FMO DATABASE

FMODB ID: 6N4NZ

Calculation Name: 4J4E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4E

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

Base Structure: X-ray

Registration Date: 2023-06-22

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-534668.538878
FMO2-HF: Nuclear repulsion	495443.983029
FMO2-HF: Total energy	-39224.555849
FMO2-MP2: Total energy	-39336.522068

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:1:LEU)

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

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.
-30.591	-33.533	17.414	-6.877	-7.594	0.037

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.043

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	3	LYS	1	0.872	0.906	1.886	-28.208	-33.208	15.987	-5.855	-5.132	0.043
4	A	4	PHE	0	0.093	0.045	5.195	-0.029	0.146	-0.001	-0.012	-0.161	0.000
5	A	5	SER	0	0.021	0.011	8.462	0.079	0.079	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.015	-0.010	6.710	0.334	0.334	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.008	0.001	9.084	-0.064	-0.064	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.121	-0.031	11.474	-0.081	-0.081	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.067	0.033	13.878	0.064	0.064	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.032	-0.028	17.261	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.012	0.012	16.294	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.004	0.009	18.410	0.026	0.026	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.035	0.004	15.308	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.002	0.015	19.323	0.011	0.011	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.007	0.002	22.419	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.055	-0.053	18.642	0.006	0.006	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.003	0.005	17.452	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.013	0.015	12.356	0.029	0.029	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.011	-0.027	16.554	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.022	-0.028	15.228	0.024	0.024	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.011	-0.007	17.185	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.826	-0.931	11.834	-0.094	-0.094	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.880	0.930	14.249	0.151	0.151	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.013	-0.019	13.229	0.024	0.024	0.000	0.000	0.000	0.000
25	A	26	ASN	0	0.001	0.008	15.084	0.011	0.011	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.038	0.034	17.860	0.022	0.022	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.012	-0.007	19.590	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	29	TYR	0	0.000	-0.013	15.920	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.024	-0.012	17.493	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.021	0.020	17.773	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.057	-0.010	15.791	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.064	0.015	17.110	0.027	0.027	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.006	0.008	11.450	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.792	-0.886	15.607	-0.153	-0.153	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.013	-0.005	11.809	-0.036	-0.036	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.015	-0.005	14.714	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.050	-0.009	14.861	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.039	-0.020	10.154	-0.051	-0.051	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.037	-0.017	11.073	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.839	-0.917	13.491	-0.132	-0.132	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.041	-0.038	16.189	0.027	0.027	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.004	-0.008	17.025	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.900	-0.953	19.527	0.034	0.034	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.002	0.006	22.272	0.011	0.011	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.036	-0.006	17.588	0.018	0.018	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.003	-0.003	15.469	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.901	0.949	12.497	0.020	0.020	0.000	0.000	0.000	0.000
48	A	49	TRP	0	-0.014	-0.007	7.863	-0.105	-0.105	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.013	0.006	10.087	0.030	0.030	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.030	-0.002	10.813	-0.057	-0.057	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.019	-0.017	12.419	-0.032	-0.032	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.025	-0.001	14.464	0.043	0.043	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.072	0.035	18.177	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.007	-0.004	19.313	0.001	0.001	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.859	-0.898	18.093	-0.220	-0.220	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.064	-0.065	14.402	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.085	-0.035	16.600	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.828	0.883	19.772	0.095	0.095	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.029	-0.031	23.308	0.004	0.004	0.000	0.000	0.000	0.000
60	A	61	THR	0	-0.003	0.011	24.124	0.004	0.004	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.050	-0.028	26.454	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.005	0.005	28.673	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.014	-0.005	30.204	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.024	0.005	32.056	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.069	-0.036	34.482	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.058	-0.051	32.109	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.827	-0.886	28.593	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.009	0.004	24.574	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.005	0.007	24.822	0.001	0.001	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.021	-0.009	21.980	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.783	-0.838	21.445	-0.077	-0.077	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.872	0.937	14.843	0.226	0.226	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.036	0.016	10.601	0.010	0.010	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.945	0.963	3.332	-0.296	0.264	0.073	-0.163	-0.470	0.000
75	A	77	ALA	0	0.029	0.016	8.705	0.014	0.014	0.000	0.000	0.000	0.000
76	A	78	GLN	0	0.005	0.004	7.471	-0.138	-0.138	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.026	-0.012	5.118	-0.167	-0.087	-0.001	-0.001	-0.079	0.000
78	A	80	PHE	0	0.019	0.011	6.742	-0.097	-0.097	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.018	-0.015	2.348	-1.419	-0.356	1.357	-0.812	-1.608	-0.006
80	A	82	SER	0	0.008	0.005	5.768	0.098	0.098	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.028	-0.017	4.156	-0.964	-0.784	-0.001	-0.034	-0.144	0.000
82	A	84	LYS	1	0.929	0.961	5.657	0.112	0.112	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.002	0.004	8.041	0.292	0.292	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.005	-0.011	10.773	-0.134	-0.134	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.016	0.005	14.175	0.008	0.008	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.854	-0.931	17.087	0.175	0.175	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.924	-0.939	14.823	0.489	0.489	0.000	0.000	0.000	0.000
88	A	90	HIS	1	0.811	0.887	17.219	-0.315	-0.315	0.000	0.000	0.000	0.000
89	A	91	ILE	0	-0.045	0.000	19.618	-0.023	-0.023	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.064	0.041	22.200	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.018	-0.023	25.712	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.022	-0.013	28.720	0.000	0.000	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.857	-0.936	31.584	0.051	0.051	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.016	0.020	33.323	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.053	-0.026	30.916	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.005	-0.008	24.769	0.007	0.007	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.838	0.922	26.296	-0.085	-0.085	0.000	0.000	0.000	0.000
98	A	100	TYR	0	0.000	0.006	18.804	0.017	0.017	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.916	-0.953	22.866	0.173	0.173	0.000	0.000	0.000	0.000

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