FMO DATABASE

FMODB ID: V5Y51

Calculation Name: 4J4G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4G

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	-509459.939729
FMO2-HF: Nuclear repulsion	470235.27554
FMO2-HF: Total energy	-39224.664189
FMO2-MP2: Total energy	-39336.617396

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.
-24.954	-26.515	9.484	-3.975	-3.948	0.03

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 : 0.061 / q_NPA : 0.027

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	0.878	0.921	2.053	-25.092	-26.653	9.484	-3.975	-3.948	0.030
4	A	4	PHE	0	0.099	0.045	5.634	-0.017	-0.017	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.011	-0.002	8.844	0.031	0.031	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.039	-0.025	6.991	0.513	0.513	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.027	0.027	10.113	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.110	-0.031	12.267	-0.079	-0.079	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.005	-0.021	14.300	0.064	0.064	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.023	-0.026	17.640	-0.013	-0.013	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.005	0.011	15.242	-0.034	-0.034	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.006	0.018	17.895	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.009	-0.004	16.067	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.002	0.005	19.989	0.004	0.004	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.002	0.005	22.398	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.022	-0.030	19.286	0.017	0.017	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.008	0.000	17.990	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.003	0.015	12.677	0.028	0.028	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.017	0.007	16.868	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.005	-0.017	15.318	0.028	0.028	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.003	-0.007	17.424	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.779	-0.883	14.208	0.097	0.097	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.891	0.946	14.939	0.081	0.081	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.000	-0.012	14.589	0.020	0.020	0.000	0.000	0.000	0.000
25	A	26	ASN	0	-0.013	-0.006	16.103	0.007	0.007	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.042	0.031	18.667	0.008	0.008	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.023	0.005	20.150	0.011	0.011	0.000	0.000	0.000	0.000
28	A	29	TYR	0	0.009	-0.012	18.147	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.053	-0.038	17.574	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.010	0.020	18.082	0.006	0.006	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.029	-0.008	16.070	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.016	-0.020	17.458	0.019	0.019	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.017	-0.006	11.820	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.748	-0.853	15.978	-0.094	-0.094	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.015	0.009	12.618	-0.036	-0.036	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.030	-0.022	15.080	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.055	-0.024	15.410	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.016	-0.009	10.746	-0.050	-0.050	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.038	-0.015	11.682	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.822	-0.893	13.979	-0.158	-0.158	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.016	-0.026	17.015	0.033	0.033	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.002	-0.003	18.346	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.913	-0.961	20.717	0.029	0.029	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.003	0.018	23.016	0.010	0.010	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.073	-0.027	17.454	0.025	0.025	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.005	-0.003	15.715	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.799	0.876	13.103	0.189	0.189	0.000	0.000	0.000	0.000
48	A	49	TRP	0	0.018	0.010	8.366	-0.081	-0.081	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.030	-0.002	11.014	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.007	-0.009	10.273	-0.095	-0.095	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.045	-0.028	11.245	0.070	0.070	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.037	0.020	11.831	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.062	0.047	13.532	0.023	0.023	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.034	0.004	16.399	0.016	0.016	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.846	-0.899	11.404	-0.215	-0.215	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.070	-0.056	14.516	0.036	0.036	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.058	-0.023	17.049	0.012	0.012	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.862	0.909	20.677	0.037	0.037	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.055	-0.053	23.688	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	61	THR	0	-0.004	0.013	24.508	0.002	0.002	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.041	-0.025	27.462	0.003	0.003	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.014	0.015	30.235	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.000	0.006	32.789	0.004	0.004	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.005	-0.010	35.479	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.016	-0.020	37.351	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.056	-0.048	33.654	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.882	-0.907	31.812	-0.057	-0.057	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.024	-0.005	24.727	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.011	0.017	28.353	0.002	0.002	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.017	-0.014	24.664	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.805	-0.850	25.286	-0.035	-0.035	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.804	0.889	13.968	0.139	0.139	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.022	0.014	18.225	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.952	0.966	15.417	-0.093	-0.093	0.000	0.000	0.000	0.000
75	A	77	ALA	0	0.031	0.020	14.125	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	78	GLN	0	0.006	0.005	15.986	0.008	0.008	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.015	-0.006	15.015	0.051	0.051	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.011	0.005	18.326	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.009	-0.015	19.333	0.035	0.035	0.000	0.000	0.000	0.000
80	A	82	SER	0	-0.001	0.003	21.314	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	83	THR	0	0.005	0.001	23.664	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.939	0.961	26.609	-0.145	-0.145	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.031	0.019	30.360	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.023	-0.019	33.584	0.006	0.006	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.023	0.007	36.725	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.854	-0.929	39.597	0.067	0.067	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.904	-0.926	37.542	0.070	0.070	0.000	0.000	0.000	0.000
88	A	90	HIS	1	0.817	0.888	40.115	-0.058	-0.058	0.000	0.000	0.000	0.000
89	A	91	ILE	0	-0.048	-0.009	42.020	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.050	0.037	44.684	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.006	-0.019	48.160	0.000	0.000	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.027	-0.017	50.984	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.904	-0.957	54.156	0.035	0.035	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.000	0.012	54.601	0.000	0.000	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.053	-0.019	52.364	0.002	0.002	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.018	-0.008	46.178	0.000	0.000	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.839	0.903	48.754	-0.042	-0.042	0.000	0.000	0.000	0.000
98	A	100	TYR	0	0.029	0.016	41.792	0.003	0.003	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.887	-0.925	45.754	0.038	0.038	0.000	0.000	0.000	0.000

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