FMO DATABASE

FMODB ID: QV12Y

Calculation Name: 1YVI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YVI

Chain ID: A

ChEMBL ID:

UniProt ID: Q6VAK4

Base Structure: X-ray

Registration Date: 2023-09-21

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1279686.896965
FMO2-HF: Nuclear repulsion	1222121.883147
FMO2-HF: Total energy	-57565.013818
FMO2-MP2: Total energy	-57728.135736

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:1:SER)

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

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.
-8.678	-3.309	4.28	-3.991	-5.656	0.019

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.026

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	3	ALA	0	0.059	0.025	2.800	-2.408	0.765	0.363	-1.642	-1.893	0.007
4	A	4	ALA	0	-0.066	-0.027	2.153	-4.773	-3.349	3.898	-2.130	-3.192	0.011
5	A	5	ALA	0	0.074	0.034	3.667	-0.177	0.438	0.020	-0.207	-0.428	0.001
6	A	6	LEU	0	0.020	0.014	5.611	0.482	0.482	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.994	1.002	4.218	-1.537	-1.380	-0.001	-0.012	-0.143	0.000
8	A	8	ASP	-1	-0.902	-0.933	6.315	-1.659	-1.659	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.042	-0.034	9.239	0.053	0.053	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.022	0.018	11.482	0.066	0.066	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.004	-0.014	11.644	0.061	0.061	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.019	-0.012	13.302	0.036	0.036	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.016	0.009	15.159	0.041	0.041	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.060	0.034	15.889	0.025	0.025	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.028	0.014	17.864	0.019	0.019	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.115	-0.051	19.259	0.015	0.015	0.000	0.000	0.000	0.000
17	A	17	MET	0	0.004	0.003	21.188	0.013	0.013	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.010	0.006	21.094	0.011	0.011	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.065	-0.048	22.663	0.004	0.004	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.045	-0.026	23.322	0.012	0.012	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.010	0.009	27.013	0.008	0.008	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.039	-0.023	25.468	0.010	0.010	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.048	-0.021	24.665	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.823	-0.901	28.121	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.906	-0.976	27.642	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.007	-0.003	27.911	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.010	0.010	21.478	0.007	0.007	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.019	0.002	23.305	0.016	0.016	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.019	0.007	23.839	0.017	0.017	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.010	0.005	24.640	0.011	0.011	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.015	-0.021	18.084	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	MET	0	0.002	0.006	21.317	0.022	0.022	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.001	-0.007	23.373	0.011	0.011	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.032	0.007	17.397	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.952	-0.958	18.544	0.188	0.188	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.999	-1.011	21.292	0.091	0.091	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.040	-0.021	24.887	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.023	0.002	21.987	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.057	-0.034	21.293	0.029	0.029	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.030	-0.004	17.063	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.052	0.036	17.655	0.018	0.018	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.037	-0.018	19.829	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.024	0.006	19.997	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.009	-0.040	18.907	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.935	-0.946	21.466	0.060	0.060	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.028	-0.009	24.784	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.019	-0.013	22.997	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.007	-0.007	24.012	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.015	0.013	26.416	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.007	-0.004	28.961	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	51	CYS	0	-0.091	-0.057	27.099	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.837	-0.902	29.795	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.855	-0.917	32.534	0.002	0.002	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.001	-0.002	33.504	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.822	-0.902	34.047	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.833	0.893	35.987	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.018	-0.011	37.837	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.006	-0.003	36.337	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	ASN	0	0.035	0.017	38.480	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.824	-0.853	41.971	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.037	-0.026	42.197	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.028	-0.012	44.013	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.041	0.018	45.792	0.001	0.001	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.070	-0.036	48.092	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.022	-0.016	47.198	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.905	-0.953	47.440	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.082	-0.026	51.762	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.014	0.004	54.723	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.019	-0.012	58.179	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.005	0.023	52.625	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ASN	0	0.011	0.005	53.383	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.078	0.016	52.388	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.806	-0.877	51.659	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.892	0.948	48.187	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.016	0.009	47.449	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.762	-0.863	46.877	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.013	-0.002	46.768	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.037	-0.066	43.851	0.002	0.002	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.032	0.027	42.458	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	HIS	0	0.020	0.013	42.102	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.004	-0.006	40.798	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.022	0.030	36.439	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.864	0.936	37.155	0.008	0.008	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.005	0.002	37.374	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.047	0.024	34.346	0.001	0.001	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.014	-0.018	33.024	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.040	-0.029	32.478	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.054	-0.036	32.734	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.005	0.001	28.086	0.005	0.005	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.032	0.028	28.159	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.040	0.024	29.866	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.064	-0.063	30.735	0.007	0.007	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.842	0.916	31.309	0.075	0.075	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.082	0.042	33.261	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.865	0.950	34.153	0.030	0.030	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.005	-0.021	35.431	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.000	-0.015	38.107	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	CYS	0	-0.054	-0.030	38.892	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	MET	0	-0.080	-0.041	41.098	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.004	0.010	43.363	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	PHE	0	0.003	-0.010	43.317	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.855	0.878	46.020	0.012	0.012	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.061	-0.021	48.466	0.001	0.001	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.041	0.019	47.263	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.061	-0.016	48.930	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.037	-0.008	52.117	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.874	-0.945	54.054	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.759	0.873	55.256	0.010	0.010	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.048	0.040	53.750	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.871	0.911	52.680	0.017	0.017	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.858	-0.937	51.274	-0.025	-0.025	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.022	0.017	50.236	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	113	CYS	0	-0.018	-0.010	48.193	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.018	-0.002	46.714	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	115	MET	0	-0.027	-0.016	45.769	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.020	0.012	44.301	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.018	-0.010	41.575	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.010	0.001	41.164	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.019	-0.003	39.124	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.029	0.007	37.975	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.919	0.958	36.699	0.032	0.032	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.021	-0.005	35.382	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.797	-0.889	33.599	-0.061	-0.061	0.000	0.000	0.000	0.000
124	A	124	PHE	0	-0.056	-0.017	31.689	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	125	TYR	0	-0.053	-0.055	31.031	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.845	-0.905	28.922	-0.104	-0.104	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.008	0.018	26.148	-0.011	-0.011	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.850	0.911	26.305	0.032	0.032	0.000	0.000	0.000	0.000
129	A	129	ASN	0	0.004	0.001	24.219	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.824	0.918	22.564	0.112	0.112	0.000	0.000	0.000	0.000
131	A	131	PHE	0	0.078	0.020	21.546	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	132	GLN	0	0.018	0.020	21.738	0.013	0.013	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.041	-0.024	17.857	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	134	MET	0	-0.014	-0.015	17.498	-0.015	-0.015	0.000	0.000	0.000	0.000
135	A	135	LEU	0	0.002	0.019	17.066	0.022	0.022	0.000	0.000	0.000	0.000
136	A	136	GLN	0	-0.036	-0.005	15.914	0.036	0.036	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.013	-0.011	12.289	0.009	0.009	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.774	-0.878	12.750	0.185	0.185	0.000	0.000	0.000	0.000
139	A	139	GLN	0	-0.030	-0.001	14.191	0.065	0.065	0.000	0.000	0.000	0.000
140	A	140	GLN	0	-0.036	-0.028	11.124	0.029	0.029	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.065	-0.028	8.936	0.131	0.131	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.012	-0.011	10.336	0.175	0.175	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.108	-0.035	10.499	0.092	0.092	0.000	0.000	0.000	0.000

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