FMO DATABASE

FMODB ID: 894NY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1220136.46962
FMO2-HF: Nuclear repulsion	1166681.43353
FMO2-HF: Total energy	-53455.036091
FMO2-MP2: Total energy	-53609.840206

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.
-198.115	-190.622	20.892	-11.891	-16.494	-0.112

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 : 0.876 / 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	0.097	0.047	3.811	-3.604	-2.328	-0.006	-0.606	-0.665	0.001
4	A	8	THR	0	0.047	0.016	6.520	0.570	0.570	0.000	0.000	0.000	0.000
5	A	9	TYR	0	-0.042	-0.024	2.262	-8.094	-6.529	8.862	-3.611	-6.816	-0.043
6	A	10	TRP	0	0.059	0.001	2.455	-14.679	-11.064	2.560	-2.116	-4.059	0.003
7	A	11	ALA	0	0.022	0.024	5.917	1.922	1.922	0.000	0.000	0.000	0.000
8	A	12	THR	0	-0.019	-0.019	8.023	2.348	2.348	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.045	-0.022	3.893	0.612	0.765	-0.001	-0.022	-0.130	0.000
10	A	14	ILE	0	-0.016	0.001	7.768	2.092	2.092	0.000	0.000	0.000	0.000
11	A	15	THR	0	0.028	-0.006	10.405	1.430	1.430	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.012	0.016	9.985	1.530	1.530	0.000	0.000	0.000	0.000
13	A	17	PHE	0	-0.004	-0.008	10.067	1.439	1.439	0.000	0.000	0.000	0.000
14	A	18	LEU	0	0.013	-0.005	11.878	1.770	1.770	0.000	0.000	0.000	0.000
15	A	19	LYS	1	0.891	0.957	15.067	18.536	18.536	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.021	-0.016	13.657	1.085	1.085	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.043	-0.036	15.152	1.061	1.061	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.012	-0.007	17.652	1.157	1.157	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.783	0.897	19.201	16.241	16.241	0.000	0.000	0.000	0.000
20	A	24	VAL	0	0.004	0.007	19.599	0.711	0.711	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.950	-0.969	20.811	-11.983	-11.983	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.987	-0.982	22.240	-12.938	-12.938	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.014	-0.013	18.220	-0.766	-0.766	0.000	0.000	0.000	0.000
24	A	28	ASP	-1	-0.837	-0.905	15.977	-16.842	-16.842	0.000	0.000	0.000	0.000
25	A	29	CYS	0	-0.094	-0.057	14.617	-1.229	-1.229	0.000	0.000	0.000	0.000
26	A	30	VAL	0	0.031	0.017	9.659	-0.838	-0.838	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.915	-0.952	7.432	-31.006	-31.006	0.000	0.000	0.000	0.000
28	A	32	SER	0	0.008	-0.008	8.916	-1.355	-1.355	0.000	0.000	0.000	0.000
29	A	33	ALA	0	-0.012	-0.016	3.940	-0.036	0.042	-0.001	-0.009	-0.068	0.000
30	A	34	VAL	0	0.066	0.034	4.992	-6.608	-6.527	-0.001	-0.002	-0.077	0.000
31	A	35	LEU	0	0.045	0.030	6.002	0.925	0.925	0.000	0.000	0.000	0.000
32	A	36	VAL	0	0.003	-0.002	6.574	1.485	1.485	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.765	-0.889	1.830	-115.437	-115.772	9.424	-5.220	-3.870	-0.074
34	A	38	VAL	0	0.026	0.026	5.587	3.538	3.538	0.000	0.000	0.000	0.000
35	A	39	SER	0	0.009	0.001	8.708	3.309	3.309	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.796	0.908	4.926	51.964	51.964	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.010	-0.004	6.539	2.038	2.038	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.028	0.022	10.135	2.178	2.178	0.000	0.000	0.000	0.000
39	A	43	THR	0	-0.015	-0.003	13.016	1.958	1.958	0.000	0.000	0.000	0.000
40	A	44	LEU	0	-0.013	-0.007	10.174	1.429	1.429	0.000	0.000	0.000	0.000
41	A	45	THR	0	-0.058	-0.029	13.637	1.594	1.594	0.000	0.000	0.000	0.000
42	A	46	GLN	0	0.020	0.012	15.952	0.617	0.617	0.000	0.000	0.000	0.000
43	A	47	GLU	-1	-0.794	-0.867	17.399	-13.666	-13.666	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.048	-0.020	17.369	0.786	0.786	0.000	0.000	0.000	0.000
45	A	49	ARG	1	0.852	0.915	19.284	14.742	14.742	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.890	0.940	21.787	13.938	13.938	0.000	0.000	0.000	0.000
47	A	51	HIS	0	-0.109	-0.055	21.566	0.771	0.771	0.000	0.000	0.000	0.000
48	A	52	TYR	0	-0.061	-0.032	23.509	0.534	0.534	0.000	0.000	0.000	0.000
49	A	53	ASP	-1	-0.855	-0.942	25.234	-11.531	-11.531	0.000	0.000	0.000	0.000
50	A	54	SER	0	-0.123	-0.057	27.326	0.505	0.505	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.076	-0.025	27.722	0.402	0.402	0.000	0.000	0.000	0.000
52	A	56	TYR	0	-0.040	-0.018	27.086	0.596	0.596	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.951	0.970	30.666	8.837	8.837	0.000	0.000	0.000	0.000
54	A	58	ALA	0	-0.049	-0.024	31.377	0.023	0.023	0.000	0.000	0.000	0.000
55	A	59	ASP	-1	-0.695	-0.828	27.757	-11.537	-11.537	0.000	0.000	0.000	0.000
56	A	60	TYR	0	-0.073	-0.065	21.238	0.328	0.328	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.040	0.028	27.174	0.101	0.101	0.000	0.000	0.000	0.000
58	A	62	PRO	0	-0.108	-0.063	29.540	0.132	0.132	0.000	0.000	0.000	0.000
59	A	63	ALA	0	0.017	-0.003	28.647	0.176	0.176	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.001	0.019	23.995	-0.097	-0.097	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.943	0.982	28.051	9.001	9.001	0.000	0.000	0.000	0.000
62	A	66	ASN	0	-0.014	-0.010	30.410	0.247	0.247	0.000	0.000	0.000	0.000
63	A	67	TRP	0	0.082	0.031	22.794	-0.177	-0.177	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.833	0.908	25.823	10.702	10.702	0.000	0.000	0.000	0.000
65	A	69	ARG	1	0.920	0.948	27.114	9.564	9.564	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.856	-0.908	27.405	-10.201	-10.201	0.000	0.000	0.000	0.000
67	A	71	LEU	0	0.010	0.021	20.229	-0.057	-0.057	0.000	0.000	0.000	0.000
68	A	72	SER	0	0.060	0.016	21.189	-0.259	-0.259	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.832	0.914	21.942	10.185	10.185	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.002	0.006	22.686	0.037	0.037	0.000	0.000	0.000	0.000
71	A	75	PHE	0	0.063	0.012	17.991	-0.187	-0.187	0.000	0.000	0.000	0.000
72	A	76	THR	0	0.015	-0.007	18.973	-0.412	-0.412	0.000	0.000	0.000	0.000
73	A	77	SER	0	-0.032	-0.024	20.537	0.160	0.160	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.075	-0.012	18.337	0.232	0.232	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.002	-0.022	15.366	-0.521	-0.521	0.000	0.000	0.000	0.000
76	A	80	VAL	0	-0.021	0.014	18.525	0.020	0.020	0.000	0.000	0.000	0.000
77	A	81	ASP	-1	-0.817	-0.866	21.347	-12.873	-12.873	0.000	0.000	0.000	0.000
78	A	82	VAL	0	-0.040	-0.018	17.748	-0.074	-0.074	0.000	0.000	0.000	0.000
79	A	83	ILE	0	0.046	0.025	12.230	-0.237	-0.237	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.008	-0.003	14.443	-0.437	-0.437	0.000	0.000	0.000	0.000
81	A	85	SER	0	0.074	0.011	11.501	0.010	0.010	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.017	0.022	13.129	-0.518	-0.518	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.782	0.838	16.250	14.549	14.549	0.000	0.000	0.000	0.000
84	A	88	ILE	0	0.008	0.015	10.292	0.328	0.328	0.000	0.000	0.000	0.000
85	A	89	VAL	0	-0.003	0.003	12.259	-0.575	-0.575	0.000	0.000	0.000	0.000
86	A	90	GLY	0	0.043	0.019	14.062	0.435	0.435	0.000	0.000	0.000	0.000
87	A	91	PHE	0	-0.038	-0.020	12.211	0.685	0.685	0.000	0.000	0.000	0.000
88	A	92	PHE	0	0.012	-0.003	9.167	0.027	0.027	0.000	0.000	0.000	0.000
89	A	93	ASP	-1	-0.745	-0.843	14.452	-15.217	-15.217	0.000	0.000	0.000	0.000
90	A	94	VAL	0	-0.026	-0.008	17.408	0.887	0.887	0.000	0.000	0.000	0.000
91	A	95	GLY	0	0.048	0.019	17.002	0.667	0.667	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.832	0.900	16.564	16.517	16.517	0.000	0.000	0.000	0.000
93	A	97	TYR	0	-0.033	-0.040	18.239	0.638	0.638	0.000	0.000	0.000	0.000
94	A	98	VAL	0	0.024	0.015	21.353	0.618	0.618	0.000	0.000	0.000	0.000
95	A	99	CYS	0	-0.085	-0.036	19.156	0.319	0.319	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.858	-0.922	20.328	-15.072	-15.072	0.000	0.000	0.000	0.000
97	A	101	GLU	-1	-0.899	-0.949	23.227	-12.217	-12.217	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.114	-0.047	25.542	0.510	0.510	0.000	0.000	0.000	0.000
99	A	103	LEU	0	-0.053	-0.031	22.902	0.427	0.427	0.000	0.000	0.000	0.000
100	A	104	CYS	0	0.005	-0.002	26.335	0.176	0.176	0.000	0.000	0.000	0.000
101	A	105	PRO	0	-0.015	-0.010	24.225	-0.315	-0.315	0.000	0.000	0.000	0.000
102	A	106	GLY	0	0.030	0.010	23.879	0.480	0.480	0.000	0.000	0.000	0.000
103	A	107	SER	0	-0.062	-0.027	25.180	0.012	0.012	0.000	0.000	0.000	0.000
104	A	108	TRP	0	-0.011	-0.017	17.148	-0.790	-0.790	0.000	0.000	0.000	0.000
105	A	109	THR	0	-0.018	-0.038	23.279	0.433	0.433	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.850	-0.938	23.874	-11.277	-11.277	0.000	0.000	0.000	0.000
107	A	111	ASP	-1	-0.822	-0.899	24.445	-11.558	-11.558	0.000	0.000	0.000	0.000
108	A	112	HIS	0	0.076	0.058	20.716	-0.117	-0.117	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.862	-0.913	19.925	-14.920	-14.920	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.029	-0.001	20.117	-0.420	-0.420	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.013	-0.020	17.976	-0.374	-0.374	0.000	0.000	0.000	0.000
112	A	116	ASN	0	0.028	0.011	14.985	-1.849	-1.849	0.000	0.000	0.000	0.000
113	A	117	ASP	-1	-0.861	-0.910	15.719	-17.777	-17.777	0.000	0.000	0.000	0.000
114	A	118	CYS	0	-0.091	-0.021	16.942	-0.383	-0.383	0.000	0.000	0.000	0.000
115	A	119	MET	0	-0.007	-0.005	13.689	-0.080	-0.080	0.000	0.000	0.000	0.000
116	A	120	THR	0	-0.001	-0.020	11.306	-1.821	-1.821	0.000	0.000	0.000	0.000
117	A	121	HIS	0	-0.044	-0.034	12.457	-0.689	-0.689	0.000	0.000	0.000	0.000
118	A	122	PHE	0	0.015	0.017	13.800	-0.130	-0.130	0.000	0.000	0.000	0.000
119	A	123	PHE	0	0.014	0.007	6.652	-0.459	-0.459	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.031	-0.031	8.462	-1.130	-1.130	0.000	0.000	0.000	0.000
121	A	125	GLU	-1	-0.924	-0.944	9.877	-16.383	-16.383	0.000	0.000	0.000	0.000
122	A	126	ASN	0	-0.107	-0.060	12.267	1.178	1.178	0.000	0.000	0.000	0.000
123	A	127	ASN	0	-0.053	-0.021	7.926	-0.857	-0.857	0.000	0.000	0.000	0.000
124	A	128	LEU	0	0.053	0.020	8.265	-0.585	-0.585	0.000	0.000	0.000	0.000
125	A	129	MET	0	-0.029	0.000	3.121	-0.988	-0.249	0.057	-0.278	-0.517	0.001
126	A	130	ASN	0	-0.064	-0.038	5.026	-3.047	-2.924	-0.001	-0.002	-0.119	0.000
127	A	131	HIS	0	-0.027	-0.002	6.370	2.060	2.060	0.000	0.000	0.000	0.000
128	A	132	PHE	0	-0.005	-0.013	7.200	1.519	1.519	0.000	0.000	0.000	0.000
129	A	133	PRO	0	0.033	0.031	5.772	-5.981	-5.981	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.037	-0.006	3.847	2.600	2.798	-0.001	-0.025	-0.173	0.000
131	A	135	GLU	-1	-0.962	-0.985	5.945	-25.538	-25.538	0.000	0.000	0.000	0.000

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