FMO DATABASE

FMODB ID: G5ZY1

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1219037.992513
FMO2-HF: Nuclear repulsion	1165583.736784
FMO2-HF: Total energy	-53454.255728
FMO2-MP2: Total energy	-53609.090633

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.
-176.444	-163.494	6.972	-7.746	-12.173	-0.065

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 : 0.928 / q_NPA : 0.963

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	0.098	0.048	3.675	-3.883	-2.532	-0.007	-0.616	-0.728	0.001
4	A	8	THR	0	0.043	0.021	6.520	1.506	1.506	0.000	0.000	0.000	0.000
5	A	9	TYR	0	-0.085	-0.100	2.537	-8.171	-4.920	5.210	-2.897	-5.564	-0.040
6	A	10	TRP	0	0.059	0.007	2.586	-10.303	-6.836	0.931	-1.513	-2.884	0.005
7	A	11	ALA	0	0.021	0.023	6.043	2.227	2.227	0.000	0.000	0.000	0.000
8	A	12	THR	0	-0.012	-0.009	7.932	2.506	2.506	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.053	-0.025	4.072	1.122	1.242	-0.001	-0.013	-0.106	0.000
10	A	14	ILE	0	0.001	0.008	7.801	2.267	2.267	0.000	0.000	0.000	0.000
11	A	15	THR	0	0.022	0.004	10.630	1.554	1.554	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.015	0.017	10.055	1.593	1.593	0.000	0.000	0.000	0.000
13	A	17	PHE	0	0.001	-0.008	10.300	1.458	1.458	0.000	0.000	0.000	0.000
14	A	18	LEU	0	0.010	-0.004	12.079	1.742	1.742	0.000	0.000	0.000	0.000
15	A	19	LYS	1	0.887	0.955	15.190	18.882	18.882	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.027	-0.023	13.871	1.063	1.063	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.041	-0.026	15.477	0.949	0.949	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.009	-0.003	17.933	1.133	1.133	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.872	0.935	19.836	14.929	14.929	0.000	0.000	0.000	0.000
20	A	24	VAL	0	0.009	0.010	19.715	0.704	0.704	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.961	-0.975	20.976	-11.884	-11.884	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.981	-0.981	22.257	-12.937	-12.937	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.033	-0.019	18.178	-0.739	-0.739	0.000	0.000	0.000	0.000
24	A	28	ASP	-1	-0.817	-0.904	15.881	-16.905	-16.905	0.000	0.000	0.000	0.000
25	A	29	CYS	0	-0.097	-0.059	14.615	-1.192	-1.192	0.000	0.000	0.000	0.000
26	A	30	VAL	0	0.034	0.028	9.664	-0.808	-0.808	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.916	-0.958	7.337	-31.827	-31.827	0.000	0.000	0.000	0.000
28	A	32	SER	0	0.014	-0.012	8.953	-1.417	-1.417	0.000	0.000	0.000	0.000
29	A	33	ALA	0	-0.017	-0.015	3.910	0.207	0.286	-0.001	-0.009	-0.068	0.000
30	A	34	VAL	0	0.084	0.043	5.233	-5.086	-5.086	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.031	0.021	6.122	1.358	1.358	0.000	0.000	0.000	0.000
32	A	36	VAL	0	-0.008	-0.004	7.037	1.814	1.814	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.791	-0.870	2.480	-93.974	-90.299	0.741	-2.420	-1.996	-0.031
34	A	38	VAL	0	0.021	0.023	6.034	3.312	3.312	0.000	0.000	0.000	0.000
35	A	39	SER	0	-0.031	-0.016	9.066	3.007	3.007	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.912	0.955	6.279	41.857	41.857	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.005	0.001	6.919	1.910	1.910	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.031	0.023	10.565	1.965	1.965	0.000	0.000	0.000	0.000
39	A	43	THR	0	-0.006	0.010	13.499	1.909	1.909	0.000	0.000	0.000	0.000
40	A	44	LEU	0	-0.012	-0.007	10.718	1.327	1.327	0.000	0.000	0.000	0.000
41	A	45	THR	0	-0.054	-0.022	14.026	1.542	1.542	0.000	0.000	0.000	0.000
42	A	46	GLN	0	0.003	-0.002	16.356	0.545	0.545	0.000	0.000	0.000	0.000
43	A	47	GLU	-1	-0.840	-0.902	17.834	-13.705	-13.705	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.057	-0.032	17.773	0.713	0.713	0.000	0.000	0.000	0.000
45	A	49	ARG	1	0.909	0.951	19.690	14.652	14.652	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.908	0.965	22.217	13.722	13.722	0.000	0.000	0.000	0.000
47	A	51	HIS	0	-0.080	-0.043	22.013	0.341	0.341	0.000	0.000	0.000	0.000
48	A	52	TYR	0	-0.047	-0.021	23.853	0.479	0.479	0.000	0.000	0.000	0.000
49	A	53	ASP	-1	-0.855	-0.942	25.606	-11.270	-11.270	0.000	0.000	0.000	0.000
50	A	54	SER	0	-0.125	-0.048	27.790	0.497	0.497	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.065	-0.021	28.173	0.385	0.385	0.000	0.000	0.000	0.000
52	A	56	TYR	0	-0.048	-0.022	27.619	0.579	0.579	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.961	0.972	31.036	8.652	8.652	0.000	0.000	0.000	0.000
54	A	58	ALA	0	-0.070	-0.031	31.695	0.026	0.026	0.000	0.000	0.000	0.000
55	A	59	ASP	-1	-0.724	-0.834	28.521	-11.291	-11.291	0.000	0.000	0.000	0.000
56	A	60	TYR	0	-0.078	-0.096	21.559	0.325	0.325	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.043	0.033	27.441	0.089	0.089	0.000	0.000	0.000	0.000
58	A	62	PRO	0	-0.096	-0.057	29.792	0.115	0.115	0.000	0.000	0.000	0.000
59	A	63	ALA	0	0.029	0.001	28.844	0.163	0.163	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.002	0.019	24.073	-0.100	-0.100	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.948	0.989	28.220	8.951	8.951	0.000	0.000	0.000	0.000
62	A	66	ASN	0	-0.016	-0.017	30.687	0.209	0.209	0.000	0.000	0.000	0.000
63	A	67	TRP	0	0.094	0.038	23.115	-0.139	-0.139	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.913	0.965	26.128	10.510	10.510	0.000	0.000	0.000	0.000
65	A	69	ARG	1	0.909	0.942	27.399	9.533	9.533	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.903	-0.932	27.197	-10.251	-10.251	0.000	0.000	0.000	0.000
67	A	71	LEU	0	0.004	0.005	20.614	-0.081	-0.081	0.000	0.000	0.000	0.000
68	A	72	SER	0	0.049	0.001	21.103	-0.431	-0.431	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.904	0.961	21.757	10.187	10.187	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.007	0.001	22.519	0.060	0.060	0.000	0.000	0.000	0.000
71	A	75	PHE	0	0.064	0.017	17.803	-0.167	-0.167	0.000	0.000	0.000	0.000
72	A	76	THR	0	0.025	0.006	18.814	-0.393	-0.393	0.000	0.000	0.000	0.000
73	A	77	SER	0	-0.073	-0.043	20.382	-0.020	-0.020	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.035	0.004	18.051	0.198	0.198	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.012	-0.033	15.062	-0.526	-0.526	0.000	0.000	0.000	0.000
76	A	80	VAL	0	-0.019	0.013	18.412	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	81	ASP	-1	-0.840	-0.897	21.249	-12.772	-12.772	0.000	0.000	0.000	0.000
78	A	82	VAL	0	-0.039	-0.013	17.643	-0.072	-0.072	0.000	0.000	0.000	0.000
79	A	83	ILE	0	0.051	0.028	12.118	-0.238	-0.238	0.000	0.000	0.000	0.000
80	A	84	ASN	0	0.000	0.000	14.425	-0.406	-0.406	0.000	0.000	0.000	0.000
81	A	85	SER	0	0.068	0.012	11.901	-0.147	-0.147	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.014	0.016	13.599	-0.445	-0.445	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.821	0.881	16.766	14.499	14.499	0.000	0.000	0.000	0.000
84	A	88	ILE	0	0.009	0.018	10.345	0.329	0.329	0.000	0.000	0.000	0.000
85	A	89	VAL	0	-0.006	0.000	12.763	-0.538	-0.538	0.000	0.000	0.000	0.000
86	A	90	GLY	0	0.049	0.020	14.363	0.410	0.410	0.000	0.000	0.000	0.000
87	A	91	PHE	0	-0.045	-0.018	12.889	0.608	0.608	0.000	0.000	0.000	0.000
88	A	92	PHE	0	0.019	-0.005	9.410	0.016	0.016	0.000	0.000	0.000	0.000
89	A	93	ASP	-1	-0.763	-0.857	14.686	-14.996	-14.996	0.000	0.000	0.000	0.000
90	A	94	VAL	0	-0.044	-0.011	17.708	0.871	0.871	0.000	0.000	0.000	0.000
91	A	95	GLY	0	0.042	0.012	17.184	0.652	0.652	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.849	0.920	16.931	16.361	16.361	0.000	0.000	0.000	0.000
93	A	97	TYR	0	-0.017	-0.038	18.514	0.593	0.593	0.000	0.000	0.000	0.000
94	A	98	VAL	0	0.024	0.025	21.377	0.598	0.598	0.000	0.000	0.000	0.000
95	A	99	CYS	0	-0.074	-0.034	19.252	0.306	0.306	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.900	-0.951	20.300	-14.641	-14.641	0.000	0.000	0.000	0.000
97	A	101	GLU	-1	-0.952	-0.974	23.508	-11.451	-11.451	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.136	-0.055	25.766	0.498	0.498	0.000	0.000	0.000	0.000
99	A	103	LEU	0	-0.053	-0.033	22.957	0.415	0.415	0.000	0.000	0.000	0.000
100	A	104	CYS	0	0.011	0.002	26.511	0.177	0.177	0.000	0.000	0.000	0.000
101	A	105	PRO	0	-0.026	-0.011	24.436	-0.329	-0.329	0.000	0.000	0.000	0.000
102	A	106	GLY	0	0.028	0.005	24.077	0.472	0.472	0.000	0.000	0.000	0.000
103	A	107	SER	0	-0.061	-0.026	25.332	0.013	0.013	0.000	0.000	0.000	0.000
104	A	108	TRP	0	0.023	0.008	17.442	-0.707	-0.707	0.000	0.000	0.000	0.000
105	A	109	THR	0	-0.019	-0.032	23.344	0.395	0.395	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.855	-0.935	24.101	-11.297	-11.297	0.000	0.000	0.000	0.000
107	A	111	ASP	-1	-0.920	-0.960	24.651	-11.577	-11.577	0.000	0.000	0.000	0.000
108	A	112	HIS	0	0.065	0.044	20.756	-0.184	-0.184	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.908	-0.948	20.131	-14.509	-14.509	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.002	0.016	20.291	-0.425	-0.425	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.020	-0.025	18.305	-0.399	-0.399	0.000	0.000	0.000	0.000
112	A	116	ASN	0	0.042	0.010	15.058	-1.854	-1.854	0.000	0.000	0.000	0.000
113	A	117	ASP	-1	-0.897	-0.915	15.916	-17.539	-17.539	0.000	0.000	0.000	0.000
114	A	118	CYS	0	-0.079	-0.015	17.074	-0.385	-0.385	0.000	0.000	0.000	0.000
115	A	119	MET	0	-0.021	-0.013	14.230	-0.173	-0.173	0.000	0.000	0.000	0.000
116	A	120	THR	0	0.002	-0.032	11.395	-1.762	-1.762	0.000	0.000	0.000	0.000
117	A	121	HIS	0	-0.047	-0.033	12.299	-0.604	-0.604	0.000	0.000	0.000	0.000
118	A	122	PHE	0	0.020	0.021	13.599	-0.183	-0.183	0.000	0.000	0.000	0.000
119	A	123	PHE	0	0.014	0.009	6.423	-0.485	-0.485	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.039	-0.037	8.250	-1.270	-1.270	0.000	0.000	0.000	0.000
121	A	125	GLU	-1	-0.943	-0.955	9.682	-16.719	-16.719	0.000	0.000	0.000	0.000
122	A	126	ASN	0	-0.107	-0.058	12.089	1.208	1.208	0.000	0.000	0.000	0.000
123	A	127	ASN	0	-0.028	-0.006	7.810	-1.068	-1.068	0.000	0.000	0.000	0.000
124	A	128	LEU	0	0.070	0.019	8.192	-0.683	-0.683	0.000	0.000	0.000	0.000
125	A	129	MET	0	-0.029	0.000	2.836	-0.743	0.004	0.101	-0.266	-0.582	0.000
126	A	130	ASN	0	-0.089	-0.049	4.992	-0.571	-0.447	-0.001	-0.003	-0.120	0.000
127	A	131	HIS	0	-0.016	0.003	6.383	2.250	2.250	0.000	0.000	0.000	0.000
128	A	132	PHE	0	-0.016	-0.017	7.308	1.894	1.894	0.000	0.000	0.000	0.000
129	A	133	PRO	0	0.026	0.017	6.194	-5.523	-5.523	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.041	0.007	4.100	2.856	2.992	-0.001	-0.009	-0.125	0.000
131	A	135	GLU	-1	-0.995	-1.008	6.163	-24.436	-24.436	0.000	0.000	0.000	0.000

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