FMO DATABASE

FMODB ID: 2RLYR

Calculation Name: 3POA-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphothreonine

Ligand 3-letter code: TPO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3POA

Chain ID: A

ChEMBL ID:

UniProt ID: P71590

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	-695560.03307
FMO2-HF: Nuclear repulsion	658636.260782
FMO2-HF: Total energy	-36923.772288
FMO2-MP2: Total energy	-37033.085969

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:THR)

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

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.
-168.996	-156.933	8.041	-7.952	-12.151	-0.075

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.821 / 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	6	VAL	0	0.063	0.017	2.742	-0.133	2.145	0.675	-1.078	-1.875	-0.011
4	A	7	THR	0	-0.065	-0.026	4.654	3.506	3.522	-0.001	-0.010	-0.006	0.000
48	A	51	TRP	0	0.012	0.010	2.161	-1.302	-0.837	2.369	-0.802	-2.032	-0.004
50	A	53	GLY	0	0.055	0.037	4.134	0.693	0.811	-0.001	-0.037	-0.080	0.000
51	A	54	GLN	0	-0.107	-0.067	2.652	-25.928	-22.103	0.843	-2.431	-2.237	-0.027
52	A	55	VAL	0	0.005	-0.008	4.166	-1.753	-1.458	0.000	-0.059	-0.235	0.000
93	A	96	MET	0	-0.023	-0.011	2.846	-4.258	-3.696	0.288	-0.145	-0.705	-0.001
94	A	97	HIS	0	0.033	0.019	3.669	3.569	4.152	0.031	-0.159	-0.455	-0.001
95	A	98	PRO	0	-0.015	-0.019	2.136	-18.696	-15.606	3.682	-3.417	-3.355	-0.025
96	A	99	LEU	-1	-0.927	-0.953	3.001	-42.707	-41.876	0.155	0.186	-1.171	-0.006
5	A	8	LEU	0	-0.004	0.009	8.286	0.404	0.404	0.000	0.000	0.000	0.000
6	A	9	GLN	0	0.049	0.006	11.297	-0.549	-0.549	0.000	0.000	0.000	0.000
7	A	10	LEU	0	-0.065	-0.027	13.964	0.211	0.211	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.913	-0.958	17.472	-14.390	-14.390	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.831	-0.883	19.582	-12.604	-12.604	0.000	0.000	0.000	0.000
10	A	13	GLY	0	0.002	0.002	22.111	0.554	0.554	0.000	0.000	0.000	0.000
11	A	14	SER	0	-0.105	-0.096	21.872	-0.030	-0.030	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.025	0.013	19.254	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.820	0.915	18.159	13.236	13.236	0.000	0.000	0.000	0.000
14	A	17	THR	0	0.022	0.001	13.177	-0.539	-0.539	0.000	0.000	0.000	0.000
15	A	18	TYR	0	-0.050	-0.047	12.343	1.416	1.416	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.004	0.010	8.058	-2.226	-2.226	0.000	0.000	0.000	0.000
17	A	20	LEU	0	-0.033	-0.017	6.969	2.253	2.253	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.928	0.959	8.648	17.869	17.869	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.904	-0.943	6.972	-38.352	-38.352	0.000	0.000	0.000	0.000
20	A	23	GLY	0	-0.057	-0.023	10.131	2.764	2.764	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.078	-0.083	12.490	-0.550	-0.550	0.000	0.000	0.000	0.000
22	A	25	ASN	0	0.017	0.023	11.021	0.006	0.006	0.000	0.000	0.000	0.000
23	A	26	ILE	0	-0.003	0.001	14.585	0.384	0.384	0.000	0.000	0.000	0.000
24	A	27	ILE	0	0.047	0.023	13.940	-0.045	-0.045	0.000	0.000	0.000	0.000
25	A	28	GLY	0	0.028	0.001	18.231	0.543	0.543	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.852	0.940	21.928	10.388	10.388	0.000	0.000	0.000	0.000
27	A	30	GLY	0	-0.032	-0.014	24.677	0.447	0.447	0.000	0.000	0.000	0.000
28	A	31	GLN	0	-0.057	-0.045	24.415	-0.207	-0.207	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.848	-0.921	24.439	-11.819	-11.819	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.051	-0.006	20.417	-0.542	-0.542	0.000	0.000	0.000	0.000
31	A	34	GLN	0	-0.014	-0.005	16.181	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	35	PHE	0	-0.008	0.005	15.707	-0.201	-0.201	0.000	0.000	0.000	0.000
33	A	36	ARG	1	0.894	0.957	17.827	14.229	14.229	0.000	0.000	0.000	0.000
34	A	37	LEU	0	0.074	0.028	19.165	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	38	PRO	0	0.007	-0.009	22.945	0.271	0.271	0.000	0.000	0.000	0.000
36	A	39	ASP	-1	-0.732	-0.827	25.150	-10.740	-10.740	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.002	-0.020	27.092	-0.200	-0.200	0.000	0.000	0.000	0.000
38	A	41	GLY	0	0.027	0.027	28.474	0.183	0.183	0.000	0.000	0.000	0.000
39	A	42	VAL	0	-0.027	0.013	22.708	-0.169	-0.169	0.000	0.000	0.000	0.000
40	A	43	SER	0	0.034	0.003	25.051	0.613	0.613	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.921	0.947	24.788	9.336	9.336	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.990	0.994	21.980	13.025	13.025	0.000	0.000	0.000	0.000
43	A	46	HIS	0	0.021	0.022	21.177	0.693	0.693	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.048	0.029	15.671	0.186	0.186	0.000	0.000	0.000	0.000
45	A	48	GLU	-1	-0.874	-0.913	15.468	-17.614	-17.614	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.017	0.005	10.057	-0.088	-0.088	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.916	0.965	12.079	19.549	19.549	0.000	0.000	0.000	0.000
49	A	52	ASP	-1	-0.824	-0.910	7.000	-33.860	-33.860	0.000	0.000	0.000	0.000
53	A	56	ALA	0	-0.004	0.002	6.526	0.794	0.794	0.000	0.000	0.000	0.000
54	A	57	LEU	0	-0.005	0.000	7.876	1.742	1.742	0.000	0.000	0.000	0.000
55	A	58	LEU	0	-0.016	-0.002	11.592	0.297	0.297	0.000	0.000	0.000	0.000
56	A	59	ALA	0	0.060	0.019	14.060	0.610	0.610	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.745	-0.823	17.729	-12.766	-12.766	0.000	0.000	0.000	0.000
58	A	61	LEU	0	-0.088	-0.053	20.036	0.275	0.275	0.000	0.000	0.000	0.000
59	A	62	ASN	0	-0.049	-0.020	22.993	0.537	0.537	0.000	0.000	0.000	0.000
60	A	63	SER	0	-0.066	-0.044	23.998	0.554	0.554	0.000	0.000	0.000	0.000
61	A	64	THR	0	-0.045	-0.039	26.160	0.168	0.168	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.054	-0.044	27.178	0.546	0.546	0.000	0.000	0.000	0.000
63	A	66	GLY	0	0.037	0.046	25.063	0.030	0.030	0.000	0.000	0.000	0.000
64	A	67	THR	0	-0.011	-0.032	18.497	-0.265	-0.265	0.000	0.000	0.000	0.000
65	A	68	THR	0	-0.053	-0.022	20.600	0.243	0.243	0.000	0.000	0.000	0.000
66	A	69	VAL	0	0.054	0.020	14.216	-0.570	-0.570	0.000	0.000	0.000	0.000
67	A	70	ASN	0	-0.025	-0.026	14.541	0.564	0.564	0.000	0.000	0.000	0.000
68	A	71	ASN	0	-0.015	-0.009	18.556	0.407	0.407	0.000	0.000	0.000	0.000
69	A	72	ALA	0	0.021	0.031	20.109	0.650	0.650	0.000	0.000	0.000	0.000
70	A	73	PRO	0	-0.014	-0.014	20.760	-0.543	-0.543	0.000	0.000	0.000	0.000
71	A	74	VAL	0	-0.026	-0.015	17.639	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	75	GLN	0	-0.030	0.000	20.830	0.551	0.551	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.944	-0.988	17.151	-15.927	-15.927	0.000	0.000	0.000	0.000
74	A	77	TRP	0	-0.006	-0.015	13.150	1.059	1.059	0.000	0.000	0.000	0.000
75	A	78	GLN	0	-0.010	0.003	8.433	0.454	0.454	0.000	0.000	0.000	0.000
76	A	79	LEU	0	-0.039	-0.017	8.707	0.710	0.710	0.000	0.000	0.000	0.000
77	A	80	ALA	0	0.002	-0.004	7.510	-2.624	-2.624	0.000	0.000	0.000	0.000
78	A	81	ASP	-1	-0.860	-0.944	6.581	-29.717	-29.717	0.000	0.000	0.000	0.000
79	A	82	GLY	0	-0.008	-0.002	8.136	1.848	1.848	0.000	0.000	0.000	0.000
80	A	83	ASP	-1	-0.812	-0.881	10.882	-19.261	-19.261	0.000	0.000	0.000	0.000
81	A	84	VAL	0	-0.027	-0.020	12.753	-0.425	-0.425	0.000	0.000	0.000	0.000
82	A	85	ILE	0	0.001	0.003	12.465	0.692	0.692	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.788	0.864	16.525	13.746	13.746	0.000	0.000	0.000	0.000
84	A	87	LEU	0	0.014	-0.003	18.637	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	88	GLY	0	-0.024	-0.004	22.179	0.047	0.047	0.000	0.000	0.000	0.000
86	A	89	HIS	0	-0.075	-0.065	25.729	0.390	0.390	0.000	0.000	0.000	0.000
87	A	90	SER	0	-0.052	-0.031	21.293	-0.077	-0.077	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.785	-0.865	19.460	-13.304	-13.304	0.000	0.000	0.000	0.000
89	A	92	ILE	0	-0.034	-0.031	13.500	-0.119	-0.119	0.000	0.000	0.000	0.000
90	A	93	ILE	0	0.008	0.020	12.283	-0.270	-0.270	0.000	0.000	0.000	0.000
91	A	94	VAL	0	-0.018	-0.015	7.628	-0.912	-0.912	0.000	0.000	0.000	0.000
92	A	95	ARG	1	0.849	0.928	7.843	24.120	24.120	0.000	0.000	0.000	0.000

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