FMO DATABASE

FMODB ID: 67RJZ

Calculation Name: 4YTD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4YTD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8BR07

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	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-457787.906497
FMO2-HF: Nuclear repulsion	417821.21194
FMO2-HF: Total energy	-39966.694557
FMO2-MP2: Total energy	-40079.422567

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:708:GLY)

Summations of interaction energy for fragment #1(A:708:GLY)

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.
40.208	41.758	-0.006	-0.688	-0.856	-0.003

Interaction energy analysis for fragmet #1(A:708:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.901 / q_NPA : 0.935

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	710	GLY	0	0.082	0.048	3.841	9.613	11.163	-0.006	-0.688	-0.856	-0.003
4	A	711	ASN	0	0.009	-0.015	5.669	-0.705	-0.705	0.000	0.000	0.000	0.000
5	A	712	LYS	1	0.986	0.990	6.279	46.279	46.279	0.000	0.000	0.000	0.000
6	A	713	TYR	0	0.055	0.047	9.008	2.804	2.804	0.000	0.000	0.000	0.000
7	A	714	GLU	-1	-0.800	-0.907	10.251	-21.945	-21.945	0.000	0.000	0.000	0.000
8	A	715	ASN	0	-0.022	-0.012	11.920	1.638	1.638	0.000	0.000	0.000	0.000
9	A	716	GLU	-1	-0.927	-0.959	13.560	-19.875	-19.875	0.000	0.000	0.000	0.000
10	A	717	LYS	1	0.886	0.931	14.624	22.291	22.291	0.000	0.000	0.000	0.000
11	A	718	ALA	0	-0.029	0.012	16.327	1.318	1.318	0.000	0.000	0.000	0.000
12	A	719	MET	0	0.078	0.041	16.262	1.224	1.224	0.000	0.000	0.000	0.000
13	A	720	VAL	0	0.006	0.014	19.450	1.181	1.181	0.000	0.000	0.000	0.000
14	A	721	THR	0	-0.029	-0.024	20.279	1.059	1.059	0.000	0.000	0.000	0.000
15	A	722	GLU	-1	-0.921	-0.959	20.240	-14.736	-14.736	0.000	0.000	0.000	0.000
16	A	723	THR	0	-0.029	-0.026	23.489	0.856	0.856	0.000	0.000	0.000	0.000
17	A	724	MET	0	-0.017	-0.013	25.041	0.913	0.913	0.000	0.000	0.000	0.000
18	A	725	THR	0	-0.039	-0.027	26.163	0.628	0.628	0.000	0.000	0.000	0.000
19	A	726	LYS	1	0.957	0.980	28.280	11.082	11.082	0.000	0.000	0.000	0.000
20	A	727	LEU	0	0.058	0.024	28.899	0.404	0.404	0.000	0.000	0.000	0.000
21	A	728	ARG	1	0.895	0.943	29.124	11.071	11.071	0.000	0.000	0.000	0.000
22	A	729	ASN	0	-0.008	-0.005	32.134	0.456	0.456	0.000	0.000	0.000	0.000
23	A	730	GLU	-1	-0.935	-0.956	34.310	-9.055	-9.055	0.000	0.000	0.000	0.000
24	A	731	LEU	0	-0.018	-0.027	34.134	0.309	0.309	0.000	0.000	0.000	0.000
25	A	732	LYS	1	0.805	0.902	37.021	8.421	8.421	0.000	0.000	0.000	0.000
26	A	733	ALA	0	0.064	0.035	38.818	0.225	0.225	0.000	0.000	0.000	0.000
27	A	734	LEU	0	0.042	0.015	38.969	0.220	0.220	0.000	0.000	0.000	0.000
28	A	735	LYS	1	0.891	0.943	38.522	8.485	8.485	0.000	0.000	0.000	0.000
29	A	736	GLU	-1	-0.883	-0.926	42.322	-7.639	-7.639	0.000	0.000	0.000	0.000
30	A	737	ASP	-1	-0.866	-0.926	44.942	-7.009	-7.009	0.000	0.000	0.000	0.000
31	A	738	ALA	0	-0.019	-0.008	45.966	0.197	0.197	0.000	0.000	0.000	0.000
32	A	739	ALA	0	-0.045	-0.015	47.514	0.152	0.152	0.000	0.000	0.000	0.000
33	A	740	THR	0	-0.019	-0.018	49.304	0.201	0.201	0.000	0.000	0.000	0.000
34	A	741	PHE	0	0.025	0.024	47.856	0.173	0.173	0.000	0.000	0.000	0.000
35	A	742	SER	0	-0.002	-0.012	53.000	0.108	0.108	0.000	0.000	0.000	0.000
36	A	743	SER	0	-0.032	-0.016	55.270	0.127	0.127	0.000	0.000	0.000	0.000
37	A	744	LEU	0	0.026	0.016	53.889	0.125	0.125	0.000	0.000	0.000	0.000
38	A	745	ARG	1	0.960	0.971	54.353	5.981	5.981	0.000	0.000	0.000	0.000
39	A	746	ALA	0	0.028	0.026	58.847	0.092	0.092	0.000	0.000	0.000	0.000
40	A	747	MET	0	0.005	0.020	60.899	0.107	0.107	0.000	0.000	0.000	0.000
41	A	748	PHE	0	-0.016	-0.024	57.311	0.069	0.069	0.000	0.000	0.000	0.000
42	A	749	ALA	0	0.024	0.020	62.891	0.077	0.077	0.000	0.000	0.000	0.000
43	A	750	THR	0	0.027	0.005	64.801	0.086	0.086	0.000	0.000	0.000	0.000
44	A	751	ARG	1	0.810	0.885	65.872	4.923	4.923	0.000	0.000	0.000	0.000
45	A	752	CYS	0	-0.063	-0.040	65.794	0.050	0.050	0.000	0.000	0.000	0.000
46	A	753	ASP	-1	-0.842	-0.920	68.675	-4.666	-4.666	0.000	0.000	0.000	0.000
47	A	754	GLU	-1	-0.863	-0.901	69.900	-4.640	-4.640	0.000	0.000	0.000	0.000
48	A	755	TYR	0	-0.032	-0.025	68.910	0.046	0.046	0.000	0.000	0.000	0.000
49	A	756	VAL	0	-0.013	-0.002	72.204	0.062	0.062	0.000	0.000	0.000	0.000
50	A	757	THR	0	0.006	-0.004	74.726	0.076	0.076	0.000	0.000	0.000	0.000
51	A	758	GLN	0	-0.036	-0.024	76.484	0.117	0.117	0.000	0.000	0.000	0.000
52	A	759	LEU	0	-0.058	-0.019	74.674	0.057	0.057	0.000	0.000	0.000	0.000
53	A	760	ASP	-1	-0.847	-0.923	78.310	-4.165	-4.165	0.000	0.000	0.000	0.000
54	A	761	GLU	-1	-0.770	-0.833	80.747	-3.776	-3.776	0.000	0.000	0.000	0.000
55	A	762	MET	0	-0.010	-0.013	81.660	0.069	0.069	0.000	0.000	0.000	0.000
56	A	763	GLN	0	-0.035	-0.018	80.356	0.048	0.048	0.000	0.000	0.000	0.000
57	A	764	ARG	1	0.803	0.868	84.472	3.816	3.816	0.000	0.000	0.000	0.000
58	A	765	GLN	0	-0.086	-0.062	85.992	0.073	0.073	0.000	0.000	0.000	0.000
59	A	766	LEU	0	-0.012	-0.002	86.174	0.049	0.049	0.000	0.000	0.000	0.000
60	A	767	ALA	0	-0.006	-0.005	88.572	0.043	0.043	0.000	0.000	0.000	0.000
61	A	768	ALA	0	0.032	0.028	90.334	0.042	0.042	0.000	0.000	0.000	0.000
62	A	769	ALA	0	0.061	0.033	91.810	0.047	0.047	0.000	0.000	0.000	0.000
63	A	770	GLU	-1	-0.843	-0.913	91.202	-3.506	-3.506	0.000	0.000	0.000	0.000
64	A	771	ASP	-1	-0.902	-0.944	94.116	-3.441	-3.441	0.000	0.000	0.000	0.000
65	A	772	GLU	-1	-0.957	-0.976	96.092	-3.384	-3.384	0.000	0.000	0.000	0.000
66	A	773	LYS	1	0.835	0.903	94.095	3.546	3.546	0.000	0.000	0.000	0.000
67	A	774	LYS	1	0.949	0.973	97.731	3.358	3.358	0.000	0.000	0.000	0.000
68	A	775	THR	0	-0.040	-0.020	99.597	0.051	0.051	0.000	0.000	0.000	0.000
69	A	776	LEU	0	0.030	0.008	100.749	0.048	0.048	0.000	0.000	0.000	0.000
70	A	777	ASN	0	-0.005	-0.002	101.673	0.037	0.037	0.000	0.000	0.000	0.000
71	A	778	THR	0	-0.038	-0.029	103.221	0.026	0.026	0.000	0.000	0.000	0.000
72	A	779	LEU	0	0.028	-0.001	105.595	0.036	0.036	0.000	0.000	0.000	0.000
73	A	780	LEU	0	-0.005	0.011	105.566	0.035	0.035	0.000	0.000	0.000	0.000
74	A	781	ARG	1	0.890	0.938	102.561	3.207	3.207	0.000	0.000	0.000	0.000
75	A	782	MET	0	-0.018	-0.001	109.326	0.018	0.018	0.000	0.000	0.000	0.000
76	A	783	ALA	0	0.049	0.027	111.553	0.032	0.032	0.000	0.000	0.000	0.000
77	A	784	ILE	0	-0.030	-0.015	109.503	0.029	0.029	0.000	0.000	0.000	0.000
78	A	785	GLN	0	0.019	0.002	112.778	0.045	0.045	0.000	0.000	0.000	0.000
79	A	786	GLN	0	-0.015	-0.004	115.381	0.020	0.020	0.000	0.000	0.000	0.000
80	A	787	LYS	1	0.970	0.988	115.325	2.853	2.853	0.000	0.000	0.000	0.000
81	A	788	LEU	0	-0.043	-0.004	114.981	0.021	0.021	0.000	0.000	0.000	0.000
82	A	789	ALA	0	0.022	0.012	118.981	0.023	0.023	0.000	0.000	0.000	0.000
83	A	790	LEU	0	-0.044	-0.033	120.674	0.026	0.026	0.000	0.000	0.000	0.000
84	A	791	THR	0	-0.055	-0.035	120.784	0.011	0.011	0.000	0.000	0.000	0.000
85	A	792	GLN	0	-0.029	-0.018	123.127	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	793	ARG	1	0.957	0.978	125.020	2.573	2.573	0.000	0.000	0.000	0.000
87	A	794	LEU	0	-0.058	-0.016	126.468	0.019	0.019	0.000	0.000	0.000	0.000
88	A	795	GLU	-1	-0.882	-0.951	124.800	-2.627	-2.627	0.000	0.000	0.000	0.000
89	A	796	ASP	-1	-0.886	-0.936	128.716	-2.556	-2.556	0.000	0.000	0.000	0.000
90	A	797	LEU	0	-0.056	-0.037	130.996	0.021	0.021	0.000	0.000	0.000	0.000
91	A	798	GLU	-1	-0.961	-0.983	130.335	-2.514	-2.514	0.000	0.000	0.000	0.000
92	A	799	PHE	0	-0.014	0.001	133.187	0.021	0.021	0.000	0.000	0.000	0.000
93	A	800	ASP	-1	-0.955	-0.985	134.939	-2.416	-2.416	0.000	0.000	0.000	0.000
94	A	801	HIS	0	-0.111	-0.063	135.984	0.033	0.033	0.000	0.000	0.000	0.000
95	A	802	GLU	-1	-1.001	-0.991	135.760	-2.426	-2.426	0.000	0.000	0.000	0.000
96	A	803	GLN	-1	-1.036	-0.997	138.971	-2.284	-2.284	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:708:GLY)