FMO DATABASE

FMODB ID: R52Y8

Calculation Name: 1YQ5-A-Xray372

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: 2023-06-20

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1137205.425661
FMO2-HF: Nuclear repulsion	1086003.825866
FMO2-HF: Total energy	-51201.599796
FMO2-MP2: Total energy	-51349.766441

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.
1.753	2.519	-0.01	-0.47	-0.286	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 : 0.009 / 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	199	VAL	0	-0.016	-0.006	3.788	1.650	2.416	-0.010	-0.470	-0.286	0.002
4	A	200	THR	0	-0.010	-0.039	6.824	-0.263	-0.263	0.000	0.000	0.000	0.000
5	A	201	ASP	-1	-0.779	-0.865	8.607	-0.272	-0.272	0.000	0.000	0.000	0.000
6	A	202	ALA	0	-0.007	-0.014	11.651	0.055	0.055	0.000	0.000	0.000	0.000
7	A	203	LEU	0	-0.016	0.014	13.583	-0.026	-0.026	0.000	0.000	0.000	0.000
8	A	204	SER	0	-0.032	-0.018	16.822	0.035	0.035	0.000	0.000	0.000	0.000
9	A	205	LEU	0	0.004	-0.009	18.579	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	206	MET	0	0.025	0.025	22.360	0.014	0.014	0.000	0.000	0.000	0.000
11	A	207	TYR	0	-0.020	-0.019	25.313	0.002	0.002	0.000	0.000	0.000	0.000
12	A	208	SER	0	0.066	0.000	28.423	0.006	0.006	0.000	0.000	0.000	0.000
13	A	209	THR	0	-0.010	0.001	31.877	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	210	SER	0	-0.005	-0.002	33.622	0.001	0.001	0.000	0.000	0.000	0.000
15	A	211	THR	0	-0.090	-0.047	28.975	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	212	GLY	0	0.070	0.019	30.357	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	213	GLY	0	0.011	0.028	32.478	0.003	0.003	0.000	0.000	0.000	0.000
18	A	214	PRO	0	-0.019	-0.004	33.685	0.001	0.001	0.000	0.000	0.000	0.000
19	A	215	ALA	0	0.044	0.019	37.197	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	216	SER	0	-0.032	-0.035	39.716	0.001	0.001	0.000	0.000	0.000	0.000
21	A	217	ILE	0	-0.031	0.007	33.867	0.001	0.001	0.000	0.000	0.000	0.000
22	A	218	ALA	0	0.022	0.001	38.244	0.002	0.002	0.000	0.000	0.000	0.000
23	A	219	ALA	0	0.010	0.010	39.550	0.000	0.000	0.000	0.000	0.000	0.000
24	A	220	ASN	0	-0.041	-0.022	40.238	0.002	0.002	0.000	0.000	0.000	0.000
25	A	221	ALA	0	0.031	0.008	39.164	0.002	0.002	0.000	0.000	0.000	0.000
26	A	222	LEU	0	-0.014	-0.006	33.515	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	223	THR	0	0.004	0.007	36.031	0.003	0.003	0.000	0.000	0.000	0.000
28	A	224	ASP	-1	-0.849	-0.939	31.506	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	225	PHE	0	0.006	-0.012	29.000	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	226	ASP	-1	-0.779	-0.830	30.338	-0.065	-0.065	0.000	0.000	0.000	0.000
31	A	227	LEU	0	-0.028	-0.033	25.053	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	228	SER	0	-0.082	-0.061	27.512	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	229	GLY	0	0.024	0.004	29.029	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	230	ALA	0	-0.006	0.015	26.063	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	231	LEU	0	0.000	0.013	24.839	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	232	THR	0	-0.006	-0.010	20.197	0.010	0.010	0.000	0.000	0.000	0.000
37	A	233	VAL	0	-0.017	0.003	19.073	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	234	ASN	0	0.010	-0.007	12.961	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	235	SER	0	0.012	0.000	16.123	0.065	0.065	0.000	0.000	0.000	0.000
40	A	236	VAL	0	-0.040	-0.005	9.608	-0.060	-0.060	0.000	0.000	0.000	0.000
41	A	237	GLY	0	0.053	0.038	12.717	0.064	0.064	0.000	0.000	0.000	0.000
42	A	238	THR	0	-0.024	-0.028	13.276	0.034	0.034	0.000	0.000	0.000	0.000
43	A	239	GLY	0	-0.016	-0.012	15.155	0.044	0.044	0.000	0.000	0.000	0.000
44	A	240	LEU	0	-0.022	0.002	14.975	0.044	0.044	0.000	0.000	0.000	0.000
45	A	241	THR	0	-0.009	0.001	18.213	-0.027	-0.027	0.000	0.000	0.000	0.000
46	A	242	LYS	1	0.885	0.936	21.311	0.172	0.172	0.000	0.000	0.000	0.000
47	A	243	SER	0	-0.026	-0.043	24.278	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	244	ALA	0	0.044	0.013	27.723	0.002	0.002	0.000	0.000	0.000	0.000
49	A	245	ALA	0	-0.047	-0.009	29.201	0.006	0.006	0.000	0.000	0.000	0.000
50	A	246	GLY	0	0.035	0.011	26.979	0.009	0.009	0.000	0.000	0.000	0.000
51	A	247	ILE	0	-0.044	-0.017	20.146	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	248	GLN	0	0.013	0.025	23.307	0.018	0.018	0.000	0.000	0.000	0.000
53	A	249	LEU	0	0.013	0.002	19.123	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	250	ALA	0	-0.025	-0.004	18.677	0.010	0.010	0.000	0.000	0.000	0.000
55	A	251	ALA	0	0.072	0.012	20.024	0.020	0.020	0.000	0.000	0.000	0.000
56	A	252	GLY	0	0.008	0.005	19.330	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	253	LYS	1	0.823	0.915	13.061	0.154	0.154	0.000	0.000	0.000	0.000
58	A	254	SER	0	0.096	0.072	17.271	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	255	GLY	0	-0.047	-0.028	15.562	0.038	0.038	0.000	0.000	0.000	0.000
60	A	256	LEU	0	0.001	0.008	13.518	-0.038	-0.038	0.000	0.000	0.000	0.000
61	A	257	TYR	0	-0.011	-0.044	13.706	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	258	GLN	0	0.016	0.023	13.341	0.055	0.055	0.000	0.000	0.000	0.000
63	A	259	ILE	0	-0.013	-0.026	15.192	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	260	THR	0	0.006	0.000	18.245	0.022	0.022	0.000	0.000	0.000	0.000
65	A	261	MET	0	-0.049	0.002	20.159	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	262	THR	0	-0.038	-0.021	22.966	0.009	0.009	0.000	0.000	0.000	0.000
67	A	263	VAL	0	0.039	0.018	25.530	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	264	LYS	1	0.886	0.964	28.875	0.042	0.042	0.000	0.000	0.000	0.000
69	A	265	ASN	0	0.120	0.039	31.329	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	266	ASN	0	0.036	-0.015	34.031	0.005	0.005	0.000	0.000	0.000	0.000
71	A	267	THR	0	0.009	0.021	36.700	0.001	0.001	0.000	0.000	0.000	0.000
72	A	268	VAL	0	0.004	0.023	38.333	0.002	0.002	0.000	0.000	0.000	0.000
73	A	269	THR	0	-0.035	-0.008	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	0.065	0.045	40.254	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	272	ASN	0	-0.043	-0.035	36.746	0.002	0.002	0.000	0.000	0.000	0.000
77	A	273	TYR	0	-0.004	-0.010	32.862	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	274	LEU	0	-0.007	-0.005	33.592	0.005	0.005	0.000	0.000	0.000	0.000
79	A	275	LEU	0	-0.024	-0.016	27.363	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	276	ARG	1	0.904	0.940	29.238	0.005	0.005	0.000	0.000	0.000	0.000
81	A	277	VAL	0	-0.003	0.008	23.291	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	278	LYS	1	0.853	0.928	26.707	0.007	0.007	0.000	0.000	0.000	0.000
83	A	279	TYR	0	0.019	-0.016	23.537	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	280	GLY	0	0.026	0.027	26.199	0.010	0.010	0.000	0.000	0.000	0.000
85	A	281	SER	0	-0.051	-0.036	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	-0.944	-0.977	28.596	0.027	0.027	0.000	0.000	0.000	0.000
88	A	284	PHE	0	0.019	0.005	24.832	0.008	0.008	0.000	0.000	0.000	0.000
89	A	285	VAL	0	0.020	-0.004	28.042	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	286	VAL	0	-0.006	-0.003	28.017	0.007	0.007	0.000	0.000	0.000	0.000
91	A	287	ALA	0	0.013	0.014	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	0.051	0.029	33.161	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	290	ALA	0	-0.024	0.004	35.467	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	291	SER	0	0.016	-0.007	36.348	0.001	0.001	0.000	0.000	0.000	0.000
96	A	292	SER	0	-0.010	-0.030	37.350	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	293	LEU	0	-0.005	0.000	35.368	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	294	THR	0	-0.012	0.012	32.437	-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	0.003	-0.030	31.644	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	297	GLY	0	0.034	0.018	29.868	0.006	0.006	0.000	0.000	0.000	0.000
102	A	298	THR	0	-0.069	-0.051	23.605	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	299	ILE	0	0.039	0.036	24.351	0.008	0.008	0.000	0.000	0.000	0.000
104	A	300	SER	0	-0.002	-0.007	19.497	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	301	LEU	0	-0.026	-0.014	19.756	0.012	0.012	0.000	0.000	0.000	0.000
106	A	302	LEU	0	0.040	0.047	14.506	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	303	ILE	0	-0.009	-0.005	17.731	0.007	0.007	0.000	0.000	0.000	0.000
108	A	304	TYR	0	0.024	0.007	17.989	0.023	0.023	0.000	0.000	0.000	0.000
109	A	305	CYS	0	-0.038	-0.008	19.071	-0.020	-0.020	0.000	0.000	0.000	0.000
110	A	306	ASN	0	0.018	0.002	20.294	0.022	0.022	0.000	0.000	0.000	0.000
111	A	307	VAL	0	-0.051	-0.018	20.009	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	308	LEU	0	-0.037	-0.032	22.959	0.007	0.007	0.000	0.000	0.000	0.000
113	A	309	GLY	0	-0.028	-0.014	25.032	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	310	VAL	0	-0.037	-0.012	25.890	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	311	VAL	0	0.068	0.026	26.473	0.002	0.002	0.000	0.000	0.000	0.000
116	A	312	SER	0	-0.018	-0.021	27.728	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	313	LEU	0	-0.048	-0.022	29.211	0.002	0.002	0.000	0.000	0.000	0.000
118	A	314	ASP	-1	-0.738	-0.840	23.690	0.022	0.022	0.000	0.000	0.000	0.000
119	A	315	VAL	0	-0.033	-0.026	24.436	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	316	LEU	0	-0.017	0.000	19.687	0.011	0.011	0.000	0.000	0.000	0.000
121	A	317	LYS	1	0.937	0.972	24.362	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	318	PHE	0	0.056	0.004	21.766	0.007	0.007	0.000	0.000	0.000	0.000
123	A	319	SER	0	0.001	-0.003	27.839	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	320	LEU	0	0.032	0.001	28.955	0.004	0.004	0.000	0.000	0.000	0.000
125	A	321	CYS	0	-0.029	0.020	32.341	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	322	ASN	0	0.011	0.010	35.223	0.003	0.003	0.000	0.000	0.000	0.000
127	A	323	ASP	-1	-0.787	-0.920	37.781	0.001	0.001	0.000	0.000	0.000	0.000
128	A	324	GLY	0	0.012	0.014	40.408	0.001	0.001	0.000	0.000	0.000	0.000
129	A	325	ALA	0	-0.046	-0.030	41.531	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	326	ALA	0	0.002	0.005	40.583	0.000	0.000	0.000	0.000	0.000	0.000
131	A	327	LEU	0	-0.037	-0.010	34.750	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	328	SER	0	0.009	0.000	38.316	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	329	ASN	0	-0.077	-0.045	37.132	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	330	TYR	0	-0.019	-0.010	31.732	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	331	ILE	0	-0.012	0.001	27.712	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	332	ILE	0	-0.001	-0.007	26.570	0.005	0.005	0.000	0.000	0.000	0.000
137	A	333	ASN	0	-0.038	0.000	22.269	-0.024	-0.024	0.000	0.000	0.000	0.000
138	A	334	ILE	0	0.021	0.007	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	0.016	0.014	16.613	0.038	0.038	0.000	0.000	0.000	0.000
141	A	337	ALA	0	0.020	0.003	11.077	-0.070	-0.070	0.000	0.000	0.000	0.000
142	A	338	LYS	1	0.897	0.969	11.980	-0.128	-0.128	0.000	0.000	0.000	0.000
143	A	339	ILE	0	-0.001	-0.019	8.982	-0.060	-0.060	0.000	0.000	0.000	0.000
144	A	340	ASN	0	-0.020	0.017	8.982	0.395	0.395	0.000	0.000	0.000	0.000

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