FMO DATABASE

FMODB ID: R8V28

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	OptH
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	-667089.757119
FMO2-HF: Nuclear repulsion	630876.752413
FMO2-HF: Total energy	-36213.004707
FMO2-MP2: Total energy	-36319.067705

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.
-2.473	0.471	0.886	-1.139	-2.691	0.003

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 : 0.003 / q_NPA : -0.007

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	0.010	0.007	3.827	-0.263	1.302	-0.018	-0.671	-0.876	0.002
4	A	2696	PHE	0	0.024	-0.010	6.461	0.051	0.051	0.000	0.000	0.000	0.000
5	A	2697	ASN	0	-0.033	-0.020	9.930	-0.129	-0.129	0.000	0.000	0.000	0.000
6	A	2698	ASP	-1	-0.842	-0.927	13.136	0.304	0.304	0.000	0.000	0.000	0.000
7	A	2699	GLU	-1	-0.905	-0.955	16.024	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	2700	SER	0	-0.031	-0.035	18.926	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	2701	GLY	0	0.036	0.014	20.681	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	2702	GLU	-1	-0.855	-0.917	21.444	0.183	0.183	0.000	0.000	0.000	0.000
11	A	2703	ASN	0	0.016	0.008	21.683	0.030	0.030	0.000	0.000	0.000	0.000
12	A	2704	ALA	0	0.073	0.012	19.053	0.026	0.026	0.000	0.000	0.000	0.000
13	A	2705	GLU	-1	-0.893	-0.942	18.751	0.397	0.397	0.000	0.000	0.000	0.000
14	A	2706	LYS	1	0.859	0.919	20.034	-0.183	-0.183	0.000	0.000	0.000	0.000
15	A	2707	LEU	0	0.006	0.009	14.938	0.063	0.063	0.000	0.000	0.000	0.000
16	A	2708	LEU	0	-0.006	-0.005	14.135	0.121	0.121	0.000	0.000	0.000	0.000
17	A	2709	GLN	0	0.002	0.001	15.344	0.086	0.086	0.000	0.000	0.000	0.000
18	A	2710	PHE	0	0.020	0.014	14.990	0.042	0.042	0.000	0.000	0.000	0.000
19	A	2711	LYS	1	0.959	0.984	10.990	-0.802	-0.802	0.000	0.000	0.000	0.000
20	A	2712	ARG	1	0.964	0.993	12.064	-0.386	-0.386	0.000	0.000	0.000	0.000
21	A	2713	TRP	0	-0.088	-0.054	14.063	0.017	0.017	0.000	0.000	0.000	0.000
22	A	2714	PHE	0	0.057	0.017	8.862	-0.102	-0.102	0.000	0.000	0.000	0.000
23	A	2715	TRP	0	0.066	0.029	5.894	0.078	0.078	0.000	0.000	0.000	0.000
24	A	2716	SER	0	-0.049	0.006	10.889	-0.172	-0.172	0.000	0.000	0.000	0.000
25	A	2717	ILE	0	-0.033	-0.035	14.216	-0.095	-0.095	0.000	0.000	0.000	0.000
26	A	2718	VAL	0	0.058	0.023	9.014	-0.098	-0.098	0.000	0.000	0.000	0.000
27	A	2719	GLU	-1	-0.939	-0.981	10.158	1.040	1.040	0.000	0.000	0.000	0.000
28	A	2720	LYS	1	0.817	0.915	12.772	-0.551	-0.551	0.000	0.000	0.000	0.000
29	A	2721	MET	0	-0.016	0.038	13.421	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	2722	SER	0	0.021	0.028	15.195	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	2723	MET	0	0.036	-0.004	13.727	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	2724	THR	0	0.005	-0.003	14.418	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	2725	GLU	-1	-0.859	-0.934	15.615	0.128	0.128	0.000	0.000	0.000	0.000
34	A	2726	ARG	1	0.913	0.936	10.429	-0.179	-0.179	0.000	0.000	0.000	0.000
35	A	2727	GLN	0	-0.016	-0.006	10.502	-0.030	-0.030	0.000	0.000	0.000	0.000
36	A	2728	ASP	-1	-0.766	-0.866	11.956	-0.098	-0.098	0.000	0.000	0.000	0.000
37	A	2729	LEU	0	-0.054	-0.026	9.517	0.001	0.001	0.000	0.000	0.000	0.000
38	A	2730	VAL	0	0.000	-0.008	6.288	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	2731	TYR	0	0.017	0.052	8.577	-0.112	-0.112	0.000	0.000	0.000	0.000
40	A	2732	PHE	0	-0.001	0.002	11.483	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	2733	TRP	0	-0.071	-0.035	6.786	0.196	0.196	0.000	0.000	0.000	0.000
42	A	2734	THR	0	-0.005	-0.055	5.673	-0.075	-0.075	0.000	0.000	0.000	0.000
43	A	2735	SER	0	-0.084	-0.029	8.960	0.011	0.011	0.000	0.000	0.000	0.000
44	A	2736	SER	0	-0.018	0.001	8.370	0.024	0.024	0.000	0.000	0.000	0.000
45	A	2737	PRO	0	0.017	0.000	9.723	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	2750	PRO	0	0.057	0.014	2.520	-1.678	-0.210	0.894	-0.680	-1.682	0.001
47	A	2751	SER	0	-0.020	0.026	3.538	0.540	0.451	0.010	0.212	-0.133	0.000
48	A	2752	ILE	0	0.025	0.017	6.833	0.090	0.090	0.000	0.000	0.000	0.000
49	A	2753	THR	0	0.001	0.007	10.113	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	2754	ILE	0	-0.031	-0.007	12.983	0.031	0.031	0.000	0.000	0.000	0.000
51	A	2755	ARG	1	0.902	0.948	16.103	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	2756	PRO	0	0.025	0.004	19.464	0.032	0.032	0.000	0.000	0.000	0.000
53	A	2757	PRO	0	-0.046	-0.012	22.922	0.000	0.000	0.000	0.000	0.000	0.000
54	A	2758	ASP	-1	-0.829	-0.920	23.996	0.075	0.075	0.000	0.000	0.000	0.000
55	A	2759	ASP	-1	-0.815	-0.916	24.402	0.181	0.181	0.000	0.000	0.000	0.000
56	A	2760	GLN	0	-0.072	-0.044	26.172	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	2761	HIS	0	0.023	0.046	20.599	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	2762	LEU	0	-0.020	0.008	20.625	0.027	0.027	0.000	0.000	0.000	0.000
59	A	2763	PRO	0	0.007	0.004	15.841	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	2764	THR	0	-0.014	-0.005	16.212	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	2765	ALA	0	0.032	0.010	12.021	0.033	0.033	0.000	0.000	0.000	0.000
62	A	2766	ASN	0	-0.008	0.009	12.571	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	2767	THR	0	0.053	0.011	10.867	-0.053	-0.053	0.000	0.000	0.000	0.000
64	A	2768	CYS	0	-0.015	0.000	10.630	-0.078	-0.078	0.000	0.000	0.000	0.000
65	A	2769	ILE	0	-0.028	-0.012	9.914	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	2770	SER	0	-0.014	0.003	5.605	-0.229	-0.229	0.000	0.000	0.000	0.000
67	A	2771	ARG	1	0.873	0.947	6.772	0.270	0.270	0.000	0.000	0.000	0.000
68	A	2772	LEU	0	0.016	0.021	9.363	0.039	0.039	0.000	0.000	0.000	0.000
69	A	2773	TYR	0	-0.009	-0.015	11.152	0.043	0.043	0.000	0.000	0.000	0.000
70	A	2774	VAL	0	0.002	-0.017	14.269	0.005	0.005	0.000	0.000	0.000	0.000
71	A	2775	PRO	0	0.039	0.032	16.496	0.025	0.025	0.000	0.000	0.000	0.000
72	A	2776	LEU	0	-0.002	0.009	18.528	0.039	0.039	0.000	0.000	0.000	0.000
73	A	2777	TYR	0	-0.060	-0.085	19.103	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	2778	SER	0	-0.017	-0.022	21.987	0.028	0.028	0.000	0.000	0.000	0.000
75	A	2779	SER	0	0.022	0.005	23.385	0.002	0.002	0.000	0.000	0.000	0.000
76	A	2780	LYS	1	0.929	0.965	17.804	-0.428	-0.428	0.000	0.000	0.000	0.000
77	A	2781	GLN	0	-0.020	-0.022	20.719	0.013	0.013	0.000	0.000	0.000	0.000
78	A	2782	ILE	0	0.020	0.026	23.202	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	2783	LEU	0	0.007	0.016	15.476	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	2784	LYS	1	0.935	0.964	18.789	-0.235	-0.235	0.000	0.000	0.000	0.000
81	A	2785	GLN	0	0.022	0.018	19.805	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	2786	LYS	1	0.932	0.970	21.377	-0.134	-0.134	0.000	0.000	0.000	0.000
83	A	2787	LEU	0	0.015	0.012	13.644	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	2788	LEU	0	-0.021	-0.022	17.325	-0.024	-0.024	0.000	0.000	0.000	0.000
85	A	2789	LEU	0	-0.044	-0.025	19.089	-0.027	-0.027	0.000	0.000	0.000	0.000
86	A	2790	ALA	0	-0.042	-0.014	17.707	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	2791	ILE	0	-0.060	-0.021	14.045	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	2792	LYS	1	0.860	0.941	16.734	-0.046	-0.046	0.000	0.000	0.000	0.000

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