FMO DATABASE

FMODB ID: 7GQVK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-635650.255014
FMO2-HF: Nuclear repulsion	600689.585387
FMO2-HF: Total energy	-34960.669627
FMO2-MP2: Total energy	-35064.480976

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.
-2.242	-0.072999999999999	0.173	-0.791	-1.549	0.001

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 : -0.027 / q_NPA : -0.016

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	-0.031	0.000	3.874	1.243	2.607	-0.009	-0.579	-0.775	0.002
4	B	7	ILE	0	-0.017	-0.014	5.915	0.397	0.397	0.000	0.000	0.000	0.000
5	B	8	TYR	0	-0.033	-0.031	9.146	0.218	0.218	0.000	0.000	0.000	0.000
6	B	9	GLN	0	-0.024	-0.012	12.344	-0.009	-0.009	0.000	0.000	0.000	0.000
7	B	10	PHE	0	-0.008	-0.001	14.184	0.015	0.015	0.000	0.000	0.000	0.000
8	B	11	HIS	0	0.019	0.017	19.151	0.010	0.010	0.000	0.000	0.000	0.000
9	B	12	SER	0	-0.090	-0.067	22.548	0.022	0.022	0.000	0.000	0.000	0.000
10	B	13	PHE	0	0.045	0.005	20.970	-0.025	-0.025	0.000	0.000	0.000	0.000
11	B	14	GLU	-1	-0.838	-0.898	22.619	-0.239	-0.239	0.000	0.000	0.000	0.000
12	B	15	ASP	-1	-0.802	-0.879	20.191	-0.286	-0.286	0.000	0.000	0.000	0.000
13	B	16	ILE	0	-0.010	-0.008	17.286	-0.023	-0.023	0.000	0.000	0.000	0.000
14	B	17	ILE	0	-0.006	0.018	19.177	-0.028	-0.028	0.000	0.000	0.000	0.000
15	B	18	GLN	0	-0.077	-0.063	21.461	0.000	0.000	0.000	0.000	0.000	0.000
16	B	19	LEU	0	-0.006	0.012	13.869	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	20	SER	0	-0.023	-0.033	17.244	-0.043	-0.043	0.000	0.000	0.000	0.000
18	B	21	GLU	-1	-0.842	-0.903	18.380	-0.251	-0.251	0.000	0.000	0.000	0.000
19	B	22	SER	0	-0.075	-0.052	17.049	0.020	0.020	0.000	0.000	0.000	0.000
20	B	23	LEU	0	-0.012	0.002	11.942	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	24	GLN	0	0.052	0.031	15.132	0.017	0.017	0.000	0.000	0.000	0.000
22	B	25	ARG	1	0.885	0.949	17.587	0.243	0.243	0.000	0.000	0.000	0.000
23	B	26	ILE	0	-0.048	-0.008	11.750	0.039	0.039	0.000	0.000	0.000	0.000
24	B	27	GLY	0	-0.029	0.002	14.749	0.027	0.027	0.000	0.000	0.000	0.000
25	B	28	ILE	0	-0.076	-0.043	9.388	-0.045	-0.045	0.000	0.000	0.000	0.000
26	B	29	THR	0	0.019	-0.020	13.014	0.005	0.005	0.000	0.000	0.000	0.000
27	B	30	GLY	0	0.029	0.030	13.122	0.047	0.047	0.000	0.000	0.000	0.000
28	B	31	GLY	0	0.021	0.010	11.845	-0.006	-0.006	0.000	0.000	0.000	0.000
29	B	32	THR	0	-0.053	-0.014	12.269	0.222	0.222	0.000	0.000	0.000	0.000
30	B	33	VAL	0	0.019	0.006	14.150	-0.061	-0.061	0.000	0.000	0.000	0.000
31	B	34	TYR	0	0.004	-0.004	14.410	0.079	0.079	0.000	0.000	0.000	0.000
32	B	35	HIS	0	-0.045	-0.015	18.867	0.020	0.020	0.000	0.000	0.000	0.000
33	B	36	TYR	0	-0.072	-0.063	19.784	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	37	ASP	-1	-0.847	-0.912	22.180	-0.235	-0.235	0.000	0.000	0.000	0.000
35	B	38	GLY	0	-0.029	-0.007	24.329	0.013	0.013	0.000	0.000	0.000	0.000
36	B	39	GLN	0	-0.043	-0.021	20.742	0.024	0.024	0.000	0.000	0.000	0.000
37	B	40	TYR	0	-0.002	-0.012	20.088	0.001	0.001	0.000	0.000	0.000	0.000
38	B	41	PHE	0	-0.007	-0.021	14.986	0.001	0.001	0.000	0.000	0.000	0.000
39	B	42	LEU	0	0.013	0.009	12.285	0.049	0.049	0.000	0.000	0.000	0.000
40	B	43	SER	0	-0.065	-0.047	9.472	-0.116	-0.116	0.000	0.000	0.000	0.000
41	B	44	LEU	0	0.026	-0.003	7.695	0.362	0.362	0.000	0.000	0.000	0.000
42	B	45	GLU	-1	-0.816	-0.894	5.690	-2.905	-2.905	0.000	0.000	0.000	0.000
43	B	46	ASP	-1	-0.871	-0.924	4.985	-1.946	-1.904	-0.001	-0.006	-0.035	0.000
44	B	47	LEU	0	0.012	0.012	2.858	-0.184	0.252	0.122	-0.117	-0.441	-0.001
45	B	48	GLY	0	0.019	0.009	6.797	0.439	0.439	0.000	0.000	0.000	0.000
46	B	49	SER	0	-0.091	-0.050	7.950	0.067	0.067	0.000	0.000	0.000	0.000
47	B	50	HIS	1	0.782	0.885	8.322	0.624	0.624	0.000	0.000	0.000	0.000
48	B	51	THR	0	0.029	0.001	6.682	-0.078	-0.078	0.000	0.000	0.000	0.000
49	B	52	ALA	0	0.081	0.044	3.305	-0.488	-0.227	0.062	-0.087	-0.236	0.000
50	B	53	GLU	-1	-0.884	-0.952	5.228	0.531	0.597	-0.001	-0.002	-0.062	0.000
51	B	54	GLY	0	-0.025	-0.008	7.824	-0.066	-0.066	0.000	0.000	0.000	0.000
52	B	55	VAL	0	0.016	0.007	7.076	-0.005	-0.005	0.000	0.000	0.000	0.000
53	B	56	VAL	0	0.009	-0.006	5.962	-0.029	-0.029	0.000	0.000	0.000	0.000
54	B	57	ALA	0	-0.030	-0.010	8.727	0.044	0.044	0.000	0.000	0.000	0.000
55	B	58	VAL	0	0.027	0.007	12.075	0.007	0.007	0.000	0.000	0.000	0.000
56	B	59	LEU	0	-0.006	-0.005	8.896	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	60	ALA	0	-0.054	-0.025	12.844	0.025	0.025	0.000	0.000	0.000	0.000
58	B	61	GLU	-1	-0.933	-0.932	14.668	-0.194	-0.194	0.000	0.000	0.000	0.000
59	B	62	TYR	0	-0.042	-0.033	16.397	0.024	0.024	0.000	0.000	0.000	0.000
60	B	63	GLY	0	0.036	0.019	16.307	0.005	0.005	0.000	0.000	0.000	0.000
61	B	64	ASN	0	-0.088	-0.046	15.409	0.050	0.050	0.000	0.000	0.000	0.000
62	B	65	PRO	0	0.066	0.038	11.366	-0.063	-0.063	0.000	0.000	0.000	0.000
63	B	66	THR	0	0.011	0.006	11.988	0.099	0.099	0.000	0.000	0.000	0.000
64	B	67	THR	0	-0.006	-0.005	11.876	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	68	LEU	0	-0.079	-0.028	13.800	0.040	0.040	0.000	0.000	0.000	0.000
66	B	69	THR	0	0.026	0.010	11.102	-0.098	-0.098	0.000	0.000	0.000	0.000
67	B	70	ILE	0	0.096	0.041	9.277	0.109	0.109	0.000	0.000	0.000	0.000
68	B	71	TYR	0	0.013	0.001	9.015	0.156	0.156	0.000	0.000	0.000	0.000
69	B	72	ARG	1	0.950	0.983	14.372	0.316	0.316	0.000	0.000	0.000	0.000
70	B	73	LEU	0	-0.002	0.006	13.581	0.043	0.043	0.000	0.000	0.000	0.000
71	B	74	GLN	0	-0.015	-0.016	13.433	-0.018	-0.018	0.000	0.000	0.000	0.000
72	B	75	GLU	-1	-0.903	-0.923	17.348	-0.201	-0.201	0.000	0.000	0.000	0.000
73	B	76	TYR	0	-0.123	-0.080	20.109	0.040	0.040	0.000	0.000	0.000	0.000
74	B	77	GLY	0	0.009	0.015	20.108	0.020	0.020	0.000	0.000	0.000	0.000
75	B	78	LYS	1	0.857	0.927	21.099	0.305	0.305	0.000	0.000	0.000	0.000
76	B	79	LEU	0	0.030	0.016	17.563	-0.007	-0.007	0.000	0.000	0.000	0.000
77	B	80	ILE	0	-0.091	-0.044	20.148	0.058	0.058	0.000	0.000	0.000	0.000
78	B	81	MET	0	-0.029	-0.001	19.151	0.028	0.028	0.000	0.000	0.000	0.000
79	B	82	ASP	-1	-0.880	-0.943	16.599	-0.665	-0.665	0.000	0.000	0.000	0.000
80	B	83	GLY	0	0.029	0.026	13.749	0.049	0.049	0.000	0.000	0.000	0.000
81	B	84	ASN	0	0.003	-0.010	14.673	-0.053	-0.053	0.000	0.000	0.000	0.000
82	B	85	ALA	0	0.014	0.012	16.050	0.071	0.071	0.000	0.000	0.000	0.000
83	B	86	VAL	0	0.025	0.028	14.855	0.068	0.068	0.000	0.000	0.000	0.000
84	B	87	GLU	-1	-0.804	-0.911	17.680	-0.337	-0.337	0.000	0.000	0.000	0.000
85	B	88	THR	0	-0.084	-0.040	19.893	0.062	0.062	0.000	0.000	0.000	0.000
86	B	89	ILE	0	-0.019	-0.015	19.329	0.039	0.039	0.000	0.000	0.000	0.000
87	B	90	GLN	0	-0.037	-0.052	20.471	0.026	0.026	0.000	0.000	0.000	0.000
88	B	91	THR	0	-0.100	-0.048	23.245	0.036	0.036	0.000	0.000	0.000	0.000
89	B	92	HIS	0	-0.086	-0.052	25.541	0.013	0.013	0.000	0.000	0.000	0.000
90	B	93	PHE	0	-0.028	0.005	25.930	0.015	0.015	0.000	0.000	0.000	0.000

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