FMO DATABASE

FMODB ID: 72RKK

Calculation Name: 3DB0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DB0

Chain ID: A

ChEMBL ID:

UniProt ID: Q926Z8

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1046136.375249
FMO2-HF: Nuclear repulsion	996059.559385
FMO2-HF: Total energy	-50076.815864
FMO2-MP2: Total energy	-50223.815016

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.
0.557	3.892	0.188	-0.869	-2.655	0.001

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 : -0.046 / q_NPA : -0.039

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

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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	ASN	0	-0.057	-0.025	3.544	1.310	2.903	0.004	-0.463	-1.135	0.001
4	A	4	GLU	-1	-0.880	-0.927	3.367	-0.261	0.346	0.025	-0.128	-0.504	0.000
5	A	5	LEU	0	-0.020	-0.016	2.933	-0.002	1.133	0.159	-0.278	-1.016	0.000
6	A	6	GLU	-1	-0.869	-0.945	5.658	-0.809	-0.809	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.866	-0.935	8.275	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.797	0.903	8.083	0.260	0.260	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.033	0.009	8.738	0.214	0.214	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.007	0.004	11.740	0.125	0.125	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.049	0.029	13.409	0.074	0.074	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.074	-0.033	12.828	0.070	0.070	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.008	0.005	16.020	0.035	0.035	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.888	-0.950	16.772	-0.153	-0.153	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.093	-0.043	16.981	0.036	0.036	0.000	0.000	0.000	0.000
16	A	16	HIS	1	0.714	0.831	18.955	0.058	0.058	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.068	0.044	22.212	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.021	-0.007	24.590	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.026	0.015	23.335	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.064	-0.023	23.417	0.009	0.009	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.013	0.013	23.329	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.059	-0.051	23.331	0.019	0.019	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.027	-0.001	24.982	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.016	0.001	27.141	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.003	0.007	29.768	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.011	-0.006	33.329	0.008	0.008	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.901	-0.957	32.673	-0.100	-0.100	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.018	0.015	32.906	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.022	-0.004	29.440	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	30	HIS	0	-0.010	-0.006	29.906	0.010	0.010	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.012	-0.011	28.188	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.924	0.965	28.539	0.134	0.134	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.030	0.015	27.272	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.037	-0.006	26.872	0.004	0.004	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.039	0.024	27.349	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.031	-0.021	23.401	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.063	0.037	24.500	0.010	0.010	0.000	0.000	0.000	0.000
38	A	38	HIS	0	-0.047	-0.041	18.207	0.020	0.020	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.826	-0.895	20.661	-0.218	-0.218	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.021	0.022	17.061	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.023	0.005	11.915	0.070	0.070	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.075	-0.023	16.115	0.012	0.012	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.002	0.002	18.613	0.034	0.034	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.002	-0.009	21.709	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.029	-0.036	25.527	0.012	0.012	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.038	0.036	28.039	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.033	-0.032	31.890	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.004	0.011	34.193	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.932	0.951	37.549	0.068	0.068	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.706	-0.823	39.344	-0.072	-0.072	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.040	-0.005	37.004	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.027	-0.009	40.194	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.860	0.910	43.777	0.061	0.061	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.096	-0.062	45.346	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.982	-0.986	42.042	-0.073	-0.073	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.944	-0.964	40.343	-0.101	-0.101	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.009	0.001	35.782	0.002	0.002	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.939	0.958	35.213	0.119	0.119	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.850	0.926	28.530	0.174	0.174	0.000	0.000	0.000	0.000
60	A	60	ASN	0	0.008	-0.003	27.849	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.000	0.007	25.596	0.007	0.007	0.000	0.000	0.000	0.000
62	A	62	HIS	0	-0.023	-0.007	22.739	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.045	-0.015	21.917	0.030	0.030	0.000	0.000	0.000	0.000
64	A	64	CYS	0	-0.029	-0.016	18.482	-0.029	-0.029	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.001	0.018	19.399	0.037	0.037	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.011	0.002	18.660	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.038	0.010	18.603	0.019	0.019	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.074	0.028	18.108	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	69	TYR	0	-0.047	-0.015	19.603	0.026	0.026	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.807	-0.878	21.410	0.008	0.008	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.044	-0.023	22.625	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.002	-0.001	22.488	0.003	0.003	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.040	-0.003	20.669	0.020	0.020	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.023	-0.028	18.575	0.012	0.012	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.008	0.003	13.225	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.050	-0.028	15.359	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.011	0.011	12.456	0.005	0.005	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.794	-0.880	14.081	-0.237	-0.237	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.009	-0.003	13.968	-0.085	-0.085	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.015	-0.019	14.770	0.098	0.098	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.069	0.026	16.671	-0.075	-0.075	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.002	0.017	19.239	0.051	0.051	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.017	0.012	22.575	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.056	-0.040	25.238	0.013	0.013	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.008	-0.019	27.938	0.010	0.010	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.774	-0.877	28.619	-0.211	-0.211	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.864	-0.930	30.714	-0.116	-0.116	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.867	-0.905	31.537	-0.138	-0.138	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.775	-0.889	33.360	-0.110	-0.110	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.056	-0.037	32.769	0.009	0.009	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.060	-0.026	28.202	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.798	0.885	30.978	0.119	0.119	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.863	-0.933	33.339	-0.078	-0.078	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.806	0.886	25.115	0.185	0.185	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.020	-0.006	28.483	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	TRP	0	0.070	0.028	31.427	0.006	0.006	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.857	-0.938	33.135	-0.067	-0.067	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.093	-0.052	30.251	0.013	0.013	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.059	-0.022	30.887	0.004	0.004	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.017	-0.003	33.399	0.005	0.005	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.784	0.891	32.422	0.070	0.070	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.919	-0.957	37.550	-0.038	-0.038	0.000	0.000	0.000	0.000
103	A	103	TRP	0	-0.082	-0.032	40.471	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.023	-0.023	41.713	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.150	-0.076	42.969	0.005	0.005	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.078	0.049	40.299	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.909	-0.956	39.785	-0.063	-0.063	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.845	-0.938	39.092	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.003	-0.022	37.342	0.002	0.002	0.000	0.000	0.000	0.000
110	A	110	PRO	0	-0.050	-0.015	39.072	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.065	-0.052	40.683	0.005	0.005	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.054	-0.010	34.062	0.001	0.001	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.026	0.033	34.084	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.037	0.010	29.252	0.001	0.001	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.066	-0.024	26.734	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.905	0.949	24.895	0.243	0.243	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.025	-0.023	20.582	0.004	0.004	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.036	0.027	18.853	-0.016	-0.016	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.026	-0.016	14.926	0.016	0.016	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.930	-0.968	15.628	-0.456	-0.456	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.021	-0.020	11.151	-0.028	-0.028	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.042	0.034	10.517	0.137	0.137	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.779	0.875	9.554	0.196	0.196	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.039	0.028	7.808	0.067	0.067	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.063	-0.017	10.722	0.125	0.125	0.000	0.000	0.000	0.000
126	A	126	ASN	0	0.017	0.005	13.537	-0.044	-0.044	0.000	0.000	0.000	0.000

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