FMO DATABASE

FMODB ID: 7GQJK

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	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	-545026.718425
FMO2-HF: Nuclear repulsion	510074.291021
FMO2-HF: Total energy	-34952.427404
FMO2-MP2: Total energy	-35056.435022

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.
33.324	36.18	0.719	-1.029	-2.546	-0.003

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 : 1.017 / q_NPA : 1.001

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	0.893	0.966	2.411	44.434	47.083	0.713	-0.982	-2.380	-0.003
4	A	9	LYS	1	1.005	0.995	4.080	31.772	31.979	0.006	-0.047	-0.166	0.000
5	A	10	TYR	0	0.035	-0.003	5.551	-6.599	-6.599	0.000	0.000	0.000	0.000
6	A	11	THR	0	-0.008	-0.005	9.663	0.608	0.608	0.000	0.000	0.000	0.000
7	A	12	LEU	0	0.008	0.014	13.266	-0.444	-0.444	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.008	-0.017	16.041	-0.119	-0.119	0.000	0.000	0.000	0.000
9	A	14	LEU	0	0.030	0.036	19.842	-0.087	-0.087	0.000	0.000	0.000	0.000
10	A	15	HIS	0	-0.109	-0.078	22.800	-0.403	-0.403	0.000	0.000	0.000	0.000
11	A	16	PRO	0	0.052	0.017	26.366	0.245	0.245	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.847	-0.919	28.974	-10.675	-10.675	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.853	0.941	25.855	12.104	12.104	0.000	0.000	0.000	0.000
14	A	19	ALA	0	0.067	0.030	30.351	-0.139	-0.139	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.079	0.045	27.319	-0.120	-0.120	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.813	-0.911	24.835	-12.566	-12.566	0.000	0.000	0.000	0.000
17	A	22	PHE	0	-0.012	-0.002	26.695	-0.305	-0.305	0.000	0.000	0.000	0.000
18	A	23	GLN	0	0.041	0.004	29.519	0.059	0.059	0.000	0.000	0.000	0.000
19	A	24	THR	0	-0.068	-0.042	22.914	-0.254	-0.254	0.000	0.000	0.000	0.000
20	A	25	LEU	0	-0.043	-0.030	24.761	-0.345	-0.345	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.894	-0.942	26.760	-9.622	-9.622	0.000	0.000	0.000	0.000
22	A	27	ALA	0	-0.001	0.008	26.173	0.020	0.020	0.000	0.000	0.000	0.000
23	A	28	ILE	0	-0.068	-0.044	21.670	-0.317	-0.317	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.710	-0.837	25.068	-11.783	-11.783	0.000	0.000	0.000	0.000
25	A	30	SER	0	-0.088	-0.016	28.010	0.181	0.181	0.000	0.000	0.000	0.000
26	A	31	VAL	0	0.041	0.022	23.391	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	32	PRO	0	0.023	0.034	24.529	-0.237	-0.237	0.000	0.000	0.000	0.000
28	A	33	ARG	1	0.868	0.897	22.336	11.445	11.445	0.000	0.000	0.000	0.000
29	A	34	SER	0	0.000	0.001	19.913	-0.578	-0.578	0.000	0.000	0.000	0.000
30	A	35	GLU	-1	-0.883	-0.949	18.702	-12.920	-12.920	0.000	0.000	0.000	0.000
31	A	36	ARG	1	0.740	0.842	19.263	11.968	11.968	0.000	0.000	0.000	0.000
32	A	37	GLY	0	-0.020	0.003	15.542	-0.690	-0.690	0.000	0.000	0.000	0.000
33	A	38	GLU	-1	-0.958	-0.984	14.912	-18.859	-18.859	0.000	0.000	0.000	0.000
34	A	39	LEU	0	0.022	0.020	16.036	-0.420	-0.420	0.000	0.000	0.000	0.000
35	A	40	PHE	0	0.016	-0.011	15.485	-0.264	-0.264	0.000	0.000	0.000	0.000
36	A	41	ARG	1	0.925	0.974	10.917	21.539	21.539	0.000	0.000	0.000	0.000
37	A	42	ASN	0	0.010	-0.002	13.762	-1.170	-1.170	0.000	0.000	0.000	0.000
38	A	43	ALA	0	0.054	0.052	16.447	0.113	0.113	0.000	0.000	0.000	0.000
39	A	44	PHE	0	-0.010	-0.001	9.718	-0.356	-0.356	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.027	-0.027	11.036	-0.267	-0.267	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.014	-0.020	13.752	0.456	0.456	0.000	0.000	0.000	0.000
42	A	47	GLY	0	0.060	0.038	16.886	0.707	0.707	0.000	0.000	0.000	0.000
43	A	48	MET	0	-0.035	-0.034	12.134	0.510	0.510	0.000	0.000	0.000	0.000
44	A	49	ALA	0	-0.016	-0.003	15.324	0.173	0.173	0.000	0.000	0.000	0.000
45	A	50	LEU	0	0.015	-0.001	17.146	0.588	0.588	0.000	0.000	0.000	0.000
46	A	51	HIS	0	0.001	-0.002	16.230	0.796	0.796	0.000	0.000	0.000	0.000
47	A	52	GLN	0	-0.081	-0.050	14.456	-0.582	-0.582	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.043	-0.003	18.377	0.408	0.408	0.000	0.000	0.000	0.000
49	A	54	ASP	-1	-0.745	-0.858	21.653	-11.564	-11.564	0.000	0.000	0.000	0.000
50	A	55	PRO	0	-0.010	0.008	20.308	-0.139	-0.139	0.000	0.000	0.000	0.000
51	A	56	ARG	1	0.860	0.914	21.551	11.062	11.062	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.062	0.037	22.999	0.262	0.262	0.000	0.000	0.000	0.000
53	A	58	PRO	0	-0.018	0.005	19.448	0.272	0.272	0.000	0.000	0.000	0.000
54	A	59	VAL	0	-0.020	-0.005	22.164	0.072	0.072	0.000	0.000	0.000	0.000
55	A	60	LEU	0	-0.008	-0.006	24.333	0.481	0.481	0.000	0.000	0.000	0.000
56	A	61	LEU	0	-0.004	-0.005	23.935	0.360	0.360	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.038	-0.027	23.386	0.142	0.142	0.000	0.000	0.000	0.000
58	A	63	ALA	0	-0.051	-0.032	25.967	0.296	0.296	0.000	0.000	0.000	0.000
59	A	64	ILE	0	-0.031	-0.009	29.138	0.301	0.301	0.000	0.000	0.000	0.000
60	A	65	LEU	0	-0.088	-0.020	27.319	0.304	0.304	0.000	0.000	0.000	0.000
61	A	66	SER	0	0.045	0.019	30.224	0.214	0.214	0.000	0.000	0.000	0.000
62	A	67	GLU	-1	-0.946	-0.969	32.941	-8.727	-8.727	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.908	-0.946	35.039	-7.935	-7.935	0.000	0.000	0.000	0.000
64	A	69	PHE	0	-0.109	-0.039	27.306	-0.112	-0.112	0.000	0.000	0.000	0.000
65	A	70	SER	0	0.064	0.017	32.822	0.034	0.034	0.000	0.000	0.000	0.000
66	A	71	ALA	0	0.013	-0.004	31.162	-0.202	-0.202	0.000	0.000	0.000	0.000
67	A	72	ASP	-1	-0.917	-0.963	32.111	-8.678	-8.678	0.000	0.000	0.000	0.000
68	A	73	GLN	0	0.071	0.036	32.459	-0.251	-0.251	0.000	0.000	0.000	0.000
69	A	74	VAL	0	-0.015	-0.008	27.075	-0.173	-0.173	0.000	0.000	0.000	0.000
70	A	75	VAL	0	-0.007	-0.005	29.751	-0.190	-0.190	0.000	0.000	0.000	0.000
71	A	76	THR	0	0.010	0.013	31.770	0.062	0.062	0.000	0.000	0.000	0.000
72	A	77	LEU	0	-0.003	-0.003	28.699	0.003	0.003	0.000	0.000	0.000	0.000
73	A	78	LEU	0	0.009	0.002	25.706	-0.201	-0.201	0.000	0.000	0.000	0.000
74	A	79	SER	0	-0.071	-0.027	29.254	0.001	0.001	0.000	0.000	0.000	0.000
75	A	80	GLN	0	-0.041	-0.033	32.324	0.026	0.026	0.000	0.000	0.000	0.000
76	A	81	THR	0	-0.068	-0.050	26.806	0.142	0.142	0.000	0.000	0.000	0.000
77	A	82	THR	0	-0.038	-0.008	26.735	-0.349	-0.349	0.000	0.000	0.000	0.000
78	A	83	GLY	0	-0.012	0.004	29.169	0.046	0.046	0.000	0.000	0.000	0.000
79	A	84	TRP	0	-0.045	-0.028	30.555	0.297	0.297	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.983	0.973	32.597	8.381	8.381	0.000	0.000	0.000	0.000
81	A	86	PRO	0	0.025	0.031	36.065	-0.139	-0.139	0.000	0.000	0.000	0.000
82	A	87	SER	0	0.037	0.003	37.708	0.109	0.109	0.000	0.000	0.000	0.000
83	A	88	GLN	0	0.028	0.023	39.558	0.247	0.247	0.000	0.000	0.000	0.000
84	A	89	ALA	0	-0.096	-0.046	39.036	0.148	0.148	0.000	0.000	0.000	0.000
85	A	90	ASP	-1	-0.817	-0.925	41.142	-7.453	-7.453	0.000	0.000	0.000	0.000
86	A	91	ILE	0	-0.004	-0.008	43.965	0.131	0.131	0.000	0.000	0.000	0.000
87	A	92	ARG	1	0.921	0.960	41.625	7.625	7.625	0.000	0.000	0.000	0.000
88	A	93	ALA	0	0.064	0.041	43.258	0.109	0.109	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.063	-0.022	45.187	0.105	0.105	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.082	-0.028	47.953	0.202	0.202	0.000	0.000	0.000	0.000

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