FMO DATABASE

FMODB ID: LN669

Calculation Name: 1YBT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YBT

Chain ID: A

ChEMBL ID:

UniProt ID: O07732

Base Structure: X-ray

Registration Date: 2023-09-23

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1540451.2467
FMO2-HF: Nuclear repulsion	1477318.274374
FMO2-HF: Total energy	-63132.972326
FMO2-MP2: Total energy	-63314.84749

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:291:ALA)

Summations of interaction energy for fragment #1(A:291:ALA)

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.
-4.507	0.106	0.58	-2.409	-2.785	-0.013

Interaction energy analysis for fragmet #1(A:291:ALA)

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 : -0.001

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	293	ARG	1	0.933	0.984	3.857	1.703	3.118	-0.019	-0.709	-0.687	0.002
4	A	294	MET	0	0.028	0.011	6.757	0.229	0.229	0.000	0.000	0.000	0.000
5	A	295	LEU	0	-0.025	-0.006	9.308	0.185	0.185	0.000	0.000	0.000	0.000
6	A	296	ALA	0	0.004	0.005	11.850	0.000	0.000	0.000	0.000	0.000	0.000
7	A	297	THR	0	-0.003	0.008	13.661	0.063	0.063	0.000	0.000	0.000	0.000
8	A	298	ILE	0	-0.011	-0.022	12.984	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	299	MET	0	-0.004	0.001	16.604	0.009	0.009	0.000	0.000	0.000	0.000
10	A	300	PHE	0	0.007	0.001	15.687	0.009	0.009	0.000	0.000	0.000	0.000
11	A	301	THR	0	0.064	0.006	20.677	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	302	ASP	-1	-0.905	-0.960	23.507	0.051	0.051	0.000	0.000	0.000	0.000
13	A	303	ILE	0	0.049	0.042	26.124	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	304	VAL	0	-0.041	-0.018	29.622	0.004	0.004	0.000	0.000	0.000	0.000
15	A	305	GLY	0	-0.025	-0.021	32.312	0.001	0.001	0.000	0.000	0.000	0.000
16	A	306	SER	0	0.065	0.038	29.434	0.001	0.001	0.000	0.000	0.000	0.000
17	A	307	THR	0	-0.015	-0.012	32.269	0.002	0.002	0.000	0.000	0.000	0.000
18	A	308	GLN	0	0.025	-0.006	34.022	0.003	0.003	0.000	0.000	0.000	0.000
19	A	309	HIS	0	0.027	0.031	34.626	0.001	0.001	0.000	0.000	0.000	0.000
20	A	310	ALA	0	0.034	0.013	34.128	0.000	0.000	0.000	0.000	0.000	0.000
21	A	311	ALA	0	-0.063	-0.021	36.256	0.002	0.002	0.000	0.000	0.000	0.000
22	A	312	ALA	0	-0.058	-0.030	39.163	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	313	LEU	0	-0.071	-0.034	37.998	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	314	GLY	0	0.018	0.024	39.703	0.000	0.000	0.000	0.000	0.000	0.000
25	A	315	ASP	-1	-0.871	-0.954	35.844	0.077	0.077	0.000	0.000	0.000	0.000
26	A	316	ASP	-1	-0.940	-0.970	36.553	0.060	0.060	0.000	0.000	0.000	0.000
27	A	317	ARG	1	0.979	0.983	37.816	-0.034	-0.034	0.000	0.000	0.000	0.000
28	A	318	TRP	0	-0.017	0.004	30.784	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	319	ARG	1	0.893	0.920	32.413	-0.087	-0.087	0.000	0.000	0.000	0.000
30	A	320	ASP	-1	-0.858	-0.904	32.980	0.048	0.048	0.000	0.000	0.000	0.000
31	A	321	LEU	0	-0.073	-0.033	33.738	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	322	LEU	0	0.020	-0.015	28.731	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	323	ASP	-1	-0.849	-0.901	29.268	0.074	0.074	0.000	0.000	0.000	0.000
34	A	324	ASN	0	-0.097	-0.055	30.277	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	325	HIS	0	-0.027	-0.027	26.079	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	326	ASP	-1	-0.817	-0.910	25.168	0.060	0.060	0.000	0.000	0.000	0.000
37	A	327	THR	0	-0.059	-0.020	26.044	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	328	ILE	0	-0.027	-0.018	27.775	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	329	VAL	0	0.000	-0.002	23.586	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	330	CYS	0	-0.003	-0.003	22.435	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	331	HIS	0	-0.022	-0.009	23.649	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	332	GLU	-1	-0.794	-0.911	25.921	-0.059	-0.059	0.000	0.000	0.000	0.000
43	A	333	ILE	0	-0.017	-0.011	19.472	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	334	GLN	0	-0.063	-0.026	21.576	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	335	ARG	1	0.840	0.931	22.591	0.041	0.041	0.000	0.000	0.000	0.000
46	A	336	PHE	0	-0.119	-0.049	23.844	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	337	GLY	0	-0.021	-0.014	20.790	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	338	GLY	0	-0.050	-0.029	18.022	-0.039	-0.039	0.000	0.000	0.000	0.000
49	A	339	ARG	1	0.900	0.942	11.187	0.339	0.339	0.000	0.000	0.000	0.000
50	A	340	GLU	-1	-0.889	-0.946	15.335	0.059	0.059	0.000	0.000	0.000	0.000
51	A	341	VAL	0	-0.108	-0.063	11.566	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	342	ASN	0	0.029	-0.005	12.337	0.001	0.001	0.000	0.000	0.000	0.000
53	A	343	THR	0	-0.021	-0.003	13.939	0.000	0.000	0.000	0.000	0.000	0.000
54	A	344	ALA	0	0.000	0.004	16.536	0.008	0.008	0.000	0.000	0.000	0.000
55	A	345	GLY	0	-0.085	-0.058	19.344	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	346	ASP	-1	-0.913	-0.968	21.337	0.063	0.063	0.000	0.000	0.000	0.000
57	A	347	GLY	0	0.052	0.070	23.099	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	348	PHE	0	0.042	0.018	20.501	0.011	0.011	0.000	0.000	0.000	0.000
59	A	349	VAL	0	-0.015	-0.015	15.131	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	350	ALA	0	0.023	0.021	16.058	0.015	0.015	0.000	0.000	0.000	0.000
61	A	351	THR	0	-0.067	-0.023	12.175	-0.058	-0.058	0.000	0.000	0.000	0.000
62	A	352	PHE	0	0.068	0.033	15.217	0.020	0.020	0.000	0.000	0.000	0.000
63	A	353	THR	0	-0.021	-0.015	14.858	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	354	SER	0	-0.001	-0.001	16.942	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	355	PRO	0	0.081	0.021	20.047	0.022	0.022	0.000	0.000	0.000	0.000
66	A	356	SER	0	-0.015	-0.012	21.812	0.029	0.029	0.000	0.000	0.000	0.000
67	A	357	ALA	0	-0.022	-0.005	22.022	0.018	0.018	0.000	0.000	0.000	0.000
68	A	358	ALA	0	0.054	0.034	20.676	0.016	0.016	0.000	0.000	0.000	0.000
69	A	359	ILE	0	-0.014	-0.009	22.674	0.019	0.019	0.000	0.000	0.000	0.000
70	A	360	ALA	0	-0.044	-0.026	26.062	0.013	0.013	0.000	0.000	0.000	0.000
71	A	361	CYS	0	0.033	0.037	24.171	0.011	0.011	0.000	0.000	0.000	0.000
72	A	362	ALA	0	0.010	-0.009	25.219	0.013	0.013	0.000	0.000	0.000	0.000
73	A	363	ASP	-1	-0.956	-0.988	26.805	-0.056	-0.056	0.000	0.000	0.000	0.000
74	A	364	ASP	-1	-0.846	-0.928	29.691	-0.050	-0.050	0.000	0.000	0.000	0.000
75	A	365	ILE	0	-0.011	-0.004	24.848	0.008	0.008	0.000	0.000	0.000	0.000
76	A	366	VAL	0	-0.073	-0.028	29.412	0.009	0.009	0.000	0.000	0.000	0.000
77	A	367	ASP	-1	-0.802	-0.897	31.813	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	368	ALA	0	-0.013	-0.006	31.541	0.006	0.006	0.000	0.000	0.000	0.000
79	A	369	VAL	0	-0.027	-0.031	29.995	0.006	0.006	0.000	0.000	0.000	0.000
80	A	370	ALA	0	0.025	0.029	33.214	0.006	0.006	0.000	0.000	0.000	0.000
81	A	371	ALA	0	-0.046	-0.009	36.326	0.003	0.003	0.000	0.000	0.000	0.000
82	A	372	LEU	0	-0.096	-0.053	33.138	0.003	0.003	0.000	0.000	0.000	0.000
83	A	373	GLY	0	-0.028	-0.006	37.390	0.004	0.004	0.000	0.000	0.000	0.000
84	A	374	ILE	0	-0.057	-0.017	32.299	0.002	0.002	0.000	0.000	0.000	0.000
85	A	375	GLU	-1	-0.853	-0.936	34.153	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	376	VAL	0	0.008	0.006	27.864	0.006	0.006	0.000	0.000	0.000	0.000
87	A	377	ARG	1	0.873	0.935	26.986	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	378	ILE	0	0.037	-0.003	24.097	0.001	0.001	0.000	0.000	0.000	0.000
89	A	379	GLY	0	-0.027	0.005	23.466	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	380	ILE	0	-0.022	0.002	20.706	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	381	HIS	0	-0.005	-0.006	16.979	0.017	0.017	0.000	0.000	0.000	0.000
92	A	382	ALA	0	0.025	0.005	16.792	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	383	GLY	0	-0.032	-0.020	15.031	0.040	0.040	0.000	0.000	0.000	0.000
94	A	384	GLU	-1	-0.958	-0.974	9.929	-1.004	-1.004	0.000	0.000	0.000	0.000
95	A	385	VAL	0	-0.058	-0.032	8.401	0.176	0.176	0.000	0.000	0.000	0.000
96	A	386	GLU	-1	-0.973	-0.990	3.777	-0.757	-0.600	0.001	-0.026	-0.132	0.000
97	A	387	VAL	0	0.016	-0.006	4.359	0.806	0.992	-0.001	-0.028	-0.158	0.000
98	A	388	ARG	1	0.928	0.943	2.798	-6.982	-4.205	0.598	-1.622	-1.753	-0.015
99	A	389	ASP	-1	-0.912	-0.960	3.915	-0.237	-0.159	0.001	-0.024	-0.055	0.000
100	A	390	ALA	0	0.020	0.054	6.760	0.121	0.121	0.000	0.000	0.000	0.000
101	A	391	SER	0	-0.026	-0.033	8.926	-0.204	-0.204	0.000	0.000	0.000	0.000
102	A	392	HIS	0	-0.076	-0.043	11.089	0.081	0.081	0.000	0.000	0.000	0.000
103	A	393	GLY	0	0.053	0.040	11.929	-0.050	-0.050	0.000	0.000	0.000	0.000
104	A	394	THR	0	-0.020	-0.011	7.762	0.088	0.088	0.000	0.000	0.000	0.000
105	A	395	ASP	-1	-0.831	-0.911	7.777	0.769	0.769	0.000	0.000	0.000	0.000
106	A	396	VAL	0	0.009	-0.012	7.047	-0.154	-0.154	0.000	0.000	0.000	0.000
107	A	397	ALA	0	-0.029	-0.012	7.201	0.158	0.158	0.000	0.000	0.000	0.000
108	A	398	GLY	0	0.097	0.036	8.564	-0.246	-0.246	0.000	0.000	0.000	0.000
109	A	399	VAL	0	-0.003	-0.013	10.657	0.050	0.050	0.000	0.000	0.000	0.000
110	A	400	ALA	0	0.014	0.009	13.084	0.037	0.037	0.000	0.000	0.000	0.000
111	A	401	VAL	0	0.060	0.038	11.014	0.013	0.013	0.000	0.000	0.000	0.000
112	A	402	HIS	0	-0.007	0.001	13.696	0.022	0.022	0.000	0.000	0.000	0.000
113	A	403	ILE	0	-0.023	-0.014	16.835	0.014	0.014	0.000	0.000	0.000	0.000
114	A	404	GLY	0	0.009	0.003	17.525	0.011	0.011	0.000	0.000	0.000	0.000
115	A	405	ALA	0	0.051	0.033	18.264	0.012	0.012	0.000	0.000	0.000	0.000
116	A	406	ARG	1	0.877	0.929	20.014	0.017	0.017	0.000	0.000	0.000	0.000
117	A	407	VAL	0	-0.020	-0.010	22.153	0.006	0.006	0.000	0.000	0.000	0.000
118	A	408	CYS	0	0.019	0.030	22.689	0.007	0.007	0.000	0.000	0.000	0.000
119	A	409	ALA	0	-0.023	-0.010	24.390	0.005	0.005	0.000	0.000	0.000	0.000
120	A	410	LEU	0	-0.083	-0.038	26.427	0.003	0.003	0.000	0.000	0.000	0.000
121	A	411	ALA	0	-0.023	0.003	27.589	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	412	GLY	0	-0.018	-0.001	29.397	0.009	0.009	0.000	0.000	0.000	0.000
123	A	413	PRO	0	-0.024	-0.032	31.869	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	414	SER	0	0.029	0.019	32.600	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	415	GLU	-1	-0.862	-0.915	31.241	-0.048	-0.048	0.000	0.000	0.000	0.000
126	A	416	VAL	0	0.036	0.019	26.865	0.000	0.000	0.000	0.000	0.000	0.000
127	A	417	LEU	0	-0.083	-0.044	27.086	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	418	VAL	0	0.037	0.011	24.438	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	419	SER	0	0.035	0.012	21.425	0.009	0.009	0.000	0.000	0.000	0.000
130	A	420	SER	0	-0.010	-0.028	24.490	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	421	THR	0	0.038	0.018	20.032	0.001	0.001	0.000	0.000	0.000	0.000
132	A	422	VAL	0	0.026	0.028	21.209	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	423	ARG	1	0.809	0.902	23.403	0.128	0.128	0.000	0.000	0.000	0.000
134	A	424	ASP	-1	-0.927	-0.979	25.166	-0.172	-0.172	0.000	0.000	0.000	0.000
135	A	425	ILE	0	-0.040	-0.014	20.920	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	426	VAL	0	-0.047	-0.010	24.296	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	427	ALA	0	0.023	0.014	26.937	0.020	0.020	0.000	0.000	0.000	0.000
138	A	428	GLY	0	-0.013	-0.013	29.867	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	429	SER	0	-0.040	-0.002	29.307	0.010	0.010	0.000	0.000	0.000	0.000
140	A	430	ARG	1	0.981	0.974	30.704	0.110	0.110	0.000	0.000	0.000	0.000
141	A	431	HIS	0	0.018	0.013	28.614	0.014	0.014	0.000	0.000	0.000	0.000
142	A	432	ARG	1	0.896	0.950	32.466	0.095	0.095	0.000	0.000	0.000	0.000
143	A	433	PHE	0	0.047	0.015	28.601	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	434	ALA	0	0.011	0.025	33.502	0.002	0.002	0.000	0.000	0.000	0.000
145	A	435	GLU	-1	-0.898	-0.955	31.749	-0.099	-0.099	0.000	0.000	0.000	0.000
146	A	436	ARG	1	0.884	0.953	32.438	0.055	0.055	0.000	0.000	0.000	0.000
147	A	437	GLY	0	0.026	0.006	33.217	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	438	GLU	-1	-0.921	-0.980	29.295	-0.103	-0.103	0.000	0.000	0.000	0.000
149	A	439	GLN	0	-0.068	-0.037	28.713	0.015	0.015	0.000	0.000	0.000	0.000
150	A	440	GLU	-1	-0.930	-0.959	27.089	-0.052	-0.052	0.000	0.000	0.000	0.000
151	A	441	LEU	0	0.018	0.023	22.419	0.010	0.010	0.000	0.000	0.000	0.000
152	A	442	LYS	1	0.993	0.974	24.043	-0.015	-0.015	0.000	0.000	0.000	0.000
153	A	443	GLY	0	-0.024	-0.015	22.355	0.010	0.010	0.000	0.000	0.000	0.000
154	A	444	VAL	0	-0.006	-0.002	19.082	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	445	PRO	0	-0.015	0.005	18.598	0.005	0.005	0.000	0.000	0.000	0.000
156	A	446	GLY	0	0.032	0.007	21.849	-0.014	-0.014	0.000	0.000	0.000	0.000
157	A	447	ARG	1	0.881	0.958	24.492	0.086	0.086	0.000	0.000	0.000	0.000
158	A	448	TRP	0	0.036	0.017	20.029	-0.017	-0.017	0.000	0.000	0.000	0.000
159	A	449	ARG	1	0.968	0.987	26.433	0.135	0.135	0.000	0.000	0.000	0.000
160	A	450	LEU	0	-0.019	-0.002	25.362	-0.012	-0.012	0.000	0.000	0.000	0.000
161	A	451	CYS	0	-0.055	-0.039	28.284	0.005	0.005	0.000	0.000	0.000	0.000
162	A	452	VAL	0	0.057	0.040	29.246	-0.003	-0.003	0.000	0.000	0.000	0.000
163	A	453	LEU	0	0.014	0.008	29.767	-0.004	-0.004	0.000	0.000	0.000	0.000
164	A	454	MET	0	-0.107	-0.063	31.909	0.008	0.008	0.000	0.000	0.000	0.000
165	A	455	ARG	1	0.822	0.909	32.485	0.044	0.044	0.000	0.000	0.000	0.000
166	A	456	ASP	-1	-0.936	-0.973	35.900	-0.053	-0.053	0.000	0.000	0.000	0.000
167	A	457	ASP	-1	-0.994	-0.975	38.784	-0.027	-0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:291:ALA)