	0.009	30.111	0.041	0.041	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.783	-0.861	32.975	-0.093	-0.093	0.000	0.000	0.000	0.000
87	A	90	VAL	0	0.021	0.013	34.544	0.010	0.010	0.000	0.000	0.000	0.000
88	A	91	THR	0	-0.093	-0.068	37.183	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	92	ASP	-1	-0.867	-0.922	39.005	0.046	0.046	0.000	0.000	0.000	0.000
90	A	93	GLN	0	0.029	-0.001	39.719	0.003	0.003	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.880	-0.924	41.796	0.094	0.094	0.000	0.000	0.000	0.000
92	A	95	SER	0	-0.049	-0.041	36.621	0.011	0.011	0.000	0.000	0.000	0.000
93	A	96	TYR	0	-0.007	-0.010	36.601	0.011	0.011	0.000	0.000	0.000	0.000
94	A	97	ALA	0	0.022	0.017	38.268	0.006	0.006	0.000	0.000	0.000	0.000
95	A	98	ASN	0	-0.034	-0.037	37.891	0.023	0.023	0.000	0.000	0.000	0.000
96	A	99	VAL	0	-0.017	0.001	33.787	0.033	0.033	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.964	0.977	35.049	-0.038	-0.038	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.009	0.021	36.805	0.024	0.024	0.000	0.000	0.000	0.000
99	A	102	TRP	0	-0.048	-0.050	31.557	0.051	0.051	0.000	0.000	0.000	0.000
100	A	103	LEU	0	0.009	0.002	31.180	0.038	0.038	0.000	0.000	0.000	0.000
101	A	104	GLN	0	0.022	0.016	32.636	0.041	0.041	0.000	0.000	0.000	0.000
102	A	105	GLU	-1	-0.866	-0.939	31.865	0.454	0.454	0.000	0.000	0.000	0.000
103	A	106	ILE	0	-0.050	-0.033	27.438	0.063	0.063	0.000	0.000	0.000	0.000
104	A	107	ASP	-1	-0.916	-0.961	29.412	0.321	0.321	0.000	0.000	0.000	0.000
105	A	108	ARG	1	0.812	0.925	31.826	-0.345	-0.345	0.000	0.000	0.000	0.000
106	A	109	TYR	0	-0.053	-0.027	28.723	0.043	0.043	0.000	0.000	0.000	0.000
107	A	110	ALA	0	-0.023	-0.016	25.191	0.103	0.103	0.000	0.000	0.000	0.000
108	A	111	SER	0	-0.014	-0.006	22.486	0.011	0.011	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.922	-0.971	24.870	0.431	0.431	0.000	0.000	0.000	0.000
110	A	113	ASN	0	-0.091	-0.042	21.474	-0.041	-0.041	0.000	0.000	0.000	0.000
111	A	114	VAL	0	-0.023	0.008	21.927	-0.045	-0.045	0.000	0.000	0.000	0.000
112	A	115	ASN	0	0.008	-0.006	21.046	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	116	LYS	1	0.965	0.981	23.396	-0.134	-0.134	0.000	0.000	0.000	0.000
114	A	117	LEU	0	-0.001	0.004	22.928	-0.074	-0.074	0.000	0.000	0.000	0.000
115	A	118	LEU	0	-0.010	0.014	26.345	0.063	0.063	0.000	0.000	0.000	0.000
116	A	119	VAL	0	0.007	-0.015	25.827	-0.068	-0.068	0.000	0.000	0.000	0.000
117	A	120	GLY	0	0.061	0.029	29.164	0.053	0.053	0.000	0.000	0.000	0.000
118	A	121	ASN	0	-0.015	-0.025	29.735	-0.104	-0.104	0.000	0.000	0.000	0.000
119	A	122	LYS	1	0.826	0.891	31.441	0.053	0.053	0.000	0.000	0.000	0.000
120	A	123	SER	0	0.014	-0.008	31.594	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	124	ASP	-1	-0.828	-0.892	33.293	-0.274	-0.274	0.000	0.000	0.000	0.000
122	A	125	LEU	0	-0.055	-0.015	35.227	0.009	0.009	0.000	0.000	0.000	0.000
123	A	126	THR	0	0.031	-0.001	37.833	0.026	0.026	0.000	0.000	0.000	0.000
124	A	127	THR	0	-0.040	-0.022	39.948	0.013	0.013	0.000	0.000	0.000	0.000
125	A	128	LYS	1	0.918	0.954	41.096	0.133	0.133	0.000	0.000	0.000	0.000
126	A	129	LYS	1	0.826	0.925	36.703	0.269	0.269	0.000	0.000	0.000	0.000
127	A	130	VAL	0	-0.012	-0.009	41.268	0.001	0.001	0.000	0.000	0.000	0.000
128	A	131	VAL	0	-0.036	0.002	38.153	0.009	0.009	0.000	0.000	0.000	0.000
129	A	132	ASP	-1	-0.815	-0.887	39.565	-0.225	-0.225	0.000	0.000	0.000	0.000
130	A	133	ASN	0	0.000	-0.016	35.816	0.018	0.018	0.000	0.000	0.000	0.000
131	A	134	THR	0	-0.061	-0.043	37.042	-0.009	-0.009	0.000	0.000	0.000	0.000
132	A	135	THR	0	0.057	0.024	39.131	0.004	0.004	0.000	0.000	0.000	0.000
133	A	136	ALA	0	-0.018	-0.005	35.418	0.014	0.014	0.000	0.000	0.000	0.000
134	A	137	LYS	1	0.820	0.889	32.335	0.354	0.354	0.000	0.000	0.000	0.000
135	A	138	GLU	-1	-0.915	-0.961	35.706	-0.165	-0.165	0.000	0.000	0.000	0.000
136	A	139	PHE	0	-0.035	-0.016	35.193	0.021	0.021	0.000	0.000	0.000	0.000
137	A	140	ALA	0	0.000	0.011	32.196	0.022	0.022	0.000	0.000	0.000	0.000
138	A	141	ASP	-1	-0.792	-0.872	33.626	-0.286	-0.286	0.000	0.000	0.000	0.000
139	A	142	SER	0	-0.115	-0.065	34.998	0.018	0.018	0.000	0.000	0.000	0.000
140	A	143	LEU	0	-0.030	-0.019	34.299	0.033	0.033	0.000	0.000	0.000	0.000
141	A	144	GLY	0	-0.022	-0.002	32.484	0.024	0.024	0.000	0.000	0.000	0.000
142	A	145	ILE	0	-0.086	-0.036	28.924	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	146	PRO	0	0.013	0.013	25.461	-0.032	-0.032	0.000	0.000	0.000	0.000
144	A	147	PHE	0	0.022	-0.016	28.391	0.050	0.050	0.000	0.000	0.000	0.000
145	A	148	LEU	0	-0.025	0.001	24.314	-0.064	-0.064	0.000	0.000	0.000	0.000
146	A	149	GLU	-1	-0.777	-0.877	28.734	-0.222	-0.222	0.000	0.000	0.000	0.000
147	A	150	THR	0	0.006	-0.009	25.976	-0.059	-0.059	0.000	0.000	0.000	0.000
148	A	151	SER	0	-0.072	-0.050	28.038	0.049	0.049	0.000	0.000	0.000	0.000
149	A	152	ALA	0	0.018	0.012	26.617	-0.050	-0.050	0.000	0.000	0.000	0.000
150	A	153	LYS	1	0.836	0.921	27.388	0.198	0.198	0.000	0.000	0.000	0.000
151	A	154	ASN	0	0.007	-0.016	29.356	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	155	ALA	0	0.042	0.032	24.065	-0.060	-0.060	0.000	0.000	0.000	0.000
153	A	156	THR	0	0.020	0.006	24.771	-0.078	-0.078	0.000	0.000	0.000	0.000
154	A	157	ASN	0	0.003	-0.016	24.331	-0.014	-0.014	0.000	0.000	0.000	0.000
155	A	158	VAL	0	0.008	0.020	21.564	0.004	0.004	0.000	0.000	0.000	0.000
156	A	159	GLU	-1	-0.759	-0.860	17.000	-1.408	-1.408	0.000	0.000	0.000	0.000
157	A	160	GLN	0	-0.015	-0.009	18.792	-0.073	-0.073	0.000	0.000	0.000	0.000
158	A	161	ALA	0	0.039	0.037	20.954	-0.009	-0.009	0.000	0.000	0.000	0.000
159	A	162	PHE	0	0.013	-0.002	16.890	0.110	0.110	0.000	0.000	0.000	0.000
160	A	163	MET	0	-0.010	0.001	13.980	-0.041	-0.041	0.000	0.000	0.000	0.000
161	A	164	THR	0	-0.020	-0.030	17.040	-0.024	-0.024	0.000	0.000	0.000	0.000
162	A	165	MET	0	-0.004	0.031	18.750	0.061	0.061	0.000	0.000	0.000	0.000
163	A	166	ALA	0	0.002	-0.007	13.950	0.112	0.112	0.000	0.000	0.000	0.000
164	A	167	ALA	0	0.009	0.005	15.869	-0.047	-0.047	0.000	0.000	0.000	0.000
165	A	168	GLU	-1	-0.836	-0.908	17.484	-0.654	-0.654	0.000	0.000	0.000	0.000
166	A	169	ILE	0	-0.015	0.000	16.012	0.151	0.151	0.000	0.000	0.000	0.000
167	A	170	LYS	1	0.830	0.899	12.279	2.623	2.623	0.000	0.000	0.000	0.000
168	A	171	LYS	1	0.814	0.894	16.208	0.812	0.812	0.000	0.000	0.000	0.000
169	A	172	ARG	1	0.872	0.958	19.023	-0.264	-0.264	0.000	0.000	0.000	0.000
170	A	173	MET	-1	-0.939	-0.957	14.308	0.098	0.098	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLU)