FMO DATABASE

FMODB ID: Q1LKY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1101281.007525
FMO2-HF: Nuclear repulsion	1049334.993606
FMO2-HF: Total energy	-51946.013919
FMO2-MP2: Total energy	-52096.170982

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.
-1.769	-0.08	0.035	-0.847	-0.877	0

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 : 0.000 / q_NPA : -0.023

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].
3	A	6	THR	0	-0.008	-0.008	3.336	-1.872	-0.183	0.035	-0.847	-0.877
4	A	7	PHE	0	0.004	-0.010	5.702	0.398	0.398	0.000	0.000	0.000
5	A	8	VAL	0	0.005	0.002	9.250	-0.030	-0.030	0.000	0.000	0.000
6	A	9	PRO	0	-0.032	-0.002	12.789	0.048	0.048	0.000	0.000	0.000
7	A	10	ASP	-1	-0.871	-0.937	15.608	-0.209	-0.209	0.000	0.000	0.000
8	A	11	THR	0	-0.051	-0.032	19.225	-0.012	-0.012	0.000	0.000	0.000
9	A	12	PRO	0	-0.020	-0.017	20.700	0.019	0.019	0.000	0.000	0.000
10	A	13	ILE	0	-0.008	0.006	23.395	0.006	0.006	0.000	0.000	0.000
11	A	14	GLU	-1	-0.862	-0.930	26.870	-0.121	-0.121	0.000	0.000	0.000
12	A	15	SER	0	-0.014	-0.045	29.565	0.006	0.006	0.000	0.000	0.000
13	A	16	ARG	1	0.849	0.922	32.757	0.055	0.055	0.000	0.000	0.000
14	A	17	ALA	0	-0.005	0.004	35.765	0.001	0.001	0.000	0.000	0.000
15	A	18	ARG	1	0.814	0.880	31.699	0.110	0.110	0.000	0.000	0.000
16	A	19	LEU	0	-0.001	0.002	30.766	0.000	0.000	0.000	0.000	0.000
17	A	20	SER	0	-0.061	-0.027	34.853	0.004	0.004	0.000	0.000	0.000
18	A	21	LEU	0	-0.002	0.002	37.398	0.005	0.005	0.000	0.000	0.000
19	A	22	PRO	0	-0.031	-0.012	38.907	-0.002	-0.002	0.000	0.000	0.000
20	A	23	LYS	1	0.853	0.899	38.936	0.072	0.072	0.000	0.000	0.000
21	A	24	GLN	0	-0.006	0.006	39.881	-0.005	-0.005	0.000	0.000	0.000
22	A	25	LEU	0	-0.035	-0.017	41.385	0.003	0.003	0.000	0.000	0.000
23	A	26	VAL	0	0.024	0.014	37.694	-0.005	-0.005	0.000	0.000	0.000
24	A	27	LEU	0	-0.006	-0.003	35.904	0.005	0.005	0.000	0.000	0.000
25	A	28	ARG	1	0.808	0.895	36.969	0.077	0.077	0.000	0.000	0.000
26	A	29	GLN	0	-0.032	-0.022	38.828	-0.001	-0.001	0.000	0.000	0.000
27	A	30	SER	0	-0.057	-0.048	40.480	0.002	0.002	0.000	0.000	0.000
28	A	31	ILE	0	-0.014	-0.010	44.100	-0.001	-0.001	0.000	0.000	0.000
29	A	32	VAL	0	-0.077	-0.043	46.168	0.003	0.003	0.000	0.000	0.000
30	A	33	GLY	0	0.035	0.015	45.882	0.003	0.003	0.000	0.000	0.000
31	A	34	ALA	0	-0.044	-0.016	44.285	0.001	0.001	0.000	0.000	0.000
32	A	35	GLU	-1	-0.804	-0.917	40.833	-0.068	-0.068	0.000	0.000	0.000
33	A	36	VAL	0	-0.010	0.019	36.655	-0.002	-0.002	0.000	0.000	0.000
34	A	37	GLY	0	0.069	0.033	39.968	0.005	0.005	0.000	0.000	0.000
35	A	38	VAL	0	-0.028	-0.006	41.083	-0.004	-0.004	0.000	0.000	0.000
36	A	39	TRP	0	-0.025	-0.012	42.005	0.004	0.004	0.000	0.000	0.000
37	A	40	THR	0	-0.020	-0.033	42.856	-0.003	-0.003	0.000	0.000	0.000
38	A	41	GLY	0	0.031	0.020	42.008	-0.002	-0.002	0.000	0.000	0.000
39	A	42	GLU	-1	-0.830	-0.902	42.957	-0.072	-0.072	0.000	0.000	0.000
40	A	43	THR	0	-0.006	-0.020	46.012	0.000	0.000	0.000	0.000	0.000
41	A	44	ILE	0	-0.009	0.006	46.490	0.000	0.000	0.000	0.000	0.000
42	A	45	PRO	0	0.030	0.019	50.571	0.002	0.002	0.000	0.000	0.000
43	A	46	VAL	0	0.007	0.027	54.212	0.000	0.000	0.000	0.000	0.000
44	A	47	ARG	1	0.879	0.926	56.953	0.038	0.038	0.000	0.000	0.000
45	A	48	THR	0	0.002	0.011	50.339	0.000	0.000	0.000	0.000	0.000
46	A	49	CYS	0	-0.041	-0.013	52.817	0.000	0.000	0.000	0.000	0.000
47	A	50	PHE	0	0.023	0.007	47.257	-0.002	-0.002	0.000	0.000	0.000
48	A	51	GLY	0	0.032	0.018	48.689	0.002	0.002	0.000	0.000	0.000
49	A	52	PRO	0	0.006	0.005	48.479	-0.001	-0.001	0.000	0.000	0.000
50	A	53	LEU	0	0.002	-0.012	46.642	-0.002	-0.002	0.000	0.000	0.000
51	A	54	ILE	0	-0.055	-0.031	43.274	0.003	0.003	0.000	0.000	0.000
52	A	55	GLY	0	0.054	0.005	43.950	-0.003	-0.003	0.000	0.000	0.000
53	A	56	GLN	0	0.006	0.019	40.941	0.004	0.004	0.000	0.000	0.000
54	A	57	GLN	0	0.003	0.001	45.467	0.000	0.000	0.000	0.000	0.000
55	A	58	SER	0	0.000	-0.003	49.089	0.000	0.000	0.000	0.000	0.000
56	A	59	HIS	0	0.026	0.031	51.510	0.000	0.000	0.000	0.000	0.000
57	A	71	VAL	0	0.054	0.008	48.440	0.000	0.000	0.000	0.000	0.000
58	A	72	ASN	0	-0.045	-0.029	48.691	-0.001	-0.001	0.000	0.000	0.000
59	A	73	HIS	0	0.020	0.032	45.051	-0.003	-0.003	0.000	0.000	0.000
60	A	74	ILE	0	0.005	0.003	48.155	0.000	0.000	0.000	0.000	0.000
61	A	75	TRP	0	0.004	0.000	48.521	0.002	0.002	0.000	0.000	0.000
62	A	76	LYS	1	0.924	0.958	53.094	0.029	0.029	0.000	0.000	0.000
63	A	77	ILE	0	-0.003	0.016	54.174	0.000	0.000	0.000	0.000	0.000
64	A	78	TYR	0	0.012	-0.010	57.161	0.001	0.001	0.000	0.000	0.000
65	A	79	HIS	0	0.057	0.028	60.846	-0.001	-0.001	0.000	0.000	0.000
66	A	80	ASN	0	-0.031	-0.020	62.658	0.001	0.001	0.000	0.000	0.000
67	A	81	GLY	0	-0.004	0.009	65.716	0.001	0.001	0.000	0.000	0.000
68	A	82	VAL	0	-0.026	-0.003	63.101	0.000	0.000	0.000	0.000	0.000
69	A	83	LEU	0	-0.053	-0.039	57.795	-0.001	-0.001	0.000	0.000	0.000
70	A	84	GLU	-1	-0.880	-0.930	58.249	-0.022	-0.022	0.000	0.000	0.000
71	A	85	PHE	0	-0.014	-0.021	52.515	0.000	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.047	-0.017	52.967	0.000	0.000	0.000	0.000	0.000
73	A	87	ILE	0	0.004	0.003	48.009	0.000	0.000	0.000	0.000	0.000
74	A	88	ILE	0	-0.006	-0.006	45.712	0.000	0.000	0.000	0.000	0.000
75	A	89	THR	0	-0.018	-0.030	44.578	0.000	0.000	0.000	0.000	0.000
76	A	90	THR	0	0.050	-0.001	41.866	-0.001	-0.001	0.000	0.000	0.000
77	A	91	ASP	-1	-0.773	-0.867	37.535	-0.064	-0.064	0.000	0.000	0.000
78	A	92	GLU	-1	-0.746	-0.827	34.367	-0.091	-0.091	0.000	0.000	0.000
79	A	93	ASN	0	-0.056	-0.037	33.485	-0.006	-0.006	0.000	0.000	0.000
80	A	94	GLU	-1	-0.851	-0.935	36.404	-0.045	-0.045	0.000	0.000	0.000
81	A	95	CYS	0	-0.108	-0.035	40.023	0.004	0.004	0.000	0.000	0.000
82	A	96	ASN	0	0.019	0.006	40.022	-0.003	-0.003	0.000	0.000	0.000
83	A	97	TRP	0	0.056	0.009	40.172	0.001	0.001	0.000	0.000	0.000
84	A	98	MET	0	-0.054	-0.005	41.262	0.000	0.000	0.000	0.000	0.000
85	A	99	MET	0	-0.029	-0.005	39.795	0.001	0.001	0.000	0.000	0.000
86	A	100	PHE	0	-0.010	0.001	36.985	0.000	0.000	0.000	0.000	0.000
87	A	101	VAL	0	-0.024	0.000	42.687	-0.001	-0.001	0.000	0.000	0.000
88	A	102	ARG	1	0.833	0.917	42.065	0.066	0.066	0.000	0.000	0.000
89	A	103	LYS	1	0.887	0.955	48.140	0.041	0.041	0.000	0.000	0.000
90	A	104	ALA	0	0.015	0.008	51.835	-0.001	-0.001	0.000	0.000	0.000
91	A	105	ARG	1	0.823	0.880	50.852	0.052	0.052	0.000	0.000	0.000
92	A	106	ASN	0	-0.081	-0.044	55.344	0.002	0.002	0.000	0.000	0.000
93	A	107	ARG	1	0.963	0.966	57.784	0.032	0.032	0.000	0.000	0.000
94	A	108	GLU	-1	-0.872	-0.940	59.238	-0.037	-0.037	0.000	0.000	0.000
95	A	109	GLU	-1	-0.782	-0.858	53.639	-0.048	-0.048	0.000	0.000	0.000
96	A	110	GLN	0	-0.065	-0.021	54.212	-0.001	-0.001	0.000	0.000	0.000
97	A	111	ASN	0	0.009	0.002	51.054	0.000	0.000	0.000	0.000	0.000
98	A	112	LEU	0	0.019	0.017	49.648	0.000	0.000	0.000	0.000	0.000
99	A	113	VAL	0	-0.019	-0.007	54.287	0.001	0.001	0.000	0.000	0.000
100	A	114	ALA	0	0.003	-0.005	53.697	-0.001	-0.001	0.000	0.000	0.000
101	A	115	TYR	0	-0.034	-0.039	55.377	0.002	0.002	0.000	0.000	0.000
102	A	116	PRO	0	0.013	0.003	56.129	-0.001	-0.001	0.000	0.000	0.000
103	A	117	HIS	0	-0.020	-0.026	56.949	0.001	0.001	0.000	0.000	0.000
104	A	118	ASP	-1	-0.850	-0.916	56.668	-0.030	-0.030	0.000	0.000	0.000
105	A	119	GLY	0	0.001	0.008	56.585	0.000	0.000	0.000	0.000	0.000
106	A	120	LYS	1	0.816	0.909	49.686	0.037	0.037	0.000	0.000	0.000
107	A	121	ILE	0	-0.010	0.002	51.814	0.001	0.001	0.000	0.000	0.000
108	A	122	PHE	0	0.053	0.024	51.767	-0.002	-0.002	0.000	0.000	0.000
109	A	123	PHE	0	0.002	-0.007	47.742	0.001	0.001	0.000	0.000	0.000
110	A	124	CYS	0	-0.008	-0.003	52.887	0.000	0.000	0.000	0.000	0.000
111	A	125	THR	0	-0.013	-0.013	52.279	0.001	0.001	0.000	0.000	0.000
112	A	126	SER	0	-0.054	-0.029	54.941	0.001	0.001	0.000	0.000	0.000
113	A	127	GLN	0	0.012	-0.014	56.301	0.002	0.002	0.000	0.000	0.000
114	A	128	ASP	-1	-0.854	-0.924	55.235	-0.045	-0.045	0.000	0.000	0.000
115	A	129	ILE	0	-0.027	-0.008	50.177	0.000	0.000	0.000	0.000	0.000
116	A	130	PRO	0	0.008	0.008	50.918	-0.001	-0.001	0.000	0.000	0.000
117	A	131	PRO	0	0.054	0.052	45.640	0.000	0.000	0.000	0.000	0.000
118	A	132	GLU	-1	-0.843	-0.905	42.705	-0.078	-0.078	0.000	0.000	0.000
119	A	133	ASN	0	-0.063	-0.039	45.688	0.003	0.003	0.000	0.000	0.000
120	A	134	GLU	-1	-0.755	-0.843	45.314	-0.066	-0.066	0.000	0.000	0.000
121	A	135	LEU	0	-0.017	-0.010	46.064	0.003	0.003	0.000	0.000	0.000
122	A	136	LEU	0	0.004	0.001	48.288	0.000	0.000	0.000	0.000	0.000
123	A	137	PHE	0	0.005	0.004	49.755	0.003	0.003	0.000	0.000	0.000
124	A	138	TYR	0	0.024	0.004	53.255	0.001	0.001	0.000	0.000	0.000
125	A	139	TYR	0	0.010	0.020	54.116	0.000	0.000	0.000	0.000	0.000
126	A	140	SER	0	0.068	0.035	58.199	0.000	0.000	0.000	0.000	0.000
127	A	141	ARG	1	0.853	0.927	61.030	0.032	0.032	0.000	0.000	0.000

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