FMO DATABASE

FMODB ID: J4RN9

Calculation Name: 1ID0-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-adenylate ester

Ligand 3-letter code: ANP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1ID0

Chain ID: A

ChEMBL ID:

UniProt ID: P23837

Base Structure: X-ray

Registration Date: 2025-10-03

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1347493.869155
FMO2-HF: Nuclear repulsion	1290447.571529
FMO2-HF: Total energy	-57046.297626
FMO2-MP2: Total energy	-57212.042544

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:335:ARG)

Summations of interaction energy for fragment #1(A:335: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.
-371.592	-371.876	22.662	-9.878	-12.498	-0.124

Interaction energy analysis for fragmet #1(A:335:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.636 / q_NPA : 1.795

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	337	LEU	0	0.035	0.024	3.488	-5.721	-3.716	0.020	-0.904	-1.121	-0.001
4	A	338	HIS	1	0.816	0.896	4.029	95.398	95.681	-0.001	-0.036	-0.246	0.000
39	A	373	VAL	0	-0.018	-0.012	2.300	-11.364	-10.614	2.218	-1.019	-1.949	-0.016
40	A	374	GLY	0	0.034	-0.007	2.098	-0.475	0.602	2.644	-1.774	-1.946	-0.010
41	A	375	GLU	-1	-0.864	-0.912	1.675	-151.121	-156.000	17.781	-6.089	-6.813	-0.097
42	A	376	GLN	0	-0.006	-0.004	3.973	9.682	9.856	0.002	-0.026	-0.149	0.000
122	A	456	TYR	0	-0.109	-0.074	3.957	-9.582	-9.366	-0.001	-0.027	-0.188	0.000
146	A	480	HIS	-1	-0.969	-0.963	4.837	-77.715	-77.625	-0.001	-0.003	-0.086	0.000
5	A	339	PRO	0	0.046	0.028	8.473	1.153	1.153	0.000	0.000	0.000	0.000
6	A	340	VAL	0	0.034	0.012	11.288	0.245	0.245	0.000	0.000	0.000	0.000
7	A	341	ALA	0	0.034	0.024	13.439	1.282	1.282	0.000	0.000	0.000	0.000
8	A	342	PRO	0	0.033	0.000	14.693	1.074	1.074	0.000	0.000	0.000	0.000
9	A	343	LEU	0	-0.031	-0.005	9.958	0.433	0.433	0.000	0.000	0.000	0.000
10	A	344	LEU	0	0.042	0.014	14.414	1.191	1.191	0.000	0.000	0.000	0.000
11	A	345	ASP	-1	-0.905	-0.922	17.674	-26.159	-26.159	0.000	0.000	0.000	0.000
12	A	346	ASN	0	-0.021	-0.017	14.732	2.760	2.760	0.000	0.000	0.000	0.000
13	A	347	LEU	0	-0.031	-0.008	15.525	1.354	1.354	0.000	0.000	0.000	0.000
14	A	348	THR	0	0.036	0.009	18.927	1.655	1.655	0.000	0.000	0.000	0.000
15	A	349	SER	0	-0.019	-0.012	21.604	1.766	1.766	0.000	0.000	0.000	0.000
16	A	350	ALA	0	-0.078	-0.033	20.548	1.079	1.079	0.000	0.000	0.000	0.000
17	A	351	LEU	0	0.005	-0.013	21.115	1.210	1.210	0.000	0.000	0.000	0.000
18	A	352	ASN	0	0.043	0.017	24.398	1.276	1.276	0.000	0.000	0.000	0.000
19	A	353	LYS	1	0.920	0.964	24.891	23.785	23.785	0.000	0.000	0.000	0.000
20	A	354	VAL	0	-0.062	-0.022	24.694	0.778	0.778	0.000	0.000	0.000	0.000
21	A	355	TYR	0	-0.033	-0.042	26.076	1.142	1.142	0.000	0.000	0.000	0.000
22	A	356	GLN	0	0.026	0.029	30.197	0.380	0.380	0.000	0.000	0.000	0.000
23	A	357	ARG	1	0.882	0.926	32.198	16.369	16.369	0.000	0.000	0.000	0.000
24	A	358	LYS	1	0.724	0.849	31.897	19.546	19.546	0.000	0.000	0.000	0.000
25	A	359	GLY	0	-0.006	0.013	34.111	0.200	0.200	0.000	0.000	0.000	0.000
26	A	360	VAL	0	0.001	0.001	29.232	0.122	0.122	0.000	0.000	0.000	0.000
27	A	361	ASN	0	-0.015	-0.003	30.792	-0.455	-0.455	0.000	0.000	0.000	0.000
28	A	362	ILE	0	-0.001	-0.001	24.507	-0.247	-0.247	0.000	0.000	0.000	0.000
29	A	363	SER	0	-0.021	-0.002	26.853	0.132	0.132	0.000	0.000	0.000	0.000
30	A	364	LEU	0	-0.022	-0.025	21.192	-0.882	-0.882	0.000	0.000	0.000	0.000
31	A	365	ASP	-1	-0.901	-0.942	23.337	-23.290	-23.290	0.000	0.000	0.000	0.000
32	A	366	ILE	0	-0.071	-0.050	17.137	-1.214	-1.214	0.000	0.000	0.000	0.000
33	A	367	SER	0	-0.028	-0.034	18.817	1.204	1.204	0.000	0.000	0.000	0.000
34	A	368	PRO	0	-0.014	-0.026	17.531	-1.802	-1.802	0.000	0.000	0.000	0.000
35	A	369	GLU	-1	-0.846	-0.894	15.243	-34.548	-34.548	0.000	0.000	0.000	0.000
36	A	370	ILE	0	-0.022	0.010	13.441	-3.206	-3.206	0.000	0.000	0.000	0.000
37	A	371	SER	0	-0.041	-0.038	9.182	-0.393	-0.393	0.000	0.000	0.000	0.000
38	A	372	PHE	0	0.003	0.012	5.944	-0.227	-0.227	0.000	0.000	0.000	0.000
43	A	377	ASN	0	0.010	-0.007	6.411	5.949	5.949	0.000	0.000	0.000	0.000
44	A	378	ASP	-1	-0.745	-0.850	6.736	-62.884	-62.884	0.000	0.000	0.000	0.000
45	A	379	PHE	0	0.032	0.010	8.724	5.467	5.467	0.000	0.000	0.000	0.000
46	A	380	VAL	0	0.000	-0.008	10.387	4.495	4.495	0.000	0.000	0.000	0.000
47	A	381	GLU	-1	-0.914	-0.960	11.921	-38.172	-38.172	0.000	0.000	0.000	0.000
48	A	382	VAL	0	-0.026	-0.005	12.556	3.392	3.392	0.000	0.000	0.000	0.000
49	A	383	MET	0	0.001	0.006	13.898	2.750	2.750	0.000	0.000	0.000	0.000
50	A	384	GLY	0	0.034	0.014	16.018	2.211	2.211	0.000	0.000	0.000	0.000
51	A	385	ASN	0	-0.006	-0.005	17.663	2.690	2.690	0.000	0.000	0.000	0.000
52	A	386	VAL	0	-0.021	-0.005	18.630	1.736	1.736	0.000	0.000	0.000	0.000
53	A	387	LEU	0	0.038	0.017	19.543	1.480	1.480	0.000	0.000	0.000	0.000
54	A	388	ASP	-1	-0.715	-0.795	21.857	-22.398	-22.398	0.000	0.000	0.000	0.000
55	A	389	ASN	0	-0.061	-0.039	23.198	2.044	2.044	0.000	0.000	0.000	0.000
56	A	390	ALA	0	0.054	0.045	24.780	0.986	0.986	0.000	0.000	0.000	0.000
57	A	391	CYS	0	0.024	0.002	25.264	0.904	0.904	0.000	0.000	0.000	0.000
58	A	392	LYS	1	0.856	0.936	27.794	21.423	21.423	0.000	0.000	0.000	0.000
59	A	393	TYR	0	-0.043	-0.047	28.112	1.076	1.076	0.000	0.000	0.000	0.000
60	A	394	CYS	0	-0.014	0.039	30.020	0.624	0.624	0.000	0.000	0.000	0.000
61	A	395	LEU	0	-0.077	-0.028	32.066	0.429	0.429	0.000	0.000	0.000	0.000
62	A	396	GLU	-1	-0.974	-1.000	34.750	-16.609	-16.609	0.000	0.000	0.000	0.000
63	A	397	PHE	0	-0.026	-0.016	31.825	-0.501	-0.501	0.000	0.000	0.000	0.000
64	A	398	VAL	0	-0.022	-0.030	25.384	-0.284	-0.284	0.000	0.000	0.000	0.000
65	A	399	GLU	-1	-0.917	-0.946	26.668	-20.717	-20.717	0.000	0.000	0.000	0.000
66	A	400	ILE	0	-0.040	-0.024	20.080	-0.801	-0.801	0.000	0.000	0.000	0.000
67	A	401	SER	0	0.039	0.028	21.543	0.041	0.041	0.000	0.000	0.000	0.000
68	A	402	ALA	0	-0.005	-0.010	16.205	-1.203	-1.203	0.000	0.000	0.000	0.000
69	A	403	ARG	1	0.921	0.972	16.884	31.172	31.172	0.000	0.000	0.000	0.000
70	A	404	GLN	0	0.033	0.015	12.106	-3.487	-3.487	0.000	0.000	0.000	0.000
71	A	405	THR	0	-0.041	-0.026	13.715	1.837	1.837	0.000	0.000	0.000	0.000
72	A	406	ASP	-1	-0.890	-0.948	12.182	-38.357	-38.357	0.000	0.000	0.000	0.000
73	A	407	GLU	-1	-0.922	-0.958	9.834	-45.251	-45.251	0.000	0.000	0.000	0.000
74	A	408	HIS	0	-0.041	-0.013	10.136	-3.259	-3.259	0.000	0.000	0.000	0.000
75	A	409	LEU	0	-0.015	0.006	9.991	1.933	1.933	0.000	0.000	0.000	0.000
76	A	410	TYR	0	-0.049	-0.034	12.069	0.590	0.590	0.000	0.000	0.000	0.000
77	A	411	ILE	0	0.005	-0.008	13.761	0.287	0.287	0.000	0.000	0.000	0.000
78	A	412	VAL	0	-0.022	-0.010	17.105	0.464	0.464	0.000	0.000	0.000	0.000
79	A	413	VAL	0	-0.002	-0.002	20.100	-0.056	-0.056	0.000	0.000	0.000	0.000
80	A	414	GLU	-1	-0.803	-0.905	22.770	-21.578	-21.578	0.000	0.000	0.000	0.000
81	A	415	ASP	-1	-0.783	-0.889	26.573	-20.966	-20.966	0.000	0.000	0.000	0.000
82	A	416	ASP	-1	-0.679	-0.823	29.468	-18.216	-18.216	0.000	0.000	0.000	0.000
83	A	417	GLY	0	0.032	0.023	32.184	0.567	0.567	0.000	0.000	0.000	0.000
84	A	418	PRO	0	-0.094	-0.051	33.510	0.277	0.277	0.000	0.000	0.000	0.000
85	A	419	GLY	0	0.069	0.043	31.521	0.178	0.178	0.000	0.000	0.000	0.000
86	A	420	ILE	0	-0.012	-0.002	26.988	0.059	0.059	0.000	0.000	0.000	0.000
87	A	421	PRO	0	0.026	0.005	31.403	0.100	0.100	0.000	0.000	0.000	0.000
88	A	422	LEU	0	0.093	0.045	32.340	-0.377	-0.377	0.000	0.000	0.000	0.000
89	A	423	SER	0	-0.001	-0.007	32.429	-0.505	-0.505	0.000	0.000	0.000	0.000
90	A	424	LYS	1	0.852	0.906	31.350	17.710	17.710	0.000	0.000	0.000	0.000
91	A	425	ARG	1	0.801	0.892	28.097	18.851	18.851	0.000	0.000	0.000	0.000
92	A	426	GLU	-1	-0.914	-0.940	26.663	-21.197	-21.197	0.000	0.000	0.000	0.000
93	A	427	VAL	0	0.049	0.002	26.379	-0.592	-0.592	0.000	0.000	0.000	0.000
94	A	428	ILE	0	-0.052	-0.015	25.222	-0.084	-0.084	0.000	0.000	0.000	0.000
95	A	429	PHE	0	-0.045	-0.023	20.887	-0.894	-0.894	0.000	0.000	0.000	0.000
96	A	430	ASP	-1	-0.847	-0.915	22.862	-23.828	-23.828	0.000	0.000	0.000	0.000
97	A	431	ARG	1	0.778	0.845	18.894	28.307	28.307	0.000	0.000	0.000	0.000
98	A	432	GLY	0	0.048	0.035	25.394	0.879	0.879	0.000	0.000	0.000	0.000
99	A	433	GLN	0	-0.029	-0.026	27.482	-0.434	-0.434	0.000	0.000	0.000	0.000
100	A	434	ARG	1	0.867	0.935	21.630	25.852	25.852	0.000	0.000	0.000	0.000
101	A	435	VAL	0	0.002	-0.007	27.158	-0.473	-0.473	0.000	0.000	0.000	0.000
102	A	436	ASP	-1	-0.885	-0.954	28.660	-19.071	-19.071	0.000	0.000	0.000	0.000
103	A	437	THR	0	-0.036	-0.005	26.957	0.122	0.122	0.000	0.000	0.000	0.000
104	A	438	LEU	0	-0.010	0.006	25.166	-0.644	-0.644	0.000	0.000	0.000	0.000
105	A	439	ARG	1	0.811	0.865	25.584	22.821	22.821	0.000	0.000	0.000	0.000
106	A	440	PRO	0	0.005	-0.030	24.680	-0.725	-0.725	0.000	0.000	0.000	0.000
107	A	441	GLY	0	0.014	0.022	23.094	-0.636	-0.636	0.000	0.000	0.000	0.000
108	A	442	GLN	0	-0.109	-0.045	22.869	-0.767	-0.767	0.000	0.000	0.000	0.000
109	A	443	GLY	0	0.094	0.058	19.269	-0.884	-0.884	0.000	0.000	0.000	0.000
110	A	444	VAL	0	0.015	0.002	15.184	1.617	1.617	0.000	0.000	0.000	0.000
111	A	445	GLY	0	-0.045	-0.019	18.585	0.868	0.868	0.000	0.000	0.000	0.000
112	A	446	LEU	0	0.022	-0.007	19.691	-1.337	-1.337	0.000	0.000	0.000	0.000
113	A	447	ALA	0	0.011	0.019	19.879	-0.993	-0.993	0.000	0.000	0.000	0.000
114	A	448	VAL	0	0.009	0.013	15.713	-0.702	-0.702	0.000	0.000	0.000	0.000
115	A	449	ALA	0	0.001	0.002	15.540	-2.074	-2.074	0.000	0.000	0.000	0.000
116	A	450	ARG	1	0.924	0.971	15.039	26.126	26.126	0.000	0.000	0.000	0.000
117	A	451	GLU	-1	-0.770	-0.854	15.409	-32.052	-32.052	0.000	0.000	0.000	0.000
118	A	452	ILE	0	0.005	0.003	10.121	-1.883	-1.883	0.000	0.000	0.000	0.000
119	A	453	THR	0	-0.050	-0.044	10.824	-2.674	-2.674	0.000	0.000	0.000	0.000
120	A	454	GLU	-1	-0.895	-0.951	11.763	-33.778	-33.778	0.000	0.000	0.000	0.000
121	A	455	GLN	0	-0.078	-0.031	8.473	2.312	2.312	0.000	0.000	0.000	0.000
123	A	457	GLU	-1	-0.877	-0.920	9.065	-47.594	-47.594	0.000	0.000	0.000	0.000
124	A	458	GLY	0	-0.004	0.008	12.195	1.797	1.797	0.000	0.000	0.000	0.000
125	A	459	LYS	1	0.909	0.953	13.460	30.739	30.739	0.000	0.000	0.000	0.000
126	A	460	ILE	0	0.008	0.009	16.146	-0.575	-0.575	0.000	0.000	0.000	0.000
127	A	461	VAL	0	-0.049	-0.022	18.481	1.027	1.027	0.000	0.000	0.000	0.000
128	A	462	ALA	0	0.025	0.006	22.004	-0.197	-0.197	0.000	0.000	0.000	0.000
129	A	463	GLY	0	-0.047	-0.037	25.014	0.532	0.532	0.000	0.000	0.000	0.000
130	A	464	GLU	-1	-0.909	-0.925	27.917	-17.849	-17.849	0.000	0.000	0.000	0.000
131	A	465	SER	0	-0.029	-0.021	29.164	-0.211	-0.211	0.000	0.000	0.000	0.000
132	A	466	MET	0	-0.005	-0.006	30.222	0.809	0.809	0.000	0.000	0.000	0.000
133	A	467	LEU	0	-0.041	-0.017	30.873	0.695	0.695	0.000	0.000	0.000	0.000
134	A	468	GLY	0	-0.021	-0.001	33.692	0.451	0.451	0.000	0.000	0.000	0.000
135	A	469	GLY	0	0.011	0.026	32.180	0.243	0.243	0.000	0.000	0.000	0.000
136	A	470	ALA	0	-0.069	-0.055	27.594	-0.097	-0.097	0.000	0.000	0.000	0.000
137	A	471	ARG	1	0.854	0.913	23.504	23.923	23.923	0.000	0.000	0.000	0.000
138	A	472	MET	0	-0.067	-0.033	21.506	0.375	0.375	0.000	0.000	0.000	0.000
139	A	473	GLU	-1	-0.872	-0.921	19.551	-28.090	-28.090	0.000	0.000	0.000	0.000
140	A	474	VAL	0	-0.030	-0.020	14.133	0.067	0.067	0.000	0.000	0.000	0.000
141	A	475	ILE	0	-0.017	-0.010	14.103	-0.475	-0.475	0.000	0.000	0.000	0.000
142	A	476	PHE	0	0.014	-0.002	8.901	-0.184	-0.184	0.000	0.000	0.000	0.000
143	A	477	GLY	0	0.115	0.059	10.514	0.359	0.359	0.000	0.000	0.000	0.000
144	A	478	ARG	1	0.832	0.891	6.313	56.222	56.222	0.000	0.000	0.000	0.000
145	A	479	GLN	0	-0.063	-0.043	5.614	-9.657	-9.657	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:335:ARG)