FMO DATABASE

FMODB ID: KGG73

Calculation Name: 3N53-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N53

Chain ID: A

ChEMBL ID:

UniProt ID: Q3A6W4

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1165111.338361
FMO2-HF: Nuclear repulsion	1114078.119936
FMO2-HF: Total energy	-51033.218424
FMO2-MP2: Total energy	-51184.700842

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.
-10.033	-3.866	5.16	-3.497	-7.831	-0.018

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 : -0.025 / q_NPA : -0.021

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	3	LYS	1	0.846	0.901	3.242	-2.006	0.063	0.060	-0.997	-1.132	0.001
4	A	4	ILE	0	0.007	0.006	5.683	0.468	0.468	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.042	-0.011	8.279	-0.002	-0.002	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.017	0.004	11.402	0.063	0.063	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.029	-0.030	13.890	0.028	0.028	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.777	-0.887	17.538	-0.284	-0.284	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.007	0.007	19.996	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.054	-0.021	23.009	0.010	0.010	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.784	-0.877	20.618	-0.276	-0.276	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.035	-0.010	19.865	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.008	-0.029	19.892	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.752	0.853	15.966	0.312	0.312	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.028	-0.017	15.408	-0.062	-0.062	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.921	-0.940	15.040	-0.373	-0.373	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.024	-0.017	13.081	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.850	0.903	8.701	0.858	0.858	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.007	-0.003	10.125	-0.151	-0.151	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.067	-0.026	11.202	-0.048	-0.048	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.007	-0.015	8.350	-0.032	-0.032	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.816	-0.898	6.250	-1.623	-1.623	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.107	-0.045	5.355	-0.259	-0.259	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.958	-0.964	4.340	-1.132	-0.889	-0.001	-0.045	-0.197	0.000
25	A	25	TYR	0	-0.073	-0.071	2.584	-4.017	-1.602	1.263	-1.414	-2.264	-0.016
26	A	26	LEU	0	-0.004	0.013	2.298	-1.610	-0.280	3.829	-1.036	-4.124	-0.003
27	A	27	VAL	0	-0.013	-0.008	3.850	0.223	0.333	0.009	-0.005	-0.114	0.000
28	A	28	ILE	0	-0.005	0.003	7.417	0.200	0.200	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.822	-0.892	10.493	-0.431	-0.431	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.001	-0.019	13.841	0.048	0.048	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.889	0.938	17.098	0.240	0.240	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.002	-0.001	20.592	0.029	0.029	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.763	-0.875	21.091	-0.153	-0.153	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.815	0.893	21.915	0.139	0.139	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.797	-0.895	19.091	-0.260	-0.260	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.045	0.017	17.267	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.039	-0.039	17.358	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.795	-0.872	19.123	-0.163	-0.163	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.011	-0.002	13.918	-0.029	-0.029	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.031	-0.016	14.147	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.945	-0.963	15.376	-0.135	-0.135	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.111	-0.072	14.853	0.040	0.040	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.025	-0.020	9.973	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.077	-0.019	10.503	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.017	-0.003	9.315	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.806	-0.882	7.030	-0.486	-0.486	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.038	0.023	9.740	0.163	0.163	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.003	0.002	10.966	-0.108	-0.108	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.018	0.011	11.936	0.052	0.052	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.021	-0.025	15.249	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.737	-0.857	18.696	-0.237	-0.237	0.000	0.000	0.000	0.000
52	A	52	MET	0	-0.020	-0.031	21.046	0.016	0.016	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.863	-0.926	23.744	-0.213	-0.213	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.023	-0.005	21.337	0.008	0.008	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.028	-0.014	25.105	0.013	0.013	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.053	0.027	27.205	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.967	-1.014	28.815	-0.078	-0.078	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.026	-0.015	32.437	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.008	-0.009	32.393	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.066	-0.011	29.892	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	ASN	0	0.059	0.047	26.952	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.070	0.012	22.655	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	CYS	0	0.024	0.033	22.524	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.002	-0.001	23.278	0.003	0.003	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.793	0.900	24.349	0.130	0.130	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.038	0.017	18.871	0.007	0.007	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.868	0.916	19.114	0.128	0.128	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.791	0.913	22.666	0.100	0.100	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.037	0.014	20.889	0.017	0.017	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.915	0.945	21.382	0.042	0.042	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.093	0.038	17.493	0.005	0.005	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.012	0.006	15.739	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.836	0.929	17.699	0.071	0.071	0.000	0.000	0.000	0.000
74	A	74	ASN	0	0.014	0.008	16.099	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.016	0.036	13.340	0.023	0.023	0.000	0.000	0.000	0.000
76	A	76	PRO	0	-0.025	-0.001	13.344	0.002	0.002	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.028	-0.022	14.999	-0.056	-0.056	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.005	0.007	14.584	0.032	0.032	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.030	-0.021	17.878	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.002	0.001	17.388	0.010	0.010	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.027	0.006	21.519	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.036	0.015	25.205	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.001	0.004	27.814	0.007	0.007	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.977	-0.993	29.605	-0.123	-0.123	0.000	0.000	0.000	0.000
85	A	85	HIS	0	0.016	-0.002	33.328	0.006	0.006	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.813	0.900	35.798	0.072	0.072	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.662	-0.858	31.248	-0.092	-0.092	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.085	-0.020	33.343	0.007	0.007	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.045	0.031	27.214	0.004	0.004	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.018	-0.005	30.969	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.088	-0.047	32.901	0.007	0.007	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.048	0.031	32.420	0.006	0.006	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.059	-0.022	31.893	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	HIS	0	0.040	0.008	27.008	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	SER	0	0.039	0.037	26.819	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.006	-0.017	25.627	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.025	-0.010	21.228	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.794	-0.874	18.827	-0.103	-0.103	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.817	-0.895	19.134	-0.140	-0.140	0.000	0.000	0.000	0.000
100	A	100	TYR	0	-0.058	-0.029	20.930	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.007	0.011	18.656	0.006	0.006	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.009	0.015	22.408	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.756	0.886	22.404	0.224	0.224	0.000	0.000	0.000	0.000
104	A	104	PRO	0	-0.005	-0.024	23.640	0.014	0.014	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.062	0.026	16.448	0.013	0.013	0.000	0.000	0.000	0.000
106	A	106	ASN	0	-0.005	-0.001	19.707	-0.027	-0.027	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.935	0.945	15.511	0.347	0.347	0.000	0.000	0.000	0.000
108	A	108	ASN	0	0.027	0.006	15.108	-0.066	-0.066	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.881	-0.921	15.968	-0.171	-0.171	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.016	0.008	13.947	0.008	0.008	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.038	0.021	8.946	0.002	0.002	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.006	0.006	12.028	0.018	0.018	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.848	0.894	14.616	0.194	0.194	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.003	0.006	9.598	0.048	0.048	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.809	-0.878	8.452	-0.110	-0.110	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.054	-0.028	11.174	0.139	0.139	0.000	0.000	0.000	0.000
117	A	117	HIS	0	-0.047	-0.038	13.568	0.090	0.090	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.024	0.012	6.866	0.052	0.052	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.957	0.983	10.584	-0.033	-0.033	0.000	0.000	0.000	0.000
120	A	120	THR	0	-0.069	-0.041	12.033	0.067	0.067	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.020	-0.024	10.269	0.050	0.050	0.000	0.000	0.000	0.000
122	A	122	ASN	0	0.006	0.003	7.984	-0.077	-0.077	0.000	0.000	0.000	0.000
123	A	123	TYR	0	-0.016	0.014	12.235	0.010	0.010	0.000	0.000	0.000	0.000
124	A	124	TYR	0	-0.015	-0.028	15.750	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.081	-0.040	13.278	-0.016	-0.016	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.941	-0.973	13.934	0.703	0.703	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.147	-0.056	16.331	-0.075	-0.075	0.000	0.000	0.000	0.000

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