FMO DATABASE

FMODB ID: 4JR9N

Calculation Name: 1YRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YRV

Chain ID: A

ChEMBL ID:

UniProt ID: Q5VVX9

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1499551.273455
FMO2-HF: Nuclear repulsion	1437624.102581
FMO2-HF: Total energy	-61927.170875
FMO2-MP2: Total energy	-62107.528012

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:-4:VAL)

Summations of interaction energy for fragment #1(A:-4: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.
-3.26	0.618	0.935	-1.626	-3.185	-0.002

Interaction energy analysis for fragmet #1(A:-4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.008

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	-2	ARG	1	0.976	0.991	3.400	-1.348	0.176	0.033	-0.744	-0.814	0.000
4	A	-1	GLY	0	0.041	0.017	4.794	0.233	0.357	-0.001	-0.008	-0.114	0.000
5	A	0	SER	0	0.005	-0.015	2.725	-1.001	0.413	0.542	-0.684	-1.271	-0.003
6	A	1	MET	0	-0.033	-0.006	2.795	-0.454	0.133	0.353	-0.139	-0.801	0.001
7	A	2	HIS	0	0.011	-0.005	5.280	0.115	0.151	-0.001	-0.001	-0.033	0.000
8	A	3	GLY	0	0.016	0.015	7.773	0.130	0.130	0.000	0.000	0.000	0.000
9	A	4	ARG	1	0.918	0.950	9.550	0.255	0.255	0.000	0.000	0.000	0.000
10	A	5	ALA	0	0.076	0.042	11.710	0.004	0.004	0.000	0.000	0.000	0.000
11	A	6	TYR	0	0.037	0.031	6.423	0.014	0.014	0.000	0.000	0.000	0.000
12	A	7	LEU	0	-0.004	-0.003	9.781	0.028	0.028	0.000	0.000	0.000	0.000
13	A	8	LEU	0	-0.041	-0.015	11.572	0.042	0.042	0.000	0.000	0.000	0.000
14	A	9	LEU	0	0.055	0.025	11.751	0.033	0.033	0.000	0.000	0.000	0.000
15	A	10	HIS	0	-0.031	-0.016	9.128	0.099	0.099	0.000	0.000	0.000	0.000
16	A	11	ARG	1	0.860	0.919	12.511	0.276	0.276	0.000	0.000	0.000	0.000
17	A	12	ASP	-1	-0.712	-0.824	15.965	-0.213	-0.213	0.000	0.000	0.000	0.000
18	A	13	PHE	0	0.051	0.013	13.228	0.026	0.026	0.000	0.000	0.000	0.000
19	A	14	CYS	0	-0.073	-0.043	15.221	0.018	0.018	0.000	0.000	0.000	0.000
20	A	15	ASP	-1	-0.827	-0.918	18.106	-0.202	-0.202	0.000	0.000	0.000	0.000
21	A	16	LEU	0	-0.040	-0.010	19.440	0.020	0.020	0.000	0.000	0.000	0.000
22	A	17	LYS	1	0.815	0.913	15.489	0.323	0.323	0.000	0.000	0.000	0.000
23	A	18	GLU	-1	-0.942	-0.971	21.390	-0.162	-0.162	0.000	0.000	0.000	0.000
24	A	19	ASN	0	-0.088	-0.053	24.052	0.024	0.024	0.000	0.000	0.000	0.000
25	A	20	ASN	0	-0.059	-0.013	24.870	0.009	0.009	0.000	0.000	0.000	0.000
26	A	21	TYR	0	0.004	-0.010	25.004	0.008	0.008	0.000	0.000	0.000	0.000
27	A	22	LYS	1	0.860	0.906	27.599	0.063	0.063	0.000	0.000	0.000	0.000
28	A	23	GLY	0	0.013	0.006	29.452	0.002	0.002	0.000	0.000	0.000	0.000
29	A	24	ILE	0	-0.031	-0.006	23.855	0.002	0.002	0.000	0.000	0.000	0.000
30	A	25	THR	0	-0.010	0.004	21.973	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	26	ALA	0	0.006	-0.006	18.674	0.006	0.006	0.000	0.000	0.000	0.000
32	A	27	LYS	1	0.909	0.954	12.958	0.232	0.232	0.000	0.000	0.000	0.000
33	A	28	PRO	0	0.026	0.026	10.953	0.021	0.021	0.000	0.000	0.000	0.000
34	A	29	VAL	0	-0.028	-0.020	12.276	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	30	SER	0	0.023	0.001	7.536	0.030	0.030	0.000	0.000	0.000	0.000
36	A	31	GLU	-1	-0.890	-0.954	3.493	-0.842	-0.649	0.009	-0.050	-0.152	0.000
37	A	32	ASP	-1	-0.953	-0.977	4.810	-0.927	-0.927	0.000	0.000	0.000	0.000
38	A	33	MET	0	-0.075	-0.039	5.516	0.060	0.060	0.000	0.000	0.000	0.000
39	A	34	MET	0	-0.002	0.020	8.818	0.106	0.106	0.000	0.000	0.000	0.000
40	A	35	GLU	-1	-0.822	-0.875	10.533	-0.027	-0.027	0.000	0.000	0.000	0.000
41	A	36	TRP	0	-0.030	-0.035	12.314	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	37	GLU	-1	-0.901	-0.942	15.119	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	38	VAL	0	-0.054	-0.045	18.201	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	39	GLU	-1	-0.868	-0.914	21.085	-0.045	-0.045	0.000	0.000	0.000	0.000
45	A	40	ILE	0	-0.018	-0.006	24.614	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	41	GLU	-1	-0.822	-0.882	27.485	-0.055	-0.055	0.000	0.000	0.000	0.000
47	A	42	GLY	0	0.002	-0.002	31.147	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	43	LEU	0	-0.010	0.003	33.984	0.000	0.000	0.000	0.000	0.000	0.000
49	A	44	GLN	0	0.024	0.008	35.557	0.003	0.003	0.000	0.000	0.000	0.000
50	A	45	ASN	0	-0.057	-0.047	38.684	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	46	SER	0	-0.001	0.013	37.772	0.002	0.002	0.000	0.000	0.000	0.000
52	A	47	VAL	0	0.005	-0.017	40.257	0.001	0.001	0.000	0.000	0.000	0.000
53	A	48	TRP	0	0.058	0.017	34.964	0.001	0.001	0.000	0.000	0.000	0.000
54	A	49	GLN	0	-0.003	0.023	36.466	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	50	GLY	0	0.021	0.006	36.677	0.003	0.003	0.000	0.000	0.000	0.000
56	A	51	LEU	0	-0.050	-0.017	34.386	0.003	0.003	0.000	0.000	0.000	0.000
57	A	52	VAL	0	0.044	0.016	28.043	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	53	PHE	0	0.000	-0.008	28.128	0.006	0.006	0.000	0.000	0.000	0.000
59	A	54	GLN	0	-0.037	-0.019	25.511	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	55	LEU	0	-0.037	-0.019	23.074	0.007	0.007	0.000	0.000	0.000	0.000
61	A	56	THR	0	0.005	0.006	18.545	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	57	ILE	0	-0.037	-0.022	17.529	0.006	0.006	0.000	0.000	0.000	0.000
63	A	58	HIS	1	0.842	0.909	13.260	0.067	0.067	0.000	0.000	0.000	0.000
64	A	59	PHE	0	0.017	0.006	13.410	0.016	0.016	0.000	0.000	0.000	0.000
65	A	60	THR	0	0.014	-0.006	13.302	0.015	0.015	0.000	0.000	0.000	0.000
66	A	61	SER	0	0.037	-0.024	11.036	-0.031	-0.031	0.000	0.000	0.000	0.000
67	A	62	GLU	-1	-0.899	-0.928	12.602	-0.177	-0.177	0.000	0.000	0.000	0.000
68	A	63	TYR	0	-0.064	-0.044	14.881	0.022	0.022	0.000	0.000	0.000	0.000
69	A	64	ASN	0	-0.076	-0.041	16.774	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	65	TYR	0	0.021	0.005	18.493	0.007	0.007	0.000	0.000	0.000	0.000
71	A	66	ALA	0	-0.004	0.009	19.588	0.017	0.017	0.000	0.000	0.000	0.000
72	A	67	PRO	0	0.031	0.021	19.983	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	68	PRO	0	-0.035	-0.010	17.833	0.000	0.000	0.000	0.000	0.000	0.000
74	A	69	VAL	0	-0.008	-0.002	18.957	0.014	0.014	0.000	0.000	0.000	0.000
75	A	70	VAL	0	0.013	0.000	19.799	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	71	LYS	1	0.850	0.917	22.330	0.033	0.033	0.000	0.000	0.000	0.000
77	A	72	PHE	0	0.024	-0.002	23.463	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	73	ILE	0	-0.025	0.002	21.981	0.006	0.006	0.000	0.000	0.000	0.000
79	A	74	THR	0	0.012	0.001	25.107	0.009	0.009	0.000	0.000	0.000	0.000
80	A	75	ILE	0	-0.010	0.000	28.902	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	76	PRO	0	-0.001	0.021	30.543	0.003	0.003	0.000	0.000	0.000	0.000
82	A	77	PHE	0	0.028	0.014	33.530	0.001	0.001	0.000	0.000	0.000	0.000
83	A	78	HIS	0	0.026	0.008	34.370	0.001	0.001	0.000	0.000	0.000	0.000
84	A	79	PRO	0	-0.013	-0.005	36.361	0.001	0.001	0.000	0.000	0.000	0.000
85	A	80	ASN	0	-0.009	-0.026	34.673	0.001	0.001	0.000	0.000	0.000	0.000
86	A	81	VAL	0	0.012	0.015	30.122	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	82	ASP	-1	-0.758	-0.879	30.959	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	83	PRO	0	-0.029	-0.023	31.857	0.001	0.001	0.000	0.000	0.000	0.000
89	A	84	HIS	0	-0.034	-0.009	31.211	0.002	0.002	0.000	0.000	0.000	0.000
90	A	85	THR	0	-0.056	-0.044	27.387	0.005	0.005	0.000	0.000	0.000	0.000
91	A	86	GLY	0	0.032	0.013	27.055	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	87	GLN	0	-0.009	0.004	25.335	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	88	PRO	0	-0.027	-0.009	26.460	0.004	0.004	0.000	0.000	0.000	0.000
94	A	89	CYS	0	-0.020	-0.007	28.875	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	90	ILE	0	-0.015	-0.011	28.097	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	91	ASP	-1	-0.786	-0.886	29.561	-0.053	-0.053	0.000	0.000	0.000	0.000
97	A	92	PHE	0	-0.012	-0.028	25.044	0.000	0.000	0.000	0.000	0.000	0.000
98	A	93	LEU	0	-0.037	-0.023	23.383	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	94	ASP	-1	-0.809	-0.909	26.129	-0.046	-0.046	0.000	0.000	0.000	0.000
100	A	95	ASN	0	-0.045	-0.025	28.604	0.003	0.003	0.000	0.000	0.000	0.000
101	A	96	PRO	0	0.007	-0.012	27.913	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	97	GLU	-1	-0.923	-0.947	28.980	-0.050	-0.050	0.000	0.000	0.000	0.000
103	A	98	LYS	1	0.765	0.888	30.534	0.049	0.049	0.000	0.000	0.000	0.000
104	A	99	TRP	0	0.020	0.009	21.110	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	100	ASN	0	0.019	0.002	25.744	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	101	THR	0	0.014	0.021	23.170	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	102	ASN	0	-0.052	-0.034	23.331	-0.017	-0.017	0.000	0.000	0.000	0.000
108	A	103	TYR	0	-0.059	-0.012	23.848	0.000	0.000	0.000	0.000	0.000	0.000
109	A	104	THR	0	0.039	0.028	20.626	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	105	LEU	0	0.017	-0.002	16.819	0.017	0.017	0.000	0.000	0.000	0.000
111	A	106	SER	0	0.018	0.000	20.103	0.011	0.011	0.000	0.000	0.000	0.000
112	A	107	SER	0	-0.005	0.003	23.229	0.016	0.016	0.000	0.000	0.000	0.000
113	A	108	ILE	0	-0.016	-0.004	20.377	0.012	0.012	0.000	0.000	0.000	0.000
114	A	109	LEU	0	0.026	0.009	20.611	0.012	0.012	0.000	0.000	0.000	0.000
115	A	110	LEU	0	0.031	0.017	24.675	0.011	0.011	0.000	0.000	0.000	0.000
116	A	111	ALA	0	-0.021	-0.004	27.661	0.009	0.009	0.000	0.000	0.000	0.000
117	A	112	LEU	0	0.010	-0.003	24.217	0.008	0.008	0.000	0.000	0.000	0.000
118	A	113	GLN	0	-0.010	-0.001	28.285	0.004	0.004	0.000	0.000	0.000	0.000
119	A	114	VAL	0	-0.019	0.002	30.321	0.007	0.007	0.000	0.000	0.000	0.000
120	A	115	MET	0	0.005	0.001	31.325	0.005	0.005	0.000	0.000	0.000	0.000
121	A	116	LEU	0	-0.004	0.009	27.992	0.005	0.005	0.000	0.000	0.000	0.000
122	A	117	SER	0	-0.011	-0.008	32.596	0.005	0.005	0.000	0.000	0.000	0.000
123	A	118	ASN	0	-0.125	-0.072	35.543	0.005	0.005	0.000	0.000	0.000	0.000
124	A	119	PRO	0	0.007	0.006	37.275	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	120	VAL	0	0.032	0.026	36.717	0.001	0.001	0.000	0.000	0.000	0.000
126	A	121	LEU	0	-0.019	-0.032	39.202	0.002	0.002	0.000	0.000	0.000	0.000
127	A	122	GLU	-1	-0.953	-0.949	41.720	-0.023	-0.023	0.000	0.000	0.000	0.000
128	A	123	ASN	0	-0.029	-0.027	40.746	0.003	0.003	0.000	0.000	0.000	0.000
129	A	124	PRO	0	-0.048	0.000	39.008	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	125	VAL	0	0.021	0.015	34.494	0.002	0.002	0.000	0.000	0.000	0.000
131	A	126	ASN	0	-0.029	-0.003	36.784	0.004	0.004	0.000	0.000	0.000	0.000
132	A	127	LEU	0	0.088	0.027	39.289	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	128	GLU	-1	-0.818	-0.896	42.498	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	129	ALA	0	-0.014	0.001	39.760	0.000	0.000	0.000	0.000	0.000	0.000
135	A	130	ALA	0	0.032	0.006	41.659	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	131	ARG	1	0.805	0.883	43.097	0.008	0.008	0.000	0.000	0.000	0.000
137	A	132	ILE	0	-0.026	-0.021	45.036	0.000	0.000	0.000	0.000	0.000	0.000
138	A	133	LEU	0	-0.012	0.003	41.185	0.000	0.000	0.000	0.000	0.000	0.000
139	A	134	VAL	0	-0.012	-0.005	44.994	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	135	LYS	1	0.810	0.904	47.682	0.014	0.014	0.000	0.000	0.000	0.000
141	A	136	ASP	-1	-0.830	-0.914	49.111	-0.014	-0.014	0.000	0.000	0.000	0.000
142	A	137	GLU	-1	-0.703	-0.826	45.175	-0.023	-0.023	0.000	0.000	0.000	0.000
143	A	138	SER	0	0.034	0.026	45.217	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	139	LEU	0	-0.008	0.006	46.692	0.000	0.000	0.000	0.000	0.000	0.000
145	A	140	TYR	0	-0.015	-0.029	38.765	0.000	0.000	0.000	0.000	0.000	0.000
146	A	141	ARG	1	0.816	0.865	41.980	0.023	0.023	0.000	0.000	0.000	0.000
147	A	142	THR	0	-0.064	-0.029	42.187	0.000	0.000	0.000	0.000	0.000	0.000
148	A	143	ILE	0	0.005	0.001	41.039	0.001	0.001	0.000	0.000	0.000	0.000
149	A	144	LEU	0	-0.005	0.001	36.979	0.001	0.001	0.000	0.000	0.000	0.000
150	A	145	ARG	1	0.824	0.913	38.246	0.026	0.026	0.000	0.000	0.000	0.000
151	A	146	LEU	0	-0.010	-0.008	39.460	0.001	0.001	0.000	0.000	0.000	0.000
152	A	147	PHE	0	-0.001	0.010	35.672	0.002	0.002	0.000	0.000	0.000	0.000
153	A	148	ASN	0	-0.119	-0.049	34.280	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-4:VAL)