FMO DATABASE

FMODB ID: 3J6QL

Calculation Name: 1YG2-A-Xray372

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: 2023-09-24

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	OptH
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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1570549.318221
FMO2-HF: Nuclear repulsion	1503081.135819
FMO2-HF: Total energy	-67468.182402
FMO2-MP2: Total energy	-67665.764591

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:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-38.279	-40.247	25.032	-11.354	-11.711	0.022

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.041

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	PRO	0	0.093	0.037	2.434	-2.367	0.558	1.685	-1.872	-2.738	0.004
4	A	5	HIS	1	0.930	0.942	1.804	-36.019	-43.888	20.747	-6.954	-5.924	0.037
5	A	6	VAL	0	-0.004	0.024	3.468	-1.787	-1.264	0.002	-0.171	-0.354	0.000
6	A	7	ILE	0	0.001	-0.008	5.558	0.074	0.074	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.025	-0.018	7.582	-0.118	-0.118	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.001	-0.012	6.933	-0.258	-0.258	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.025	-0.002	9.527	-0.108	-0.108	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.007	-0.013	12.033	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.055	-0.025	11.692	0.028	0.028	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.117	-0.042	14.093	-0.065	-0.065	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.946	0.966	16.571	-0.136	-0.136	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.804	-0.866	17.129	0.355	0.355	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.015	-0.024	17.090	-0.045	-0.045	0.000	0.000	0.000	0.000
16	A	17	THR	0	0.040	0.012	18.579	0.017	0.017	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.048	0.000	17.135	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.012	-0.010	17.448	-0.036	-0.036	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.780	-0.877	18.621	0.028	0.028	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.065	0.026	12.779	-0.038	-0.038	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.037	-0.024	14.410	-0.075	-0.075	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.830	0.935	15.736	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.908	-0.957	13.709	-0.120	-0.120	0.000	0.000	0.000	0.000
24	A	25	PHE	0	-0.046	-0.031	7.974	-0.089	-0.089	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.053	-0.013	13.292	-0.050	-0.050	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.017	-0.009	15.955	0.028	0.028	0.000	0.000	0.000	0.000
27	A	28	SER	0	0.041	0.014	15.300	-0.072	-0.072	0.000	0.000	0.000	0.000
28	A	29	ILE	0	0.042	0.024	9.552	-0.067	-0.067	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.028	0.025	11.174	-0.183	-0.183	0.000	0.000	0.000	0.000
30	A	31	TYR	0	-0.071	-0.027	13.276	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.019	-0.003	7.001	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	TRP	0	0.001	-0.001	2.356	-2.503	-1.594	2.244	-1.652	-1.501	-0.013
33	A	34	LYS	1	0.995	1.008	8.467	0.871	0.871	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.017	-0.021	8.354	-0.170	-0.170	0.000	0.000	0.000	0.000
35	A	36	SER	0	0.000	-0.010	10.426	0.122	0.122	0.000	0.000	0.000	0.000
36	A	37	HIS	0	0.135	0.050	12.552	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.016	0.009	14.307	0.049	0.049	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.019	-0.001	9.234	0.056	0.056	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.061	0.053	9.946	0.025	0.025	0.000	0.000	0.000	0.000
40	A	41	TYR	0	0.025	0.016	10.972	0.115	0.115	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.885	0.930	11.546	0.420	0.420	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.900	-0.954	6.226	0.344	0.344	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.026	-0.002	9.350	0.212	0.212	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.042	-0.007	11.992	0.071	0.071	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.959	0.973	9.067	0.245	0.245	0.000	0.000	0.000	0.000
46	A	47	MET	0	0.003	0.010	8.454	0.115	0.115	0.000	0.000	0.000	0.000
47	A	48	GLY	0	-0.004	0.010	10.766	0.053	0.053	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.979	-0.979	13.988	0.214	0.214	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.056	-0.036	7.579	0.118	0.118	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.030	0.033	12.739	0.057	0.057	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.045	-0.005	8.356	0.078	0.078	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.001	-0.006	11.894	0.038	0.038	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.031	-0.014	14.575	-0.072	-0.072	0.000	0.000	0.000	0.000
54	A	55	CYS	0	-0.012	-0.018	18.231	0.001	0.001	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.019	0.018	20.812	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.045	-0.023	23.992	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.913	-0.959	25.342	0.158	0.158	0.000	0.000	0.000	0.000
58	A	68	VAL	0	-0.030	-0.015	21.078	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	69	TYR	0	-0.034	-0.029	16.278	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	70	SER	0	0.029	0.001	17.793	0.001	0.001	0.000	0.000	0.000	0.000
61	A	71	ILE	0	-0.016	0.003	12.019	0.060	0.060	0.000	0.000	0.000	0.000
62	A	72	THR	0	0.000	-0.024	14.865	-0.049	-0.049	0.000	0.000	0.000	0.000
63	A	73	GLN	0	0.061	0.013	15.451	0.072	0.072	0.000	0.000	0.000	0.000
64	A	74	ALA	0	0.013	0.011	13.913	0.062	0.062	0.000	0.000	0.000	0.000
65	A	75	GLY	0	0.071	0.029	11.228	0.223	0.223	0.000	0.000	0.000	0.000
66	A	76	ARG	1	0.887	0.934	11.259	-0.334	-0.334	0.000	0.000	0.000	0.000
67	A	77	SER	0	-0.010	-0.003	12.634	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	78	ALA	0	0.009	0.009	8.249	0.053	0.053	0.000	0.000	0.000	0.000
69	A	79	LEU	0	-0.068	-0.028	6.942	0.789	0.789	0.000	0.000	0.000	0.000
70	A	80	GLY	0	0.010	-0.001	8.682	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	81	GLU	-1	-0.899	-0.943	10.190	1.508	1.508	0.000	0.000	0.000	0.000
72	A	82	TRP	0	-0.064	-0.050	2.814	-0.018	1.526	0.354	-0.705	-1.194	-0.006
73	A	83	PHE	0	-0.080	-0.045	7.182	-0.568	-0.568	0.000	0.000	0.000	0.000
74	A	84	ASP	-1	-0.897	-0.942	8.912	0.547	0.547	0.000	0.000	0.000	0.000
75	A	85	GLN	0	-0.102	-0.036	7.408	0.221	0.221	0.000	0.000	0.000	0.000
76	A	86	PRO	0	-0.024	0.004	9.554	-0.096	-0.096	0.000	0.000	0.000	0.000
77	A	87	THR	0	0.000	0.003	7.942	-0.084	-0.084	0.000	0.000	0.000	0.000
78	A	88	ALA	0	0.008	-0.014	9.459	0.029	0.029	0.000	0.000	0.000	0.000
79	A	89	HIS	0	-0.010	-0.012	10.737	-0.163	-0.163	0.000	0.000	0.000	0.000
80	A	90	PRO	0	-0.006	0.000	10.428	0.033	0.033	0.000	0.000	0.000	0.000
81	A	91	THR	0	-0.019	-0.014	12.730	0.052	0.052	0.000	0.000	0.000	0.000
82	A	92	VAL	0	0.024	0.013	15.882	-0.041	-0.041	0.000	0.000	0.000	0.000
83	A	93	ARG	1	0.943	0.960	16.469	0.355	0.355	0.000	0.000	0.000	0.000
84	A	94	ASP	-1	-0.791	-0.871	18.991	-0.339	-0.339	0.000	0.000	0.000	0.000
85	A	95	GLU	-1	-0.855	-0.926	20.177	-0.280	-0.280	0.000	0.000	0.000	0.000
86	A	96	PHE	0	-0.003	0.003	20.138	0.023	0.023	0.000	0.000	0.000	0.000
87	A	97	SER	0	0.007	-0.006	23.908	0.029	0.029	0.000	0.000	0.000	0.000
88	A	98	ALA	0	-0.045	-0.020	24.583	0.020	0.020	0.000	0.000	0.000	0.000
89	A	99	LYS	1	0.909	0.950	25.480	0.257	0.257	0.000	0.000	0.000	0.000
90	A	100	LEU	0	0.058	0.025	28.034	0.013	0.013	0.000	0.000	0.000	0.000
91	A	101	MET	0	0.006	0.006	29.499	0.013	0.013	0.000	0.000	0.000	0.000
92	A	102	ALA	0	-0.027	-0.006	30.910	0.011	0.011	0.000	0.000	0.000	0.000
93	A	103	CYS	0	-0.035	-0.027	32.204	0.006	0.006	0.000	0.000	0.000	0.000
94	A	104	SER	0	-0.063	-0.009	34.685	0.009	0.009	0.000	0.000	0.000	0.000
95	A	105	VAL	0	-0.034	-0.024	35.580	0.007	0.007	0.000	0.000	0.000	0.000
96	A	106	GLN	0	-0.028	0.001	33.397	0.007	0.007	0.000	0.000	0.000	0.000
97	A	107	SER	0	-0.001	0.011	36.827	0.000	0.000	0.000	0.000	0.000	0.000
98	A	108	ALA	0	0.051	0.005	35.155	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.896	-0.958	35.045	-0.121	-0.121	0.000	0.000	0.000	0.000
100	A	110	PRO	0	-0.010	-0.006	33.043	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	111	TYR	0	-0.011	-0.030	26.951	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	112	ARG	1	0.939	0.947	30.553	0.119	0.119	0.000	0.000	0.000	0.000
103	A	113	LEU	0	-0.034	-0.018	32.363	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	114	GLN	0	-0.016	-0.011	26.965	0.007	0.007	0.000	0.000	0.000	0.000
105	A	115	LEU	0	-0.012	0.011	26.538	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	116	ALA	0	0.014	-0.008	28.056	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	117	GLU	-1	-0.954	-0.966	26.712	-0.237	-0.237	0.000	0.000	0.000	0.000
108	A	118	LEU	0	0.046	0.012	22.347	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	119	VAL	0	-0.013	0.013	24.706	-0.017	-0.017	0.000	0.000	0.000	0.000
110	A	120	GLU	-1	-0.883	-0.938	26.909	-0.167	-0.167	0.000	0.000	0.000	0.000
111	A	121	GLU	-1	-0.949	-0.985	23.478	-0.278	-0.278	0.000	0.000	0.000	0.000
112	A	122	SER	0	-0.072	-0.046	22.709	-0.022	-0.022	0.000	0.000	0.000	0.000
113	A	123	ARG	1	0.873	0.931	23.721	0.163	0.163	0.000	0.000	0.000	0.000
114	A	124	LYS	1	0.932	0.981	25.648	0.222	0.222	0.000	0.000	0.000	0.000
115	A	125	LEU	0	-0.042	-0.020	18.238	0.001	0.001	0.000	0.000	0.000	0.000
116	A	126	VAL	0	-0.019	-0.015	22.544	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	127	ALA	0	0.021	0.018	23.966	0.007	0.007	0.000	0.000	0.000	0.000
118	A	128	HIS	0	0.053	0.026	20.628	0.022	0.022	0.000	0.000	0.000	0.000
119	A	129	TYR	0	-0.002	-0.022	16.803	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	130	GLN	0	-0.004	-0.011	22.611	0.012	0.012	0.000	0.000	0.000	0.000
121	A	131	GLU	-1	-0.953	-0.963	25.867	-0.137	-0.137	0.000	0.000	0.000	0.000
122	A	132	ILE	0	-0.031	-0.014	21.111	0.012	0.012	0.000	0.000	0.000	0.000
123	A	133	GLU	-1	-0.877	-0.956	23.532	-0.150	-0.150	0.000	0.000	0.000	0.000
124	A	134	ALA	0	-0.030	-0.019	24.692	0.016	0.016	0.000	0.000	0.000	0.000
125	A	135	ALA	0	-0.011	0.001	27.281	0.012	0.012	0.000	0.000	0.000	0.000
126	A	136	TYR	0	-0.042	-0.015	23.957	0.014	0.014	0.000	0.000	0.000	0.000
127	A	137	TYR	0	-0.113	-0.087	19.481	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	138	ALA	0	0.049	0.036	24.696	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	139	ASN	0	0.024	-0.001	27.904	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	140	PRO	0	0.018	-0.015	24.397	0.006	0.006	0.000	0.000	0.000	0.000
131	A	141	ALA	0	-0.049	-0.016	25.864	0.009	0.009	0.000	0.000	0.000	0.000
132	A	142	VAL	0	-0.030	-0.012	28.585	0.008	0.008	0.000	0.000	0.000	0.000
133	A	143	LEU	0	-0.042	0.006	23.431	0.000	0.000	0.000	0.000	0.000	0.000
134	A	144	ASP	-1	-0.854	-0.938	22.738	0.014	0.014	0.000	0.000	0.000	0.000
135	A	145	LYS	1	0.908	0.917	20.062	-0.112	-0.112	0.000	0.000	0.000	0.000
136	A	146	GLN	0	0.080	0.038	14.393	0.017	0.017	0.000	0.000	0.000	0.000
137	A	147	GLN	0	0.115	0.074	17.710	-0.023	-0.023	0.000	0.000	0.000	0.000
138	A	148	ARG	1	0.915	0.969	19.865	-0.022	-0.022	0.000	0.000	0.000	0.000
139	A	149	LEU	0	-0.003	0.002	14.328	-0.023	-0.023	0.000	0.000	0.000	0.000
140	A	150	GLU	-1	-0.820	-0.890	15.387	-0.181	-0.181	0.000	0.000	0.000	0.000
141	A	151	ARG	1	0.982	1.020	16.424	0.074	0.074	0.000	0.000	0.000	0.000
142	A	152	LEU	0	-0.057	-0.030	16.453	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	153	THR	0	-0.064	-0.042	12.006	-0.041	-0.041	0.000	0.000	0.000	0.000
144	A	154	LEU	0	-0.002	0.009	14.579	-0.050	-0.050	0.000	0.000	0.000	0.000
145	A	155	ARG	1	0.870	0.918	17.487	0.166	0.166	0.000	0.000	0.000	0.000
146	A	156	ARG	1	0.956	0.993	13.184	0.628	0.628	0.000	0.000	0.000	0.000
147	A	157	ASN	0	-0.077	-0.057	14.804	-0.053	-0.053	0.000	0.000	0.000	0.000
148	A	158	LEU	0	0.011	0.015	17.223	0.014	0.014	0.000	0.000	0.000	0.000
149	A	159	LEU	0	0.027	0.016	20.450	0.012	0.012	0.000	0.000	0.000	0.000
150	A	160	VAL	0	-0.014	0.002	16.717	0.007	0.007	0.000	0.000	0.000	0.000
151	A	161	ARG	1	0.935	0.966	17.698	0.396	0.396	0.000	0.000	0.000	0.000
152	A	162	GLN	0	0.026	-0.002	20.853	0.013	0.013	0.000	0.000	0.000	0.000
153	A	163	ALA	0	0.005	0.013	22.496	0.016	0.016	0.000	0.000	0.000	0.000
154	A	164	TRP	0	-0.022	-0.018	21.367	0.010	0.010	0.000	0.000	0.000	0.000
155	A	165	ILE	0	-0.004	-0.003	23.495	0.009	0.009	0.000	0.000	0.000	0.000
156	A	166	GLN	0	-0.012	0.005	26.305	0.009	0.009	0.000	0.000	0.000	0.000
157	A	167	TRP	0	0.009	0.004	24.977	0.004	0.004	0.000	0.000	0.000	0.000
158	A	168	ALA	0	0.029	0.006	26.467	0.009	0.009	0.000	0.000	0.000	0.000
159	A	169	ASP	-1	-0.831	-0.918	28.306	-0.152	-0.152	0.000	0.000	0.000	0.000
160	A	170	GLU	-1	-0.965	-0.979	31.145	-0.132	-0.132	0.000	0.000	0.000	0.000
161	A	171	VAL	0	-0.023	-0.005	29.011	0.008	0.008	0.000	0.000	0.000	0.000
162	A	172	LEU	0	-0.047	-0.040	30.962	0.008	0.008	0.000	0.000	0.000	0.000
163	A	173	ALA	0	-0.031	-0.005	33.815	0.008	0.008	0.000	0.000	0.000	0.000
164	A	174	GLU	-1	-0.878	-0.945	35.273	-0.104	-0.104	0.000	0.000	0.000	0.000
165	A	175	LEU	0	-0.078	-0.047	32.663	0.004	0.004	0.000	0.000	0.000	0.000
166	A	176	ASN	0	-0.060	-0.006	37.044	0.001	0.001	0.000	0.000	0.000	0.000
167	A	177	ALA	0	-0.012	-0.007	40.317	0.005	0.005	0.000	0.000	0.000	0.000
168	A	178	MET	0	-0.015	0.012	38.881	0.002	0.002	0.000	0.000	0.000	0.000
169	A	179	ALA	0	-0.049	-0.011	41.792	0.005	0.005	0.000	0.000	0.000	0.000

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