FMO DATABASE

FMODB ID: QVJ6Y

Calculation Name: 3PT3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

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

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	-667686.935151
FMO2-HF: Nuclear repulsion	631473.540132
FMO2-HF: Total energy	-36213.395019
FMO2-MP2: Total energy	-36319.48551

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: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.
-2.434	0.31	1.157	-1.115	-2.786	0.004

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 : 0.010 / q_NPA : -0.005

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	2695	SER	0	-0.018	-0.004	3.827	0.163	1.640	-0.017	-0.602	-0.858	0.002
4	A	2696	PHE	0	0.023	-0.010	6.474	-0.013	-0.013	0.000	0.000	0.000	0.000
5	A	2697	ASN	0	-0.035	-0.026	9.938	-0.159	-0.159	0.000	0.000	0.000	0.000
6	A	2698	ASP	-1	-0.821	-0.901	13.155	0.312	0.312	0.000	0.000	0.000	0.000
7	A	2699	GLU	-1	-0.815	-0.882	16.033	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	2700	SER	0	-0.027	-0.051	18.937	-0.019	-0.019	0.000	0.000	0.000	0.000
9	A	2701	GLY	0	0.017	0.005	20.681	-0.016	-0.016	0.000	0.000	0.000	0.000
10	A	2702	GLU	-1	-0.829	-0.903	21.467	0.194	0.194	0.000	0.000	0.000	0.000
11	A	2703	ASN	0	0.009	0.007	21.685	0.030	0.030	0.000	0.000	0.000	0.000
12	A	2704	ALA	0	0.072	0.013	19.062	0.026	0.026	0.000	0.000	0.000	0.000
13	A	2705	GLU	-1	-0.882	-0.934	18.746	0.409	0.409	0.000	0.000	0.000	0.000
14	A	2706	LYS	1	0.830	0.901	20.034	-0.186	-0.186	0.000	0.000	0.000	0.000
15	A	2707	LEU	0	-0.006	0.003	15.040	0.064	0.064	0.000	0.000	0.000	0.000
16	A	2708	LEU	0	-0.005	-0.005	14.498	0.116	0.116	0.000	0.000	0.000	0.000
17	A	2709	GLN	0	0.004	-0.003	15.344	0.087	0.087	0.000	0.000	0.000	0.000
18	A	2710	PHE	0	0.034	0.022	15.112	0.042	0.042	0.000	0.000	0.000	0.000
19	A	2711	LYS	1	0.946	0.981	11.468	-0.780	-0.780	0.000	0.000	0.000	0.000
20	A	2712	ARG	1	0.951	0.987	12.064	-0.397	-0.397	0.000	0.000	0.000	0.000
21	A	2713	TRP	0	-0.071	-0.045	14.063	0.009	0.009	0.000	0.000	0.000	0.000
22	A	2714	PHE	0	0.062	0.023	8.733	-0.098	-0.098	0.000	0.000	0.000	0.000
23	A	2715	TRP	0	0.057	0.026	5.632	0.107	0.107	0.000	0.000	0.000	0.000
24	A	2716	SER	0	-0.038	0.007	10.850	-0.166	-0.166	0.000	0.000	0.000	0.000
25	A	2717	ILE	0	-0.005	-0.025	14.183	-0.095	-0.095	0.000	0.000	0.000	0.000
26	A	2718	VAL	0	0.052	0.021	8.952	-0.093	-0.093	0.000	0.000	0.000	0.000
27	A	2719	GLU	-1	-0.934	-0.984	10.941	0.718	0.718	0.000	0.000	0.000	0.000
28	A	2720	LYS	1	0.768	0.897	12.753	-0.586	-0.586	0.000	0.000	0.000	0.000
29	A	2721	MET	0	-0.037	0.025	13.375	-0.052	-0.052	0.000	0.000	0.000	0.000
30	A	2722	SER	0	0.014	-0.023	15.089	-0.030	-0.030	0.000	0.000	0.000	0.000
31	A	2723	MET	0	0.021	-0.011	13.389	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	2724	THR	0	0.020	0.011	14.286	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	2725	GLU	-1	-0.807	-0.868	15.482	0.078	0.078	0.000	0.000	0.000	0.000
34	A	2726	ARG	1	0.896	0.935	10.466	-0.098	-0.098	0.000	0.000	0.000	0.000
35	A	2727	GLN	0	-0.008	-0.005	10.377	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	2728	ASP	-1	-0.773	-0.871	11.875	-0.130	-0.130	0.000	0.000	0.000	0.000
37	A	2729	LEU	0	-0.052	-0.028	9.370	0.005	0.005	0.000	0.000	0.000	0.000
38	A	2730	VAL	0	0.001	-0.008	6.301	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	2731	TYR	0	0.012	0.035	8.501	-0.090	-0.090	0.000	0.000	0.000	0.000
40	A	2732	PHE	0	-0.002	0.004	11.451	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	2733	TRP	0	-0.065	-0.033	6.387	0.165	0.165	0.000	0.000	0.000	0.000
42	A	2734	THR	0	0.007	-0.026	5.703	-0.062	-0.062	0.000	0.000	0.000	0.000
43	A	2735	SER	0	-0.070	-0.021	8.935	0.024	0.024	0.000	0.000	0.000	0.000
44	A	2736	SER	0	-0.032	-0.013	8.267	0.016	0.016	0.000	0.000	0.000	0.000
45	A	2737	PRO	0	0.006	-0.004	9.963	-0.049	-0.049	0.000	0.000	0.000	0.000
46	A	2750	PRO	0	0.068	0.016	2.327	-1.618	-0.299	1.167	-0.691	-1.795	0.002
47	A	2751	SER	0	-0.046	0.015	3.589	0.517	0.465	0.007	0.178	-0.133	0.000
48	A	2752	ILE	0	0.033	0.021	6.836	0.049	0.049	0.000	0.000	0.000	0.000
49	A	2753	THR	0	-0.054	-0.024	10.099	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	2754	ILE	0	-0.028	-0.010	12.974	0.029	0.029	0.000	0.000	0.000	0.000
51	A	2755	ARG	1	0.873	0.917	16.091	-0.107	-0.107	0.000	0.000	0.000	0.000
52	A	2756	PRO	0	0.034	0.006	19.455	0.030	0.030	0.000	0.000	0.000	0.000
53	A	2757	PRO	0	-0.031	-0.007	22.865	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	2758	ASP	-1	-0.816	-0.913	23.941	0.072	0.072	0.000	0.000	0.000	0.000
55	A	2759	ASP	-1	-0.805	-0.887	24.319	0.178	0.178	0.000	0.000	0.000	0.000
56	A	2760	GLN	0	-0.048	-0.030	26.119	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	2761	HIS	0	0.032	0.035	20.944	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	2762	LEU	0	-0.030	-0.007	20.566	0.026	0.026	0.000	0.000	0.000	0.000
59	A	2763	PRO	0	0.008	0.004	15.754	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	2764	THR	0	-0.015	-0.007	16.174	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	2765	ALA	0	0.028	0.010	12.003	0.031	0.031	0.000	0.000	0.000	0.000
62	A	2766	ASN	0	-0.009	0.007	12.585	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	2767	THR	0	0.055	0.016	10.886	-0.049	-0.049	0.000	0.000	0.000	0.000
64	A	2768	CYS	0	-0.026	-0.005	10.667	-0.077	-0.077	0.000	0.000	0.000	0.000
65	A	2769	ILE	0	-0.015	-0.007	10.012	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	2770	SER	0	-0.014	0.004	5.675	-0.205	-0.205	0.000	0.000	0.000	0.000
67	A	2771	ARG	1	0.854	0.940	6.779	0.190	0.190	0.000	0.000	0.000	0.000
68	A	2772	LEU	0	0.022	0.024	9.312	0.040	0.040	0.000	0.000	0.000	0.000
69	A	2773	TYR	0	-0.015	-0.017	11.101	0.053	0.053	0.000	0.000	0.000	0.000
70	A	2774	VAL	0	0.012	-0.016	14.107	0.001	0.001	0.000	0.000	0.000	0.000
71	A	2775	PRO	0	0.040	0.031	16.421	0.028	0.028	0.000	0.000	0.000	0.000
72	A	2776	LEU	0	-0.012	0.007	18.570	0.036	0.036	0.000	0.000	0.000	0.000
73	A	2777	TYR	0	-0.038	-0.056	18.933	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	2778	SER	0	-0.014	-0.046	21.934	0.029	0.029	0.000	0.000	0.000	0.000
75	A	2779	SER	0	0.007	-0.007	23.358	0.002	0.002	0.000	0.000	0.000	0.000
76	A	2780	LYS	1	0.925	0.966	17.593	-0.421	-0.421	0.000	0.000	0.000	0.000
77	A	2781	GLN	0	-0.015	-0.020	20.673	0.014	0.014	0.000	0.000	0.000	0.000
78	A	2782	ILE	0	0.021	0.026	23.091	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	2783	LEU	0	0.002	0.015	15.420	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	2784	LYS	1	0.932	0.964	18.742	-0.207	-0.207	0.000	0.000	0.000	0.000
81	A	2785	GLN	0	0.024	0.016	19.763	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	2786	LYS	1	0.888	0.957	21.247	-0.122	-0.122	0.000	0.000	0.000	0.000
83	A	2787	LEU	0	0.009	0.008	13.590	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	2788	LEU	0	-0.012	-0.021	17.184	-0.026	-0.026	0.000	0.000	0.000	0.000
85	A	2789	LEU	0	-0.044	-0.017	18.958	-0.027	-0.027	0.000	0.000	0.000	0.000
86	A	2790	ALA	0	-0.044	-0.015	17.624	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	2791	ILE	0	-0.049	-0.019	13.828	-0.020	-0.020	0.000	0.000	0.000	0.000
88	A	2792	LYS	1	0.853	0.941	16.642	-0.023	-0.023	0.000	0.000	0.000	0.000

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