FMO DATABASE

FMODB ID: M34MZ

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	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	-544733.39638
FMO2-HF: Nuclear repulsion	509781.680313
FMO2-HF: Total energy	-34951.716067
FMO2-MP2: Total energy	-35055.7926

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.
50.019	47.924	11.393	-3.223	-6.074	-0.017

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 : 1.008 / q_NPA : 1.005

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	0.931	0.981	1.793	56.422	53.800	11.352	-3.101	-5.629	-0.015
4	A	9	LYS	1	0.997	0.993	3.602	34.360	34.807	0.042	-0.118	-0.370	-0.002
5	A	10	TYR	0	0.022	-0.008	4.685	-5.352	-5.272	-0.001	-0.004	-0.075	0.000
6	A	11	THR	0	-0.019	-0.006	8.856	1.608	1.608	0.000	0.000	0.000	0.000
7	A	12	LEU	0	0.002	0.009	12.448	-0.525	-0.525	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.016	-0.022	15.304	-0.105	-0.105	0.000	0.000	0.000	0.000
9	A	14	LEU	0	0.018	0.032	19.100	-0.125	-0.125	0.000	0.000	0.000	0.000
10	A	15	HIS	0	-0.076	-0.061	22.087	-0.281	-0.281	0.000	0.000	0.000	0.000
11	A	16	PRO	0	0.046	0.018	25.657	0.270	0.270	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.894	-0.945	28.089	-10.751	-10.751	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.884	0.944	26.686	11.668	11.668	0.000	0.000	0.000	0.000
14	A	19	ALA	0	0.065	0.032	29.701	-0.139	-0.139	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.071	0.038	26.727	-0.123	-0.123	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.810	-0.898	24.209	-12.827	-12.827	0.000	0.000	0.000	0.000
17	A	22	PHE	0	-0.007	-0.002	26.052	-0.337	-0.337	0.000	0.000	0.000	0.000
18	A	23	GLN	0	0.043	0.005	28.832	0.132	0.132	0.000	0.000	0.000	0.000
19	A	24	THR	0	-0.074	-0.047	22.287	-0.254	-0.254	0.000	0.000	0.000	0.000
20	A	25	LEU	0	-0.031	-0.026	24.249	-0.374	-0.374	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.883	-0.931	26.037	-9.773	-9.773	0.000	0.000	0.000	0.000
22	A	27	ALA	0	-0.001	0.006	25.477	0.025	0.025	0.000	0.000	0.000	0.000
23	A	28	ILE	0	-0.086	-0.051	20.777	-0.344	-0.344	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.893	-0.964	24.370	-11.605	-11.605	0.000	0.000	0.000	0.000
25	A	30	SER	0	-0.127	-0.039	27.265	0.199	0.199	0.000	0.000	0.000	0.000
26	A	31	VAL	0	0.024	0.021	23.080	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	32	PRO	0	0.037	0.029	25.115	-0.283	-0.283	0.000	0.000	0.000	0.000
28	A	33	ARG	1	0.971	0.959	22.740	11.637	11.637	0.000	0.000	0.000	0.000
29	A	34	SER	0	-0.008	-0.003	20.442	-0.573	-0.573	0.000	0.000	0.000	0.000
30	A	35	GLU	-1	-0.882	-0.947	19.156	-13.108	-13.108	0.000	0.000	0.000	0.000
31	A	36	ARG	1	0.855	0.930	19.518	12.245	12.245	0.000	0.000	0.000	0.000
32	A	37	GLY	0	-0.016	0.005	15.742	-0.732	-0.732	0.000	0.000	0.000	0.000
33	A	38	GLU	-1	-0.959	-0.984	14.707	-18.957	-18.957	0.000	0.000	0.000	0.000
34	A	39	LEU	0	0.006	0.012	16.122	-0.465	-0.465	0.000	0.000	0.000	0.000
35	A	40	PHE	0	0.016	-0.011	14.800	-0.275	-0.275	0.000	0.000	0.000	0.000
36	A	41	ARG	1	0.951	0.984	10.189	23.175	23.175	0.000	0.000	0.000	0.000
37	A	42	ASN	0	0.030	0.012	13.279	-1.528	-1.528	0.000	0.000	0.000	0.000
38	A	43	ALA	0	0.041	0.053	16.092	0.132	0.132	0.000	0.000	0.000	0.000
39	A	44	PHE	0	-0.015	-0.001	9.191	-0.418	-0.418	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.032	-0.028	11.041	-0.289	-0.289	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.015	-0.033	13.546	0.489	0.489	0.000	0.000	0.000	0.000
42	A	47	GLY	0	0.057	0.038	16.634	0.755	0.755	0.000	0.000	0.000	0.000
43	A	48	MET	0	-0.031	-0.030	11.890	0.586	0.586	0.000	0.000	0.000	0.000
44	A	49	ALA	0	-0.015	-0.004	15.210	0.208	0.208	0.000	0.000	0.000	0.000
45	A	50	LEU	0	0.020	0.001	17.173	0.624	0.624	0.000	0.000	0.000	0.000
46	A	51	HIS	0	0.000	-0.002	15.829	0.893	0.893	0.000	0.000	0.000	0.000
47	A	52	GLN	0	-0.095	-0.057	14.207	-0.902	-0.902	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.039	-0.002	18.401	0.409	0.409	0.000	0.000	0.000	0.000
49	A	54	ASP	-1	-0.784	-0.898	21.736	-11.624	-11.624	0.000	0.000	0.000	0.000
50	A	55	PRO	0	0.002	0.008	20.438	-0.164	-0.164	0.000	0.000	0.000	0.000
51	A	56	ARG	1	0.868	0.925	21.551	11.057	11.057	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.039	0.023	23.252	0.252	0.252	0.000	0.000	0.000	0.000
53	A	58	PRO	0	-0.013	0.007	19.249	0.265	0.265	0.000	0.000	0.000	0.000
54	A	59	VAL	0	-0.008	0.000	21.935	0.064	0.064	0.000	0.000	0.000	0.000
55	A	60	LEU	0	-0.002	-0.011	24.048	0.490	0.490	0.000	0.000	0.000	0.000
56	A	61	LEU	0	-0.010	-0.007	23.657	0.380	0.380	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.027	-0.009	22.933	0.153	0.153	0.000	0.000	0.000	0.000
58	A	63	ALA	0	-0.059	-0.040	25.559	0.306	0.306	0.000	0.000	0.000	0.000
59	A	64	ILE	0	-0.042	-0.014	28.747	0.327	0.327	0.000	0.000	0.000	0.000
60	A	65	LEU	0	-0.082	-0.021	26.985	0.310	0.310	0.000	0.000	0.000	0.000
61	A	66	SER	0	0.045	0.029	29.785	0.226	0.226	0.000	0.000	0.000	0.000
62	A	67	GLU	-1	-0.924	-0.962	32.470	-8.886	-8.886	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.901	-0.941	34.534	-8.101	-8.101	0.000	0.000	0.000	0.000
64	A	69	PHE	0	-0.136	-0.050	27.151	-0.124	-0.124	0.000	0.000	0.000	0.000
65	A	70	SER	0	0.063	0.019	32.504	0.032	0.032	0.000	0.000	0.000	0.000
66	A	71	ALA	0	0.016	-0.004	30.942	-0.207	-0.207	0.000	0.000	0.000	0.000
67	A	72	ASP	-1	-0.912	-0.961	31.939	-8.757	-8.757	0.000	0.000	0.000	0.000
68	A	73	GLN	0	0.080	0.034	32.216	-0.309	-0.309	0.000	0.000	0.000	0.000
69	A	74	VAL	0	-0.011	0.003	27.031	-0.170	-0.170	0.000	0.000	0.000	0.000
70	A	75	VAL	0	-0.005	-0.007	29.645	-0.195	-0.195	0.000	0.000	0.000	0.000
71	A	76	THR	0	0.003	0.003	31.693	0.077	0.077	0.000	0.000	0.000	0.000
72	A	77	LEU	0	-0.015	-0.012	28.618	0.007	0.007	0.000	0.000	0.000	0.000
73	A	78	LEU	0	0.009	0.000	26.222	-0.193	-0.193	0.000	0.000	0.000	0.000
74	A	79	SER	0	-0.040	-0.015	29.238	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	80	GLN	0	-0.020	-0.022	32.369	-0.051	-0.051	0.000	0.000	0.000	0.000
76	A	81	THR	0	-0.050	-0.014	26.832	0.027	0.027	0.000	0.000	0.000	0.000
77	A	82	THR	0	-0.074	-0.020	26.905	-0.401	-0.401	0.000	0.000	0.000	0.000
78	A	83	GLY	0	-0.008	0.002	29.194	0.047	0.047	0.000	0.000	0.000	0.000
79	A	84	TRP	0	-0.035	-0.024	30.532	0.299	0.299	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.975	0.971	32.568	8.360	8.360	0.000	0.000	0.000	0.000
81	A	86	PRO	0	0.017	0.026	35.990	-0.118	-0.118	0.000	0.000	0.000	0.000
82	A	87	SER	0	0.047	0.016	37.687	0.113	0.113	0.000	0.000	0.000	0.000
83	A	88	GLN	0	0.036	0.020	39.435	0.278	0.278	0.000	0.000	0.000	0.000
84	A	89	ALA	0	-0.097	-0.048	38.906	0.150	0.150	0.000	0.000	0.000	0.000
85	A	90	ASP	-1	-0.816	-0.923	41.033	-7.496	-7.496	0.000	0.000	0.000	0.000
86	A	91	ILE	0	-0.008	-0.007	43.895	0.131	0.131	0.000	0.000	0.000	0.000
87	A	92	ARG	1	0.915	0.953	41.244	7.697	7.697	0.000	0.000	0.000	0.000
88	A	93	ALA	0	0.072	0.044	43.276	0.110	0.110	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.069	-0.016	45.160	0.100	0.100	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.087	-0.037	47.911	0.198	0.198	0.000	0.000	0.000	0.000

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