FMO DATABASE

FMODB ID: 39G6L

Calculation Name: 3R0E-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3R0E

Chain ID: A

ChEMBL ID:
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UniProt ID: B5LYJ9

Base Structure: X-ray

Registration Date: 2023-06-26

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	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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-781753.28933
FMO2-HF: Nuclear repulsion	740038.921458
FMO2-HF: Total energy	-41714.367872
FMO2-MP2: Total energy	-41836.083958

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:LEU)

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

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.
-13.494	-12.106	20.355	-8.805	-12.936	-0.042

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.018

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	THR	0	-0.021	-0.001	3.847	-1.480	1.735	-0.023	-1.825	-1.367	0.003
4	A	4	ASN	0	0.035	0.026	6.171	-0.164	-0.164	0.000	0.000	0.000	0.000
5	A	5	TYR	0	-0.045	-0.033	7.875	0.237	0.237	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.035	0.027	6.388	-0.494	-0.494	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.008	-0.015	8.880	0.287	0.287	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.007	-0.004	11.959	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.011	-0.001	14.120	0.001	0.001	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.014	0.003	8.544	-0.148	-0.148	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.014	-0.027	7.826	0.226	0.226	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.049	-0.006	2.077	-0.985	-1.362	2.500	-0.845	-1.278	-0.002
13	A	13	ASP	-1	-0.793	-0.896	4.523	0.782	0.885	-0.001	-0.004	-0.098	0.000
14	A	14	THR	0	0.004	-0.029	5.869	0.810	0.810	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.882	-0.933	5.278	1.559	1.559	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.025	0.010	2.349	0.859	1.612	3.075	-1.879	-1.948	0.000
17	A	17	HIS	0	-0.078	-0.073	2.062	-7.995	-12.227	11.582	-1.682	-5.668	-0.008
18	A	18	LEU	0	-0.018	-0.010	2.307	-7.813	-5.967	3.223	-2.567	-2.501	-0.035
19	A	19	LYS	1	0.844	0.915	5.069	0.414	0.494	-0.001	-0.003	-0.076	0.000
20	A	20	ASN	0	-0.055	-0.055	7.671	-0.180	-0.180	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.027	0.027	11.271	0.068	0.068	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.907	-0.959	12.243	0.071	0.071	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.038	0.015	12.600	0.068	0.068	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.773	-0.878	7.406	0.408	0.408	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.045	-0.014	7.465	0.055	0.055	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.042	0.009	5.973	0.142	0.142	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.048	-0.007	6.332	-0.670	-0.670	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.018	0.013	8.045	0.257	0.257	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.879	-0.959	9.852	0.467	0.467	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.874	-0.949	11.481	0.351	0.351	0.000	0.000	0.000	0.000
31	A	31	CYS	0	-0.115	-0.014	12.626	-0.172	-0.172	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.003	0.010	14.124	-0.102	-0.102	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.019	0.016	8.748	0.111	0.111	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.010	-0.011	10.901	-0.132	-0.132	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.016	-0.002	10.794	0.070	0.070	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.001	-0.025	9.686	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.032	-0.048	13.654	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.041	0.022	15.603	-0.033	-0.033	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.105	-0.049	16.878	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	40	TRP	0	0.035	0.029	12.880	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.032	0.009	15.001	0.070	0.070	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.006	-0.001	14.895	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	43	ASN	0	-0.060	-0.029	16.554	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.015	-0.012	15.307	-0.027	-0.027	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.032	0.020	17.282	0.024	0.024	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.029	-0.014	17.746	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.065	-0.025	18.670	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.031	0.006	18.371	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.848	0.926	15.136	-0.341	-0.341	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.822	-0.915	12.466	0.310	0.310	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.858	0.940	9.133	-0.229	-0.229	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.030	0.012	7.909	-0.069	-0.069	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.062	-0.030	9.154	-0.158	-0.158	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.012	0.012	11.540	0.064	0.064	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.016	-0.016	13.570	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.859	-0.927	17.231	-0.262	-0.262	0.000	0.000	0.000	0.000
57	A	58	TYR	0	0.014	-0.007	19.821	0.014	0.014	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.048	0.020	17.974	0.020	0.020	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.841	-0.906	17.647	-0.101	-0.101	0.000	0.000	0.000	0.000
60	A	61	LEU	0	0.036	0.012	11.563	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.041	-0.034	13.940	0.055	0.055	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.042	0.030	12.164	-0.046	-0.046	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.887	0.943	13.500	0.085	0.085	0.000	0.000	0.000	0.000
64	A	65	ASN	0	0.052	0.009	13.893	0.036	0.036	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.027	0.026	15.201	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.890	-0.923	16.157	0.090	0.090	0.000	0.000	0.000	0.000
67	A	68	GLY	0	-0.031	-0.010	16.741	-0.029	-0.029	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.070	-0.047	17.790	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.047	-0.049	18.281	0.003	0.003	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.024	0.019	16.872	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	72	TRP	0	0.038	0.012	14.885	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.905	0.951	17.341	0.026	0.026	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.028	0.020	16.879	0.004	0.004	0.000	0.000	0.000	0.000
74	A	75	GLY	0	-0.013	0.011	18.742	0.004	0.004	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.031	-0.018	21.135	0.004	0.004	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.073	-0.045	21.125	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	78	SER	0	0.000	0.007	23.282	0.015	0.015	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.027	0.007	24.804	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.881	0.945	22.609	0.183	0.183	0.000	0.000	0.000	0.000
80	A	81	GLY	0	-0.026	-0.013	22.624	0.010	0.010	0.000	0.000	0.000	0.000
81	A	82	ASN	0	-0.042	-0.019	18.443	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.010	-0.022	16.991	0.028	0.028	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.002	-0.002	13.684	-0.070	-0.070	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.008	0.019	11.175	0.094	0.094	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.016	-0.026	11.181	-0.168	-0.168	0.000	0.000	0.000	0.000
86	A	87	VAL	0	0.045	0.030	8.981	0.116	0.116	0.000	0.000	0.000	0.000
87	A	88	HIS	0	-0.003	0.002	11.889	-0.022	-0.022	0.000	0.000	0.000	0.000
88	A	89	PRO	0	0.018	-0.009	15.527	0.030	0.030	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.833	-0.899	16.687	-0.098	-0.098	0.000	0.000	0.000	0.000
90	A	91	GLY	0	0.012	0.009	16.089	0.027	0.027	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.795	0.880	16.459	0.160	0.160	0.000	0.000	0.000	0.000
92	A	93	LEU	0	0.022	0.019	11.239	-0.054	-0.054	0.000	0.000	0.000	0.000
93	A	94	VAL	0	-0.055	-0.025	14.320	0.045	0.045	0.000	0.000	0.000	0.000
94	A	95	VAL	0	0.011	-0.002	14.659	-0.073	-0.073	0.000	0.000	0.000	0.000
95	A	96	PHE	0	-0.026	-0.006	16.406	0.052	0.052	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.016	0.006	18.199	-0.044	-0.044	0.000	0.000	0.000	0.000
97	A	98	PRO	0	0.021	0.018	20.952	0.021	0.021	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.035	-0.038	20.567	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	100	VAL	0	0.005	0.019	22.284	0.013	0.013	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.001	-0.008	24.353	0.015	0.015	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.876	0.927	21.229	0.261	0.261	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.019	0.023	23.546	0.020	0.020	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.833	-0.927	22.912	-0.302	-0.302	0.000	0.000	0.000	0.000
104	A	105	PRO	0	-0.013	0.004	21.434	0.023	0.023	0.000	0.000	0.000	0.000
105	A	106	TRP	0	-0.007	0.000	18.084	0.023	0.023	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.011	0.010	24.432	0.015	0.015	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.921	0.964	27.945	0.130	0.130	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.008	0.007	30.514	0.012	0.012	0.000	0.000	0.000	0.000

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