FMO DATABASE

FMODB ID: 642YZ

Calculation Name: 4HPM-D-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4HPM

Chain ID: D

ChEMBL ID:

UniProt ID: Q5H9F3

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-699848.141877
FMO2-HF: Nuclear repulsion	661426.758785
FMO2-HF: Total energy	-38421.383092
FMO2-MP2: Total energy	-38531.065894

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:164:GLY)

Summations of interaction energy for fragment #1(A:164: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.
161.189	163.274	-0.015	-1.024	-1.046	-0.006

Interaction energy analysis for fragmet #1(A:164:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.909

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	166	ARG	1	0.963	0.999	3.799	45.252	47.337	-0.015	-1.024	-1.046	-0.006
4	A	167	GLU	-1	-0.823	-0.907	5.585	-28.589	-28.589	0.000	0.000	0.000	0.000
5	A	168	GLN	0	-0.077	-0.057	4.952	0.338	0.338	0.000	0.000	0.000	0.000
6	A	169	LEU	0	0.036	0.035	9.156	1.866	1.866	0.000	0.000	0.000	0.000
7	A	170	ASN	0	-0.012	-0.014	12.480	-1.817	-1.817	0.000	0.000	0.000	0.000
8	A	171	LEU	0	0.028	0.010	14.815	0.781	0.781	0.000	0.000	0.000	0.000
9	A	172	CYS	0	-0.018	-0.005	17.490	-0.083	-0.083	0.000	0.000	0.000	0.000
10	A	173	LEU	0	-0.002	0.002	18.094	0.141	0.141	0.000	0.000	0.000	0.000
11	A	174	GLU	-1	-0.783	-0.882	22.027	-11.457	-11.457	0.000	0.000	0.000	0.000
12	A	175	ARG	1	0.755	0.874	25.859	10.348	10.348	0.000	0.000	0.000	0.000
13	A	176	LEU	0	0.057	0.017	27.959	0.302	0.302	0.000	0.000	0.000	0.000
14	A	177	SER	0	-0.010	-0.006	30.916	0.277	0.277	0.000	0.000	0.000	0.000
15	A	178	SER	0	-0.021	-0.051	28.287	-0.189	-0.189	0.000	0.000	0.000	0.000
16	A	179	GLY	0	0.020	0.008	30.228	0.276	0.276	0.000	0.000	0.000	0.000
17	A	180	LYS	1	0.833	0.915	32.107	8.734	8.734	0.000	0.000	0.000	0.000
18	A	181	ASP	-1	-0.706	-0.832	33.805	-8.622	-8.622	0.000	0.000	0.000	0.000
19	A	182	LYS	1	0.959	0.980	35.623	8.355	8.355	0.000	0.000	0.000	0.000
20	A	183	ASN	0	0.001	0.004	31.404	-0.380	-0.380	0.000	0.000	0.000	0.000
21	A	184	LYS	1	0.840	0.913	28.689	10.441	10.441	0.000	0.000	0.000	0.000
22	A	185	SER	0	-0.080	-0.055	29.572	0.151	0.151	0.000	0.000	0.000	0.000
23	A	186	VAL	0	0.005	0.011	27.316	-0.097	-0.097	0.000	0.000	0.000	0.000
24	A	187	LEU	0	-0.035	-0.010	19.701	-0.088	-0.088	0.000	0.000	0.000	0.000
25	A	188	GLN	0	0.080	0.029	23.708	-0.461	-0.461	0.000	0.000	0.000	0.000
26	A	189	ASN	0	-0.012	-0.009	19.416	0.518	0.518	0.000	0.000	0.000	0.000
27	A	190	LYS	1	0.884	0.951	19.899	11.482	11.482	0.000	0.000	0.000	0.000
28	A	191	TYR	0	0.029	0.016	18.913	0.107	0.107	0.000	0.000	0.000	0.000
29	A	192	VAL	0	0.000	0.001	13.795	-0.651	-0.651	0.000	0.000	0.000	0.000
30	A	193	ARG	1	0.943	0.979	9.488	25.489	25.489	0.000	0.000	0.000	0.000
31	A	194	CYS	0	-0.033	-0.004	8.992	-0.709	-0.709	0.000	0.000	0.000	0.000
32	A	195	SER	0	0.006	0.007	5.719	0.020	0.020	0.000	0.000	0.000	0.000
33	A	196	VAL	0	0.019	0.000	7.719	2.476	2.476	0.000	0.000	0.000	0.000
34	A	197	ARG	1	0.922	0.947	5.619	36.906	36.906	0.000	0.000	0.000	0.000
35	A	198	ALA	0	-0.027	0.004	9.715	0.653	0.653	0.000	0.000	0.000	0.000
36	A	199	GLU	-1	-0.727	-0.844	10.960	-17.967	-17.967	0.000	0.000	0.000	0.000
37	A	200	VAL	0	0.036	0.022	14.623	-0.577	-0.577	0.000	0.000	0.000	0.000
38	A	201	ARG	1	0.863	0.898	15.340	17.992	17.992	0.000	0.000	0.000	0.000
39	A	202	HIS	0	-0.054	-0.017	12.580	-0.577	-0.577	0.000	0.000	0.000	0.000
40	A	203	LEU	0	0.025	0.016	14.695	-0.144	-0.144	0.000	0.000	0.000	0.000
41	A	204	ARG	1	0.849	0.902	15.735	13.849	13.849	0.000	0.000	0.000	0.000
42	A	205	ARG	1	0.962	0.986	16.586	15.875	15.875	0.000	0.000	0.000	0.000
43	A	206	VAL	0	-0.003	-0.002	13.466	0.329	0.329	0.000	0.000	0.000	0.000
44	A	207	LEU	0	-0.001	0.004	16.821	0.483	0.483	0.000	0.000	0.000	0.000
45	A	208	CYS	0	-0.045	-0.012	20.045	0.777	0.777	0.000	0.000	0.000	0.000
46	A	209	HIS	0	-0.014	-0.007	18.770	0.511	0.511	0.000	0.000	0.000	0.000
47	A	210	ARG	1	0.913	0.954	17.993	16.290	16.290	0.000	0.000	0.000	0.000
48	A	211	LEU	0	-0.005	0.018	21.538	0.481	0.481	0.000	0.000	0.000	0.000
49	A	212	MET	0	0.007	0.015	24.312	0.658	0.658	0.000	0.000	0.000	0.000
50	A	213	LEU	0	-0.018	-0.012	25.129	0.610	0.610	0.000	0.000	0.000	0.000
51	A	214	ASN	0	0.065	0.032	25.443	-0.626	-0.626	0.000	0.000	0.000	0.000
52	A	215	PRO	0	-0.004	-0.035	22.941	0.050	0.050	0.000	0.000	0.000	0.000
53	A	216	GLN	0	-0.021	-0.009	24.917	-0.078	-0.078	0.000	0.000	0.000	0.000
54	A	217	HIS	0	0.032	0.026	28.147	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	218	VAL	0	-0.024	-0.012	23.682	0.042	0.042	0.000	0.000	0.000	0.000
56	A	219	GLN	0	0.018	0.008	25.287	-0.542	-0.542	0.000	0.000	0.000	0.000
57	A	220	LEU	0	-0.039	-0.030	19.141	-0.234	-0.234	0.000	0.000	0.000	0.000
58	A	221	LEU	0	-0.015	-0.007	23.417	0.199	0.199	0.000	0.000	0.000	0.000
59	A	222	PHE	0	0.000	-0.012	23.312	-0.663	-0.663	0.000	0.000	0.000	0.000
60	A	223	ASP	-1	-0.872	-0.932	25.607	-10.707	-10.707	0.000	0.000	0.000	0.000
61	A	224	ASN	0	-0.037	-0.029	28.933	0.360	0.360	0.000	0.000	0.000	0.000
62	A	225	GLU	-1	-0.850	-0.909	28.660	-9.953	-9.953	0.000	0.000	0.000	0.000
63	A	226	VAL	0	-0.011	-0.018	26.480	-0.476	-0.476	0.000	0.000	0.000	0.000
64	A	227	LEU	0	-0.025	-0.004	21.015	-0.060	-0.060	0.000	0.000	0.000	0.000
65	A	228	PRO	0	0.040	0.010	22.775	-0.149	-0.149	0.000	0.000	0.000	0.000
66	A	229	ASP	-1	-0.774	-0.876	20.605	-14.479	-14.479	0.000	0.000	0.000	0.000
67	A	230	HIS	0	-0.044	-0.039	17.884	-0.383	-0.383	0.000	0.000	0.000	0.000
68	A	231	MET	0	-0.002	0.033	18.163	-0.319	-0.319	0.000	0.000	0.000	0.000
69	A	232	THR	0	-0.003	-0.021	13.622	-0.412	-0.412	0.000	0.000	0.000	0.000
70	A	233	MET	0	0.037	0.016	13.024	1.105	1.105	0.000	0.000	0.000	0.000
71	A	234	LYS	1	0.963	0.987	13.081	21.343	21.343	0.000	0.000	0.000	0.000
72	A	235	GLN	0	0.048	0.033	15.229	0.757	0.757	0.000	0.000	0.000	0.000
73	A	236	ILE	0	0.047	0.041	17.920	0.803	0.803	0.000	0.000	0.000	0.000
74	A	237	TRP	0	0.008	-0.006	16.327	0.137	0.137	0.000	0.000	0.000	0.000
75	A	238	LEU	0	-0.050	-0.040	17.897	0.500	0.500	0.000	0.000	0.000	0.000
76	A	239	SER	0	-0.033	-0.029	20.760	0.705	0.705	0.000	0.000	0.000	0.000
77	A	240	ARG	1	0.851	0.942	22.748	11.919	11.919	0.000	0.000	0.000	0.000
78	A	241	TRP	0	-0.005	-0.027	20.982	0.585	0.585	0.000	0.000	0.000	0.000
79	A	242	PHE	0	0.022	0.014	21.196	-0.304	-0.304	0.000	0.000	0.000	0.000
80	A	243	GLY	0	-0.007	-0.001	23.167	0.531	0.531	0.000	0.000	0.000	0.000
81	A	244	LYS	1	0.916	0.979	23.975	11.967	11.967	0.000	0.000	0.000	0.000
82	A	245	PRO	0	0.028	0.011	22.744	-0.627	-0.627	0.000	0.000	0.000	0.000
83	A	246	SER	0	0.020	0.026	18.343	-0.641	-0.641	0.000	0.000	0.000	0.000
84	A	247	PRO	0	-0.062	-0.035	18.878	0.307	0.307	0.000	0.000	0.000	0.000
85	A	248	LEU	0	0.038	0.017	17.489	0.574	0.574	0.000	0.000	0.000	0.000
86	A	249	LEU	0	-0.018	-0.010	20.170	-0.393	-0.393	0.000	0.000	0.000	0.000
87	A	250	LEU	0	0.010	0.000	18.164	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	251	GLN	0	0.036	0.015	22.586	0.370	0.370	0.000	0.000	0.000	0.000
89	A	252	TYR	0	0.004	0.011	23.421	-0.398	-0.398	0.000	0.000	0.000	0.000
90	A	253	SER	0	0.043	0.027	25.462	0.382	0.382	0.000	0.000	0.000	0.000
91	A	254	VAL	-1	-0.842	-0.902	27.229	-10.340	-10.340	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:164:GLY)