FMO DATABASE

FMODB ID: LZKJ9

Calculation Name: 2CY9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CY9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CQR4

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1018136.122614
FMO2-HF: Nuclear repulsion	969241.740353
FMO2-HF: Total energy	-48894.382261
FMO2-MP2: Total energy	-49033.049544

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:13:LYS)

Summations of interaction energy for fragment #1(A:13: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.
-29.184	-34.739	33.903	-13.893	-14.456	-0.141

Interaction energy analysis for fragmet #1(A:13:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.884 / q_NPA : 0.905

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	15	MET	0	0.039	0.041	1.764	-59.238	-67.886	29.385	-10.911	-9.826	-0.123
4	A	16	PHE	0	0.017	0.001	4.210	7.031	7.492	0.000	-0.098	-0.363	0.000
5	A	17	LYS	1	0.871	0.942	7.013	28.669	28.669	0.000	0.000	0.000	0.000
6	A	18	VAL	0	0.083	0.038	9.080	2.807	2.807	0.000	0.000	0.000	0.000
7	A	19	PRO	0	-0.024	-0.014	10.447	1.965	1.965	0.000	0.000	0.000	0.000
8	A	20	GLY	0	-0.011	-0.018	13.664	0.406	0.406	0.000	0.000	0.000	0.000
9	A	21	PHE	0	0.024	0.013	16.400	0.393	0.393	0.000	0.000	0.000	0.000
10	A	22	ASP	-1	-0.848	-0.923	19.653	-12.742	-12.742	0.000	0.000	0.000	0.000
11	A	23	ARG	1	0.863	0.940	20.134	15.111	15.111	0.000	0.000	0.000	0.000
12	A	24	VAL	0	-0.011	0.010	22.666	0.179	0.179	0.000	0.000	0.000	0.000
13	A	25	LEU	0	-0.042	-0.029	19.640	-0.782	-0.782	0.000	0.000	0.000	0.000
14	A	26	GLU	-1	-0.803	-0.893	19.741	-14.197	-14.197	0.000	0.000	0.000	0.000
15	A	27	LYS	1	0.832	0.905	13.384	20.499	20.499	0.000	0.000	0.000	0.000
16	A	28	VAL	0	0.032	0.027	15.634	-1.036	-1.036	0.000	0.000	0.000	0.000
17	A	29	THR	0	-0.035	-0.022	12.255	0.045	0.045	0.000	0.000	0.000	0.000
18	A	30	LEU	0	0.013	0.006	9.912	-1.427	-1.427	0.000	0.000	0.000	0.000
19	A	31	VAL	0	-0.024	-0.039	4.015	-1.454	-1.358	-0.001	-0.017	-0.078	0.000
20	A	32	SER	0	-0.015	0.003	3.631	-0.228	-0.027	0.003	-0.059	-0.146	0.000
21	A	33	ALA	0	-0.009	-0.004	2.098	0.676	0.827	3.184	-1.356	-1.978	0.000
22	A	34	ALA	0	0.020	0.011	2.518	-9.576	-7.400	1.333	-1.448	-2.062	-0.018
23	A	35	PRO	0	0.024	0.008	5.250	-0.087	-0.079	-0.001	-0.004	-0.003	0.000
24	A	36	GLU	-1	-0.842	-0.913	7.918	-18.084	-18.084	0.000	0.000	0.000	0.000
25	A	37	LYS	1	0.873	0.951	8.367	21.902	21.902	0.000	0.000	0.000	0.000
26	A	38	LEU	0	-0.034	-0.024	5.504	-3.834	-3.834	0.000	0.000	0.000	0.000
27	A	39	ILE	0	0.031	0.030	6.915	2.370	2.370	0.000	0.000	0.000	0.000
28	A	40	CYS	0	-0.071	-0.028	7.335	-2.955	-2.955	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.793	-0.887	9.842	-16.527	-16.527	0.000	0.000	0.000	0.000
30	A	42	MET	0	-0.044	-0.013	12.804	-0.734	-0.734	0.000	0.000	0.000	0.000
31	A	43	LYS	1	0.908	0.968	14.659	16.786	16.786	0.000	0.000	0.000	0.000
32	A	44	VAL	0	-0.027	-0.009	19.472	-0.154	-0.154	0.000	0.000	0.000	0.000
33	A	45	GLU	-1	-0.758	-0.887	20.288	-13.114	-13.114	0.000	0.000	0.000	0.000
34	A	46	GLU	-1	-0.903	-0.959	24.313	-9.889	-9.889	0.000	0.000	0.000	0.000
35	A	47	GLN	0	0.010	0.001	22.687	0.614	0.614	0.000	0.000	0.000	0.000
36	A	48	HIS	0	-0.032	-0.010	20.348	0.255	0.255	0.000	0.000	0.000	0.000
37	A	49	THR	0	-0.092	-0.053	24.768	0.165	0.165	0.000	0.000	0.000	0.000
38	A	50	ASN	0	0.000	-0.016	27.788	0.140	0.140	0.000	0.000	0.000	0.000
39	A	51	LYS	1	0.911	0.938	31.042	9.025	9.025	0.000	0.000	0.000	0.000
40	A	52	LEU	0	-0.003	0.009	33.078	0.240	0.240	0.000	0.000	0.000	0.000
41	A	53	GLY	0	0.053	0.042	30.814	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	54	THR	0	-0.001	-0.009	27.758	-0.208	-0.208	0.000	0.000	0.000	0.000
43	A	55	LEU	0	0.009	0.020	21.244	0.093	0.093	0.000	0.000	0.000	0.000
44	A	56	HIS	0	0.033	0.012	25.757	0.321	0.321	0.000	0.000	0.000	0.000
45	A	57	GLY	0	0.057	0.007	25.817	-0.373	-0.373	0.000	0.000	0.000	0.000
46	A	58	GLY	0	-0.010	0.010	25.411	-0.290	-0.290	0.000	0.000	0.000	0.000
47	A	59	LEU	0	0.025	0.013	21.084	-0.387	-0.387	0.000	0.000	0.000	0.000
48	A	60	THR	0	0.012	0.000	21.099	-0.651	-0.651	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.016	0.012	20.737	-0.543	-0.543	0.000	0.000	0.000	0.000
50	A	62	THR	0	0.006	0.007	20.686	-0.685	-0.685	0.000	0.000	0.000	0.000
51	A	63	LEU	0	-0.040	-0.028	16.146	-0.987	-0.987	0.000	0.000	0.000	0.000
52	A	64	VAL	0	0.020	0.017	16.491	-0.749	-0.749	0.000	0.000	0.000	0.000
53	A	65	ASP	-1	-0.754	-0.868	18.019	-15.498	-15.498	0.000	0.000	0.000	0.000
54	A	66	SER	0	0.063	0.010	15.512	-1.658	-1.658	0.000	0.000	0.000	0.000
55	A	67	ILE	0	-0.001	-0.005	11.016	0.206	0.206	0.000	0.000	0.000	0.000
56	A	68	SER	0	0.015	0.012	11.883	-1.476	-1.476	0.000	0.000	0.000	0.000
57	A	69	THR	0	0.010	-0.009	13.159	-0.839	-0.839	0.000	0.000	0.000	0.000
58	A	70	MET	0	-0.071	-0.026	8.417	0.079	0.079	0.000	0.000	0.000	0.000
59	A	71	ALA	0	0.030	0.019	8.497	-2.924	-2.924	0.000	0.000	0.000	0.000
60	A	72	LEU	0	0.012	0.008	9.458	-1.566	-1.566	0.000	0.000	0.000	0.000
61	A	73	MET	0	-0.064	-0.017	9.966	0.314	0.314	0.000	0.000	0.000	0.000
62	A	74	CYS	0	-0.045	-0.016	5.909	-2.775	-2.775	0.000	0.000	0.000	0.000
63	A	75	THR	0	-0.061	-0.029	7.576	-1.383	-1.383	0.000	0.000	0.000	0.000
64	A	76	GLU	-1	-0.788	-0.872	10.231	-22.205	-22.205	0.000	0.000	0.000	0.000
65	A	77	ARG	1	0.815	0.861	11.834	20.511	20.511	0.000	0.000	0.000	0.000
66	A	78	GLY	0	-0.030	-0.013	15.217	0.110	0.110	0.000	0.000	0.000	0.000
67	A	79	ALA	0	0.007	0.004	12.751	0.411	0.411	0.000	0.000	0.000	0.000
68	A	80	PRO	0	-0.016	0.004	13.762	0.517	0.517	0.000	0.000	0.000	0.000
69	A	81	GLY	0	0.043	0.011	16.062	0.755	0.755	0.000	0.000	0.000	0.000
70	A	82	VAL	0	-0.026	-0.003	19.723	-0.209	-0.209	0.000	0.000	0.000	0.000
71	A	83	SER	0	-0.004	-0.051	22.079	-0.243	-0.243	0.000	0.000	0.000	0.000
72	A	84	VAL	0	-0.072	-0.024	23.235	0.397	0.397	0.000	0.000	0.000	0.000
73	A	85	ASP	-1	-0.852	-0.922	24.844	-10.620	-10.620	0.000	0.000	0.000	0.000
74	A	86	MET	0	-0.005	-0.002	21.896	-0.861	-0.861	0.000	0.000	0.000	0.000
75	A	87	ASN	0	-0.044	-0.001	24.563	0.501	0.501	0.000	0.000	0.000	0.000
76	A	88	ILE	0	0.032	-0.005	23.180	-0.449	-0.449	0.000	0.000	0.000	0.000
77	A	89	THR	0	-0.025	0.001	25.146	0.576	0.576	0.000	0.000	0.000	0.000
78	A	90	TYR	0	0.020	-0.010	25.032	-0.517	-0.517	0.000	0.000	0.000	0.000
79	A	91	MET	0	-0.060	-0.026	24.977	0.334	0.334	0.000	0.000	0.000	0.000
80	A	92	SER	0	0.014	0.017	25.762	0.311	0.311	0.000	0.000	0.000	0.000
81	A	93	PRO	0	-0.028	-0.003	26.497	-0.267	-0.267	0.000	0.000	0.000	0.000
82	A	94	ALA	0	0.031	0.006	23.219	-0.119	-0.119	0.000	0.000	0.000	0.000
83	A	95	LYS	1	0.880	0.909	25.310	9.624	9.624	0.000	0.000	0.000	0.000
84	A	96	ILE	0	0.032	0.003	25.663	-0.334	-0.334	0.000	0.000	0.000	0.000
85	A	97	GLY	0	-0.016	0.003	24.974	0.315	0.315	0.000	0.000	0.000	0.000
86	A	98	GLU	-1	-0.833	-0.877	23.165	-10.564	-10.564	0.000	0.000	0.000	0.000
87	A	99	GLU	-1	-0.830	-0.917	16.234	-15.473	-15.473	0.000	0.000	0.000	0.000
88	A	100	ILE	0	-0.066	-0.020	17.324	0.372	0.372	0.000	0.000	0.000	0.000
89	A	101	VAL	0	0.025	0.008	13.059	-0.793	-0.793	0.000	0.000	0.000	0.000
90	A	102	ILE	0	-0.016	-0.011	12.686	0.741	0.741	0.000	0.000	0.000	0.000
91	A	103	THR	0	-0.006	-0.017	10.991	-1.789	-1.789	0.000	0.000	0.000	0.000
92	A	104	ALA	0	0.014	0.018	11.355	1.285	1.285	0.000	0.000	0.000	0.000
93	A	105	HIS	0	0.034	0.015	11.614	-1.477	-1.477	0.000	0.000	0.000	0.000
94	A	106	ILE	0	-0.017	-0.012	11.776	1.004	1.004	0.000	0.000	0.000	0.000
95	A	107	LEU	0	-0.021	-0.003	14.497	0.208	0.208	0.000	0.000	0.000	0.000
96	A	108	LYS	1	0.923	0.952	18.024	14.009	14.009	0.000	0.000	0.000	0.000
97	A	109	GLN	0	0.054	0.030	13.009	-0.161	-0.161	0.000	0.000	0.000	0.000
98	A	110	GLY	0	0.005	-0.012	18.425	0.734	0.734	0.000	0.000	0.000	0.000
99	A	111	LYN	0	0.043	0.019	20.801	-0.655	-0.655	0.000	0.000	0.000	0.000
100	A	112	THR	0	0.008	0.009	23.191	0.177	0.177	0.000	0.000	0.000	0.000
101	A	113	LEU	0	-0.013	0.000	22.702	0.206	0.206	0.000	0.000	0.000	0.000
102	A	114	ALA	0	-0.021	0.006	17.584	-0.239	-0.239	0.000	0.000	0.000	0.000
103	A	115	PHE	0	0.011	0.000	18.864	0.479	0.479	0.000	0.000	0.000	0.000
104	A	116	ALA	0	0.029	0.020	15.666	-0.738	-0.738	0.000	0.000	0.000	0.000
105	A	117	SER	0	0.008	-0.012	16.779	1.129	1.129	0.000	0.000	0.000	0.000
106	A	118	VAL	0	-0.054	-0.022	15.036	-1.040	-1.040	0.000	0.000	0.000	0.000
107	A	119	ASP	-1	-0.840	-0.911	16.031	-12.789	-12.789	0.000	0.000	0.000	0.000
108	A	120	LEU	0	0.031	0.007	16.080	-0.934	-0.934	0.000	0.000	0.000	0.000
109	A	121	THR	0	0.033	0.011	17.306	0.569	0.569	0.000	0.000	0.000	0.000
110	A	122	ASN	0	-0.006	-0.010	18.145	-0.587	-0.587	0.000	0.000	0.000	0.000
111	A	123	LYS	1	0.792	0.874	13.941	16.045	16.045	0.000	0.000	0.000	0.000
112	A	124	THR	0	-0.024	0.002	18.332	0.052	0.052	0.000	0.000	0.000	0.000
113	A	125	THR	0	-0.007	-0.013	21.533	0.338	0.338	0.000	0.000	0.000	0.000
114	A	126	GLY	0	0.025	0.014	20.459	0.314	0.314	0.000	0.000	0.000	0.000
115	A	127	LYS	1	0.915	0.947	21.550	9.800	9.800	0.000	0.000	0.000	0.000
116	A	128	LEU	0	-0.002	0.003	20.874	-0.262	-0.262	0.000	0.000	0.000	0.000
117	A	129	ILE	0	-0.045	-0.005	21.591	0.425	0.425	0.000	0.000	0.000	0.000
118	A	130	ALA	0	0.007	-0.016	21.859	0.504	0.504	0.000	0.000	0.000	0.000
119	A	131	GLN	0	0.001	0.007	19.190	-0.620	-0.620	0.000	0.000	0.000	0.000
120	A	132	GLY	0	0.023	0.014	20.669	0.622	0.622	0.000	0.000	0.000	0.000
121	A	133	ARG	1	0.889	0.954	20.439	11.104	11.104	0.000	0.000	0.000	0.000
122	A	134	HIS	0	-0.065	-0.024	18.467	0.650	0.650	0.000	0.000	0.000	0.000
123	A	135	THR	0	0.002	0.009	20.168	-0.550	-0.550	0.000	0.000	0.000	0.000
124	A	136	LYS	1	0.847	0.930	18.089	16.166	16.166	0.000	0.000	0.000	0.000
125	A	137	HIS	1	0.855	0.922	21.446	12.338	12.338	0.000	0.000	0.000	0.000
126	A	138	LEU	0	-0.018	0.009	18.321	-0.239	-0.239	0.000	0.000	0.000	0.000
127	A	139	GLY	0	0.034	0.012	21.814	0.718	0.718	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:LYS)