FMO DATABASE

FMODB ID: R99V8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1592879.340611
FMO2-HF: Nuclear repulsion	1530313.262094
FMO2-HF: Total energy	-62566.078517
FMO2-MP2: Total energy	-62749.537163

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.
-13.003	-9.598	10.671	-6.53	-7.547	0.005

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 : 0.028 / 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	223	ILE	0	0.007	0.026	3.884	1.076	2.771	-0.017	-0.934	-0.744	0.001
4	A	224	THR	0	-0.006	-0.009	5.031	0.349	0.349	0.000	0.000	0.000	0.000
5	A	225	SER	0	0.016	0.002	2.156	-5.007	-5.125	3.953	-1.899	-1.936	-0.016
6	A	226	GLY	0	0.077	0.043	3.747	-1.153	-0.845	0.002	-0.111	-0.199	-0.001
7	A	227	GLN	0	0.010	-0.018	6.378	0.032	0.032	0.000	0.000	0.000	0.000
8	A	228	GLU	-1	-0.870	-0.902	2.074	-1.755	-0.850	3.657	-2.066	-2.496	0.001
9	A	229	LEU	0	-0.007	0.014	3.940	0.983	1.194	0.006	-0.062	-0.155	0.000
10	A	230	LEU	0	0.030	0.008	4.980	0.580	0.597	-0.001	-0.002	-0.014	0.000
11	A	231	SER	0	-0.079	-0.065	5.760	0.350	0.350	0.000	0.000	0.000	0.000
12	A	232	GLN	0	0.050	0.018	2.112	-7.980	-7.593	3.071	-1.456	-2.003	0.020
13	A	233	ALA	0	0.009	0.002	6.779	-0.219	-0.219	0.000	0.000	0.000	0.000
14	A	234	ARG	1	0.877	0.926	9.436	0.014	0.014	0.000	0.000	0.000	0.000
15	A	235	VAL	0	0.015	0.011	8.881	-0.072	-0.072	0.000	0.000	0.000	0.000
16	A	236	LEU	0	0.008	0.017	10.436	-0.067	-0.067	0.000	0.000	0.000	0.000
17	A	237	ALA	0	0.006	-0.007	12.280	-0.055	-0.055	0.000	0.000	0.000	0.000
18	A	238	LYS	1	0.778	0.859	14.568	-0.258	-0.258	0.000	0.000	0.000	0.000
19	A	239	TYR	0	0.005	0.011	15.128	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	240	LEU	0	-0.004	-0.015	16.251	-0.032	-0.032	0.000	0.000	0.000	0.000
21	A	241	ARG	1	0.779	0.872	18.707	-0.053	-0.053	0.000	0.000	0.000	0.000
22	A	242	ASP	-1	-0.821	-0.878	19.724	0.189	0.189	0.000	0.000	0.000	0.000
23	A	243	GLN	0	-0.056	-0.019	20.201	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	244	PRO	0	0.042	0.025	23.494	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	245	GLU	-1	-0.898	-0.963	26.361	0.015	0.015	0.000	0.000	0.000	0.000
26	A	246	GLY	0	0.003	0.011	23.199	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	247	TRP	0	-0.010	-0.022	22.334	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	248	LEU	0	0.021	0.010	22.732	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	249	ALA	0	0.005	0.004	19.922	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	250	ALA	0	0.008	0.006	18.215	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	251	HIS	0	0.055	0.032	18.121	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	252	ARG	1	0.819	0.868	19.152	0.109	0.109	0.000	0.000	0.000	0.000
33	A	253	LEU	0	0.012	0.032	12.486	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	254	MET	0	-0.023	-0.012	11.998	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	255	LYS	1	0.840	0.917	15.913	0.108	0.108	0.000	0.000	0.000	0.000
36	A	256	SER	0	0.051	0.020	16.682	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	257	VAL	0	-0.029	-0.012	10.340	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	258	ARG	1	0.790	0.899	12.826	0.211	0.211	0.000	0.000	0.000	0.000
39	A	259	HIS	0	0.046	0.023	15.334	0.033	0.033	0.000	0.000	0.000	0.000
40	A	260	ASP	-1	-0.820	-0.900	17.577	-0.288	-0.288	0.000	0.000	0.000	0.000
41	A	261	THR	0	-0.055	-0.032	11.953	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	262	LEU	0	-0.062	-0.024	15.193	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	263	HIS	0	0.017	0.007	17.286	0.069	0.069	0.000	0.000	0.000	0.000
44	A	264	GLN	0	-0.011	-0.002	20.590	0.030	0.030	0.000	0.000	0.000	0.000
45	A	265	LEU	0	0.042	0.012	22.170	0.000	0.000	0.000	0.000	0.000	0.000
46	A	266	PRO	0	-0.009	0.025	24.289	0.005	0.005	0.000	0.000	0.000	0.000
47	A	267	PRO	0	0.015	-0.011	20.012	0.006	0.006	0.000	0.000	0.000	0.000
48	A	268	LEU	0	-0.045	-0.043	22.465	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	269	SER	0	-0.015	-0.010	24.692	0.003	0.003	0.000	0.000	0.000	0.000
50	A	270	ALA	0	-0.018	0.004	28.217	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	271	ASP	-1	-0.856	-0.936	30.602	-0.082	-0.082	0.000	0.000	0.000	0.000
52	A	272	GLY	0	-0.020	0.002	33.510	0.005	0.005	0.000	0.000	0.000	0.000
53	A	273	ARG	1	0.812	0.902	29.892	0.067	0.067	0.000	0.000	0.000	0.000
54	A	274	THR	0	0.040	0.007	25.495	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	275	ARG	1	0.945	0.971	20.052	0.220	0.220	0.000	0.000	0.000	0.000
56	A	276	ILE	0	-0.031	-0.002	20.557	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	277	ALA	0	0.014	-0.001	22.024	0.017	0.017	0.000	0.000	0.000	0.000
58	A	278	PRO	0	0.013	0.017	23.532	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	279	PRO	0	-0.015	-0.021	23.734	0.002	0.002	0.000	0.000	0.000	0.000
60	A	280	GLY	0	0.003	0.023	24.487	0.007	0.007	0.000	0.000	0.000	0.000
61	A	281	PRO	0	-0.036	-0.031	26.750	0.001	0.001	0.000	0.000	0.000	0.000
62	A	282	ASP	-1	-0.862	-0.942	27.526	0.009	0.009	0.000	0.000	0.000	0.000
63	A	283	ARG	1	0.882	0.917	21.718	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	284	ARG	1	0.839	0.910	27.709	0.052	0.052	0.000	0.000	0.000	0.000
65	A	285	ALA	0	0.010	0.009	29.628	0.000	0.000	0.000	0.000	0.000	0.000
66	A	286	SER	0	-0.044	-0.038	29.194	0.003	0.003	0.000	0.000	0.000	0.000
67	A	287	LEU	0	0.016	0.009	26.598	0.002	0.002	0.000	0.000	0.000	0.000
68	A	288	LYS	1	0.950	0.966	30.787	0.040	0.040	0.000	0.000	0.000	0.000
69	A	289	ARG	1	0.899	0.958	31.536	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	290	LEU	0	0.022	0.010	30.197	0.001	0.001	0.000	0.000	0.000	0.000
71	A	291	TYR	0	0.008	0.000	34.245	0.000	0.000	0.000	0.000	0.000	0.000
72	A	292	LEU	0	-0.007	0.009	35.714	0.000	0.000	0.000	0.000	0.000	0.000
73	A	293	GLN	0	-0.046	-0.036	36.243	0.000	0.000	0.000	0.000	0.000	0.000
74	A	294	GLN	0	-0.010	-0.004	37.649	0.002	0.002	0.000	0.000	0.000	0.000
75	A	295	ASN	0	0.015	0.026	33.636	0.001	0.001	0.000	0.000	0.000	0.000
76	A	296	TRP	0	0.046	0.003	33.187	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	297	LEU	0	0.024	0.017	30.505	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	298	SER	0	0.002	-0.023	29.191	0.000	0.000	0.000	0.000	0.000	0.000
79	A	299	LEU	0	-0.028	-0.017	28.461	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	300	LEU	0	0.013	0.016	26.651	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	301	GLU	-1	-0.863	-0.907	24.634	0.044	0.044	0.000	0.000	0.000	0.000
82	A	302	GLN	0	0.042	0.027	23.506	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	303	CYS	0	-0.045	-0.022	24.114	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	304	ASP	-1	-0.758	-0.859	20.498	-0.038	-0.038	0.000	0.000	0.000	0.000
85	A	305	ASP	-1	-0.829	-0.887	19.362	0.044	0.044	0.000	0.000	0.000	0.000
86	A	306	MET	0	-0.054	-0.024	19.383	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	307	PHE	0	-0.024	-0.007	17.273	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	308	ALA	0	0.017	0.014	15.319	-0.040	-0.040	0.000	0.000	0.000	0.000
89	A	309	DAR	1	0.917	0.963	14.967	0.027	0.027	0.000	0.000	0.000	0.000
90	A	310	GLY	0	0.037	0.017	17.291	0.013	0.013	0.000	0.000	0.000	0.000
91	A	311	ALA	0	0.004	0.005	16.804	-0.037	-0.037	0.000	0.000	0.000	0.000
92	A	312	SER	0	-0.005	-0.029	16.306	0.002	0.002	0.000	0.000	0.000	0.000
93	A	313	HIS	0	-0.015	-0.018	17.348	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	314	LEU	0	0.044	0.041	20.324	0.005	0.005	0.000	0.000	0.000	0.000
95	A	315	TRP	0	-0.024	-0.002	22.990	0.012	0.012	0.000	0.000	0.000	0.000
96	A	316	LEU	0	0.060	0.024	25.106	0.006	0.006	0.000	0.000	0.000	0.000
97	A	317	ASP	-1	-0.748	-0.868	27.086	-0.056	-0.056	0.000	0.000	0.000	0.000
98	A	318	LEU	0	-0.086	-0.032	22.933	0.008	0.008	0.000	0.000	0.000	0.000
99	A	319	GLN	0	0.003	-0.004	24.020	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	320	TRP	0	0.075	0.052	27.352	0.006	0.006	0.000	0.000	0.000	0.000
101	A	321	TYR	0	-0.009	-0.002	29.148	0.007	0.007	0.000	0.000	0.000	0.000
102	A	322	ILE	0	-0.012	-0.010	24.331	0.006	0.006	0.000	0.000	0.000	0.000
103	A	323	HIS	0	-0.015	-0.006	28.847	0.003	0.003	0.000	0.000	0.000	0.000
104	A	324	GLN	0	0.044	0.019	31.529	0.002	0.002	0.000	0.000	0.000	0.000
105	A	325	ALA	0	-0.019	-0.007	30.819	0.005	0.005	0.000	0.000	0.000	0.000
106	A	326	LEU	0	-0.035	-0.026	28.370	0.005	0.005	0.000	0.000	0.000	0.000
107	A	327	LEU	0	0.014	0.015	32.661	0.003	0.003	0.000	0.000	0.000	0.000
108	A	328	GLN	0	-0.004	0.000	36.260	0.001	0.001	0.000	0.000	0.000	0.000
109	A	329	THR	0	-0.059	-0.012	32.898	0.005	0.005	0.000	0.000	0.000	0.000
110	A	330	GLY	0	0.040	0.018	36.334	0.003	0.003	0.000	0.000	0.000	0.000
111	A	331	LYS	1	0.836	0.921	31.787	0.003	0.003	0.000	0.000	0.000	0.000
112	A	332	GLU	-1	-0.865	-0.942	33.391	-0.036	-0.036	0.000	0.000	0.000	0.000
113	A	333	ASN	0	-0.019	-0.011	32.084	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	334	TYR	0	0.015	-0.004	27.980	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	335	ALA	0	0.037	0.016	29.729	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	336	ALA	0	0.012	0.003	31.521	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	337	ILE	0	0.002	0.000	26.600	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	338	ILE	0	-0.035	-0.006	26.319	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	339	GLN	0	0.054	0.029	28.159	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	340	TYR	0	-0.012	-0.009	29.156	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	341	ASP	-1	-0.804	-0.874	23.943	-0.150	-0.150	0.000	0.000	0.000	0.000
122	A	342	LEU	0	-0.033	-0.012	25.552	-0.017	-0.017	0.000	0.000	0.000	0.000
123	A	343	LYS	1	0.897	0.941	27.279	0.091	0.091	0.000	0.000	0.000	0.000
124	A	344	GLY	0	0.001	0.000	26.524	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	345	LEU	0	-0.031	-0.021	22.150	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	346	LEU	0	-0.003	-0.009	25.194	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	347	LEU	0	-0.041	-0.005	28.563	0.002	0.002	0.000	0.000	0.000	0.000
128	A	348	ARG	1	0.798	0.876	20.569	0.281	0.281	0.000	0.000	0.000	0.000
129	A	349	LEU	0	-0.068	-0.028	22.283	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	350	PRO	0	0.042	0.014	27.003	0.008	0.008	0.000	0.000	0.000	0.000
131	A	351	GLY	0	0.011	0.009	30.077	0.008	0.008	0.000	0.000	0.000	0.000
132	A	352	LEU	0	-0.018	-0.011	24.250	0.005	0.005	0.000	0.000	0.000	0.000
133	A	353	GLU	-1	-0.881	-0.968	28.417	-0.096	-0.096	0.000	0.000	0.000	0.000
134	A	354	THR	0	-0.016	-0.006	30.905	0.009	0.009	0.000	0.000	0.000	0.000
135	A	355	LEU	0	-0.031	0.014	27.190	0.002	0.002	0.000	0.000	0.000	0.000
136	A	356	ALA	0	0.049	0.021	29.727	0.006	0.006	0.000	0.000	0.000	0.000
137	A	357	PHE	0	-0.023	0.009	24.016	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	358	ASN	0	0.013	-0.013	24.754	0.008	0.008	0.000	0.000	0.000	0.000
139	A	359	ASP	-1	-0.783	-0.890	28.661	-0.061	-0.061	0.000	0.000	0.000	0.000
140	A	360	GLY	0	0.016	0.010	31.188	0.006	0.006	0.000	0.000	0.000	0.000
141	A	361	MET	0	-0.072	-0.004	30.722	0.002	0.002	0.000	0.000	0.000	0.000
142	A	362	PRO	0	0.067	0.030	30.742	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	363	PHE	0	-0.016	-0.038	25.280	0.000	0.000	0.000	0.000	0.000	0.000
144	A	364	ALA	0	-0.016	-0.010	28.886	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	365	ASP	-1	-0.861	-0.928	31.697	-0.051	-0.051	0.000	0.000	0.000	0.000
146	A	366	ASP	-1	-0.874	-0.943	35.090	-0.054	-0.054	0.000	0.000	0.000	0.000
147	A	367	VAL	0	-0.040	-0.015	36.542	0.000	0.000	0.000	0.000	0.000	0.000
148	A	368	THR	0	-0.078	-0.055	32.504	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	369	LEU	0	0.030	0.006	34.088	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	370	SER	0	-0.026	-0.001	35.256	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	371	TRP	0	-0.041	-0.036	29.780	-0.003	-0.003	0.000	0.000	0.000	0.000
152	A	372	ILE	0	0.020	-0.002	30.664	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	373	GLN	0	0.015	0.009	34.370	0.003	0.003	0.000	0.000	0.000	0.000
154	A	374	GLN	0	-0.030	-0.007	37.176	0.000	0.000	0.000	0.000	0.000	0.000
155	A	375	GLN	0	-0.053	-0.011	36.635	0.005	0.005	0.000	0.000	0.000	0.000
156	A	376	VAL	0	-0.003	0.012	31.476	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	377	MET	0	-0.058	-0.009	33.355	-0.008	-0.008	0.000	0.000	0.000	0.000

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