FMO DATABASE

FMODB ID: R5LQ8

Calculation Name: 3DB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UKN5

Base Structure: X-ray

Registration Date: 2023-03-14

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1101787.000157
FMO2-HF: Nuclear repulsion	1049841.480158
FMO2-HF: Total energy	-51945.519999
FMO2-MP2: Total energy	-52095.702491

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:4:PRO)

Summations of interaction energy for fragment #1(A:4:PRO)

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.
-1.194	0.499	-0.004	-0.776	-0.913	0.001

Interaction energy analysis for fragmet #1(A:4:PRO)

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 : -0.014

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	6	THR	0	0.007	0.000	3.563	-1.292	0.401	-0.004	-0.776	-0.913	0.001
4	A	7	PHE	0	-0.003	-0.013	5.878	0.417	0.417	0.000	0.000	0.000	0.000
5	A	8	VAL	0	0.001	-0.006	9.004	0.004	0.004	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.030	-0.002	12.541	0.061	0.061	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.875	-0.929	15.216	-0.249	-0.249	0.000	0.000	0.000	0.000
8	A	11	THR	0	-0.060	-0.044	18.810	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	12	PRO	0	-0.023	-0.015	20.535	0.021	0.021	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.009	0.001	23.028	0.007	0.007	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.907	-0.955	26.520	-0.142	-0.142	0.000	0.000	0.000	0.000
12	A	15	SER	0	-0.012	-0.040	29.386	0.006	0.006	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.910	0.938	32.500	0.064	0.064	0.000	0.000	0.000	0.000
14	A	17	ALA	0	-0.012	0.002	35.388	0.000	0.000	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.842	0.879	32.346	0.119	0.119	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.008	0.009	30.609	0.000	0.000	0.000	0.000	0.000	0.000
17	A	20	SER	0	-0.075	-0.036	34.642	0.004	0.004	0.000	0.000	0.000	0.000
18	A	21	LEU	0	-0.008	0.000	37.417	0.005	0.005	0.000	0.000	0.000	0.000
19	A	22	PRO	0	-0.010	-0.003	38.776	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.853	0.913	38.854	0.083	0.083	0.000	0.000	0.000	0.000
21	A	24	GLN	0	-0.018	-0.009	39.800	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.025	-0.004	41.475	0.003	0.003	0.000	0.000	0.000	0.000
23	A	26	VAL	0	0.038	0.008	37.992	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.024	0.007	35.911	0.006	0.006	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.920	0.961	37.093	0.085	0.085	0.000	0.000	0.000	0.000
26	A	29	GLN	0	-0.069	-0.025	38.928	0.000	0.000	0.000	0.000	0.000	0.000
27	A	30	SER	0	-0.064	-0.067	40.542	0.002	0.002	0.000	0.000	0.000	0.000
28	A	31	ILE	0	-0.007	0.006	44.150	0.000	0.000	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.092	-0.062	46.973	0.002	0.002	0.000	0.000	0.000	0.000
30	A	33	GLY	0	0.044	0.016	46.151	0.003	0.003	0.000	0.000	0.000	0.000
31	A	34	ALA	0	-0.040	-0.007	44.050	0.002	0.002	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.810	-0.913	40.555	-0.074	-0.074	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.040	0.005	36.584	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	37	GLY	0	0.071	0.035	39.938	0.005	0.005	0.000	0.000	0.000	0.000
35	A	38	VAL	0	-0.023	-0.012	41.118	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	39	TRP	0	-0.037	-0.026	42.046	0.005	0.005	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.011	-0.011	43.093	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	41	GLY	0	0.048	0.032	42.230	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.823	-0.900	43.093	-0.083	-0.083	0.000	0.000	0.000	0.000
40	A	43	THR	0	-0.008	-0.024	46.302	0.001	0.001	0.000	0.000	0.000	0.000
41	A	44	ILE	0	-0.023	-0.001	46.728	0.000	0.000	0.000	0.000	0.000	0.000
42	A	45	PRO	0	0.027	0.026	50.817	0.002	0.002	0.000	0.000	0.000	0.000
43	A	46	VAL	0	0.020	0.027	54.342	0.000	0.000	0.000	0.000	0.000	0.000
44	A	47	ARG	1	0.877	0.934	56.718	0.043	0.043	0.000	0.000	0.000	0.000
45	A	48	THR	0	0.024	0.021	50.481	0.000	0.000	0.000	0.000	0.000	0.000
46	A	49	CYS	0	-0.050	-0.025	52.908	0.000	0.000	0.000	0.000	0.000	0.000
47	A	50	PHE	0	0.039	0.018	46.954	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.012	0.018	48.308	0.002	0.002	0.000	0.000	0.000	0.000
49	A	52	PRO	0	0.009	-0.006	48.375	0.000	0.000	0.000	0.000	0.000	0.000
50	A	53	LEU	0	-0.019	-0.037	46.148	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	54	ILE	0	-0.061	-0.026	42.802	0.002	0.002	0.000	0.000	0.000	0.000
52	A	55	GLY	0	0.036	-0.016	44.033	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	56	GLN	0	0.032	0.023	41.211	0.002	0.002	0.000	0.000	0.000	0.000
54	A	57	GLN	0	-0.007	-0.005	45.398	0.000	0.000	0.000	0.000	0.000	0.000
55	A	58	SER	0	0.011	0.011	48.717	0.000	0.000	0.000	0.000	0.000	0.000
56	A	59	HIS	0	0.036	0.025	50.939	0.000	0.000	0.000	0.000	0.000	0.000
57	A	71	VAL	0	0.034	-0.003	48.267	0.000	0.000	0.000	0.000	0.000	0.000
58	A	72	ASN	0	-0.030	-0.020	48.708	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	73	HIS	0	0.005	0.016	45.401	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	74	ILE	0	0.021	0.003	48.174	0.000	0.000	0.000	0.000	0.000	0.000
61	A	75	TRP	0	-0.011	-0.002	48.541	0.002	0.002	0.000	0.000	0.000	0.000
62	A	76	LYS	1	0.947	0.977	52.930	0.033	0.033	0.000	0.000	0.000	0.000
63	A	77	ILE	0	0.008	0.012	54.094	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	78	TYR	0	0.000	-0.017	57.068	0.001	0.001	0.000	0.000	0.000	0.000
65	A	79	HIS	0	0.030	0.019	60.564	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	80	ASN	0	-0.022	-0.019	62.463	0.001	0.001	0.000	0.000	0.000	0.000
67	A	81	GLY	0	-0.002	0.008	65.418	0.001	0.001	0.000	0.000	0.000	0.000
68	A	82	VAL	0	0.022	0.022	62.679	0.001	0.001	0.000	0.000	0.000	0.000
69	A	83	LEU	0	-0.072	-0.038	57.453	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	84	GLU	-1	-0.892	-0.945	57.950	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	85	PHE	0	-0.021	-0.021	52.181	0.000	0.000	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.049	-0.024	52.465	0.000	0.000	0.000	0.000	0.000	0.000
73	A	87	ILE	0	-0.006	0.014	47.748	0.000	0.000	0.000	0.000	0.000	0.000
74	A	88	ILE	0	0.026	0.012	45.257	0.000	0.000	0.000	0.000	0.000	0.000
75	A	89	THR	0	-0.035	-0.041	44.295	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	90	THR	0	0.050	0.007	41.331	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	91	ASP	-1	-0.806	-0.877	37.118	-0.075	-0.075	0.000	0.000	0.000	0.000
78	A	92	GLU	-1	-0.726	-0.820	34.336	-0.102	-0.102	0.000	0.000	0.000	0.000
79	A	93	ASN	0	-0.067	-0.047	33.211	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	94	GLU	-1	-0.883	-0.944	36.224	-0.053	-0.053	0.000	0.000	0.000	0.000
81	A	95	CYS	0	-0.091	-0.021	39.483	0.005	0.005	0.000	0.000	0.000	0.000
82	A	96	ASN	0	0.015	0.009	39.532	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	97	TRP	0	0.094	0.025	39.958	0.001	0.001	0.000	0.000	0.000	0.000
84	A	98	MET	0	-0.080	-0.010	41.058	0.000	0.000	0.000	0.000	0.000	0.000
85	A	99	MET	0	-0.025	-0.002	39.535	0.002	0.002	0.000	0.000	0.000	0.000
86	A	100	PHE	0	-0.027	-0.017	36.777	0.001	0.001	0.000	0.000	0.000	0.000
87	A	101	VAL	0	-0.054	-0.009	42.644	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	102	ARG	1	0.904	0.953	41.618	0.074	0.074	0.000	0.000	0.000	0.000
89	A	103	LYS	1	0.894	0.958	47.852	0.045	0.045	0.000	0.000	0.000	0.000
90	A	104	ALA	0	0.013	0.016	51.569	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	105	ARG	1	0.830	0.883	51.214	0.057	0.057	0.000	0.000	0.000	0.000
92	A	106	ASN	0	-0.070	-0.033	55.398	0.002	0.002	0.000	0.000	0.000	0.000
93	A	107	ARG	1	0.975	0.970	57.756	0.035	0.035	0.000	0.000	0.000	0.000
94	A	108	GLU	-1	-0.891	-0.951	59.060	-0.041	-0.041	0.000	0.000	0.000	0.000
95	A	109	GLU	-1	-0.775	-0.851	53.760	-0.053	-0.053	0.000	0.000	0.000	0.000
96	A	110	GLN	0	-0.060	-0.029	54.248	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	111	ASN	0	0.006	-0.007	51.162	0.001	0.001	0.000	0.000	0.000	0.000
98	A	112	LEU	0	0.031	0.029	49.555	0.000	0.000	0.000	0.000	0.000	0.000
99	A	113	VAL	0	-0.010	-0.002	54.246	0.001	0.001	0.000	0.000	0.000	0.000
100	A	114	ALA	0	0.007	-0.004	53.592	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	115	TYR	0	-0.041	-0.040	55.254	0.002	0.002	0.000	0.000	0.000	0.000
102	A	116	PRO	0	0.019	0.000	56.099	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	117	HIS	0	-0.046	-0.030	56.654	0.001	0.001	0.000	0.000	0.000	0.000
104	A	118	ASP	-1	-0.844	-0.918	56.736	-0.034	-0.034	0.000	0.000	0.000	0.000
105	A	119	GLY	0	-0.004	-0.001	56.626	0.000	0.000	0.000	0.000	0.000	0.000
106	A	120	LYS	1	0.862	0.936	50.002	0.041	0.041	0.000	0.000	0.000	0.000
107	A	121	ILE	0	-0.001	0.014	51.440	0.001	0.001	0.000	0.000	0.000	0.000
108	A	122	PHE	0	0.050	0.024	51.445	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	123	PHE	0	-0.007	-0.007	47.638	0.001	0.001	0.000	0.000	0.000	0.000
110	A	124	CYS	0	0.002	0.005	52.461	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	125	THR	0	-0.016	-0.016	52.334	0.001	0.001	0.000	0.000	0.000	0.000
112	A	126	SER	0	-0.047	-0.031	54.865	0.001	0.001	0.000	0.000	0.000	0.000
113	A	127	GLN	0	-0.013	-0.012	56.284	0.003	0.003	0.000	0.000	0.000	0.000
114	A	128	ASP	-1	-0.815	-0.912	55.159	-0.051	-0.051	0.000	0.000	0.000	0.000
115	A	129	ILE	0	-0.058	-0.015	50.268	0.001	0.001	0.000	0.000	0.000	0.000
116	A	130	PRO	0	0.007	0.002	51.060	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	131	PRO	0	0.044	0.034	46.227	0.000	0.000	0.000	0.000	0.000	0.000
118	A	132	GLU	-1	-0.925	-0.972	43.313	-0.086	-0.086	0.000	0.000	0.000	0.000
119	A	133	ASN	0	-0.088	-0.044	45.965	0.004	0.004	0.000	0.000	0.000	0.000
120	A	134	GLU	-1	-0.760	-0.845	45.446	-0.073	-0.073	0.000	0.000	0.000	0.000
121	A	135	LEU	0	-0.023	-0.016	46.138	0.004	0.004	0.000	0.000	0.000	0.000
122	A	136	LEU	0	0.003	-0.006	48.318	0.000	0.000	0.000	0.000	0.000	0.000
123	A	137	PHE	0	0.005	0.011	49.680	0.003	0.003	0.000	0.000	0.000	0.000
124	A	138	TYR	0	-0.004	-0.018	53.053	0.001	0.001	0.000	0.000	0.000	0.000
125	A	139	TYR	0	0.021	0.036	54.156	0.000	0.000	0.000	0.000	0.000	0.000
126	A	140	SER	0	0.074	0.030	58.154	0.000	0.000	0.000	0.000	0.000	0.000
127	A	141	ARG	1	0.858	0.927	60.949	0.036	0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:PRO)