FMO DATABASE

FMODB ID: 9GZV2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-633021.419051
FMO2-HF: Nuclear repulsion	598061.530168
FMO2-HF: Total energy	-34959.888883
FMO2-MP2: Total energy	-35063.686845

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.
-2.835	-0.209	0.203	-1.029	-1.798	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 : -0.040 / q_NPA : -0.022

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	-0.067	-0.023	3.356	0.881	2.774	0.011	-0.821	-1.083	0.003
4	B	7	ILE	0	0.009	-0.006	5.516	0.112	0.112	0.000	0.000	0.000	0.000
5	B	8	TYR	0	0.002	-0.010	8.331	0.224	0.224	0.000	0.000	0.000	0.000
6	B	9	GLN	0	0.019	0.017	11.893	-0.046	-0.046	0.000	0.000	0.000	0.000
7	B	10	PHE	0	-0.003	-0.005	13.535	0.024	0.024	0.000	0.000	0.000	0.000
8	B	11	HIS	0	0.062	0.040	18.560	-0.011	-0.011	0.000	0.000	0.000	0.000
9	B	12	SER	0	-0.043	-0.019	21.873	0.012	0.012	0.000	0.000	0.000	0.000
10	B	13	PHE	0	0.022	-0.004	20.900	-0.018	-0.018	0.000	0.000	0.000	0.000
11	B	14	GLU	-1	-0.913	-0.953	22.078	-0.195	-0.195	0.000	0.000	0.000	0.000
12	B	15	ASP	-1	-0.837	-0.917	19.469	-0.212	-0.212	0.000	0.000	0.000	0.000
13	B	16	ILE	0	-0.038	-0.025	16.922	-0.019	-0.019	0.000	0.000	0.000	0.000
14	B	17	ILE	0	-0.011	0.000	18.819	-0.025	-0.025	0.000	0.000	0.000	0.000
15	B	18	GLN	0	-0.023	-0.013	21.295	0.000	0.000	0.000	0.000	0.000	0.000
16	B	19	LEU	0	0.021	0.017	13.617	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	20	SER	0	-0.022	-0.015	16.941	-0.044	-0.044	0.000	0.000	0.000	0.000
18	B	21	GLU	-1	-0.843	-0.907	18.004	-0.244	-0.244	0.000	0.000	0.000	0.000
19	B	22	SER	0	-0.070	-0.038	16.770	0.022	0.022	0.000	0.000	0.000	0.000
20	B	23	LEU	0	-0.010	-0.010	11.744	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	24	GLN	0	0.079	0.038	14.895	0.001	0.001	0.000	0.000	0.000	0.000
22	B	25	ARG	1	0.874	0.944	17.478	0.184	0.184	0.000	0.000	0.000	0.000
23	B	26	ILE	0	-0.061	-0.017	12.059	0.031	0.031	0.000	0.000	0.000	0.000
24	B	27	GLY	0	-0.021	-0.019	14.701	0.019	0.019	0.000	0.000	0.000	0.000
25	B	28	ILE	0	-0.041	-0.006	8.989	-0.044	-0.044	0.000	0.000	0.000	0.000
26	B	29	THR	0	0.056	-0.003	12.590	0.031	0.031	0.000	0.000	0.000	0.000
27	B	30	GLY	0	0.050	0.042	13.102	0.052	0.052	0.000	0.000	0.000	0.000
28	B	31	GLY	0	0.022	0.007	11.967	0.060	0.060	0.000	0.000	0.000	0.000
29	B	32	THR	0	-0.004	0.003	12.828	0.135	0.135	0.000	0.000	0.000	0.000
30	B	33	VAL	0	0.002	0.005	14.326	-0.033	-0.033	0.000	0.000	0.000	0.000
31	B	34	TYR	0	0.001	-0.010	14.412	0.068	0.068	0.000	0.000	0.000	0.000
32	B	35	HIS	0	-0.015	-0.001	18.476	0.028	0.028	0.000	0.000	0.000	0.000
33	B	36	TYR	0	-0.004	-0.024	19.537	0.000	0.000	0.000	0.000	0.000	0.000
34	B	37	ASP	-1	-0.884	-0.938	21.792	-0.179	-0.179	0.000	0.000	0.000	0.000
35	B	38	GLY	0	-0.045	-0.009	24.041	0.012	0.012	0.000	0.000	0.000	0.000
36	B	39	GLN	0	-0.067	-0.039	20.083	0.022	0.022	0.000	0.000	0.000	0.000
37	B	40	TYR	0	-0.013	-0.019	19.133	-0.008	-0.008	0.000	0.000	0.000	0.000
38	B	41	PHE	0	-0.016	-0.021	14.520	0.007	0.007	0.000	0.000	0.000	0.000
39	B	42	LEU	0	0.008	0.013	11.799	0.002	0.002	0.000	0.000	0.000	0.000
40	B	43	SER	0	-0.042	-0.020	9.909	-0.145	-0.145	0.000	0.000	0.000	0.000
41	B	44	LEU	0	0.006	-0.015	7.375	0.217	0.217	0.000	0.000	0.000	0.000
42	B	45	GLU	-1	-0.897	-0.945	5.785	-2.688	-2.688	0.000	0.000	0.000	0.000
43	B	46	ASP	-1	-0.890	-0.938	5.048	-2.522	-2.529	-0.001	-0.006	0.015	0.000
44	B	47	LEU	0	-0.011	-0.009	2.801	0.290	0.696	0.129	-0.112	-0.422	-0.001
45	B	48	GLY	0	0.033	0.022	6.805	0.529	0.529	0.000	0.000	0.000	0.000
46	B	49	SER	0	-0.089	-0.051	8.496	0.028	0.028	0.000	0.000	0.000	0.000
47	B	50	HIS	1	0.833	0.925	8.699	0.642	0.642	0.000	0.000	0.000	0.000
48	B	51	THR	0	0.022	0.004	7.011	-0.116	-0.116	0.000	0.000	0.000	0.000
49	B	52	ALA	0	0.084	0.035	3.248	-0.522	-0.248	0.065	-0.088	-0.251	0.000
50	B	53	GLU	-1	-0.878	-0.950	5.141	1.007	1.067	-0.001	-0.002	-0.057	0.000
51	B	54	GLY	0	-0.041	-0.015	7.858	-0.100	-0.100	0.000	0.000	0.000	0.000
52	B	55	VAL	0	0.022	0.009	6.932	-0.040	-0.040	0.000	0.000	0.000	0.000
53	B	56	VAL	0	-0.007	-0.011	5.841	-0.047	-0.047	0.000	0.000	0.000	0.000
54	B	57	ALA	0	-0.047	-0.020	8.449	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	58	VAL	0	0.043	0.023	11.826	-0.004	-0.004	0.000	0.000	0.000	0.000
56	B	59	LEU	0	-0.015	-0.010	8.430	-0.025	-0.025	0.000	0.000	0.000	0.000
57	B	60	ALA	0	-0.035	-0.023	12.303	0.015	0.015	0.000	0.000	0.000	0.000
58	B	61	GLU	-1	-1.002	-0.981	13.827	-0.102	-0.102	0.000	0.000	0.000	0.000
59	B	62	TYR	0	-0.004	0.001	16.032	0.008	0.008	0.000	0.000	0.000	0.000
60	B	63	GLY	0	0.021	-0.003	15.572	0.002	0.002	0.000	0.000	0.000	0.000
61	B	64	ASN	0	-0.122	-0.055	14.931	0.034	0.034	0.000	0.000	0.000	0.000
62	B	65	PRO	0	0.050	0.029	10.764	-0.067	-0.067	0.000	0.000	0.000	0.000
63	B	66	THR	0	-0.001	0.005	11.270	0.073	0.073	0.000	0.000	0.000	0.000
64	B	67	THR	0	0.015	-0.001	11.599	0.007	0.007	0.000	0.000	0.000	0.000
65	B	68	LEU	0	-0.062	-0.022	13.240	0.017	0.017	0.000	0.000	0.000	0.000
66	B	69	THR	0	0.020	0.016	11.189	-0.067	-0.067	0.000	0.000	0.000	0.000
67	B	70	ILE	0	0.124	0.040	9.860	0.079	0.079	0.000	0.000	0.000	0.000
68	B	71	TYR	0	-0.002	-0.007	10.022	0.110	0.110	0.000	0.000	0.000	0.000
69	B	72	ARG	1	0.951	0.987	14.699	0.252	0.252	0.000	0.000	0.000	0.000
70	B	73	LEU	0	-0.001	0.009	13.460	0.037	0.037	0.000	0.000	0.000	0.000
71	B	74	GLN	0	-0.028	-0.006	13.500	-0.066	-0.066	0.000	0.000	0.000	0.000
72	B	75	GLU	-1	-0.973	-0.971	17.754	-0.216	-0.216	0.000	0.000	0.000	0.000
73	B	76	TYR	0	-0.064	-0.045	20.181	0.035	0.035	0.000	0.000	0.000	0.000
74	B	77	GLY	0	-0.016	0.000	20.014	0.021	0.021	0.000	0.000	0.000	0.000
75	B	78	LYS	1	0.895	0.951	21.027	0.293	0.293	0.000	0.000	0.000	0.000
76	B	79	LEU	0	0.016	-0.003	18.080	-0.009	-0.009	0.000	0.000	0.000	0.000
77	B	80	ILE	0	-0.091	-0.041	20.349	0.045	0.045	0.000	0.000	0.000	0.000
78	B	81	MET	0	-0.022	-0.010	18.943	0.018	0.018	0.000	0.000	0.000	0.000
79	B	82	ASP	-1	-0.884	-0.946	17.287	-0.671	-0.671	0.000	0.000	0.000	0.000
80	B	83	GLY	0	0.080	0.041	14.478	0.023	0.023	0.000	0.000	0.000	0.000
81	B	84	ASN	0	-0.047	-0.023	15.321	-0.034	-0.034	0.000	0.000	0.000	0.000
82	B	85	ALA	0	0.005	-0.004	15.612	0.071	0.071	0.000	0.000	0.000	0.000
83	B	86	VAL	0	0.002	0.012	14.623	0.068	0.068	0.000	0.000	0.000	0.000
84	B	87	GLU	-1	-0.920	-0.954	17.466	-0.330	-0.330	0.000	0.000	0.000	0.000
85	B	88	THR	0	-0.037	-0.024	20.017	0.061	0.061	0.000	0.000	0.000	0.000
86	B	89	ILE	0	-0.050	-0.022	19.063	0.037	0.037	0.000	0.000	0.000	0.000
87	B	90	GLN	0	-0.027	-0.031	20.393	0.021	0.021	0.000	0.000	0.000	0.000
88	B	91	THR	0	-0.052	-0.014	23.031	0.035	0.035	0.000	0.000	0.000	0.000
89	B	92	HIS	0	-0.099	-0.027	25.551	0.014	0.014	0.000	0.000	0.000	0.000
90	B	93	PHE	0	-0.040	-0.033	25.765	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)