FMO DATABASE

FMODB ID: Q892Y

Calculation Name: 1YQ5-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQ5

Chain ID: A

ChEMBL ID:

UniProt ID: P22536

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1136949.231706
FMO2-HF: Nuclear repulsion	1085748.092551
FMO2-HF: Total energy	-51201.139155
FMO2-MP2: Total energy	-51349.291267

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:197:GLY )

Summations of interaction energy for fragment #1(A:197:GLY )

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.
2.075	2.84	-0.007	-0.475	-0.284	0.002

Interaction energy analysis for fragmet #1(A:197:GLY )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.009

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	199	VAL	0	-0.007	-0.001	3.788	1.618	2.383	-0.007	-0.475	-0.284	0.002
4	A	200	THR	0	-0.003	-0.034	6.824	-0.282	-0.282	0.000	0.000	0.000	0.000
5	A	201	ASP	-1	-0.783	-0.867	8.601	-0.281	-0.281	0.000	0.000	0.000	0.000
6	A	202	ALA	0	-0.002	-0.012	11.651	0.055	0.055	0.000	0.000	0.000	0.000
7	A	203	LEU	0	-0.021	0.011	13.583	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	204	SER	0	-0.031	-0.017	16.822	0.036	0.036	0.000	0.000	0.000	0.000
9	A	205	LEU	0	0.001	-0.010	18.579	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	206	MET	0	0.025	0.023	22.360	0.015	0.015	0.000	0.000	0.000	0.000
11	A	207	TYR	0	-0.018	-0.018	25.312	0.002	0.002	0.000	0.000	0.000	0.000
12	A	208	SER	0	0.064	-0.001	28.423	0.007	0.007	0.000	0.000	0.000	0.000
13	A	209	THR	0	-0.016	0.000	31.877	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	210	SER	0	-0.004	-0.001	33.622	0.001	0.001	0.000	0.000	0.000	0.000
15	A	211	THR	0	-0.090	-0.048	28.974	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	212	GLY	0	0.067	0.018	30.357	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	213	GLY	0	0.017	0.030	32.478	0.003	0.003	0.000	0.000	0.000	0.000
18	A	214	PRO	0	-0.018	-0.004	33.685	0.001	0.001	0.000	0.000	0.000	0.000
19	A	215	ALA	0	0.041	0.019	37.197	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	216	SER	0	-0.033	-0.035	39.716	0.001	0.001	0.000	0.000	0.000	0.000
21	A	217	ILE	0	-0.032	0.007	33.867	0.001	0.001	0.000	0.000	0.000	0.000
22	A	218	ALA	0	0.024	0.002	38.244	0.002	0.002	0.000	0.000	0.000	0.000
23	A	219	ALA	0	0.008	0.010	39.550	0.000	0.000	0.000	0.000	0.000	0.000
24	A	220	ASN	0	-0.041	-0.023	40.238	0.002	0.002	0.000	0.000	0.000	0.000
25	A	221	ALA	0	0.033	0.009	39.164	0.002	0.002	0.000	0.000	0.000	0.000
26	A	222	LEU	0	-0.015	-0.006	33.515	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	223	THR	0	0.002	0.005	36.032	0.003	0.003	0.000	0.000	0.000	0.000
28	A	224	ASP	-1	-0.846	-0.937	31.506	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	225	PHE	0	0.004	-0.013	29.001	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	226	ASP	-1	-0.782	-0.831	30.338	-0.066	-0.066	0.000	0.000	0.000	0.000
31	A	227	LEU	0	-0.030	-0.033	25.054	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	228	SER	0	-0.074	-0.058	27.512	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	229	GLY	0	0.018	0.001	29.029	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	230	ALA	0	-0.004	0.015	26.063	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	231	LEU	0	-0.002	0.012	24.839	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	232	THR	0	-0.005	-0.009	20.197	0.009	0.009	0.000	0.000	0.000	0.000
37	A	233	VAL	0	-0.019	0.001	19.073	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	234	ASN	0	0.009	-0.008	12.961	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	235	SER	0	0.008	-0.002	16.123	0.064	0.064	0.000	0.000	0.000	0.000
40	A	236	VAL	0	-0.035	-0.004	9.608	-0.061	-0.061	0.000	0.000	0.000	0.000
41	A	237	GLY	0	0.054	0.039	12.712	0.064	0.064	0.000	0.000	0.000	0.000
42	A	238	THR	0	-0.028	-0.030	13.271	0.038	0.038	0.000	0.000	0.000	0.000
43	A	239	GLY	0	-0.014	-0.010	15.149	0.046	0.046	0.000	0.000	0.000	0.000
44	A	240	LEU	0	-0.020	0.005	14.975	0.044	0.044	0.000	0.000	0.000	0.000
45	A	241	THR	0	-0.010	-0.001	18.207	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	242	LYS	1	0.881	0.934	21.306	0.173	0.173	0.000	0.000	0.000	0.000
47	A	243	SER	0	-0.025	-0.043	24.278	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	244	ALA	0	0.038	0.010	27.717	0.002	0.002	0.000	0.000	0.000	0.000
49	A	245	ALA	0	-0.047	-0.009	29.195	0.006	0.006	0.000	0.000	0.000	0.000
50	A	246	GLY	0	0.030	0.009	26.979	0.009	0.009	0.000	0.000	0.000	0.000
51	A	247	ILE	0	-0.036	-0.016	20.146	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	248	GLN	0	0.006	0.023	23.307	0.018	0.018	0.000	0.000	0.000	0.000
53	A	249	LEU	0	0.024	0.008	19.117	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	250	ALA	0	-0.032	-0.008	18.671	0.011	0.011	0.000	0.000	0.000	0.000
55	A	251	ALA	0	0.068	0.010	20.018	0.020	0.020	0.000	0.000	0.000	0.000
56	A	252	GLY	0	0.002	0.001	19.324	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	253	LYS	1	0.825	0.917	13.056	0.160	0.160	0.000	0.000	0.000	0.000
58	A	254	SER	0	0.072	0.057	17.265	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	255	GLY	0	0.020	0.012	15.545	0.031	0.031	0.000	0.000	0.000	0.000
60	A	256	LEU	0	-0.038	-0.005	13.521	-0.046	-0.046	0.000	0.000	0.000	0.000
61	A	257	TYR	0	-0.010	-0.043	13.706	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	258	GLN	0	0.004	0.017	13.341	0.053	0.053	0.000	0.000	0.000	0.000
63	A	259	ILE	0	-0.013	-0.027	15.192	-0.057	-0.057	0.000	0.000	0.000	0.000
64	A	260	THR	0	0.001	-0.002	18.245	0.022	0.022	0.000	0.000	0.000	0.000
65	A	261	MET	0	-0.051	0.001	20.159	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	262	THR	0	-0.042	-0.021	22.967	0.009	0.009	0.000	0.000	0.000	0.000
67	A	263	VAL	0	0.040	0.018	25.530	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	264	LYS	1	0.888	0.964	28.875	0.042	0.042	0.000	0.000	0.000	0.000
69	A	265	ASN	0	0.115	0.037	31.329	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	266	ASN	0	0.037	-0.014	34.032	0.005	0.005	0.000	0.000	0.000	0.000
71	A	267	THR	0	0.009	0.021	36.700	0.002	0.002	0.000	0.000	0.000	0.000
72	A	268	VAL	0	0.002	0.023	38.333	0.002	0.002	0.000	0.000	0.000	0.000
73	A	269	THR	0	-0.036	-0.007	38.110	0.000	0.000	0.000	0.000	0.000	0.000
74	A	270	THR	0	0.025	0.017	39.878	0.002	0.002	0.000	0.000	0.000	0.000
75	A	271	GLY	0	0.063	0.044	40.254	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	272	ASN	0	-0.042	-0.036	36.746	0.002	0.002	0.000	0.000	0.000	0.000
77	A	273	TYR	0	-0.009	-0.012	32.862	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	274	LEU	0	-0.004	-0.003	33.592	0.005	0.005	0.000	0.000	0.000	0.000
79	A	275	LEU	0	-0.021	-0.014	27.363	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	276	ARG	1	0.901	0.938	29.238	0.006	0.006	0.000	0.000	0.000	0.000
81	A	277	VAL	0	0.000	0.009	23.291	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	278	LYS	1	0.852	0.928	26.707	0.008	0.008	0.000	0.000	0.000	0.000
83	A	279	TYR	0	0.020	-0.015	23.531	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	280	GLY	0	0.033	0.030	26.199	0.010	0.010	0.000	0.000	0.000	0.000
85	A	281	SER	0	-0.057	-0.039	28.686	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	282	SER	0	-0.012	0.008	26.897	0.005	0.005	0.000	0.000	0.000	0.000
87	A	283	ASP	-1	-0.943	-0.977	28.596	0.026	0.026	0.000	0.000	0.000	0.000
88	A	284	PHE	0	0.021	0.007	24.832	0.008	0.008	0.000	0.000	0.000	0.000
89	A	285	VAL	0	0.017	-0.005	28.042	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	286	VAL	0	-0.003	-0.003	28.017	0.007	0.007	0.000	0.000	0.000	0.000
91	A	287	ALA	0	0.010	0.012	30.600	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	288	CYS	0	-0.058	-0.025	30.434	0.004	0.004	0.000	0.000	0.000	0.000
93	A	289	PRO	0	0.050	0.028	33.161	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	290	ALA	0	-0.025	0.005	35.467	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	291	SER	0	0.015	-0.009	36.348	0.001	0.001	0.000	0.000	0.000	0.000
96	A	292	SER	0	-0.012	-0.031	37.350	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	293	LEU	0	-0.007	0.000	35.368	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	294	THR	0	-0.010	0.013	32.435	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	295	ALA	0	0.010	0.028	33.899	0.002	0.002	0.000	0.000	0.000	0.000
100	A	296	GLY	0	0.002	-0.029	31.644	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	297	GLY	0	0.028	0.016	29.868	0.006	0.006	0.000	0.000	0.000	0.000
102	A	298	THR	0	-0.060	-0.049	23.606	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	299	ILE	0	0.038	0.034	24.351	0.008	0.008	0.000	0.000	0.000	0.000
104	A	300	SER	0	-0.006	-0.009	19.497	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	301	LEU	0	-0.029	-0.017	19.756	0.012	0.012	0.000	0.000	0.000	0.000
106	A	302	LEU	0	0.043	0.050	14.506	-0.010	-0.010	0.000	0.000	0.000	0.000
107	A	303	ILE	0	-0.019	-0.011	17.731	0.006	0.006	0.000	0.000	0.000	0.000
108	A	304	TYR	0	0.029	0.013	17.989	0.019	0.019	0.000	0.000	0.000	0.000
109	A	305	CYS	0	-0.047	-0.014	19.071	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	306	ASN	0	0.018	0.003	20.294	0.020	0.020	0.000	0.000	0.000	0.000
111	A	307	VAL	0	-0.049	-0.016	20.003	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	308	LEU	0	-0.039	-0.034	22.953	0.007	0.007	0.000	0.000	0.000	0.000
113	A	309	GLY	0	-0.028	-0.015	25.026	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	310	VAL	0	-0.044	-0.017	25.884	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	311	VAL	0	0.071	0.027	26.467	0.002	0.002	0.000	0.000	0.000	0.000
116	A	312	SER	0	-0.021	-0.021	27.722	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	313	LEU	0	-0.052	-0.025	29.205	0.002	0.002	0.000	0.000	0.000	0.000
118	A	314	ASP	-1	-0.736	-0.837	23.683	0.019	0.019	0.000	0.000	0.000	0.000
119	A	315	VAL	0	-0.030	-0.025	24.430	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	316	LEU	0	-0.017	0.001	19.686	0.011	0.011	0.000	0.000	0.000	0.000
121	A	317	LYS	1	0.936	0.971	24.362	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	318	PHE	0	0.059	0.005	21.766	0.007	0.007	0.000	0.000	0.000	0.000
123	A	319	SER	0	-0.004	-0.005	27.839	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	320	LEU	0	0.033	0.001	28.956	0.004	0.004	0.000	0.000	0.000	0.000
125	A	321	CYS	0	-0.027	0.020	32.341	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	322	ASN	0	0.008	0.010	35.223	0.003	0.003	0.000	0.000	0.000	0.000
127	A	323	ASP	-1	-0.789	-0.919	37.781	0.001	0.001	0.000	0.000	0.000	0.000
128	A	324	GLY	0	0.013	0.015	40.408	0.001	0.001	0.000	0.000	0.000	0.000
129	A	325	ALA	0	-0.048	-0.032	41.531	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	326	ALA	0	0.001	0.005	40.583	0.000	0.000	0.000	0.000	0.000	0.000
131	A	327	LEU	0	-0.038	-0.010	34.751	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	328	SER	0	0.009	0.001	38.316	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	329	ASN	0	-0.077	-0.046	37.132	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	330	TYR	0	-0.018	-0.010	31.732	0.000	0.000	0.000	0.000	0.000	0.000
135	A	331	ILE	0	-0.013	0.000	27.711	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	332	ILE	0	-0.003	-0.008	26.570	0.005	0.005	0.000	0.000	0.000	0.000
137	A	333	ASN	0	-0.035	0.001	22.269	-0.024	-0.024	0.000	0.000	0.000	0.000
138	A	334	ILE	0	0.020	0.006	21.527	0.016	0.016	0.000	0.000	0.000	0.000
139	A	335	THR	0	-0.008	0.005	15.615	-0.038	-0.038	0.000	0.000	0.000	0.000
140	A	336	ALA	0	0.012	0.012	16.613	0.038	0.038	0.000	0.000	0.000	0.000
141	A	337	ALA	0	0.015	-0.002	11.075	-0.072	-0.072	0.000	0.000	0.000	0.000
142	A	338	LYS	1	0.854	0.941	11.961	-0.145	-0.145	0.000	0.000	0.000	0.000
143	A	339	ILE	0	-0.041	-0.042	8.982	-0.074	-0.074	0.000	0.000	0.000	0.000
144	A	340	ASN	-1	-0.843	-0.898	8.982	0.839	0.839	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:197:GLY )