FMO DATABASE

FMODB ID: YY832

Calculation Name: 2YMB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YMB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HD42

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1674299.858366
FMO2-HF: Nuclear repulsion	1609241.114603
FMO2-HF: Total energy	-65058.743763
FMO2-MP2: Total energy	-65248.189778

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:89:HIS)

Summations of interaction energy for fragment #1(A:89:HIS)

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.
-153.738	-146.835	21.921	-12.331	-16.493	-0.144

Interaction energy analysis for fragmet #1(A:89:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.914

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	91	GLN	0	-0.035	-0.030	3.773	-6.041	-3.702	0.002	-1.084	-1.256	0.002
4	A	92	ILE	0	-0.009	-0.002	5.430	5.255	5.255	0.000	0.000	0.000	0.000
5	A	93	LYS	1	0.831	0.896	9.109	20.476	20.476	0.000	0.000	0.000	0.000
6	A	94	ILE	0	-0.014	0.007	11.105	1.640	1.640	0.000	0.000	0.000	0.000
7	A	95	GLU	-1	-0.791	-0.905	14.153	-19.644	-19.644	0.000	0.000	0.000	0.000
8	A	96	GLU	-1	-0.773	-0.886	16.839	-13.709	-13.709	0.000	0.000	0.000	0.000
9	A	97	ASN	0	-0.092	-0.028	19.891	0.776	0.776	0.000	0.000	0.000	0.000
10	A	98	ALA	0	-0.002	0.021	18.311	0.493	0.493	0.000	0.000	0.000	0.000
11	A	99	THR	0	-0.021	-0.021	20.393	0.320	0.320	0.000	0.000	0.000	0.000
12	A	100	GLY	0	-0.005	0.004	19.933	-0.507	-0.507	0.000	0.000	0.000	0.000
13	A	101	PHE	0	0.037	0.007	14.024	-0.984	-0.984	0.000	0.000	0.000	0.000
14	A	102	SER	0	-0.009	-0.027	17.587	-0.529	-0.529	0.000	0.000	0.000	0.000
15	A	103	TYR	0	0.018	-0.023	16.469	-0.430	-0.430	0.000	0.000	0.000	0.000
16	A	104	GLU	-1	-0.830	-0.888	17.252	-13.716	-13.716	0.000	0.000	0.000	0.000
17	A	105	SER	0	-0.036	-0.054	17.820	0.274	0.274	0.000	0.000	0.000	0.000
18	A	106	LEU	0	-0.040	-0.010	11.148	-0.614	-0.614	0.000	0.000	0.000	0.000
19	A	107	PHE	0	0.028	-0.010	11.536	-1.674	-1.674	0.000	0.000	0.000	0.000
20	A	108	ARG	1	0.869	0.954	14.055	16.037	16.037	0.000	0.000	0.000	0.000
21	A	109	GLU	-1	-0.882	-0.922	10.605	-22.937	-22.937	0.000	0.000	0.000	0.000
22	A	110	TYR	0	-0.080	-0.057	8.492	-1.324	-1.324	0.000	0.000	0.000	0.000
23	A	111	LEU	0	0.014	0.016	12.257	0.338	0.338	0.000	0.000	0.000	0.000
24	A	112	ASN	0	0.052	0.032	15.399	1.015	1.015	0.000	0.000	0.000	0.000
25	A	113	GLH	0	0.031	0.010	18.768	0.249	0.249	0.000	0.000	0.000	0.000
26	A	114	THR	0	-0.049	-0.030	16.760	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	115	VAL	0	-0.025	0.011	15.869	-0.183	-0.183	0.000	0.000	0.000	0.000
28	A	116	THR	0	-0.002	-0.013	18.587	0.469	0.469	0.000	0.000	0.000	0.000
29	A	117	GLU	-1	-0.861	-0.913	19.301	-13.524	-13.524	0.000	0.000	0.000	0.000
30	A	118	VAL	0	-0.011	-0.004	15.969	-0.922	-0.922	0.000	0.000	0.000	0.000
31	A	119	TRP	0	-0.011	-0.014	15.481	0.656	0.656	0.000	0.000	0.000	0.000
32	A	120	ILE	0	-0.015	-0.005	14.882	-1.315	-1.315	0.000	0.000	0.000	0.000
33	A	121	GLU	-1	-0.849	-0.905	14.176	-18.789	-18.789	0.000	0.000	0.000	0.000
34	A	122	ASP	-1	-0.755	-0.901	14.426	-19.695	-19.695	0.000	0.000	0.000	0.000
35	A	123	PRO	0	-0.039	0.001	16.244	1.080	1.080	0.000	0.000	0.000	0.000
36	A	124	TYR	0	-0.027	-0.019	18.007	0.568	0.568	0.000	0.000	0.000	0.000
37	A	125	ILE	0	-0.011	-0.001	18.754	-0.030	-0.030	0.000	0.000	0.000	0.000
38	A	126	ARG	1	0.861	0.916	22.323	12.574	12.574	0.000	0.000	0.000	0.000
39	A	127	HIS	0	-0.002	-0.002	25.113	0.074	0.074	0.000	0.000	0.000	0.000
40	A	128	THR	0	0.020	-0.018	26.682	-0.306	-0.306	0.000	0.000	0.000	0.000
41	A	129	HIS	0	-0.054	-0.050	23.328	0.457	0.457	0.000	0.000	0.000	0.000
42	A	130	GLN	0	0.008	0.001	22.334	-0.089	-0.089	0.000	0.000	0.000	0.000
43	A	131	LEU	0	0.031	0.023	23.195	-0.473	-0.473	0.000	0.000	0.000	0.000
44	A	132	TYR	0	0.024	0.005	25.440	-0.077	-0.077	0.000	0.000	0.000	0.000
45	A	133	ASN	0	-0.057	-0.015	20.450	0.226	0.226	0.000	0.000	0.000	0.000
46	A	134	PHE	0	0.079	0.030	20.490	-0.511	-0.511	0.000	0.000	0.000	0.000
47	A	135	LEU	0	0.000	0.016	21.983	-0.145	-0.145	0.000	0.000	0.000	0.000
48	A	136	ARG	1	0.890	0.949	21.782	13.346	13.346	0.000	0.000	0.000	0.000
49	A	137	PHE	0	-0.030	-0.009	15.832	-0.219	-0.219	0.000	0.000	0.000	0.000
50	A	138	CYS	0	-0.025	-0.016	20.621	-0.176	-0.176	0.000	0.000	0.000	0.000
51	A	139	GLU	-1	-0.925	-0.978	23.104	-11.175	-11.175	0.000	0.000	0.000	0.000
52	A	140	MET	0	-0.086	-0.029	17.468	0.207	0.207	0.000	0.000	0.000	0.000
53	A	141	LEU	0	0.037	0.015	17.629	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	142	ILE	0	-0.036	-0.008	21.550	0.122	0.122	0.000	0.000	0.000	0.000
55	A	143	LYS	1	0.806	0.875	24.381	13.030	13.030	0.000	0.000	0.000	0.000
56	A	144	ARG	1	0.945	0.968	26.391	10.228	10.228	0.000	0.000	0.000	0.000
57	A	145	PRO	0	-0.042	-0.024	23.567	-0.024	-0.024	0.000	0.000	0.000	0.000
58	A	146	CYS	0	-0.016	0.017	21.109	-0.070	-0.070	0.000	0.000	0.000	0.000
59	A	147	LYS	1	0.918	0.939	22.530	11.807	11.807	0.000	0.000	0.000	0.000
60	A	148	VAL	0	0.028	0.029	20.369	0.155	0.155	0.000	0.000	0.000	0.000
61	A	149	LYS	1	0.825	0.901	23.134	11.395	11.395	0.000	0.000	0.000	0.000
62	A	150	THR	0	0.019	0.014	22.990	0.582	0.582	0.000	0.000	0.000	0.000
63	A	151	ILE	0	0.010	0.001	20.421	-0.734	-0.734	0.000	0.000	0.000	0.000
64	A	152	HIS	1	0.779	0.856	19.842	14.508	14.508	0.000	0.000	0.000	0.000
65	A	153	LEU	0	0.009	0.009	19.434	-0.974	-0.974	0.000	0.000	0.000	0.000
66	A	154	LEU	0	-0.006	0.010	18.446	0.684	0.684	0.000	0.000	0.000	0.000
67	A	155	THR	0	-0.012	-0.031	19.190	-0.586	-0.586	0.000	0.000	0.000	0.000
68	A	156	SER	0	0.000	0.009	21.058	0.582	0.582	0.000	0.000	0.000	0.000
69	A	157	LEU	0	-0.005	0.000	23.024	0.048	0.048	0.000	0.000	0.000	0.000
70	A	158	ASP	-1	-0.857	-0.926	26.670	-10.751	-10.751	0.000	0.000	0.000	0.000
71	A	159	GLU	-1	-0.926	-0.961	28.516	-10.496	-10.496	0.000	0.000	0.000	0.000
72	A	160	GLY	0	-0.003	0.010	31.196	0.383	0.383	0.000	0.000	0.000	0.000
73	A	161	ILE	0	0.012	-0.017	33.624	-0.074	-0.074	0.000	0.000	0.000	0.000
74	A	162	GLU	-1	-0.861	-0.920	30.282	-10.071	-10.071	0.000	0.000	0.000	0.000
75	A	163	GLN	0	0.015	0.009	30.932	-0.064	-0.064	0.000	0.000	0.000	0.000
76	A	164	VAL	0	-0.011	-0.005	31.985	-0.065	-0.065	0.000	0.000	0.000	0.000
77	A	165	GLN	0	0.008	0.019	32.559	-0.180	-0.180	0.000	0.000	0.000	0.000
78	A	166	GLN	0	0.021	0.017	25.427	0.241	0.241	0.000	0.000	0.000	0.000
79	A	167	SER	0	0.015	0.009	29.787	-0.175	-0.175	0.000	0.000	0.000	0.000
80	A	168	ARG	1	0.808	0.875	31.462	8.486	8.486	0.000	0.000	0.000	0.000
81	A	169	GLY	0	0.068	0.036	31.336	0.025	0.025	0.000	0.000	0.000	0.000
82	A	170	LEU	0	-0.027	-0.020	25.227	-0.190	-0.190	0.000	0.000	0.000	0.000
83	A	171	GLN	0	-0.004	-0.003	28.964	0.080	0.080	0.000	0.000	0.000	0.000
84	A	172	GLU	-1	-0.811	-0.871	31.907	-8.801	-8.801	0.000	0.000	0.000	0.000
85	A	173	ILE	0	-0.034	-0.018	26.424	0.025	0.025	0.000	0.000	0.000	0.000
86	A	174	GLU	-1	-0.846	-0.904	28.990	-10.172	-10.172	0.000	0.000	0.000	0.000
87	A	175	GLU	-1	-0.839	-0.898	30.152	-8.584	-8.584	0.000	0.000	0.000	0.000
88	A	176	SER	0	-0.015	0.000	31.291	0.162	0.162	0.000	0.000	0.000	0.000
89	A	177	LEU	0	-0.003	0.002	25.955	0.037	0.037	0.000	0.000	0.000	0.000
90	A	178	ARG	1	0.812	0.877	29.974	9.437	9.437	0.000	0.000	0.000	0.000
91	A	179	SER	0	-0.037	-0.011	32.408	0.255	0.255	0.000	0.000	0.000	0.000
92	A	180	HIS	1	0.773	0.868	30.661	9.868	9.868	0.000	0.000	0.000	0.000
93	A	181	GLY	0	0.004	0.011	31.209	-0.165	-0.165	0.000	0.000	0.000	0.000
94	A	182	VAL	0	-0.067	-0.029	25.659	-0.235	-0.235	0.000	0.000	0.000	0.000
95	A	183	LEU	0	0.023	0.016	27.386	0.223	0.223	0.000	0.000	0.000	0.000
96	A	184	LEU	0	-0.023	-0.010	24.023	-0.549	-0.549	0.000	0.000	0.000	0.000
97	A	185	GLU	-1	-0.815	-0.871	24.597	-12.099	-12.099	0.000	0.000	0.000	0.000
98	A	186	VAL	0	0.002	-0.014	24.230	-0.655	-0.655	0.000	0.000	0.000	0.000
99	A	187	GLN	0	-0.056	-0.031	23.599	0.352	0.352	0.000	0.000	0.000	0.000
100	A	188	TYR	0	0.037	-0.005	23.902	-0.513	-0.513	0.000	0.000	0.000	0.000
101	A	189	SER	0	0.015	-0.002	22.352	0.444	0.444	0.000	0.000	0.000	0.000
102	A	190	SER	0	-0.004	0.008	22.637	-0.564	-0.564	0.000	0.000	0.000	0.000
103	A	191	SER	0	-0.014	-0.011	22.463	0.229	0.229	0.000	0.000	0.000	0.000
104	A	192	ILE	0	0.000	0.024	17.195	-0.573	-0.573	0.000	0.000	0.000	0.000
105	A	193	HIS	0	0.012	-0.024	16.690	0.737	0.737	0.000	0.000	0.000	0.000
106	A	194	ASP	-1	-0.846	-0.904	10.300	-29.319	-29.319	0.000	0.000	0.000	0.000
107	A	195	ARG	1	0.882	0.936	11.104	22.209	22.209	0.000	0.000	0.000	0.000
108	A	196	GLU	-1	-0.881	-0.931	8.786	-33.765	-33.765	0.000	0.000	0.000	0.000
109	A	197	ILE	0	0.004	0.006	10.201	2.784	2.784	0.000	0.000	0.000	0.000
110	A	198	ARG	1	0.849	0.927	10.413	17.616	17.616	0.000	0.000	0.000	0.000
111	A	199	PHE	0	0.060	0.020	11.357	2.060	2.060	0.000	0.000	0.000	0.000
112	A	200	ASN	0	0.043	0.016	13.520	-1.192	-1.192	0.000	0.000	0.000	0.000
113	A	201	ASN	0	-0.016	-0.008	13.166	-0.603	-0.603	0.000	0.000	0.000	0.000
114	A	202	GLY	0	0.019	0.014	11.373	0.057	0.057	0.000	0.000	0.000	0.000
115	A	203	TRP	0	-0.032	-0.008	5.368	-3.492	-3.492	0.000	0.000	0.000	0.000
116	A	204	MET	0	-0.014	-0.013	6.938	2.866	2.866	0.000	0.000	0.000	0.000
117	A	205	ILE	0	-0.016	-0.004	6.117	-5.989	-5.989	0.000	0.000	0.000	0.000
118	A	206	LYS	1	0.828	0.903	5.290	37.000	37.000	0.000	0.000	0.000	0.000
119	A	207	ILE	0	-0.006	0.004	6.740	-3.009	-3.009	0.000	0.000	0.000	0.000
120	A	208	GLY	0	0.038	0.024	9.388	1.785	1.785	0.000	0.000	0.000	0.000
121	A	209	ARG	1	0.873	0.919	10.750	18.666	18.666	0.000	0.000	0.000	0.000
122	A	210	GLY	0	0.012	0.021	12.675	1.363	1.363	0.000	0.000	0.000	0.000
123	A	211	LEU	0	0.024	-0.008	14.201	-0.352	-0.352	0.000	0.000	0.000	0.000
124	A	212	ASP	-1	-0.831	-0.878	16.447	-13.512	-13.512	0.000	0.000	0.000	0.000
125	A	213	TYR	0	-0.028	-0.019	14.899	-0.181	-0.181	0.000	0.000	0.000	0.000
126	A	214	PHE	0	0.046	0.017	17.569	0.190	0.190	0.000	0.000	0.000	0.000
127	A	215	LYS	1	0.788	0.877	20.998	13.849	13.849	0.000	0.000	0.000	0.000
128	A	216	LYS	1	0.892	0.942	24.235	10.150	10.150	0.000	0.000	0.000	0.000
129	A	217	PRO	0	0.027	0.027	27.797	-0.169	-0.169	0.000	0.000	0.000	0.000
130	A	218	GLN	0	0.059	0.031	29.830	0.209	0.209	0.000	0.000	0.000	0.000
131	A	219	SER	0	0.012	-0.018	32.015	0.239	0.239	0.000	0.000	0.000	0.000
132	A	220	ARG	1	0.989	0.975	34.389	7.519	7.519	0.000	0.000	0.000	0.000
133	A	221	PHE	0	0.027	0.019	36.050	0.031	0.031	0.000	0.000	0.000	0.000
134	A	222	SER	0	-0.036	0.011	32.062	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	223	LEU	0	0.080	0.017	30.912	-0.162	-0.162	0.000	0.000	0.000	0.000
136	A	224	GLY	0	0.078	0.049	27.642	-0.151	-0.151	0.000	0.000	0.000	0.000
137	A	225	TYR	0	-0.086	-0.026	27.695	-0.285	-0.285	0.000	0.000	0.000	0.000
138	A	226	CYS	0	-0.009	-0.012	29.156	-0.098	-0.098	0.000	0.000	0.000	0.000
139	A	227	ASP	-1	-0.803	-0.887	25.935	-12.284	-12.284	0.000	0.000	0.000	0.000
140	A	228	PHE	0	0.005	-0.029	22.007	-0.031	-0.031	0.000	0.000	0.000	0.000
141	A	229	ASP	-1	-0.775	-0.823	20.831	-15.806	-15.806	0.000	0.000	0.000	0.000
142	A	230	LEU	0	0.012	0.005	22.949	-0.021	-0.021	0.000	0.000	0.000	0.000
143	A	231	ARG	1	0.764	0.871	23.317	12.254	12.254	0.000	0.000	0.000	0.000
144	A	232	PRO	0	-0.005	-0.001	22.613	-0.566	-0.566	0.000	0.000	0.000	0.000
145	A	233	CYS	0	-0.017	0.002	17.948	-0.079	-0.079	0.000	0.000	0.000	0.000
146	A	234	HIS	0	-0.034	-0.031	18.431	0.685	0.685	0.000	0.000	0.000	0.000
147	A	235	GLU	-1	-0.873	-0.918	14.887	-19.670	-19.670	0.000	0.000	0.000	0.000
148	A	236	THR	0	-0.038	-0.034	11.430	0.399	0.399	0.000	0.000	0.000	0.000
149	A	237	THR	0	0.007	0.019	7.549	1.049	1.049	0.000	0.000	0.000	0.000
150	A	238	VAL	0	0.012	0.004	7.431	1.674	1.674	0.000	0.000	0.000	0.000
151	A	239	ASP	-1	-0.835	-0.907	2.150	-100.407	-99.377	6.742	-3.736	-4.037	-0.051
152	A	240	ILE	0	0.003	0.009	3.554	5.317	6.462	0.027	-0.387	-0.784	-0.001
153	A	241	PHE	0	0.003	-0.022	1.852	-49.529	-47.401	15.147	-7.043	-10.233	-0.093
154	A	242	HIS	0	0.006	-0.001	3.655	8.994	9.255	0.003	-0.081	-0.183	-0.001
155	A	243	LYS	1	0.960	0.995	6.290	24.461	24.461	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:89:HIS)