FMO DATABASE

FMODB ID: 43R1N

Calculation Name: 2YMB-A-Xray320

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: 2021-09-07

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	157
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1671805.659589
FMO2-HF: Nuclear repulsion	1606578.794472
FMO2-HF: Total energy	-65226.865117
FMO2-MP2: Total energy	-65416.897581

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:88:ACE )

Summations of interaction energy for fragment #1(A:88: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.
-0.722	0.891	0.214	-0.822	-1.005	-0.003

Interaction energy analysis for fragmet #1(A:88:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.014

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	90	LYS	1	0.957	0.985	3.810	0.291	1.384	-0.007	-0.514	-0.571	-0.002
4	A	91	GLN	0	0.004	0.007	6.130	0.011	0.011	0.000	0.000	0.000	0.000
5	A	92	ILE	0	-0.020	-0.015	9.620	0.134	0.134	0.000	0.000	0.000	0.000
6	A	93	LYS	1	0.956	0.971	12.189	0.221	0.221	0.000	0.000	0.000	0.000
7	A	94	ILE	0	-0.033	0.004	15.814	0.032	0.032	0.000	0.000	0.000	0.000
8	A	95	GLU	-1	-0.841	-0.928	18.279	-0.124	-0.124	0.000	0.000	0.000	0.000
9	A	96	GLU	-1	-0.803	-0.923	21.600	-0.086	-0.086	0.000	0.000	0.000	0.000
10	A	97	ASN	0	-0.094	-0.023	25.039	0.010	0.010	0.000	0.000	0.000	0.000
11	A	98	ALA	0	0.036	0.043	21.574	0.008	0.008	0.000	0.000	0.000	0.000
12	A	99	THR	0	-0.028	-0.037	23.050	0.003	0.003	0.000	0.000	0.000	0.000
13	A	100	GLY	0	0.005	0.014	21.744	0.000	0.000	0.000	0.000	0.000	0.000
14	A	101	PHE	0	0.024	-0.002	16.152	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	102	SER	0	0.040	0.014	19.830	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	103	TYR	0	0.013	-0.031	18.238	0.002	0.002	0.000	0.000	0.000	0.000
17	A	104	GLU	-1	-0.907	-0.950	17.818	0.004	0.004	0.000	0.000	0.000	0.000
18	A	105	SER	0	-0.080	-0.083	18.060	0.022	0.022	0.000	0.000	0.000	0.000
19	A	106	LEU	0	-0.068	-0.023	13.773	0.014	0.014	0.000	0.000	0.000	0.000
20	A	107	PHE	0	-0.005	-0.016	12.972	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	108	ARG	1	0.933	0.987	14.043	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	109	GLU	-1	-0.937	-0.972	9.939	0.222	0.222	0.000	0.000	0.000	0.000
23	A	110	TYR	0	-0.045	-0.022	7.233	-0.034	-0.034	0.000	0.000	0.000	0.000
24	A	111	LEU	0	0.034	0.033	10.686	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	112	ASN	0	0.069	0.049	12.870	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	113	GLH	0	0.008	-0.032	16.484	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	114	THR	0	-0.098	-0.063	14.665	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	115	VAL	0	-0.006	0.019	14.316	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	116	THR	0	-0.017	-0.013	16.892	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	117	GLU	-1	-0.896	-0.956	18.357	-0.055	-0.055	0.000	0.000	0.000	0.000
31	A	118	VAL	0	-0.005	-0.003	16.518	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	119	TRP	0	-0.017	-0.023	15.430	0.003	0.003	0.000	0.000	0.000	0.000
33	A	120	ILE	0	-0.016	0.004	17.120	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	121	GLU	-1	-0.902	-0.941	18.656	-0.200	-0.200	0.000	0.000	0.000	0.000
35	A	122	ASP	-1	-0.789	-0.939	19.859	-0.181	-0.181	0.000	0.000	0.000	0.000
36	A	123	PRO	0	-0.030	-0.004	22.520	0.017	0.017	0.000	0.000	0.000	0.000
37	A	124	TYR	0	-0.031	-0.024	25.228	0.008	0.008	0.000	0.000	0.000	0.000
38	A	125	ILE	0	-0.016	0.005	23.963	0.001	0.001	0.000	0.000	0.000	0.000
39	A	126	ARG	1	0.899	0.937	27.889	0.093	0.093	0.000	0.000	0.000	0.000
40	A	127	HIS	0	-0.011	-0.002	31.388	0.002	0.002	0.000	0.000	0.000	0.000
41	A	128	THR	0	0.060	0.018	32.061	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	129	HIS	0	-0.042	-0.042	28.817	0.007	0.007	0.000	0.000	0.000	0.000
43	A	130	GLN	0	0.006	0.007	27.993	0.001	0.001	0.000	0.000	0.000	0.000
44	A	131	LEU	0	0.043	0.026	27.551	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	132	TYR	0	0.015	0.002	29.021	0.002	0.002	0.000	0.000	0.000	0.000
46	A	133	ASN	0	-0.023	-0.001	24.541	0.010	0.010	0.000	0.000	0.000	0.000
47	A	134	PHE	0	0.068	0.030	23.354	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	135	LEU	0	0.020	0.013	25.171	0.003	0.003	0.000	0.000	0.000	0.000
49	A	136	ARG	1	0.903	0.950	24.513	0.065	0.065	0.000	0.000	0.000	0.000
50	A	137	PHE	0	-0.045	-0.011	17.480	0.006	0.006	0.000	0.000	0.000	0.000
51	A	138	CYS	0	0.005	-0.005	22.049	0.005	0.005	0.000	0.000	0.000	0.000
52	A	139	GLU	-1	-0.947	-0.968	24.267	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	140	MET	0	-0.082	-0.033	17.290	0.007	0.007	0.000	0.000	0.000	0.000
54	A	141	LEU	0	0.008	0.003	18.291	0.011	0.011	0.000	0.000	0.000	0.000
55	A	142	ILE	0	-0.039	-0.007	21.481	0.009	0.009	0.000	0.000	0.000	0.000
56	A	143	LYS	1	0.963	1.001	23.612	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	144	ARG	1	0.901	0.844	25.339	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	145	PRO	0	-0.016	-0.151	22.528	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	146	CYS	0	0.023	0.178	19.907	0.007	0.007	0.000	0.000	0.000	0.000
60	A	147	LYS	1	0.871	1.008	21.262	-0.061	-0.061	0.000	0.000	0.000	0.000
61	A	148	VAL	0	0.049	0.037	19.960	0.001	0.001	0.000	0.000	0.000	0.000
62	A	149	LYS	1	0.916	0.951	22.449	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	150	THR	0	0.001	0.005	23.177	0.001	0.001	0.000	0.000	0.000	0.000
64	A	151	ILE	0	0.008	0.005	21.649	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	152	HIS	1	0.781	0.870	21.569	0.078	0.078	0.000	0.000	0.000	0.000
66	A	153	LEU	0	0.000	-0.009	21.957	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	154	LEU	0	0.017	0.024	22.651	0.008	0.008	0.000	0.000	0.000	0.000
68	A	155	THR	0	0.001	-0.006	23.960	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	156	SER	0	-0.004	-0.001	26.559	0.007	0.007	0.000	0.000	0.000	0.000
70	A	157	LEU	0	-0.013	-0.004	29.066	0.002	0.002	0.000	0.000	0.000	0.000
71	A	158	ASP	-1	-0.914	-0.965	32.548	-0.069	-0.069	0.000	0.000	0.000	0.000
72	A	159	GLU	-1	-0.910	-0.964	34.771	-0.065	-0.065	0.000	0.000	0.000	0.000
73	A	160	GLY	0	-0.010	0.014	37.641	0.004	0.004	0.000	0.000	0.000	0.000
74	A	161	ILE	0	0.038	-0.003	40.018	0.000	0.000	0.000	0.000	0.000	0.000
75	A	162	GLU	-1	-0.896	-0.946	36.807	-0.054	-0.054	0.000	0.000	0.000	0.000
76	A	163	GLN	0	0.029	0.020	36.695	0.001	0.001	0.000	0.000	0.000	0.000
77	A	164	VAL	0	-0.046	-0.021	37.609	0.000	0.000	0.000	0.000	0.000	0.000
78	A	165	GLN	0	-0.032	-0.029	37.764	0.000	0.000	0.000	0.000	0.000	0.000
79	A	166	GLN	0	0.049	0.044	31.124	0.003	0.003	0.000	0.000	0.000	0.000
80	A	167	SER	0	0.000	-0.002	34.392	0.000	0.000	0.000	0.000	0.000	0.000
81	A	168	ARG	1	0.944	0.966	35.925	0.033	0.033	0.000	0.000	0.000	0.000
82	A	169	GLY	0	0.052	0.029	35.516	0.002	0.002	0.000	0.000	0.000	0.000
83	A	170	LEU	0	-0.008	-0.017	29.546	0.001	0.001	0.000	0.000	0.000	0.000
84	A	171	GLN	0	-0.006	0.006	32.512	0.003	0.003	0.000	0.000	0.000	0.000
85	A	172	GLU	-1	-0.892	-0.929	35.121	-0.030	-0.030	0.000	0.000	0.000	0.000
86	A	173	ILE	0	-0.055	-0.027	29.096	0.003	0.003	0.000	0.000	0.000	0.000
87	A	174	GLU	-1	-0.890	-0.942	31.084	-0.040	-0.040	0.000	0.000	0.000	0.000
88	A	175	GLU	-1	-0.941	-0.984	32.082	-0.024	-0.024	0.000	0.000	0.000	0.000
89	A	176	SER	0	-0.015	-0.011	33.149	0.005	0.005	0.000	0.000	0.000	0.000
90	A	177	LEU	0	-0.003	-0.013	27.408	0.004	0.004	0.000	0.000	0.000	0.000
91	A	178	ARG	1	0.936	0.985	31.035	0.033	0.033	0.000	0.000	0.000	0.000
92	A	179	SER	0	-0.070	-0.030	33.177	0.004	0.004	0.000	0.000	0.000	0.000
93	A	180	HIS	1	0.818	0.901	30.723	0.015	0.015	0.000	0.000	0.000	0.000
94	A	181	GLY	0	-0.032	0.004	31.249	0.004	0.004	0.000	0.000	0.000	0.000
95	A	182	VAL	0	-0.070	-0.041	26.061	0.002	0.002	0.000	0.000	0.000	0.000
96	A	183	LEU	0	-0.005	0.005	27.637	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	184	LEU	0	-0.007	-0.003	26.121	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	185	GLU	-1	-0.835	-0.892	26.074	-0.070	-0.070	0.000	0.000	0.000	0.000
99	A	186	VAL	0	0.020	0.008	26.633	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	187	GLN	0	-0.043	-0.015	27.255	0.001	0.001	0.000	0.000	0.000	0.000
101	A	188	TYR	0	0.041	0.005	27.862	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	189	SER	0	-0.001	-0.018	27.663	0.004	0.004	0.000	0.000	0.000	0.000
103	A	190	SER	0	-0.024	0.000	28.559	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	191	SER	0	-0.030	-0.016	28.489	0.002	0.002	0.000	0.000	0.000	0.000
105	A	192	ILE	0	0.028	0.031	23.282	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	193	HIS	0	0.009	-0.019	23.174	0.015	0.015	0.000	0.000	0.000	0.000
107	A	194	ASP	-1	-0.935	-0.954	17.999	-0.294	-0.294	0.000	0.000	0.000	0.000
108	A	195	ARG	1	0.887	0.959	18.199	0.211	0.211	0.000	0.000	0.000	0.000
109	A	196	GLU	-1	-0.888	-0.962	13.633	-0.446	-0.446	0.000	0.000	0.000	0.000
110	A	197	ILE	0	0.024	0.010	14.053	0.056	0.056	0.000	0.000	0.000	0.000
111	A	198	ARG	1	0.888	0.964	12.649	0.149	0.149	0.000	0.000	0.000	0.000
112	A	199	PHE	0	0.061	0.025	11.550	0.054	0.054	0.000	0.000	0.000	0.000
113	A	200	ASN	0	0.045	0.029	12.697	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	201	ASN	0	0.026	0.000	11.631	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	202	GLY	0	-0.002	0.001	8.834	0.088	0.088	0.000	0.000	0.000	0.000
116	A	203	TRP	0	-0.011	0.009	4.311	-0.159	-0.086	0.000	-0.012	-0.061	0.000
117	A	204	MET	0	-0.011	-0.010	7.877	0.046	0.046	0.000	0.000	0.000	0.000
118	A	205	ILE	0	-0.018	-0.003	8.775	-0.209	-0.209	0.000	0.000	0.000	0.000
119	A	206	LYS	1	0.944	0.986	11.080	0.577	0.577	0.000	0.000	0.000	0.000
120	A	207	ILE	0	-0.004	0.019	12.978	-0.028	-0.028	0.000	0.000	0.000	0.000
121	A	208	GLY	0	0.036	0.010	15.481	0.017	0.017	0.000	0.000	0.000	0.000
122	A	209	ARG	1	0.876	0.914	17.842	0.158	0.158	0.000	0.000	0.000	0.000
123	A	210	GLY	0	0.035	0.031	18.972	0.018	0.018	0.000	0.000	0.000	0.000
124	A	211	LEU	0	0.001	-0.008	19.039	0.000	0.000	0.000	0.000	0.000	0.000
125	A	212	ASP	-1	-0.854	-0.902	21.349	-0.079	-0.079	0.000	0.000	0.000	0.000
126	A	213	TYR	0	-0.011	-0.012	18.967	-0.009	-0.009	0.000	0.000	0.000	0.000
127	A	214	PHE	0	0.020	0.012	21.683	0.005	0.005	0.000	0.000	0.000	0.000
128	A	215	LYS	1	0.790	0.888	25.645	0.073	0.073	0.000	0.000	0.000	0.000
129	A	216	LYS	1	0.970	0.984	28.968	0.048	0.048	0.000	0.000	0.000	0.000
130	A	217	PRO	0	-0.004	0.001	32.250	0.001	0.001	0.000	0.000	0.000	0.000
131	A	218	GLN	0	-0.018	-0.004	33.621	0.001	0.001	0.000	0.000	0.000	0.000
132	A	219	SER	0	0.042	0.001	35.981	0.001	0.001	0.000	0.000	0.000	0.000
133	A	220	ARG	1	0.975	0.969	37.662	0.019	0.019	0.000	0.000	0.000	0.000
134	A	221	PHE	0	0.014	0.009	38.708	0.000	0.000	0.000	0.000	0.000	0.000
135	A	222	SER	0	-0.031	0.016	35.238	0.001	0.001	0.000	0.000	0.000	0.000
136	A	223	LEU	0	0.078	0.013	32.688	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	224	GLY	0	0.060	0.039	29.813	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	225	TYR	0	-0.074	-0.022	30.197	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	226	CYS	0	-0.028	-0.031	31.508	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	227	ASP	-1	-0.785	-0.877	26.457	-0.016	-0.016	0.000	0.000	0.000	0.000
141	A	228	PHE	0	-0.031	-0.034	24.642	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	229	ASP	-1	-0.791	-0.845	22.137	-0.031	-0.031	0.000	0.000	0.000	0.000
143	A	230	LEU	0	-0.003	-0.013	24.475	0.001	0.001	0.000	0.000	0.000	0.000
144	A	231	ARG	1	0.779	0.890	26.352	0.049	0.049	0.000	0.000	0.000	0.000
145	A	232	PRO	0	-0.002	0.001	25.617	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	233	CYS	0	-0.029	0.000	22.362	-0.003	-0.003	0.000	0.000	0.000	0.000
147	A	234	HIS	0	-0.007	-0.017	23.974	0.005	0.005	0.000	0.000	0.000	0.000
148	A	235	GLU	-1	-0.914	-0.942	21.642	-0.138	-0.138	0.000	0.000	0.000	0.000
149	A	236	THR	0	-0.043	-0.035	17.749	-0.011	-0.011	0.000	0.000	0.000	0.000
150	A	237	THR	0	-0.010	-0.006	14.762	0.018	0.018	0.000	0.000	0.000	0.000
151	A	238	VAL	0	-0.020	-0.009	10.937	0.004	0.004	0.000	0.000	0.000	0.000
152	A	239	ASP	-1	-0.842	-0.915	9.390	-0.787	-0.787	0.000	0.000	0.000	0.000
153	A	240	ILE	0	-0.023	-0.001	5.297	0.126	0.126	0.000	0.000	0.000	0.000
154	A	241	PHE	0	0.013	-0.006	4.658	-0.984	-1.032	0.000	-0.031	0.078	0.000
155	A	242	HIS	0	-0.032	-0.039	2.710	0.466	0.944	0.221	-0.262	-0.437	-0.001
156	A	243	LYS	1	0.937	0.971	4.542	0.162	0.179	0.000	-0.003	-0.014	0.000
157	A	244	NME	0	0.014	0.027	7.150	0.081	0.081	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:88:ACE )