FMO DATABASE

FMODB ID: 9G3R2

Calculation Name: 1AY9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AY9

Chain ID: A

ChEMBL ID:

UniProt ID: P0AG11

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-723121.529126
FMO2-HF: Nuclear repulsion	682291.47358
FMO2-HF: Total energy	-40830.055545
FMO2-MP2: Total energy	-40949.211244

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:32:ASP)

Summations of interaction energy for fragment #1(A:32:ASP)

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.
22.837	26.459	0.038	-1.739	-1.92	0.006

Interaction energy analysis for fragmet #1(A:32:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.898 / q_NPA : -0.955

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	34	VAL	0	0.013	0.015	3.752	-0.499	3.091	0.039	-1.736	-1.893	0.006
4	A	35	GLU	-1	-0.823	-0.894	5.143	20.335	20.367	-0.001	-0.003	-0.027	0.000
5	A	36	GLN	0	-0.004	0.006	8.173	-3.294	-3.294	0.000	0.000	0.000	0.000
6	A	37	ARG	1	0.813	0.890	11.096	-24.163	-24.163	0.000	0.000	0.000	0.000
7	A	38	ILE	0	0.022	0.014	14.065	-0.429	-0.429	0.000	0.000	0.000	0.000
8	A	39	ASP	-1	-0.771	-0.884	17.583	14.388	14.388	0.000	0.000	0.000	0.000
9	A	40	LEU	0	0.012	-0.013	20.190	-0.295	-0.295	0.000	0.000	0.000	0.000
10	A	41	ASN	0	-0.040	-0.021	23.361	-0.991	-0.991	0.000	0.000	0.000	0.000
11	A	42	GLN	0	-0.029	-0.020	18.830	-0.111	-0.111	0.000	0.000	0.000	0.000
12	A	43	LEU	0	-0.046	-0.010	21.825	-0.119	-0.119	0.000	0.000	0.000	0.000
13	A	44	LEU	0	-0.027	-0.005	23.833	-0.353	-0.353	0.000	0.000	0.000	0.000
14	A	45	ILE	0	0.005	0.010	27.318	-0.519	-0.519	0.000	0.000	0.000	0.000
15	A	46	GLN	0	0.013	0.006	28.362	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	47	HIS	1	0.800	0.881	30.225	-9.331	-9.331	0.000	0.000	0.000	0.000
17	A	48	PRO	0	0.058	0.028	28.530	-0.305	-0.305	0.000	0.000	0.000	0.000
18	A	49	SER	0	-0.040	-0.019	31.472	-0.068	-0.068	0.000	0.000	0.000	0.000
19	A	50	ALA	0	0.006	0.011	34.382	-0.255	-0.255	0.000	0.000	0.000	0.000
20	A	51	THR	0	-0.024	-0.004	32.676	-0.116	-0.116	0.000	0.000	0.000	0.000
21	A	52	TYR	0	-0.042	-0.039	34.817	0.120	0.120	0.000	0.000	0.000	0.000
22	A	53	PHE	0	-0.028	-0.021	34.427	0.147	0.147	0.000	0.000	0.000	0.000
23	A	54	VAL	0	0.032	0.019	36.810	-0.168	-0.168	0.000	0.000	0.000	0.000
24	A	55	LYS	1	0.845	0.922	38.406	-7.999	-7.999	0.000	0.000	0.000	0.000
25	A	56	ALA	0	0.030	0.024	40.668	-0.180	-0.180	0.000	0.000	0.000	0.000
26	A	57	SER	0	-0.036	-0.031	42.678	0.001	0.001	0.000	0.000	0.000	0.000
27	A	58	GLY	0	0.014	0.008	46.120	-0.090	-0.090	0.000	0.000	0.000	0.000
28	A	59	ASP	-1	-0.816	-0.908	46.714	6.487	6.487	0.000	0.000	0.000	0.000
29	A	60	SER	0	0.016	0.025	48.395	0.041	0.041	0.000	0.000	0.000	0.000
30	A	61	MET	0	-0.049	-0.017	45.096	-0.120	-0.120	0.000	0.000	0.000	0.000
31	A	62	ILE	0	0.031	0.027	44.629	0.171	0.171	0.000	0.000	0.000	0.000
32	A	63	ASP	-1	-0.885	-0.940	44.486	6.674	6.674	0.000	0.000	0.000	0.000
33	A	64	GLY	0	-0.043	-0.030	43.483	0.051	0.051	0.000	0.000	0.000	0.000
34	A	65	GLY	0	-0.044	-0.014	40.268	0.205	0.205	0.000	0.000	0.000	0.000
35	A	66	ILE	0	-0.006	0.003	40.126	0.189	0.189	0.000	0.000	0.000	0.000
36	A	67	SER	0	-0.031	-0.034	41.328	-0.151	-0.151	0.000	0.000	0.000	0.000
37	A	68	ASP	-1	-0.844	-0.906	42.028	7.164	7.164	0.000	0.000	0.000	0.000
38	A	69	GLY	0	0.011	0.010	41.163	0.094	0.094	0.000	0.000	0.000	0.000
39	A	70	ASP	-1	-0.793	-0.876	37.672	8.473	8.473	0.000	0.000	0.000	0.000
40	A	71	LEU	0	-0.052	-0.031	33.475	-0.166	-0.166	0.000	0.000	0.000	0.000
41	A	72	LEU	0	0.021	0.021	35.451	0.230	0.230	0.000	0.000	0.000	0.000
42	A	73	ILE	0	-0.006	-0.005	30.802	0.010	0.010	0.000	0.000	0.000	0.000
43	A	74	VAL	0	-0.002	-0.003	35.082	-0.096	-0.096	0.000	0.000	0.000	0.000
44	A	75	ASP	-1	-0.733	-0.848	35.445	9.078	9.078	0.000	0.000	0.000	0.000
45	A	76	SER	0	-0.002	-0.015	37.338	-0.265	-0.265	0.000	0.000	0.000	0.000
46	A	77	ALA	0	-0.059	-0.025	37.116	-0.181	-0.181	0.000	0.000	0.000	0.000
47	A	78	ILE	0	-0.061	-0.035	37.040	0.102	0.102	0.000	0.000	0.000	0.000
48	A	79	THR	0	-0.014	-0.007	40.336	-0.067	-0.067	0.000	0.000	0.000	0.000
49	A	80	ALA	0	0.040	0.033	43.875	0.035	0.035	0.000	0.000	0.000	0.000
50	A	81	SER	0	-0.036	-0.019	44.441	-0.213	-0.213	0.000	0.000	0.000	0.000
51	A	82	HIS	0	-0.056	-0.036	46.351	-0.050	-0.050	0.000	0.000	0.000	0.000
52	A	83	GLY	0	-0.033	-0.030	45.527	0.018	0.018	0.000	0.000	0.000	0.000
53	A	84	ASP	-1	-0.771	-0.871	42.861	7.586	7.586	0.000	0.000	0.000	0.000
54	A	85	ILE	0	-0.008	-0.004	41.716	-0.204	-0.204	0.000	0.000	0.000	0.000
55	A	86	VAL	0	-0.009	-0.005	42.418	0.188	0.188	0.000	0.000	0.000	0.000
56	A	87	ILE	0	0.004	0.007	41.878	-0.089	-0.089	0.000	0.000	0.000	0.000
57	A	88	ALA	0	0.015	-0.003	45.068	0.009	0.009	0.000	0.000	0.000	0.000
58	A	89	ALA	0	-0.019	-0.005	48.719	0.022	0.022	0.000	0.000	0.000	0.000
59	A	90	VAL	0	0.027	0.007	51.987	0.000	0.000	0.000	0.000	0.000	0.000
60	A	91	ASP	-1	-0.797	-0.868	55.577	5.405	5.405	0.000	0.000	0.000	0.000
61	A	92	GLY	0	-0.028	-0.007	55.869	-0.078	-0.078	0.000	0.000	0.000	0.000
62	A	93	GLU	-1	-0.979	-0.981	54.522	5.724	5.724	0.000	0.000	0.000	0.000
63	A	94	PHE	0	-0.024	-0.017	48.293	0.047	0.047	0.000	0.000	0.000	0.000
64	A	95	THR	0	-0.055	-0.027	49.551	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	96	VAL	0	0.028	0.018	43.597	0.121	0.121	0.000	0.000	0.000	0.000
66	A	97	LYS	1	0.860	0.910	46.690	-6.609	-6.609	0.000	0.000	0.000	0.000
67	A	98	LYS	1	0.897	0.965	46.144	-6.580	-6.580	0.000	0.000	0.000	0.000
68	A	99	LEU	0	0.028	0.029	47.163	-0.192	-0.192	0.000	0.000	0.000	0.000
69	A	100	GLN	0	-0.041	-0.017	49.025	0.202	0.202	0.000	0.000	0.000	0.000
70	A	101	LEU	0	0.051	0.012	50.019	-0.072	-0.072	0.000	0.000	0.000	0.000
71	A	102	ARG	1	0.943	0.986	50.317	-6.326	-6.326	0.000	0.000	0.000	0.000
72	A	103	PRO	0	-0.011	-0.026	55.238	0.094	0.094	0.000	0.000	0.000	0.000
73	A	104	THR	0	0.022	0.001	57.719	-0.050	-0.050	0.000	0.000	0.000	0.000
74	A	105	VAL	0	0.024	0.018	54.405	0.105	0.105	0.000	0.000	0.000	0.000
75	A	106	GLN	0	-0.006	0.007	54.582	-0.123	-0.123	0.000	0.000	0.000	0.000
76	A	107	LEU	0	0.035	0.031	50.046	0.153	0.153	0.000	0.000	0.000	0.000
77	A	108	ILE	0	-0.028	-0.024	50.759	-0.127	-0.127	0.000	0.000	0.000	0.000
78	A	109	PRO	0	0.027	0.006	50.256	0.173	0.173	0.000	0.000	0.000	0.000
79	A	110	MET	0	-0.045	-0.021	44.807	0.067	0.067	0.000	0.000	0.000	0.000
80	A	111	ASN	0	0.033	0.004	48.226	0.008	0.008	0.000	0.000	0.000	0.000
81	A	112	SER	0	-0.008	-0.001	50.972	-0.135	-0.135	0.000	0.000	0.000	0.000
82	A	113	ALA	0	-0.023	0.006	54.142	-0.125	-0.125	0.000	0.000	0.000	0.000
83	A	114	TYR	0	-0.076	-0.057	52.306	-0.094	-0.094	0.000	0.000	0.000	0.000
84	A	115	SER	0	-0.008	-0.011	55.813	-0.037	-0.037	0.000	0.000	0.000	0.000
85	A	116	PRO	0	-0.063	-0.050	55.612	0.082	0.082	0.000	0.000	0.000	0.000
86	A	117	ILE	0	0.041	0.039	54.324	-0.088	-0.088	0.000	0.000	0.000	0.000
87	A	118	THR	0	-0.050	-0.049	56.526	0.067	0.067	0.000	0.000	0.000	0.000
88	A	119	ILE	0	-0.024	-0.001	55.696	0.010	0.010	0.000	0.000	0.000	0.000
89	A	120	SER	0	-0.062	-0.046	59.107	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	121	SER	0	-0.093	-0.079	61.784	0.051	0.051	0.000	0.000	0.000	0.000
91	A	122	GLU	-1	-0.939	-0.955	64.019	4.892	4.892	0.000	0.000	0.000	0.000
92	A	123	ASP	-1	-0.808	-0.856	60.104	5.217	5.217	0.000	0.000	0.000	0.000
93	A	124	THR	0	-0.081	-0.088	58.032	0.067	0.067	0.000	0.000	0.000	0.000
94	A	125	LEU	0	-0.048	-0.016	51.666	0.074	0.074	0.000	0.000	0.000	0.000
95	A	126	ASP	-1	-0.891	-0.940	50.740	6.360	6.360	0.000	0.000	0.000	0.000
96	A	127	VAL	0	-0.050	-0.046	46.017	0.061	0.061	0.000	0.000	0.000	0.000
97	A	128	PHE	0	0.024	0.014	44.890	0.092	0.092	0.000	0.000	0.000	0.000
98	A	129	GLY	0	0.022	0.013	41.560	0.205	0.205	0.000	0.000	0.000	0.000
99	A	130	VAL	0	-0.017	0.008	39.197	-0.162	-0.162	0.000	0.000	0.000	0.000
100	A	131	VAL	0	-0.020	-0.024	38.356	0.228	0.228	0.000	0.000	0.000	0.000
101	A	132	ILE	0	-0.034	-0.011	32.594	-0.030	-0.030	0.000	0.000	0.000	0.000
102	A	133	HIS	0	-0.021	-0.021	30.290	0.172	0.172	0.000	0.000	0.000	0.000
103	A	134	VAL	0	0.021	0.005	34.321	-0.216	-0.216	0.000	0.000	0.000	0.000
104	A	135	VAL	0	-0.012	-0.001	30.842	0.178	0.178	0.000	0.000	0.000	0.000
105	A	136	LYS	1	0.828	0.902	33.289	-8.385	-8.385	0.000	0.000	0.000	0.000
106	A	137	ALA	0	-0.019	-0.004	33.179	0.320	0.320	0.000	0.000	0.000	0.000
107	A	138	MET	0	0.006	-0.008	32.116	-0.051	-0.051	0.000	0.000	0.000	0.000
108	A	139	ARG	1	0.958	0.988	29.917	-8.734	-8.734	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:32:ASP)