FMO DATABASE

FMODB ID: 946R2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1046769.414985
FMO2-HF: Nuclear repulsion	996693.683803
FMO2-HF: Total energy	-50075.731182
FMO2-MP2: Total energy	-50222.676784

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.
1.721	4.897	0.216	-0.672	-2.722	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 : -0.034 / 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	0.012	-0.018	3.450	2.041	3.386	0.014	-0.241	-1.118	0.001
4	A	4	GLU	-1	-0.919	-0.942	3.300	0.373	1.128	0.035	-0.178	-0.614	0.000
5	A	5	LEU	0	-0.007	-0.016	3.022	0.470	1.546	0.167	-0.253	-0.990	0.000
6	A	6	GLU	-1	-0.931	-0.964	5.781	-1.313	-1.313	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.883	-0.931	8.063	-0.144	-0.144	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.831	0.925	8.389	0.331	0.331	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.042	0.000	8.558	0.217	0.217	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.040	0.015	11.885	0.124	0.124	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.031	0.029	13.352	0.091	0.091	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.070	-0.030	13.217	0.075	0.075	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.016	-0.005	15.922	0.045	0.045	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.917	-0.953	17.493	-0.202	-0.202	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.096	-0.039	17.819	0.050	0.050	0.000	0.000	0.000	0.000
16	A	16	HIS	1	0.728	0.826	18.972	0.106	0.106	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.050	0.031	22.397	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.032	0.008	24.851	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.030	0.010	23.003	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.051	-0.021	22.992	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.017	0.011	23.083	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.059	-0.045	23.250	0.020	0.020	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.005	-0.007	24.928	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.022	0.004	27.078	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.027	-0.009	29.617	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.013	-0.002	33.229	0.009	0.009	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.901	-0.962	32.619	-0.106	-0.106	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.008	0.000	33.177	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.041	-0.004	29.112	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	30	HIS	0	-0.002	-0.005	29.666	0.012	0.012	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.002	-0.010	28.076	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.935	0.970	28.313	0.150	0.150	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.011	0.019	26.592	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.038	-0.012	26.678	0.007	0.007	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.059	0.028	26.938	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.057	-0.023	22.998	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.060	0.026	24.615	0.010	0.010	0.000	0.000	0.000	0.000
38	A	38	HIS	0	-0.046	-0.038	18.430	0.020	0.020	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.914	-0.948	20.922	-0.309	-0.309	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.010	0.008	16.761	-0.044	-0.044	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.015	-0.009	11.460	0.075	0.075	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.057	-0.017	15.963	0.014	0.014	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.016	-0.003	18.629	0.037	0.037	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.002	-0.010	21.513	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.031	-0.039	25.287	0.015	0.015	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.062	0.049	27.698	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.042	-0.034	31.474	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.006	0.000	33.618	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.934	0.964	37.085	0.081	0.081	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.742	-0.859	39.515	-0.082	-0.082	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.052	-0.020	36.448	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.031	-0.017	40.115	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.909	0.967	42.907	0.070	0.070	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.071	-0.048	44.837	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-1.007	-1.006	41.629	-0.087	-0.087	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.919	-0.945	40.076	-0.113	-0.113	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.003	0.009	35.322	0.002	0.002	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.944	0.961	34.653	0.129	0.129	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.899	0.942	28.038	0.200	0.200	0.000	0.000	0.000	0.000
60	A	60	ASN	0	0.041	0.017	27.422	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.029	-0.007	25.575	0.008	0.008	0.000	0.000	0.000	0.000
62	A	62	HIS	0	0.021	0.017	22.376	-0.032	-0.032	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.037	-0.013	21.556	0.030	0.030	0.000	0.000	0.000	0.000
64	A	64	CYS	0	-0.015	-0.001	18.812	-0.028	-0.028	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.018	0.010	19.257	0.037	0.037	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.009	0.010	18.322	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.042	0.003	18.133	0.021	0.021	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.047	0.020	17.932	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	TYR	0	-0.051	-0.019	19.691	0.036	0.036	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.797	-0.864	21.353	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.034	-0.024	22.759	0.011	0.011	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.017	-0.005	22.670	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.035	-0.022	20.959	0.020	0.020	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.011	0.000	18.858	0.017	0.017	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.027	0.025	13.666	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.087	-0.051	15.472	-0.043	-0.043	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.008	0.002	12.191	0.007	0.007	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.839	-0.916	13.808	-0.212	-0.212	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.011	-0.011	13.820	-0.085	-0.085	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.012	0.002	15.107	0.110	0.110	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.069	0.023	16.354	-0.087	-0.087	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.024	0.008	18.932	0.055	0.055	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.006	0.003	22.246	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.071	-0.044	25.018	0.011	0.011	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.016	0.008	27.899	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.872	-0.949	28.080	-0.245	-0.245	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.937	-0.982	30.306	-0.146	-0.146	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.877	-0.928	31.355	-0.164	-0.164	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.855	-0.950	33.281	-0.130	-0.130	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.027	-0.003	33.255	0.009	0.009	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.096	-0.045	28.346	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.882	0.948	31.101	0.137	0.137	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.878	-0.932	33.213	-0.098	-0.098	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.926	0.965	25.372	0.219	0.219	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.001	0.003	28.363	0.002	0.002	0.000	0.000	0.000	0.000
96	A	96	TRP	0	0.065	0.036	31.272	0.007	0.007	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.850	-0.924	32.793	-0.095	-0.095	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.099	-0.071	29.987	0.011	0.011	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.051	-0.040	30.795	0.004	0.004	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.075	-0.031	33.184	0.007	0.007	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.812	0.927	32.347	0.092	0.092	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.975	-0.983	37.777	-0.053	-0.053	0.000	0.000	0.000	0.000
103	A	103	TRP	0	-0.001	-0.003	40.007	0.001	0.001	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.054	-0.028	41.291	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.119	-0.069	42.536	0.005	0.005	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.081	0.059	40.298	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.898	-0.952	39.476	-0.077	-0.077	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.835	-0.935	39.020	-0.107	-0.107	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.023	-0.009	37.276	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	PRO	0	-0.051	-0.013	38.952	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.059	-0.042	40.510	0.007	0.007	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.035	0.012	33.561	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.008	0.010	33.403	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.044	0.016	28.834	0.001	0.001	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.074	-0.030	26.327	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.989	0.995	23.271	0.325	0.325	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.034	-0.037	19.945	0.007	0.007	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.029	0.021	18.561	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.007	-0.002	14.469	0.027	0.027	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.927	-0.968	15.103	-0.532	-0.532	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.055	-0.047	11.122	-0.045	-0.045	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.040	0.026	10.133	0.136	0.136	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.850	0.930	9.075	0.213	0.213	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.057	0.032	8.244	0.037	0.037	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.075	-0.033	10.695	0.157	0.157	0.000	0.000	0.000	0.000
126	A	126	ASN	0	0.034	0.014	13.211	-0.069	-0.069	0.000	0.000	0.000	0.000

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