FMO DATABASE

FMODB ID: 229KR

Calculation Name: 2JD3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JD3

Chain ID: A

ChEMBL ID:

UniProt ID:

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	-545004.439768
FMO2-HF: Nuclear repulsion	510051.539883
FMO2-HF: Total energy	-34952.899885
FMO2-MP2: Total energy	-35056.849508

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:6:LYS)

Summations of interaction energy for fragment #1(A:6:LYS)

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.
27.778	30.202	0.225	-0.844	-1.803	-0.002

Interaction energy analysis for fragmet #1(A:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.024 / q_NPA : 1.004

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	8	LYS	1	0.879	0.954	2.678	43.071	45.315	0.224	-0.815	-1.652	-0.002
4	A	9	LYS	1	1.006	1.014	4.383	28.668	28.848	0.001	-0.029	-0.151	0.000
5	A	10	TYR	0	0.056	0.013	6.357	-6.121	-6.121	0.000	0.000	0.000	0.000
6	A	11	THR	0	-0.013	-0.018	10.143	0.509	0.509	0.000	0.000	0.000	0.000
7	A	12	LEU	0	0.004	0.017	13.810	-0.601	-0.601	0.000	0.000	0.000	0.000
8	A	13	TYR	0	0.004	-0.010	16.726	-0.185	-0.185	0.000	0.000	0.000	0.000
9	A	14	LEU	0	0.008	0.014	20.551	-0.161	-0.161	0.000	0.000	0.000	0.000
10	A	15	HIS	0	-0.086	-0.051	23.713	-0.400	-0.400	0.000	0.000	0.000	0.000
11	A	16	PRO	0	0.027	0.011	27.230	0.194	0.194	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.825	-0.907	29.890	-10.380	-10.380	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.780	0.883	26.269	11.838	11.838	0.000	0.000	0.000	0.000
14	A	19	ALA	0	0.065	0.022	30.590	-0.219	-0.219	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.081	0.051	28.110	-0.070	-0.070	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.763	-0.869	25.807	-12.243	-12.243	0.000	0.000	0.000	0.000
17	A	22	PHE	0	-0.021	-0.001	27.304	-0.291	-0.291	0.000	0.000	0.000	0.000
18	A	23	GLN	0	0.067	0.028	30.020	-0.023	-0.023	0.000	0.000	0.000	0.000
19	A	24	THR	0	-0.057	-0.040	23.593	-0.257	-0.257	0.000	0.000	0.000	0.000
20	A	25	LEU	0	-0.048	-0.037	25.108	-0.359	-0.359	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.892	-0.947	27.197	-9.460	-9.460	0.000	0.000	0.000	0.000
22	A	27	ALA	0	-0.001	0.010	27.101	0.027	0.027	0.000	0.000	0.000	0.000
23	A	28	ILE	0	-0.041	-0.026	22.094	-0.290	-0.290	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.769	-0.854	25.608	-11.718	-11.718	0.000	0.000	0.000	0.000
25	A	30	SER	0	-0.073	-0.029	28.230	0.195	0.195	0.000	0.000	0.000	0.000
26	A	31	VAL	0	-0.002	0.017	23.073	0.056	0.056	0.000	0.000	0.000	0.000
27	A	32	PRO	0	0.042	0.031	24.657	-0.109	-0.109	0.000	0.000	0.000	0.000
28	A	33	ARG	1	0.828	0.862	22.589	11.213	11.213	0.000	0.000	0.000	0.000
29	A	34	SER	0	-0.013	-0.017	20.028	-0.543	-0.543	0.000	0.000	0.000	0.000
30	A	35	GLU	-1	-0.832	-0.904	18.762	-13.009	-13.009	0.000	0.000	0.000	0.000
31	A	36	ARG	1	0.763	0.859	19.058	11.724	11.724	0.000	0.000	0.000	0.000
32	A	37	GLY	0	-0.014	0.006	15.257	-0.621	-0.621	0.000	0.000	0.000	0.000
33	A	38	GLU	-1	-0.810	-0.900	15.014	-19.749	-19.749	0.000	0.000	0.000	0.000
34	A	39	LEU	0	0.018	0.023	16.180	-0.501	-0.501	0.000	0.000	0.000	0.000
35	A	40	PHE	0	0.020	-0.008	15.991	-0.284	-0.284	0.000	0.000	0.000	0.000
36	A	41	ARG	1	0.822	0.913	11.263	20.564	20.564	0.000	0.000	0.000	0.000
37	A	42	ASN	0	-0.023	-0.035	14.058	-1.068	-1.068	0.000	0.000	0.000	0.000
38	A	43	ALA	0	0.045	0.049	16.614	0.190	0.190	0.000	0.000	0.000	0.000
39	A	44	PHE	0	-0.019	-0.004	9.858	-0.232	-0.232	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.023	-0.017	11.496	-0.378	-0.378	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.020	-0.023	14.106	0.427	0.427	0.000	0.000	0.000	0.000
42	A	47	GLY	0	0.054	0.030	17.501	0.605	0.605	0.000	0.000	0.000	0.000
43	A	48	MET	0	-0.039	-0.025	12.230	0.450	0.450	0.000	0.000	0.000	0.000
44	A	49	ALA	0	0.007	0.001	15.439	0.304	0.304	0.000	0.000	0.000	0.000
45	A	50	LEU	0	0.012	0.002	17.364	0.654	0.654	0.000	0.000	0.000	0.000
46	A	51	HIS	0	0.003	-0.003	16.726	0.732	0.732	0.000	0.000	0.000	0.000
47	A	52	GLN	0	-0.090	-0.054	14.294	-0.694	-0.694	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.030	-0.001	18.349	0.401	0.401	0.000	0.000	0.000	0.000
49	A	54	ASP	-1	-0.735	-0.857	21.786	-11.558	-11.558	0.000	0.000	0.000	0.000
50	A	55	PRO	0	-0.017	0.009	20.459	-0.144	-0.144	0.000	0.000	0.000	0.000
51	A	56	ARG	1	0.826	0.895	21.757	11.125	11.125	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.018	0.024	23.090	0.248	0.248	0.000	0.000	0.000	0.000
53	A	58	PRO	0	0.004	0.011	19.906	0.277	0.277	0.000	0.000	0.000	0.000
54	A	59	VAL	0	-0.001	0.004	22.512	0.244	0.244	0.000	0.000	0.000	0.000
55	A	60	LEU	0	0.002	-0.004	24.914	0.428	0.428	0.000	0.000	0.000	0.000
56	A	61	LEU	0	-0.001	-0.008	24.346	0.351	0.351	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.050	-0.041	24.025	0.092	0.092	0.000	0.000	0.000	0.000
58	A	63	ALA	0	-0.058	-0.031	26.539	0.269	0.269	0.000	0.000	0.000	0.000
59	A	64	ILE	0	-0.006	0.008	29.853	0.325	0.325	0.000	0.000	0.000	0.000
60	A	65	LEU	0	-0.078	-0.007	27.526	0.260	0.260	0.000	0.000	0.000	0.000
61	A	66	SER	0	0.021	-0.004	30.465	0.183	0.183	0.000	0.000	0.000	0.000
62	A	67	GLU	-1	-0.927	-0.965	33.486	-8.519	-8.519	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.913	-0.947	35.810	-7.908	-7.908	0.000	0.000	0.000	0.000
64	A	69	PHE	0	-0.093	-0.032	27.789	-0.114	-0.114	0.000	0.000	0.000	0.000
65	A	70	SER	0	0.034	0.008	33.173	0.022	0.022	0.000	0.000	0.000	0.000
66	A	71	ALA	0	-0.005	-0.021	31.348	-0.164	-0.164	0.000	0.000	0.000	0.000
67	A	72	ASP	-1	-0.899	-0.941	32.414	-8.577	-8.577	0.000	0.000	0.000	0.000
68	A	73	GLN	0	0.083	0.045	32.919	-0.260	-0.260	0.000	0.000	0.000	0.000
69	A	74	VAL	0	-0.006	0.001	27.449	-0.166	-0.166	0.000	0.000	0.000	0.000
70	A	75	VAL	0	-0.012	-0.005	30.000	-0.204	-0.204	0.000	0.000	0.000	0.000
71	A	76	THR	0	0.016	0.010	32.111	0.077	0.077	0.000	0.000	0.000	0.000
72	A	77	LEU	0	0.004	0.005	28.951	0.036	0.036	0.000	0.000	0.000	0.000
73	A	78	LEU	0	0.008	-0.004	25.993	-0.123	-0.123	0.000	0.000	0.000	0.000
74	A	79	SER	0	-0.082	-0.050	29.702	0.064	0.064	0.000	0.000	0.000	0.000
75	A	80	GLN	0	-0.061	-0.033	32.964	0.142	0.142	0.000	0.000	0.000	0.000
76	A	81	THR	0	-0.080	-0.052	27.202	0.129	0.129	0.000	0.000	0.000	0.000
77	A	82	THR	0	-0.013	-0.006	26.548	-0.266	-0.266	0.000	0.000	0.000	0.000
78	A	83	GLY	0	-0.003	0.013	29.056	0.031	0.031	0.000	0.000	0.000	0.000
79	A	84	TRP	0	-0.027	-0.013	30.643	0.280	0.280	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.952	0.956	32.649	8.445	8.445	0.000	0.000	0.000	0.000
81	A	86	PRO	0	0.031	0.032	35.906	-0.164	-0.164	0.000	0.000	0.000	0.000
82	A	87	SER	0	0.016	0.000	37.914	0.042	0.042	0.000	0.000	0.000	0.000
83	A	88	GLN	0	0.024	0.009	40.119	0.223	0.223	0.000	0.000	0.000	0.000
84	A	89	ALA	0	-0.028	-0.009	39.159	0.128	0.128	0.000	0.000	0.000	0.000
85	A	90	ASP	-1	-0.831	-0.930	41.312	-7.462	-7.462	0.000	0.000	0.000	0.000
86	A	91	ILE	0	-0.024	-0.014	44.019	0.156	0.156	0.000	0.000	0.000	0.000
87	A	92	ARG	1	0.924	0.955	41.902	7.609	7.609	0.000	0.000	0.000	0.000
88	A	93	ALA	0	0.000	0.009	43.515	0.080	0.080	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.024	-0.005	45.441	0.094	0.094	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.062	-0.012	48.288	0.191	0.191	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:LYS)