FMO DATABASE

FMODB ID: 64NMZ

Calculation Name: 1VKK-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VKK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ERL7

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1365530.241466
FMO2-HF: Nuclear repulsion	1308145.173537
FMO2-HF: Total energy	-57385.067929
FMO2-MP2: Total energy	-57550.381388

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:6:VAL)

Summations of interaction energy for fragment #1(A:6:VAL)

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.
-16.967	-12.013	1.606	-1.984	-4.575	-0.018

Interaction energy analysis for fragmet #1(A:6:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.919

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	8	CYS	0	-0.007	0.012	3.297	0.779	3.071	0.140	-0.747	-1.685	-0.004
4	A	9	GLU	-1	-0.848	-0.923	4.088	-22.583	-22.514	0.000	-0.013	-0.057	0.000
33	A	38	LYS	1	0.887	0.905	4.728	34.474	34.553	-0.001	-0.001	-0.076	0.000
36	A	41	GLN	0	-0.026	-0.005	2.641	-9.655	-7.902	1.306	-1.076	-1.984	-0.014
37	A	42	MET	0	-0.031	-0.009	4.903	-0.200	-0.145	-0.001	-0.002	-0.051	0.000
98	A	103	MET	0	-0.032	0.000	2.723	-5.706	-5.081	0.164	-0.130	-0.659	0.000
99	A	104	TYR	0	0.022	0.025	4.669	-1.794	-1.774	-0.001	-0.008	-0.010	0.000
102	A	107	SER	0	-0.010	-0.020	4.750	-1.783	-1.722	-0.001	-0.007	-0.053	0.000
5	A	10	VAL	0	-0.032	-0.008	7.326	-0.631	-0.631	0.000	0.000	0.000	0.000
6	A	11	ASP	-1	-0.728	-0.864	10.450	-17.710	-17.710	0.000	0.000	0.000	0.000
7	A	12	PRO	0	-0.004	-0.020	12.455	0.737	0.737	0.000	0.000	0.000	0.000
8	A	13	GLU	-1	-0.883	-0.929	15.651	-13.817	-13.817	0.000	0.000	0.000	0.000
9	A	14	LEU	0	-0.033	-0.001	13.071	0.661	0.661	0.000	0.000	0.000	0.000
10	A	15	LYS	1	0.858	0.936	12.351	21.022	21.022	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.781	-0.857	17.029	-11.670	-11.670	0.000	0.000	0.000	0.000
12	A	17	THR	0	-0.032	-0.020	19.457	0.741	0.741	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.001	-0.015	15.914	0.471	0.471	0.000	0.000	0.000	0.000
14	A	19	ARG	1	0.846	0.905	20.228	12.477	12.477	0.000	0.000	0.000	0.000
15	A	20	LYS	1	0.864	0.908	22.481	12.350	12.350	0.000	0.000	0.000	0.000
16	A	21	PHE	0	0.006	0.002	22.974	0.401	0.401	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.836	0.908	22.158	13.382	13.382	0.000	0.000	0.000	0.000
18	A	23	PHE	0	-0.077	-0.037	25.283	0.297	0.297	0.000	0.000	0.000	0.000
19	A	24	ARG	1	0.846	0.927	27.341	10.693	10.693	0.000	0.000	0.000	0.000
20	A	25	LYS	1	0.924	0.948	29.928	8.608	8.608	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.889	-0.932	32.072	-9.121	-9.121	0.000	0.000	0.000	0.000
22	A	27	THR	0	-0.034	-0.018	33.264	-0.188	-0.188	0.000	0.000	0.000	0.000
23	A	28	ASN	0	-0.005	-0.012	32.988	0.003	0.003	0.000	0.000	0.000	0.000
24	A	29	ASN	0	0.049	0.029	30.037	-0.158	-0.158	0.000	0.000	0.000	0.000
25	A	30	ALA	0	0.003	0.003	27.520	0.168	0.168	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.005	0.002	22.971	-0.240	-0.240	0.000	0.000	0.000	0.000
27	A	32	ILE	0	0.024	0.030	18.552	0.090	0.090	0.000	0.000	0.000	0.000
28	A	33	ILE	0	0.050	0.020	17.469	-0.585	-0.585	0.000	0.000	0.000	0.000
29	A	34	MET	0	-0.025	-0.001	13.642	-0.328	-0.328	0.000	0.000	0.000	0.000
30	A	35	LYS	1	0.911	0.934	11.869	17.915	17.915	0.000	0.000	0.000	0.000
31	A	36	VAL	0	-0.031	-0.021	5.192	-0.624	-0.624	0.000	0.000	0.000	0.000
32	A	37	ASP	-1	-0.851	-0.913	8.563	-22.693	-22.693	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.917	-0.940	5.740	-28.330	-28.330	0.000	0.000	0.000	0.000
35	A	40	ARG	1	0.833	0.892	7.836	20.314	20.314	0.000	0.000	0.000	0.000
38	A	43	VAL	0	-0.021	-0.006	7.401	0.156	0.156	0.000	0.000	0.000	0.000
39	A	44	VAL	0	0.026	0.000	9.490	1.178	1.178	0.000	0.000	0.000	0.000
40	A	45	LEU	0	0.017	0.001	12.748	-0.293	-0.293	0.000	0.000	0.000	0.000
41	A	46	GLU	-1	-0.853	-0.870	16.202	-17.364	-17.364	0.000	0.000	0.000	0.000
42	A	47	ASP	-1	-0.819	-0.916	17.824	-12.585	-12.585	0.000	0.000	0.000	0.000
43	A	48	GLU	-1	-0.940	-0.988	20.966	-12.498	-12.498	0.000	0.000	0.000	0.000
44	A	49	LEU	0	0.007	0.017	23.673	0.496	0.496	0.000	0.000	0.000	0.000
45	A	50	GLN	0	0.041	0.000	26.573	0.191	0.191	0.000	0.000	0.000	0.000
46	A	51	ASN	0	-0.035	-0.015	29.870	0.279	0.279	0.000	0.000	0.000	0.000
47	A	52	ILE	0	0.034	0.063	25.918	0.154	0.154	0.000	0.000	0.000	0.000
48	A	53	SER	0	-0.014	-0.040	29.587	-0.191	-0.191	0.000	0.000	0.000	0.000
49	A	54	PRO	0	0.021	-0.014	27.788	-0.300	-0.300	0.000	0.000	0.000	0.000
50	A	55	GLU	-1	-0.855	-0.907	27.683	-9.721	-9.721	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.764	-0.856	28.736	-9.716	-9.716	0.000	0.000	0.000	0.000
52	A	57	LEU	0	-0.006	-0.006	22.158	-0.375	-0.375	0.000	0.000	0.000	0.000
53	A	58	LYS	1	0.814	0.890	23.904	9.782	9.782	0.000	0.000	0.000	0.000
54	A	59	LEU	0	-0.043	-0.021	24.530	-0.283	-0.283	0.000	0.000	0.000	0.000
55	A	60	GLU	-1	-0.915	-0.949	23.371	-11.594	-11.594	0.000	0.000	0.000	0.000
56	A	61	LEU	0	-0.083	-0.033	18.584	-0.916	-0.916	0.000	0.000	0.000	0.000
57	A	62	PRO	0	-0.019	-0.015	17.322	0.246	0.246	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.795	-0.887	18.965	-12.755	-12.755	0.000	0.000	0.000	0.000
59	A	64	ARG	1	0.825	0.890	18.609	12.961	12.961	0.000	0.000	0.000	0.000
60	A	65	GLN	0	-0.057	-0.036	14.039	-0.419	-0.419	0.000	0.000	0.000	0.000
61	A	66	PRO	0	-0.029	-0.004	10.802	0.639	0.639	0.000	0.000	0.000	0.000
62	A	67	ARG	1	0.794	0.869	13.237	18.007	18.007	0.000	0.000	0.000	0.000
63	A	68	PHE	0	-0.028	-0.008	8.686	-0.242	-0.242	0.000	0.000	0.000	0.000
64	A	69	VAL	0	0.027	0.024	14.625	0.434	0.434	0.000	0.000	0.000	0.000
65	A	70	VAL	0	-0.014	-0.005	18.154	-0.301	-0.301	0.000	0.000	0.000	0.000
66	A	71	TYR	0	-0.037	-0.042	20.446	0.402	0.402	0.000	0.000	0.000	0.000
67	A	72	SER	0	-0.011	0.008	24.003	0.195	0.195	0.000	0.000	0.000	0.000
68	A	73	TYR	0	-0.017	-0.048	27.243	0.159	0.159	0.000	0.000	0.000	0.000
69	A	74	LYS	1	0.946	0.975	29.772	8.311	8.311	0.000	0.000	0.000	0.000
70	A	75	TYR	0	-0.011	-0.010	32.219	0.147	0.147	0.000	0.000	0.000	0.000
71	A	76	VAL	0	-0.010	-0.006	34.465	0.143	0.143	0.000	0.000	0.000	0.000
72	A	77	HIS	0	-0.043	-0.037	37.104	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.881	-0.942	40.010	-7.670	-7.670	0.000	0.000	0.000	0.000
74	A	79	ASP	-1	-0.835	-0.894	42.938	-7.176	-7.176	0.000	0.000	0.000	0.000
75	A	80	GLY	0	0.000	0.005	43.682	0.146	0.146	0.000	0.000	0.000	0.000
76	A	81	ARG	1	0.819	0.898	40.781	7.558	7.558	0.000	0.000	0.000	0.000
77	A	82	VAL	0	-0.013	-0.011	37.047	-0.137	-0.137	0.000	0.000	0.000	0.000
78	A	83	SER	0	-0.050	-0.021	34.496	0.014	0.014	0.000	0.000	0.000	0.000
79	A	84	TYR	0	0.061	0.020	32.088	0.032	0.032	0.000	0.000	0.000	0.000
80	A	85	PRO	0	-0.081	-0.023	28.598	-0.194	-0.194	0.000	0.000	0.000	0.000
81	A	86	LEU	0	0.047	0.032	23.593	-0.058	-0.058	0.000	0.000	0.000	0.000
82	A	87	CYS	0	-0.040	-0.018	23.672	0.027	0.027	0.000	0.000	0.000	0.000
83	A	88	PHE	0	0.038	0.011	13.718	-0.437	-0.437	0.000	0.000	0.000	0.000
84	A	89	ILE	0	0.013	0.003	18.782	0.343	0.343	0.000	0.000	0.000	0.000
85	A	90	PHE	0	-0.065	-0.030	11.014	-0.917	-0.917	0.000	0.000	0.000	0.000
86	A	91	SER	0	0.049	0.035	15.895	0.684	0.684	0.000	0.000	0.000	0.000
87	A	92	SER	0	0.046	0.010	14.312	-2.036	-2.036	0.000	0.000	0.000	0.000
88	A	93	PRO	0	0.039	0.034	15.420	0.140	0.140	0.000	0.000	0.000	0.000
89	A	94	VAL	0	0.000	-0.011	16.864	-1.039	-1.039	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.007	0.021	18.752	-0.019	-0.019	0.000	0.000	0.000	0.000
91	A	96	CYS	0	-0.083	-0.018	14.060	-0.601	-0.601	0.000	0.000	0.000	0.000
92	A	97	LYS	1	1.000	0.987	11.933	19.938	19.938	0.000	0.000	0.000	0.000
93	A	98	PRO	0	0.069	0.019	11.344	-1.745	-1.745	0.000	0.000	0.000	0.000
94	A	99	GLU	-1	-0.901	-0.942	6.134	-35.666	-35.666	0.000	0.000	0.000	0.000
95	A	100	GLN	0	0.011	-0.007	6.570	-3.572	-3.572	0.000	0.000	0.000	0.000
96	A	101	GLN	0	0.037	0.000	8.215	-2.878	-2.878	0.000	0.000	0.000	0.000
97	A	102	MET	0	0.036	0.018	5.305	-1.186	-1.186	0.000	0.000	0.000	0.000
100	A	105	ALA	0	0.019	-0.002	7.442	0.429	0.429	0.000	0.000	0.000	0.000
101	A	106	GLY	0	-0.009	-0.009	5.556	1.946	1.946	0.000	0.000	0.000	0.000
103	A	108	LYS	1	0.901	0.973	7.138	25.079	25.079	0.000	0.000	0.000	0.000
104	A	109	ASN	0	0.016	-0.001	10.798	2.508	2.508	0.000	0.000	0.000	0.000
105	A	110	ARG	1	0.923	0.960	5.756	37.211	37.211	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.020	0.020	10.928	1.779	1.779	0.000	0.000	0.000	0.000
107	A	112	VAL	0	-0.008	-0.005	12.417	1.537	1.537	0.000	0.000	0.000	0.000
108	A	113	GLN	0	-0.019	-0.010	14.521	0.513	0.513	0.000	0.000	0.000	0.000
109	A	114	THR	0	-0.018	-0.019	13.232	0.892	0.892	0.000	0.000	0.000	0.000
110	A	115	ALA	0	0.006	0.013	15.714	0.891	0.891	0.000	0.000	0.000	0.000
111	A	116	GLU	-1	-0.927	-0.953	18.259	-12.400	-12.400	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.072	-0.037	18.852	0.794	0.794	0.000	0.000	0.000	0.000
113	A	118	THR	0	0.029	0.002	20.364	-0.504	-0.504	0.000	0.000	0.000	0.000
114	A	119	LYS	1	0.885	0.967	23.056	11.114	11.114	0.000	0.000	0.000	0.000
115	A	120	VAL	0	-0.010	0.004	17.543	-0.198	-0.198	0.000	0.000	0.000	0.000
116	A	121	PHE	0	-0.018	-0.013	20.248	0.293	0.293	0.000	0.000	0.000	0.000
117	A	122	GLU	-1	-0.888	-0.956	15.650	-21.114	-21.114	0.000	0.000	0.000	0.000
118	A	123	ILE	0	0.018	0.027	18.637	0.658	0.658	0.000	0.000	0.000	0.000
119	A	124	ARG	1	0.891	0.925	16.138	17.116	17.116	0.000	0.000	0.000	0.000
120	A	125	THR	0	0.014	0.018	20.355	-0.398	-0.398	0.000	0.000	0.000	0.000
121	A	126	THR	0	0.067	0.026	21.005	-0.312	-0.312	0.000	0.000	0.000	0.000
122	A	127	ASP	-1	-0.908	-0.959	22.975	-11.221	-11.221	0.000	0.000	0.000	0.000
123	A	128	ASP	-1	-0.876	-0.947	24.202	-12.196	-12.196	0.000	0.000	0.000	0.000
124	A	129	LEU	0	-0.090	-0.026	22.556	0.166	0.166	0.000	0.000	0.000	0.000
125	A	130	THR	0	0.039	0.012	25.896	0.419	0.419	0.000	0.000	0.000	0.000
126	A	131	GLU	-1	-0.811	-0.898	29.337	-9.432	-9.432	0.000	0.000	0.000	0.000
127	A	132	THR	0	-0.002	0.002	31.640	0.011	0.011	0.000	0.000	0.000	0.000
128	A	133	TRP	0	0.064	0.036	22.900	-0.115	-0.115	0.000	0.000	0.000	0.000
129	A	134	LEU	0	-0.005	0.001	26.130	-0.201	-0.201	0.000	0.000	0.000	0.000
130	A	135	LYS	1	0.907	0.938	28.812	8.559	8.559	0.000	0.000	0.000	0.000
131	A	136	GLU	-1	-0.890	-0.948	31.325	-9.493	-9.493	0.000	0.000	0.000	0.000
132	A	137	LYS	1	0.880	0.940	24.672	12.484	12.484	0.000	0.000	0.000	0.000
133	A	138	LEU	0	-0.031	-0.038	27.461	-0.172	-0.172	0.000	0.000	0.000	0.000
134	A	139	ALA	0	-0.009	0.004	29.937	0.144	0.144	0.000	0.000	0.000	0.000
135	A	140	PHE	0	-0.040	-0.013	27.679	0.145	0.145	0.000	0.000	0.000	0.000
136	A	141	PHE	0	-0.044	-0.030	25.613	-0.182	-0.182	0.000	0.000	0.000	0.000
137	A	142	ARG	0	-0.030	0.014	31.637	0.665	0.665	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:VAL)