FMO DATABASE

FMODB ID: ZVY4N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1270755.837478
FMO2-HF: Nuclear repulsion	1213192.316162
FMO2-HF: Total energy	-57563.521316
FMO2-MP2: Total energy	-57726.720708

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.
-11.112	-5.604	3.147	-3.491	-5.164	0.023

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 : 0.034 / q_NPA : 0.007

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	0.051	0.024	2.995	-1.769	0.929	0.123	-1.331	-1.491	0.005
4	A	4	ALA	0	-0.037	-0.022	2.297	-6.368	-4.442	3.009	-1.938	-2.997	0.018
5	A	5	ALA	0	0.053	0.033	3.556	-0.741	-0.135	0.017	-0.201	-0.422	0.000
6	A	6	LEU	0	0.031	0.016	5.275	0.495	0.617	-0.001	-0.008	-0.112	0.000
7	A	7	ARG	1	0.997	0.994	4.337	-3.450	-3.294	-0.001	-0.013	-0.142	0.000
8	A	8	ASP	-1	-0.893	-0.931	7.182	-1.086	-1.086	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.054	-0.036	9.279	-0.180	-0.180	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.023	0.016	11.460	0.047	0.047	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.001	0.001	11.733	0.054	0.054	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.033	-0.017	13.382	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.033	-0.006	15.212	0.029	0.029	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.074	0.020	16.177	0.014	0.014	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.032	-0.009	17.852	0.014	0.014	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.060	-0.036	19.474	0.008	0.008	0.000	0.000	0.000	0.000
17	A	17	MET	0	0.006	0.014	21.408	0.006	0.006	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.023	0.020	21.600	0.008	0.008	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.059	-0.031	22.970	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.051	-0.035	23.897	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.011	0.007	27.212	0.003	0.003	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.037	-0.008	25.689	0.008	0.008	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.020	-0.010	24.518	0.007	0.007	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.855	-0.930	27.980	0.017	0.017	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.944	-0.987	27.663	0.044	0.044	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.038	-0.024	28.020	0.008	0.008	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.024	0.015	21.513	0.010	0.010	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.018	-0.014	23.464	0.025	0.025	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.048	0.010	23.960	0.022	0.022	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.001	0.020	24.566	0.014	0.014	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.002	-0.013	18.333	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	MET	0	-0.007	0.008	21.245	0.036	0.036	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.025	0.006	23.589	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.015	0.015	17.554	-0.039	-0.039	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.936	-0.927	18.662	0.385	0.385	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-1.047	-1.044	21.237	0.185	0.185	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.088	-0.049	25.112	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.001	0.006	22.396	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.046	-0.013	21.650	0.035	0.035	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.048	0.000	17.478	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.051	0.038	18.105	0.017	0.017	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.036	-0.036	19.979	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.044	0.022	20.317	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.007	-0.006	18.913	-0.036	-0.036	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.926	-0.946	21.655	0.110	0.110	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.034	-0.001	24.923	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.029	-0.013	23.433	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.008	-0.028	24.407	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.027	0.024	26.828	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.015	0.009	29.090	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	51	CYS	0	-0.089	-0.054	27.611	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.885	-0.933	30.517	0.022	0.022	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.905	-0.963	32.838	0.035	0.035	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.059	-0.040	33.745	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.909	-0.953	34.359	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.941	0.978	36.139	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.044	-0.030	38.045	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.009	-0.007	36.753	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.018	-0.008	38.837	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.947	-0.969	42.237	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.048	-0.031	42.527	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.017	-0.018	44.371	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.075	0.044	46.234	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.062	-0.033	48.145	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.048	-0.031	47.538	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.935	-0.949	48.174	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.086	-0.029	52.269	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.021	0.012	55.255	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.015	-0.009	58.671	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.021	0.023	53.227	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.005	-0.002	53.829	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.061	-0.006	52.933	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.860	-0.913	52.246	0.006	0.006	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.906	0.956	49.438	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.013	0.004	47.844	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.754	-0.860	47.212	0.005	0.005	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.028	-0.018	46.950	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.014	-0.005	43.411	0.002	0.002	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.033	0.021	42.752	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.041	-0.012	42.232	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.006	-0.017	40.881	0.001	0.001	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.019	0.032	36.318	0.003	0.003	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.930	0.982	37.439	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.012	-0.013	37.704	0.001	0.001	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.054	0.013	34.599	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.019	-0.007	33.272	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.071	-0.050	32.796	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.033	-0.008	32.808	0.004	0.004	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.002	0.011	28.251	0.009	0.009	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.045	0.032	28.085	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.020	0.023	29.958	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.048	-0.057	31.219	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.969	0.981	32.069	0.054	0.054	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.087	0.058	33.445	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.921	0.972	35.288	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	96	PHE	0	-0.016	-0.048	35.826	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.019	0.012	38.327	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	CYS	0	-0.025	-0.012	39.362	0.001	0.001	0.000	0.000	0.000	0.000
99	A	99	MET	0	-0.078	-0.038	41.521	0.002	0.002	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.012	0.013	43.730	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	PHE	0	0.018	-0.005	43.382	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.856	0.903	46.355	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.044	-0.011	48.800	0.001	0.001	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.046	0.019	47.084	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.043	-0.001	49.649	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.023	-0.007	52.545	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.903	-0.953	54.732	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.862	0.934	55.724	0.001	0.001	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.037	0.032	53.807	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.864	0.900	52.981	0.011	0.011	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.871	-0.939	51.580	-0.020	-0.020	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.011	0.009	50.544	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	113	CYS	0	-0.021	-0.006	48.482	0.000	0.000	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.001	0.000	46.961	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	115	MET	0	-0.030	-0.010	45.993	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.014	0.003	44.546	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.005	0.001	41.972	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.035	-0.015	41.247	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.020	0.017	39.443	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.014	-0.004	38.095	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.929	0.978	36.729	0.026	0.026	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.021	-0.008	35.291	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.814	-0.909	33.629	-0.043	-0.043	0.000	0.000	0.000	0.000
124	A	124	PHE	0	-0.029	-0.013	31.683	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	125	TYR	0	-0.015	-0.027	31.114	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.923	-0.943	29.390	-0.086	-0.086	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.037	-0.024	26.453	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.966	0.989	26.415	0.030	0.030	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.040	-0.020	24.516	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.925	0.960	22.092	0.126	0.126	0.000	0.000	0.000	0.000
131	A	131	PHE	0	0.086	0.024	21.577	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.011	-0.005	21.945	0.024	0.024	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.027	-0.009	17.737	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	134	MET	0	0.010	0.001	17.583	-0.016	-0.016	0.000	0.000	0.000	0.000
135	A	135	LEU	0	0.013	0.021	17.112	0.032	0.032	0.000	0.000	0.000	0.000
136	A	136	GLN	0	-0.020	0.012	16.974	0.041	0.041	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.022	-0.024	12.523	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.890	-0.953	12.975	0.384	0.384	0.000	0.000	0.000	0.000
139	A	139	GLN	0	-0.057	-0.034	14.108	0.080	0.080	0.000	0.000	0.000	0.000
140	A	140	GLN	0	-0.057	-0.040	11.178	0.044	0.044	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.053	-0.018	8.930	0.176	0.176	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.022	-0.017	10.418	0.222	0.222	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.067	-0.008	10.361	0.077	0.077	0.000	0.000	0.000	0.000

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