FMO DATABASE

FMODB ID: 983G2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1571902.137168
FMO2-HF: Nuclear repulsion	1504432.576485
FMO2-HF: Total energy	-67469.560683
FMO2-MP2: Total energy	-67666.981574

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.
-37.468	-33.835	18.272	-9.894	-12.011	0.01

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 : 0.029 / q_NPA : 0.035

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	0.061	0.012	2.616	-2.684	0.178	1.396	-1.744	-2.513	0.007
4	A	5	HIS	1	0.919	0.949	1.944	-33.334	-36.404	13.415	-4.910	-5.436	0.032
5	A	6	VAL	0	0.003	0.023	3.704	-1.806	-1.346	0.000	-0.141	-0.319	0.000
6	A	7	ILE	0	-0.004	-0.009	5.724	0.101	0.101	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.004	-0.002	6.988	-0.144	-0.144	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.012	-0.008	6.744	-0.261	-0.261	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.006	0.006	9.284	-0.104	-0.104	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.004	0.001	11.947	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.050	-0.036	11.499	0.006	0.006	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.128	-0.059	13.913	-0.074	-0.074	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.874	0.921	16.328	-0.144	-0.144	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.799	-0.868	16.921	0.390	0.390	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.002	-0.003	16.585	-0.049	-0.049	0.000	0.000	0.000	0.000
16	A	17	THR	0	0.015	-0.018	18.506	0.016	0.016	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.045	0.010	17.420	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	TYR	0	0.025	0.029	17.913	-0.037	-0.037	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.790	-0.860	18.703	0.044	0.044	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.051	0.019	12.548	-0.034	-0.034	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.043	-0.042	14.126	-0.070	-0.070	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.851	0.934	15.564	-0.059	-0.059	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.781	-0.882	13.491	-0.042	-0.042	0.000	0.000	0.000	0.000
24	A	25	PHE	0	-0.060	-0.035	8.038	-0.081	-0.081	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.099	-0.048	13.393	-0.039	-0.039	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.011	0.007	16.080	0.025	0.025	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.013	-0.018	15.665	-0.055	-0.055	0.000	0.000	0.000	0.000
28	A	29	ILE	0	0.025	0.007	9.404	-0.059	-0.059	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.030	0.031	11.301	-0.171	-0.171	0.000	0.000	0.000	0.000
30	A	31	TYR	0	-0.069	-0.036	13.646	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.007	-0.017	7.008	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	TRP	0	0.025	0.009	2.503	-2.536	-1.474	2.033	-1.623	-1.472	-0.012
33	A	34	LYS	1	0.989	1.001	8.310	0.765	0.765	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.040	-0.016	8.388	-0.105	-0.105	0.000	0.000	0.000	0.000
35	A	36	SER	0	0.000	-0.020	10.428	0.121	0.121	0.000	0.000	0.000	0.000
36	A	37	HIS	0	0.099	0.029	12.690	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.064	0.042	14.507	0.006	0.006	0.000	0.000	0.000	0.000
38	A	39	GLN	0	0.019	0.025	9.519	0.077	0.077	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.049	0.028	10.058	0.041	0.041	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.021	-0.019	11.097	0.114	0.114	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.892	0.943	11.786	0.329	0.329	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.818	-0.899	5.900	-0.246	-0.246	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.017	0.001	9.352	0.214	0.214	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.031	-0.003	11.925	0.041	0.041	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.828	0.906	6.911	0.387	0.387	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.005	0.011	8.092	0.154	0.154	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.000	0.009	10.440	0.040	0.040	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.964	-0.977	13.543	0.196	0.196	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.056	-0.040	7.359	0.139	0.139	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.033	0.032	12.546	0.075	0.075	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.041	0.001	7.972	0.072	0.072	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.022	-0.024	11.773	0.034	0.034	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.020	-0.005	14.343	-0.072	-0.072	0.000	0.000	0.000	0.000
54	A	55	CYS	0	-0.013	-0.016	17.902	0.009	0.009	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.022	0.017	20.499	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.002	0.003	23.742	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.956	-0.982	25.236	0.156	0.156	0.000	0.000	0.000	0.000
58	A	68	VAL	0	-0.041	-0.019	21.046	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	69	TYR	0	-0.003	-0.020	15.848	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	70	SER	0	0.007	-0.013	17.608	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	71	ILE	0	-0.002	0.006	12.000	0.060	0.060	0.000	0.000	0.000	0.000
62	A	72	THR	0	-0.006	-0.021	14.724	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	73	GLN	0	0.066	0.021	15.216	0.073	0.073	0.000	0.000	0.000	0.000
64	A	74	ALA	0	0.016	0.014	13.468	0.058	0.058	0.000	0.000	0.000	0.000
65	A	75	GLY	0	0.063	0.023	10.783	0.233	0.233	0.000	0.000	0.000	0.000
66	A	76	ARG	1	0.876	0.919	10.764	-0.329	-0.329	0.000	0.000	0.000	0.000
67	A	77	SER	0	-0.006	0.005	12.218	0.015	0.015	0.000	0.000	0.000	0.000
68	A	78	ALA	0	0.014	0.007	7.824	0.046	0.046	0.000	0.000	0.000	0.000
69	A	79	LEU	0	-0.079	-0.035	6.369	1.234	1.234	0.000	0.000	0.000	0.000
70	A	80	GLY	0	0.014	0.006	8.365	-0.055	-0.055	0.000	0.000	0.000	0.000
71	A	81	GLU	-1	-0.914	-0.961	9.309	1.802	1.802	0.000	0.000	0.000	0.000
72	A	82	TRP	0	-0.019	-0.026	2.698	-1.656	0.663	1.428	-1.476	-2.271	-0.017
73	A	83	PHE	0	-0.076	-0.033	7.177	-0.529	-0.529	0.000	0.000	0.000	0.000
74	A	84	ASP	-1	-0.884	-0.942	8.950	0.450	0.450	0.000	0.000	0.000	0.000
75	A	85	GLN	0	-0.102	-0.040	7.104	0.067	0.067	0.000	0.000	0.000	0.000
76	A	86	PRO	0	-0.019	-0.007	9.436	-0.125	-0.125	0.000	0.000	0.000	0.000
77	A	87	THR	0	-0.021	-0.006	7.697	-0.154	-0.154	0.000	0.000	0.000	0.000
78	A	88	ALA	0	0.007	-0.007	9.111	0.079	0.079	0.000	0.000	0.000	0.000
79	A	89	HIS	0	-0.008	-0.002	10.491	-0.181	-0.181	0.000	0.000	0.000	0.000
80	A	90	PRO	0	0.009	0.002	10.517	0.037	0.037	0.000	0.000	0.000	0.000
81	A	91	THR	0	-0.038	-0.021	12.827	0.057	0.057	0.000	0.000	0.000	0.000
82	A	92	VAL	0	0.037	0.016	16.252	-0.032	-0.032	0.000	0.000	0.000	0.000
83	A	93	ARG	1	0.924	0.952	16.375	0.364	0.364	0.000	0.000	0.000	0.000
84	A	94	ASP	-1	-0.788	-0.869	19.706	-0.306	-0.306	0.000	0.000	0.000	0.000
85	A	95	GLU	-1	-0.779	-0.886	20.591	-0.241	-0.241	0.000	0.000	0.000	0.000
86	A	96	PHE	0	0.000	0.006	20.011	0.021	0.021	0.000	0.000	0.000	0.000
87	A	97	SER	0	0.039	-0.003	24.377	0.027	0.027	0.000	0.000	0.000	0.000
88	A	98	ALA	0	-0.053	-0.015	24.989	0.017	0.017	0.000	0.000	0.000	0.000
89	A	99	LYS	1	0.831	0.900	24.920	0.249	0.249	0.000	0.000	0.000	0.000
90	A	100	LEU	0	0.044	0.037	28.378	0.012	0.012	0.000	0.000	0.000	0.000
91	A	101	MET	0	0.003	-0.003	29.921	0.012	0.012	0.000	0.000	0.000	0.000
92	A	102	ALA	0	-0.013	0.006	30.902	0.011	0.011	0.000	0.000	0.000	0.000
93	A	103	CYS	0	-0.049	-0.024	32.357	0.007	0.007	0.000	0.000	0.000	0.000
94	A	104	SER	0	-0.061	-0.031	34.947	0.008	0.008	0.000	0.000	0.000	0.000
95	A	105	VAL	0	-0.062	-0.036	35.807	0.007	0.007	0.000	0.000	0.000	0.000
96	A	106	GLN	0	-0.025	-0.007	34.034	0.004	0.004	0.000	0.000	0.000	0.000
97	A	107	SER	0	-0.048	-0.028	37.130	0.001	0.001	0.000	0.000	0.000	0.000
98	A	108	ALA	0	0.078	0.023	35.556	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.855	-0.910	35.192	-0.117	-0.117	0.000	0.000	0.000	0.000
100	A	110	PRO	0	-0.014	-0.011	32.942	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	111	TYR	0	0.016	-0.007	27.362	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	112	ARG	1	0.923	0.944	30.792	0.110	0.110	0.000	0.000	0.000	0.000
103	A	113	LEU	0	-0.038	-0.018	32.727	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	114	GLN	0	0.015	0.002	27.686	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	115	LEU	0	-0.015	0.005	26.946	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	116	ALA	0	0.018	0.003	28.192	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	117	GLU	-1	-0.955	-0.975	27.209	-0.198	-0.198	0.000	0.000	0.000	0.000
108	A	118	LEU	0	0.018	0.002	22.645	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	119	VAL	0	0.018	0.035	24.982	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	120	GLU	-1	-0.818	-0.898	27.230	-0.157	-0.157	0.000	0.000	0.000	0.000
111	A	121	GLU	-1	-0.929	-0.948	23.379	-0.235	-0.235	0.000	0.000	0.000	0.000
112	A	122	SER	0	-0.068	-0.050	22.922	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	123	ARG	1	0.805	0.876	23.967	0.151	0.151	0.000	0.000	0.000	0.000
114	A	124	LYS	1	0.870	0.935	25.937	0.196	0.196	0.000	0.000	0.000	0.000
115	A	125	LEU	0	-0.027	-0.004	18.307	0.000	0.000	0.000	0.000	0.000	0.000
116	A	126	VAL	0	-0.009	-0.009	22.429	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	127	ALA	0	0.015	0.011	24.011	0.006	0.006	0.000	0.000	0.000	0.000
118	A	128	HIS	0	0.054	0.028	20.023	0.024	0.024	0.000	0.000	0.000	0.000
119	A	129	TYR	0	-0.010	-0.026	16.217	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	130	GLN	0	0.004	-0.008	22.490	0.004	0.004	0.000	0.000	0.000	0.000
121	A	131	GLU	-1	-0.938	-0.959	25.859	-0.120	-0.120	0.000	0.000	0.000	0.000
122	A	132	ILE	0	-0.014	-0.002	21.053	0.011	0.011	0.000	0.000	0.000	0.000
123	A	133	GLU	-1	-0.795	-0.886	23.502	-0.143	-0.143	0.000	0.000	0.000	0.000
124	A	134	ALA	0	-0.037	-0.029	24.615	0.015	0.015	0.000	0.000	0.000	0.000
125	A	135	ALA	0	-0.012	0.006	27.140	0.011	0.011	0.000	0.000	0.000	0.000
126	A	136	TYR	0	-0.039	-0.017	23.939	0.014	0.014	0.000	0.000	0.000	0.000
127	A	137	TYR	0	-0.079	-0.067	19.278	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	138	ALA	0	0.038	0.024	24.530	0.000	0.000	0.000	0.000	0.000	0.000
129	A	139	ASN	0	0.012	-0.002	27.544	0.003	0.003	0.000	0.000	0.000	0.000
130	A	140	PRO	0	0.032	-0.008	24.237	0.007	0.007	0.000	0.000	0.000	0.000
131	A	141	ALA	0	-0.028	-0.003	25.750	0.008	0.008	0.000	0.000	0.000	0.000
132	A	142	VAL	0	-0.025	-0.015	28.516	0.009	0.009	0.000	0.000	0.000	0.000
133	A	143	LEU	0	-0.045	0.015	22.651	0.003	0.003	0.000	0.000	0.000	0.000
134	A	144	ASP	-1	-0.788	-0.885	22.619	0.044	0.044	0.000	0.000	0.000	0.000
135	A	145	LYS	1	0.914	0.934	19.987	-0.109	-0.109	0.000	0.000	0.000	0.000
136	A	146	GLN	0	0.024	0.005	14.496	0.022	0.022	0.000	0.000	0.000	0.000
137	A	147	GLN	0	0.084	0.038	17.539	-0.028	-0.028	0.000	0.000	0.000	0.000
138	A	148	ARG	1	0.849	0.919	19.827	-0.015	-0.015	0.000	0.000	0.000	0.000
139	A	149	LEU	0	0.022	0.013	14.225	-0.025	-0.025	0.000	0.000	0.000	0.000
140	A	150	GLU	-1	-0.782	-0.848	15.231	-0.179	-0.179	0.000	0.000	0.000	0.000
141	A	151	ARG	1	0.915	0.965	16.247	0.077	0.077	0.000	0.000	0.000	0.000
142	A	152	LEU	0	-0.035	-0.012	16.132	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	153	THR	0	-0.052	-0.035	11.708	-0.043	-0.043	0.000	0.000	0.000	0.000
144	A	154	LEU	0	-0.002	0.007	14.427	-0.045	-0.045	0.000	0.000	0.000	0.000
145	A	155	ARG	1	0.849	0.891	17.532	0.163	0.163	0.000	0.000	0.000	0.000
146	A	156	ARG	1	0.883	0.950	12.739	0.591	0.591	0.000	0.000	0.000	0.000
147	A	157	ASN	0	-0.053	-0.024	14.961	-0.082	-0.082	0.000	0.000	0.000	0.000
148	A	158	LEU	0	-0.022	0.007	17.334	0.013	0.013	0.000	0.000	0.000	0.000
149	A	159	LEU	0	0.026	0.010	20.792	0.012	0.012	0.000	0.000	0.000	0.000
150	A	160	VAL	0	0.006	0.009	17.080	0.011	0.011	0.000	0.000	0.000	0.000
151	A	161	ARG	1	0.895	0.938	18.396	0.346	0.346	0.000	0.000	0.000	0.000
152	A	162	GLN	0	0.021	-0.002	21.275	0.015	0.015	0.000	0.000	0.000	0.000
153	A	163	ALA	0	0.012	0.010	22.928	0.013	0.013	0.000	0.000	0.000	0.000
154	A	164	TRP	0	-0.027	-0.015	21.523	0.009	0.009	0.000	0.000	0.000	0.000
155	A	165	ILE	0	-0.014	-0.010	23.787	0.009	0.009	0.000	0.000	0.000	0.000
156	A	166	GLN	0	-0.060	-0.024	26.700	0.007	0.007	0.000	0.000	0.000	0.000
157	A	167	TRP	0	0.026	0.011	25.733	0.003	0.003	0.000	0.000	0.000	0.000
158	A	168	ALA	0	0.022	0.007	26.595	0.008	0.008	0.000	0.000	0.000	0.000
159	A	169	ASP	-1	-0.813	-0.902	28.535	-0.143	-0.143	0.000	0.000	0.000	0.000
160	A	170	GLU	-1	-0.913	-0.946	31.425	-0.133	-0.133	0.000	0.000	0.000	0.000
161	A	171	VAL	0	0.003	-0.003	29.340	0.008	0.008	0.000	0.000	0.000	0.000
162	A	172	LEU	0	-0.040	-0.029	31.125	0.007	0.007	0.000	0.000	0.000	0.000
163	A	173	ALA	0	-0.025	0.005	33.981	0.008	0.008	0.000	0.000	0.000	0.000
164	A	174	GLU	-1	-0.852	-0.938	35.431	-0.098	-0.098	0.000	0.000	0.000	0.000
165	A	175	LEU	0	-0.056	-0.037	32.690	0.005	0.005	0.000	0.000	0.000	0.000
166	A	176	ASN	0	-0.066	-0.020	37.133	0.002	0.002	0.000	0.000	0.000	0.000
167	A	177	ALA	0	-0.003	0.026	40.343	0.005	0.005	0.000	0.000	0.000	0.000
168	A	178	MET	0	-0.034	-0.005	38.421	0.002	0.002	0.000	0.000	0.000	0.000
169	A	179	ALA	0	-0.095	-0.055	41.867	0.006	0.006	0.000	0.000	0.000	0.000

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