FMO DATABASE

FMODB ID: 3MZ7L

Calculation Name: 2J0S-C-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-adenylate ester | magnesium ion

Ligand 3-letter code: ANP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2J0S

Chain ID: C

ChEMBL ID:

UniProt ID: O15234

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
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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1386350.552042
FMO2-HF: Nuclear repulsion	1328117.324195
FMO2-HF: Total energy	-58233.227847
FMO2-MP2: Total energy	-58405.631759

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:ASP)

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

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.
-3.194	1.244	-4.336808689942E-18	-1.787	-2.65	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.087 / q_NPA : -0.046

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	TYR	0	-0.063	-0.052	3.812	1.462	4.000	-0.032	-1.195	-1.311	-0.002
25	A	28	PRO	0	0.049	0.019	3.338	-0.709	-0.476	0.013	-0.087	-0.160	0.000
26	A	29	ASP	-1	-0.850	-0.907	5.217	0.057	0.117	-0.001	0.000	-0.059	0.000
88	A	91	VAL	0	-0.020	0.001	4.207	0.451	0.706	0.000	-0.019	-0.236	0.000
89	A	92	ILE	0	-0.011	-0.015	5.300	-3.219	-3.157	-0.001	-0.020	-0.040	0.000
90	A	93	GLY	0	-0.034	-0.009	3.317	0.938	1.588	0.016	-0.230	-0.436	-0.001
91	A	94	ASP	-1	-0.943	-0.972	3.741	-1.497	-0.857	0.005	-0.236	-0.408	-0.001
4	A	7	LEU	0	0.052	0.038	6.659	-0.209	-0.209	0.000	0.000	0.000	0.000
5	A	8	ARG	1	0.756	0.875	10.352	0.712	0.712	0.000	0.000	0.000	0.000
6	A	9	TYR	0	0.048	0.007	13.411	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	10	TYR	0	-0.044	-0.035	16.917	0.113	0.113	0.000	0.000	0.000	0.000
8	A	11	VAL	0	0.018	0.006	20.203	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	12	GLY	0	0.021	0.009	23.836	0.024	0.024	0.000	0.000	0.000	0.000
10	A	13	HIS	0	-0.013	-0.003	26.970	-0.022	-0.022	0.000	0.000	0.000	0.000
11	A	14	LYS	1	0.938	0.971	27.718	0.070	0.070	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.048	0.020	32.472	0.001	0.001	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.936	0.967	36.089	0.138	0.138	0.000	0.000	0.000	0.000
14	A	17	PHE	0	0.008	0.009	36.079	0.011	0.011	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.088	0.062	34.309	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	19	HIS	0	-0.033	-0.026	25.379	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.784	-0.846	29.792	-0.222	-0.222	0.000	0.000	0.000	0.000
18	A	21	PHE	0	-0.032	-0.021	22.716	0.004	0.004	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.004	0.013	21.743	0.014	0.014	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.830	-0.916	18.032	-0.310	-0.310	0.000	0.000	0.000	0.000
21	A	24	PHE	0	-0.025	-0.015	15.596	0.091	0.091	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.789	-0.865	12.271	-0.193	-0.193	0.000	0.000	0.000	0.000
23	A	26	PHE	0	0.016	0.009	9.904	0.197	0.197	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.865	0.909	8.170	-1.094	-1.094	0.000	0.000	0.000	0.000
27	A	30	GLY	0	0.036	0.011	8.167	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	31	LYS	1	0.770	0.896	9.999	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.010	0.015	11.806	-0.195	-0.195	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.762	0.863	14.384	0.466	0.466	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.047	0.009	16.755	-0.102	-0.102	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.043	-0.035	19.824	0.118	0.118	0.000	0.000	0.000	0.000
33	A	36	ASN	0	0.001	0.003	22.659	-0.033	-0.033	0.000	0.000	0.000	0.000
34	A	37	ASN	0	0.008	-0.009	25.923	0.060	0.060	0.000	0.000	0.000	0.000
35	A	38	SER	0	0.029	-0.022	28.852	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	39	ASN	0	-0.025	-0.009	32.382	0.022	0.022	0.000	0.000	0.000	0.000
37	A	40	TYR	0	0.008	-0.004	35.712	0.017	0.017	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.867	0.929	37.851	0.163	0.163	0.000	0.000	0.000	0.000
39	A	42	ASN	0	-0.021	-0.010	38.892	0.003	0.003	0.000	0.000	0.000	0.000
40	A	43	ASP	-1	-0.857	-0.893	34.824	-0.189	-0.189	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.016	-0.022	32.339	0.024	0.024	0.000	0.000	0.000	0.000
42	A	45	MET	0	-0.044	-0.009	26.364	-0.035	-0.035	0.000	0.000	0.000	0.000
43	A	46	ILE	0	-0.006	0.006	26.387	0.010	0.010	0.000	0.000	0.000	0.000
44	A	47	ARG	1	0.948	0.956	22.761	0.039	0.039	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.893	0.964	22.210	0.468	0.468	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.834	-0.912	18.277	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	50	ALA	0	0.011	0.009	17.348	0.043	0.043	0.000	0.000	0.000	0.000
48	A	51	TYR	0	0.012	0.006	12.811	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.009	0.002	12.291	0.068	0.068	0.000	0.000	0.000	0.000
50	A	53	HIS	0	0.055	0.040	12.933	-0.310	-0.310	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.884	0.921	5.342	7.993	7.993	0.000	0.000	0.000	0.000
52	A	55	SER	0	0.031	-0.003	9.979	-0.697	-0.697	0.000	0.000	0.000	0.000
53	A	56	VAL	0	0.012	0.007	12.541	-0.188	-0.188	0.000	0.000	0.000	0.000
54	A	57	MET	0	-0.023	-0.008	7.165	0.139	0.139	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.791	-0.875	6.584	-10.931	-10.931	0.000	0.000	0.000	0.000
56	A	59	GLU	-1	-0.822	-0.898	9.497	-2.522	-2.522	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.054	-0.021	10.485	0.158	0.158	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.873	0.922	4.985	11.801	11.801	0.000	0.000	0.000	0.000
59	A	62	ARG	1	0.792	0.879	9.591	2.816	2.816	0.000	0.000	0.000	0.000
60	A	63	ILE	0	-0.023	-0.006	12.712	0.363	0.363	0.000	0.000	0.000	0.000
61	A	64	ILE	0	-0.039	-0.021	10.703	0.319	0.319	0.000	0.000	0.000	0.000
62	A	65	ASP	-1	-0.874	-0.939	10.290	-5.505	-5.505	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.833	-0.906	13.060	-2.038	-2.038	0.000	0.000	0.000	0.000
64	A	67	SER	0	-0.111	-0.063	15.627	0.333	0.333	0.000	0.000	0.000	0.000
65	A	68	GLU	-1	-0.934	-0.971	15.935	-1.414	-1.414	0.000	0.000	0.000	0.000
66	A	69	ILE	0	-0.012	-0.008	14.018	0.143	0.143	0.000	0.000	0.000	0.000
67	A	70	THR	0	-0.090	-0.081	10.717	0.287	0.287	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.806	0.892	13.664	2.519	2.519	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.896	-0.939	17.229	-0.896	-0.896	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.898	-0.966	18.134	-0.484	-0.484	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.821	-0.918	20.541	-0.497	-0.497	0.000	0.000	0.000	0.000
72	A	75	ALA	0	-0.005	0.004	22.349	0.064	0.064	0.000	0.000	0.000	0.000
73	A	76	LEU	0	-0.068	-0.036	24.862	0.053	0.053	0.000	0.000	0.000	0.000
74	A	77	TRP	0	-0.062	-0.035	20.204	0.008	0.008	0.000	0.000	0.000	0.000
75	A	78	PRO	0	-0.013	-0.006	26.819	0.050	0.050	0.000	0.000	0.000	0.000
76	A	79	PRO	0	0.072	0.051	26.783	-0.033	-0.033	0.000	0.000	0.000	0.000
77	A	80	PRO	0	-0.035	-0.024	24.968	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	81	ASP	-1	-0.770	-0.861	27.777	-0.233	-0.233	0.000	0.000	0.000	0.000
79	A	82	ARG	1	0.804	0.887	31.372	0.148	0.148	0.000	0.000	0.000	0.000
80	A	83	VAL	0	-0.032	-0.012	32.677	0.012	0.012	0.000	0.000	0.000	0.000
81	A	84	GLY	0	-0.046	-0.038	29.557	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	85	ARG	1	0.841	0.921	21.733	0.183	0.183	0.000	0.000	0.000	0.000
83	A	86	GLN	0	0.005	-0.003	22.168	-0.077	-0.077	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.787	-0.870	18.017	-0.203	-0.203	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.013	-0.007	14.822	-0.043	-0.043	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.858	-0.908	11.001	-0.154	-0.154	0.000	0.000	0.000	0.000
87	A	90	ILE	0	0.001	-0.010	9.176	-0.218	-0.218	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.781	-0.834	6.437	-1.780	-1.780	0.000	0.000	0.000	0.000
93	A	96	HIS	0	-0.025	-0.035	7.209	-1.239	-1.239	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.025	0.028	9.424	0.277	0.277	0.000	0.000	0.000	0.000
95	A	98	SER	0	-0.018	-0.027	11.986	-0.115	-0.115	0.000	0.000	0.000	0.000
96	A	99	PHE	0	0.034	0.041	14.599	0.075	0.075	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.069	-0.058	18.098	0.035	0.035	0.000	0.000	0.000	0.000
98	A	101	THR	0	0.003	-0.002	21.132	0.023	0.023	0.000	0.000	0.000	0.000
99	A	102	SER	0	-0.011	-0.027	24.462	0.013	0.013	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.819	0.908	26.266	0.296	0.296	0.000	0.000	0.000	0.000
101	A	104	ILE	0	0.032	0.026	25.036	0.028	0.028	0.000	0.000	0.000	0.000
102	A	105	GLY	0	-0.029	-0.008	28.797	-0.023	-0.023	0.000	0.000	0.000	0.000
103	A	106	SER	0	-0.043	-0.034	31.882	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	107	LEU	0	0.054	0.013	29.855	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	108	ILE	0	-0.029	-0.007	32.429	0.007	0.007	0.000	0.000	0.000	0.000
106	A	109	ASP	-1	-0.836	-0.919	31.488	-0.409	-0.409	0.000	0.000	0.000	0.000
107	A	110	VAL	0	0.021	0.022	28.193	0.005	0.005	0.000	0.000	0.000	0.000
108	A	111	ASN	0	-0.017	-0.006	30.613	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	112	GLN	0	-0.058	-0.018	33.718	0.036	0.036	0.000	0.000	0.000	0.000
110	A	113	SER	0	-0.028	-0.006	30.084	0.023	0.023	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.902	0.933	31.000	0.291	0.291	0.000	0.000	0.000	0.000
112	A	115	ASP	-1	-0.725	-0.823	25.044	-0.653	-0.653	0.000	0.000	0.000	0.000
113	A	116	PRO	0	-0.021	-0.002	27.386	-0.051	-0.051	0.000	0.000	0.000	0.000
114	A	117	GLU	0	-0.091	-0.088	25.260	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	118	GLY	0	0.149	0.090	22.992	-0.063	-0.063	0.000	0.000	0.000	0.000
116	A	119	LEU	0	-0.033	-0.023	22.952	-0.072	-0.072	0.000	0.000	0.000	0.000
117	A	120	ARG	1	0.856	0.920	25.163	0.670	0.670	0.000	0.000	0.000	0.000
118	A	121	VAL	0	0.045	0.038	19.878	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	122	PHE	0	0.012	0.001	19.091	-0.080	-0.080	0.000	0.000	0.000	0.000
120	A	123	TYR	0	-0.014	-0.021	21.469	-0.016	-0.016	0.000	0.000	0.000	0.000
121	A	124	TYR	0	-0.018	-0.003	23.845	0.061	0.061	0.000	0.000	0.000	0.000
122	A	125	LEU	0	0.108	0.071	15.757	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	126	VAL	0	-0.005	-0.013	19.471	-0.060	-0.060	0.000	0.000	0.000	0.000
124	A	127	GLN	0	-0.123	-0.067	20.976	0.093	0.093	0.000	0.000	0.000	0.000
125	A	128	ASP	-1	-0.872	-0.928	19.653	-1.403	-1.403	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.002	-0.007	14.791	-0.023	-0.023	0.000	0.000	0.000	0.000
127	A	130	LYS	1	0.876	0.950	18.460	0.886	0.886	0.000	0.000	0.000	0.000
128	A	131	CYS	0	-0.028	0.001	21.457	0.087	0.087	0.000	0.000	0.000	0.000
129	A	132	LEU	0	0.049	0.040	15.213	0.095	0.095	0.000	0.000	0.000	0.000
130	A	133	VAL	0	0.017	0.000	16.976	0.085	0.085	0.000	0.000	0.000	0.000
131	A	134	PHE	0	-0.033	-0.042	19.414	0.121	0.121	0.000	0.000	0.000	0.000
132	A	135	SER	0	-0.007	-0.005	21.957	0.118	0.118	0.000	0.000	0.000	0.000
133	A	136	LEU	0	-0.032	-0.007	16.575	0.082	0.082	0.000	0.000	0.000	0.000
134	A	137	ILE	0	-0.033	-0.025	20.289	0.114	0.114	0.000	0.000	0.000	0.000
135	A	138	GLY	0	-0.017	-0.008	22.566	0.099	0.099	0.000	0.000	0.000	0.000
136	A	139	LEU	0	-0.024	-0.031	23.439	0.074	0.074	0.000	0.000	0.000	0.000
137	A	140	HIS	0	0.002	0.017	22.139	-0.012	-0.012	0.000	0.000	0.000	0.000
138	A	141	PHE	0	-0.034	-0.022	21.529	0.063	0.063	0.000	0.000	0.000	0.000
139	A	142	LYS	1	0.880	0.955	26.794	0.519	0.519	0.000	0.000	0.000	0.000
140	A	143	ILE	0	0.038	0.021	29.681	-0.014	-0.014	0.000	0.000	0.000	0.000
141	A	144	LYS	1	0.878	0.927	32.895	0.427	0.427	0.000	0.000	0.000	0.000
142	A	145	PRO	0	-0.052	-0.038	34.194	0.016	0.016	0.000	0.000	0.000	0.000
143	A	146	ILE	-1	-0.836	-0.888	37.398	-0.351	-0.351	0.000	0.000	0.000	0.000

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