FMO DATABASE

FMODB ID: 98222

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	OptHSide
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	-1540556.841319
FMO2-HF: Nuclear repulsion	1477422.864102
FMO2-HF: Total energy	-63133.977217
FMO2-MP2: Total energy	-63315.790557

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.
-3.874	0.629	0.969	-2.494	-2.979	-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 : -0.010 / q_NPA : -0.004

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	0.841	0.922	3.857	1.552	3.018	-0.019	-0.733	-0.714	0.002
4	A	294	MET	0	0.024	0.006	6.754	0.222	0.222	0.000	0.000	0.000	0.000
5	A	295	LEU	0	-0.042	-0.014	9.295	0.184	0.184	0.000	0.000	0.000	0.000
6	A	296	ALA	0	0.004	0.004	11.728	0.000	0.000	0.000	0.000	0.000	0.000
7	A	297	THR	0	0.007	0.007	13.638	0.058	0.058	0.000	0.000	0.000	0.000
8	A	298	ILE	0	-0.004	-0.018	12.814	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	299	MET	0	-0.005	0.006	16.582	0.007	0.007	0.000	0.000	0.000	0.000
10	A	300	PHE	0	0.006	-0.006	15.522	0.012	0.012	0.000	0.000	0.000	0.000
11	A	301	THR	0	0.073	0.016	20.659	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	302	ASP	-1	-0.834	-0.916	23.489	0.049	0.049	0.000	0.000	0.000	0.000
13	A	303	ILE	0	0.053	0.048	26.108	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	304	VAL	0	-0.007	0.002	29.605	0.004	0.004	0.000	0.000	0.000	0.000
15	A	305	GLY	0	-0.016	-0.021	32.299	0.001	0.001	0.000	0.000	0.000	0.000
16	A	306	SER	0	0.055	0.033	29.422	0.001	0.001	0.000	0.000	0.000	0.000
17	A	307	THR	0	-0.007	-0.011	32.064	0.001	0.001	0.000	0.000	0.000	0.000
18	A	308	GLN	0	0.000	-0.015	34.013	0.002	0.002	0.000	0.000	0.000	0.000
19	A	309	HIS	0	0.030	0.035	34.457	0.001	0.001	0.000	0.000	0.000	0.000
20	A	310	ALA	0	0.040	0.015	34.082	0.000	0.000	0.000	0.000	0.000	0.000
21	A	311	ALA	0	-0.061	-0.020	36.242	0.001	0.001	0.000	0.000	0.000	0.000
22	A	312	ALA	0	-0.052	-0.026	39.152	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	313	LEU	0	-0.065	-0.038	37.930	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	314	GLY	0	0.011	0.022	39.698	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	315	ASP	-1	-0.843	-0.938	36.022	0.079	0.079	0.000	0.000	0.000	0.000
26	A	316	ASP	-1	-0.933	-0.969	36.533	0.061	0.061	0.000	0.000	0.000	0.000
27	A	317	ARG	1	0.964	0.985	37.880	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	318	TRP	0	-0.008	0.007	30.637	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	319	ARG	1	0.865	0.905	32.310	-0.087	-0.087	0.000	0.000	0.000	0.000
30	A	320	ASP	-1	-0.844	-0.903	33.041	0.050	0.050	0.000	0.000	0.000	0.000
31	A	321	LEU	0	-0.047	-0.014	33.922	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	322	LEU	0	-0.006	-0.009	28.270	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	323	ASP	-1	-0.836	-0.899	29.324	0.078	0.078	0.000	0.000	0.000	0.000
34	A	324	ASN	0	-0.159	-0.093	30.328	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	325	HIS	0	-0.034	-0.041	25.948	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	326	ASP	-1	-0.819	-0.895	25.526	0.066	0.066	0.000	0.000	0.000	0.000
37	A	327	THR	0	-0.066	-0.031	26.089	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	328	ILE	0	-0.016	-0.013	27.814	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	329	VAL	0	0.007	0.002	23.646	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	330	CYS	0	-0.033	-0.013	21.525	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	331	HIS	0	-0.016	0.004	23.680	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	332	GLU	-1	-0.747	-0.872	25.944	-0.045	-0.045	0.000	0.000	0.000	0.000
43	A	333	ILE	0	-0.022	-0.016	19.537	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	334	GLN	0	-0.053	-0.019	21.572	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	335	ARG	1	0.768	0.875	22.610	0.029	0.029	0.000	0.000	0.000	0.000
46	A	336	PHE	0	-0.111	-0.047	23.977	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	337	GLY	0	-0.025	-0.015	20.794	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	338	GLY	0	-0.041	-0.024	18.033	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	339	ARG	1	0.895	0.935	10.320	0.325	0.325	0.000	0.000	0.000	0.000
50	A	340	GLU	-1	-0.868	-0.931	15.365	0.063	0.063	0.000	0.000	0.000	0.000
51	A	341	VAL	0	-0.101	-0.062	11.601	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	342	ASN	0	0.031	-0.003	12.256	-0.051	-0.051	0.000	0.000	0.000	0.000
53	A	343	THR	0	-0.014	0.001	13.920	0.002	0.002	0.000	0.000	0.000	0.000
54	A	344	ALA	0	0.007	0.007	16.519	0.007	0.007	0.000	0.000	0.000	0.000
55	A	345	GLY	0	-0.078	-0.052	19.326	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	346	ASP	-1	-0.916	-0.967	21.326	0.070	0.070	0.000	0.000	0.000	0.000
57	A	347	GLY	0	0.034	0.053	23.077	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	348	PHE	0	0.043	0.016	20.459	0.012	0.012	0.000	0.000	0.000	0.000
59	A	349	VAL	0	-0.012	-0.018	15.244	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	350	ALA	0	0.021	0.022	16.107	0.017	0.017	0.000	0.000	0.000	0.000
61	A	351	THR	0	-0.049	-0.022	12.050	-0.057	-0.057	0.000	0.000	0.000	0.000
62	A	352	PHE	0	0.068	0.032	15.236	0.019	0.019	0.000	0.000	0.000	0.000
63	A	353	THR	0	-0.024	-0.014	14.844	-0.025	-0.025	0.000	0.000	0.000	0.000
64	A	354	SER	0	0.002	0.000	16.929	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	355	PRO	0	0.082	0.027	20.069	0.021	0.021	0.000	0.000	0.000	0.000
66	A	356	SER	0	-0.018	-0.016	21.808	0.028	0.028	0.000	0.000	0.000	0.000
67	A	357	ALA	0	-0.010	-0.005	22.077	0.017	0.017	0.000	0.000	0.000	0.000
68	A	358	ALA	0	0.053	0.037	20.716	0.016	0.016	0.000	0.000	0.000	0.000
69	A	359	ILE	0	-0.028	-0.014	22.685	0.018	0.018	0.000	0.000	0.000	0.000
70	A	360	ALA	0	-0.036	-0.023	26.034	0.012	0.012	0.000	0.000	0.000	0.000
71	A	361	CYS	0	-0.012	0.029	24.150	0.012	0.012	0.000	0.000	0.000	0.000
72	A	362	ALA	0	0.040	-0.005	25.148	0.012	0.012	0.000	0.000	0.000	0.000
73	A	363	ASP	-1	-0.945	-0.971	26.779	-0.051	-0.051	0.000	0.000	0.000	0.000
74	A	364	ASP	-1	-0.812	-0.916	29.614	-0.045	-0.045	0.000	0.000	0.000	0.000
75	A	365	ILE	0	-0.032	-0.013	24.919	0.008	0.008	0.000	0.000	0.000	0.000
76	A	366	VAL	0	-0.059	-0.022	29.443	0.009	0.009	0.000	0.000	0.000	0.000
77	A	367	ASP	-1	-0.782	-0.857	31.786	-0.029	-0.029	0.000	0.000	0.000	0.000
78	A	368	ALA	0	-0.016	-0.005	31.559	0.005	0.005	0.000	0.000	0.000	0.000
79	A	369	VAL	0	-0.010	-0.027	29.993	0.006	0.006	0.000	0.000	0.000	0.000
80	A	370	ALA	0	0.026	0.032	33.256	0.005	0.005	0.000	0.000	0.000	0.000
81	A	371	ALA	0	-0.045	-0.011	36.361	0.003	0.003	0.000	0.000	0.000	0.000
82	A	372	LEU	0	-0.085	-0.046	33.171	0.003	0.003	0.000	0.000	0.000	0.000
83	A	373	GLY	0	-0.030	-0.007	37.437	0.004	0.004	0.000	0.000	0.000	0.000
84	A	374	ILE	0	-0.063	-0.022	32.310	0.002	0.002	0.000	0.000	0.000	0.000
85	A	375	GLU	-1	-0.825	-0.891	34.133	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	376	VAL	0	0.002	-0.001	27.714	0.006	0.006	0.000	0.000	0.000	0.000
87	A	377	ARG	1	0.803	0.910	27.023	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	378	ILE	0	0.040	-0.007	24.130	0.002	0.002	0.000	0.000	0.000	0.000
89	A	379	GLY	0	-0.023	0.009	23.454	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	380	ILE	0	-0.034	-0.007	20.734	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	381	HIS	0	0.004	0.016	16.971	0.017	0.017	0.000	0.000	0.000	0.000
92	A	382	ALA	0	0.026	0.009	16.763	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	383	GLY	0	-0.028	-0.022	15.026	0.037	0.037	0.000	0.000	0.000	0.000
94	A	384	GLU	-1	-0.866	-0.912	9.811	-1.052	-1.052	0.000	0.000	0.000	0.000
95	A	385	VAL	0	-0.056	-0.029	8.733	0.172	0.172	0.000	0.000	0.000	0.000
96	A	386	GLU	-1	-0.904	-0.941	3.756	-0.361	-0.181	0.001	-0.027	-0.154	0.000
97	A	387	VAL	0	0.006	-0.014	4.338	0.787	0.971	-0.001	-0.029	-0.155	0.000
98	A	388	ARG	1	0.872	0.907	2.469	-6.249	-3.648	0.987	-1.682	-1.906	-0.015
99	A	389	ASP	-1	-0.919	-0.958	3.974	-0.458	-0.386	0.001	-0.023	-0.050	0.000
100	A	390	ALA	0	0.017	0.045	6.796	0.083	0.083	0.000	0.000	0.000	0.000
101	A	391	SER	0	-0.016	-0.026	8.971	-0.197	-0.197	0.000	0.000	0.000	0.000
102	A	392	HIS	0	-0.083	-0.036	11.045	0.078	0.078	0.000	0.000	0.000	0.000
103	A	393	GLY	0	0.042	0.025	11.996	-0.050	-0.050	0.000	0.000	0.000	0.000
104	A	394	THR	0	-0.027	-0.014	7.811	0.094	0.094	0.000	0.000	0.000	0.000
105	A	395	ASP	-1	-0.842	-0.912	7.624	0.828	0.828	0.000	0.000	0.000	0.000
106	A	396	VAL	0	0.006	-0.018	7.019	-0.123	-0.123	0.000	0.000	0.000	0.000
107	A	397	ALA	0	-0.012	-0.002	7.182	0.138	0.138	0.000	0.000	0.000	0.000
108	A	398	GLY	0	0.080	0.026	8.570	-0.240	-0.240	0.000	0.000	0.000	0.000
109	A	399	VAL	0	0.001	-0.014	10.672	0.045	0.045	0.000	0.000	0.000	0.000
110	A	400	ALA	0	0.012	0.013	12.890	0.034	0.034	0.000	0.000	0.000	0.000
111	A	401	VAL	0	0.054	0.036	10.957	0.010	0.010	0.000	0.000	0.000	0.000
112	A	402	HIS	0	0.003	0.002	14.085	0.017	0.017	0.000	0.000	0.000	0.000
113	A	403	ILE	0	-0.024	-0.008	16.842	0.012	0.012	0.000	0.000	0.000	0.000
114	A	404	GLY	0	0.011	0.003	17.524	0.009	0.009	0.000	0.000	0.000	0.000
115	A	405	ALA	0	0.041	0.027	18.268	0.011	0.011	0.000	0.000	0.000	0.000
116	A	406	ARG	1	0.841	0.910	20.011	0.007	0.007	0.000	0.000	0.000	0.000
117	A	407	VAL	0	-0.020	-0.014	22.151	0.005	0.005	0.000	0.000	0.000	0.000
118	A	408	CYS	0	-0.007	0.013	22.544	0.006	0.006	0.000	0.000	0.000	0.000
119	A	409	ALA	0	-0.029	-0.013	24.391	0.004	0.004	0.000	0.000	0.000	0.000
120	A	410	LEU	0	-0.077	-0.034	26.423	0.003	0.003	0.000	0.000	0.000	0.000
121	A	411	ALA	0	-0.022	0.003	27.545	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	412	GLY	0	-0.017	-0.013	29.388	0.009	0.009	0.000	0.000	0.000	0.000
123	A	413	PRO	0	-0.025	-0.036	31.855	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	414	SER	0	0.009	-0.019	32.600	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	415	GLU	-1	-0.807	-0.847	31.417	-0.043	-0.043	0.000	0.000	0.000	0.000
126	A	416	VAL	0	0.045	0.017	26.783	0.000	0.000	0.000	0.000	0.000	0.000
127	A	417	LEU	0	-0.086	-0.044	27.103	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	418	VAL	0	0.023	0.003	24.316	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	419	SER	0	0.049	0.002	21.391	0.007	0.007	0.000	0.000	0.000	0.000
130	A	420	SER	0	0.034	-0.008	24.484	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	421	THR	0	-0.016	0.000	20.016	0.000	0.000	0.000	0.000	0.000	0.000
132	A	422	VAL	0	0.028	0.025	21.039	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	423	ARG	1	0.759	0.870	23.389	0.122	0.122	0.000	0.000	0.000	0.000
134	A	424	ASP	-1	-0.883	-0.946	25.428	-0.155	-0.155	0.000	0.000	0.000	0.000
135	A	425	ILE	0	-0.022	-0.008	20.759	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	426	VAL	0	-0.032	0.002	24.280	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	427	ALA	0	0.023	0.024	26.915	0.019	0.019	0.000	0.000	0.000	0.000
138	A	428	GLY	0	-0.007	-0.009	29.849	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	429	SER	0	-0.045	-0.018	29.262	0.009	0.009	0.000	0.000	0.000	0.000
140	A	430	ARG	1	0.988	0.988	31.046	0.099	0.099	0.000	0.000	0.000	0.000
141	A	431	HIS	0	0.018	0.015	28.053	0.015	0.015	0.000	0.000	0.000	0.000
142	A	432	ARG	1	0.869	0.927	32.443	0.091	0.091	0.000	0.000	0.000	0.000
143	A	433	PHE	0	0.061	0.018	28.381	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	434	ALA	0	0.017	0.030	33.487	0.001	0.001	0.000	0.000	0.000	0.000
145	A	435	GLU	-1	-0.834	-0.909	31.765	-0.099	-0.099	0.000	0.000	0.000	0.000
146	A	436	ARG	1	0.819	0.884	31.909	0.048	0.048	0.000	0.000	0.000	0.000
147	A	437	GLY	0	0.009	-0.005	33.216	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	438	GLU	-1	-0.876	-0.937	29.770	-0.089	-0.089	0.000	0.000	0.000	0.000
149	A	439	GLN	0	-0.070	-0.028	28.731	0.013	0.013	0.000	0.000	0.000	0.000
150	A	440	GLU	-1	-0.823	-0.893	27.099	-0.053	-0.053	0.000	0.000	0.000	0.000
151	A	441	LEU	0	0.024	0.027	22.401	0.010	0.010	0.000	0.000	0.000	0.000
152	A	442	LYS	1	0.986	0.969	24.060	-0.016	-0.016	0.000	0.000	0.000	0.000
153	A	443	GLY	0	-0.002	-0.006	22.376	0.010	0.010	0.000	0.000	0.000	0.000
154	A	444	VAL	0	-0.003	0.000	19.318	0.002	0.002	0.000	0.000	0.000	0.000
155	A	445	PRO	0	-0.012	0.004	18.686	0.004	0.004	0.000	0.000	0.000	0.000
156	A	446	GLY	0	0.028	0.008	21.877	-0.013	-0.013	0.000	0.000	0.000	0.000
157	A	447	ARG	1	0.763	0.866	24.511	0.075	0.075	0.000	0.000	0.000	0.000
158	A	448	TRP	0	-0.005	-0.009	19.868	-0.018	-0.018	0.000	0.000	0.000	0.000
159	A	449	ARG	1	0.931	0.959	26.440	0.127	0.127	0.000	0.000	0.000	0.000
160	A	450	LEU	0	-0.019	-0.006	25.358	-0.011	-0.011	0.000	0.000	0.000	0.000
161	A	451	CYS	0	-0.057	-0.039	28.273	0.005	0.005	0.000	0.000	0.000	0.000
162	A	452	VAL	0	0.059	0.043	29.234	-0.003	-0.003	0.000	0.000	0.000	0.000
163	A	453	LEU	0	0.011	0.002	29.503	-0.004	-0.004	0.000	0.000	0.000	0.000
164	A	454	MET	0	-0.110	-0.061	31.890	0.008	0.008	0.000	0.000	0.000	0.000
165	A	455	ARG	1	0.784	0.849	32.679	0.038	0.038	0.000	0.000	0.000	0.000
166	A	456	ASP	-1	-0.967	-0.983	35.877	-0.048	-0.048	0.000	0.000	0.000	0.000
167	A	457	ASP	-1	-0.965	-0.966	38.754	-0.024	-0.024	0.000	0.000	0.000	0.000

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