FMO DATABASE

FMODB ID: ZYM6N

Calculation Name: 1GO4-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GO4

Chain ID: E

ChEMBL ID:

UniProt ID: Q9Y6D9

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-413859.814356
FMO2-HF: Nuclear repulsion	376959.294781
FMO2-HF: Total energy	-36900.519575
FMO2-MP2: Total energy	-37006.233242

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(E:493:PHE)

Summations of interaction energy for fragment #1(E:493:PHE)

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.
-15.875	-29.919	45.473	-10.323	-21.105	0.015

Interaction energy analysis for fragmet #1(E:493:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.032

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	E	495	ARG	1	0.961	0.971	1.968	-8.874	-5.941	6.713	-3.533	-6.113	0.027
4	E	496	GLU	-1	-0.874	-0.939	1.900	-1.852	-19.960	38.439	-7.705	-12.626	-0.010
5	E	497	GLU	-1	-0.913	-0.945	2.729	-6.546	-5.629	0.321	0.951	-2.188	-0.002
6	E	498	ALA	0	-0.009	0.004	4.194	0.531	0.745	0.000	-0.036	-0.178	0.000
7	E	499	ASP	-1	-0.917	-0.960	5.966	0.311	0.311	0.000	0.000	0.000	0.000
8	E	500	THR	0	-0.059	-0.035	6.578	-0.110	-0.110	0.000	0.000	0.000	0.000
9	E	501	LEU	0	-0.015	-0.019	7.318	0.159	0.159	0.000	0.000	0.000	0.000
10	E	502	ARG	1	0.907	0.948	9.772	0.112	0.112	0.000	0.000	0.000	0.000
11	E	503	LEU	0	0.036	0.036	11.210	0.068	0.068	0.000	0.000	0.000	0.000
12	E	504	LYS	1	0.996	0.996	11.711	0.861	0.861	0.000	0.000	0.000	0.000
13	E	505	VAL	0	-0.047	-0.038	13.347	0.038	0.038	0.000	0.000	0.000	0.000
14	E	506	GLU	-1	-0.927	-0.958	15.543	-0.119	-0.119	0.000	0.000	0.000	0.000
15	E	507	GLU	-1	-0.981	-0.990	16.074	-0.322	-0.322	0.000	0.000	0.000	0.000
16	E	508	LEU	0	-0.031	-0.019	16.496	0.018	0.018	0.000	0.000	0.000	0.000
17	E	509	GLU	-1	-0.922	-0.954	19.692	-0.222	-0.222	0.000	0.000	0.000	0.000
18	E	510	GLY	0	-0.026	-0.014	21.688	0.024	0.024	0.000	0.000	0.000	0.000
19	E	511	GLU	-1	-0.947	-0.967	20.949	-0.258	-0.258	0.000	0.000	0.000	0.000
20	E	512	ARG	1	0.954	0.979	23.713	0.190	0.190	0.000	0.000	0.000	0.000
21	E	513	SER	0	-0.051	-0.025	25.527	0.017	0.017	0.000	0.000	0.000	0.000
22	E	514	ARG	1	0.994	0.997	26.587	0.151	0.151	0.000	0.000	0.000	0.000
23	E	515	LEU	0	0.033	0.015	26.598	0.009	0.009	0.000	0.000	0.000	0.000
24	E	516	GLU	-1	-0.956	-0.975	29.417	-0.127	-0.127	0.000	0.000	0.000	0.000
25	E	517	GLU	-1	-0.998	-1.015	31.827	-0.084	-0.084	0.000	0.000	0.000	0.000
26	E	518	GLU	-1	-0.887	-0.941	31.614	-0.127	-0.127	0.000	0.000	0.000	0.000
27	E	519	LYS	1	0.894	0.941	32.938	0.127	0.127	0.000	0.000	0.000	0.000
28	E	520	ARG	1	0.923	0.971	33.941	0.097	0.097	0.000	0.000	0.000	0.000
29	E	521	MET	0	-0.008	-0.002	37.552	0.006	0.006	0.000	0.000	0.000	0.000
30	E	522	LEU	0	0.004	0.002	36.580	0.005	0.005	0.000	0.000	0.000	0.000
31	E	523	GLU	-1	-0.911	-0.958	38.259	-0.091	-0.091	0.000	0.000	0.000	0.000
32	E	524	ALA	0	0.002	0.003	41.628	0.005	0.005	0.000	0.000	0.000	0.000
33	E	525	GLN	0	-0.149	-0.084	41.566	0.002	0.002	0.000	0.000	0.000	0.000
34	E	526	LEU	0	-0.011	-0.021	42.472	0.004	0.004	0.000	0.000	0.000	0.000
35	E	527	GLU	-1	-0.888	-0.930	45.890	-0.062	-0.062	0.000	0.000	0.000	0.000
36	E	528	ARG	1	0.906	0.970	46.573	0.063	0.063	0.000	0.000	0.000	0.000
37	E	529	ARG	1	0.870	0.934	46.037	0.069	0.069	0.000	0.000	0.000	0.000
38	E	530	ALA	0	0.042	0.018	50.992	0.000	0.000	0.000	0.000	0.000	0.000
39	E	531	LEU	0	-0.044	-0.011	52.080	0.002	0.002	0.000	0.000	0.000	0.000
40	E	532	GLN	0	0.035	0.001	50.080	-0.003	-0.003	0.000	0.000	0.000	0.000
41	E	533	GLY	0	-0.038	-0.004	52.454	-0.002	-0.002	0.000	0.000	0.000	0.000
42	E	534	ASP	-1	-0.909	-0.958	50.856	-0.064	-0.064	0.000	0.000	0.000	0.000
43	E	535	TYR	0	-0.042	-0.011	52.849	0.000	0.000	0.000	0.000	0.000	0.000
44	E	536	ASP	-1	-0.748	-0.848	47.561	-0.083	-0.083	0.000	0.000	0.000	0.000
45	E	537	GLN	0	-0.017	-0.030	50.838	0.001	0.001	0.000	0.000	0.000	0.000
46	E	538	SER	0	-0.103	-0.068	47.097	-0.001	-0.001	0.000	0.000	0.000	0.000
47	E	539	ARG	1	0.888	0.939	45.759	0.081	0.081	0.000	0.000	0.000	0.000
48	E	540	THR	0	-0.020	0.005	50.242	0.002	0.002	0.000	0.000	0.000	0.000
49	E	541	LYS	1	0.954	0.977	53.949	0.061	0.061	0.000	0.000	0.000	0.000
50	E	542	VAL	0	0.031	0.017	57.126	0.001	0.001	0.000	0.000	0.000	0.000
51	E	543	LEU	0	-0.029	-0.014	60.707	0.000	0.000	0.000	0.000	0.000	0.000
52	E	544	HIS	0	0.004	-0.006	63.489	0.002	0.002	0.000	0.000	0.000	0.000
53	E	545	MET	0	0.016	0.009	67.299	0.000	0.000	0.000	0.000	0.000	0.000
54	E	546	SER	0	0.036	0.013	70.148	0.000	0.000	0.000	0.000	0.000	0.000
55	E	547	LEU	0	-0.023	0.002	71.515	0.001	0.001	0.000	0.000	0.000	0.000
56	E	548	ASN	0	0.022	0.004	72.346	0.001	0.001	0.000	0.000	0.000	0.000
57	E	549	PRO	0	0.073	0.021	75.416	0.001	0.001	0.000	0.000	0.000	0.000
58	E	550	THR	0	0.022	0.017	74.651	0.001	0.001	0.000	0.000	0.000	0.000
59	E	551	SER	0	-0.022	-0.010	75.087	0.001	0.001	0.000	0.000	0.000	0.000
60	E	552	VAL	0	0.043	0.017	76.971	0.001	0.001	0.000	0.000	0.000	0.000
61	E	553	ALA	0	0.024	0.013	80.116	0.001	0.001	0.000	0.000	0.000	0.000
62	E	554	ARG	1	0.940	0.961	73.151	0.035	0.035	0.000	0.000	0.000	0.000
63	E	555	GLN	0	-0.048	-0.024	80.696	0.000	0.000	0.000	0.000	0.000	0.000
64	E	556	ARG	1	1.004	0.997	82.405	0.028	0.028	0.000	0.000	0.000	0.000
65	E	557	LEU	0	0.026	0.039	82.861	0.000	0.000	0.000	0.000	0.000	0.000
66	E	558	ARG	1	0.911	0.960	78.954	0.031	0.031	0.000	0.000	0.000	0.000
67	E	559	GLU	-1	-0.904	-0.957	85.490	-0.027	-0.027	0.000	0.000	0.000	0.000
68	E	560	ASP	-1	-0.854	-0.927	88.316	-0.024	-0.024	0.000	0.000	0.000	0.000
69	E	561	HIS	0	-0.034	-0.029	86.436	0.001	0.001	0.000	0.000	0.000	0.000
70	E	562	SER	0	-0.028	-0.013	88.682	0.000	0.000	0.000	0.000	0.000	0.000
71	E	563	GLN	0	0.011	0.007	91.097	0.000	0.000	0.000	0.000	0.000	0.000
72	E	564	LEU	0	0.000	0.000	93.039	0.001	0.001	0.000	0.000	0.000	0.000
73	E	565	GLN	0	-0.033	-0.020	90.136	0.000	0.000	0.000	0.000	0.000	0.000
74	E	566	ALA	0	0.002	-0.010	94.623	0.000	0.000	0.000	0.000	0.000	0.000
75	E	567	GLU	-1	-0.920	-0.962	96.951	-0.019	-0.019	0.000	0.000	0.000	0.000
76	E	568	CYS	0	-0.059	-0.022	97.616	0.001	0.001	0.000	0.000	0.000	0.000
77	E	569	GLU	-1	-0.870	-0.933	98.663	-0.019	-0.019	0.000	0.000	0.000	0.000
78	E	570	ARG	1	0.975	0.982	100.413	0.019	0.019	0.000	0.000	0.000	0.000
79	E	571	LEU	0	0.025	0.016	102.991	0.000	0.000	0.000	0.000	0.000	0.000
80	E	572	ARG	1	0.920	0.958	101.628	0.019	0.019	0.000	0.000	0.000	0.000
81	E	573	GLY	0	-0.090	-0.047	104.599	0.000	0.000	0.000	0.000	0.000	0.000
82	E	574	LEU	0	-0.052	-0.023	105.915	0.000	0.000	0.000	0.000	0.000	0.000
83	E	575	LEU	0	-0.024	-0.020	106.614	0.000	0.000	0.000	0.000	0.000	0.000
84	E	576	ARG	1	0.925	0.967	106.594	0.017	0.017	0.000	0.000	0.000	0.000
85	E	577	ALA	0	0.011	0.031	110.062	0.000	0.000	0.000	0.000	0.000	0.000
86	E	578	MET	0	-0.088	-0.051	112.606	0.000	0.000	0.000	0.000	0.000	0.000
87	E	579	GLU	-1	-0.948	-0.962	113.142	-0.015	-0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:493:PHE)