FMO DATABASE

FMODB ID: NN1GQ

Calculation Name: 1Y71-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y71

Chain ID: A

ChEMBL ID:

UniProt ID: Q816F1

Base Structure: X-ray

Registration Date: 2023-09-21

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-861085.671365
FMO2-HF: Nuclear repulsion	817568.11512
FMO2-HF: Total energy	-43517.556245
FMO2-MP2: Total energy	-43646.018909

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:THR)

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

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.
-9.389	-5.436	3.729	-3.356	-4.325	-0.017

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.033

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	6	GLU	-1	-0.874	-0.926	3.137	-5.329	-3.163	0.090	-0.990	-1.266	-0.001
4	A	7	ILE	0	-0.044	-0.038	5.177	0.615	0.666	-0.001	-0.001	-0.049	0.000
5	A	8	GLY	0	0.012	0.000	7.871	0.094	0.094	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.863	-0.910	7.409	-0.127	-0.127	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.024	0.020	9.839	0.046	0.046	0.000	0.000	0.000	0.000
8	A	11	VAL	0	0.019	0.002	8.055	0.131	0.131	0.000	0.000	0.000	0.000
9	A	12	THR	0	-0.063	-0.041	11.404	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	13	GLY	0	0.038	0.020	11.573	0.047	0.047	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.048	-0.022	13.336	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	15	TYR	0	0.067	0.015	15.215	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.953	0.978	17.530	0.099	0.099	0.000	0.000	0.000	0.000
14	A	17	THR	0	0.001	0.000	20.310	0.003	0.003	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.046	0.052	21.021	0.013	0.013	0.000	0.000	0.000	0.000
16	A	19	LYS	1	0.935	0.958	15.901	-0.176	-0.176	0.000	0.000	0.000	0.000
17	A	20	TYR	0	0.040	0.032	16.849	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	21	ILE	0	0.053	0.030	15.842	0.026	0.026	0.000	0.000	0.000	0.000
19	A	22	GLY	0	0.032	-0.001	14.583	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.794	-0.858	12.407	-0.442	-0.442	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.009	0.003	6.113	0.065	0.065	0.000	0.000	0.000	0.000
22	A	25	THR	0	-0.016	-0.024	9.599	-0.052	-0.052	0.000	0.000	0.000	0.000
23	A	26	ASN	0	0.001	-0.010	8.628	-0.078	-0.078	0.000	0.000	0.000	0.000
24	A	27	SER	0	0.010	0.012	3.624	-0.502	-0.167	0.016	-0.112	-0.239	0.000
25	A	28	ARG	1	0.902	0.956	6.003	0.866	0.866	0.000	0.000	0.000	0.000
26	A	29	PRO	0	0.052	0.015	6.104	-0.255	-0.255	0.000	0.000	0.000	0.000
27	A	30	GLY	0	0.038	0.031	6.396	0.218	0.218	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.077	-0.046	6.729	0.373	0.373	0.000	0.000	0.000	0.000
29	A	32	TYR	0	0.033	-0.002	2.284	-2.234	-1.344	3.620	-2.076	-2.434	-0.015
30	A	33	VAL	0	-0.052	-0.014	7.965	0.262	0.262	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.014	0.001	10.343	-0.096	-0.096	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.808	0.894	12.710	0.494	0.494	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.014	-0.007	15.711	0.012	0.012	0.000	0.000	0.000	0.000
34	A	37	LEU	0	-0.008	-0.018	16.960	0.001	0.001	0.000	0.000	0.000	0.000
35	A	38	ALA	0	0.031	0.022	19.503	0.015	0.015	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.014	-0.010	20.033	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.008	-0.009	18.197	0.011	0.011	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.830	0.906	21.894	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	42	HIS	0	0.106	0.075	22.869	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	43	PRO	0	-0.029	0.000	23.662	0.013	0.013	0.000	0.000	0.000	0.000
41	A	44	VAL	0	0.013	-0.002	25.111	0.001	0.001	0.000	0.000	0.000	0.000
42	A	45	GLN	0	-0.043	-0.080	27.744	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	61	GLU	-1	-0.761	-0.809	31.412	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	62	ARG	1	0.875	0.938	25.121	0.014	0.014	0.000	0.000	0.000	0.000
45	A	63	ARG	1	0.982	0.996	27.829	0.077	0.077	0.000	0.000	0.000	0.000
46	A	64	ALA	0	-0.020	-0.010	24.360	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.038	-0.013	18.329	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	66	ALA	0	0.024	0.024	22.490	0.011	0.011	0.000	0.000	0.000	0.000
49	A	67	PHE	0	0.036	0.016	22.095	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	68	ARG	1	0.888	0.938	20.090	0.184	0.184	0.000	0.000	0.000	0.000
51	A	69	GLU	-1	-0.900	-0.931	20.066	-0.187	-0.187	0.000	0.000	0.000	0.000
52	A	70	GLN	0	0.013	0.009	15.190	-0.073	-0.073	0.000	0.000	0.000	0.000
53	A	71	THR	0	0.006	-0.007	15.482	0.023	0.023	0.000	0.000	0.000	0.000
54	A	72	ASN	0	0.000	0.005	11.677	-0.126	-0.126	0.000	0.000	0.000	0.000
55	A	73	ILE	0	-0.040	-0.016	11.281	0.095	0.095	0.000	0.000	0.000	0.000
56	A	74	PRO	0	0.025	0.012	10.126	-0.117	-0.117	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.813	-0.900	3.835	-3.185	-2.674	0.004	-0.177	-0.337	-0.001
58	A	76	GLN	0	0.043	0.019	7.604	0.316	0.316	0.000	0.000	0.000	0.000
59	A	77	MET	0	-0.082	-0.039	9.995	0.148	0.148	0.000	0.000	0.000	0.000
60	A	78	VAL	0	-0.018	-0.003	7.454	-0.072	-0.072	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.874	0.932	8.220	-0.399	-0.399	0.000	0.000	0.000	0.000
62	A	80	LYS	1	0.906	0.962	8.239	-0.208	-0.208	0.000	0.000	0.000	0.000
63	A	81	TYR	0	-0.125	-0.081	9.845	0.033	0.033	0.000	0.000	0.000	0.000
64	A	82	GLU	-1	-0.881	-0.960	12.800	0.167	0.167	0.000	0.000	0.000	0.000
65	A	83	GLY	0	-0.014	0.020	15.819	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	84	GLU	-1	-0.910	-0.954	19.007	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	85	ILE	0	-0.030	-0.024	17.617	0.009	0.009	0.000	0.000	0.000	0.000
68	A	86	PRO	0	-0.012	0.011	21.149	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	87	ASP	-1	-0.738	-0.885	23.751	-0.091	-0.091	0.000	0.000	0.000	0.000
70	A	88	TYR	0	-0.012	-0.022	22.806	0.010	0.010	0.000	0.000	0.000	0.000
71	A	89	THR	0	-0.006	0.003	25.349	0.006	0.006	0.000	0.000	0.000	0.000
72	A	90	GLU	-1	-0.924	-0.961	28.787	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	91	SER	0	-0.051	-0.030	24.556	0.007	0.007	0.000	0.000	0.000	0.000
74	A	92	LEU	0	-0.022	-0.012	26.614	0.009	0.009	0.000	0.000	0.000	0.000
75	A	93	LYS	1	0.880	0.921	27.599	0.025	0.025	0.000	0.000	0.000	0.000
76	A	94	LEU	0	0.032	0.018	27.613	0.005	0.005	0.000	0.000	0.000	0.000
77	A	95	ALA	0	-0.015	-0.003	25.907	0.008	0.008	0.000	0.000	0.000	0.000
78	A	96	LEU	0	-0.013	-0.013	27.877	0.006	0.006	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.800	-0.882	30.709	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	98	THR	0	-0.034	-0.019	28.711	0.006	0.006	0.000	0.000	0.000	0.000
81	A	99	GLN	0	-0.002	-0.006	28.848	0.000	0.000	0.000	0.000	0.000	0.000
82	A	100	MET	0	-0.039	-0.007	31.118	0.001	0.001	0.000	0.000	0.000	0.000
83	A	101	ASN	0	0.020	-0.003	34.536	0.000	0.000	0.000	0.000	0.000	0.000
84	A	102	SER	0	-0.112	-0.060	32.063	0.004	0.004	0.000	0.000	0.000	0.000
85	A	103	PHE	0	-0.008	-0.005	33.092	0.002	0.002	0.000	0.000	0.000	0.000
86	A	104	SER	0	0.034	0.022	37.035	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	105	GLU	-1	-1.019	-1.016	39.594	0.029	0.029	0.000	0.000	0.000	0.000
88	A	106	ASP	-1	-0.843	-0.887	37.589	0.024	0.024	0.000	0.000	0.000	0.000
89	A	107	ASP	-1	-0.948	-0.970	40.717	0.015	0.015	0.000	0.000	0.000	0.000
90	A	108	SER	0	-0.060	-0.050	39.289	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	109	PRO	0	0.049	-0.006	41.363	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	110	PHE	0	-0.053	-0.020	31.758	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	111	ALA	0	0.063	0.040	36.938	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.929	-0.955	38.047	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	113	ARG	1	0.941	0.948	34.270	0.009	0.009	0.000	0.000	0.000	0.000
96	A	114	SER	0	-0.090	-0.045	34.060	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	115	LEU	0	-0.005	0.000	35.598	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	116	GLU	-1	-0.895	-0.932	37.653	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	117	THR	0	-0.083	-0.064	33.854	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	118	LEU	0	-0.036	-0.024	31.084	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	119	GLN	0	0.028	0.014	34.688	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	120	GLN	0	-0.043	-0.017	37.360	0.001	0.001	0.000	0.000	0.000	0.000
103	A	121	LEU	0	0.008	-0.002	30.597	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	122	LYS	1	0.901	0.953	33.942	0.014	0.014	0.000	0.000	0.000	0.000
105	A	123	LYS	1	0.888	0.939	35.299	0.022	0.022	0.000	0.000	0.000	0.000
106	A	124	ASP	-1	-0.880	-0.928	34.043	-0.048	-0.048	0.000	0.000	0.000	0.000
107	A	125	TYR	0	-0.101	-0.079	28.850	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	126	LYS	1	0.905	0.962	33.159	0.059	0.059	0.000	0.000	0.000	0.000
109	A	127	LEU	0	-0.048	-0.015	33.178	0.000	0.000	0.000	0.000	0.000	0.000

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