FMO DATABASE

FMODB ID: V59M1

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	OptHSide
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	-1067019.64212
FMO2-HF: Nuclear repulsion	1017628.729941
FMO2-HF: Total energy	-49390.912179
FMO2-MP2: Total energy	-49536.022465

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.
-12.06	-6.3	8.919	-4.946	-9.734	-0.027

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 : -0.011 / q_NPA : -0.011

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	0.829	0.886	2.182	-1.761	-0.721	3.541	-1.419	-3.163	0.005
4	G	15	GLN	0	-0.015	0.022	4.962	0.023	0.171	-0.001	-0.013	-0.134	0.000
5	G	16	THR	0	-0.038	-0.035	7.703	0.202	0.202	0.000	0.000	0.000	0.000
6	G	17	GLY	0	-0.009	0.014	9.747	0.026	0.026	0.000	0.000	0.000	0.000
7	G	18	SER	0	-0.040	-0.010	7.693	0.035	0.035	0.000	0.000	0.000	0.000
8	G	19	SER	0	-0.005	-0.037	7.866	-0.089	-0.089	0.000	0.000	0.000	0.000
9	G	20	ALA	0	-0.024	0.003	2.982	-0.018	0.309	0.060	-0.089	-0.298	0.000
10	G	21	GLU	-1	-0.824	-0.863	4.003	-0.662	-0.542	-0.001	-0.028	-0.091	0.000
11	G	22	ILE	0	0.016	0.010	3.615	-1.593	-0.900	0.012	-0.211	-0.494	-0.001
12	G	23	THR	0	-0.009	0.001	5.471	0.464	0.464	0.000	0.000	0.000	0.000
13	G	24	CYS	0	-0.001	0.023	7.896	-0.043	-0.043	0.000	0.000	0.000	0.000
14	G	25	ASP	-1	-0.866	-0.901	10.513	-0.502	-0.502	0.000	0.000	0.000	0.000
15	G	26	LEU	0	0.078	0.025	12.827	0.075	0.075	0.000	0.000	0.000	0.000
16	G	27	ALA	0	0.032	0.015	15.807	0.020	0.020	0.000	0.000	0.000	0.000
17	G	28	GLU	-1	-0.810	-0.903	17.521	-0.161	-0.161	0.000	0.000	0.000	0.000
18	G	29	GLY	0	-0.025	-0.004	16.397	0.009	0.009	0.000	0.000	0.000	0.000
19	G	30	SER	0	-0.045	-0.017	17.426	0.000	0.000	0.000	0.000	0.000	0.000
20	G	31	THR	0	0.032	0.000	19.477	0.000	0.000	0.000	0.000	0.000	0.000
21	G	32	GLY	0	0.022	0.026	22.099	0.006	0.006	0.000	0.000	0.000	0.000
22	G	33	TYR	0	0.004	-0.016	21.567	-0.006	-0.006	0.000	0.000	0.000	0.000
23	G	34	ILE	0	-0.017	0.003	14.883	-0.004	-0.004	0.000	0.000	0.000	0.000
24	G	35	HIS	0	-0.052	-0.022	16.912	-0.005	-0.005	0.000	0.000	0.000	0.000
25	G	36	TRP	0	0.066	0.015	8.421	-0.049	-0.049	0.000	0.000	0.000	0.000
26	G	37	TYR	0	-0.021	-0.018	13.111	0.076	0.076	0.000	0.000	0.000	0.000
27	G	38	LEU	0	-0.004	0.005	9.371	-0.156	-0.156	0.000	0.000	0.000	0.000
28	G	39	HIS	0	0.019	-0.002	11.730	0.114	0.114	0.000	0.000	0.000	0.000
29	G	40	GLN	0	-0.049	-0.036	11.485	-0.067	-0.067	0.000	0.000	0.000	0.000
30	G	41	GLU	-1	-0.913	-0.957	13.895	-0.250	-0.250	0.000	0.000	0.000	0.000
31	G	42	GLY	0	-0.018	-0.014	16.317	0.022	0.022	0.000	0.000	0.000	0.000
32	G	43	LYN	0	-0.072	-0.042	17.939	0.041	0.041	0.000	0.000	0.000	0.000
33	G	44	ALA	0	0.075	0.053	17.049	-0.057	-0.057	0.000	0.000	0.000	0.000
34	G	45	PRO	0	-0.036	-0.013	15.791	-0.011	-0.011	0.000	0.000	0.000	0.000
35	G	46	GLN	0	-0.005	0.008	16.179	0.098	0.098	0.000	0.000	0.000	0.000
36	G	47	ARG	1	0.769	0.873	15.968	0.264	0.264	0.000	0.000	0.000	0.000
37	G	48	LEU	0	0.007	0.005	12.139	0.031	0.031	0.000	0.000	0.000	0.000
38	G	49	LEU	0	-0.004	-0.008	14.300	0.049	0.049	0.000	0.000	0.000	0.000
39	G	50	TYR	0	-0.024	-0.025	17.609	-0.019	-0.019	0.000	0.000	0.000	0.000
40	G	51	TYR	0	-0.004	0.006	17.130	0.013	0.013	0.000	0.000	0.000	0.000
41	G	52	ASP	-1	-0.811	-0.893	19.199	-0.194	-0.194	0.000	0.000	0.000	0.000
42	G	53	SER	0	0.037	0.006	20.190	0.015	0.015	0.000	0.000	0.000	0.000
43	G	54	TYR	0	-0.057	-0.010	21.492	0.017	0.017	0.000	0.000	0.000	0.000
44	G	55	THR	0	-0.061	-0.063	25.312	0.008	0.008	0.000	0.000	0.000	0.000
45	G	56	SER	0	-0.033	-0.018	21.480	0.004	0.004	0.000	0.000	0.000	0.000
46	G	57	SER	0	-0.014	0.019	21.991	-0.009	-0.009	0.000	0.000	0.000	0.000
47	G	58	VAL	0	0.016	-0.013	18.041	-0.025	-0.025	0.000	0.000	0.000	0.000
48	G	59	VAL	0	-0.030	-0.006	21.064	0.020	0.020	0.000	0.000	0.000	0.000
49	G	60	LEU	0	-0.016	-0.009	17.764	-0.027	-0.027	0.000	0.000	0.000	0.000
50	G	61	GLU	-1	-0.715	-0.828	19.690	-0.295	-0.295	0.000	0.000	0.000	0.000
51	G	62	SER	0	-0.015	-0.016	21.734	0.006	0.006	0.000	0.000	0.000	0.000
52	G	63	GLY	0	0.019	0.008	21.845	-0.016	-0.016	0.000	0.000	0.000	0.000
53	G	64	ILE	0	-0.057	-0.015	16.437	-0.010	-0.010	0.000	0.000	0.000	0.000
54	G	65	SER	0	0.029	0.013	17.026	0.015	0.015	0.000	0.000	0.000	0.000
55	G	66	PRO	0	0.001	-0.001	17.966	-0.021	-0.021	0.000	0.000	0.000	0.000
56	G	67	GLY	0	-0.001	-0.011	17.528	0.027	0.027	0.000	0.000	0.000	0.000
57	G	68	LYS	1	0.787	0.909	11.811	0.582	0.582	0.000	0.000	0.000	0.000
58	G	69	TYR	0	0.052	0.003	10.521	-0.004	-0.004	0.000	0.000	0.000	0.000
59	G	70	ASP	-1	-0.784	-0.856	12.297	-0.268	-0.268	0.000	0.000	0.000	0.000
60	G	71	THR	0	-0.009	-0.003	11.954	-0.073	-0.073	0.000	0.000	0.000	0.000
61	G	72	TYR	0	-0.006	-0.022	12.624	0.057	0.057	0.000	0.000	0.000	0.000
62	G	73	GLY	0	0.011	0.001	13.960	0.011	0.011	0.000	0.000	0.000	0.000
63	G	74	SER	0	-0.030	-0.022	13.397	-0.004	-0.004	0.000	0.000	0.000	0.000
64	G	75	THR	0	0.007	0.004	15.446	0.005	0.005	0.000	0.000	0.000	0.000
65	G	76	ARG	1	0.840	0.909	16.233	0.141	0.141	0.000	0.000	0.000	0.000
66	G	77	LYS	1	0.858	0.935	13.385	0.293	0.293	0.000	0.000	0.000	0.000
67	G	78	ASN	0	-0.017	-0.006	13.606	-0.032	-0.032	0.000	0.000	0.000	0.000
68	G	79	LEU	0	0.025	0.030	13.122	-0.019	-0.019	0.000	0.000	0.000	0.000
69	G	80	ARG	1	0.815	0.877	8.700	0.261	0.261	0.000	0.000	0.000	0.000
70	G	81	MET	0	-0.010	-0.007	8.927	0.087	0.087	0.000	0.000	0.000	0.000
71	G	82	ILE	0	-0.031	-0.015	7.818	-0.186	-0.186	0.000	0.000	0.000	0.000
72	G	83	LEU	0	-0.015	0.006	6.873	0.096	0.096	0.000	0.000	0.000	0.000
73	G	84	ARG	1	0.854	0.908	8.310	0.294	0.294	0.000	0.000	0.000	0.000
74	G	85	ASN	0	-0.018	-0.047	10.993	0.027	0.027	0.000	0.000	0.000	0.000
75	G	86	LEU	0	-0.037	0.002	5.254	-0.057	-0.057	0.000	0.000	0.000	0.000
76	G	87	ILE	0	0.039	0.010	9.574	0.067	0.067	0.000	0.000	0.000	0.000
77	G	88	GLU	-1	-0.770	-0.892	10.342	-0.404	-0.404	0.000	0.000	0.000	0.000
78	G	89	ASN	0	-0.016	-0.007	11.877	-0.007	-0.007	0.000	0.000	0.000	0.000
79	G	90	ASP	-1	-0.805	-0.886	8.869	-0.750	-0.750	0.000	0.000	0.000	0.000
80	G	91	SER	0	0.013	0.028	7.210	-0.366	-0.366	0.000	0.000	0.000	0.000
81	G	92	GLY	0	0.051	0.034	7.008	0.339	0.339	0.000	0.000	0.000	0.000
82	G	93	VAL	0	-0.035	-0.014	6.787	-0.664	-0.664	0.000	0.000	0.000	0.000
83	G	94	TYR	0	0.014	-0.007	6.121	0.454	0.454	0.000	0.000	0.000	0.000
84	G	95	TYR	0	0.014	-0.006	8.620	-0.058	-0.058	0.000	0.000	0.000	0.000
85	G	97	ALA	0	0.024	-0.006	12.729	0.025	0.025	0.000	0.000	0.000	0.000
86	G	98	THR	0	0.003	0.001	16.412	0.020	0.020	0.000	0.000	0.000	0.000
87	G	99	TRP	0	0.015	-0.003	19.756	-0.005	-0.005	0.000	0.000	0.000	0.000
88	G	100	ASP	-1	-0.844	-0.908	23.324	-0.173	-0.173	0.000	0.000	0.000	0.000
89	G	101	GLN	0	-0.014	-0.010	24.704	-0.005	-0.005	0.000	0.000	0.000	0.000
90	G	102	ASN	0	-0.039	-0.026	27.623	-0.004	-0.004	0.000	0.000	0.000	0.000
91	G	103	TYR	0	-0.006	-0.016	26.922	0.000	0.000	0.000	0.000	0.000	0.000
92	G	104	TYR	0	0.024	0.036	28.784	0.000	0.000	0.000	0.000	0.000	0.000
93	G	105	LYS	1	0.919	0.940	23.982	0.179	0.179	0.000	0.000	0.000	0.000
94	G	106	LYS	1	0.881	0.951	19.690	0.312	0.312	0.000	0.000	0.000	0.000
95	G	107	LEU	0	-0.020	0.010	19.261	-0.008	-0.008	0.000	0.000	0.000	0.000
96	G	108	PHE	0	0.019	-0.020	14.956	-0.019	-0.019	0.000	0.000	0.000	0.000
97	G	109	GLY	0	-0.001	0.006	12.195	0.035	0.035	0.000	0.000	0.000	0.000
98	G	110	SER	0	-0.062	-0.059	10.043	-0.005	-0.005	0.000	0.000	0.000	0.000
99	G	111	GLY	0	-0.008	0.004	8.394	0.006	0.006	0.000	0.000	0.000	0.000
100	G	112	THR	0	-0.072	-0.047	2.423	0.431	-0.799	3.381	-0.593	-1.558	-0.001
101	G	113	SER	0	-0.004	0.003	3.862	-0.416	-0.038	0.002	-0.082	-0.298	0.000
102	G	114	LEU	0	-0.005	0.004	2.550	-9.232	-5.377	1.919	-2.462	-3.311	-0.030
103	G	115	VAL	0	0.058	0.042	3.651	1.293	1.722	0.006	-0.049	-0.387	0.000
104	G	167	TYR	0	0.001	0.015	32.851	0.001	0.001	0.000	0.000	0.000	0.000
105	G	168	TYR	0	-0.070	-0.050	30.488	0.008	0.008	0.000	0.000	0.000	0.000
106	G	169	ILE	0	-0.009	0.002	29.115	-0.009	-0.009	0.000	0.000	0.000	0.000
107	G	170	PHE	0	-0.040	-0.018	25.253	0.001	0.001	0.000	0.000	0.000	0.000
108	G	171	TRP	0	0.031	0.015	22.243	-0.001	-0.001	0.000	0.000	0.000	0.000
109	G	227	ALA	0	0.022	0.022	23.611	-0.006	-0.006	0.000	0.000	0.000	0.000
110	G	228	LEU	0	-0.009	-0.020	25.687	0.009	0.009	0.000	0.000	0.000	0.000
111	G	229	GLY	0	0.042	-0.004	26.798	-0.023	-0.023	0.000	0.000	0.000	0.000
112	G	230	GLU	-1	-0.922	-0.945	28.578	-0.152	-0.152	0.000	0.000	0.000	0.000
113	G	231	SER	0	0.017	-0.004	30.549	0.012	0.012	0.000	0.000	0.000	0.000
114	G	232	LEU	0	-0.025	0.011	29.445	-0.013	-0.013	0.000	0.000	0.000	0.000
115	G	233	THR	0	-0.002	-0.029	28.617	0.007	0.007	0.000	0.000	0.000	0.000
116	G	234	ARG	1	0.953	0.986	25.445	0.154	0.154	0.000	0.000	0.000	0.000
117	G	235	ALA	0	0.000	-0.004	24.170	-0.022	-0.022	0.000	0.000	0.000	0.000
118	G	236	ASP	-1	-0.858	-0.903	24.707	-0.208	-0.208	0.000	0.000	0.000	0.000
119	G	237	LYS	1	0.821	0.900	20.955	0.299	0.299	0.000	0.000	0.000	0.000
120	G	238	LEU	0	-0.009	0.004	22.111	0.016	0.016	0.000	0.000	0.000	0.000
121	G	239	ILE	0	0.001	-0.008	22.194	-0.035	-0.035	0.000	0.000	0.000	0.000
122	G	240	PHE	0	0.035	0.012	20.019	0.018	0.018	0.000	0.000	0.000	0.000
123	G	241	GLY	0	-0.008	0.003	21.881	-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)