FMO DATABASE

FMODB ID: 2JJGR

Calculation Name: 4U3Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U3Q

Chain ID: A

ChEMBL ID:

UniProt ID: P29722

Base Structure: X-ray

Registration Date: 2023-06-21

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-745846.601378
FMO2-HF: Nuclear repulsion	705694.167143
FMO2-HF: Total energy	-40152.434235
FMO2-MP2: Total energy	-40267.498753

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:10:LYS)

Summations of interaction energy for fragment #1(A:10: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.
-88.682	-78.036	2.087	-5.752	-6.98	-0.044

Interaction energy analysis for fragmet #1(A:10:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.050 / q_NPA : 1.020

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

Sort

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	12	LYS	1	0.945	0.968	3.687	21.186	22.777	-0.008	-0.677	-0.905	0.003
4	A	13	ALA	0	0.059	0.033	2.915	1.968	2.626	0.159	-0.203	-0.614	0.000
5	A	14	GLU	-1	-0.845	-0.929	2.818	-66.949	-62.858	0.359	-2.030	-2.420	-0.022
6	A	15	LYS	1	0.921	0.960	5.095	31.095	31.200	-0.001	-0.004	-0.100	0.000
7	A	16	VAL	0	-0.031	-0.012	7.855	2.933	2.933	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.883	-0.939	6.247	-41.569	-41.569	0.000	0.000	0.000	0.000
9	A	18	CYS	0	-0.077	-0.053	8.047	2.735	2.735	0.000	0.000	0.000	0.000
10	A	19	ALA	0	-0.031	-0.006	10.836	2.056	2.056	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.013	-0.002	12.448	1.791	1.791	0.000	0.000	0.000	0.000
12	A	21	LYS	1	0.910	0.977	9.745	30.973	30.973	0.000	0.000	0.000	0.000
13	A	22	GLY	0	-0.058	-0.024	14.962	0.146	0.146	0.000	0.000	0.000	0.000
14	A	23	GLY	0	-0.054	-0.020	18.049	1.051	1.051	0.000	0.000	0.000	0.000
15	A	24	ILE	0	0.004	0.001	19.833	-0.213	-0.213	0.000	0.000	0.000	0.000
16	A	25	PHE	0	-0.035	-0.022	17.776	0.206	0.206	0.000	0.000	0.000	0.000
17	A	26	ARG	1	0.864	0.898	23.097	10.043	10.043	0.000	0.000	0.000	0.000
18	A	27	GLY	0	0.015	-0.007	26.319	-0.121	-0.121	0.000	0.000	0.000	0.000
19	A	28	THR	0	-0.026	-0.002	27.970	0.003	0.003	0.000	0.000	0.000	0.000
20	A	29	LEU	0	-0.016	0.014	25.605	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	30	PRO	0	0.013	-0.007	28.912	0.303	0.303	0.000	0.000	0.000	0.000
22	A	31	ALA	0	0.025	0.017	31.734	-0.205	-0.205	0.000	0.000	0.000	0.000
23	A	32	ALA	0	-0.040	-0.029	34.390	0.139	0.139	0.000	0.000	0.000	0.000
24	A	33	ASP	-1	-0.912	-0.948	36.446	-7.290	-7.290	0.000	0.000	0.000	0.000
25	A	34	CYS	0	-0.077	-0.028	37.945	0.190	0.190	0.000	0.000	0.000	0.000
26	A	35	PRO	0	0.015	0.006	37.827	-0.124	-0.124	0.000	0.000	0.000	0.000
27	A	36	GLY	0	0.020	0.003	34.358	-0.162	-0.162	0.000	0.000	0.000	0.000
28	A	37	ILE	0	-0.001	0.003	31.856	0.213	0.213	0.000	0.000	0.000	0.000
29	A	38	ASP	-1	-0.852	-0.895	31.198	-10.042	-10.042	0.000	0.000	0.000	0.000
30	A	39	THR	0	0.014	0.004	26.153	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	40	THR	0	-0.039	-0.027	25.946	-0.132	-0.132	0.000	0.000	0.000	0.000
32	A	41	VAL	0	0.019	0.004	20.358	0.053	0.053	0.000	0.000	0.000	0.000
33	A	42	THR	0	-0.040	-0.024	21.167	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	43	PHE	0	0.054	0.026	16.017	0.038	0.038	0.000	0.000	0.000	0.000
35	A	44	ASN	0	0.008	-0.005	17.312	-0.116	-0.116	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.025	-0.020	14.489	-1.152	-1.152	0.000	0.000	0.000	0.000
37	A	46	ASP	-1	-0.860	-0.892	13.696	-18.859	-18.859	0.000	0.000	0.000	0.000
38	A	47	GLY	0	0.021	0.019	13.607	-0.660	-0.660	0.000	0.000	0.000	0.000
39	A	48	THR	0	-0.056	-0.046	14.271	0.668	0.668	0.000	0.000	0.000	0.000
40	A	49	ALA	0	0.002	-0.023	17.825	-0.504	-0.504	0.000	0.000	0.000	0.000
41	A	50	GLN	0	-0.026	-0.004	19.938	0.818	0.818	0.000	0.000	0.000	0.000
42	A	51	LYS	1	0.867	0.947	23.614	11.830	11.830	0.000	0.000	0.000	0.000
43	A	52	VAL	0	-0.030	-0.015	25.670	0.304	0.304	0.000	0.000	0.000	0.000
44	A	53	GLU	-1	-0.841	-0.926	29.027	-10.658	-10.658	0.000	0.000	0.000	0.000
45	A	54	LEU	0	0.011	0.015	31.487	0.268	0.268	0.000	0.000	0.000	0.000
46	A	63	SER	0	-0.032	-0.026	38.080	0.080	0.080	0.000	0.000	0.000	0.000
47	A	64	PRO	0	0.008	0.003	34.514	-0.115	-0.115	0.000	0.000	0.000	0.000
48	A	65	LEU	0	0.019	0.027	32.739	0.025	0.025	0.000	0.000	0.000	0.000
49	A	66	THR	0	-0.038	-0.036	28.789	-0.264	-0.264	0.000	0.000	0.000	0.000
50	A	67	TYR	0	-0.010	0.013	26.323	0.091	0.091	0.000	0.000	0.000	0.000
51	A	68	ARG	1	0.921	0.945	24.207	11.293	11.293	0.000	0.000	0.000	0.000
52	A	69	GLY	0	0.058	0.029	21.501	0.310	0.310	0.000	0.000	0.000	0.000
53	A	70	THR	0	-0.016	0.010	15.954	0.062	0.062	0.000	0.000	0.000	0.000
54	A	71	TRP	0	-0.037	-0.019	11.397	-0.069	-0.069	0.000	0.000	0.000	0.000
55	A	72	MET	0	-0.011	-0.008	11.390	-1.659	-1.659	0.000	0.000	0.000	0.000
56	A	73	VAL	0	-0.015	0.006	7.168	1.986	1.986	0.000	0.000	0.000	0.000
57	A	74	ARG	1	0.865	0.954	7.683	17.535	17.535	0.000	0.000	0.000	0.000
58	A	75	GLU	-1	-0.894	-0.973	2.264	-54.304	-50.251	1.578	-2.759	-2.872	-0.025
59	A	76	ASP	-1	-0.867	-0.940	3.987	-23.416	-23.268	0.000	-0.079	-0.069	0.000
60	A	77	GLY	0	-0.040	-0.033	6.717	1.570	1.570	0.000	0.000	0.000	0.000
61	A	78	ILE	0	-0.046	-0.014	7.905	0.751	0.751	0.000	0.000	0.000	0.000
62	A	79	VAL	0	-0.005	-0.008	10.465	-1.764	-1.764	0.000	0.000	0.000	0.000
63	A	80	GLU	-1	-0.900	-0.972	12.726	-17.981	-17.981	0.000	0.000	0.000	0.000
64	A	81	LEU	0	-0.020	-0.001	14.964	-0.849	-0.849	0.000	0.000	0.000	0.000
65	A	82	SER	0	0.003	-0.004	18.081	0.777	0.777	0.000	0.000	0.000	0.000
66	A	83	LEU	0	-0.024	-0.009	20.531	-0.140	-0.140	0.000	0.000	0.000	0.000
67	A	84	VAL	0	0.038	0.023	23.645	0.264	0.264	0.000	0.000	0.000	0.000
68	A	94	GLU	-1	-0.922	-0.972	24.374	-12.135	-12.135	0.000	0.000	0.000	0.000
69	A	95	LYS	1	0.886	0.950	16.915	16.702	16.702	0.000	0.000	0.000	0.000
70	A	96	GLU	-1	-0.843	-0.907	20.082	-12.444	-12.444	0.000	0.000	0.000	0.000
71	A	97	LEU	0	-0.021	-0.010	15.587	-1.005	-1.005	0.000	0.000	0.000	0.000
72	A	98	TYR	0	-0.038	-0.041	15.590	1.064	1.064	0.000	0.000	0.000	0.000
73	A	99	GLU	-1	-0.859	-0.946	13.521	-16.988	-16.988	0.000	0.000	0.000	0.000
74	A	100	LEU	0	-0.026	-0.003	12.276	0.508	0.508	0.000	0.000	0.000	0.000
75	A	101	ILE	0	-0.077	-0.027	14.118	-0.087	-0.087	0.000	0.000	0.000	0.000
76	A	102	ASP	-1	-0.803	-0.912	16.184	-14.293	-14.293	0.000	0.000	0.000	0.000
77	A	103	SER	0	-0.011	-0.022	15.888	-0.817	-0.817	0.000	0.000	0.000	0.000
78	A	104	ASN	0	-0.063	-0.029	16.921	-0.416	-0.416	0.000	0.000	0.000	0.000
79	A	105	SER	0	-0.003	0.002	19.045	0.964	0.964	0.000	0.000	0.000	0.000
80	A	106	VAL	0	0.025	0.016	16.234	-0.866	-0.866	0.000	0.000	0.000	0.000
81	A	107	ARG	1	0.914	0.964	17.811	14.437	14.437	0.000	0.000	0.000	0.000
82	A	108	TYR	0	0.045	0.021	18.791	-0.723	-0.723	0.000	0.000	0.000	0.000
83	A	109	MET	0	-0.067	-0.030	16.024	0.239	0.239	0.000	0.000	0.000	0.000
84	A	110	GLY	0	0.011	0.021	20.366	0.429	0.429	0.000	0.000	0.000	0.000
85	A	111	ALA	0	0.041	0.021	20.873	-0.626	-0.626	0.000	0.000	0.000	0.000
86	A	112	PRO	0	-0.021	-0.020	18.394	-0.078	-0.078	0.000	0.000	0.000	0.000
87	A	113	GLY	0	-0.002	0.005	19.657	0.408	0.408	0.000	0.000	0.000	0.000
88	A	114	ALA	0	0.091	0.043	21.107	0.565	0.565	0.000	0.000	0.000	0.000
89	A	115	GLY	0	-0.040	-0.023	20.169	0.314	0.314	0.000	0.000	0.000	0.000
90	A	116	LYS	1	0.877	0.948	20.985	9.637	9.637	0.000	0.000	0.000	0.000
91	A	117	PRO	0	0.055	0.035	22.448	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	118	SER	0	0.009	-0.007	24.217	0.363	0.363	0.000	0.000	0.000	0.000
93	A	119	LYS	1	0.956	0.953	23.154	11.448	11.448	0.000	0.000	0.000	0.000
94	A	120	GLU	-1	-0.951	-0.948	26.810	-9.113	-9.113	0.000	0.000	0.000	0.000
95	A	121	MET	0	0.041	0.015	28.190	0.125	0.125	0.000	0.000	0.000	0.000
96	A	122	ALA	0	0.014	-0.006	23.109	-0.168	-0.168	0.000	0.000	0.000	0.000
97	A	123	PRO	0	0.001	-0.018	24.800	-0.340	-0.340	0.000	0.000	0.000	0.000
98	A	124	PHE	0	0.016	0.016	26.303	-0.073	-0.073	0.000	0.000	0.000	0.000
99	A	125	TYR	0	0.016	0.006	23.730	0.129	0.129	0.000	0.000	0.000	0.000
100	A	126	VAL	0	-0.071	-0.022	22.279	-0.628	-0.628	0.000	0.000	0.000	0.000
101	A	127	LEU	0	-0.009	0.009	21.618	0.369	0.369	0.000	0.000	0.000	0.000
102	A	128	LYS	1	0.957	0.975	21.961	10.900	10.900	0.000	0.000	0.000	0.000
103	A	129	LYS	1	0.944	0.981	17.925	16.639	16.639	0.000	0.000	0.000	0.000
104	A	130	THR	0	-0.037	-0.016	23.050	0.496	0.496	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:LYS)