FMO DATABASE

FMODB ID: LZ869

Calculation Name: 2A61-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A61

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZG9

Base Structure: X-ray

Registration Date: 2023-09-20

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1227260.273501
FMO2-HF: Nuclear repulsion	1170482.892574
FMO2-HF: Total energy	-56777.380927
FMO2-MP2: Total energy	-56945.394059

3D Structure Molmil

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.
95.821	99.862	5.611	-4.071	-5.582	0.001

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 : 1.022 / q_NPA : 0.997

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	PRO	0	0.030	0.007	2.694	-1.482	1.288	1.262	-1.644	-2.388	0.012
4	A	8	PHE	0	0.049	0.017	1.878	-0.951	-0.441	4.333	-2.167	-2.677	-0.010
5	A	9	GLU	-1	-0.810	-0.875	3.544	-27.874	-27.113	0.016	-0.260	-0.517	-0.001
6	A	10	ARG	1	0.930	0.962	5.472	31.634	31.634	0.000	0.000	0.000	0.000
7	A	11	ILE	0	0.069	0.041	6.487	1.911	1.911	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.009	0.003	6.869	1.686	1.686	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.842	0.900	8.942	26.733	26.733	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.916	-0.961	11.463	-16.765	-16.765	0.000	0.000	0.000	0.000
11	A	15	ILE	0	0.007	0.002	11.051	1.191	1.191	0.000	0.000	0.000	0.000
12	A	16	CYS	0	-0.048	-0.032	12.561	1.047	1.047	0.000	0.000	0.000	0.000
13	A	17	PHE	0	-0.023	-0.011	15.382	0.980	0.980	0.000	0.000	0.000	0.000
14	A	18	MET	0	0.033	0.013	15.782	1.050	1.050	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.040	0.028	17.873	0.732	0.732	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.895	0.950	19.514	14.417	14.417	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.021	-0.018	21.250	0.617	0.617	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.815	-0.882	23.026	-9.840	-9.840	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.052	0.016	24.280	0.420	0.420	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.768	0.844	24.838	12.092	12.092	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.841	0.917	26.185	10.789	10.789	0.000	0.000	0.000	0.000
22	A	26	VAL	0	0.028	0.021	29.812	0.270	0.270	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.043	-0.013	29.095	0.211	0.211	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.919	0.965	32.824	8.614	8.614	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.894	-0.952	34.992	-8.165	-8.165	0.000	0.000	0.000	0.000
26	A	30	PHE	0	-0.032	-0.015	35.109	0.188	0.188	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.022	0.025	37.283	0.135	0.135	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.065	-0.018	32.914	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.001	-0.031	33.105	-0.275	-0.275	0.000	0.000	0.000	0.000
30	A	34	PRO	0	0.026	-0.014	27.576	-0.089	-0.089	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.053	0.032	28.937	-0.200	-0.200	0.000	0.000	0.000	0.000
32	A	36	GLN	0	0.066	0.043	30.347	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	37	PHE	0	0.077	0.025	26.352	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.808	-0.867	25.478	-12.276	-12.276	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.020	-0.004	28.347	-0.122	-0.122	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.015	0.008	31.332	0.036	0.036	0.000	0.000	0.000	0.000
37	A	41	GLN	0	0.002	-0.021	23.802	0.030	0.030	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.828	0.922	23.749	12.422	12.422	0.000	0.000	0.000	0.000
39	A	43	ILE	0	-0.013	-0.004	28.592	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	44	TYR	0	-0.012	-0.002	29.285	0.034	0.034	0.000	0.000	0.000	0.000
41	A	45	PHE	0	-0.031	-0.013	25.787	0.004	0.004	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.848	-0.908	25.514	-12.116	-12.116	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.019	0.024	29.809	0.175	0.175	0.000	0.000	0.000	0.000
44	A	48	PRO	0	-0.012	-0.024	33.204	-0.135	-0.135	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.884	0.953	28.907	10.394	10.394	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.818	0.901	34.479	8.738	8.738	0.000	0.000	0.000	0.000
47	A	51	PRO	0	0.028	0.000	34.733	-0.284	-0.284	0.000	0.000	0.000	0.000
48	A	52	GLY	0	-0.042	-0.035	34.761	-0.161	-0.161	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.776	-0.893	30.962	-9.793	-9.793	0.000	0.000	0.000	0.000
50	A	54	LEU	0	0.026	0.014	29.936	-0.397	-0.397	0.000	0.000	0.000	0.000
51	A	55	SER	0	-0.094	-0.060	30.475	-0.165	-0.165	0.000	0.000	0.000	0.000
52	A	56	VAL	0	-0.001	-0.005	26.706	-0.199	-0.199	0.000	0.000	0.000	0.000
53	A	57	LEU	0	-0.017	-0.001	25.182	-0.419	-0.419	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.060	-0.034	25.511	-0.383	-0.383	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.043	0.039	26.626	-0.302	-0.302	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.042	-0.012	27.586	0.157	0.157	0.000	0.000	0.000	0.000
57	A	61	ALA	0	0.063	0.039	31.077	0.089	0.089	0.000	0.000	0.000	0.000
58	A	62	LYS	1	1.004	0.986	34.448	9.069	9.069	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.035	0.029	36.894	0.028	0.028	0.000	0.000	0.000	0.000
60	A	64	THR	0	0.042	0.019	33.824	0.137	0.137	0.000	0.000	0.000	0.000
61	A	65	VAL	0	0.005	0.012	33.534	0.064	0.064	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.030	-0.019	36.076	0.158	0.158	0.000	0.000	0.000	0.000
63	A	67	GLY	0	-0.010	-0.008	39.444	0.166	0.166	0.000	0.000	0.000	0.000
64	A	68	LEU	0	-0.062	-0.041	33.419	0.123	0.123	0.000	0.000	0.000	0.000
65	A	69	VAL	0	0.040	0.015	36.799	0.013	0.013	0.000	0.000	0.000	0.000
66	A	70	LYS	1	0.987	1.002	38.946	7.285	7.285	0.000	0.000	0.000	0.000
67	A	71	ARG	1	0.926	0.969	36.971	8.296	8.296	0.000	0.000	0.000	0.000
68	A	72	LEU	0	0.020	0.021	35.419	0.049	0.049	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.818	-0.876	40.048	-7.387	-7.387	0.000	0.000	0.000	0.000
70	A	74	ALA	0	-0.036	-0.012	43.005	0.133	0.133	0.000	0.000	0.000	0.000
71	A	75	ASP	-1	-0.903	-0.946	41.820	-7.231	-7.231	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.012	0.017	43.361	0.005	0.005	0.000	0.000	0.000	0.000
73	A	77	TYR	0	-0.024	-0.012	37.718	-0.038	-0.038	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.022	-0.016	36.011	-0.228	-0.228	0.000	0.000	0.000	0.000
75	A	79	THR	0	0.040	0.015	40.013	0.243	0.243	0.000	0.000	0.000	0.000
76	A	80	ARG	1	0.807	0.871	41.261	7.074	7.074	0.000	0.000	0.000	0.000
77	A	81	THR	0	0.039	0.026	41.643	0.205	0.205	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.006	0.002	43.222	-0.160	-0.160	0.000	0.000	0.000	0.000
79	A	83	ASP	-1	-0.754	-0.861	41.394	-7.853	-7.853	0.000	0.000	0.000	0.000
80	A	84	PRO	0	-0.025	-0.008	42.932	0.152	0.152	0.000	0.000	0.000	0.000
81	A	85	ALA	0	-0.001	-0.009	43.337	0.172	0.172	0.000	0.000	0.000	0.000
82	A	86	ASP	-1	-0.852	-0.932	44.058	-7.035	-7.035	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.907	0.952	45.928	6.344	6.344	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.909	0.957	45.422	6.960	6.960	0.000	0.000	0.000	0.000
85	A	89	ALA	0	-0.029	0.010	41.685	-0.112	-0.112	0.000	0.000	0.000	0.000
86	A	90	TYR	0	-0.020	-0.030	41.133	0.164	0.164	0.000	0.000	0.000	0.000
87	A	91	PHE	0	-0.021	-0.014	36.363	-0.207	-0.207	0.000	0.000	0.000	0.000
88	A	92	LEU	0	-0.027	-0.018	37.030	0.227	0.227	0.000	0.000	0.000	0.000
89	A	93	VAL	0	0.024	-0.007	37.197	-0.258	-0.258	0.000	0.000	0.000	0.000
90	A	94	ILE	0	0.005	0.016	34.059	0.107	0.107	0.000	0.000	0.000	0.000
91	A	95	THR	0	-0.032	-0.023	37.876	0.089	0.089	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.848	0.850	36.594	7.929	7.929	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.907	0.959	39.048	7.163	7.163	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.007	-0.013	37.027	-0.123	-0.123	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.841	-0.914	34.676	-8.492	-8.492	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.866	-0.925	34.288	-7.766	-7.766	0.000	0.000	0.000	0.000
97	A	101	VAL	0	-0.064	-0.006	32.578	-0.127	-0.127	0.000	0.000	0.000	0.000
98	A	102	ILE	0	-0.045	-0.026	28.843	-0.257	-0.257	0.000	0.000	0.000	0.000
99	A	103	GLU	-1	-0.782	-0.864	30.015	-8.748	-8.748	0.000	0.000	0.000	0.000
100	A	104	LYS	1	0.949	0.974	31.576	7.839	7.839	0.000	0.000	0.000	0.000
101	A	105	VAL	0	-0.064	-0.024	26.564	-0.181	-0.181	0.000	0.000	0.000	0.000
102	A	106	ILE	0	-0.046	-0.032	26.338	-0.392	-0.392	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.855	-0.910	27.364	-8.796	-8.796	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.894	0.955	27.720	9.395	9.395	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.871	0.931	19.919	12.644	12.644	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.892	-0.943	24.509	-10.426	-10.426	0.000	0.000	0.000	0.000
107	A	111	ASN	0	-0.011	-0.012	26.432	0.130	0.130	0.000	0.000	0.000	0.000
108	A	112	PHE	0	-0.031	-0.020	20.218	-0.039	-0.039	0.000	0.000	0.000	0.000
109	A	113	ILE	0	0.000	-0.011	19.711	-0.215	-0.215	0.000	0.000	0.000	0.000
110	A	114	GLU	-1	-0.872	-0.919	23.096	-9.293	-9.293	0.000	0.000	0.000	0.000
111	A	115	LYS	1	0.869	0.927	26.100	9.437	9.437	0.000	0.000	0.000	0.000
112	A	116	ILE	0	0.004	0.016	19.082	-0.056	-0.056	0.000	0.000	0.000	0.000
113	A	117	THR	0	-0.038	-0.047	21.310	0.046	0.046	0.000	0.000	0.000	0.000
114	A	118	SER	0	-0.028	-0.011	23.039	0.201	0.201	0.000	0.000	0.000	0.000
115	A	119	ASP	-1	-0.947	-0.961	23.255	-10.052	-10.052	0.000	0.000	0.000	0.000
116	A	120	LEU	0	-0.116	-0.049	18.230	-0.104	-0.104	0.000	0.000	0.000	0.000
117	A	121	GLY	0	0.054	0.038	22.182	0.056	0.056	0.000	0.000	0.000	0.000
118	A	122	LYS	1	1.009	0.992	23.619	8.822	8.822	0.000	0.000	0.000	0.000
119	A	123	GLU	-1	-0.852	-0.905	23.500	-10.868	-10.868	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.985	0.986	18.470	11.459	11.459	0.000	0.000	0.000	0.000
121	A	125	SER	0	0.039	0.013	19.257	-0.693	-0.693	0.000	0.000	0.000	0.000
122	A	126	SER	0	-0.045	-0.030	20.103	-0.261	-0.261	0.000	0.000	0.000	0.000
123	A	127	LYS	1	0.882	0.932	17.935	11.310	11.310	0.000	0.000	0.000	0.000
124	A	128	ILE	0	0.010	0.009	14.762	-0.662	-0.662	0.000	0.000	0.000	0.000
125	A	129	LEU	0	-0.005	-0.004	15.847	-0.742	-0.742	0.000	0.000	0.000	0.000
126	A	130	ASP	-1	-0.837	-0.917	17.888	-13.073	-13.073	0.000	0.000	0.000	0.000
127	A	131	TYR	0	0.018	0.009	12.626	-0.382	-0.382	0.000	0.000	0.000	0.000
128	A	132	LEU	0	-0.017	-0.007	12.542	-1.253	-1.253	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.858	0.929	14.523	12.158	12.158	0.000	0.000	0.000	0.000
130	A	134	GLU	-1	-0.920	-0.956	14.027	-17.519	-17.519	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.052	-0.026	7.947	-1.168	-1.168	0.000	0.000	0.000	0.000
132	A	136	LYS	1	0.828	0.885	11.817	14.195	14.195	0.000	0.000	0.000	0.000
133	A	137	GLY	0	0.050	0.032	14.478	-0.062	-0.062	0.000	0.000	0.000	0.000
134	A	138	VAL	0	-0.047	-0.030	10.429	-0.094	-0.094	0.000	0.000	0.000	0.000
135	A	139	MET	0	-0.034	-0.021	8.737	-0.636	-0.636	0.000	0.000	0.000	0.000
136	A	140	GLU	-1	-0.786	-0.883	12.369	-15.698	-15.698	0.000	0.000	0.000	0.000
137	A	141	ARG	1	0.907	0.970	14.547	19.783	19.783	0.000	0.000	0.000	0.000
138	A	142	ASN	0	-0.074	-0.059	10.806	-0.800	-0.800	0.000	0.000	0.000	0.000
139	A	143	PHE	0	-0.009	0.006	12.630	-0.906	-0.906	0.000	0.000	0.000	0.000
140	A	144	SER	0	0.021	0.021	14.347	0.069	0.069	0.000	0.000	0.000	0.000
141	A	145	LYS	1	0.924	0.978	8.737	31.847	31.847	0.000	0.000	0.000	0.000
142	A	146	GLN	0	-0.004	-0.002	13.202	0.187	0.187	0.000	0.000	0.000	0.000

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