FMO DATABASE

FMODB ID: 43Z7N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1664015.291578
FMO2-HF: Nuclear repulsion	1598958.813982
FMO2-HF: Total energy	-65056.477595
FMO2-MP2: Total energy	-65245.96625

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.
-100.88	-91.451	9.318	-8.664	-10.081	-0.086

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 : 0.877 / q_NPA : 0.940

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	-0.007	0.000	3.804	-0.429	1.591	-0.032	-0.858	-1.130	0.002
4	A	92	ILE	0	-0.006	-0.007	6.188	4.527	4.527	0.000	0.000	0.000	0.000
5	A	93	LYS	1	0.957	0.971	9.616	26.087	26.087	0.000	0.000	0.000	0.000
6	A	94	ILE	0	-0.028	0.007	11.839	1.408	1.408	0.000	0.000	0.000	0.000
7	A	95	GLU	-1	-0.840	-0.927	14.760	-18.387	-18.387	0.000	0.000	0.000	0.000
8	A	96	GLU	-1	-0.804	-0.923	17.649	-13.949	-13.949	0.000	0.000	0.000	0.000
9	A	97	ASN	0	-0.086	-0.020	20.637	0.696	0.696	0.000	0.000	0.000	0.000
10	A	98	ALA	0	0.034	0.041	19.209	0.403	0.403	0.000	0.000	0.000	0.000
11	A	99	THR	0	-0.027	-0.036	21.189	0.443	0.443	0.000	0.000	0.000	0.000
12	A	100	GLY	0	0.005	0.015	20.706	-0.434	-0.434	0.000	0.000	0.000	0.000
13	A	101	PHE	0	0.019	-0.005	15.097	-0.899	-0.899	0.000	0.000	0.000	0.000
14	A	102	SER	0	0.043	0.017	18.550	-0.583	-0.583	0.000	0.000	0.000	0.000
15	A	103	TYR	0	0.015	-0.030	17.324	-0.458	-0.458	0.000	0.000	0.000	0.000
16	A	104	GLU	-1	-0.909	-0.951	17.514	-13.375	-13.375	0.000	0.000	0.000	0.000
17	A	105	SER	0	-0.080	-0.082	17.775	0.003	0.003	0.000	0.000	0.000	0.000
18	A	106	LEU	0	-0.072	-0.025	12.627	-0.611	-0.611	0.000	0.000	0.000	0.000
19	A	107	PHE	0	-0.008	-0.018	12.165	-1.616	-1.616	0.000	0.000	0.000	0.000
20	A	108	ARG	1	0.935	0.987	13.962	16.218	16.218	0.000	0.000	0.000	0.000
21	A	109	GLU	-1	-0.933	-0.969	10.295	-21.633	-21.633	0.000	0.000	0.000	0.000
22	A	110	TYR	0	-0.048	-0.026	7.486	-0.889	-0.889	0.000	0.000	0.000	0.000
23	A	111	LEU	0	0.030	0.029	11.393	0.082	0.082	0.000	0.000	0.000	0.000
24	A	112	ASN	0	0.058	0.049	14.401	0.742	0.742	0.000	0.000	0.000	0.000
25	A	113	GLH	0	-0.004	-0.019	17.685	0.405	0.405	0.000	0.000	0.000	0.000
26	A	114	THR	0	-0.070	-0.059	16.321	0.090	0.090	0.000	0.000	0.000	0.000
27	A	115	VAL	0	-0.011	0.018	15.487	-0.041	-0.041	0.000	0.000	0.000	0.000
28	A	116	THR	0	-0.014	-0.012	18.179	0.408	0.408	0.000	0.000	0.000	0.000
29	A	117	GLU	-1	-0.892	-0.955	19.565	-13.439	-13.439	0.000	0.000	0.000	0.000
30	A	118	VAL	0	-0.005	-0.003	16.121	-0.860	-0.860	0.000	0.000	0.000	0.000
31	A	119	TRP	0	-0.017	-0.023	15.587	0.521	0.521	0.000	0.000	0.000	0.000
32	A	120	ILE	0	-0.017	0.002	15.320	-1.443	-1.443	0.000	0.000	0.000	0.000
33	A	121	GLU	-1	-0.903	-0.940	14.605	-18.895	-18.895	0.000	0.000	0.000	0.000
34	A	122	ASP	-1	-0.791	-0.940	15.144	-18.933	-18.933	0.000	0.000	0.000	0.000
35	A	123	PRO	0	-0.031	-0.004	16.864	0.977	0.977	0.000	0.000	0.000	0.000
36	A	124	TYR	0	-0.032	-0.025	18.847	0.503	0.503	0.000	0.000	0.000	0.000
37	A	125	ILE	0	-0.014	0.005	19.743	-0.109	-0.109	0.000	0.000	0.000	0.000
38	A	126	ARG	1	0.898	0.938	23.388	12.457	12.457	0.000	0.000	0.000	0.000
39	A	127	HIS	0	-0.008	0.001	25.858	0.088	0.088	0.000	0.000	0.000	0.000
40	A	128	THR	0	0.062	0.019	27.875	-0.177	-0.177	0.000	0.000	0.000	0.000
41	A	129	HIS	0	-0.042	-0.042	24.139	0.397	0.397	0.000	0.000	0.000	0.000
42	A	130	GLN	0	0.001	0.004	23.206	-0.051	-0.051	0.000	0.000	0.000	0.000
43	A	131	LEU	0	0.046	0.027	24.154	-0.501	-0.501	0.000	0.000	0.000	0.000
44	A	132	TYR	0	0.015	0.003	26.563	-0.036	-0.036	0.000	0.000	0.000	0.000
45	A	133	ASN	0	-0.027	-0.002	21.595	0.236	0.236	0.000	0.000	0.000	0.000
46	A	134	PHE	0	0.071	0.030	21.141	-0.482	-0.482	0.000	0.000	0.000	0.000
47	A	135	LEU	0	0.016	0.012	23.007	-0.099	-0.099	0.000	0.000	0.000	0.000
48	A	136	ARG	1	0.905	0.951	22.551	13.099	13.099	0.000	0.000	0.000	0.000
49	A	137	PHE	0	-0.043	-0.011	16.091	-0.195	-0.195	0.000	0.000	0.000	0.000
50	A	138	CYS	0	0.005	-0.005	21.455	-0.214	-0.214	0.000	0.000	0.000	0.000
51	A	139	GLU	-1	-0.950	-0.969	23.635	-10.994	-10.994	0.000	0.000	0.000	0.000
52	A	140	MET	0	-0.076	-0.030	17.248	0.295	0.295	0.000	0.000	0.000	0.000
53	A	141	LEU	0	0.010	0.004	18.521	-0.167	-0.167	0.000	0.000	0.000	0.000
54	A	142	ILE	0	-0.050	-0.012	21.730	0.045	0.045	0.000	0.000	0.000	0.000
55	A	143	LYS	1	0.970	1.005	24.150	12.396	12.396	0.000	0.000	0.000	0.000
56	A	144	ARG	1	0.932	0.845	25.941	9.912	9.912	0.000	0.000	0.000	0.000
57	A	145	PRO	0	-0.038	-0.138	23.692	0.149	0.149	0.000	0.000	0.000	0.000
58	A	146	CYS	0	-0.015	0.139	20.825	-0.197	-0.197	0.000	0.000	0.000	0.000
59	A	147	LYS	1	0.908	1.022	22.259	11.765	11.765	0.000	0.000	0.000	0.000
60	A	148	VAL	0	0.047	0.040	20.693	-0.075	-0.075	0.000	0.000	0.000	0.000
61	A	149	LYS	1	0.917	0.951	23.322	10.919	10.919	0.000	0.000	0.000	0.000
62	A	150	THR	0	0.003	0.006	23.941	0.568	0.568	0.000	0.000	0.000	0.000
63	A	151	ILE	0	0.008	0.005	20.610	-0.714	-0.714	0.000	0.000	0.000	0.000
64	A	152	HIS	1	0.781	0.870	20.401	14.216	14.216	0.000	0.000	0.000	0.000
65	A	153	LEU	0	0.003	-0.009	20.097	-0.892	-0.892	0.000	0.000	0.000	0.000
66	A	154	LEU	0	0.016	0.024	18.601	0.617	0.617	0.000	0.000	0.000	0.000
67	A	155	THR	0	-0.001	-0.006	19.742	-0.517	-0.517	0.000	0.000	0.000	0.000
68	A	156	SER	0	-0.003	0.000	21.617	0.486	0.486	0.000	0.000	0.000	0.000
69	A	157	LEU	0	-0.013	-0.004	23.592	0.042	0.042	0.000	0.000	0.000	0.000
70	A	158	ASP	-1	-0.916	-0.966	27.291	-10.588	-10.588	0.000	0.000	0.000	0.000
71	A	159	GLU	-1	-0.907	-0.962	28.989	-9.944	-9.944	0.000	0.000	0.000	0.000
72	A	160	GLY	0	-0.010	0.014	31.421	0.352	0.352	0.000	0.000	0.000	0.000
73	A	161	ILE	0	0.038	-0.002	33.940	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	162	GLU	-1	-0.896	-0.946	31.489	-9.821	-9.821	0.000	0.000	0.000	0.000
75	A	163	GLN	0	0.030	0.019	31.727	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	164	VAL	0	-0.045	-0.020	32.753	-0.072	-0.072	0.000	0.000	0.000	0.000
77	A	165	GLN	0	-0.034	-0.029	33.975	-0.166	-0.166	0.000	0.000	0.000	0.000
78	A	166	GLN	0	0.048	0.043	26.594	0.207	0.207	0.000	0.000	0.000	0.000
79	A	167	SER	0	0.001	-0.002	30.800	-0.185	-0.185	0.000	0.000	0.000	0.000
80	A	168	ARG	1	0.945	0.967	32.241	8.186	8.186	0.000	0.000	0.000	0.000
81	A	169	GLY	0	0.052	0.029	32.520	0.087	0.087	0.000	0.000	0.000	0.000
82	A	170	LEU	0	-0.007	-0.017	26.393	-0.146	-0.146	0.000	0.000	0.000	0.000
83	A	171	GLN	0	-0.009	0.004	30.208	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	172	GLU	-1	-0.886	-0.927	32.944	-8.778	-8.778	0.000	0.000	0.000	0.000
85	A	173	ILE	0	-0.059	-0.028	27.344	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	174	GLU	-1	-0.889	-0.941	29.783	-10.278	-10.278	0.000	0.000	0.000	0.000
87	A	175	GLU	-1	-0.941	-0.984	30.668	-8.523	-8.523	0.000	0.000	0.000	0.000
88	A	176	SER	0	-0.013	-0.010	32.251	0.154	0.154	0.000	0.000	0.000	0.000
89	A	177	LEU	0	-0.006	-0.014	26.457	0.041	0.041	0.000	0.000	0.000	0.000
90	A	178	ARG	1	0.936	0.984	30.587	9.283	9.283	0.000	0.000	0.000	0.000
91	A	179	SER	0	-0.060	-0.027	32.940	0.258	0.258	0.000	0.000	0.000	0.000
92	A	180	HIS	1	0.807	0.897	31.090	9.763	9.763	0.000	0.000	0.000	0.000
93	A	181	GLY	0	-0.030	0.004	31.878	-0.069	-0.069	0.000	0.000	0.000	0.000
94	A	182	VAL	0	-0.069	-0.041	26.040	-0.229	-0.229	0.000	0.000	0.000	0.000
95	A	183	LEU	0	-0.004	0.006	27.708	0.234	0.234	0.000	0.000	0.000	0.000
96	A	184	LEU	0	-0.006	-0.004	24.631	-0.525	-0.525	0.000	0.000	0.000	0.000
97	A	185	GLU	-1	-0.833	-0.891	24.765	-12.162	-12.162	0.000	0.000	0.000	0.000
98	A	186	VAL	0	0.022	0.008	24.779	-0.681	-0.681	0.000	0.000	0.000	0.000
99	A	187	GLN	0	-0.043	-0.015	24.425	0.342	0.342	0.000	0.000	0.000	0.000
100	A	188	TYR	0	0.043	0.005	24.243	-0.539	-0.539	0.000	0.000	0.000	0.000
101	A	189	SER	0	-0.003	-0.018	22.901	0.352	0.352	0.000	0.000	0.000	0.000
102	A	190	SER	0	-0.026	0.000	23.089	-0.473	-0.473	0.000	0.000	0.000	0.000
103	A	191	SER	0	-0.024	-0.014	22.579	0.203	0.203	0.000	0.000	0.000	0.000
104	A	192	ILE	0	0.029	0.031	17.662	-0.440	-0.440	0.000	0.000	0.000	0.000
105	A	193	HIS	0	0.010	-0.018	16.429	0.873	0.873	0.000	0.000	0.000	0.000
106	A	194	ASP	-1	-0.939	-0.956	11.497	-24.831	-24.831	0.000	0.000	0.000	0.000
107	A	195	ARG	1	0.892	0.963	11.915	20.604	20.604	0.000	0.000	0.000	0.000
108	A	196	GLU	-1	-0.896	-0.967	10.008	-30.500	-30.500	0.000	0.000	0.000	0.000
109	A	197	ILE	0	0.029	0.013	10.752	2.350	2.350	0.000	0.000	0.000	0.000
110	A	198	ARG	1	0.886	0.962	10.743	18.131	18.131	0.000	0.000	0.000	0.000
111	A	199	PHE	0	0.061	0.026	11.547	1.818	1.818	0.000	0.000	0.000	0.000
112	A	200	ASN	0	0.045	0.029	13.725	-1.363	-1.363	0.000	0.000	0.000	0.000
113	A	201	ASN	0	0.031	0.002	13.027	-0.241	-0.241	0.000	0.000	0.000	0.000
114	A	202	GLY	0	0.009	0.007	10.602	-0.112	-0.112	0.000	0.000	0.000	0.000
115	A	203	TRP	0	-0.013	0.008	5.006	-3.839	-3.839	0.000	0.000	0.000	0.000
116	A	204	MET	0	-0.014	-0.012	7.303	2.262	2.262	0.000	0.000	0.000	0.000
117	A	205	ILE	0	-0.020	-0.005	6.610	-5.537	-5.537	0.000	0.000	0.000	0.000
118	A	206	LYS	1	0.939	0.981	5.599	37.384	37.384	0.000	0.000	0.000	0.000
119	A	207	ILE	0	0.002	0.021	7.520	-2.724	-2.724	0.000	0.000	0.000	0.000
120	A	208	GLY	0	0.031	0.008	10.153	1.031	1.031	0.000	0.000	0.000	0.000
121	A	209	ARG	1	0.882	0.917	11.062	18.214	18.214	0.000	0.000	0.000	0.000
122	A	210	GLY	0	0.031	0.031	13.358	1.215	1.215	0.000	0.000	0.000	0.000
123	A	211	LEU	0	0.004	-0.007	14.941	-0.355	-0.355	0.000	0.000	0.000	0.000
124	A	212	ASP	-1	-0.850	-0.901	17.611	-13.072	-13.072	0.000	0.000	0.000	0.000
125	A	213	TYR	0	-0.016	-0.015	16.274	-0.347	-0.347	0.000	0.000	0.000	0.000
126	A	214	PHE	0	0.016	0.012	18.697	0.150	0.150	0.000	0.000	0.000	0.000
127	A	215	LYS	1	0.793	0.890	21.989	13.362	13.362	0.000	0.000	0.000	0.000
128	A	216	LYS	1	0.970	0.984	24.845	10.045	10.045	0.000	0.000	0.000	0.000
129	A	217	PRO	0	-0.003	0.002	28.334	-0.086	-0.086	0.000	0.000	0.000	0.000
130	A	218	GLN	0	-0.017	-0.004	30.549	0.443	0.443	0.000	0.000	0.000	0.000
131	A	219	SER	0	0.042	0.001	32.808	0.220	0.220	0.000	0.000	0.000	0.000
132	A	220	ARG	1	0.975	0.969	35.078	7.455	7.455	0.000	0.000	0.000	0.000
133	A	221	PHE	0	0.015	0.008	36.743	-0.043	-0.043	0.000	0.000	0.000	0.000
134	A	222	SER	0	-0.033	0.016	33.175	0.029	0.029	0.000	0.000	0.000	0.000
135	A	223	LEU	0	0.079	0.014	31.769	-0.118	-0.118	0.000	0.000	0.000	0.000
136	A	224	GLY	0	0.059	0.039	28.699	-0.147	-0.147	0.000	0.000	0.000	0.000
137	A	225	TYR	0	-0.074	-0.023	28.607	-0.339	-0.339	0.000	0.000	0.000	0.000
138	A	226	CYS	0	-0.029	-0.031	30.344	0.003	0.003	0.000	0.000	0.000	0.000
139	A	227	ASP	-1	-0.779	-0.874	25.969	-12.047	-12.047	0.000	0.000	0.000	0.000
140	A	228	PHE	0	-0.034	-0.036	23.094	0.064	0.064	0.000	0.000	0.000	0.000
141	A	229	ASP	-1	-0.792	-0.846	21.583	-14.755	-14.755	0.000	0.000	0.000	0.000
142	A	230	LEU	0	-0.001	-0.012	23.667	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	231	ARG	1	0.781	0.892	24.386	12.056	12.056	0.000	0.000	0.000	0.000
144	A	232	PRO	0	0.000	0.002	23.455	-0.550	-0.550	0.000	0.000	0.000	0.000
145	A	233	CYS	0	-0.031	-0.001	18.805	-0.029	-0.029	0.000	0.000	0.000	0.000
146	A	234	HIS	0	-0.009	-0.017	19.105	0.378	0.378	0.000	0.000	0.000	0.000
147	A	235	GLU	-1	-0.912	-0.942	15.794	-18.455	-18.455	0.000	0.000	0.000	0.000
148	A	236	THR	0	-0.040	-0.033	12.236	-0.218	-0.218	0.000	0.000	0.000	0.000
149	A	237	THR	0	-0.010	-0.006	8.355	0.568	0.568	0.000	0.000	0.000	0.000
150	A	238	VAL	0	-0.011	-0.003	7.930	0.495	0.495	0.000	0.000	0.000	0.000
151	A	239	ASP	-1	-0.871	-0.929	2.650	-69.085	-67.394	0.221	-1.029	-0.883	-0.010
152	A	240	ILE	0	-0.003	0.012	3.541	4.879	5.656	0.007	-0.241	-0.543	-0.001
153	A	241	PHE	0	-0.019	-0.035	2.128	-41.548	-36.781	9.122	-6.499	-7.389	-0.077
154	A	242	HIS	0	-0.029	-0.029	4.119	7.284	7.458	0.000	-0.037	-0.136	0.000
155	A	243	LYS	1	0.978	1.007	5.765	23.462	23.462	0.000	0.000	0.000	0.000

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