FMO DATABASE

FMODB ID: YQ282

Calculation Name: 1YG2-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YG2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X399

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	172
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1584056.378522
FMO2-HF: Nuclear repulsion	1516266.862615
FMO2-HF: Total energy	-67789.515907
FMO2-MP2: Total energy	-67988.095825

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:1:ACE )

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

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.
9.575	-3.099	27.52	-9.792	-5.053	-0.032

Interaction energy analysis for fragmet #1(A:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : -0.053

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	3	LEU	0	0.015	0.007	3.622	1.050	1.450	-0.005	0.035	-0.430	0.000
4	A	4	PRO	0	0.093	0.032	5.155	0.154	0.154	0.000	0.000	0.000	0.000
5	A	5	HIS	0	0.084	0.078	2.430	-0.497	-2.747	6.876	-2.749	-1.877	-0.014
6	A	6	VAL	0	-0.011	0.019	5.630	0.285	0.285	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.014	-0.016	8.086	0.194	0.194	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.024	-0.019	7.407	0.088	0.088	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.000	-0.012	8.562	0.095	0.095	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.032	-0.006	11.020	0.044	0.044	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.009	-0.014	13.587	0.033	0.033	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.056	-0.025	12.439	0.046	0.046	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.122	-0.044	14.976	0.018	0.018	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.940	0.962	17.961	0.096	0.096	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.803	-0.866	18.593	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.009	-0.023	18.993	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.041	0.014	20.197	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.036	-0.008	19.502	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.014	-0.004	20.173	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.775	-0.878	20.786	-0.105	-0.105	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.067	0.031	15.097	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.073	-0.035	17.147	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.857	0.934	18.762	0.105	0.105	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.905	-0.953	16.474	-0.179	-0.179	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.044	-0.031	11.169	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.098	-0.024	16.702	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.027	0.006	19.259	0.021	0.021	0.000	0.000	0.000	0.000
28	A	28	SER	0	0.028	0.006	18.194	-0.031	-0.031	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.041	0.024	12.597	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.035	0.029	14.338	-0.067	-0.067	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.080	-0.032	16.704	0.010	0.010	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.023	-0.004	9.847	0.012	0.012	0.000	0.000	0.000	0.000
33	A	33	TRP	0	0.010	0.006	5.609	-0.226	-0.226	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.991	1.006	11.984	0.381	0.381	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.007	-0.015	12.314	-0.052	-0.052	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.008	-0.014	14.423	0.043	0.043	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.123	0.039	16.808	-0.024	-0.024	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.013	0.008	18.392	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.011	0.002	13.805	0.008	0.008	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.066	0.057	13.776	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.018	0.013	14.812	0.013	0.013	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.881	0.928	15.907	0.220	0.220	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.891	-0.949	9.590	-0.306	-0.306	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.026	-0.001	12.929	0.037	0.037	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.049	-0.011	14.661	0.040	0.040	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.960	0.973	12.703	0.134	0.134	0.000	0.000	0.000	0.000
47	A	47	MET	0	0.012	0.015	10.167	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.011	0.007	13.129	0.032	0.032	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.986	-0.983	16.769	0.025	0.025	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.049	-0.032	10.267	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.024	0.030	14.781	0.029	0.029	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.036	0.001	9.267	0.014	0.014	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.004	-0.004	13.113	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.033	-0.015	15.678	0.008	0.008	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.021	-0.022	19.481	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.026	0.022	22.290	0.009	0.009	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.027	-0.026	25.236	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.900	-0.939	26.606	-0.035	-0.035	0.000	0.000	0.000	0.000
59	A	59	NME	0	-0.051	-0.031	30.222	0.001	0.001	0.000	0.000	0.000	0.000
60	A	67	ACE	0	-0.019	-0.019	25.601	0.001	0.001	0.000	0.000	0.000	0.000
61	A	68	VAL	0	0.005	0.003	22.453	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	69	TYR	0	-0.035	-0.017	17.668	0.003	0.003	0.000	0.000	0.000	0.000
63	A	70	SER	0	0.031	0.001	18.653	0.001	0.001	0.000	0.000	0.000	0.000
64	A	71	ILE	0	-0.007	0.008	11.978	0.007	0.007	0.000	0.000	0.000	0.000
65	A	72	THR	0	-0.008	-0.029	15.144	0.014	0.014	0.000	0.000	0.000	0.000
66	A	73	GLN	0	0.056	0.011	15.116	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	74	ALA	0	0.011	0.010	13.988	0.027	0.027	0.000	0.000	0.000	0.000
68	A	75	GLY	0	0.077	0.031	11.173	0.054	0.054	0.000	0.000	0.000	0.000
69	A	76	ARG	1	0.884	0.934	10.510	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	77	SER	0	-0.019	-0.007	11.587	0.017	0.017	0.000	0.000	0.000	0.000
71	A	78	ALA	0	0.013	0.010	7.516	0.066	0.066	0.000	0.000	0.000	0.000
72	A	79	LEU	0	-0.049	-0.018	6.827	0.232	0.232	0.000	0.000	0.000	0.000
73	A	80	GLY	0	0.000	-0.005	7.629	0.091	0.091	0.000	0.000	0.000	0.000
74	A	81	GLU	-1	-0.906	-0.948	7.960	0.862	0.862	0.000	0.000	0.000	0.000
75	A	82	TRP	0	-0.061	0.014	1.906	6.183	-4.861	20.649	-7.060	-2.545	-0.018
76	A	83	PHE	0	-0.083	-0.045	5.216	-0.074	-0.039	0.000	-0.006	-0.029	0.000
77	A	84	ASP	-1	-0.907	-0.948	7.815	0.323	0.323	0.000	0.000	0.000	0.000
78	A	85	GLN	0	-0.100	-0.036	5.198	0.447	0.632	0.000	-0.012	-0.172	0.000
79	A	86	PRO	0	-0.031	0.001	7.403	-0.089	-0.089	0.000	0.000	0.000	0.000
80	A	87	THR	0	0.008	0.007	6.335	0.060	0.060	0.000	0.000	0.000	0.000
81	A	88	ALA	0	0.004	-0.017	7.641	-0.041	-0.041	0.000	0.000	0.000	0.000
82	A	89	HIS	0	-0.011	-0.013	9.562	-0.094	-0.094	0.000	0.000	0.000	0.000
83	A	90	PRO	0	0.000	0.003	10.061	0.037	0.037	0.000	0.000	0.000	0.000
84	A	91	THR	0	-0.021	-0.015	12.073	0.022	0.022	0.000	0.000	0.000	0.000
85	A	92	VAL	0	0.024	0.013	15.158	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	93	ARG	1	0.940	0.958	16.739	0.063	0.063	0.000	0.000	0.000	0.000
87	A	94	ASP	-1	-0.793	-0.872	19.898	-0.120	-0.120	0.000	0.000	0.000	0.000
88	A	95	GLU	-1	-0.854	-0.926	21.604	-0.083	-0.083	0.000	0.000	0.000	0.000
89	A	96	PHE	0	-0.004	0.003	22.379	0.008	0.008	0.000	0.000	0.000	0.000
90	A	97	SER	0	0.010	-0.005	25.146	0.011	0.011	0.000	0.000	0.000	0.000
91	A	98	ALA	0	-0.048	-0.021	25.540	0.008	0.008	0.000	0.000	0.000	0.000
92	A	99	LYS	1	0.908	0.949	27.273	0.085	0.085	0.000	0.000	0.000	0.000
93	A	100	LEU	0	0.062	0.027	29.467	0.005	0.005	0.000	0.000	0.000	0.000
94	A	101	MET	0	0.006	0.007	30.197	0.005	0.005	0.000	0.000	0.000	0.000
95	A	102	ALA	0	-0.035	-0.010	32.150	0.004	0.004	0.000	0.000	0.000	0.000
96	A	103	CYS	0	-0.033	-0.026	33.851	0.001	0.001	0.000	0.000	0.000	0.000
97	A	104	SER	0	-0.054	-0.003	36.176	0.003	0.003	0.000	0.000	0.000	0.000
98	A	105	VAL	0	-0.040	-0.027	36.730	0.002	0.002	0.000	0.000	0.000	0.000
99	A	106	GLN	0	-0.034	-0.004	34.961	0.002	0.002	0.000	0.000	0.000	0.000
100	A	107	SER	0	0.001	0.012	38.450	0.000	0.000	0.000	0.000	0.000	0.000
101	A	108	ALA	0	0.062	0.011	37.168	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	109	GLU	-1	-0.894	-0.956	37.289	-0.042	-0.042	0.000	0.000	0.000	0.000
103	A	110	PRO	0	-0.016	-0.009	35.391	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	111	TYR	0	-0.012	-0.032	28.713	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	112	ARG	1	0.942	0.949	33.037	0.043	0.043	0.000	0.000	0.000	0.000
106	A	113	LEU	0	-0.037	-0.019	34.950	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	114	GLN	0	-0.020	-0.014	29.655	0.002	0.002	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.013	0.011	28.846	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	116	ALA	0	0.016	-0.006	30.736	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	117	GLU	-1	-0.955	-0.967	29.949	-0.099	-0.099	0.000	0.000	0.000	0.000
111	A	118	LEU	0	0.045	0.011	25.204	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	119	VAL	0	-0.014	0.013	27.635	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	120	GLU	-1	-0.878	-0.936	29.727	-0.076	-0.076	0.000	0.000	0.000	0.000
114	A	121	GLU	-1	-0.952	-0.987	26.971	-0.124	-0.124	0.000	0.000	0.000	0.000
115	A	122	SER	0	-0.072	-0.046	25.691	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	123	ARG	1	0.874	0.932	26.652	0.069	0.069	0.000	0.000	0.000	0.000
117	A	124	LYS	1	0.928	0.979	29.052	0.103	0.103	0.000	0.000	0.000	0.000
118	A	125	LEU	0	-0.043	-0.020	21.488	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	126	VAL	0	-0.021	-0.015	25.416	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	127	ALA	0	0.025	0.020	26.658	0.002	0.002	0.000	0.000	0.000	0.000
121	A	128	HIS	0	0.051	0.026	24.006	0.009	0.009	0.000	0.000	0.000	0.000
122	A	129	TYR	0	0.001	-0.020	20.099	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	130	GLN	0	-0.007	-0.013	25.388	0.004	0.004	0.000	0.000	0.000	0.000
124	A	131	GLU	-1	-0.953	-0.964	28.306	-0.081	-0.081	0.000	0.000	0.000	0.000
125	A	132	ILE	0	-0.030	-0.013	24.130	0.004	0.004	0.000	0.000	0.000	0.000
126	A	133	GLU	-1	-0.881	-0.957	25.803	-0.091	-0.091	0.000	0.000	0.000	0.000
127	A	134	ALA	0	-0.028	-0.018	27.126	0.006	0.006	0.000	0.000	0.000	0.000
128	A	135	ALA	0	-0.014	0.000	30.088	0.005	0.005	0.000	0.000	0.000	0.000
129	A	136	TYR	0	-0.041	-0.015	26.754	0.005	0.005	0.000	0.000	0.000	0.000
130	A	137	TYR	0	-0.112	-0.087	22.271	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	138	ALA	0	0.045	0.036	27.102	0.001	0.001	0.000	0.000	0.000	0.000
132	A	139	ASN	0	0.025	-0.002	30.109	0.002	0.002	0.000	0.000	0.000	0.000
133	A	140	PRO	0	0.018	-0.015	26.036	0.000	0.000	0.000	0.000	0.000	0.000
134	A	141	ALA	0	-0.050	-0.015	27.690	0.001	0.001	0.000	0.000	0.000	0.000
135	A	142	VAL	0	-0.032	-0.014	30.421	0.004	0.004	0.000	0.000	0.000	0.000
136	A	143	LEU	0	-0.041	0.006	25.742	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	144	ASP	-1	-0.855	-0.939	24.856	-0.052	-0.052	0.000	0.000	0.000	0.000
138	A	145	LYS	1	0.906	0.916	21.638	0.010	0.010	0.000	0.000	0.000	0.000
139	A	146	GLN	0	0.085	0.041	16.581	0.011	0.011	0.000	0.000	0.000	0.000
140	A	147	GLN	0	0.115	0.074	20.017	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	148	ARG	1	0.912	0.967	22.171	0.040	0.040	0.000	0.000	0.000	0.000
142	A	149	LEU	0	-0.003	0.002	16.092	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	150	GLU	-1	-0.813	-0.887	17.718	-0.164	-0.164	0.000	0.000	0.000	0.000
144	A	151	ARG	1	0.977	1.018	18.896	0.069	0.069	0.000	0.000	0.000	0.000
145	A	152	LEU	0	-0.055	-0.030	18.041	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	153	THR	0	-0.062	-0.041	14.213	-0.014	-0.014	0.000	0.000	0.000	0.000
147	A	154	LEU	0	-0.003	0.008	16.573	-0.015	-0.015	0.000	0.000	0.000	0.000
148	A	155	ARG	1	0.869	0.916	19.720	0.099	0.099	0.000	0.000	0.000	0.000
149	A	156	ARG	1	0.959	0.995	14.169	0.303	0.303	0.000	0.000	0.000	0.000
150	A	157	ASN	0	-0.075	-0.056	17.378	-0.015	-0.015	0.000	0.000	0.000	0.000
151	A	158	LEU	0	0.007	0.014	19.278	0.012	0.012	0.000	0.000	0.000	0.000
152	A	159	LEU	0	0.026	0.015	21.381	0.009	0.009	0.000	0.000	0.000	0.000
153	A	160	VAL	0	-0.015	0.001	17.700	0.006	0.006	0.000	0.000	0.000	0.000
154	A	161	ARG	1	0.939	0.968	20.596	0.178	0.178	0.000	0.000	0.000	0.000
155	A	162	GLN	0	0.020	-0.004	22.836	0.008	0.008	0.000	0.000	0.000	0.000
156	A	163	ALA	0	0.008	0.014	23.512	0.008	0.008	0.000	0.000	0.000	0.000
157	A	164	TRP	0	-0.024	-0.018	23.008	0.005	0.005	0.000	0.000	0.000	0.000
158	A	165	ILE	0	-0.006	-0.005	25.073	0.005	0.005	0.000	0.000	0.000	0.000
159	A	166	GLN	0	-0.014	0.004	28.246	0.004	0.004	0.000	0.000	0.000	0.000
160	A	167	TRP	0	0.011	0.004	26.622	0.002	0.002	0.000	0.000	0.000	0.000
161	A	168	ALA	0	0.028	0.005	28.451	0.005	0.005	0.000	0.000	0.000	0.000
162	A	169	ASP	-1	-0.833	-0.919	30.105	-0.062	-0.062	0.000	0.000	0.000	0.000
163	A	170	GLU	-1	-0.964	-0.979	32.333	-0.045	-0.045	0.000	0.000	0.000	0.000
164	A	171	VAL	0	-0.028	-0.007	30.437	0.004	0.004	0.000	0.000	0.000	0.000
165	A	172	LEU	0	-0.050	-0.042	33.305	0.003	0.003	0.000	0.000	0.000	0.000
166	A	173	ALA	0	-0.035	-0.008	35.723	0.003	0.003	0.000	0.000	0.000	0.000
167	A	174	GLU	-1	-0.883	-0.948	36.372	-0.033	-0.033	0.000	0.000	0.000	0.000
168	A	175	LEU	0	-0.091	-0.054	34.509	0.002	0.002	0.000	0.000	0.000	0.000
169	A	176	ASN	0	-0.059	-0.007	38.738	0.000	0.000	0.000	0.000	0.000	0.000
170	A	177	ALA	0	0.005	0.007	41.950	0.002	0.002	0.000	0.000	0.000	0.000
171	A	178	MET	0	-0.060	-0.015	40.324	0.001	0.001	0.000	0.000	0.000	0.000
172	A	179	ALA	-1	-0.977	-0.974	43.318	-0.027	-0.027	0.000	0.000	0.000	0.000

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