FMO DATABASE

FMODB ID: G5RN1

Calculation Name: 3O7X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3O7X

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TC59

Base Structure: X-ray

Registration Date: 2023-09-22

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-918223.781773
FMO2-HF: Nuclear repulsion	869579.061806
FMO2-HF: Total energy	-48644.719968
FMO2-MP2: Total energy	-48784.095606

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:386:SER)

Summations of interaction energy for fragment #1(A:386: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.
-4.074	-2.91	-0.008	-0.399	-0.757	0.001

Interaction energy analysis for fragmet #1(A:386:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.029

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	388	ASP	-1	-0.830	-0.903	3.862	-3.727	-2.563	-0.008	-0.399	-0.757	0.001
4	A	389	CYS	0	-0.097	-0.034	5.697	0.436	0.436	0.000	0.000	0.000	0.000
5	A	390	VAL	0	0.046	0.004	7.460	-0.139	-0.139	0.000	0.000	0.000	0.000
6	A	391	LEU	0	0.000	-0.001	8.825	0.051	0.051	0.000	0.000	0.000	0.000
7	A	392	ASP	-1	-0.802	-0.911	10.266	-1.093	-1.093	0.000	0.000	0.000	0.000
8	A	393	VAL	0	0.008	0.005	5.257	0.009	0.009	0.000	0.000	0.000	0.000
9	A	394	MET	0	-0.044	-0.026	8.451	0.241	0.241	0.000	0.000	0.000	0.000
10	A	395	HIS	0	0.002	0.008	11.561	0.146	0.146	0.000	0.000	0.000	0.000
11	A	396	ALA	0	0.000	0.005	10.284	0.134	0.134	0.000	0.000	0.000	0.000
12	A	397	ILE	0	0.014	0.007	8.716	0.145	0.145	0.000	0.000	0.000	0.000
13	A	398	TYR	0	0.011	0.013	12.722	0.179	0.179	0.000	0.000	0.000	0.000
14	A	399	GLN	0	-0.052	-0.040	15.739	0.092	0.092	0.000	0.000	0.000	0.000
15	A	400	GLN	0	0.026	0.013	11.473	0.059	0.059	0.000	0.000	0.000	0.000
16	A	401	ASN	0	-0.066	-0.043	15.568	0.139	0.139	0.000	0.000	0.000	0.000
17	A	402	LYS	1	0.900	0.964	18.633	0.528	0.528	0.000	0.000	0.000	0.000
18	A	403	GLU	-1	-0.860	-0.921	19.030	-0.551	-0.551	0.000	0.000	0.000	0.000
19	A	404	HIS	0	-0.037	-0.016	20.748	0.025	0.025	0.000	0.000	0.000	0.000
20	A	405	PHE	0	0.014	-0.006	22.487	0.044	0.044	0.000	0.000	0.000	0.000
21	A	406	GLN	0	-0.002	-0.007	24.709	0.017	0.017	0.000	0.000	0.000	0.000
22	A	407	ASP	-1	-0.828	-0.921	25.182	-0.294	-0.294	0.000	0.000	0.000	0.000
23	A	408	GLU	-1	-1.020	-0.986	26.514	-0.254	-0.254	0.000	0.000	0.000	0.000
24	A	409	CYS	0	-0.010	-0.004	28.256	0.027	0.027	0.000	0.000	0.000	0.000
25	A	410	THR	0	-0.003	-0.007	29.942	0.020	0.020	0.000	0.000	0.000	0.000
26	A	411	LYS	1	0.857	0.918	26.935	0.286	0.286	0.000	0.000	0.000	0.000
27	A	412	LEU	0	-0.016	0.011	32.159	0.013	0.013	0.000	0.000	0.000	0.000
28	A	413	LEU	0	0.009	-0.006	34.407	0.014	0.014	0.000	0.000	0.000	0.000
29	A	414	VAL	0	-0.016	-0.001	34.970	0.012	0.012	0.000	0.000	0.000	0.000
30	A	415	GLY	0	-0.025	-0.009	37.362	0.002	0.002	0.000	0.000	0.000	0.000
31	A	416	ASN	0	-0.085	-0.042	38.761	0.015	0.015	0.000	0.000	0.000	0.000
32	A	417	ILE	0	-0.012	-0.006	42.072	0.000	0.000	0.000	0.000	0.000	0.000
33	A	418	VAL	0	0.028	0.020	41.935	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	419	ILE	0	0.000	-0.005	45.216	0.005	0.005	0.000	0.000	0.000	0.000
35	A	420	THR	0	0.030	0.017	46.222	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	421	ARG	1	0.911	0.954	47.506	0.104	0.104	0.000	0.000	0.000	0.000
37	A	422	TYR	0	0.015	0.026	46.648	0.005	0.005	0.000	0.000	0.000	0.000
38	A	423	ASN	0	0.021	0.004	50.937	0.002	0.002	0.000	0.000	0.000	0.000
39	A	424	ASN	0	-0.051	-0.025	52.662	0.000	0.000	0.000	0.000	0.000	0.000
40	A	425	ARG	1	0.932	0.998	51.364	0.095	0.095	0.000	0.000	0.000	0.000
41	A	426	THR	0	-0.034	-0.027	48.749	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	427	TYR	0	-0.011	-0.013	45.821	0.004	0.004	0.000	0.000	0.000	0.000
43	A	428	ARG	1	0.819	0.883	43.196	0.121	0.121	0.000	0.000	0.000	0.000
44	A	429	ILE	0	0.020	0.017	37.867	0.000	0.000	0.000	0.000	0.000	0.000
45	A	430	ASP	-1	-0.810	-0.890	39.709	-0.131	-0.131	0.000	0.000	0.000	0.000
46	A	431	ASP	-1	-0.781	-0.891	34.293	-0.207	-0.207	0.000	0.000	0.000	0.000
47	A	432	VAL	0	-0.029	-0.022	32.732	0.010	0.010	0.000	0.000	0.000	0.000
48	A	433	ASP	-1	-0.789	-0.869	32.683	-0.231	-0.231	0.000	0.000	0.000	0.000
49	A	434	TRP	0	-0.001	-0.030	28.386	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	435	ASN	0	-0.097	-0.043	29.198	-0.032	-0.032	0.000	0.000	0.000	0.000
51	A	436	LYS	1	0.866	0.935	31.041	0.196	0.196	0.000	0.000	0.000	0.000
52	A	437	THR	0	0.003	-0.003	33.803	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	438	PRO	0	-0.045	-0.033	35.559	0.010	0.010	0.000	0.000	0.000	0.000
54	A	439	LYS	1	0.831	0.901	33.686	0.216	0.216	0.000	0.000	0.000	0.000
55	A	440	ASP	-1	-0.829	-0.893	36.156	-0.194	-0.194	0.000	0.000	0.000	0.000
56	A	441	SER	0	-0.079	-0.074	39.065	0.005	0.005	0.000	0.000	0.000	0.000
57	A	442	PHE	0	-0.038	-0.017	41.928	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	443	THR	0	0.009	0.011	44.625	0.003	0.003	0.000	0.000	0.000	0.000
59	A	444	MET	0	-0.037	-0.014	47.608	0.002	0.002	0.000	0.000	0.000	0.000
60	A	445	SER	0	0.002	-0.015	51.106	0.000	0.000	0.000	0.000	0.000	0.000
61	A	446	ASP	-1	-0.925	-0.970	54.047	-0.087	-0.087	0.000	0.000	0.000	0.000
62	A	447	GLY	0	-0.013	-0.005	50.953	0.001	0.001	0.000	0.000	0.000	0.000
63	A	448	LYS	1	0.924	0.977	50.004	0.087	0.087	0.000	0.000	0.000	0.000
64	A	449	GLU	-1	-0.861	-0.907	43.998	-0.135	-0.135	0.000	0.000	0.000	0.000
65	A	450	ILE	0	-0.077	-0.038	46.757	0.005	0.005	0.000	0.000	0.000	0.000
66	A	451	THR	0	0.059	0.003	42.422	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	452	PHE	0	0.018	0.002	40.297	0.008	0.008	0.000	0.000	0.000	0.000
68	A	453	LEU	0	0.017	0.017	40.261	0.006	0.006	0.000	0.000	0.000	0.000
69	A	454	GLU	-1	-0.805	-0.855	44.079	-0.107	-0.107	0.000	0.000	0.000	0.000
70	A	455	TYR	0	0.018	0.022	46.501	0.008	0.008	0.000	0.000	0.000	0.000
71	A	456	TYR	0	0.006	-0.017	44.278	0.004	0.004	0.000	0.000	0.000	0.000
72	A	457	SER	0	-0.026	-0.024	47.858	0.006	0.006	0.000	0.000	0.000	0.000
73	A	458	LYS	1	0.812	0.890	49.761	0.106	0.106	0.000	0.000	0.000	0.000
74	A	459	ASN	0	-0.043	-0.027	51.724	0.002	0.002	0.000	0.000	0.000	0.000
75	A	460	TYR	0	-0.048	-0.034	50.230	0.004	0.004	0.000	0.000	0.000	0.000
76	A	461	GLY	0	0.007	0.026	52.812	0.002	0.002	0.000	0.000	0.000	0.000
77	A	462	ILE	0	-0.071	-0.038	46.620	0.000	0.000	0.000	0.000	0.000	0.000
78	A	463	THR	0	0.014	0.004	45.073	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	464	VAL	0	-0.022	-0.003	40.629	0.001	0.001	0.000	0.000	0.000	0.000
80	A	465	LYS	1	0.789	0.880	40.672	0.125	0.125	0.000	0.000	0.000	0.000
81	A	466	GLU	-1	-0.884	-0.937	34.726	-0.198	-0.198	0.000	0.000	0.000	0.000
82	A	467	GLU	-1	-0.913	-0.968	36.288	-0.168	-0.168	0.000	0.000	0.000	0.000
83	A	468	ASP	-1	-0.825	-0.898	30.434	-0.249	-0.249	0.000	0.000	0.000	0.000
84	A	469	GLN	0	-0.080	-0.031	32.216	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	470	PRO	0	0.060	0.019	31.130	0.005	0.005	0.000	0.000	0.000	0.000
86	A	471	LEU	0	-0.018	0.003	33.847	0.014	0.014	0.000	0.000	0.000	0.000
87	A	472	LEU	0	-0.020	-0.011	36.279	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	473	ILE	0	0.014	0.013	36.714	0.007	0.007	0.000	0.000	0.000	0.000
89	A	474	HIS	0	0.019	0.018	40.075	0.002	0.002	0.000	0.000	0.000	0.000
90	A	475	ARG	1	0.760	0.850	37.017	0.170	0.170	0.000	0.000	0.000	0.000
91	A	476	PRO	0	0.017	0.002	44.601	0.004	0.004	0.000	0.000	0.000	0.000
92	A	477	SER	0	-0.006	-0.014	47.350	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	478	GLU	-1	-0.842	-0.895	49.214	-0.083	-0.083	0.000	0.000	0.000	0.000
94	A	479	ARG	1	0.934	0.970	42.934	0.125	0.125	0.000	0.000	0.000	0.000
95	A	480	GLN	0	-0.003	0.000	43.117	0.000	0.000	0.000	0.000	0.000	0.000
96	A	481	ASP	-1	-0.868	-0.939	47.497	-0.083	-0.083	0.000	0.000	0.000	0.000
97	A	482	ASN	0	0.030	0.024	50.477	0.004	0.004	0.000	0.000	0.000	0.000
98	A	483	HIS	0	-0.056	-0.061	48.575	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	484	GLY	0	0.026	0.021	44.760	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	485	MET	0	-0.033	0.007	44.767	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	486	LEU	0	-0.032	-0.012	43.650	0.000	0.000	0.000	0.000	0.000	0.000
102	A	487	LEU	0	0.008	-0.007	47.481	0.003	0.003	0.000	0.000	0.000	0.000
103	A	488	LYS	1	0.733	0.856	49.102	0.092	0.092	0.000	0.000	0.000	0.000
104	A	489	GLY	0	0.029	0.018	46.225	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	490	GLU	-1	-0.851	-0.924	39.872	-0.159	-0.159	0.000	0.000	0.000	0.000
106	A	491	ILE	0	-0.036	-0.021	44.289	0.002	0.002	0.000	0.000	0.000	0.000
107	A	492	LEU	0	0.027	0.021	39.246	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	493	LEU	0	-0.046	-0.021	41.138	0.008	0.008	0.000	0.000	0.000	0.000
109	A	494	LEU	0	0.057	0.030	39.541	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	495	PRO	0	0.046	0.028	36.156	0.009	0.009	0.000	0.000	0.000	0.000
111	A	496	GLU	-1	-0.786	-0.886	39.234	-0.134	-0.134	0.000	0.000	0.000	0.000
112	A	497	LEU	0	-0.067	-0.029	41.001	0.008	0.008	0.000	0.000	0.000	0.000
113	A	498	SER	0	-0.032	-0.036	41.728	0.008	0.008	0.000	0.000	0.000	0.000
114	A	499	PHE	0	-0.012	-0.005	42.211	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	500	MET	0	0.044	0.023	38.814	0.001	0.001	0.000	0.000	0.000	0.000
116	A	501	THR	0	-0.036	-0.012	43.427	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:386:SER)