FMO DATABASE

FMODB ID: 72L4K

Calculation Name: 1Y0O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y0O

Chain ID: A

ChEMBL ID:

UniProt ID: Q9SCY2

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-973484.036804
FMO2-HF: Nuclear repulsion	927138.881157
FMO2-HF: Total energy	-46345.155647
FMO2-MP2: Total energy	-46479.546878

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:5:CYS)

Summations of interaction energy for fragment #1(A:5:CYS)

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.
-4.386	-2.348	8.575	-3.493	-7.12	-0.007

Interaction energy analysis for fragmet #1(A:5:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.020

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	7	PHE	0	-0.047	-0.039	3.028	-0.523	2.252	0.914	-1.242	-2.447	-0.004
4	A	8	SER	0	0.037	0.041	4.737	0.270	0.314	-0.001	-0.007	-0.036	0.000
5	A	9	VAL	0	-0.019	-0.041	8.289	0.172	0.172	0.000	0.000	0.000	0.000
6	A	10	SER	0	-0.009	-0.001	10.346	0.137	0.137	0.000	0.000	0.000	0.000
7	A	11	PRO	0	0.044	-0.002	13.387	-0.063	-0.063	0.000	0.000	0.000	0.000
8	A	12	SER	0	-0.018	0.005	15.425	0.007	0.007	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.017	0.009	13.416	0.030	0.030	0.000	0.000	0.000	0.000
10	A	14	LEU	0	-0.090	-0.034	11.214	-0.120	-0.120	0.000	0.000	0.000	0.000
11	A	15	ALA	0	0.035	0.032	7.134	-0.076	-0.076	0.000	0.000	0.000	0.000
12	A	16	PHE	0	-0.017	-0.012	6.314	0.236	0.236	0.000	0.000	0.000	0.000
13	A	17	CYS	0	0.038	0.009	2.935	1.434	-1.023	6.505	-1.508	-2.540	-0.005
14	A	18	ASP	-1	-0.799	-0.895	4.962	1.979	2.154	-0.002	-0.051	-0.122	0.000
15	A	19	LYS	1	0.811	0.906	3.091	-8.292	-7.609	0.820	-0.359	-1.144	0.001
16	A	20	VAL	0	0.001	-0.002	6.773	-0.387	-0.387	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.034	0.025	10.549	-0.045	-0.045	0.000	0.000	0.000	0.000
18	A	22	GLY	0	-0.004	-0.002	12.806	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	23	TYR	0	0.014	0.003	15.714	-0.071	-0.071	0.000	0.000	0.000	0.000
20	A	24	GLY	0	-0.009	-0.004	19.157	-0.063	-0.063	0.000	0.000	0.000	0.000
21	A	25	PRO	0	-0.012	-0.019	20.315	0.004	0.004	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.870	-0.926	19.098	0.264	0.264	0.000	0.000	0.000	0.000
23	A	27	ALA	0	-0.050	-0.015	18.751	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.035	0.012	20.499	-0.032	-0.032	0.000	0.000	0.000	0.000
25	A	29	LYS	1	0.948	0.949	23.729	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.016	0.001	24.900	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	31	GLN	0	-0.017	-0.003	23.829	0.014	0.014	0.000	0.000	0.000	0.000
28	A	32	LEU	0	-0.018	0.001	24.623	0.009	0.009	0.000	0.000	0.000	0.000
29	A	33	ILE	0	-0.005	-0.003	18.998	0.005	0.005	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.927	0.968	21.467	-0.344	-0.344	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.024	0.012	16.259	0.039	0.039	0.000	0.000	0.000	0.000
32	A	36	HIS	0	0.058	0.060	16.344	-0.077	-0.077	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.030	-0.058	13.390	0.089	0.089	0.000	0.000	0.000	0.000
34	A	38	VAL	0	0.004	-0.005	11.809	-0.131	-0.131	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.020	0.018	11.655	0.163	0.163	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.942	0.959	9.488	-1.096	-1.096	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.029	0.016	12.184	-0.043	-0.043	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.756	-0.878	9.621	-0.901	-0.901	0.000	0.000	0.000	0.000
39	A	43	ASN	0	0.008	0.008	11.870	-0.048	-0.048	0.000	0.000	0.000	0.000
40	A	44	GLY	0	-0.003	-0.001	11.677	0.028	0.028	0.000	0.000	0.000	0.000
41	A	45	LYS	1	0.877	0.958	12.620	0.010	0.010	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.001	-0.009	14.227	0.016	0.016	0.000	0.000	0.000	0.000
43	A	47	PHE	0	-0.038	-0.021	14.155	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	48	ASP	-1	-0.771	-0.863	17.005	0.309	0.309	0.000	0.000	0.000	0.000
45	A	49	SER	0	-0.002	0.004	16.374	0.083	0.083	0.000	0.000	0.000	0.000
46	A	50	SER	0	0.007	0.007	17.383	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	51	TYR	0	-0.034	-0.055	15.216	-0.097	-0.097	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.033	0.000	19.981	-0.049	-0.049	0.000	0.000	0.000	0.000
49	A	53	ARG	1	0.837	0.908	21.168	-0.339	-0.339	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.009	0.015	23.275	-0.025	-0.025	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.910	0.957	23.203	-0.271	-0.271	0.000	0.000	0.000	0.000
52	A	56	PRO	0	-0.007	0.000	20.617	0.016	0.016	0.000	0.000	0.000	0.000
53	A	57	LEU	0	0.008	0.009	19.406	-0.044	-0.044	0.000	0.000	0.000	0.000
54	A	58	THR	0	-0.076	-0.062	21.347	0.019	0.019	0.000	0.000	0.000	0.000
55	A	59	PHE	0	0.009	0.009	18.341	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.891	0.944	23.772	-0.151	-0.151	0.000	0.000	0.000	0.000
57	A	61	ILE	0	-0.002	0.013	18.370	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.065	-0.006	21.667	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.094	-0.051	23.040	-0.026	-0.026	0.000	0.000	0.000	0.000
60	A	64	GLY	0	0.009	0.018	24.068	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	65	GLU	-1	-0.867	-0.923	24.210	0.181	0.181	0.000	0.000	0.000	0.000
62	A	66	VAL	0	-0.023	-0.004	19.278	0.014	0.014	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.035	-0.004	15.648	-0.029	-0.029	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.992	0.980	18.778	0.104	0.104	0.000	0.000	0.000	0.000
65	A	69	GLY	0	0.045	0.019	14.942	0.003	0.003	0.000	0.000	0.000	0.000
66	A	70	TRP	0	-0.034	-0.020	14.219	0.069	0.069	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.772	-0.897	15.922	0.211	0.211	0.000	0.000	0.000	0.000
68	A	72	GLN	0	-0.019	-0.023	16.311	0.018	0.018	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.031	0.031	12.869	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	74	ILE	0	-0.036	-0.011	12.743	0.132	0.132	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.030	-0.002	15.162	0.014	0.014	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.024	0.026	15.739	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	77	SER	0	-0.070	-0.053	16.744	-0.028	-0.028	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.844	-0.902	17.384	-0.135	-0.135	0.000	0.000	0.000	0.000
75	A	79	GLY	0	-0.014	-0.026	15.458	-0.044	-0.044	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.090	-0.049	11.960	-0.058	-0.058	0.000	0.000	0.000	0.000
77	A	81	PRO	0	0.058	0.046	12.572	0.028	0.028	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.056	0.050	14.172	0.071	0.071	0.000	0.000	0.000	0.000
79	A	83	MET	0	-0.055	-0.010	11.444	0.039	0.039	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.009	0.008	14.536	-0.081	-0.081	0.000	0.000	0.000	0.000
81	A	85	THR	0	-0.064	-0.060	16.048	0.082	0.082	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.017	0.000	17.062	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.012	0.025	13.272	0.061	0.061	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.787	0.877	8.446	-2.057	-2.057	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.746	0.829	7.284	-0.468	-0.468	0.000	0.000	0.000	0.000
86	A	90	THR	0	-0.045	-0.035	3.520	0.036	0.829	0.340	-0.322	-0.811	0.001
87	A	91	LEU	0	-0.032	-0.013	5.646	-0.702	-0.677	-0.001	-0.004	-0.020	0.000
88	A	92	ARG	1	0.873	0.916	6.278	1.539	1.539	0.000	0.000	0.000	0.000
89	A	93	ILE	0	-0.030	-0.021	8.089	-0.079	-0.079	0.000	0.000	0.000	0.000
90	A	94	PRO	0	0.072	0.045	11.861	0.019	0.019	0.000	0.000	0.000	0.000
91	A	95	PRO	0	0.078	0.034	14.393	0.076	0.076	0.000	0.000	0.000	0.000
92	A	96	GLU	-1	-0.901	-0.937	17.652	-0.161	-0.161	0.000	0.000	0.000	0.000
93	A	97	LEU	0	-0.025	-0.008	15.132	0.039	0.039	0.000	0.000	0.000	0.000
94	A	98	ALA	0	0.022	-0.006	15.975	0.061	0.061	0.000	0.000	0.000	0.000
95	A	99	TYR	0	-0.047	-0.034	18.091	0.008	0.008	0.000	0.000	0.000	0.000
96	A	100	GLY	0	0.020	0.010	20.233	0.003	0.003	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.851	-0.926	21.820	-0.153	-0.153	0.000	0.000	0.000	0.000
98	A	102	ARG	1	0.889	0.966	23.095	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.052	0.035	22.195	0.003	0.003	0.000	0.000	0.000	0.000
100	A	104	ALA	0	-0.012	-0.033	21.788	0.014	0.014	0.000	0.000	0.000	0.000
101	A	105	GLY	0	0.018	0.006	23.644	0.004	0.004	0.000	0.000	0.000	0.000
102	A	106	CYS	0	-0.035	-0.020	25.597	0.000	0.000	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.983	0.998	28.043	-0.066	-0.066	0.000	0.000	0.000	0.000
104	A	108	GLY	0	0.037	0.023	31.206	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	109	GLY	0	0.031	0.005	30.311	0.001	0.001	0.000	0.000	0.000	0.000
106	A	110	SER	0	-0.012	0.008	27.816	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	111	CYS	0	-0.030	-0.021	24.102	0.013	0.013	0.000	0.000	0.000	0.000
108	A	112	LEU	0	-0.039	-0.007	21.289	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	113	ILE	0	-0.025	-0.014	18.030	0.006	0.006	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.036	0.016	19.348	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	115	PRO	0	0.026	0.033	20.665	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	116	ALA	0	0.006	-0.017	20.162	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	117	SER	0	-0.035	-0.031	16.511	-0.048	-0.048	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.036	-0.011	10.907	0.026	0.026	0.000	0.000	0.000	0.000
115	A	119	LEU	0	-0.075	-0.042	12.477	0.053	0.053	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.014	0.025	6.260	-0.048	-0.048	0.000	0.000	0.000	0.000
117	A	121	PHE	0	-0.001	-0.010	8.776	-0.017	-0.017	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.792	-0.858	6.315	4.583	4.583	0.000	0.000	0.000	0.000
119	A	123	ILE	0	-0.008	-0.026	8.842	-0.361	-0.361	0.000	0.000	0.000	0.000
120	A	124	GLU	-1	-0.758	-0.843	11.064	1.419	1.419	0.000	0.000	0.000	0.000
121	A	125	TYR	0	0.013	0.006	13.554	-0.165	-0.165	0.000	0.000	0.000	0.000
122	A	126	ILE	0	-0.009	-0.011	15.949	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	127	GLY	0	0.079	0.042	18.950	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	128	LYS	1	0.957	0.989	21.361	-0.250	-0.250	0.000	0.000	0.000	0.000
125	A	129	ALA	0	-0.033	-0.030	24.386	0.005	0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:5:CYS)