FMO DATABASE

FMODB ID: 6NN8Z

Calculation Name: 4YO3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YO3

Chain ID: A

ChEMBL ID:

UniProt ID: D3GUX1

Base Structure: X-ray

Registration Date: 2023-06-21

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	157
LigandCharge	DAR=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1583018.023669
FMO2-HF: Nuclear repulsion	1520453.38286
FMO2-HF: Total energy	-62564.640809
FMO2-MP2: Total energy	-62748.184845

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:221:SER)

Summations of interaction energy for fragment #1(A:221:SER)

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.
-4.675	-7.189	15.078	-6.749	-5.818	-0.022

Interaction energy analysis for fragmet #1(A:221:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.012

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	223	ILE	0	0.000	0.014	3.890	1.055	2.722	-0.015	-0.922	-0.730	0.002
4	A	224	THR	0	0.023	0.017	5.601	-0.057	-0.057	0.000	0.000	0.000	0.000
5	A	225	SER	0	-0.013	-0.012	1.827	-2.863	-9.114	12.374	-3.759	-2.365	-0.027
6	A	226	GLY	0	0.089	0.053	3.782	-1.296	-0.995	0.002	-0.164	-0.139	-0.001
7	A	227	GLN	0	-0.023	-0.035	6.569	0.135	0.135	0.000	0.000	0.000	0.000
8	A	228	GLU	-1	-0.844	-0.917	2.136	-2.649	-1.384	2.715	-1.759	-2.221	0.003
9	A	229	LEU	0	0.005	0.016	4.406	0.735	0.852	-0.001	-0.017	-0.100	0.000
10	A	230	LEU	0	-0.018	-0.011	5.638	0.467	0.467	0.000	0.000	0.000	0.000
11	A	231	SER	0	-0.076	-0.054	6.210	0.276	0.276	0.000	0.000	0.000	0.000
12	A	232	GLN	0	0.077	0.029	3.637	-0.607	-0.220	0.003	-0.128	-0.263	0.001
13	A	233	ALA	0	0.002	0.005	7.219	-0.029	-0.029	0.000	0.000	0.000	0.000
14	A	234	ARG	1	0.928	0.958	10.136	0.189	0.189	0.000	0.000	0.000	0.000
15	A	235	VAL	0	-0.003	0.010	9.288	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	236	LEU	0	0.007	0.013	10.768	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	237	ALA	0	0.000	-0.009	12.950	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	238	LYS	1	0.787	0.865	15.216	-0.118	-0.118	0.000	0.000	0.000	0.000
19	A	239	TYR	0	0.037	0.030	15.696	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	240	LEU	0	-0.005	-0.018	16.726	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	241	ARG	1	0.863	0.933	19.628	0.022	0.022	0.000	0.000	0.000	0.000
22	A	242	ASP	-1	-0.842	-0.889	20.389	0.096	0.096	0.000	0.000	0.000	0.000
23	A	243	GLN	0	-0.076	-0.026	20.997	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	244	PRO	0	0.034	0.016	24.047	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	245	GLU	-1	-0.943	-0.976	27.084	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	246	GLY	0	0.024	0.025	23.884	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	247	TRP	0	-0.009	-0.020	22.857	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	248	LEU	0	0.055	0.022	22.917	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	249	ALA	0	0.010	0.013	20.903	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	250	ALA	0	0.031	0.016	18.628	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	251	HIS	0	-0.019	-0.012	18.446	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	252	ARG	1	0.872	0.904	19.804	0.111	0.111	0.000	0.000	0.000	0.000
33	A	253	LEU	0	0.011	0.028	13.332	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	254	MET	0	-0.018	-0.008	12.571	-0.050	-0.050	0.000	0.000	0.000	0.000
35	A	255	LYS	1	0.858	0.931	16.433	0.122	0.122	0.000	0.000	0.000	0.000
36	A	256	SER	0	0.044	0.027	16.911	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	257	VAL	0	-0.030	-0.007	11.013	-0.043	-0.043	0.000	0.000	0.000	0.000
38	A	258	ARG	1	0.781	0.903	13.533	0.245	0.245	0.000	0.000	0.000	0.000
39	A	259	HIS	0	0.025	-0.007	15.881	0.018	0.018	0.000	0.000	0.000	0.000
40	A	260	ASP	-1	-0.869	-0.918	17.700	-0.256	-0.256	0.000	0.000	0.000	0.000
41	A	261	THR	0	-0.073	-0.033	12.889	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	262	LEU	0	-0.036	-0.013	16.000	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	263	HIS	0	0.049	0.018	16.736	0.056	0.056	0.000	0.000	0.000	0.000
44	A	264	GLN	0	-0.039	-0.011	20.891	0.016	0.016	0.000	0.000	0.000	0.000
45	A	265	LEU	0	0.045	0.001	22.579	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	266	PRO	0	-0.003	0.031	23.913	0.006	0.006	0.000	0.000	0.000	0.000
47	A	267	PRO	0	-0.021	-0.022	19.992	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	268	LEU	0	-0.034	-0.026	22.337	0.003	0.003	0.000	0.000	0.000	0.000
49	A	269	SER	0	0.025	0.001	25.095	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	270	ALA	0	-0.034	-0.002	28.564	0.001	0.001	0.000	0.000	0.000	0.000
51	A	271	ASP	-1	-0.884	-0.946	30.649	-0.071	-0.071	0.000	0.000	0.000	0.000
52	A	272	GLY	0	-0.035	-0.010	33.669	0.005	0.005	0.000	0.000	0.000	0.000
53	A	273	ARG	1	0.909	0.959	30.464	0.064	0.064	0.000	0.000	0.000	0.000
54	A	274	THR	0	0.013	0.004	25.588	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	275	ARG	1	0.933	0.967	20.197	0.187	0.187	0.000	0.000	0.000	0.000
56	A	276	ILE	0	-0.027	-0.009	20.357	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	277	ALA	0	0.056	0.017	22.525	0.013	0.013	0.000	0.000	0.000	0.000
58	A	278	PRO	0	0.000	0.009	23.835	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	279	PRO	0	-0.013	-0.010	24.281	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	280	GLY	0	0.007	0.009	24.825	0.001	0.001	0.000	0.000	0.000	0.000
61	A	281	PRO	0	-0.032	-0.033	27.195	0.002	0.002	0.000	0.000	0.000	0.000
62	A	282	ASP	-1	-0.882	-0.943	27.659	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	283	ARG	1	1.005	0.991	22.997	0.036	0.036	0.000	0.000	0.000	0.000
64	A	284	ARG	1	0.963	0.990	28.003	0.065	0.065	0.000	0.000	0.000	0.000
65	A	285	ALA	0	-0.030	-0.011	30.030	0.001	0.001	0.000	0.000	0.000	0.000
66	A	286	SER	0	-0.042	-0.033	29.696	0.005	0.005	0.000	0.000	0.000	0.000
67	A	287	LEU	0	0.032	0.020	27.202	0.003	0.003	0.000	0.000	0.000	0.000
68	A	288	LYS	1	0.983	0.996	31.501	0.047	0.047	0.000	0.000	0.000	0.000
69	A	289	ARG	1	0.923	0.979	32.352	0.017	0.017	0.000	0.000	0.000	0.000
70	A	290	LEU	0	0.040	0.018	30.803	0.002	0.002	0.000	0.000	0.000	0.000
71	A	291	TYR	0	0.015	0.007	34.812	0.000	0.000	0.000	0.000	0.000	0.000
72	A	292	LEU	0	-0.010	0.006	36.227	0.001	0.001	0.000	0.000	0.000	0.000
73	A	293	GLN	0	-0.052	-0.042	37.276	0.000	0.000	0.000	0.000	0.000	0.000
74	A	294	GLN	0	0.004	0.008	38.219	0.001	0.001	0.000	0.000	0.000	0.000
75	A	295	ASN	0	-0.005	0.013	34.319	0.001	0.001	0.000	0.000	0.000	0.000
76	A	296	TRP	0	0.043	-0.002	33.829	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	297	LEU	0	0.029	0.005	31.008	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	298	SER	0	0.019	0.031	29.764	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	299	LEU	0	-0.024	-0.004	28.770	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	300	LEU	0	-0.016	-0.014	27.509	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	301	GLU	-1	-0.902	-0.951	25.167	0.001	0.001	0.000	0.000	0.000	0.000
82	A	302	GLN	0	0.022	0.012	23.996	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	303	CYS	0	-0.048	-0.028	24.293	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	304	ASP	-1	-0.795	-0.895	20.769	-0.078	-0.078	0.000	0.000	0.000	0.000
85	A	305	ASP	-1	-0.921	-0.953	19.456	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	306	MET	0	-0.098	-0.054	19.514	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	307	PHE	0	-0.035	-0.008	17.849	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	308	ALA	0	0.024	0.014	15.208	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	309	DAR	1	0.912	0.957	15.306	0.063	0.063	0.000	0.000	0.000	0.000
90	A	310	GLY	0	0.037	0.002	17.232	0.022	0.022	0.000	0.000	0.000	0.000
91	A	311	ALA	0	0.046	0.028	17.123	-0.038	-0.038	0.000	0.000	0.000	0.000
92	A	312	SER	0	-0.052	-0.041	17.021	0.002	0.002	0.000	0.000	0.000	0.000
93	A	313	HIS	0	-0.004	-0.014	17.958	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	314	LEU	0	0.073	0.056	21.061	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	315	TRP	0	-0.060	-0.015	23.734	0.010	0.010	0.000	0.000	0.000	0.000
96	A	316	LEU	0	0.050	0.009	26.043	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	317	ASP	-1	-0.769	-0.892	27.894	-0.072	-0.072	0.000	0.000	0.000	0.000
98	A	318	LEU	0	-0.086	-0.042	23.389	0.006	0.006	0.000	0.000	0.000	0.000
99	A	319	GLN	0	0.031	0.016	24.450	0.000	0.000	0.000	0.000	0.000	0.000
100	A	320	TRP	0	0.073	0.050	27.960	0.005	0.005	0.000	0.000	0.000	0.000
101	A	321	TYR	0	-0.007	-0.017	29.689	0.009	0.009	0.000	0.000	0.000	0.000
102	A	322	ILE	0	-0.017	-0.013	24.966	0.006	0.006	0.000	0.000	0.000	0.000
103	A	323	HIS	0	-0.008	0.003	29.494	0.004	0.004	0.000	0.000	0.000	0.000
104	A	324	GLN	0	0.031	0.013	32.184	0.001	0.001	0.000	0.000	0.000	0.000
105	A	325	ALA	0	-0.015	-0.006	31.616	0.005	0.005	0.000	0.000	0.000	0.000
106	A	326	LEU	0	-0.055	-0.045	28.995	0.005	0.005	0.000	0.000	0.000	0.000
107	A	327	LEU	0	0.021	0.019	33.293	0.002	0.002	0.000	0.000	0.000	0.000
108	A	328	GLN	0	-0.006	-0.006	36.862	0.004	0.004	0.000	0.000	0.000	0.000
109	A	329	THR	0	-0.112	-0.032	33.068	0.004	0.004	0.000	0.000	0.000	0.000
110	A	330	GLY	0	0.038	0.021	36.480	0.003	0.003	0.000	0.000	0.000	0.000
111	A	331	LYS	1	0.880	0.954	31.735	0.024	0.024	0.000	0.000	0.000	0.000
112	A	332	GLU	-1	-0.854	-0.947	34.145	-0.044	-0.044	0.000	0.000	0.000	0.000
113	A	333	ASN	0	-0.017	-0.014	32.884	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	334	TYR	0	-0.001	-0.015	28.691	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	335	ALA	0	0.051	0.024	30.440	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	336	ALA	0	0.029	0.017	32.458	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	337	ILE	0	-0.027	-0.013	27.229	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	338	ILE	0	-0.024	-0.006	26.532	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	339	GLN	0	0.076	0.040	28.568	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	340	TYR	0	-0.009	-0.005	29.919	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	341	ASP	-1	-0.849	-0.927	24.982	-0.145	-0.145	0.000	0.000	0.000	0.000
122	A	342	LEU	0	-0.039	-0.016	26.122	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	343	LYS	1	0.898	0.945	27.774	0.085	0.085	0.000	0.000	0.000	0.000
124	A	344	GLY	0	0.027	0.008	27.215	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	345	LEU	0	-0.043	-0.022	22.666	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	346	LEU	0	0.015	-0.004	25.757	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	347	LEU	0	-0.037	0.004	29.039	0.006	0.006	0.000	0.000	0.000	0.000
128	A	348	ARG	1	0.828	0.904	21.286	0.240	0.240	0.000	0.000	0.000	0.000
129	A	349	LEU	0	-0.062	-0.029	22.621	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	350	PRO	0	0.035	0.016	27.195	0.005	0.005	0.000	0.000	0.000	0.000
131	A	351	GLY	0	0.010	-0.001	30.900	0.005	0.005	0.000	0.000	0.000	0.000
132	A	352	LEU	0	-0.009	-0.011	24.554	0.003	0.003	0.000	0.000	0.000	0.000
133	A	353	GLU	-1	-0.913	-0.974	28.601	-0.091	-0.091	0.000	0.000	0.000	0.000
134	A	354	THR	0	-0.001	0.008	31.161	0.006	0.006	0.000	0.000	0.000	0.000
135	A	355	LEU	0	-0.054	0.001	27.468	0.003	0.003	0.000	0.000	0.000	0.000
136	A	356	ALA	0	0.032	0.011	30.358	0.004	0.004	0.000	0.000	0.000	0.000
137	A	357	PHE	0	-0.021	0.006	24.039	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	358	ASN	0	0.017	-0.004	25.754	0.002	0.002	0.000	0.000	0.000	0.000
139	A	359	ASP	-1	-0.899	-0.978	28.857	-0.069	-0.069	0.000	0.000	0.000	0.000
140	A	360	GLY	0	-0.034	-0.018	31.473	0.006	0.006	0.000	0.000	0.000	0.000
141	A	361	MET	0	-0.051	0.001	30.834	0.002	0.002	0.000	0.000	0.000	0.000
142	A	362	PRO	0	0.060	0.026	30.950	-0.007	-0.007	0.000	0.000	0.000	0.000
143	A	363	PHE	0	-0.035	-0.030	25.188	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	364	ALA	0	0.041	0.010	29.407	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	365	ASP	-1	-0.870	-0.929	32.339	-0.060	-0.060	0.000	0.000	0.000	0.000
146	A	366	ASP	-1	-0.887	-0.948	35.608	-0.055	-0.055	0.000	0.000	0.000	0.000
147	A	367	VAL	0	-0.036	-0.017	36.614	0.000	0.000	0.000	0.000	0.000	0.000
148	A	368	THR	0	-0.054	-0.021	33.029	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	369	LEU	0	0.049	0.012	35.070	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	370	SER	0	0.021	0.019	36.109	0.000	0.000	0.000	0.000	0.000	0.000
151	A	371	TRP	0	-0.058	-0.029	30.689	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	372	ILE	0	0.025	0.004	31.634	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	373	GLN	0	0.025	0.008	35.278	0.002	0.002	0.000	0.000	0.000	0.000
154	A	374	GLN	0	-0.048	-0.027	38.138	0.001	0.001	0.000	0.000	0.000	0.000
155	A	375	GLN	0	-0.074	-0.025	37.448	0.003	0.003	0.000	0.000	0.000	0.000
156	A	376	VAL	0	-0.004	0.019	32.407	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	377	MET	0	-0.054	-0.010	34.304	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:221:SER)