FMO DATABASE

FMODB ID: LN1J9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1570635.237485
FMO2-HF: Nuclear repulsion	1503166.069913
FMO2-HF: Total energy	-67469.167573
FMO2-MP2: Total energy	-67666.658753

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.
-39.074	-37.647	20.474	-10.497	-11.406	0.025

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 : 0.036

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	0.083	0.028	2.522	-2.831	0.010	1.671	-1.793	-2.720	0.010
4	A	5	HIS	1	0.926	0.948	1.870	-35.349	-40.031	16.023	-5.860	-5.481	0.037
5	A	6	VAL	0	-0.002	0.019	3.497	-1.748	-1.244	0.002	-0.166	-0.341	0.000
6	A	7	ILE	0	-0.005	-0.007	5.528	0.067	0.067	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.023	-0.013	7.253	-0.111	-0.111	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.007	-0.003	6.919	-0.277	-0.277	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.019	0.001	9.494	-0.107	-0.107	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.012	-0.015	11.992	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.052	-0.030	11.666	0.029	0.029	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.118	-0.042	14.056	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.911	0.960	16.535	-0.142	-0.142	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.808	-0.871	17.090	0.388	0.388	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.011	-0.012	16.788	-0.049	-0.049	0.000	0.000	0.000	0.000
16	A	17	THR	0	0.042	-0.003	18.539	0.026	0.026	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.060	0.006	17.203	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.003	0.005	17.503	-0.036	-0.036	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.773	-0.853	18.843	0.049	0.049	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.062	0.025	12.696	-0.038	-0.038	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.044	-0.035	14.410	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.835	0.925	15.736	-0.056	-0.056	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.853	-0.935	13.574	-0.064	-0.064	0.000	0.000	0.000	0.000
24	A	25	PHE	0	-0.054	-0.035	7.990	-0.087	-0.087	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.072	-0.018	13.295	-0.052	-0.052	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.008	-0.010	15.953	0.023	0.023	0.000	0.000	0.000	0.000
27	A	28	SER	0	0.007	0.000	15.682	-0.066	-0.066	0.000	0.000	0.000	0.000
28	A	29	ILE	0	0.032	0.018	9.465	-0.074	-0.074	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.030	0.028	11.166	-0.185	-0.185	0.000	0.000	0.000	0.000
30	A	31	TYR	0	-0.086	-0.048	13.273	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.024	-0.017	7.102	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	33	TRP	0	0.005	0.002	2.375	-2.597	-1.706	2.389	-1.766	-1.515	-0.013
33	A	34	LYS	1	0.997	1.008	8.465	0.829	0.829	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.032	-0.024	8.365	-0.147	-0.147	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.011	-0.021	10.446	0.131	0.131	0.000	0.000	0.000	0.000
36	A	37	HIS	0	0.125	0.041	12.647	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.024	0.022	14.439	0.047	0.047	0.000	0.000	0.000	0.000
38	A	39	GLN	0	0.035	0.030	9.169	0.102	0.102	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.045	0.035	10.093	0.066	0.066	0.000	0.000	0.000	0.000
40	A	41	TYR	0	0.002	0.002	11.120	0.131	0.131	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.898	0.938	11.843	0.280	0.280	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.827	-0.894	5.956	0.426	0.426	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.028	0.002	9.536	0.224	0.224	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.029	-0.005	11.975	0.035	0.035	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.840	0.897	7.374	0.084	0.084	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.021	-0.002	8.283	0.171	0.171	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.003	0.013	10.706	0.029	0.029	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.976	-0.982	13.829	0.284	0.284	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.050	-0.029	7.432	0.219	0.219	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.029	0.033	12.703	0.044	0.044	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.048	-0.008	8.341	0.070	0.070	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.001	-0.013	11.862	0.028	0.028	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.027	-0.010	14.484	-0.073	-0.073	0.000	0.000	0.000	0.000
54	A	55	CYS	0	-0.021	-0.019	18.129	0.006	0.006	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.031	0.022	20.695	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.017	-0.007	23.885	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.947	-0.977	25.364	0.171	0.171	0.000	0.000	0.000	0.000
58	A	68	VAL	0	-0.052	-0.026	21.408	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	69	TYR	0	-0.009	-0.018	16.164	0.003	0.003	0.000	0.000	0.000	0.000
60	A	70	SER	0	0.032	-0.004	17.710	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	71	ILE	0	-0.017	0.001	11.815	0.072	0.072	0.000	0.000	0.000	0.000
62	A	72	THR	0	-0.007	-0.016	14.817	-0.062	-0.062	0.000	0.000	0.000	0.000
63	A	73	GLN	0	0.080	0.026	15.438	0.074	0.074	0.000	0.000	0.000	0.000
64	A	74	ALA	0	0.016	0.014	14.028	0.055	0.055	0.000	0.000	0.000	0.000
65	A	75	GLY	0	0.068	0.024	11.212	0.223	0.223	0.000	0.000	0.000	0.000
66	A	76	ARG	1	0.872	0.918	11.221	-0.353	-0.353	0.000	0.000	0.000	0.000
67	A	77	SER	0	-0.015	-0.004	12.600	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	78	ALA	0	0.008	0.006	8.336	0.047	0.047	0.000	0.000	0.000	0.000
69	A	79	LEU	0	-0.067	-0.028	6.651	0.766	0.766	0.000	0.000	0.000	0.000
70	A	80	GLY	0	0.011	0.005	8.660	-0.069	-0.069	0.000	0.000	0.000	0.000
71	A	81	GLU	-1	-0.913	-0.955	10.171	1.544	1.544	0.000	0.000	0.000	0.000
72	A	82	TRP	0	-0.052	-0.047	2.904	-0.755	1.118	0.389	-0.912	-1.349	-0.009
73	A	83	PHE	0	-0.076	-0.042	7.190	-0.569	-0.569	0.000	0.000	0.000	0.000
74	A	84	ASP	-1	-0.889	-0.938	8.908	0.430	0.430	0.000	0.000	0.000	0.000
75	A	85	GLN	0	-0.108	-0.034	7.632	-0.041	-0.041	0.000	0.000	0.000	0.000
76	A	86	PRO	0	-0.012	0.004	9.544	-0.108	-0.108	0.000	0.000	0.000	0.000
77	A	87	THR	0	-0.003	0.000	7.967	-0.101	-0.101	0.000	0.000	0.000	0.000
78	A	88	ALA	0	-0.004	-0.015	9.438	0.056	0.056	0.000	0.000	0.000	0.000
79	A	89	HIS	0	-0.002	-0.006	10.712	-0.184	-0.184	0.000	0.000	0.000	0.000
80	A	90	PRO	0	0.002	0.001	10.422	0.033	0.033	0.000	0.000	0.000	0.000
81	A	91	THR	0	-0.028	-0.021	12.710	0.061	0.061	0.000	0.000	0.000	0.000
82	A	92	VAL	0	0.025	0.013	15.875	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	93	ARG	1	0.942	0.961	16.388	0.398	0.398	0.000	0.000	0.000	0.000
84	A	94	ASP	-1	-0.789	-0.876	18.995	-0.357	-0.357	0.000	0.000	0.000	0.000
85	A	95	GLU	-1	-0.808	-0.890	20.201	-0.272	-0.272	0.000	0.000	0.000	0.000
86	A	96	PHE	0	-0.004	0.003	20.015	0.026	0.026	0.000	0.000	0.000	0.000
87	A	97	SER	0	0.021	-0.008	23.925	0.030	0.030	0.000	0.000	0.000	0.000
88	A	98	ALA	0	-0.050	-0.021	24.593	0.020	0.020	0.000	0.000	0.000	0.000
89	A	99	LYS	1	0.854	0.914	24.609	0.274	0.274	0.000	0.000	0.000	0.000
90	A	100	LEU	0	0.047	0.024	28.040	0.014	0.014	0.000	0.000	0.000	0.000
91	A	101	MET	0	0.017	0.008	29.525	0.014	0.014	0.000	0.000	0.000	0.000
92	A	102	ALA	0	-0.024	-0.001	30.916	0.011	0.011	0.000	0.000	0.000	0.000
93	A	103	CYS	0	-0.048	-0.030	32.095	0.006	0.006	0.000	0.000	0.000	0.000
94	A	104	SER	0	-0.063	-0.017	34.693	0.009	0.009	0.000	0.000	0.000	0.000
95	A	105	VAL	0	-0.044	-0.033	35.760	0.007	0.007	0.000	0.000	0.000	0.000
96	A	106	GLN	0	-0.022	0.006	33.735	0.007	0.007	0.000	0.000	0.000	0.000
97	A	107	SER	0	-0.028	-0.025	36.839	0.000	0.000	0.000	0.000	0.000	0.000
98	A	108	ALA	0	0.041	0.006	35.163	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.865	-0.924	35.054	-0.122	-0.122	0.000	0.000	0.000	0.000
100	A	110	PRO	0	-0.007	-0.004	32.986	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	111	TYR	0	0.009	-0.011	27.074	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	112	ARG	1	0.928	0.944	30.562	0.121	0.121	0.000	0.000	0.000	0.000
103	A	113	LEU	0	-0.030	-0.015	32.370	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	114	GLN	0	0.013	0.007	27.303	0.001	0.001	0.000	0.000	0.000	0.000
105	A	115	LEU	0	-0.024	0.000	26.659	-0.016	-0.016	0.000	0.000	0.000	0.000
106	A	116	ALA	0	0.017	-0.007	28.061	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	117	GLU	-1	-0.956	-0.965	27.062	-0.218	-0.218	0.000	0.000	0.000	0.000
108	A	118	LEU	0	0.020	-0.004	22.375	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	119	VAL	0	0.015	0.034	24.709	-0.020	-0.020	0.000	0.000	0.000	0.000
110	A	120	GLU	-1	-0.817	-0.893	26.908	-0.173	-0.173	0.000	0.000	0.000	0.000
111	A	121	GLU	-1	-0.895	-0.933	23.621	-0.253	-0.253	0.000	0.000	0.000	0.000
112	A	122	SER	0	-0.057	-0.044	22.714	-0.025	-0.025	0.000	0.000	0.000	0.000
113	A	123	ARG	1	0.810	0.877	23.721	0.167	0.167	0.000	0.000	0.000	0.000
114	A	124	LYS	1	0.853	0.931	25.794	0.217	0.217	0.000	0.000	0.000	0.000
115	A	125	LEU	0	-0.049	-0.022	18.280	0.000	0.000	0.000	0.000	0.000	0.000
116	A	126	VAL	0	-0.016	-0.017	22.538	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	127	ALA	0	0.026	0.022	23.958	0.007	0.007	0.000	0.000	0.000	0.000
118	A	128	HIS	0	0.046	0.024	20.273	0.024	0.024	0.000	0.000	0.000	0.000
119	A	129	TYR	0	-0.002	-0.024	16.383	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	130	GLN	0	-0.013	-0.013	22.601	0.008	0.008	0.000	0.000	0.000	0.000
121	A	131	GLU	-1	-0.944	-0.960	25.854	-0.134	-0.134	0.000	0.000	0.000	0.000
122	A	132	ILE	0	-0.024	-0.010	21.308	0.012	0.012	0.000	0.000	0.000	0.000
123	A	133	GLU	-1	-0.801	-0.889	23.561	-0.164	-0.164	0.000	0.000	0.000	0.000
124	A	134	ALA	0	-0.030	-0.021	24.701	0.015	0.015	0.000	0.000	0.000	0.000
125	A	135	ALA	0	-0.006	0.007	27.217	0.012	0.012	0.000	0.000	0.000	0.000
126	A	136	TYR	0	-0.032	-0.013	23.987	0.015	0.015	0.000	0.000	0.000	0.000
127	A	137	TYR	0	-0.090	-0.079	19.326	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	138	ALA	0	0.051	0.040	24.700	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	139	ASN	0	0.019	-0.005	27.912	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	140	PRO	0	0.030	-0.005	24.331	0.006	0.006	0.000	0.000	0.000	0.000
131	A	141	ALA	0	-0.031	-0.008	25.869	0.009	0.009	0.000	0.000	0.000	0.000
132	A	142	VAL	0	-0.024	-0.008	28.621	0.009	0.009	0.000	0.000	0.000	0.000
133	A	143	LEU	0	-0.029	0.023	22.922	0.002	0.002	0.000	0.000	0.000	0.000
134	A	144	ASP	-1	-0.856	-0.923	22.899	0.013	0.013	0.000	0.000	0.000	0.000
135	A	145	LYS	1	0.934	0.937	20.064	-0.097	-0.097	0.000	0.000	0.000	0.000
136	A	146	GLN	0	0.054	0.025	14.626	0.016	0.016	0.000	0.000	0.000	0.000
137	A	147	GLN	0	0.099	0.046	17.703	-0.030	-0.030	0.000	0.000	0.000	0.000
138	A	148	ARG	1	0.880	0.938	19.865	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	149	LEU	0	0.005	0.007	14.526	-0.025	-0.025	0.000	0.000	0.000	0.000
140	A	150	GLU	-1	-0.797	-0.872	15.389	-0.203	-0.203	0.000	0.000	0.000	0.000
141	A	151	ARG	1	0.913	0.963	16.425	0.096	0.096	0.000	0.000	0.000	0.000
142	A	152	LEU	0	-0.038	-0.019	16.527	-0.020	-0.020	0.000	0.000	0.000	0.000
143	A	153	THR	0	-0.057	-0.032	11.927	-0.047	-0.047	0.000	0.000	0.000	0.000
144	A	154	LEU	0	-0.006	0.002	14.594	-0.051	-0.051	0.000	0.000	0.000	0.000
145	A	155	ARG	1	0.835	0.887	17.502	0.186	0.186	0.000	0.000	0.000	0.000
146	A	156	ARG	1	0.911	0.962	13.069	0.677	0.677	0.000	0.000	0.000	0.000
147	A	157	ASN	0	-0.032	-0.015	14.725	-0.064	-0.064	0.000	0.000	0.000	0.000
148	A	158	LEU	0	0.000	0.014	17.208	0.015	0.015	0.000	0.000	0.000	0.000
149	A	159	LEU	0	0.029	0.015	20.472	0.014	0.014	0.000	0.000	0.000	0.000
150	A	160	VAL	0	-0.006	0.003	16.740	0.009	0.009	0.000	0.000	0.000	0.000
151	A	161	ARG	1	0.910	0.943	17.859	0.400	0.400	0.000	0.000	0.000	0.000
152	A	162	GLN	0	0.019	-0.005	20.843	0.017	0.017	0.000	0.000	0.000	0.000
153	A	163	ALA	0	0.010	0.014	22.512	0.017	0.017	0.000	0.000	0.000	0.000
154	A	164	TRP	0	-0.033	-0.022	21.355	0.010	0.010	0.000	0.000	0.000	0.000
155	A	165	ILE	0	-0.010	-0.007	23.487	0.010	0.010	0.000	0.000	0.000	0.000
156	A	166	GLN	0	-0.054	-0.020	26.298	0.011	0.011	0.000	0.000	0.000	0.000
157	A	167	TRP	0	0.020	0.008	25.264	0.004	0.004	0.000	0.000	0.000	0.000
158	A	168	ALA	0	0.024	0.004	26.408	0.010	0.010	0.000	0.000	0.000	0.000
159	A	169	ASP	-1	-0.823	-0.900	28.303	-0.159	-0.159	0.000	0.000	0.000	0.000
160	A	170	GLU	-1	-0.916	-0.952	31.141	-0.149	-0.149	0.000	0.000	0.000	0.000
161	A	171	VAL	0	-0.009	-0.003	29.052	0.009	0.009	0.000	0.000	0.000	0.000
162	A	172	LEU	0	-0.041	-0.036	31.072	0.009	0.009	0.000	0.000	0.000	0.000
163	A	173	ALA	0	-0.029	-0.002	33.815	0.009	0.009	0.000	0.000	0.000	0.000
164	A	174	GLU	-1	-0.862	-0.934	35.261	-0.110	-0.110	0.000	0.000	0.000	0.000
165	A	175	LEU	0	-0.075	-0.046	32.644	0.005	0.005	0.000	0.000	0.000	0.000
166	A	176	ASN	0	-0.057	-0.011	37.045	0.002	0.002	0.000	0.000	0.000	0.000
167	A	177	ALA	0	-0.010	-0.004	40.319	0.005	0.005	0.000	0.000	0.000	0.000
168	A	178	MET	0	-0.020	0.015	38.529	0.002	0.002	0.000	0.000	0.000	0.000
169	A	179	ALA	0	-0.068	-0.029	41.740	0.008	0.008	0.000	0.000	0.000	0.000

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