FMO DATABASE

FMODB ID: JL539

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1018617.029705
FMO2-HF: Nuclear repulsion	969731.284317
FMO2-HF: Total energy	-48885.745388
FMO2-MP2: Total energy	-49025.297761

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.
-19.191	-33.046	37.661	-10.589	-13.217	-0.085

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 : 0.962 / q_NPA : 0.977

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	0.004	-0.015	1.892	-47.254	-65.406	35.404	-8.029	-9.222	-0.072
4	A	16	PHE	0	0.063	0.002	4.472	6.911	7.303	-0.001	-0.086	-0.306	0.000
5	A	17	LYS	1	0.982	1.000	7.471	25.887	25.887	0.000	0.000	0.000	0.000
6	A	18	VAL	0	0.069	0.042	8.824	2.173	2.173	0.000	0.000	0.000	0.000
7	A	19	PRO	0	-0.063	-0.035	11.331	1.709	1.709	0.000	0.000	0.000	0.000
8	A	20	GLY	0	-0.014	-0.035	14.457	0.310	0.310	0.000	0.000	0.000	0.000
9	A	21	PHE	0	-0.064	-0.052	16.831	0.367	0.367	0.000	0.000	0.000	0.000
10	A	22	ASP	-1	-0.831	-0.881	19.842	-12.288	-12.288	0.000	0.000	0.000	0.000
11	A	23	ARG	1	0.930	0.961	20.783	14.252	14.252	0.000	0.000	0.000	0.000
12	A	24	VAL	0	-0.015	-0.003	23.422	0.360	0.360	0.000	0.000	0.000	0.000
13	A	25	LEU	0	-0.053	-0.034	19.943	-0.852	-0.852	0.000	0.000	0.000	0.000
14	A	26	GLU	-1	-0.862	-0.898	20.710	-12.803	-12.803	0.000	0.000	0.000	0.000
15	A	27	LYS	1	0.832	0.901	12.441	20.115	20.115	0.000	0.000	0.000	0.000
16	A	28	VAL	0	0.107	0.077	17.338	-0.087	-0.087	0.000	0.000	0.000	0.000
17	A	29	THR	0	-0.056	-0.029	13.875	-0.181	-0.181	0.000	0.000	0.000	0.000
18	A	30	LEU	0	0.049	0.014	11.365	-1.132	-1.132	0.000	0.000	0.000	0.000
19	A	31	VAL	0	-0.143	-0.085	5.334	-2.629	-2.587	-0.001	-0.007	-0.034	0.000
20	A	32	SER	0	0.057	0.012	4.271	0.057	0.292	0.001	-0.067	-0.169	0.000
21	A	33	ALA	0	-0.022	0.051	2.122	-0.847	0.081	1.726	-0.972	-1.682	0.003
22	A	34	ALA	0	0.060	0.013	2.798	-9.429	-6.772	0.533	-1.425	-1.765	-0.016
23	A	35	PRO	0	0.007	0.001	5.383	-1.328	-1.285	-0.001	-0.003	-0.039	0.000
24	A	36	GLU	-1	-0.866	-0.952	8.098	-15.665	-15.665	0.000	0.000	0.000	0.000
25	A	37	LYS	1	0.914	0.938	8.558	20.954	20.954	0.000	0.000	0.000	0.000
26	A	38	LEU	0	-0.121	-0.049	6.873	-2.243	-2.243	0.000	0.000	0.000	0.000
27	A	39	ILE	0	0.043	0.020	7.678	1.167	1.167	0.000	0.000	0.000	0.000
28	A	40	CYS	0	0.020	0.032	8.502	-2.022	-2.022	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.873	-0.963	10.927	-17.172	-17.172	0.000	0.000	0.000	0.000
30	A	42	MET	0	-0.077	-0.024	14.034	-0.698	-0.698	0.000	0.000	0.000	0.000
31	A	43	LYS	1	0.934	0.983	15.682	16.488	16.488	0.000	0.000	0.000	0.000
32	A	44	VAL	0	-0.018	0.007	20.499	-0.068	-0.068	0.000	0.000	0.000	0.000
33	A	45	GLU	-1	-0.890	-0.961	21.984	-12.589	-12.589	0.000	0.000	0.000	0.000
34	A	46	GLU	-1	-0.833	-0.940	25.837	-10.000	-10.000	0.000	0.000	0.000	0.000
35	A	47	GLN	0	0.022	0.011	24.177	0.517	0.517	0.000	0.000	0.000	0.000
36	A	48	HIS	0	-0.094	-0.016	21.871	0.283	0.283	0.000	0.000	0.000	0.000
37	A	49	THR	0	-0.007	-0.036	26.166	0.107	0.107	0.000	0.000	0.000	0.000
38	A	50	ASN	0	0.059	0.028	28.932	0.009	0.009	0.000	0.000	0.000	0.000
39	A	51	LYS	1	0.914	0.938	32.126	8.924	8.924	0.000	0.000	0.000	0.000
40	A	52	LEU	0	-0.013	0.001	33.865	0.187	0.187	0.000	0.000	0.000	0.000
41	A	53	GLY	0	0.033	0.036	31.734	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	54	THR	0	-0.072	-0.066	29.075	-0.213	-0.213	0.000	0.000	0.000	0.000
43	A	55	LEU	0	0.015	0.024	23.091	0.266	0.266	0.000	0.000	0.000	0.000
44	A	56	HIS	0	0.045	0.014	27.288	0.259	0.259	0.000	0.000	0.000	0.000
45	A	57	GLY	0	0.007	-0.033	26.109	-0.368	-0.368	0.000	0.000	0.000	0.000
46	A	58	GLY	0	0.076	0.033	25.884	-0.204	-0.204	0.000	0.000	0.000	0.000
47	A	59	LEU	0	0.019	0.008	21.651	-0.323	-0.323	0.000	0.000	0.000	0.000
48	A	60	THR	0	0.045	0.004	21.949	-0.554	-0.554	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.029	0.040	21.390	-0.436	-0.436	0.000	0.000	0.000	0.000
50	A	62	THR	0	-0.052	-0.017	21.372	-0.714	-0.714	0.000	0.000	0.000	0.000
51	A	63	LEU	0	-0.009	-0.007	17.781	-0.666	-0.666	0.000	0.000	0.000	0.000
52	A	64	VAL	0	-0.061	0.004	16.934	-0.823	-0.823	0.000	0.000	0.000	0.000
53	A	65	ASP	-1	-0.906	-0.983	17.711	-14.675	-14.675	0.000	0.000	0.000	0.000
54	A	66	SER	0	0.075	-0.031	15.442	-1.352	-1.352	0.000	0.000	0.000	0.000
55	A	67	ILE	0	-0.026	-0.023	11.704	-0.176	-0.176	0.000	0.000	0.000	0.000
56	A	68	SER	0	0.054	0.045	13.250	0.073	0.073	0.000	0.000	0.000	0.000
57	A	69	THR	0	-0.060	0.002	13.622	-0.630	-0.630	0.000	0.000	0.000	0.000
58	A	70	MET	0	-0.061	-0.019	9.121	-0.222	-0.222	0.000	0.000	0.000	0.000
59	A	71	ALA	0	-0.030	-0.017	9.092	-2.345	-2.345	0.000	0.000	0.000	0.000
60	A	72	LEU	0	0.036	0.007	10.123	-0.158	-0.158	0.000	0.000	0.000	0.000
61	A	73	MET	0	-0.053	-0.008	10.725	0.702	0.702	0.000	0.000	0.000	0.000
62	A	74	CYS	0	-0.098	-0.042	6.290	-1.853	-1.853	0.000	0.000	0.000	0.000
63	A	75	THR	0	-0.043	-0.036	8.357	-0.345	-0.345	0.000	0.000	0.000	0.000
64	A	76	GLU	-1	-0.715	-0.819	10.274	-21.012	-21.012	0.000	0.000	0.000	0.000
65	A	77	ARG	1	0.784	0.854	12.045	18.183	18.183	0.000	0.000	0.000	0.000
66	A	78	GLY	0	-0.007	-0.009	15.325	0.110	0.110	0.000	0.000	0.000	0.000
67	A	79	ALA	0	0.008	0.011	13.572	0.481	0.481	0.000	0.000	0.000	0.000
68	A	80	PRO	0	0.028	0.035	15.204	0.132	0.132	0.000	0.000	0.000	0.000
69	A	81	GLY	0	0.009	-0.002	16.484	0.729	0.729	0.000	0.000	0.000	0.000
70	A	82	VAL	0	-0.060	-0.041	20.112	-0.137	-0.137	0.000	0.000	0.000	0.000
71	A	83	SER	0	0.064	0.014	22.500	-0.210	-0.210	0.000	0.000	0.000	0.000
72	A	84	VAL	0	-0.061	-0.046	23.724	0.304	0.304	0.000	0.000	0.000	0.000
73	A	85	ASP	-1	-0.885	-0.914	25.414	-9.628	-9.628	0.000	0.000	0.000	0.000
74	A	86	MET	0	0.022	-0.003	22.342	-0.779	-0.779	0.000	0.000	0.000	0.000
75	A	87	ASN	0	-0.077	0.001	24.673	0.382	0.382	0.000	0.000	0.000	0.000
76	A	88	ILE	0	0.048	-0.025	23.765	-0.409	-0.409	0.000	0.000	0.000	0.000
77	A	89	THR	0	-0.008	0.021	25.956	0.529	0.529	0.000	0.000	0.000	0.000
78	A	90	TYR	0	0.017	-0.016	26.167	-0.466	-0.466	0.000	0.000	0.000	0.000
79	A	91	MET	0	-0.034	-0.007	25.674	0.336	0.336	0.000	0.000	0.000	0.000
80	A	92	SER	0	0.044	0.038	26.309	0.235	0.235	0.000	0.000	0.000	0.000
81	A	93	PRO	0	-0.032	-0.018	27.280	-0.247	-0.247	0.000	0.000	0.000	0.000
82	A	94	ALA	0	0.038	0.009	24.495	-0.183	-0.183	0.000	0.000	0.000	0.000
83	A	95	LYS	1	0.982	0.997	26.434	8.992	8.992	0.000	0.000	0.000	0.000
84	A	96	ILE	0	0.003	0.048	26.272	-0.339	-0.339	0.000	0.000	0.000	0.000
85	A	97	GLY	0	-0.018	-0.011	25.541	0.250	0.250	0.000	0.000	0.000	0.000
86	A	98	GLU	-1	-0.935	-0.942	23.454	-10.651	-10.651	0.000	0.000	0.000	0.000
87	A	99	GLU	-1	-0.881	-0.975	16.806	-15.252	-15.252	0.000	0.000	0.000	0.000
88	A	100	ILE	0	0.000	0.016	17.177	0.071	0.071	0.000	0.000	0.000	0.000
89	A	101	VAL	0	-0.004	-0.028	13.730	-0.738	-0.738	0.000	0.000	0.000	0.000
90	A	102	ILE	0	-0.036	-0.027	13.649	0.630	0.630	0.000	0.000	0.000	0.000
91	A	103	THR	0	-0.043	-0.014	11.482	-1.351	-1.351	0.000	0.000	0.000	0.000
92	A	104	ALA	0	0.110	0.080	11.485	0.867	0.867	0.000	0.000	0.000	0.000
93	A	105	HIS	0	-0.001	-0.025	11.704	-1.347	-1.347	0.000	0.000	0.000	0.000
94	A	106	ILE	0	-0.110	-0.044	11.800	0.947	0.947	0.000	0.000	0.000	0.000
95	A	107	LEU	0	0.041	0.021	14.390	0.187	0.187	0.000	0.000	0.000	0.000
96	A	108	LYS	1	0.918	0.950	17.848	13.030	13.030	0.000	0.000	0.000	0.000
97	A	109	GLN	0	0.064	0.016	12.779	-0.138	-0.138	0.000	0.000	0.000	0.000
98	A	110	GLY	0	-0.104	-0.065	18.245	-0.112	-0.112	0.000	0.000	0.000	0.000
99	A	111	LYN	0	0.154	0.123	20.915	-0.416	-0.416	0.000	0.000	0.000	0.000
100	A	112	THR	0	0.032	0.020	23.154	0.041	0.041	0.000	0.000	0.000	0.000
101	A	113	LEU	0	-0.006	0.002	22.786	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	114	ALA	0	-0.017	0.009	17.886	-0.122	-0.122	0.000	0.000	0.000	0.000
103	A	115	PHE	0	0.014	0.018	19.189	0.353	0.353	0.000	0.000	0.000	0.000
104	A	116	ALA	0	0.049	0.019	16.128	-0.680	-0.680	0.000	0.000	0.000	0.000
105	A	117	SER	0	0.017	-0.005	16.746	1.011	1.011	0.000	0.000	0.000	0.000
106	A	118	VAL	0	-0.118	-0.034	15.203	-0.686	-0.686	0.000	0.000	0.000	0.000
107	A	119	ASP	-1	-0.822	-0.931	16.761	-12.351	-12.351	0.000	0.000	0.000	0.000
108	A	120	LEU	0	-0.012	-0.004	16.737	-0.751	-0.751	0.000	0.000	0.000	0.000
109	A	121	THR	0	0.054	0.027	17.532	0.436	0.436	0.000	0.000	0.000	0.000
110	A	122	ASN	0	-0.010	-0.018	19.385	-0.780	-0.780	0.000	0.000	0.000	0.000
111	A	123	LYS	1	0.950	0.976	14.583	15.613	15.613	0.000	0.000	0.000	0.000
112	A	124	THR	0	-0.036	-0.003	18.958	0.198	0.198	0.000	0.000	0.000	0.000
113	A	125	THR	0	-0.052	-0.039	21.875	0.199	0.199	0.000	0.000	0.000	0.000
114	A	126	GLY	0	0.078	0.055	20.444	0.250	0.250	0.000	0.000	0.000	0.000
115	A	127	LYS	1	0.891	0.926	21.346	9.710	9.710	0.000	0.000	0.000	0.000
116	A	128	LEU	0	-0.018	0.006	21.086	-0.115	-0.115	0.000	0.000	0.000	0.000
117	A	129	ILE	0	-0.038	0.007	22.117	0.406	0.406	0.000	0.000	0.000	0.000
118	A	130	ALA	0	0.002	-0.019	22.727	0.419	0.419	0.000	0.000	0.000	0.000
119	A	131	GLN	0	-0.007	0.019	21.409	-0.677	-0.677	0.000	0.000	0.000	0.000
120	A	132	GLY	0	0.075	0.039	21.443	0.563	0.563	0.000	0.000	0.000	0.000
121	A	133	ARG	1	0.914	0.958	20.749	10.645	10.645	0.000	0.000	0.000	0.000
122	A	134	HIS	0	-0.052	-0.028	19.460	0.593	0.593	0.000	0.000	0.000	0.000
123	A	135	THR	0	-0.080	0.004	20.446	-0.576	-0.576	0.000	0.000	0.000	0.000
124	A	136	LYS	1	0.942	0.949	18.240	15.362	15.362	0.000	0.000	0.000	0.000
125	A	137	HIS	1	0.894	0.924	22.056	11.632	11.632	0.000	0.000	0.000	0.000
126	A	138	LEU	0	-0.022	-0.018	18.695	-0.160	-0.160	0.000	0.000	0.000	0.000
127	A	139	GLY	0	0.002	0.009	22.072	0.591	0.591	0.000	0.000	0.000	0.000

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