FMO DATABASE

FMODB ID: QV7YY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1501257.01692
FMO2-HF: Nuclear repulsion	1439331.645162
FMO2-HF: Total energy	-61925.371759
FMO2-MP2: Total energy	-62105.988778

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.
-3.088	0.554	0.71	-1.563	-2.786	-0.003

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 : 0.031 / q_NPA : 0.006

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	1.024	1.013	2.936	-2.121	-0.259	0.227	-0.941	-1.147	-0.003
4	A	-1	GLY	0	-0.011	-0.019	4.976	0.282	0.393	-0.001	-0.006	-0.103	0.000
5	A	0	SER	0	0.035	0.004	2.546	-0.430	0.650	0.469	-0.512	-1.036	0.000
6	A	1	MET	0	-0.051	0.002	3.364	-0.109	0.308	0.012	-0.066	-0.364	0.000
7	A	2	HIS	0	0.005	-0.010	5.600	0.189	0.189	0.000	0.000	0.000	0.000
8	A	3	GLY	0	0.010	0.012	8.082	0.153	0.153	0.000	0.000	0.000	0.000
9	A	4	ARG	1	0.991	0.977	9.971	0.289	0.289	0.000	0.000	0.000	0.000
10	A	5	ALA	0	0.069	0.035	11.783	0.001	0.001	0.000	0.000	0.000	0.000
11	A	6	TYR	0	0.046	0.029	7.139	0.001	0.001	0.000	0.000	0.000	0.000
12	A	7	LEU	0	0.021	0.005	10.312	0.029	0.029	0.000	0.000	0.000	0.000
13	A	8	LEU	0	-0.077	-0.019	12.144	0.049	0.049	0.000	0.000	0.000	0.000
14	A	9	LEU	0	0.044	0.024	12.170	0.029	0.029	0.000	0.000	0.000	0.000
15	A	10	HIS	0	-0.021	-0.003	10.172	0.078	0.078	0.000	0.000	0.000	0.000
16	A	11	ARG	1	0.874	0.914	13.064	0.292	0.292	0.000	0.000	0.000	0.000
17	A	12	ASP	-1	-0.758	-0.875	16.417	-0.224	-0.224	0.000	0.000	0.000	0.000
18	A	13	PHE	0	0.021	-0.001	13.971	0.028	0.028	0.000	0.000	0.000	0.000
19	A	14	CYS	0	-0.080	-0.043	15.752	0.018	0.018	0.000	0.000	0.000	0.000
20	A	15	ASP	-1	-0.847	-0.922	18.408	-0.204	-0.204	0.000	0.000	0.000	0.000
21	A	16	LEU	0	-0.068	-0.019	20.024	0.020	0.020	0.000	0.000	0.000	0.000
22	A	17	LYS	1	0.870	0.926	16.125	0.312	0.312	0.000	0.000	0.000	0.000
23	A	18	GLU	-1	-0.955	-0.966	21.746	-0.171	-0.171	0.000	0.000	0.000	0.000
24	A	19	ASN	0	-0.081	-0.048	24.340	0.016	0.016	0.000	0.000	0.000	0.000
25	A	20	ASN	0	-0.052	-0.005	25.254	0.010	0.010	0.000	0.000	0.000	0.000
26	A	21	TYR	0	0.016	0.002	25.940	0.011	0.011	0.000	0.000	0.000	0.000
27	A	22	LYS	1	0.979	0.978	27.910	0.064	0.064	0.000	0.000	0.000	0.000
28	A	23	GLY	0	0.018	0.009	30.063	0.001	0.001	0.000	0.000	0.000	0.000
29	A	24	ILE	0	-0.026	-0.001	24.503	0.003	0.003	0.000	0.000	0.000	0.000
30	A	25	THR	0	0.006	0.018	21.825	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	26	ALA	0	0.009	-0.003	19.101	0.007	0.007	0.000	0.000	0.000	0.000
32	A	27	LYS	1	0.919	0.964	14.576	0.191	0.191	0.000	0.000	0.000	0.000
33	A	28	PRO	0	-0.004	0.008	11.532	0.021	0.021	0.000	0.000	0.000	0.000
34	A	29	VAL	0	-0.026	-0.025	12.809	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	30	SER	0	0.013	-0.015	8.561	0.030	0.030	0.000	0.000	0.000	0.000
36	A	31	GLU	-1	-0.878	-0.950	3.682	-0.983	-0.811	0.003	-0.038	-0.136	0.000
37	A	32	ASP	-1	-0.944	-0.960	5.526	-0.750	-0.750	0.000	0.000	0.000	0.000
38	A	33	MET	0	-0.092	-0.043	6.598	-0.027	-0.027	0.000	0.000	0.000	0.000
39	A	34	MET	0	-0.027	-0.001	9.588	0.078	0.078	0.000	0.000	0.000	0.000
40	A	35	GLU	-1	-0.812	-0.867	11.326	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	36	TRP	0	-0.044	-0.022	13.101	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	37	GLU	-1	-0.898	-0.949	15.855	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	38	VAL	0	-0.048	-0.040	18.749	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	39	GLU	-1	-0.860	-0.935	21.779	-0.041	-0.041	0.000	0.000	0.000	0.000
45	A	40	ILE	0	-0.061	-0.029	25.373	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	41	GLU	-1	-0.927	-0.961	28.028	-0.054	-0.054	0.000	0.000	0.000	0.000
47	A	42	GLY	0	-0.023	-0.020	31.542	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	43	LEU	0	0.004	0.007	34.490	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	44	GLN	0	0.020	0.015	36.076	0.003	0.003	0.000	0.000	0.000	0.000
50	A	45	ASN	0	-0.123	-0.077	39.227	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	46	SER	0	0.036	0.019	38.441	0.001	0.001	0.000	0.000	0.000	0.000
52	A	47	VAL	0	0.027	-0.003	40.499	0.001	0.001	0.000	0.000	0.000	0.000
53	A	48	TRP	0	0.035	-0.001	35.554	0.001	0.001	0.000	0.000	0.000	0.000
54	A	49	GLN	0	0.021	0.038	36.849	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	50	GLY	0	-0.049	-0.025	37.254	0.003	0.003	0.000	0.000	0.000	0.000
56	A	51	LEU	0	-0.065	-0.015	34.945	0.002	0.002	0.000	0.000	0.000	0.000
57	A	52	VAL	0	0.039	0.016	28.762	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	53	PHE	0	-0.035	-0.016	28.724	0.006	0.006	0.000	0.000	0.000	0.000
59	A	54	GLN	0	0.003	0.013	25.578	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	55	LEU	0	-0.039	-0.032	23.514	0.007	0.007	0.000	0.000	0.000	0.000
61	A	56	THR	0	0.010	0.024	18.822	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	57	ILE	0	-0.019	-0.022	18.256	0.006	0.006	0.000	0.000	0.000	0.000
63	A	58	HIS	1	0.875	0.918	14.251	0.064	0.064	0.000	0.000	0.000	0.000
64	A	59	PHE	0	0.014	0.009	14.102	0.012	0.012	0.000	0.000	0.000	0.000
65	A	60	THR	0	0.051	0.019	14.145	0.004	0.004	0.000	0.000	0.000	0.000
66	A	61	SER	0	0.005	-0.005	11.322	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	62	GLU	-1	-0.907	-0.961	12.976	-0.177	-0.177	0.000	0.000	0.000	0.000
68	A	63	TYR	0	-0.059	-0.042	15.404	0.014	0.014	0.000	0.000	0.000	0.000
69	A	64	ASN	0	-0.061	-0.017	17.139	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	65	TYR	0	0.007	-0.004	19.052	0.011	0.011	0.000	0.000	0.000	0.000
71	A	66	ALA	0	-0.025	-0.009	19.799	0.019	0.019	0.000	0.000	0.000	0.000
72	A	67	PRO	0	0.013	0.014	20.321	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	68	PRO	0	-0.020	-0.002	18.553	0.003	0.003	0.000	0.000	0.000	0.000
74	A	69	VAL	0	0.006	-0.005	19.453	0.015	0.015	0.000	0.000	0.000	0.000
75	A	70	VAL	0	0.003	0.003	20.547	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	71	LYS	1	0.871	0.920	22.359	0.023	0.023	0.000	0.000	0.000	0.000
77	A	72	PHE	0	0.012	-0.003	24.034	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	73	ILE	0	-0.025	0.008	22.193	0.007	0.007	0.000	0.000	0.000	0.000
79	A	74	THR	0	0.009	-0.008	25.480	0.009	0.009	0.000	0.000	0.000	0.000
80	A	75	ILE	0	-0.009	0.000	29.191	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	76	PRO	0	-0.009	0.016	30.802	0.002	0.002	0.000	0.000	0.000	0.000
82	A	77	PHE	0	0.013	0.017	33.766	0.001	0.001	0.000	0.000	0.000	0.000
83	A	78	HIS	0	-0.004	-0.008	34.866	0.001	0.001	0.000	0.000	0.000	0.000
84	A	79	PRO	0	0.031	0.008	36.960	0.002	0.002	0.000	0.000	0.000	0.000
85	A	80	ASN	0	0.033	0.010	34.979	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	81	VAL	0	0.015	0.029	30.843	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	82	ASP	-1	-0.780	-0.888	31.513	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	83	PRO	0	-0.034	-0.015	32.451	0.001	0.001	0.000	0.000	0.000	0.000
89	A	84	HIS	0	0.001	-0.002	32.552	0.002	0.002	0.000	0.000	0.000	0.000
90	A	85	THR	0	-0.078	-0.047	27.589	0.005	0.005	0.000	0.000	0.000	0.000
91	A	86	GLY	0	0.005	0.002	27.877	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	87	GLN	0	0.056	0.024	25.978	0.002	0.002	0.000	0.000	0.000	0.000
93	A	88	PRO	0	-0.041	-0.013	27.026	0.004	0.004	0.000	0.000	0.000	0.000
94	A	89	CYS	0	0.001	0.007	29.615	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	90	ILE	0	-0.019	-0.004	29.098	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	91	ASP	-1	-0.784	-0.903	30.384	-0.050	-0.050	0.000	0.000	0.000	0.000
97	A	92	PHE	0	-0.082	-0.047	25.505	0.000	0.000	0.000	0.000	0.000	0.000
98	A	93	LEU	0	-0.050	-0.038	24.367	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	94	ASP	-1	-0.847	-0.926	26.788	-0.046	-0.046	0.000	0.000	0.000	0.000
100	A	95	ASN	0	-0.026	-0.013	29.500	0.003	0.003	0.000	0.000	0.000	0.000
101	A	96	PRO	0	0.014	-0.006	28.420	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	97	GLU	-1	-0.962	-0.978	29.455	-0.056	-0.056	0.000	0.000	0.000	0.000
103	A	98	LYS	1	0.853	0.925	31.357	0.056	0.056	0.000	0.000	0.000	0.000
104	A	99	TRP	0	-0.023	0.003	22.021	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	100	ASN	0	0.048	0.012	26.785	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	101	THR	0	-0.016	-0.002	23.636	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	102	ASN	0	-0.070	-0.040	23.915	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	103	TYR	0	-0.034	-0.010	24.427	0.001	0.001	0.000	0.000	0.000	0.000
109	A	104	THR	0	0.023	0.023	21.436	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	105	LEU	0	0.033	0.005	17.034	0.016	0.016	0.000	0.000	0.000	0.000
111	A	106	SER	0	0.041	0.006	20.603	0.017	0.017	0.000	0.000	0.000	0.000
112	A	107	SER	0	-0.018	0.010	23.759	0.016	0.016	0.000	0.000	0.000	0.000
113	A	108	ILE	0	0.015	0.008	21.146	0.012	0.012	0.000	0.000	0.000	0.000
114	A	109	LEU	0	0.006	0.013	21.202	0.011	0.011	0.000	0.000	0.000	0.000
115	A	110	LEU	0	0.023	0.011	25.282	0.011	0.011	0.000	0.000	0.000	0.000
116	A	111	ALA	0	-0.026	-0.022	28.295	0.008	0.008	0.000	0.000	0.000	0.000
117	A	112	LEU	0	0.017	-0.005	24.836	0.008	0.008	0.000	0.000	0.000	0.000
118	A	113	GLN	0	-0.008	0.016	28.952	0.006	0.006	0.000	0.000	0.000	0.000
119	A	114	VAL	0	0.003	-0.005	30.894	0.007	0.007	0.000	0.000	0.000	0.000
120	A	115	MET	0	-0.020	-0.006	31.900	0.005	0.005	0.000	0.000	0.000	0.000
121	A	116	LEU	0	0.024	0.017	28.918	0.005	0.005	0.000	0.000	0.000	0.000
122	A	117	SER	0	-0.027	-0.007	33.316	0.006	0.006	0.000	0.000	0.000	0.000
123	A	118	ASN	0	-0.122	-0.074	36.175	0.005	0.005	0.000	0.000	0.000	0.000
124	A	119	PRO	0	0.023	0.002	37.763	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	120	VAL	0	0.011	0.017	37.546	0.000	0.000	0.000	0.000	0.000	0.000
126	A	121	LEU	0	-0.044	-0.055	40.181	0.002	0.002	0.000	0.000	0.000	0.000
127	A	122	GLU	-1	-0.956	-0.964	42.330	-0.022	-0.022	0.000	0.000	0.000	0.000
128	A	123	ASN	0	-0.020	-0.011	41.731	0.003	0.003	0.000	0.000	0.000	0.000
129	A	124	PRO	0	-0.064	-0.012	39.630	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	125	VAL	0	0.052	0.037	35.183	0.002	0.002	0.000	0.000	0.000	0.000
131	A	126	ASN	0	-0.039	-0.008	37.672	0.004	0.004	0.000	0.000	0.000	0.000
132	A	127	LEU	0	0.077	0.017	39.699	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	128	GLU	-1	-0.929	-0.975	43.352	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	129	ALA	0	-0.003	0.006	40.296	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	130	ALA	0	0.059	0.016	42.281	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	131	ARG	1	0.926	0.967	43.611	0.006	0.006	0.000	0.000	0.000	0.000
137	A	132	ILE	0	-0.052	-0.041	45.310	0.000	0.000	0.000	0.000	0.000	0.000
138	A	133	LEU	0	-0.017	0.009	41.664	0.000	0.000	0.000	0.000	0.000	0.000
139	A	134	VAL	0	-0.018	-0.004	45.438	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	135	LYS	1	0.879	0.933	48.183	0.013	0.013	0.000	0.000	0.000	0.000
141	A	136	ASP	-1	-0.843	-0.911	49.911	-0.013	-0.013	0.000	0.000	0.000	0.000
142	A	137	GLU	-1	-0.791	-0.910	45.919	-0.024	-0.024	0.000	0.000	0.000	0.000
143	A	138	SER	0	-0.071	-0.041	45.984	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	139	LEU	0	-0.023	-0.008	47.151	0.000	0.000	0.000	0.000	0.000	0.000
145	A	140	TYR	0	0.036	-0.005	39.118	0.000	0.000	0.000	0.000	0.000	0.000
146	A	141	ARG	1	0.947	0.970	42.349	0.022	0.022	0.000	0.000	0.000	0.000
147	A	142	THR	0	-0.069	-0.018	42.586	0.000	0.000	0.000	0.000	0.000	0.000
148	A	143	ILE	0	0.010	-0.001	41.453	0.001	0.001	0.000	0.000	0.000	0.000
149	A	144	LEU	0	-0.007	0.009	37.667	0.001	0.001	0.000	0.000	0.000	0.000
150	A	145	ARG	1	0.932	0.955	38.739	0.023	0.023	0.000	0.000	0.000	0.000
151	A	146	LEU	0	-0.028	-0.010	39.904	0.001	0.001	0.000	0.000	0.000	0.000
152	A	147	PHE	0	-0.049	-0.015	36.662	0.002	0.002	0.000	0.000	0.000	0.000
153	A	148	ASN	0	-0.081	-0.022	35.160	-0.003	-0.003	0.000	0.000	0.000	0.000

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