FMO DATABASE

FMODB ID: 536MZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1666195.111166
FMO2-HF: Nuclear repulsion	1601136.974444
FMO2-HF: Total energy	-65058.136722
FMO2-MP2: Total energy	-65247.555602

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.
-138.102	-130.844	19.678	-12.227	-14.709	-0.137

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 : 0.911

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	-0.034	-0.032	3.804	0.779	2.870	-0.034	-0.866	-1.191	0.002
4	A	92	ILE	0	-0.019	-0.016	5.978	5.202	5.202	0.000	0.000	0.000	0.000
5	A	93	LYS	1	0.836	0.898	9.297	20.703	20.703	0.000	0.000	0.000	0.000
6	A	94	ILE	0	-0.027	0.004	11.582	1.609	1.609	0.000	0.000	0.000	0.000
7	A	95	GLU	-1	-0.788	-0.892	14.407	-19.338	-19.338	0.000	0.000	0.000	0.000
8	A	96	GLU	-1	-0.778	-0.897	17.368	-13.807	-13.807	0.000	0.000	0.000	0.000
9	A	97	ASN	0	-0.072	-0.025	20.333	0.524	0.524	0.000	0.000	0.000	0.000
10	A	98	ALA	0	0.028	0.038	18.789	0.410	0.410	0.000	0.000	0.000	0.000
11	A	99	THR	0	-0.028	-0.039	20.808	0.455	0.455	0.000	0.000	0.000	0.000
12	A	100	GLY	0	-0.010	0.012	20.643	-0.427	-0.427	0.000	0.000	0.000	0.000
13	A	101	PHE	0	0.035	0.004	14.446	-0.877	-0.877	0.000	0.000	0.000	0.000
14	A	102	SER	0	-0.009	-0.024	18.277	-0.576	-0.576	0.000	0.000	0.000	0.000
15	A	103	TYR	0	0.037	-0.011	17.098	-0.397	-0.397	0.000	0.000	0.000	0.000
16	A	104	GLU	-1	-0.829	-0.891	17.448	-13.179	-13.179	0.000	0.000	0.000	0.000
17	A	105	SER	0	-0.028	-0.043	17.978	0.106	0.106	0.000	0.000	0.000	0.000
18	A	106	LEU	0	-0.071	-0.016	12.065	-0.558	-0.558	0.000	0.000	0.000	0.000
19	A	107	PHE	0	0.003	-0.018	11.974	-1.437	-1.437	0.000	0.000	0.000	0.000
20	A	108	ARG	1	0.910	0.974	14.025	15.833	15.833	0.000	0.000	0.000	0.000
21	A	109	GLU	-1	-0.870	-0.924	10.948	-21.536	-21.536	0.000	0.000	0.000	0.000
22	A	110	TYR	0	-0.113	-0.067	8.627	-0.900	-0.900	0.000	0.000	0.000	0.000
23	A	111	LEU	0	0.025	0.024	12.045	0.004	0.004	0.000	0.000	0.000	0.000
24	A	112	ASN	0	0.056	0.033	14.673	1.086	1.086	0.000	0.000	0.000	0.000
25	A	113	GLH	0	0.010	0.006	18.131	0.378	0.378	0.000	0.000	0.000	0.000
26	A	114	THR	0	-0.055	-0.040	16.339	0.046	0.046	0.000	0.000	0.000	0.000
27	A	115	VAL	0	-0.028	0.012	15.511	-0.057	-0.057	0.000	0.000	0.000	0.000
28	A	116	THR	0	-0.001	-0.017	18.180	0.463	0.463	0.000	0.000	0.000	0.000
29	A	117	GLU	-1	-0.868	-0.917	19.428	-13.406	-13.406	0.000	0.000	0.000	0.000
30	A	118	VAL	0	-0.009	-0.003	15.782	-0.878	-0.878	0.000	0.000	0.000	0.000
31	A	119	TRP	0	-0.015	-0.023	15.313	0.590	0.590	0.000	0.000	0.000	0.000
32	A	120	ILE	0	-0.021	0.000	14.920	-1.446	-1.446	0.000	0.000	0.000	0.000
33	A	121	GLU	-1	-0.871	-0.927	14.211	-18.981	-18.981	0.000	0.000	0.000	0.000
34	A	122	ASP	-1	-0.769	-0.925	14.657	-19.294	-19.294	0.000	0.000	0.000	0.000
35	A	123	PRO	0	-0.039	0.012	16.449	1.016	1.016	0.000	0.000	0.000	0.000
36	A	124	TYR	0	-0.026	-0.019	18.172	0.513	0.513	0.000	0.000	0.000	0.000
37	A	125	ILE	0	-0.007	0.004	19.263	-0.079	-0.079	0.000	0.000	0.000	0.000
38	A	126	ARG	1	0.874	0.926	22.878	12.496	12.496	0.000	0.000	0.000	0.000
39	A	127	HIS	0	-0.027	-0.011	25.403	0.064	0.064	0.000	0.000	0.000	0.000
40	A	128	THR	0	0.050	0.009	27.350	-0.211	-0.211	0.000	0.000	0.000	0.000
41	A	129	HIS	0	-0.045	-0.046	23.661	0.434	0.434	0.000	0.000	0.000	0.000
42	A	130	GLN	0	0.000	-0.008	22.541	-0.040	-0.040	0.000	0.000	0.000	0.000
43	A	131	LEU	0	0.041	0.028	23.597	-0.506	-0.506	0.000	0.000	0.000	0.000
44	A	132	TYR	0	0.008	-0.001	25.986	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	133	ASN	0	-0.040	-0.005	21.051	0.265	0.265	0.000	0.000	0.000	0.000
46	A	134	PHE	0	0.076	0.033	20.780	-0.482	-0.482	0.000	0.000	0.000	0.000
47	A	135	LEU	0	0.020	0.018	22.524	-0.099	-0.099	0.000	0.000	0.000	0.000
48	A	136	ARG	1	0.898	0.945	22.363	13.108	13.108	0.000	0.000	0.000	0.000
49	A	137	PHE	0	-0.049	-0.017	15.861	-0.184	-0.184	0.000	0.000	0.000	0.000
50	A	138	CYS	0	-0.005	-0.009	21.174	-0.213	-0.213	0.000	0.000	0.000	0.000
51	A	139	GLU	-1	-0.943	-0.974	23.311	-10.963	-10.963	0.000	0.000	0.000	0.000
52	A	140	MET	0	-0.084	-0.031	17.413	0.231	0.231	0.000	0.000	0.000	0.000
53	A	141	LEU	0	0.037	0.017	17.855	-0.145	-0.145	0.000	0.000	0.000	0.000
54	A	142	ILE	0	-0.072	-0.021	21.674	0.052	0.052	0.000	0.000	0.000	0.000
55	A	143	LYS	1	0.855	0.922	24.358	12.690	12.690	0.000	0.000	0.000	0.000
56	A	144	ARG	1	0.944	0.924	26.246	9.885	9.885	0.000	0.000	0.000	0.000
57	A	145	PRO	0	-0.086	-0.029	23.744	0.092	0.092	0.000	0.000	0.000	0.000
58	A	146	CYS	0	0.017	0.023	21.302	-0.182	-0.182	0.000	0.000	0.000	0.000
59	A	147	LYS	1	0.910	0.941	22.533	11.583	11.583	0.000	0.000	0.000	0.000
60	A	148	VAL	0	0.063	0.049	20.628	-0.050	-0.050	0.000	0.000	0.000	0.000
61	A	149	LYS	1	0.824	0.899	23.356	11.243	11.243	0.000	0.000	0.000	0.000
62	A	150	THR	0	0.017	0.011	23.422	0.582	0.582	0.000	0.000	0.000	0.000
63	A	151	ILE	0	0.000	-0.002	20.188	-0.728	-0.728	0.000	0.000	0.000	0.000
64	A	152	HIS	1	0.768	0.850	19.914	14.374	14.374	0.000	0.000	0.000	0.000
65	A	153	LEU	0	-0.003	-0.011	19.699	-0.897	-0.897	0.000	0.000	0.000	0.000
66	A	154	LEU	0	0.016	0.022	18.246	0.621	0.621	0.000	0.000	0.000	0.000
67	A	155	THR	0	-0.012	-0.029	19.289	-0.556	-0.556	0.000	0.000	0.000	0.000
68	A	156	SER	0	0.008	0.004	21.255	0.503	0.503	0.000	0.000	0.000	0.000
69	A	157	LEU	0	-0.014	0.000	23.190	0.039	0.039	0.000	0.000	0.000	0.000
70	A	158	ASP	-1	-0.873	-0.946	26.874	-10.720	-10.720	0.000	0.000	0.000	0.000
71	A	159	GLU	-1	-0.926	-0.964	28.575	-10.263	-10.263	0.000	0.000	0.000	0.000
72	A	160	GLY	0	0.003	0.018	31.051	0.370	0.370	0.000	0.000	0.000	0.000
73	A	161	ILE	0	0.042	-0.004	33.543	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	162	GLU	-1	-0.898	-0.936	30.699	-9.940	-9.940	0.000	0.000	0.000	0.000
75	A	163	GLN	0	0.031	0.015	31.262	-0.095	-0.095	0.000	0.000	0.000	0.000
76	A	164	VAL	0	-0.028	-0.014	32.295	-0.074	-0.074	0.000	0.000	0.000	0.000
77	A	165	GLN	0	-0.020	-0.015	33.285	-0.172	-0.172	0.000	0.000	0.000	0.000
78	A	166	GLN	0	0.035	0.032	25.958	0.191	0.191	0.000	0.000	0.000	0.000
79	A	167	SER	0	0.012	0.001	30.279	-0.196	-0.196	0.000	0.000	0.000	0.000
80	A	168	ARG	1	0.829	0.889	31.739	8.330	8.330	0.000	0.000	0.000	0.000
81	A	169	GLY	0	0.043	0.023	31.971	0.084	0.084	0.000	0.000	0.000	0.000
82	A	170	LEU	0	-0.010	-0.017	25.751	-0.137	-0.137	0.000	0.000	0.000	0.000
83	A	171	GLN	0	0.002	0.007	29.665	0.059	0.059	0.000	0.000	0.000	0.000
84	A	172	GLU	-1	-0.802	-0.867	32.490	-8.681	-8.681	0.000	0.000	0.000	0.000
85	A	173	ILE	0	-0.031	-0.014	27.055	0.016	0.016	0.000	0.000	0.000	0.000
86	A	174	GLU	-1	-0.854	-0.915	29.158	-10.061	-10.061	0.000	0.000	0.000	0.000
87	A	175	GLU	-1	-0.840	-0.907	30.295	-8.485	-8.485	0.000	0.000	0.000	0.000
88	A	176	SER	0	-0.021	-0.008	31.904	0.157	0.157	0.000	0.000	0.000	0.000
89	A	177	LEU	0	-0.004	0.000	26.189	0.048	0.048	0.000	0.000	0.000	0.000
90	A	178	ARG	1	0.820	0.893	30.216	9.261	9.261	0.000	0.000	0.000	0.000
91	A	179	SER	0	-0.060	-0.015	32.548	0.271	0.271	0.000	0.000	0.000	0.000
92	A	180	HIS	1	0.784	0.871	30.801	9.783	9.783	0.000	0.000	0.000	0.000
93	A	181	GLY	0	-0.009	0.014	31.747	-0.075	-0.075	0.000	0.000	0.000	0.000
94	A	182	VAL	0	-0.066	-0.034	25.650	-0.241	-0.241	0.000	0.000	0.000	0.000
95	A	183	LEU	0	0.020	0.020	27.383	0.221	0.221	0.000	0.000	0.000	0.000
96	A	184	LEU	0	-0.001	-0.005	24.178	-0.532	-0.532	0.000	0.000	0.000	0.000
97	A	185	GLU	-1	-0.814	-0.875	24.599	-12.112	-12.112	0.000	0.000	0.000	0.000
98	A	186	VAL	0	0.009	-0.001	24.381	-0.672	-0.672	0.000	0.000	0.000	0.000
99	A	187	GLN	0	-0.049	-0.028	23.973	0.390	0.390	0.000	0.000	0.000	0.000
100	A	188	TYR	0	0.036	-0.002	23.808	-0.566	-0.566	0.000	0.000	0.000	0.000
101	A	189	SER	0	0.003	-0.012	22.512	0.371	0.371	0.000	0.000	0.000	0.000
102	A	190	SER	0	-0.013	0.010	22.750	-0.520	-0.520	0.000	0.000	0.000	0.000
103	A	191	SER	0	-0.016	-0.014	22.322	0.198	0.198	0.000	0.000	0.000	0.000
104	A	192	ILE	0	0.014	0.023	17.347	-0.533	-0.533	0.000	0.000	0.000	0.000
105	A	193	HIS	0	0.010	-0.021	16.216	0.796	0.796	0.000	0.000	0.000	0.000
106	A	194	ASP	-1	-0.892	-0.930	10.367	-27.804	-27.804	0.000	0.000	0.000	0.000
107	A	195	ARG	1	0.894	0.963	11.525	21.286	21.286	0.000	0.000	0.000	0.000
108	A	196	GLU	-1	-0.865	-0.932	9.363	-33.094	-33.094	0.000	0.000	0.000	0.000
109	A	197	ILE	0	0.006	0.001	10.394	2.622	2.622	0.000	0.000	0.000	0.000
110	A	198	ARG	1	0.855	0.941	10.343	17.992	17.992	0.000	0.000	0.000	0.000
111	A	199	PHE	0	0.060	0.022	11.442	1.948	1.948	0.000	0.000	0.000	0.000
112	A	200	ASN	0	0.040	0.028	13.536	-1.242	-1.242	0.000	0.000	0.000	0.000
113	A	201	ASN	0	0.017	-0.010	12.851	-0.330	-0.330	0.000	0.000	0.000	0.000
114	A	202	GLY	0	0.008	0.015	10.498	0.001	0.001	0.000	0.000	0.000	0.000
115	A	203	TRP	0	-0.011	0.003	5.102	-3.686	-3.686	0.000	0.000	0.000	0.000
116	A	204	MET	0	-0.013	-0.010	6.817	2.231	2.231	0.000	0.000	0.000	0.000
117	A	205	ILE	0	-0.020	-0.011	6.216	-5.855	-5.855	0.000	0.000	0.000	0.000
118	A	206	LYS	1	0.877	0.929	5.312	36.778	36.778	0.000	0.000	0.000	0.000
119	A	207	ILE	0	0.001	0.019	6.976	-2.912	-2.912	0.000	0.000	0.000	0.000
120	A	208	GLY	0	0.036	0.014	9.709	1.119	1.119	0.000	0.000	0.000	0.000
121	A	209	ARG	1	0.872	0.911	10.664	18.351	18.351	0.000	0.000	0.000	0.000
122	A	210	GLY	0	0.015	0.022	12.865	1.322	1.322	0.000	0.000	0.000	0.000
123	A	211	LEU	0	0.010	-0.005	14.423	-0.323	-0.323	0.000	0.000	0.000	0.000
124	A	212	ASP	-1	-0.826	-0.887	17.052	-13.129	-13.129	0.000	0.000	0.000	0.000
125	A	213	TYR	0	-0.013	-0.012	15.768	-0.346	-0.346	0.000	0.000	0.000	0.000
126	A	214	PHE	0	0.020	0.011	18.211	0.177	0.177	0.000	0.000	0.000	0.000
127	A	215	LYS	1	0.771	0.878	21.492	13.636	13.636	0.000	0.000	0.000	0.000
128	A	216	LYS	1	0.933	0.965	24.386	10.075	10.075	0.000	0.000	0.000	0.000
129	A	217	PRO	0	0.010	0.011	27.856	-0.090	-0.090	0.000	0.000	0.000	0.000
130	A	218	GLN	0	0.019	0.012	30.059	0.288	0.288	0.000	0.000	0.000	0.000
131	A	219	SER	0	0.025	-0.012	32.352	0.230	0.230	0.000	0.000	0.000	0.000
132	A	220	ARG	1	0.986	0.984	34.579	7.479	7.479	0.000	0.000	0.000	0.000
133	A	221	PHE	0	0.012	0.002	36.218	-0.042	-0.042	0.000	0.000	0.000	0.000
134	A	222	SER	0	-0.024	0.022	32.665	0.042	0.042	0.000	0.000	0.000	0.000
135	A	223	LEU	0	0.079	0.014	31.562	-0.120	-0.120	0.000	0.000	0.000	0.000
136	A	224	GLY	0	0.056	0.037	28.357	-0.152	-0.152	0.000	0.000	0.000	0.000
137	A	225	TYR	0	-0.072	-0.024	28.095	-0.340	-0.340	0.000	0.000	0.000	0.000
138	A	226	CYS	0	-0.030	-0.030	30.019	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	227	ASP	-1	-0.787	-0.877	25.978	-12.084	-12.084	0.000	0.000	0.000	0.000
140	A	228	PHE	0	-0.028	-0.036	22.773	0.055	0.055	0.000	0.000	0.000	0.000
141	A	229	ASP	-1	-0.770	-0.840	21.136	-15.141	-15.141	0.000	0.000	0.000	0.000
142	A	230	LEU	0	0.008	-0.004	23.601	-0.010	-0.010	0.000	0.000	0.000	0.000
143	A	231	ARG	1	0.785	0.899	23.818	12.151	12.151	0.000	0.000	0.000	0.000
144	A	232	PRO	0	0.004	0.002	22.979	-0.562	-0.562	0.000	0.000	0.000	0.000
145	A	233	CYS	0	-0.033	0.000	18.338	-0.025	-0.025	0.000	0.000	0.000	0.000
146	A	234	HIS	0	-0.004	-0.019	18.569	0.372	0.372	0.000	0.000	0.000	0.000
147	A	235	GLU	-1	-0.881	-0.919	15.451	-19.283	-19.283	0.000	0.000	0.000	0.000
148	A	236	THR	0	-0.043	-0.035	11.902	0.035	0.035	0.000	0.000	0.000	0.000
149	A	237	THR	0	0.012	0.012	7.945	0.818	0.818	0.000	0.000	0.000	0.000
150	A	238	VAL	0	-0.006	-0.006	7.652	0.590	0.590	0.000	0.000	0.000	0.000
151	A	239	ASP	-1	-0.816	-0.887	2.285	-91.511	-89.826	4.604	-3.324	-2.965	-0.043
152	A	240	ILE	0	0.001	0.014	3.499	5.639	6.678	0.014	-0.365	-0.688	-0.001
153	A	241	PHE	0	-0.010	-0.022	1.854	-49.700	-47.532	15.093	-7.592	-9.669	-0.094
154	A	242	HIS	0	-0.013	-0.017	3.855	8.408	8.683	0.001	-0.080	-0.196	-0.001
155	A	243	LYS	1	0.971	1.005	5.676	24.078	24.078	0.000	0.000	0.000	0.000

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