FMO DATABASE

FMODB ID: VRVZ1

Calculation Name: 1AYY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AYY

Chain ID: A

ChEMBL ID:

UniProt ID: Q47898

Base Structure: X-ray

Registration Date: 2023-03-13

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1151112.542568
FMO2-HF: Nuclear repulsion	1097106.628218
FMO2-HF: Total energy	-54005.91435
FMO2-MP2: Total energy	-54161.656459

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:2:THR)

Summations of interaction energy for fragment #1(A:2: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.
-8.892	-6.119	4.503	-2.753	-4.521	0.023

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.022

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	4	LYS	1	0.949	0.991	2.279	-8.665	-5.912	4.504	-2.745	-4.511	0.023
4	A	5	PRO	0	0.012	0.004	4.898	-0.257	-0.237	-0.001	-0.008	-0.010	0.000
5	A	6	ILE	0	-0.009	-0.015	6.809	-0.186	-0.186	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.006	-0.003	9.073	0.124	0.124	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.016	-0.008	11.951	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	9	SER	0	0.007	-0.012	14.745	0.029	0.029	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.003	0.001	18.443	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	11	TRP	0	0.037	0.014	21.698	0.002	0.002	0.000	0.000	0.000	0.000
11	A	12	ASN	0	0.001	-0.005	23.118	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.073	0.040	24.720	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.055	0.030	21.464	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.064	-0.027	20.030	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	16	HIS	0	0.050	0.009	20.764	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.035	0.027	21.404	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	18	ASN	0	0.011	0.010	16.696	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.006	0.007	17.464	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.775	-0.872	19.529	-0.120	-0.120	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.018	0.017	16.022	0.005	0.005	0.000	0.000	0.000	0.000
21	A	22	TRP	0	0.019	0.006	10.301	0.011	0.011	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.785	0.898	16.117	0.111	0.111	0.000	0.000	0.000	0.000
23	A	24	VAL	0	0.022	0.031	16.075	0.014	0.014	0.000	0.000	0.000	0.000
24	A	25	LEU	0	0.022	0.005	10.859	0.011	0.011	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.088	-0.064	12.348	0.006	0.006	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.823	0.900	13.904	0.157	0.157	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.002	0.012	12.166	0.038	0.038	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.015	0.002	13.215	0.051	0.051	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.855	0.906	13.781	-0.059	-0.059	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.046	0.013	11.596	-0.028	-0.028	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.052	0.027	13.703	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.779	-0.861	17.111	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.011	-0.001	15.088	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	35	VAL	0	0.023	-0.001	15.214	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.748	-0.820	17.842	-0.038	-0.038	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.738	0.830	20.727	0.059	0.059	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.005	0.009	19.894	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	39	VAL	0	0.012	-0.011	20.867	0.003	0.003	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.814	0.879	23.198	0.062	0.062	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.044	-0.007	24.620	0.005	0.005	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.003	-0.011	24.702	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.787	-0.879	27.391	-0.049	-0.049	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.780	-0.886	29.482	-0.049	-0.049	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.860	-0.898	30.564	-0.062	-0.062	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.035	-0.018	32.349	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.078	-0.067	33.644	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.818	-0.894	29.067	-0.072	-0.072	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.767	0.855	32.342	0.040	0.040	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.158	-0.109	30.305	0.003	0.003	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.021	-0.017	27.448	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.047	0.021	30.810	0.001	0.001	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.051	-0.021	32.360	0.005	0.005	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.005	0.005	34.743	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.015	0.021	34.964	0.001	0.001	0.000	0.000	0.000	0.000
55	A	56	ARG	1	0.779	0.858	35.601	0.045	0.045	0.000	0.000	0.000	0.000
56	A	57	PRO	0	-0.030	-0.004	37.719	0.000	0.000	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.779	-0.890	40.388	-0.023	-0.023	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.915	0.944	41.577	0.018	0.018	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.896	-0.949	44.999	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.043	-0.014	44.939	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.827	0.882	42.532	0.018	0.018	0.000	0.000	0.000	0.000
62	A	63	VAL	0	0.000	-0.004	37.049	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.046	-0.019	37.526	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.026	-0.009	32.545	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.850	-0.918	30.914	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	67	ALA	0	-0.022	-0.007	26.742	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	68	CYS	0	-0.031	-0.015	23.200	0.006	0.006	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.015	0.001	20.777	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	70	MET	0	0.004	0.001	17.927	0.004	0.004	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.838	-0.904	16.752	0.026	0.026	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.843	-0.919	12.765	0.065	0.065	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.084	-0.046	14.423	0.036	0.036	0.000	0.000	0.000	0.000
73	A	74	TYR	0	-0.015	-0.017	16.554	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.031	0.001	19.442	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	76	ILE	0	0.015	-0.022	20.997	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.023	0.015	23.549	0.005	0.005	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.057	-0.050	25.730	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.013	0.005	28.411	0.004	0.004	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.041	0.019	31.046	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	81	CYS	0	-0.026	-0.024	33.623	0.003	0.003	0.000	0.000	0.000	0.000
81	A	82	MET	0	0.017	0.029	32.964	0.002	0.002	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.770	-0.869	36.582	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.006	-0.018	38.820	0.001	0.001	0.000	0.000	0.000	0.000
84	A	85	ILE	0	0.023	0.019	33.859	0.000	0.000	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.853	0.926	32.765	0.039	0.039	0.000	0.000	0.000	0.000
86	A	87	ASN	0	-0.032	-0.021	29.397	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.058	0.025	29.365	0.003	0.003	0.000	0.000	0.000	0.000
88	A	89	ILE	0	-0.002	0.001	22.605	0.003	0.003	0.000	0.000	0.000	0.000
89	A	90	SER	0	0.002	-0.037	26.117	0.002	0.002	0.000	0.000	0.000	0.000
90	A	91	VAL	0	-0.023	0.006	27.550	0.005	0.005	0.000	0.000	0.000	0.000
91	A	92	ALA	0	0.001	0.010	26.463	0.004	0.004	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.751	0.832	21.919	0.022	0.022	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.004	-0.010	26.054	0.006	0.006	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.049	-0.022	29.405	0.004	0.004	0.000	0.000	0.000	0.000
95	A	96	MET	0	-0.016	0.002	21.631	0.002	0.002	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.879	-0.916	24.181	0.004	0.004	0.000	0.000	0.000	0.000
97	A	98	LYS	1	0.830	0.914	27.696	0.006	0.006	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.010	-0.003	31.132	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.041	-0.004	31.441	0.001	0.001	0.000	0.000	0.000	0.000
100	A	101	HIS	0	-0.002	0.001	32.196	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	VAL	0	0.060	0.022	27.696	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	MET	0	-0.053	-0.034	28.865	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.013	0.017	31.526	0.002	0.002	0.000	0.000	0.000	0.000
104	A	105	VAL	0	0.009	-0.018	34.144	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.018	0.021	36.806	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	ASP	-1	-0.911	-0.966	39.139	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.070	0.041	40.231	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.021	-0.013	35.140	0.001	0.001	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.005	-0.002	36.645	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.929	-0.975	38.880	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	112	PHE	0	-0.004	0.003	32.335	0.000	0.000	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.046	0.028	35.262	0.000	0.000	0.000	0.000	0.000	0.000
113	A	114	LEU	0	-0.031	-0.017	36.206	0.000	0.000	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.098	-0.057	37.969	0.001	0.001	0.000	0.000	0.000	0.000
115	A	116	GLN	0	-0.057	-0.035	33.752	0.002	0.002	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.016	0.000	35.362	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	118	PHE	0	-0.056	-0.023	30.444	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.854	0.910	36.343	0.029	0.029	0.000	0.000	0.000	0.000
119	A	120	LYS	1	0.927	0.975	38.124	0.017	0.017	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.848	-0.909	37.559	-0.033	-0.033	0.000	0.000	0.000	0.000
121	A	122	ASN	0	-0.023	-0.021	41.009	0.000	0.000	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.019	0.015	35.917	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	124	LEU	0	0.043	0.033	39.121	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	125	THR	0	0.037	0.022	39.053	0.002	0.002	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.035	0.000	41.973	0.001	0.001	0.000	0.000	0.000	0.000
126	A	127	GLU	-1	-0.822	-0.891	40.507	-0.039	-0.039	0.000	0.000	0.000	0.000
127	A	128	SER	0	0.039	0.015	39.230	0.001	0.001	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.805	-0.863	42.315	-0.022	-0.022	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.747	0.855	45.742	0.027	0.027	0.000	0.000	0.000	0.000
130	A	131	GLU	-1	-0.734	-0.823	41.034	-0.035	-0.035	0.000	0.000	0.000	0.000
131	A	132	TRP	0	-0.009	0.000	44.196	0.001	0.001	0.000	0.000	0.000	0.000
132	A	133	LYS	1	0.867	0.911	45.680	0.022	0.022	0.000	0.000	0.000	0.000
133	A	134	GLU	-1	-0.877	-0.947	48.180	-0.020	-0.020	0.000	0.000	0.000	0.000
134	A	135	TRP	0	-0.013	-0.001	45.001	0.001	0.001	0.000	0.000	0.000	0.000
135	A	136	LEU	0	-0.024	-0.019	47.641	0.001	0.001	0.000	0.000	0.000	0.000
136	A	137	LYS	1	0.824	0.946	50.311	0.020	0.020	0.000	0.000	0.000	0.000
137	A	138	THR	0	-0.035	-0.023	48.893	0.001	0.001	0.000	0.000	0.000	0.000
138	A	139	SER	0	-0.066	-0.013	47.608	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)