FMO DATABASE

FMODB ID: NNJ2Q

Calculation Name: 3BL2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BL2

Chain ID: A

ChEMBL ID:

UniProt ID: P89884

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1223651.952253
FMO2-HF: Nuclear repulsion	1170196.635128
FMO2-HF: Total energy	-53455.317125
FMO2-MP2: Total energy	-53610.11436

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:5:LYS)

Summations of interaction energy for fragment #1(A:5: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.
-209.755	-212.839	38.301	-16.407	-18.811	-0.135

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.934

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	7	GLY	0	0.089	0.041	3.899	-2.867	-1.758	-0.006	-0.501	-0.602	0.001
4	A	8	THR	0	0.046	0.020	6.572	0.254	0.254	0.000	0.000	0.000	0.000
5	A	9	TYR	0	-0.036	-0.019	2.198	-7.385	-5.056	7.986	-3.810	-6.506	-0.045
6	A	10	TRP	0	0.045	-0.017	1.943	-15.978	-19.541	13.699	-4.245	-5.891	0.000
7	A	11	ALA	0	0.029	0.020	5.681	1.723	1.723	0.000	0.000	0.000	0.000
8	A	12	THR	0	-0.010	-0.012	8.134	2.010	2.010	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.037	-0.018	3.992	0.658	0.802	-0.001	-0.019	-0.124	0.000
10	A	14	ILE	0	-0.026	-0.002	7.845	1.949	1.949	0.000	0.000	0.000	0.000
11	A	15	THR	0	0.022	-0.013	10.590	1.452	1.452	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.004	0.009	9.954	1.419	1.419	0.000	0.000	0.000	0.000
13	A	17	PHE	0	-0.014	-0.007	10.176	1.365	1.365	0.000	0.000	0.000	0.000
14	A	18	LEU	0	0.020	0.009	11.948	1.729	1.729	0.000	0.000	0.000	0.000
15	A	19	LYS	1	0.862	0.936	15.234	18.166	18.166	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.013	-0.012	13.610	1.054	1.054	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.018	-0.019	15.151	1.100	1.100	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.026	-0.015	17.539	1.239	1.239	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.752	0.866	19.386	16.082	16.082	0.000	0.000	0.000	0.000
20	A	24	VAL	0	-0.015	0.005	19.625	0.644	0.644	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.939	-0.966	20.833	-11.981	-11.981	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.995	-0.986	22.201	-12.924	-12.924	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.006	-0.011	18.306	-0.782	-0.782	0.000	0.000	0.000	0.000
24	A	28	ASP	-1	-0.808	-0.898	15.846	-17.180	-17.180	0.000	0.000	0.000	0.000
25	A	29	CYS	0	-0.096	-0.041	14.703	-1.223	-1.223	0.000	0.000	0.000	0.000
26	A	30	VAL	0	0.019	0.009	9.783	-0.603	-0.603	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.907	-0.952	7.221	-31.519	-31.519	0.000	0.000	0.000	0.000
28	A	32	SER	0	-0.001	-0.005	8.473	-2.023	-2.023	0.000	0.000	0.000	0.000
29	A	33	ALA	0	0.011	-0.005	3.782	0.271	0.369	-0.001	-0.015	-0.083	0.000
30	A	34	VAL	0	0.050	0.034	4.837	-7.394	-7.298	-0.001	-0.005	-0.090	0.000
31	A	35	LEU	0	0.043	0.018	6.008	1.089	1.089	0.000	0.000	0.000	0.000
32	A	36	VAL	0	-0.006	-0.004	6.334	1.782	1.782	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.745	-0.854	1.695	-124.041	-128.448	16.529	-7.446	-4.676	-0.093
34	A	38	VAL	0	0.023	0.013	5.374	3.791	3.807	-0.001	0.000	-0.014	0.000
35	A	39	SER	0	0.020	0.016	8.713	3.269	3.269	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.775	0.893	4.448	56.857	56.908	-0.001	0.000	-0.049	0.000
37	A	41	ILE	0	0.006	0.008	6.763	2.436	2.436	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.033	0.019	10.065	2.287	2.287	0.000	0.000	0.000	0.000
39	A	43	THR	0	-0.017	-0.011	12.879	2.026	2.026	0.000	0.000	0.000	0.000
40	A	44	LEU	0	-0.023	-0.015	9.993	1.442	1.442	0.000	0.000	0.000	0.000
41	A	45	THR	0	-0.074	-0.043	13.507	1.561	1.561	0.000	0.000	0.000	0.000
42	A	46	GLN	0	0.012	0.009	15.829	0.610	0.610	0.000	0.000	0.000	0.000
43	A	47	GLU	-1	-0.757	-0.854	17.351	-13.711	-13.711	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.046	-0.006	17.214	0.702	0.702	0.000	0.000	0.000	0.000
45	A	49	ARG	1	0.796	0.883	19.148	14.865	14.865	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.875	0.930	21.786	13.941	13.941	0.000	0.000	0.000	0.000
47	A	51	HIS	0	-0.101	-0.056	21.187	0.990	0.990	0.000	0.000	0.000	0.000
48	A	52	TYR	0	-0.047	-0.032	23.318	0.521	0.521	0.000	0.000	0.000	0.000
49	A	53	ASP	-1	-0.833	-0.943	25.064	-11.672	-11.672	0.000	0.000	0.000	0.000
50	A	54	SER	0	-0.131	-0.070	26.840	0.557	0.557	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.083	-0.032	27.840	0.335	0.335	0.000	0.000	0.000	0.000
52	A	56	TYR	0	-0.039	-0.013	26.826	0.554	0.554	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.923	0.956	30.339	8.882	8.882	0.000	0.000	0.000	0.000
54	A	58	ALA	0	-0.024	-0.004	31.741	0.216	0.216	0.000	0.000	0.000	0.000
55	A	59	ASP	-1	-0.718	-0.839	27.934	-11.500	-11.500	0.000	0.000	0.000	0.000
56	A	60	TYR	0	-0.017	-0.025	21.314	0.367	0.367	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.054	0.044	27.323	0.088	0.088	0.000	0.000	0.000	0.000
58	A	62	PRO	0	-0.101	-0.063	29.404	0.205	0.205	0.000	0.000	0.000	0.000
59	A	63	ALA	0	0.011	0.019	28.813	0.302	0.302	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.024	0.004	23.763	0.022	0.022	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.885	0.937	27.795	9.152	9.152	0.000	0.000	0.000	0.000
62	A	66	ASN	0	-0.031	-0.022	30.159	0.337	0.337	0.000	0.000	0.000	0.000
63	A	67	TRP	0	0.018	0.008	22.921	-0.173	-0.173	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.849	0.910	25.644	10.686	10.686	0.000	0.000	0.000	0.000
65	A	69	ARG	1	0.908	0.951	27.267	9.636	9.636	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.828	-0.892	27.143	-10.279	-10.279	0.000	0.000	0.000	0.000
67	A	71	LEU	0	0.018	0.027	20.180	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	72	SER	0	0.073	0.028	20.651	-0.277	-0.277	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.831	0.921	21.696	10.217	10.217	0.000	0.000	0.000	0.000
70	A	74	LEU	0	0.008	0.011	22.534	0.050	0.050	0.000	0.000	0.000	0.000
71	A	75	PHE	0	0.051	0.004	17.901	-0.131	-0.131	0.000	0.000	0.000	0.000
72	A	76	THR	0	0.018	-0.016	19.069	-0.341	-0.341	0.000	0.000	0.000	0.000
73	A	77	SER	0	-0.039	-0.028	20.620	0.191	0.191	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.068	-0.011	18.191	0.270	0.270	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.001	-0.024	15.163	-0.711	-0.711	0.000	0.000	0.000	0.000
76	A	80	VAL	0	-0.022	0.012	18.406	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	81	ASP	-1	-0.809	-0.857	21.182	-12.837	-12.837	0.000	0.000	0.000	0.000
78	A	82	VAL	0	-0.036	-0.022	17.572	-0.070	-0.070	0.000	0.000	0.000	0.000
79	A	83	ILE	0	0.036	0.029	12.018	-0.208	-0.208	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.013	-0.014	13.870	-0.402	-0.402	0.000	0.000	0.000	0.000
81	A	85	SER	0	0.055	-0.003	11.142	0.230	0.230	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.010	0.017	12.563	-0.529	-0.529	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.786	0.837	15.693	14.591	14.591	0.000	0.000	0.000	0.000
84	A	88	ILE	0	-0.014	0.011	10.144	0.404	0.404	0.000	0.000	0.000	0.000
85	A	89	VAL	0	-0.005	0.003	12.180	-0.581	-0.581	0.000	0.000	0.000	0.000
86	A	90	GLY	0	0.050	0.025	13.956	0.466	0.466	0.000	0.000	0.000	0.000
87	A	91	PHE	0	-0.031	-0.021	12.010	0.714	0.714	0.000	0.000	0.000	0.000
88	A	92	PHE	0	0.021	0.004	9.200	0.032	0.032	0.000	0.000	0.000	0.000
89	A	93	ASP	-1	-0.723	-0.844	14.435	-15.239	-15.239	0.000	0.000	0.000	0.000
90	A	94	VAL	0	-0.019	-0.005	17.428	0.981	0.981	0.000	0.000	0.000	0.000
91	A	95	GLY	0	0.042	0.013	17.048	0.629	0.629	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.830	0.900	16.650	16.441	16.441	0.000	0.000	0.000	0.000
93	A	97	TYR	0	-0.029	-0.036	18.341	0.633	0.633	0.000	0.000	0.000	0.000
94	A	98	VAL	0	0.014	-0.006	21.371	0.591	0.591	0.000	0.000	0.000	0.000
95	A	99	CYS	0	-0.058	-0.031	19.035	0.203	0.203	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.861	-0.906	19.654	-15.533	-15.533	0.000	0.000	0.000	0.000
97	A	101	GLU	-1	-0.860	-0.928	23.087	-12.512	-12.512	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.124	-0.044	25.376	0.539	0.539	0.000	0.000	0.000	0.000
99	A	103	LEU	0	-0.040	-0.016	22.921	0.468	0.468	0.000	0.000	0.000	0.000
100	A	104	CYS	0	-0.044	-0.027	25.937	0.094	0.094	0.000	0.000	0.000	0.000
101	A	105	PRO	0	0.009	0.010	23.873	-0.315	-0.315	0.000	0.000	0.000	0.000
102	A	106	GLY	0	0.014	0.005	23.751	0.597	0.597	0.000	0.000	0.000	0.000
103	A	107	SER	0	-0.026	-0.020	24.935	-0.095	-0.095	0.000	0.000	0.000	0.000
104	A	108	TRP	0	-0.012	-0.034	17.161	-0.860	-0.860	0.000	0.000	0.000	0.000
105	A	109	THR	0	-0.016	-0.030	23.433	0.591	0.591	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.851	-0.940	23.695	-11.246	-11.246	0.000	0.000	0.000	0.000
107	A	111	ASP	-1	-0.825	-0.890	24.353	-11.602	-11.602	0.000	0.000	0.000	0.000
108	A	112	HIS	0	0.074	0.046	20.561	-0.164	-0.164	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.855	-0.903	19.650	-15.136	-15.136	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.023	-0.006	19.838	-0.448	-0.448	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.027	-0.022	17.889	-0.346	-0.346	0.000	0.000	0.000	0.000
112	A	116	ASN	0	0.054	0.026	14.755	-1.781	-1.781	0.000	0.000	0.000	0.000
113	A	117	ASP	-1	-0.848	-0.905	15.419	-18.035	-18.035	0.000	0.000	0.000	0.000
114	A	118	CYS	0	-0.101	-0.032	16.891	-0.230	-0.230	0.000	0.000	0.000	0.000
115	A	119	MET	0	-0.015	-0.006	13.501	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	120	THR	0	0.004	-0.014	11.181	-1.602	-1.602	0.000	0.000	0.000	0.000
117	A	121	HIS	0	-0.049	-0.031	12.211	-0.730	-0.730	0.000	0.000	0.000	0.000
118	A	122	PHE	0	0.006	0.014	13.496	-0.171	-0.171	0.000	0.000	0.000	0.000
119	A	123	PHE	0	0.011	-0.004	6.349	-0.403	-0.403	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.030	-0.019	8.379	-1.244	-1.244	0.000	0.000	0.000	0.000
121	A	125	GLU	-1	-0.906	-0.938	9.698	-16.321	-16.321	0.000	0.000	0.000	0.000
122	A	126	ASN	0	-0.089	-0.049	12.404	0.980	0.980	0.000	0.000	0.000	0.000
123	A	127	ASN	0	-0.055	-0.035	8.017	-0.841	-0.841	0.000	0.000	0.000	0.000
124	A	128	LEU	0	0.028	0.016	8.205	-0.719	-0.719	0.000	0.000	0.000	0.000
125	A	129	MET	0	0.002	0.011	3.209	-1.103	-0.281	0.099	-0.341	-0.580	0.002
126	A	130	ASN	0	-0.060	-0.030	5.276	-3.213	-3.213	0.000	0.000	0.000	0.000
127	A	131	HIS	0	-0.021	-0.007	6.436	2.276	2.276	0.000	0.000	0.000	0.000
128	A	132	PHE	0	-0.002	0.003	6.780	1.625	1.625	0.000	0.000	0.000	0.000
129	A	133	PRO	0	0.037	0.022	5.599	-6.392	-6.392	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.014	0.009	4.043	2.732	2.953	-0.001	-0.025	-0.196	0.000
131	A	135	GLU	-1	-0.995	-0.992	5.417	-31.249	-31.249	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)