FMO DATABASE

FMODB ID: 175ZZ

Calculation Name: 1O13-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O13

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X2D6

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-779649.887472
FMO2-HF: Nuclear repulsion	739878.510871
FMO2-HF: Total energy	-39771.376601
FMO2-MP2: Total energy	-39888.998413

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:1:MET)

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

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.
-7.857	1.192	2.27	-3.846	-7.474	-0.013

Interaction energy analysis for fragmet #1(A:1:MET)

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 : 0.016

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	3	ILE	0	0.016	0.016	3.120	-0.663	2.500	0.103	-1.317	-1.949	0.003
4	A	4	ALA	0	0.016	0.008	5.468	-0.398	-0.398	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.002	-0.002	8.551	0.302	0.302	0.000	0.000	0.000	0.000
6	A	6	PRO	0	-0.044	0.008	11.977	-0.100	-0.100	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.028	-0.002	15.068	0.047	0.047	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.001	-0.024	17.740	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.907	-0.949	20.726	-0.065	-0.065	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.033	0.019	19.619	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.908	0.939	19.571	0.122	0.122	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.059	0.036	17.466	0.003	0.003	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.855	0.925	14.716	0.152	0.152	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.843	-0.928	15.667	-0.079	-0.079	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.060	-0.036	16.459	0.032	0.032	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.026	0.025	16.903	0.022	0.022	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.003	0.010	14.559	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.057	-0.048	17.439	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.956	-1.000	19.395	0.098	0.098	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.008	-0.008	21.444	0.028	0.028	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.071	0.018	14.216	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.035	-0.019	18.926	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.989	0.980	20.740	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.008	0.033	18.822	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.054	0.029	20.898	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.020	0.014	18.055	-0.016	-0.016	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.013	-0.005	13.420	0.067	0.067	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.011	0.012	12.272	-0.056	-0.056	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.009	-0.027	9.148	0.095	0.095	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.029	0.003	6.385	-0.042	-0.042	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.958	0.994	4.699	1.059	1.128	-0.001	-0.043	-0.025	0.000
32	A	32	VAL	0	0.030	0.023	2.500	0.739	2.173	0.538	-0.484	-1.488	0.000
33	A	33	LYS	1	0.937	0.951	2.552	-3.950	-2.209	0.665	-1.162	-1.244	-0.016
34	A	34	ASN	0	-0.039	-0.024	5.104	0.416	0.461	-0.001	-0.001	-0.042	0.000
35	A	35	ASN	0	-0.011	-0.004	6.153	0.432	0.432	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.059	0.042	7.111	0.180	0.180	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.037	0.012	6.979	-0.628	-0.628	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.089	-0.046	6.735	0.163	0.163	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.954	-0.983	8.284	-1.027	-1.027	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.011	0.006	9.224	-0.244	-0.244	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.013	0.010	11.456	0.176	0.176	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.024	-0.016	13.270	0.009	0.009	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.823	-0.904	13.795	-0.669	-0.669	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.907	-0.958	17.429	-0.170	-0.170	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.055	-0.026	18.976	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.030	0.002	19.358	0.026	0.026	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.071	-0.036	20.171	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.054	-0.011	22.709	0.019	0.019	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.023	-0.006	24.365	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.879	-0.939	27.630	-0.033	-0.033	0.000	0.000	0.000	0.000
51	A	51	HIS	0	-0.083	-0.057	30.699	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.008	0.032	25.922	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.051	-0.034	25.064	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.024	0.003	23.860	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.005	-0.005	20.232	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.064	0.033	16.829	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.036	-0.025	14.884	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	58	ASN	0	0.032	0.008	13.975	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.086	0.060	15.026	-0.040	-0.040	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.014	-0.018	10.350	-0.060	-0.060	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.953	0.971	9.733	0.060	0.060	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.981	-0.990	10.489	-0.371	-0.371	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.820	0.913	11.019	0.499	0.499	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.023	-0.013	7.271	-0.272	-0.272	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.061	-0.021	5.525	-0.371	-0.371	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.901	-0.950	2.768	-0.577	0.380	0.179	-0.271	-0.865	-0.001
67	A	67	LEU	0	-0.070	-0.040	4.567	0.086	0.517	0.011	-0.061	-0.382	0.000
68	A	68	VAL	0	-0.013	-0.001	6.198	-0.520	-0.520	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.009	0.012	7.344	0.132	0.132	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.006	-0.022	10.842	-0.178	-0.178	0.000	0.000	0.000	0.000
71	A	71	ARG	1	1.013	1.056	14.618	-0.075	-0.075	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.034	-0.001	17.905	0.027	0.027	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.007	-0.015	15.752	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.006	0.009	19.633	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	ARG	1	1.011	0.979	20.246	-0.115	-0.115	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.985	0.994	20.941	-0.043	-0.043	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.036	0.030	17.577	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.016	-0.004	15.936	0.003	0.003	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.046	0.028	16.394	0.017	0.017	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.014	-0.010	17.715	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.031	0.002	11.934	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.929	-0.962	13.098	0.292	0.292	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.037	-0.018	14.377	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.081	-0.038	13.279	-0.042	-0.042	0.000	0.000	0.000	0.000
85	A	85	GLY	0	-0.020	0.000	11.072	-0.030	-0.030	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.019	0.006	8.052	0.039	0.039	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.932	0.966	6.340	-0.718	-0.718	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.038	0.012	8.953	0.081	0.081	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.022	0.023	8.003	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.901	0.941	11.798	-0.363	-0.363	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.045	-0.017	15.292	0.029	0.029	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.045	0.034	13.770	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.069	-0.065	15.885	-0.069	-0.069	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.069	0.045	17.336	0.033	0.033	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.011	0.004	16.662	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.016	-0.004	11.089	0.056	0.056	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.872	-0.934	11.698	-0.080	-0.080	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.882	-0.935	12.325	0.176	0.176	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.017	-0.012	11.062	0.113	0.113	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.005	0.002	6.541	0.233	0.233	0.000	0.000	0.000	0.000
101	A	101	ASN	0	0.025	-0.004	8.668	0.348	0.348	0.000	0.000	0.000	0.000
102	A	102	GLN	0	-0.040	-0.003	10.992	0.125	0.125	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.028	-0.012	2.711	-2.102	-0.893	0.776	-0.507	-1.479	0.001
104	A	104	LEU	0	-0.052	-0.028	4.897	0.285	0.285	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.054	-0.022	7.978	-0.098	-0.098	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.008	0.004	10.256	-0.130	-0.130	0.000	0.000	0.000	0.000
107	A	107	GLN	0	-0.043	-0.018	11.465	-0.055	-0.055	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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