FMO DATABASE

FMODB ID: MN22Z

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	OptAll
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	-1542718.02323
FMO2-HF: Nuclear repulsion	1479583.439491
FMO2-HF: Total energy	-63134.583739
FMO2-MP2: Total energy	-63316.360703

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.
-8.057	-5.861	7.52	-4.617	-5.098	-0.037

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 : -0.010

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	0.830	0.903	3.876	1.625	2.781	-0.010	-0.546	-0.600	0.002
4	A	294	MET	0	0.016	0.010	6.210	0.421	0.421	0.000	0.000	0.000	0.000
5	A	295	LEU	0	-0.040	-0.013	9.125	0.185	0.185	0.000	0.000	0.000	0.000
6	A	296	ALA	0	0.029	0.015	11.205	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	297	THR	0	-0.015	-0.010	13.206	0.077	0.077	0.000	0.000	0.000	0.000
8	A	298	ILE	0	-0.012	-0.017	12.265	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	299	MET	0	-0.010	0.002	16.051	0.011	0.011	0.000	0.000	0.000	0.000
10	A	300	PHE	0	0.015	0.003	15.244	0.011	0.011	0.000	0.000	0.000	0.000
11	A	301	THR	0	0.035	0.005	20.323	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	302	ASP	-1	-0.803	-0.884	23.417	0.055	0.055	0.000	0.000	0.000	0.000
13	A	303	ILE	0	0.069	0.053	25.919	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	304	VAL	0	-0.013	-0.008	29.292	0.005	0.005	0.000	0.000	0.000	0.000
15	A	305	GLY	0	-0.007	0.004	31.684	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	306	SER	0	0.015	0.007	28.812	0.000	0.000	0.000	0.000	0.000	0.000
17	A	307	THR	0	-0.004	-0.009	31.482	0.000	0.000	0.000	0.000	0.000	0.000
18	A	308	GLN	0	-0.030	-0.024	33.509	0.000	0.000	0.000	0.000	0.000	0.000
19	A	309	HIS	0	0.020	0.021	33.801	0.000	0.000	0.000	0.000	0.000	0.000
20	A	310	ALA	0	0.044	0.019	33.749	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	311	ALA	0	-0.063	-0.026	35.885	0.000	0.000	0.000	0.000	0.000	0.000
22	A	312	ALA	0	-0.036	-0.014	38.948	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	313	LEU	0	-0.058	-0.035	36.972	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	314	GLY	0	0.013	0.015	39.356	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	315	ASP	-1	-0.839	-0.929	35.285	0.086	0.086	0.000	0.000	0.000	0.000
26	A	316	ASP	-1	-0.913	-0.958	35.733	0.065	0.065	0.000	0.000	0.000	0.000
27	A	317	ARG	1	0.933	0.963	36.578	-0.039	-0.039	0.000	0.000	0.000	0.000
28	A	318	TRP	0	-0.006	0.001	29.883	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	319	ARG	1	0.794	0.895	31.511	-0.089	-0.089	0.000	0.000	0.000	0.000
30	A	320	ASP	-1	-0.857	-0.916	32.361	0.048	0.048	0.000	0.000	0.000	0.000
31	A	321	LEU	0	-0.032	-0.013	33.338	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	322	LEU	0	0.005	0.009	27.061	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	323	ASP	-1	-0.859	-0.931	28.804	0.077	0.077	0.000	0.000	0.000	0.000
34	A	324	ASN	0	-0.113	-0.064	29.388	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	325	HIS	0	-0.022	-0.033	25.381	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	326	ASP	-1	-0.830	-0.910	24.932	0.066	0.066	0.000	0.000	0.000	0.000
37	A	327	THR	0	-0.074	-0.047	25.200	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	328	ILE	0	-0.027	-0.008	27.029	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	329	VAL	0	0.011	0.010	22.595	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	330	CYS	0	-0.051	-0.026	20.520	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	331	HIS	0	-0.016	0.007	22.636	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	332	GLU	-1	-0.729	-0.877	25.087	-0.052	-0.052	0.000	0.000	0.000	0.000
43	A	333	ILE	0	-0.031	-0.024	18.511	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	334	GLN	0	-0.046	-0.023	21.037	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	335	ARG	1	0.727	0.838	22.136	0.037	0.037	0.000	0.000	0.000	0.000
46	A	336	PHE	0	-0.091	-0.031	23.107	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	337	GLY	0	-0.039	-0.020	20.444	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	338	GLY	0	-0.023	-0.010	17.348	-0.044	-0.044	0.000	0.000	0.000	0.000
49	A	339	ARG	1	0.787	0.863	8.965	0.488	0.488	0.000	0.000	0.000	0.000
50	A	340	GLU	-1	-0.807	-0.905	14.365	0.029	0.029	0.000	0.000	0.000	0.000
51	A	341	VAL	0	-0.082	-0.049	10.944	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	342	ASN	0	-0.048	-0.044	10.347	-0.123	-0.123	0.000	0.000	0.000	0.000
53	A	343	THR	0	-0.047	-0.015	13.154	0.018	0.018	0.000	0.000	0.000	0.000
54	A	344	ALA	0	0.000	-0.010	16.200	0.018	0.018	0.000	0.000	0.000	0.000
55	A	345	GLY	0	-0.038	-0.020	19.266	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	346	ASP	-1	-0.877	-0.925	21.537	0.070	0.070	0.000	0.000	0.000	0.000
57	A	347	GLY	0	0.041	0.028	22.864	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	348	PHE	0	0.013	0.010	19.823	0.017	0.017	0.000	0.000	0.000	0.000
59	A	349	VAL	0	-0.032	-0.029	15.079	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	350	ALA	0	0.018	0.023	15.398	0.015	0.015	0.000	0.000	0.000	0.000
61	A	351	THR	0	-0.052	-0.028	11.372	-0.064	-0.064	0.000	0.000	0.000	0.000
62	A	352	PHE	0	0.060	0.023	14.571	0.013	0.013	0.000	0.000	0.000	0.000
63	A	353	THR	0	-0.010	-0.009	14.850	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	354	SER	0	0.005	0.002	16.685	0.002	0.002	0.000	0.000	0.000	0.000
65	A	355	PRO	0	0.077	0.037	19.470	0.023	0.023	0.000	0.000	0.000	0.000
66	A	356	SER	0	-0.010	-0.012	21.335	0.032	0.032	0.000	0.000	0.000	0.000
67	A	357	ALA	0	0.019	0.014	21.711	0.021	0.021	0.000	0.000	0.000	0.000
68	A	358	ALA	0	0.033	0.023	20.018	0.017	0.017	0.000	0.000	0.000	0.000
69	A	359	ILE	0	-0.006	-0.018	21.966	0.020	0.020	0.000	0.000	0.000	0.000
70	A	360	ALA	0	-0.057	-0.026	25.355	0.014	0.014	0.000	0.000	0.000	0.000
71	A	361	CYS	0	-0.032	0.010	23.313	0.013	0.013	0.000	0.000	0.000	0.000
72	A	362	ALA	0	0.039	-0.002	24.558	0.013	0.013	0.000	0.000	0.000	0.000
73	A	363	ASP	-1	-0.918	-0.959	26.083	-0.057	-0.057	0.000	0.000	0.000	0.000
74	A	364	ASP	-1	-0.825	-0.904	28.535	-0.054	-0.054	0.000	0.000	0.000	0.000
75	A	365	ILE	0	0.004	-0.005	24.050	0.009	0.009	0.000	0.000	0.000	0.000
76	A	366	VAL	0	-0.045	-0.012	28.562	0.010	0.010	0.000	0.000	0.000	0.000
77	A	367	ASP	-1	-0.793	-0.864	31.205	-0.033	-0.033	0.000	0.000	0.000	0.000
78	A	368	ALA	0	-0.024	-0.008	30.450	0.006	0.006	0.000	0.000	0.000	0.000
79	A	369	VAL	0	-0.016	-0.029	28.857	0.007	0.007	0.000	0.000	0.000	0.000
80	A	370	ALA	0	0.028	0.033	32.153	0.006	0.006	0.000	0.000	0.000	0.000
81	A	371	ALA	0	-0.045	-0.017	35.436	0.003	0.003	0.000	0.000	0.000	0.000
82	A	372	LEU	0	-0.061	-0.026	32.137	0.003	0.003	0.000	0.000	0.000	0.000
83	A	373	GLY	0	-0.050	-0.017	36.402	0.004	0.004	0.000	0.000	0.000	0.000
84	A	374	ILE	0	-0.052	-0.024	31.991	0.003	0.003	0.000	0.000	0.000	0.000
85	A	375	GLU	-1	-0.831	-0.891	33.907	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	376	VAL	0	-0.002	-0.006	27.412	0.007	0.007	0.000	0.000	0.000	0.000
87	A	377	ARG	1	0.776	0.887	26.556	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	378	ILE	0	0.028	-0.004	23.709	0.002	0.002	0.000	0.000	0.000	0.000
89	A	379	GLY	0	-0.023	0.001	23.066	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	380	ILE	0	-0.027	-0.010	20.416	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	381	HIS	0	0.011	0.021	16.543	0.023	0.023	0.000	0.000	0.000	0.000
92	A	382	ALA	0	0.040	0.009	16.374	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	383	GLY	0	-0.028	-0.019	14.844	0.049	0.049	0.000	0.000	0.000	0.000
94	A	384	GLU	-1	-0.869	-0.916	9.503	-1.078	-1.078	0.000	0.000	0.000	0.000
95	A	385	VAL	0	-0.050	-0.023	8.171	0.221	0.221	0.000	0.000	0.000	0.000
96	A	386	GLU	-1	-0.877	-0.925	3.141	0.067	0.440	0.035	-0.080	-0.327	0.000
97	A	387	VAL	0	0.031	0.003	3.976	0.848	1.309	0.001	-0.192	-0.270	0.000
98	A	388	ARG	1	0.830	0.891	1.993	-11.889	-11.697	7.470	-3.874	-3.788	-0.039
99	A	389	ASP	-1	-0.764	-0.841	3.372	-0.516	-0.502	0.024	0.075	-0.113	0.000
100	A	390	ALA	0	0.021	0.018	6.287	0.390	0.390	0.000	0.000	0.000	0.000
101	A	391	SER	0	-0.042	-0.035	8.711	-0.169	-0.169	0.000	0.000	0.000	0.000
102	A	392	HIS	0	-0.037	-0.010	10.105	0.097	0.097	0.000	0.000	0.000	0.000
103	A	393	GLY	0	0.048	0.036	11.725	-0.039	-0.039	0.000	0.000	0.000	0.000
104	A	394	THR	0	-0.041	-0.036	7.289	0.221	0.221	0.000	0.000	0.000	0.000
105	A	395	ASP	-1	-0.803	-0.885	6.638	1.201	1.201	0.000	0.000	0.000	0.000
106	A	396	VAL	0	0.005	-0.012	6.292	-0.279	-0.279	0.000	0.000	0.000	0.000
107	A	397	ALA	0	-0.020	0.006	6.614	0.187	0.187	0.000	0.000	0.000	0.000
108	A	398	GLY	0	0.075	0.027	7.793	-0.313	-0.313	0.000	0.000	0.000	0.000
109	A	399	VAL	0	-0.009	-0.016	10.079	0.052	0.052	0.000	0.000	0.000	0.000
110	A	400	ALA	0	0.016	0.006	12.641	0.040	0.040	0.000	0.000	0.000	0.000
111	A	401	VAL	0	0.065	0.039	10.721	0.007	0.007	0.000	0.000	0.000	0.000
112	A	402	HIS	0	0.025	0.009	13.872	0.007	0.007	0.000	0.000	0.000	0.000
113	A	403	ILE	0	-0.032	-0.010	16.585	0.011	0.011	0.000	0.000	0.000	0.000
114	A	404	GLY	0	0.024	0.012	17.194	0.010	0.010	0.000	0.000	0.000	0.000
115	A	405	ALA	0	0.041	0.028	17.942	0.012	0.012	0.000	0.000	0.000	0.000
116	A	406	ARG	1	0.824	0.901	19.675	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	407	VAL	0	-0.033	-0.019	21.801	0.005	0.005	0.000	0.000	0.000	0.000
118	A	408	CYS	0	0.001	0.006	21.965	0.006	0.006	0.000	0.000	0.000	0.000
119	A	409	ALA	0	-0.024	-0.015	23.825	0.004	0.004	0.000	0.000	0.000	0.000
120	A	410	LEU	0	-0.074	-0.033	25.830	0.003	0.003	0.000	0.000	0.000	0.000
121	A	411	ALA	0	-0.026	0.007	27.204	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	412	GLY	0	-0.010	-0.017	28.990	0.009	0.009	0.000	0.000	0.000	0.000
123	A	413	PRO	0	-0.022	-0.028	31.531	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	414	SER	0	0.020	-0.009	32.635	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	415	GLU	-1	-0.813	-0.845	30.824	-0.045	-0.045	0.000	0.000	0.000	0.000
126	A	416	VAL	0	0.054	0.020	26.404	0.000	0.000	0.000	0.000	0.000	0.000
127	A	417	LEU	0	-0.074	-0.028	26.538	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	418	VAL	0	0.010	0.003	24.404	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	419	SER	0	0.024	-0.024	21.060	0.008	0.008	0.000	0.000	0.000	0.000
130	A	420	SER	0	-0.043	-0.037	24.133	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	421	THR	0	-0.006	0.000	19.615	0.000	0.000	0.000	0.000	0.000	0.000
132	A	422	VAL	0	0.020	0.027	20.600	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	423	ARG	1	0.771	0.859	22.886	0.123	0.123	0.000	0.000	0.000	0.000
134	A	424	ASP	-1	-0.829	-0.906	25.349	-0.154	-0.154	0.000	0.000	0.000	0.000
135	A	425	ILE	0	-0.032	-0.016	20.899	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	426	VAL	0	-0.031	-0.005	24.172	-0.007	-0.007	0.000	0.000	0.000	0.000
137	A	427	ALA	0	0.002	0.010	26.681	0.018	0.018	0.000	0.000	0.000	0.000
138	A	428	GLY	0	0.005	0.003	29.900	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	429	SER	0	-0.042	-0.018	28.664	0.009	0.009	0.000	0.000	0.000	0.000
140	A	430	ARG	1	0.996	0.984	30.441	0.109	0.109	0.000	0.000	0.000	0.000
141	A	431	HIS	0	-0.015	0.010	27.201	0.017	0.017	0.000	0.000	0.000	0.000
142	A	432	ARG	1	0.848	0.913	31.656	0.100	0.100	0.000	0.000	0.000	0.000
143	A	433	PHE	0	0.073	0.021	28.019	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	434	ALA	0	0.012	0.021	33.241	0.002	0.002	0.000	0.000	0.000	0.000
145	A	435	GLU	-1	-0.794	-0.889	30.774	-0.104	-0.104	0.000	0.000	0.000	0.000
146	A	436	ARG	1	0.804	0.870	31.267	0.049	0.049	0.000	0.000	0.000	0.000
147	A	437	GLY	0	0.008	-0.005	32.249	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	438	GLU	-1	-0.886	-0.934	29.152	-0.085	-0.085	0.000	0.000	0.000	0.000
149	A	439	GLN	0	-0.007	-0.008	28.126	0.013	0.013	0.000	0.000	0.000	0.000
150	A	440	GLU	-1	-0.766	-0.853	26.558	-0.052	-0.052	0.000	0.000	0.000	0.000
151	A	441	LEU	0	0.033	0.025	21.935	0.011	0.011	0.000	0.000	0.000	0.000
152	A	442	LYS	1	0.937	0.952	23.033	-0.018	-0.018	0.000	0.000	0.000	0.000
153	A	443	GLY	0	0.008	0.002	21.693	0.013	0.013	0.000	0.000	0.000	0.000
154	A	444	VAL	0	0.000	0.013	18.676	0.005	0.005	0.000	0.000	0.000	0.000
155	A	445	PRO	0	-0.014	-0.009	18.759	0.004	0.004	0.000	0.000	0.000	0.000
156	A	446	GLY	0	0.023	0.014	21.666	-0.013	-0.013	0.000	0.000	0.000	0.000
157	A	447	ARG	1	0.707	0.818	24.337	0.071	0.071	0.000	0.000	0.000	0.000
158	A	448	TRP	0	0.006	-0.005	19.401	-0.022	-0.022	0.000	0.000	0.000	0.000
159	A	449	ARG	1	0.915	0.965	25.991	0.133	0.133	0.000	0.000	0.000	0.000
160	A	450	LEU	0	0.003	0.008	24.997	-0.013	-0.013	0.000	0.000	0.000	0.000
161	A	451	CYS	0	-0.043	-0.019	27.991	0.005	0.005	0.000	0.000	0.000	0.000
162	A	452	VAL	0	0.047	0.029	28.965	-0.003	-0.003	0.000	0.000	0.000	0.000
163	A	453	LEU	0	0.016	-0.006	28.700	-0.004	-0.004	0.000	0.000	0.000	0.000
164	A	454	MET	0	-0.110	-0.052	31.542	0.009	0.009	0.000	0.000	0.000	0.000
165	A	455	ARG	1	0.771	0.833	32.450	0.041	0.041	0.000	0.000	0.000	0.000
166	A	456	ASP	-1	-0.977	-0.974	35.292	-0.052	-0.052	0.000	0.000	0.000	0.000
167	A	457	ASP	-1	-0.933	-0.950	37.732	-0.028	-0.028	0.000	0.000	0.000	0.000

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