FMO DATABASE

FMODB ID: 6YLMZ

Calculation Name: 2QIY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QIY

Chain ID: A

ChEMBL ID:

UniProt ID: P53741

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1356732.099264
FMO2-HF: Nuclear repulsion	1299546.427839
FMO2-HF: Total energy	-57185.671425
FMO2-MP2: Total energy	-57352.536772

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:3:VAL)

Summations of interaction energy for fragment #1(A:3:VAL)

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.
-4.064	0.504	3.399	-3.081	-4.886	-0.011

Interaction energy analysis for fragmet #1(A:3:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.010

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	5	VAL	0	0.069	0.019	2.946	-2.965	-0.378	0.200	-1.341	-1.446	-0.004
4	A	6	GLN	0	0.033	0.012	5.578	0.230	0.230	0.000	0.000	0.000	0.000
5	A	7	ASP	-1	-0.877	-0.939	2.544	-2.177	-0.319	1.081	-1.202	-1.736	-0.008
6	A	8	ILE	0	-0.055	-0.021	2.207	-0.150	-0.113	2.118	-0.516	-1.640	0.001
7	A	9	CYS	0	-0.034	-0.008	4.416	0.217	0.303	0.000	-0.022	-0.064	0.000
8	A	10	PHE	0	0.025	0.019	7.313	0.123	0.123	0.000	0.000	0.000	0.000
9	A	11	ALA	0	0.022	0.008	5.873	0.089	0.089	0.000	0.000	0.000	0.000
10	A	12	PHE	0	-0.040	-0.019	7.827	0.082	0.082	0.000	0.000	0.000	0.000
11	A	13	LEU	0	0.014	-0.001	9.576	0.067	0.067	0.000	0.000	0.000	0.000
12	A	14	GLN	0	-0.011	0.008	11.553	0.029	0.029	0.000	0.000	0.000	0.000
13	A	15	ASN	0	0.025	-0.006	8.936	0.077	0.077	0.000	0.000	0.000	0.000
14	A	16	TYR	0	-0.110	-0.070	12.712	0.037	0.037	0.000	0.000	0.000	0.000
15	A	17	TYR	0	0.015	-0.025	15.132	0.021	0.021	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.942	-0.972	15.277	-0.129	-0.129	0.000	0.000	0.000	0.000
17	A	19	ARG	1	0.940	0.975	13.491	0.285	0.285	0.000	0.000	0.000	0.000
18	A	20	MET	0	-0.041	-0.001	18.327	0.017	0.017	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.964	0.999	18.687	0.120	0.120	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.075	-0.053	19.293	0.009	0.009	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.858	-0.927	21.817	-0.102	-0.102	0.000	0.000	0.000	0.000
22	A	24	PRO	0	0.015	0.009	22.364	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	25	SER	0	-0.046	-0.024	24.102	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.964	0.982	20.623	0.123	0.123	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.031	0.001	18.972	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	28	ALA	0	0.006	-0.003	19.248	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	29	TYR	0	-0.031	-0.015	15.587	0.005	0.005	0.000	0.000	0.000	0.000
28	A	30	PHE	0	-0.008	-0.007	13.288	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	31	TYR	0	-0.039	-0.017	15.953	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.105	0.056	18.361	0.010	0.010	0.000	0.000	0.000	0.000
31	A	33	SER	0	-0.004	-0.020	19.468	0.011	0.011	0.000	0.000	0.000	0.000
32	A	34	THR	0	0.012	-0.002	22.791	0.011	0.011	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.033	0.009	20.811	0.002	0.002	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.946	-0.967	22.570	-0.123	-0.123	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.022	-0.004	22.544	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	38	THR	0	-0.053	-0.036	24.592	0.016	0.016	0.000	0.000	0.000	0.000
37	A	39	HIS	0	0.082	0.021	22.881	0.003	0.003	0.000	0.000	0.000	0.000
38	A	40	THR	0	0.089	0.032	26.791	0.006	0.006	0.000	0.000	0.000	0.000
39	A	41	ASN	0	-0.001	0.000	28.988	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	42	TYR	0	0.032	0.001	26.399	0.007	0.007	0.000	0.000	0.000	0.000
41	A	43	GLN	0	-0.008	-0.005	32.943	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	44	SER	0	-0.040	-0.009	35.805	0.004	0.004	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.968	1.000	37.793	0.051	0.051	0.000	0.000	0.000	0.000
44	A	46	SER	0	-0.003	-0.008	40.002	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	47	THR	0	-0.065	-0.045	38.563	0.000	0.000	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.000	-0.024	41.605	0.000	0.000	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.876	-0.940	43.731	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.917	0.970	37.228	0.049	0.049	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.936	-0.939	37.492	-0.050	-0.050	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.790	-0.853	34.571	-0.055	-0.055	0.000	0.000	0.000	0.000
51	A	53	VAL	0	-0.032	-0.013	32.523	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.026	-0.010	30.454	0.003	0.003	0.000	0.000	0.000	0.000
53	A	55	PRO	0	-0.008	0.006	32.259	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	56	THR	0	-0.008	-0.010	28.457	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	57	VAL	0	-0.043	-0.021	30.298	0.006	0.006	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.945	0.976	29.267	0.096	0.096	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.033	-0.009	27.493	0.008	0.008	0.000	0.000	0.000	0.000
58	A	60	THR	0	0.064	0.031	27.207	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	61	GLY	0	0.022	0.014	26.053	0.009	0.009	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.875	0.925	19.951	0.193	0.193	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.891	-0.945	24.866	-0.104	-0.104	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.035	-0.029	28.158	0.011	0.011	0.000	0.000	0.000	0.000
63	A	65	ILE	0	0.013	0.017	22.907	0.006	0.006	0.000	0.000	0.000	0.000
64	A	66	ASN	0	0.047	0.012	25.631	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	67	LYS	1	0.875	0.949	26.507	0.095	0.095	0.000	0.000	0.000	0.000
66	A	68	PHE	0	-0.045	-0.023	26.768	0.008	0.008	0.000	0.000	0.000	0.000
67	A	69	PHE	0	0.040	-0.001	22.360	0.006	0.006	0.000	0.000	0.000	0.000
68	A	70	SER	0	0.017	0.007	27.034	0.005	0.005	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.858	0.932	29.080	0.084	0.084	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.038	-0.004	29.453	0.011	0.011	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.782	-0.880	28.142	-0.091	-0.091	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.053	0.011	28.587	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.946	0.969	30.182	0.068	0.068	0.000	0.000	0.000	0.000
74	A	76	VAL	0	0.005	0.024	24.354	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.899	0.949	25.330	0.085	0.085	0.000	0.000	0.000	0.000
76	A	78	SER	0	-0.145	-0.079	26.171	0.004	0.004	0.000	0.000	0.000	0.000
77	A	79	LEU	0	-0.008	0.000	22.169	0.005	0.005	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.889	0.944	23.648	0.064	0.064	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.010	-0.009	18.997	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.933	0.992	21.942	0.054	0.054	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.005	-0.013	14.664	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	84	ASP	-1	-0.879	-0.947	18.992	-0.070	-0.070	0.000	0.000	0.000	0.000
83	A	85	THR	0	-0.018	0.009	17.663	0.008	0.008	0.000	0.000	0.000	0.000
84	A	86	ILE	0	-0.008	-0.018	11.561	-0.022	-0.022	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.914	-0.929	14.965	-0.153	-0.153	0.000	0.000	0.000	0.000
86	A	88	PHE	0	0.011	-0.024	10.053	-0.066	-0.066	0.000	0.000	0.000	0.000
87	A	89	GLN	0	-0.026	-0.010	13.285	0.032	0.032	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.003	0.013	6.590	-0.077	-0.077	0.000	0.000	0.000	0.000
89	A	91	THR	0	0.020	0.000	13.103	0.071	0.071	0.000	0.000	0.000	0.000
90	A	92	GLY	0	0.030	0.015	15.068	-0.031	-0.031	0.000	0.000	0.000	0.000
91	A	93	HIS	0	0.045	0.013	17.230	0.009	0.009	0.000	0.000	0.000	0.000
92	A	94	LEU	0	-0.008	-0.014	15.478	-0.036	-0.036	0.000	0.000	0.000	0.000
93	A	95	HIS	0	0.011	0.004	14.061	-0.035	-0.035	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.916	0.965	10.083	0.371	0.371	0.000	0.000	0.000	0.000
95	A	97	SER	0	0.004	0.011	10.417	-0.070	-0.070	0.000	0.000	0.000	0.000
96	A	98	ILE	0	-0.025	-0.015	7.163	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	99	LEU	0	0.000	0.000	11.793	0.035	0.035	0.000	0.000	0.000	0.000
98	A	100	ILE	0	0.006	-0.001	10.313	-0.025	-0.025	0.000	0.000	0.000	0.000
99	A	101	MET	0	0.000	-0.004	14.222	0.033	0.033	0.000	0.000	0.000	0.000
100	A	102	ALA	0	0.029	0.014	16.019	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.039	-0.032	17.626	0.017	0.017	0.000	0.000	0.000	0.000
102	A	104	GLY	0	0.068	0.028	20.283	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	105	GLU	-1	-0.915	-0.942	22.634	-0.055	-0.055	0.000	0.000	0.000	0.000
104	A	106	MET	0	0.000	0.006	22.747	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	107	PHE	0	-0.001	-0.014	25.881	0.008	0.008	0.000	0.000	0.000	0.000
106	A	108	TRP	0	-0.010	0.002	27.296	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	109	THR	0	-0.011	-0.033	29.594	0.004	0.004	0.000	0.000	0.000	0.000
108	A	110	GLY	0	-0.001	0.004	31.442	0.001	0.001	0.000	0.000	0.000	0.000
109	A	111	THR	0	-0.047	-0.021	32.202	0.001	0.001	0.000	0.000	0.000	0.000
110	A	112	PRO	0	0.007	0.009	33.160	0.000	0.000	0.000	0.000	0.000	0.000
111	A	113	VAL	0	0.025	0.012	29.194	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	114	TYR	0	0.008	0.007	29.178	0.004	0.004	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.922	0.968	26.956	0.060	0.060	0.000	0.000	0.000	0.000
114	A	116	PHE	0	-0.032	-0.018	20.370	0.002	0.002	0.000	0.000	0.000	0.000
115	A	117	CYS	0	0.020	0.025	22.288	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	118	GLN	0	0.013	-0.026	19.292	0.016	0.016	0.000	0.000	0.000	0.000
117	A	119	THR	0	-0.031	-0.005	18.304	-0.013	-0.013	0.000	0.000	0.000	0.000
118	A	120	PHE	0	0.018	-0.006	14.862	0.009	0.009	0.000	0.000	0.000	0.000
119	A	121	ILE	0	-0.025	0.001	15.332	-0.014	-0.014	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.013	0.004	9.812	0.018	0.018	0.000	0.000	0.000	0.000
121	A	123	LEU	0	0.028	0.006	12.628	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	124	PRO	0	-0.022	-0.008	9.757	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	125	SER	0	0.034	0.017	11.057	0.038	0.038	0.000	0.000	0.000	0.000
124	A	126	SER	0	0.014	-0.020	12.928	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	127	ASN	0	-0.040	-0.030	13.539	-0.017	-0.017	0.000	0.000	0.000	0.000
126	A	128	GLY	0	0.010	0.036	9.913	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	129	SER	0	-0.026	-0.030	6.489	0.040	0.040	0.000	0.000	0.000	0.000
128	A	130	THR	0	-0.024	0.007	6.390	-0.094	-0.094	0.000	0.000	0.000	0.000
129	A	131	PHE	0	-0.006	-0.014	5.694	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	132	ASP	-1	-0.874	-0.913	10.638	-0.281	-0.281	0.000	0.000	0.000	0.000
131	A	133	ILE	0	-0.056	-0.036	14.328	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	134	THR	0	0.008	-0.019	16.243	0.020	0.020	0.000	0.000	0.000	0.000
133	A	135	ASN	0	-0.001	0.002	18.339	0.012	0.012	0.000	0.000	0.000	0.000
134	A	136	ASP	-1	-0.720	-0.798	18.628	-0.221	-0.221	0.000	0.000	0.000	0.000
135	A	137	ILE	0	0.014	0.009	20.615	0.019	0.019	0.000	0.000	0.000	0.000
136	A	138	ILE	0	-0.006	0.017	22.284	-0.008	-0.008	0.000	0.000	0.000	0.000
137	A	139	ARG	1	0.913	0.950	24.340	0.098	0.098	0.000	0.000	0.000	0.000
138	A	140	PHE	0	0.004	-0.010	26.631	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	141	ILE	0	-0.060	-0.038	26.522	0.002	0.002	0.000	0.000	0.000	0.000
140	A	142	SER	0	-0.015	-0.048	30.359	0.002	0.002	0.000	0.000	0.000	0.000
141	A	143	ASN	0	-0.024	-0.011	32.395	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:VAL)