FMO DATABASE

FMODB ID: M341Z

Calculation Name: 3JTO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JTO

Chain ID: B

ChEMBL ID:

UniProt ID: P50734

Base Structure: X-ray

Registration Date: 2023-06-19

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	OptHSide
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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-633397.874139
FMO2-HF: Nuclear repulsion	598437.532811
FMO2-HF: Total energy	-34960.341328
FMO2-MP2: Total energy	-35064.129945

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(B:4:ALA)

Summations of interaction energy for fragment #1(B:4:ALA)

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.
-2.632	0.0059999999999995	0.249	-1.048	-1.837	0.002

Interaction energy analysis for fragmet #1(B:4:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.017

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	B	6	ILE	0	-0.040	-0.012	3.402	0.815	2.664	-0.003	-0.818	-1.028	0.003
4	B	7	ILE	0	-0.014	-0.020	5.590	0.068	0.068	0.000	0.000	0.000	0.000
5	B	8	TYR	0	0.008	0.004	8.608	0.228	0.228	0.000	0.000	0.000	0.000
6	B	9	GLN	0	-0.004	-0.004	11.965	-0.054	-0.054	0.000	0.000	0.000	0.000
7	B	10	PHE	0	-0.004	-0.011	13.668	0.026	0.026	0.000	0.000	0.000	0.000
8	B	11	HIS	0	0.038	0.028	18.628	-0.010	-0.010	0.000	0.000	0.000	0.000
9	B	12	SER	0	-0.059	-0.034	21.961	0.011	0.011	0.000	0.000	0.000	0.000
10	B	13	PHE	0	0.038	-0.001	20.504	-0.016	-0.016	0.000	0.000	0.000	0.000
11	B	14	GLU	-1	-0.858	-0.912	22.132	-0.188	-0.188	0.000	0.000	0.000	0.000
12	B	15	ASP	-1	-0.821	-0.903	19.615	-0.200	-0.200	0.000	0.000	0.000	0.000
13	B	16	ILE	0	-0.033	-0.021	16.761	-0.016	-0.016	0.000	0.000	0.000	0.000
14	B	17	ILE	0	-0.006	0.009	18.870	-0.024	-0.024	0.000	0.000	0.000	0.000
15	B	18	GLN	0	-0.071	-0.049	21.405	0.005	0.005	0.000	0.000	0.000	0.000
16	B	19	LEU	0	-0.010	0.013	13.587	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	20	SER	0	-0.029	-0.029	16.966	-0.041	-0.041	0.000	0.000	0.000	0.000
18	B	21	GLU	-1	-0.826	-0.893	18.034	-0.216	-0.216	0.000	0.000	0.000	0.000
19	B	22	SER	0	-0.084	-0.045	16.671	0.017	0.017	0.000	0.000	0.000	0.000
20	B	23	LEU	0	-0.016	-0.010	11.737	-0.003	-0.003	0.000	0.000	0.000	0.000
21	B	24	GLN	0	0.074	0.032	14.925	0.004	0.004	0.000	0.000	0.000	0.000
22	B	25	ARG	1	0.877	0.946	17.496	0.167	0.167	0.000	0.000	0.000	0.000
23	B	26	ILE	0	-0.052	-0.009	11.528	0.032	0.032	0.000	0.000	0.000	0.000
24	B	27	GLY	0	-0.021	-0.016	14.703	0.021	0.021	0.000	0.000	0.000	0.000
25	B	28	ILE	0	-0.060	-0.013	9.101	-0.044	-0.044	0.000	0.000	0.000	0.000
26	B	29	THR	0	0.060	0.005	12.598	0.024	0.024	0.000	0.000	0.000	0.000
27	B	30	GLY	0	0.042	0.039	13.109	0.046	0.046	0.000	0.000	0.000	0.000
28	B	31	GLY	0	0.020	0.006	11.982	0.060	0.060	0.000	0.000	0.000	0.000
29	B	32	THR	0	-0.008	0.001	12.826	0.135	0.135	0.000	0.000	0.000	0.000
30	B	33	VAL	0	0.001	0.006	14.345	-0.031	-0.031	0.000	0.000	0.000	0.000
31	B	34	TYR	0	0.012	-0.007	14.748	0.062	0.062	0.000	0.000	0.000	0.000
32	B	35	HIS	0	-0.034	-0.008	18.476	0.031	0.031	0.000	0.000	0.000	0.000
33	B	36	TYR	0	-0.045	-0.039	19.696	-0.008	-0.008	0.000	0.000	0.000	0.000
34	B	37	ASP	-1	-0.851	-0.922	21.871	-0.188	-0.188	0.000	0.000	0.000	0.000
35	B	38	GLY	0	-0.028	-0.007	24.060	0.013	0.013	0.000	0.000	0.000	0.000
36	B	39	GLN	0	-0.054	-0.028	20.110	0.020	0.020	0.000	0.000	0.000	0.000
37	B	40	TYR	0	-0.013	-0.019	19.294	-0.010	-0.010	0.000	0.000	0.000	0.000
38	B	41	PHE	0	0.004	-0.012	14.574	0.011	0.011	0.000	0.000	0.000	0.000
39	B	42	LEU	0	0.011	0.017	12.149	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	43	SER	0	-0.028	-0.016	9.123	-0.029	-0.029	0.000	0.000	0.000	0.000
41	B	44	LEU	0	-0.005	-0.014	7.325	0.194	0.194	0.000	0.000	0.000	0.000
42	B	45	GLU	-1	-0.897	-0.949	5.777	-2.620	-2.620	0.000	0.000	0.000	0.000
43	B	46	ASP	-1	-0.860	-0.923	5.021	-2.429	-2.436	-0.001	-0.007	0.016	0.000
44	B	47	LEU	0	0.001	0.001	2.754	0.182	0.635	0.194	-0.134	-0.512	-0.001
45	B	48	GLY	0	0.040	0.025	6.791	0.519	0.519	0.000	0.000	0.000	0.000
46	B	49	SER	0	-0.089	-0.050	8.455	0.038	0.038	0.000	0.000	0.000	0.000
47	B	50	HIS	1	0.812	0.898	8.571	0.602	0.602	0.000	0.000	0.000	0.000
48	B	51	THR	0	0.021	0.005	6.998	-0.088	-0.088	0.000	0.000	0.000	0.000
49	B	52	ALA	0	0.079	0.036	3.301	-0.537	-0.265	0.060	-0.087	-0.245	0.000
50	B	53	GLU	-1	-0.883	-0.955	5.167	1.143	1.214	-0.001	-0.002	-0.068	0.000
51	B	54	GLY	0	-0.036	-0.013	7.836	-0.118	-0.118	0.000	0.000	0.000	0.000
52	B	55	VAL	0	0.024	0.009	6.987	-0.056	-0.056	0.000	0.000	0.000	0.000
53	B	56	VAL	0	-0.003	-0.011	5.735	-0.063	-0.063	0.000	0.000	0.000	0.000
54	B	57	ALA	0	-0.045	-0.017	8.472	-0.021	-0.021	0.000	0.000	0.000	0.000
55	B	58	VAL	0	0.034	0.008	11.857	-0.008	-0.008	0.000	0.000	0.000	0.000
56	B	59	LEU	0	0.007	0.006	8.351	-0.027	-0.027	0.000	0.000	0.000	0.000
57	B	60	ALA	0	-0.047	-0.031	12.352	0.010	0.010	0.000	0.000	0.000	0.000
58	B	61	GLU	-1	-0.941	-0.939	13.868	-0.090	-0.090	0.000	0.000	0.000	0.000
59	B	62	TYR	0	-0.033	-0.027	15.847	0.000	0.000	0.000	0.000	0.000	0.000
60	B	63	GLY	0	0.021	0.008	15.626	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	64	ASN	0	-0.099	-0.050	14.949	0.038	0.038	0.000	0.000	0.000	0.000
62	B	65	PRO	0	0.050	0.036	10.773	-0.066	-0.066	0.000	0.000	0.000	0.000
63	B	66	THR	0	-0.008	-0.003	11.347	0.064	0.064	0.000	0.000	0.000	0.000
64	B	67	THR	0	-0.004	-0.003	11.616	0.011	0.011	0.000	0.000	0.000	0.000
65	B	68	LEU	0	-0.079	-0.028	13.254	0.013	0.013	0.000	0.000	0.000	0.000
66	B	69	THR	0	0.033	0.016	11.204	-0.060	-0.060	0.000	0.000	0.000	0.000
67	B	70	ILE	0	0.116	0.039	9.728	0.093	0.093	0.000	0.000	0.000	0.000
68	B	71	TYR	0	-0.005	-0.007	9.568	0.148	0.148	0.000	0.000	0.000	0.000
69	B	72	ARG	1	0.959	0.991	14.709	0.265	0.265	0.000	0.000	0.000	0.000
70	B	73	LEU	0	0.004	0.012	13.526	0.040	0.040	0.000	0.000	0.000	0.000
71	B	74	GLN	0	-0.004	0.001	13.709	-0.043	-0.043	0.000	0.000	0.000	0.000
72	B	75	GLU	-1	-0.980	-0.975	17.769	-0.221	-0.221	0.000	0.000	0.000	0.000
73	B	76	TYR	0	-0.063	-0.045	20.191	0.037	0.037	0.000	0.000	0.000	0.000
74	B	77	GLY	0	-0.010	0.003	20.031	0.023	0.023	0.000	0.000	0.000	0.000
75	B	78	LYS	1	0.853	0.921	21.044	0.299	0.299	0.000	0.000	0.000	0.000
76	B	79	LEU	0	0.034	0.011	18.107	-0.007	-0.007	0.000	0.000	0.000	0.000
77	B	80	ILE	0	-0.072	-0.026	20.348	0.047	0.047	0.000	0.000	0.000	0.000
78	B	81	MET	0	-0.016	-0.003	19.019	0.019	0.019	0.000	0.000	0.000	0.000
79	B	82	ASP	-1	-0.893	-0.955	17.295	-0.670	-0.670	0.000	0.000	0.000	0.000
80	B	83	GLY	0	0.070	0.039	14.447	0.023	0.023	0.000	0.000	0.000	0.000
81	B	84	ASN	0	-0.050	-0.027	15.294	-0.028	-0.028	0.000	0.000	0.000	0.000
82	B	85	ALA	0	0.005	0.002	15.611	0.072	0.072	0.000	0.000	0.000	0.000
83	B	86	VAL	0	0.008	0.007	14.643	0.066	0.066	0.000	0.000	0.000	0.000
84	B	87	GLU	-1	-0.904	-0.940	17.488	-0.315	-0.315	0.000	0.000	0.000	0.000
85	B	88	THR	0	-0.058	-0.037	20.028	0.060	0.060	0.000	0.000	0.000	0.000
86	B	89	ILE	0	-0.050	-0.022	18.956	0.035	0.035	0.000	0.000	0.000	0.000
87	B	90	GLN	0	-0.029	-0.042	20.392	0.023	0.023	0.000	0.000	0.000	0.000
88	B	91	THR	0	-0.059	-0.020	23.053	0.033	0.033	0.000	0.000	0.000	0.000
89	B	92	HIS	0	-0.091	-0.025	25.568	0.015	0.015	0.000	0.000	0.000	0.000
90	B	93	PHE	0	-0.039	-0.033	25.566	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:ALA)