FMO DATABASE

FMODB ID: 3JRML

Calculation Name: 3ON9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ON9

Chain ID: A

ChEMBL ID:

UniProt ID: Q7TDW8

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:

Apendix: None

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1552730.262731
FMO2-HF: Nuclear repulsion	1488812.787196
FMO2-HF: Total energy	-63917.475534
FMO2-MP2: Total energy	-64098.69083

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:161:GLY)

Summations of interaction energy for fragment #1(A:161:GLY)

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.
-1.31	0.835	0.291	-1.151	-1.284	0.002

Interaction energy analysis for fragmet #1(A:161:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.015

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	163	PHE	0	0.050	0.013	3.863	-0.826	0.649	-0.004	-0.849	-0.621	0.004
4	A	164	ASN	0	-0.031	-0.051	6.751	-0.151	-0.151	0.000	0.000	0.000	0.000
5	A	165	SER	0	-0.030	0.001	8.526	0.283	0.283	0.000	0.000	0.000	0.000
6	A	166	ILE	0	-0.001	-0.003	11.543	-0.199	-0.199	0.000	0.000	0.000	0.000
7	A	167	ASH	0	-0.077	-0.068	14.294	0.111	0.111	0.000	0.000	0.000	0.000
8	A	168	VAL	0	0.017	0.001	17.516	-0.042	-0.042	0.000	0.000	0.000	0.000
9	A	169	GLU	-1	-0.838	-0.866	20.620	-0.330	-0.330	0.000	0.000	0.000	0.000
10	A	170	ILE	0	-0.021	-0.031	23.504	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	171	ASN	0	0.037	0.047	26.648	0.019	0.019	0.000	0.000	0.000	0.000
12	A	172	MET	0	-0.019	-0.010	29.798	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	173	TYR	0	0.038	0.041	33.407	0.009	0.009	0.000	0.000	0.000	0.000
14	A	174	PRO	0	-0.037	-0.014	37.025	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	175	VAL	0	0.022	0.005	36.054	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	176	ASN	0	-0.083	-0.074	39.386	0.009	0.009	0.000	0.000	0.000	0.000
17	A	177	LYS	1	0.834	0.923	39.892	0.101	0.101	0.000	0.000	0.000	0.000
18	A	178	THR	0	0.064	0.040	38.345	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	179	SER	0	0.005	0.007	37.534	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	180	CYS	0	-0.070	-0.036	30.514	0.004	0.004	0.000	0.000	0.000	0.000
21	A	181	ASN	0	-0.071	-0.033	34.677	0.013	0.013	0.000	0.000	0.000	0.000
22	A	182	SER	0	0.019	-0.018	28.788	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	183	SER	0	0.013	-0.008	30.114	0.017	0.017	0.000	0.000	0.000	0.000
24	A	184	ILE	0	0.018	0.031	24.187	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	185	GLY	0	0.014	0.004	25.508	0.019	0.019	0.000	0.000	0.000	0.000
26	A	186	SER	0	-0.009	-0.010	23.685	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	187	SER	0	-0.007	0.001	24.536	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	188	SER	0	-0.012	0.009	24.575	0.017	0.017	0.000	0.000	0.000	0.000
29	A	189	THR	0	-0.028	-0.017	26.690	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	190	ILE	0	0.048	0.039	27.111	0.007	0.007	0.000	0.000	0.000	0.000
31	A	191	SER	0	-0.028	-0.004	31.106	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	192	THR	0	0.049	0.028	34.822	0.007	0.007	0.000	0.000	0.000	0.000
33	A	193	SER	0	0.008	-0.004	38.037	0.000	0.000	0.000	0.000	0.000	0.000
34	A	194	GLU	-1	-0.843	-0.926	39.197	-0.109	-0.109	0.000	0.000	0.000	0.000
35	A	195	LEU	0	0.015	0.002	34.954	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	196	THR	0	-0.007	0.000	33.078	0.006	0.006	0.000	0.000	0.000	0.000
37	A	197	ILE	0	-0.006	-0.002	27.907	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	198	THR	0	0.020	-0.006	28.727	0.006	0.006	0.000	0.000	0.000	0.000
39	A	199	LEU	0	-0.014	0.006	21.125	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	200	THR	0	-0.039	-0.019	23.431	0.012	0.012	0.000	0.000	0.000	0.000
41	A	201	HIS	0	0.032	-0.014	18.286	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	202	GLU	-1	-0.881	-0.938	18.496	-0.287	-0.287	0.000	0.000	0.000	0.000
43	A	203	ASP	-1	-0.858	-0.929	15.576	-0.397	-0.397	0.000	0.000	0.000	0.000
44	A	204	CYS	0	-0.095	-0.008	13.092	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	205	THR	0	0.031	0.016	11.366	0.025	0.025	0.000	0.000	0.000	0.000
46	A	206	PRO	0	-0.009	-0.008	10.793	0.090	0.090	0.000	0.000	0.000	0.000
47	A	207	VAL	0	-0.010	0.010	13.627	0.011	0.011	0.000	0.000	0.000	0.000
48	A	208	PHE	0	0.048	-0.001	17.448	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	209	ILE	0	-0.081	-0.042	19.042	0.033	0.033	0.000	0.000	0.000	0.000
50	A	210	GLY	0	0.022	0.010	21.690	0.028	0.028	0.000	0.000	0.000	0.000
51	A	211	ASP	-1	-0.884	-0.908	23.051	-0.216	-0.216	0.000	0.000	0.000	0.000
52	A	212	TYR	0	0.022	0.017	23.576	0.011	0.011	0.000	0.000	0.000	0.000
53	A	213	TYR	0	-0.029	-0.057	28.082	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	214	SER	0	-0.029	0.010	31.139	0.015	0.015	0.000	0.000	0.000	0.000
55	A	215	VAL	0	-0.008	-0.016	33.128	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	216	VAL	0	-0.004	0.004	35.784	0.008	0.008	0.000	0.000	0.000	0.000
57	A	217	ASP	-1	-0.846	-0.925	38.175	-0.098	-0.098	0.000	0.000	0.000	0.000
58	A	218	LYS	1	0.802	0.906	40.133	0.095	0.095	0.000	0.000	0.000	0.000
59	A	219	LEU	0	0.007	0.005	33.619	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	220	ALA	0	-0.001	-0.001	33.475	0.005	0.005	0.000	0.000	0.000	0.000
61	A	221	THR	0	-0.003	-0.016	27.990	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	222	SER	0	-0.012	-0.027	28.266	0.016	0.016	0.000	0.000	0.000	0.000
63	A	223	GLY	0	0.034	0.014	24.304	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	224	PHE	0	0.003	-0.001	21.959	0.024	0.024	0.000	0.000	0.000	0.000
65	A	225	PHE	0	0.001	0.000	18.491	-0.039	-0.039	0.000	0.000	0.000	0.000
66	A	226	THR	0	0.006	0.001	14.250	0.008	0.008	0.000	0.000	0.000	0.000
67	A	227	ASN	0	0.008	0.008	15.624	0.021	0.021	0.000	0.000	0.000	0.000
68	A	228	ASP	-1	-0.768	-0.854	12.266	-0.345	-0.345	0.000	0.000	0.000	0.000
69	A	229	LYS	1	0.795	0.877	11.011	0.130	0.130	0.000	0.000	0.000	0.000
70	A	230	VAL	0	-0.002	-0.004	10.830	0.121	0.121	0.000	0.000	0.000	0.000
71	A	231	HIS	1	0.774	0.877	4.463	1.215	1.319	-0.001	-0.016	-0.087	0.000
72	A	232	GLN	0	0.016	0.007	7.527	0.292	0.292	0.000	0.000	0.000	0.000
73	A	233	ASP	-1	-0.824	-0.876	6.913	-0.465	-0.465	0.000	0.000	0.000	0.000
74	A	234	LEU	0	0.012	-0.010	4.248	-0.141	-0.081	-0.001	-0.012	-0.048	0.000
75	A	235	THR	0	-0.079	-0.051	8.505	0.042	0.042	0.000	0.000	0.000	0.000
76	A	236	THR	0	-0.049	-0.015	11.893	0.030	0.030	0.000	0.000	0.000	0.000
77	A	237	GLN	0	-0.021	-0.023	11.845	-0.218	-0.218	0.000	0.000	0.000	0.000
78	A	239	LYS	1	0.832	0.904	14.816	0.367	0.367	0.000	0.000	0.000	0.000
79	A	240	ILE	0	0.017	0.019	16.706	0.046	0.046	0.000	0.000	0.000	0.000
80	A	241	ASN	0	-0.032	-0.015	19.422	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	242	LEU	0	0.015	0.003	23.204	0.013	0.013	0.000	0.000	0.000	0.000
82	A	243	GLU	-1	-0.893	-0.947	25.500	-0.171	-0.171	0.000	0.000	0.000	0.000
83	A	244	ILE	0	0.018	0.010	28.004	0.001	0.001	0.000	0.000	0.000	0.000
84	A	245	LYS	1	0.896	0.956	31.663	0.136	0.136	0.000	0.000	0.000	0.000
85	A	246	CYS	0	-0.032	-0.002	35.096	0.005	0.005	0.000	0.000	0.000	0.000
86	A	247	ASN	0	0.018	0.006	38.266	0.004	0.004	0.000	0.000	0.000	0.000
87	A	248	SER	0	-0.041	-0.029	41.082	0.003	0.003	0.000	0.000	0.000	0.000
88	A	249	GLY	0	-0.050	-0.028	39.504	0.002	0.002	0.000	0.000	0.000	0.000
89	A	250	ARG	1	0.818	0.880	40.553	0.106	0.106	0.000	0.000	0.000	0.000
90	A	251	GLU	-1	-0.933	-0.957	39.189	-0.119	-0.119	0.000	0.000	0.000	0.000
91	A	252	SER	0	-0.016	-0.007	34.332	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	253	ARG	1	0.948	0.972	33.497	0.176	0.176	0.000	0.000	0.000	0.000
93	A	254	GLN	0	0.034	0.019	28.086	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	255	LEU	0	-0.046	-0.021	27.867	0.016	0.016	0.000	0.000	0.000	0.000
95	A	256	THR	0	-0.004	-0.016	26.333	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	257	PRO	0	0.020	0.030	21.839	0.017	0.017	0.000	0.000	0.000	0.000
97	A	258	THR	0	-0.027	-0.032	22.195	0.019	0.019	0.000	0.000	0.000	0.000
98	A	259	THR	0	-0.050	-0.035	19.249	0.032	0.032	0.000	0.000	0.000	0.000
99	A	260	LYS	1	0.953	0.971	19.109	0.304	0.304	0.000	0.000	0.000	0.000
100	A	261	VAL	0	-0.035	-0.017	15.413	0.018	0.018	0.000	0.000	0.000	0.000
101	A	262	TYR	0	-0.043	-0.028	12.615	0.062	0.062	0.000	0.000	0.000	0.000
102	A	263	LEU	0	0.001	-0.003	7.772	0.103	0.103	0.000	0.000	0.000	0.000
103	A	264	MET	0	-0.061	-0.014	5.892	-0.826	-0.826	0.000	0.000	0.000	0.000
104	A	265	PRO	0	-0.026	-0.016	7.652	0.327	0.327	0.000	0.000	0.000	0.000
105	A	266	HIS	1	0.796	0.879	10.611	1.043	1.043	0.000	0.000	0.000	0.000
106	A	267	SER	0	-0.067	-0.031	13.598	0.089	0.089	0.000	0.000	0.000	0.000
107	A	268	GLU	-1	-0.762	-0.841	16.556	-0.742	-0.742	0.000	0.000	0.000	0.000
108	A	269	THR	0	-0.050	-0.024	19.851	0.038	0.038	0.000	0.000	0.000	0.000
109	A	270	VAL	0	0.053	0.031	23.500	0.000	0.000	0.000	0.000	0.000	0.000
110	A	271	THR	0	-0.037	-0.013	25.995	0.016	0.016	0.000	0.000	0.000	0.000
111	A	272	VAL	0	-0.014	0.003	29.734	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	273	VAL	0	0.006	-0.004	32.797	0.006	0.006	0.000	0.000	0.000	0.000
113	A	274	GLY	0	0.023	-0.006	35.921	0.006	0.006	0.000	0.000	0.000	0.000
114	A	275	ASP	-1	-0.865	-0.908	37.803	-0.122	-0.122	0.000	0.000	0.000	0.000
115	A	277	LEU	0	0.022	0.015	34.275	0.001	0.001	0.000	0.000	0.000	0.000
116	A	278	SER	0	-0.009	-0.012	37.770	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	279	ASN	0	-0.060	-0.037	34.299	0.006	0.006	0.000	0.000	0.000	0.000
118	A	280	LEU	0	0.039	0.027	29.928	0.004	0.004	0.000	0.000	0.000	0.000
119	A	281	ASP	-1	-0.776	-0.865	27.499	-0.225	-0.225	0.000	0.000	0.000	0.000
120	A	282	VAL	0	0.018	-0.002	23.223	0.005	0.005	0.000	0.000	0.000	0.000
121	A	283	TYR	0	0.018	0.004	20.575	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	284	ILE	0	0.017	0.032	16.947	0.008	0.008	0.000	0.000	0.000	0.000
123	A	285	VAL	0	-0.008	-0.010	14.373	-0.038	-0.038	0.000	0.000	0.000	0.000
124	A	286	TYR	0	-0.003	-0.034	10.699	0.027	0.027	0.000	0.000	0.000	0.000
125	A	287	ALA	0	0.042	0.005	9.956	-0.121	-0.121	0.000	0.000	0.000	0.000
126	A	288	ASN	0	0.062	0.023	2.755	0.945	1.451	0.297	-0.274	-0.528	-0.002
127	A	289	THR	0	-0.015	-0.011	6.689	0.184	0.184	0.000	0.000	0.000	0.000
128	A	290	ASP	-1	-0.891	-0.920	4.835	0.444	0.444	0.000	0.000	0.000	0.000
129	A	291	ALA	0	-0.064	-0.020	5.175	0.366	0.366	0.000	0.000	0.000	0.000
130	A	292	ILE	0	-0.017	0.000	7.208	0.156	0.156	0.000	0.000	0.000	0.000
131	A	293	TYR	0	0.026	-0.004	10.361	-0.175	-0.175	0.000	0.000	0.000	0.000
132	A	294	SER	0	-0.060	-0.051	11.623	0.014	0.014	0.000	0.000	0.000	0.000
133	A	295	ASP	-1	-0.852	-0.915	7.599	-0.888	-0.888	0.000	0.000	0.000	0.000
134	A	296	MET	0	-0.049	-0.017	8.613	-0.407	-0.407	0.000	0.000	0.000	0.000
135	A	297	ASP	-1	-0.710	-0.833	10.664	-1.405	-1.405	0.000	0.000	0.000	0.000
136	A	298	VAL	0	0.021	0.008	12.566	0.063	0.063	0.000	0.000	0.000	0.000
137	A	299	VAL	0	-0.030	-0.001	16.232	0.048	0.048	0.000	0.000	0.000	0.000
138	A	300	ALA	0	0.014	0.015	18.655	0.034	0.034	0.000	0.000	0.000	0.000
139	A	301	TYR	0	0.009	-0.005	20.970	0.026	0.026	0.000	0.000	0.000	0.000
140	A	302	HIS	1	0.861	0.902	25.173	0.281	0.281	0.000	0.000	0.000	0.000
141	A	303	THR	0	-0.038	-0.006	29.123	0.001	0.001	0.000	0.000	0.000	0.000
142	A	304	SER	0	-0.031	-0.013	32.583	0.013	0.013	0.000	0.000	0.000	0.000
143	A	305	TYR	0	-0.032	-0.020	32.724	-0.010	-0.010	0.000	0.000	0.000	0.000
144	A	306	ILE	0	-0.007	0.007	27.506	0.001	0.001	0.000	0.000	0.000	0.000
145	A	307	LEU	0	-0.052	-0.017	31.146	0.013	0.013	0.000	0.000	0.000	0.000
146	A	308	ASN	0	-0.080	-0.045	29.936	-0.009	-0.009	0.000	0.000	0.000	0.000
147	A	309	VAL	0	0.025	-0.007	28.156	0.009	0.009	0.000	0.000	0.000	0.000
148	A	310	ASP	-1	-0.838	-0.902	28.631	-0.186	-0.186	0.000	0.000	0.000	0.000
149	A	311	HIS	0	-0.072	-0.053	29.224	0.012	0.012	0.000	0.000	0.000	0.000
150	A	312	ILE	0	-0.013	0.012	30.844	0.012	0.012	0.000	0.000	0.000	0.000
151	A	313	PRO	0	-0.023	-0.001	29.633	-0.011	-0.011	0.000	0.000	0.000	0.000
152	A	314	PRO	0	0.030	0.013	25.757	0.002	0.002	0.000	0.000	0.000	0.000
153	A	315	ASN	0	-0.046	-0.033	28.223	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	316	ASP	-1	-0.762	-0.876	29.134	-0.134	-0.134	0.000	0.000	0.000	0.000
155	A	318	GLU	-1	-0.968	-0.962	32.459	-0.099	-0.099	0.000	0.000	0.000	0.000
156	A	319	ARG	1	0.826	0.888	35.106	0.098	0.098	0.000	0.000	0.000	0.000
157	A	320	ASP	-1	-0.970	-0.970	37.287	-0.072	-0.072	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:161:GLY)