FMO DATABASE

FMODB ID: KGM53

Calculation Name: 3PT3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PT3

Chain ID: A

ChEMBL ID:

UniProt ID: O95071

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-668411.897186
FMO2-HF: Nuclear repulsion	632198.312998
FMO2-HF: Total energy	-36213.584188
FMO2-MP2: Total energy	-36319.66409

3D Structure

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:2693:PHE)

Summations of interaction energy for fragment #1(A:2693:PHE)

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.
-2.458	-0.171	1.569	-1.05	-2.805	0.005

Interaction energy analysis for fragmet #1(A:2693:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.004

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

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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	2695	SER	0	0.013	0.001	3.873	0.245	1.613	0.006	-0.523	-0.851	0.003
4	A	2696	PHE	0	0.016	-0.013	6.541	0.051	0.051	0.000	0.000	0.000	0.000
5	A	2697	ASN	0	-0.033	-0.011	9.595	-0.159	-0.159	0.000	0.000	0.000	0.000
6	A	2698	ASP	-1	-0.817	-0.899	12.861	0.357	0.357	0.000	0.000	0.000	0.000
7	A	2699	GLU	-1	-0.794	-0.863	16.095	0.034	0.034	0.000	0.000	0.000	0.000
8	A	2700	SER	0	-0.052	-0.059	19.170	-0.026	-0.026	0.000	0.000	0.000	0.000
9	A	2701	GLY	0	0.018	0.008	21.091	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	2702	GLU	-1	-0.813	-0.895	21.467	0.203	0.203	0.000	0.000	0.000	0.000
11	A	2703	ASN	0	-0.004	0.003	22.149	0.029	0.029	0.000	0.000	0.000	0.000
12	A	2704	ALA	0	0.062	0.013	19.287	0.027	0.027	0.000	0.000	0.000	0.000
13	A	2705	GLU	-1	-0.873	-0.926	18.672	0.421	0.421	0.000	0.000	0.000	0.000
14	A	2706	LYS	1	0.840	0.902	19.676	-0.187	-0.187	0.000	0.000	0.000	0.000
15	A	2707	LEU	0	0.012	0.012	15.379	0.061	0.061	0.000	0.000	0.000	0.000
16	A	2708	LEU	0	-0.015	-0.005	14.851	0.119	0.119	0.000	0.000	0.000	0.000
17	A	2709	GLN	0	-0.008	-0.012	15.237	0.082	0.082	0.000	0.000	0.000	0.000
18	A	2710	PHE	0	0.030	0.015	15.223	0.039	0.039	0.000	0.000	0.000	0.000
19	A	2711	LYS	1	0.941	0.978	11.352	-0.787	-0.787	0.000	0.000	0.000	0.000
20	A	2712	ARG	1	0.945	0.975	11.986	-0.379	-0.379	0.000	0.000	0.000	0.000
21	A	2713	TRP	0	-0.068	-0.043	14.060	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	2714	PHE	0	0.074	0.032	8.660	-0.103	-0.103	0.000	0.000	0.000	0.000
23	A	2715	TRP	0	0.067	0.035	5.398	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	2716	SER	0	-0.009	0.011	10.861	-0.193	-0.193	0.000	0.000	0.000	0.000
25	A	2717	ILE	0	-0.041	-0.017	13.796	-0.122	-0.122	0.000	0.000	0.000	0.000
26	A	2718	VAL	0	0.056	0.017	8.784	-0.092	-0.092	0.000	0.000	0.000	0.000
27	A	2719	GLU	-1	-0.886	-0.949	11.174	0.563	0.563	0.000	0.000	0.000	0.000
28	A	2720	LYS	1	0.777	0.880	12.621	-0.479	-0.479	0.000	0.000	0.000	0.000
29	A	2721	MET	0	-0.009	0.041	12.796	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	2722	SER	0	0.021	-0.014	14.939	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	2723	MET	0	0.023	-0.007	13.097	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	2724	THR	0	0.031	0.012	13.944	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	2725	GLU	-1	-0.791	-0.856	14.986	0.035	0.035	0.000	0.000	0.000	0.000
34	A	2726	ARG	1	0.836	0.900	10.113	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	2727	GLN	0	0.009	-0.003	10.009	-0.044	-0.044	0.000	0.000	0.000	0.000
36	A	2728	ASP	-1	-0.775	-0.873	11.716	-0.126	-0.126	0.000	0.000	0.000	0.000
37	A	2729	LEU	0	-0.034	-0.012	8.815	0.002	0.002	0.000	0.000	0.000	0.000
38	A	2730	VAL	0	0.001	-0.007	5.902	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	2731	TYR	0	0.004	0.035	8.259	-0.056	-0.056	0.000	0.000	0.000	0.000
40	A	2732	PHE	0	-0.011	-0.009	11.497	0.000	0.000	0.000	0.000	0.000	0.000
41	A	2733	TRP	0	-0.080	-0.040	5.886	0.131	0.131	0.000	0.000	0.000	0.000
42	A	2734	THR	0	0.000	-0.027	5.982	-0.057	-0.057	0.000	0.000	0.000	0.000
43	A	2735	SER	0	-0.034	-0.001	9.200	0.032	0.032	0.000	0.000	0.000	0.000
44	A	2736	SER	0	-0.020	-0.011	8.759	0.021	0.021	0.000	0.000	0.000	0.000
45	A	2737	PRO	0	-0.014	-0.017	9.558	-0.053	-0.053	0.000	0.000	0.000	0.000
46	A	2750	PRO	0	0.073	0.019	2.213	-1.500	-0.500	1.551	-0.778	-1.773	0.002
47	A	2751	SER	0	-0.055	-0.007	3.414	0.342	0.261	0.012	0.251	-0.181	0.000
48	A	2752	ILE	0	0.031	0.024	6.763	0.061	0.061	0.000	0.000	0.000	0.000
49	A	2753	THR	0	-0.033	-0.020	9.670	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	2754	ILE	0	-0.036	-0.018	12.914	0.022	0.022	0.000	0.000	0.000	0.000
51	A	2755	ARG	1	0.889	0.923	16.077	-0.136	-0.136	0.000	0.000	0.000	0.000
52	A	2756	PRO	0	0.032	0.006	19.196	0.030	0.030	0.000	0.000	0.000	0.000
53	A	2757	PRO	0	-0.022	-0.003	22.455	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	2758	ASP	-1	-0.786	-0.893	23.836	0.077	0.077	0.000	0.000	0.000	0.000
55	A	2759	ASP	-1	-0.823	-0.887	24.159	0.177	0.177	0.000	0.000	0.000	0.000
56	A	2760	GLN	0	-0.051	-0.028	26.119	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	2761	HIS	0	0.079	0.060	20.349	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	2762	LEU	0	-0.024	-0.012	20.348	0.019	0.019	0.000	0.000	0.000	0.000
59	A	2763	PRO	0	-0.001	-0.004	15.353	0.001	0.001	0.000	0.000	0.000	0.000
60	A	2764	THR	0	-0.007	-0.005	15.891	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	2765	ALA	0	0.025	0.001	11.993	0.030	0.030	0.000	0.000	0.000	0.000
62	A	2766	ASN	0	-0.002	0.005	12.327	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	2767	THR	0	0.043	0.014	10.605	-0.036	-0.036	0.000	0.000	0.000	0.000
64	A	2768	CYS	0	-0.013	0.001	10.444	-0.077	-0.077	0.000	0.000	0.000	0.000
65	A	2769	ILE	0	-0.032	-0.009	10.206	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	2770	SER	0	-0.013	-0.007	5.541	-0.148	-0.148	0.000	0.000	0.000	0.000
67	A	2771	ARG	1	0.838	0.933	6.592	0.092	0.092	0.000	0.000	0.000	0.000
68	A	2772	LEU	0	0.026	0.021	8.984	0.026	0.026	0.000	0.000	0.000	0.000
69	A	2773	TYR	0	-0.007	-0.019	10.839	0.039	0.039	0.000	0.000	0.000	0.000
70	A	2774	VAL	0	0.003	-0.016	14.002	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	2775	PRO	0	0.044	0.031	16.275	0.027	0.027	0.000	0.000	0.000	0.000
72	A	2776	LEU	0	-0.001	0.014	18.664	0.035	0.035	0.000	0.000	0.000	0.000
73	A	2777	TYR	0	-0.046	-0.051	18.782	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	2778	SER	0	-0.011	-0.046	21.873	0.030	0.030	0.000	0.000	0.000	0.000
75	A	2779	SER	0	0.004	-0.009	23.251	0.002	0.002	0.000	0.000	0.000	0.000
76	A	2780	LYS	1	0.864	0.941	17.148	-0.394	-0.394	0.000	0.000	0.000	0.000
77	A	2781	GLN	0	-0.015	-0.010	20.603	0.008	0.008	0.000	0.000	0.000	0.000
78	A	2782	ILE	0	0.022	0.026	23.071	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	2783	LEU	0	0.017	0.019	15.506	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	2784	LYS	1	0.941	0.967	18.578	-0.164	-0.164	0.000	0.000	0.000	0.000
81	A	2785	GLN	0	-0.013	-0.008	19.650	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	2786	LYS	1	0.804	0.895	20.942	-0.126	-0.126	0.000	0.000	0.000	0.000
83	A	2787	LEU	0	0.004	0.006	13.185	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	2788	LEU	0	-0.029	-0.022	16.607	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	2789	LEU	0	-0.035	-0.017	18.529	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	2790	ALA	0	-0.027	-0.001	17.501	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	2791	ILE	0	-0.062	-0.026	13.364	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	2792	LYS	1	0.843	0.933	16.264	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2693:PHE)