FMO DATABASE

FMODB ID: YZ432

Calculation Name: 3OMZ-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OMZ

Chain ID: G

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-19

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1067039.934868
FMO2-HF: Nuclear repulsion	1017649.363896
FMO2-HF: Total energy	-49390.570972
FMO2-MP2: Total energy	-49535.689922

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(G:12:VAL)

Summations of interaction energy for fragment #1(G:12:VAL)

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.
-12.331	-6.586	9.669	-5.167	-10.244	-0.031

Interaction energy analysis for fragmet #1(G:12:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.010

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	G	14	ARG	1	0.844	0.893	2.117	-1.506	-0.248	3.051	-1.382	-2.927	0.004
4	G	15	GLN	0	-0.044	0.013	4.946	0.011	0.150	-0.001	-0.013	-0.124	0.000
5	G	16	THR	0	-0.025	-0.029	7.782	0.214	0.214	0.000	0.000	0.000	0.000
6	G	17	GLY	0	-0.023	0.019	9.447	0.037	0.037	0.000	0.000	0.000	0.000
7	G	18	SER	0	-0.029	-0.010	7.671	0.055	0.055	0.000	0.000	0.000	0.000
8	G	19	SER	0	-0.009	-0.037	7.805	-0.060	-0.060	0.000	0.000	0.000	0.000
9	G	20	ALA	0	-0.032	0.006	2.829	-0.082	0.293	0.122	-0.120	-0.377	0.000
10	G	21	GLU	-1	-0.842	-0.876	4.103	-0.545	-0.426	-0.001	-0.024	-0.094	0.000
11	G	22	ILE	0	0.017	0.011	3.684	-1.326	-0.675	0.011	-0.176	-0.485	-0.001
12	G	23	THR	0	-0.002	0.003	5.454	0.403	0.403	0.000	0.000	0.000	0.000
13	G	24	CYS	0	-0.018	0.015	7.971	-0.053	-0.053	0.000	0.000	0.000	0.000
14	G	25	ASP	-1	-0.876	-0.911	10.564	-0.441	-0.441	0.000	0.000	0.000	0.000
15	G	26	LEU	0	0.063	0.010	12.920	0.069	0.069	0.000	0.000	0.000	0.000
16	G	27	ALA	0	0.039	0.026	15.859	0.019	0.019	0.000	0.000	0.000	0.000
17	G	28	GLU	-1	-0.819	-0.909	17.668	-0.112	-0.112	0.000	0.000	0.000	0.000
18	G	29	GLY	0	-0.022	-0.006	16.527	0.013	0.013	0.000	0.000	0.000	0.000
19	G	30	SER	0	-0.051	-0.018	17.546	-0.005	-0.005	0.000	0.000	0.000	0.000
20	G	31	THR	0	0.026	-0.004	19.483	0.004	0.004	0.000	0.000	0.000	0.000
21	G	32	GLY	0	0.028	0.027	22.121	0.005	0.005	0.000	0.000	0.000	0.000
22	G	33	TYR	0	0.002	-0.016	21.513	-0.007	-0.007	0.000	0.000	0.000	0.000
23	G	34	ILE	0	-0.027	-0.004	14.872	-0.005	-0.005	0.000	0.000	0.000	0.000
24	G	35	HIS	0	-0.046	-0.019	16.818	-0.010	-0.010	0.000	0.000	0.000	0.000
25	G	36	TRP	0	0.070	0.022	8.516	-0.051	-0.051	0.000	0.000	0.000	0.000
26	G	37	TYR	0	-0.004	-0.013	12.937	0.082	0.082	0.000	0.000	0.000	0.000
27	G	38	LEU	0	-0.001	0.005	9.192	-0.149	-0.149	0.000	0.000	0.000	0.000
28	G	39	HIS	0	0.000	-0.003	11.597	0.103	0.103	0.000	0.000	0.000	0.000
29	G	40	GLN	0	-0.015	-0.004	11.498	-0.073	-0.073	0.000	0.000	0.000	0.000
30	G	41	GLU	-1	-0.913	-0.957	13.717	-0.291	-0.291	0.000	0.000	0.000	0.000
31	G	42	GLY	0	-0.015	-0.014	16.309	0.027	0.027	0.000	0.000	0.000	0.000
32	G	43	LYN	0	-0.060	-0.033	17.964	0.049	0.049	0.000	0.000	0.000	0.000
33	G	44	ALA	0	0.050	0.039	17.152	-0.054	-0.054	0.000	0.000	0.000	0.000
34	G	45	PRO	0	-0.060	-0.032	15.732	-0.008	-0.008	0.000	0.000	0.000	0.000
35	G	46	GLN	0	0.033	0.035	16.072	0.099	0.099	0.000	0.000	0.000	0.000
36	G	47	ARG	1	0.847	0.930	15.877	0.277	0.277	0.000	0.000	0.000	0.000
37	G	48	LEU	0	-0.011	0.001	11.788	0.031	0.031	0.000	0.000	0.000	0.000
38	G	49	LEU	0	0.003	-0.007	14.065	0.051	0.051	0.000	0.000	0.000	0.000
39	G	50	TYR	0	-0.023	-0.023	17.461	-0.016	-0.016	0.000	0.000	0.000	0.000
40	G	51	TYR	0	-0.014	0.000	16.608	0.021	0.021	0.000	0.000	0.000	0.000
41	G	52	ASP	-1	-0.813	-0.906	19.118	-0.184	-0.184	0.000	0.000	0.000	0.000
42	G	53	SER	0	0.022	-0.002	20.200	0.014	0.014	0.000	0.000	0.000	0.000
43	G	54	TYR	0	-0.053	-0.010	21.482	0.016	0.016	0.000	0.000	0.000	0.000
44	G	55	THR	0	-0.045	-0.040	25.269	0.007	0.007	0.000	0.000	0.000	0.000
45	G	56	SER	0	-0.030	-0.016	21.637	0.006	0.006	0.000	0.000	0.000	0.000
46	G	57	SER	0	-0.026	0.014	21.942	-0.010	-0.010	0.000	0.000	0.000	0.000
47	G	58	VAL	0	0.033	-0.008	17.940	-0.025	-0.025	0.000	0.000	0.000	0.000
48	G	59	VAL	0	-0.032	-0.003	20.924	0.019	0.019	0.000	0.000	0.000	0.000
49	G	60	LEU	0	-0.026	-0.018	17.257	-0.028	-0.028	0.000	0.000	0.000	0.000
50	G	61	GLU	-1	-0.792	-0.877	19.509	-0.316	-0.316	0.000	0.000	0.000	0.000
51	G	62	SER	0	-0.012	-0.015	21.462	0.005	0.005	0.000	0.000	0.000	0.000
52	G	63	GLY	0	0.024	0.009	21.595	-0.018	-0.018	0.000	0.000	0.000	0.000
53	G	64	ILE	0	-0.061	-0.015	16.139	-0.013	-0.013	0.000	0.000	0.000	0.000
54	G	65	SER	0	0.036	0.009	16.708	0.010	0.010	0.000	0.000	0.000	0.000
55	G	66	PRO	0	0.007	0.005	17.795	-0.021	-0.021	0.000	0.000	0.000	0.000
56	G	67	GLY	0	0.012	-0.003	17.330	0.031	0.031	0.000	0.000	0.000	0.000
57	G	68	LYS	1	0.870	0.978	12.177	0.554	0.554	0.000	0.000	0.000	0.000
58	G	69	TYR	0	0.050	-0.002	10.624	-0.007	-0.007	0.000	0.000	0.000	0.000
59	G	70	ASP	-1	-0.759	-0.838	12.177	-0.275	-0.275	0.000	0.000	0.000	0.000
60	G	71	THR	0	-0.010	-0.025	11.904	-0.061	-0.061	0.000	0.000	0.000	0.000
61	G	72	TYR	0	0.007	0.012	12.716	0.053	0.053	0.000	0.000	0.000	0.000
62	G	73	GLY	0	0.004	-0.009	14.003	0.010	0.010	0.000	0.000	0.000	0.000
63	G	74	SER	0	-0.025	-0.017	13.392	0.000	0.000	0.000	0.000	0.000	0.000
64	G	75	THR	0	0.015	0.004	15.484	0.001	0.001	0.000	0.000	0.000	0.000
65	G	76	ARG	1	0.839	0.913	16.343	0.090	0.090	0.000	0.000	0.000	0.000
66	G	77	LYS	1	0.874	0.942	13.623	0.225	0.225	0.000	0.000	0.000	0.000
67	G	78	ASN	0	-0.030	-0.006	13.780	-0.018	-0.018	0.000	0.000	0.000	0.000
68	G	79	LEU	0	0.020	0.019	13.063	-0.017	-0.017	0.000	0.000	0.000	0.000
69	G	80	ARG	1	0.832	0.891	8.787	0.154	0.154	0.000	0.000	0.000	0.000
70	G	81	MET	0	-0.026	-0.017	8.911	0.067	0.067	0.000	0.000	0.000	0.000
71	G	82	ILE	0	-0.037	-0.018	7.792	-0.181	-0.181	0.000	0.000	0.000	0.000
72	G	83	LEU	0	0.007	0.011	6.743	0.102	0.102	0.000	0.000	0.000	0.000
73	G	84	ARG	1	0.847	0.892	8.147	0.290	0.290	0.000	0.000	0.000	0.000
74	G	85	ASN	0	-0.043	-0.053	10.857	0.018	0.018	0.000	0.000	0.000	0.000
75	G	86	LEU	0	-0.022	0.011	5.009	-0.004	-0.004	0.000	0.000	0.000	0.000
76	G	87	ILE	0	0.040	0.007	9.206	0.051	0.051	0.000	0.000	0.000	0.000
77	G	88	GLU	-1	-0.773	-0.895	10.032	-0.547	-0.547	0.000	0.000	0.000	0.000
78	G	89	ASN	0	-0.033	-0.023	11.714	-0.040	-0.040	0.000	0.000	0.000	0.000
79	G	90	ASP	-1	-0.849	-0.927	8.657	-0.815	-0.815	0.000	0.000	0.000	0.000
80	G	91	SER	0	-0.009	0.016	7.035	-0.440	-0.440	0.000	0.000	0.000	0.000
81	G	92	GLY	0	0.048	0.021	6.820	0.384	0.384	0.000	0.000	0.000	0.000
82	G	93	VAL	0	-0.040	-0.016	6.626	-0.733	-0.733	0.000	0.000	0.000	0.000
83	G	94	TYR	0	0.007	-0.017	6.102	0.524	0.524	0.000	0.000	0.000	0.000
84	G	95	TYR	0	0.018	-0.002	8.439	-0.026	-0.026	0.000	0.000	0.000	0.000
85	G	97	ALA	0	0.035	0.000	12.654	0.026	0.026	0.000	0.000	0.000	0.000
86	G	98	THR	0	0.000	0.002	16.341	0.019	0.019	0.000	0.000	0.000	0.000
87	G	99	TRP	0	0.020	0.002	19.705	-0.005	-0.005	0.000	0.000	0.000	0.000
88	G	100	ASP	-1	-0.848	-0.910	23.269	-0.159	-0.159	0.000	0.000	0.000	0.000
89	G	101	GLN	0	-0.008	-0.003	24.800	-0.005	-0.005	0.000	0.000	0.000	0.000
90	G	102	ASN	0	-0.045	-0.028	27.620	-0.004	-0.004	0.000	0.000	0.000	0.000
91	G	103	TYR	0	0.001	-0.009	26.906	-0.002	-0.002	0.000	0.000	0.000	0.000
92	G	104	TYR	0	0.038	0.043	28.795	-0.001	-0.001	0.000	0.000	0.000	0.000
93	G	105	LYS	1	0.921	0.946	24.091	0.167	0.167	0.000	0.000	0.000	0.000
94	G	106	LYS	1	0.856	0.940	19.463	0.316	0.316	0.000	0.000	0.000	0.000
95	G	107	LEU	0	-0.023	0.004	19.297	-0.008	-0.008	0.000	0.000	0.000	0.000
96	G	108	PHE	0	0.026	-0.016	14.726	-0.022	-0.022	0.000	0.000	0.000	0.000
97	G	109	GLY	0	-0.005	-0.002	12.178	0.039	0.039	0.000	0.000	0.000	0.000
98	G	110	SER	0	-0.046	-0.040	10.090	-0.010	-0.010	0.000	0.000	0.000	0.000
99	G	111	GLY	0	-0.008	0.004	8.388	0.001	0.001	0.000	0.000	0.000	0.000
100	G	112	THR	0	-0.073	-0.048	2.340	0.734	-0.736	3.696	-0.623	-1.602	-0.001
101	G	113	SER	0	-0.018	-0.004	3.792	-0.730	-0.320	0.003	-0.093	-0.321	0.000
102	G	114	LEU	0	0.023	0.015	2.529	-9.924	-6.033	2.775	-2.783	-3.882	-0.033
103	G	115	VAL	0	0.051	0.036	3.443	1.536	1.908	0.013	0.047	-0.432	0.000
104	G	167	TYR	0	0.007	0.008	32.700	0.003	0.003	0.000	0.000	0.000	0.000
105	G	168	TYR	0	-0.077	-0.045	30.320	0.008	0.008	0.000	0.000	0.000	0.000
106	G	169	ILE	0	-0.010	0.002	29.113	-0.010	-0.010	0.000	0.000	0.000	0.000
107	G	170	PHE	0	-0.037	-0.020	25.153	0.003	0.003	0.000	0.000	0.000	0.000
108	G	171	TRP	0	0.022	0.011	22.221	-0.002	-0.002	0.000	0.000	0.000	0.000
109	G	227	ALA	0	0.034	0.030	23.676	-0.007	-0.007	0.000	0.000	0.000	0.000
110	G	228	LEU	0	-0.018	-0.023	25.647	0.011	0.011	0.000	0.000	0.000	0.000
111	G	229	GLY	0	0.043	-0.004	26.642	-0.023	-0.023	0.000	0.000	0.000	0.000
112	G	230	GLU	-1	-0.928	-0.939	28.429	-0.155	-0.155	0.000	0.000	0.000	0.000
113	G	231	SER	0	0.035	-0.006	30.380	0.014	0.014	0.000	0.000	0.000	0.000
114	G	232	LEU	0	-0.030	0.012	29.345	-0.013	-0.013	0.000	0.000	0.000	0.000
115	G	233	THR	0	-0.008	0.000	28.512	0.007	0.007	0.000	0.000	0.000	0.000
116	G	234	ARG	1	0.959	0.981	25.366	0.151	0.151	0.000	0.000	0.000	0.000
117	G	235	ALA	0	-0.015	-0.018	24.074	-0.021	-0.021	0.000	0.000	0.000	0.000
118	G	236	ASP	-1	-0.866	-0.935	24.572	-0.213	-0.213	0.000	0.000	0.000	0.000
119	G	237	LYS	1	0.822	0.891	20.769	0.315	0.315	0.000	0.000	0.000	0.000
120	G	238	LEU	0	0.007	0.009	22.008	0.019	0.019	0.000	0.000	0.000	0.000
121	G	239	ILE	0	-0.030	-0.016	22.022	-0.036	-0.036	0.000	0.000	0.000	0.000
122	G	240	PHE	0	0.014	-0.011	19.905	0.020	0.020	0.000	0.000	0.000	0.000
123	G	241	GLY	0	0.018	0.022	21.354	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:12:VAL)