FMO DATABASE

FMODB ID: ZYJ3N

Calculation Name: 2VY1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VY1

Chain ID: A

ChEMBL ID:

UniProt ID: Q00958

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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1663473.055385
FMO2-HF: Nuclear repulsion	1597191.451137
FMO2-HF: Total energy	-66281.604248
FMO2-MP2: Total energy	-66473.349963

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:237:ARG)

Summations of interaction energy for fragment #1(A:237:ARG)

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.
190.534	194.384	0.816	-2.187	-2.479	-0.013

Interaction energy analysis for fragmet #1(A:237:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.975 / q_NPA : 0.988

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	239	HIS	0	0.051	0.027	2.555	-14.826	-10.976	0.816	-2.187	-2.479	-0.013
4	A	240	PRO	0	-0.034	-0.011	4.840	1.598	1.598	0.000	0.000	0.000	0.000
5	A	241	PHE	0	0.022	0.003	6.375	1.991	1.991	0.000	0.000	0.000	0.000
6	A	242	ILE	0	-0.014	-0.024	9.835	-0.817	-0.817	0.000	0.000	0.000	0.000
7	A	243	VAL	0	0.029	0.003	13.003	0.172	0.172	0.000	0.000	0.000	0.000
8	A	244	THR	0	-0.001	0.023	15.616	-0.076	-0.076	0.000	0.000	0.000	0.000
9	A	245	GLU	-1	-0.779	-0.873	18.313	-11.682	-11.682	0.000	0.000	0.000	0.000
10	A	246	PRO	0	0.009	-0.013	21.093	-0.413	-0.413	0.000	0.000	0.000	0.000
11	A	247	GLY	0	0.009	0.014	21.669	0.425	0.425	0.000	0.000	0.000	0.000
12	A	248	GLU	-1	-0.843	-0.898	18.935	-14.289	-14.289	0.000	0.000	0.000	0.000
13	A	249	VAL	0	-0.006	-0.002	16.864	-0.789	-0.789	0.000	0.000	0.000	0.000
14	A	250	ALA	0	-0.031	-0.017	13.429	0.163	0.163	0.000	0.000	0.000	0.000
15	A	251	ARG	1	1.011	1.005	15.049	13.815	13.815	0.000	0.000	0.000	0.000
16	A	252	GLY	0	0.025	0.010	13.802	-0.779	-0.779	0.000	0.000	0.000	0.000
17	A	253	LYS	1	0.945	0.974	8.201	24.587	24.587	0.000	0.000	0.000	0.000
18	A	254	LYS	1	0.925	0.958	8.488	24.655	24.655	0.000	0.000	0.000	0.000
19	A	255	ASN	0	0.021	0.025	7.357	2.903	2.903	0.000	0.000	0.000	0.000
20	A	256	GLY	0	0.077	0.017	10.670	-0.115	-0.115	0.000	0.000	0.000	0.000
21	A	257	LEU	0	-0.039	-0.024	13.493	-0.923	-0.923	0.000	0.000	0.000	0.000
22	A	258	ASP	-1	-0.706	-0.819	15.640	-14.117	-14.117	0.000	0.000	0.000	0.000
23	A	259	TYR	0	-0.045	-0.038	9.042	1.022	1.022	0.000	0.000	0.000	0.000
24	A	260	LEU	0	-0.029	-0.011	11.965	-0.299	-0.299	0.000	0.000	0.000	0.000
25	A	261	PHE	0	0.027	-0.008	13.824	-0.079	-0.079	0.000	0.000	0.000	0.000
26	A	262	HIS	0	0.081	0.049	16.259	-0.207	-0.207	0.000	0.000	0.000	0.000
27	A	263	LEU	0	0.011	0.001	10.257	0.136	0.136	0.000	0.000	0.000	0.000
28	A	264	TYR	0	-0.023	-0.045	14.649	-0.091	-0.091	0.000	0.000	0.000	0.000
29	A	265	GLU	-1	-0.797	-0.884	17.473	-12.033	-12.033	0.000	0.000	0.000	0.000
30	A	266	GLN	0	0.060	0.037	13.994	0.085	0.085	0.000	0.000	0.000	0.000
31	A	267	CYS	0	-0.093	-0.039	15.224	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	268	ARG	1	0.980	0.989	17.734	11.732	11.732	0.000	0.000	0.000	0.000
33	A	269	GLU	-1	-0.915	-0.952	20.578	-11.973	-11.973	0.000	0.000	0.000	0.000
34	A	270	PHE	0	0.008	-0.014	15.197	0.340	0.340	0.000	0.000	0.000	0.000
35	A	271	LEU	0	-0.050	-0.027	20.437	0.256	0.256	0.000	0.000	0.000	0.000
36	A	272	LEU	0	0.023	0.017	22.785	0.407	0.407	0.000	0.000	0.000	0.000
37	A	273	GLN	0	0.049	0.037	20.985	0.359	0.359	0.000	0.000	0.000	0.000
38	A	274	VAL	0	-0.033	-0.023	21.974	0.222	0.222	0.000	0.000	0.000	0.000
39	A	275	GLN	0	-0.065	-0.055	24.973	0.420	0.420	0.000	0.000	0.000	0.000
40	A	276	THR	0	-0.039	-0.026	28.040	0.408	0.408	0.000	0.000	0.000	0.000
41	A	277	ILE	0	0.028	0.019	26.819	0.237	0.237	0.000	0.000	0.000	0.000
42	A	278	ALA	0	-0.006	0.002	28.773	0.204	0.204	0.000	0.000	0.000	0.000
43	A	279	LYS	1	0.916	0.945	30.455	9.348	9.348	0.000	0.000	0.000	0.000
44	A	280	ASP	-1	-0.937	-0.948	32.827	-8.201	-8.201	0.000	0.000	0.000	0.000
45	A	281	ARG	1	0.848	0.915	27.501	10.019	10.019	0.000	0.000	0.000	0.000
46	A	282	GLY	0	0.012	0.023	34.345	0.118	0.118	0.000	0.000	0.000	0.000
47	A	283	GLU	-1	-0.891	-0.932	29.990	-9.754	-9.754	0.000	0.000	0.000	0.000
48	A	284	LYS	1	0.945	0.962	29.880	9.836	9.836	0.000	0.000	0.000	0.000
49	A	285	CYS	0	0.035	0.016	30.119	-0.345	-0.345	0.000	0.000	0.000	0.000
50	A	286	PRO	0	-0.073	-0.016	25.691	0.026	0.026	0.000	0.000	0.000	0.000
51	A	287	THR	0	0.088	0.032	28.019	-0.079	-0.079	0.000	0.000	0.000	0.000
52	A	288	LYS	1	0.879	0.948	24.555	10.711	10.711	0.000	0.000	0.000	0.000
53	A	289	VAL	0	0.043	0.033	18.276	-0.094	-0.094	0.000	0.000	0.000	0.000
54	A	290	THR	0	0.045	0.017	21.087	-0.253	-0.253	0.000	0.000	0.000	0.000
55	A	291	ASN	0	0.044	0.003	18.230	-1.229	-1.229	0.000	0.000	0.000	0.000
56	A	292	GLN	0	0.013	0.015	18.368	-0.519	-0.519	0.000	0.000	0.000	0.000
57	A	293	VAL	0	0.048	0.036	18.301	-0.153	-0.153	0.000	0.000	0.000	0.000
58	A	294	PHE	0	0.035	0.009	13.891	-0.367	-0.367	0.000	0.000	0.000	0.000
59	A	295	ARG	1	0.944	0.969	14.701	13.218	13.218	0.000	0.000	0.000	0.000
60	A	296	TYR	0	0.017	0.007	16.505	-0.189	-0.189	0.000	0.000	0.000	0.000
61	A	297	ALA	0	0.046	0.021	13.996	0.095	0.095	0.000	0.000	0.000	0.000
62	A	298	LYS	1	0.946	0.970	9.869	22.048	22.048	0.000	0.000	0.000	0.000
63	A	299	LYS	1	0.849	0.929	13.186	13.474	13.474	0.000	0.000	0.000	0.000
64	A	300	SER	0	-0.032	-0.011	15.984	0.550	0.550	0.000	0.000	0.000	0.000
65	A	301	GLY	0	0.070	0.048	12.507	0.263	0.263	0.000	0.000	0.000	0.000
66	A	302	ALA	0	0.013	0.021	11.260	-0.893	-0.893	0.000	0.000	0.000	0.000
67	A	303	SER	0	-0.030	-0.028	7.193	-0.745	-0.745	0.000	0.000	0.000	0.000
68	A	304	TYR	0	-0.017	-0.012	6.096	-2.060	-2.060	0.000	0.000	0.000	0.000
69	A	305	ILE	0	-0.003	0.015	7.161	-1.033	-1.033	0.000	0.000	0.000	0.000
70	A	306	ASN	0	0.006	-0.014	6.489	0.491	0.491	0.000	0.000	0.000	0.000
71	A	307	LYS	1	0.932	0.958	10.023	18.051	18.051	0.000	0.000	0.000	0.000
72	A	308	PRO	0	0.006	-0.001	9.804	1.121	1.121	0.000	0.000	0.000	0.000
73	A	309	LYS	1	0.888	0.954	6.597	31.090	31.090	0.000	0.000	0.000	0.000
74	A	310	MET	0	0.005	0.012	10.069	0.485	0.485	0.000	0.000	0.000	0.000
75	A	311	ARG	1	0.867	0.933	13.270	16.826	16.826	0.000	0.000	0.000	0.000
76	A	312	HIS	0	-0.035	-0.004	11.915	1.422	1.422	0.000	0.000	0.000	0.000
77	A	313	TYR	0	0.065	0.025	10.155	-0.132	-0.132	0.000	0.000	0.000	0.000
78	A	314	VAL	0	0.051	0.042	15.303	0.767	0.767	0.000	0.000	0.000	0.000
79	A	315	HIS	0	-0.001	-0.015	18.261	0.447	0.447	0.000	0.000	0.000	0.000
80	A	316	CYS	0	-0.061	-0.032	17.584	0.282	0.282	0.000	0.000	0.000	0.000
81	A	317	TYR	0	-0.002	0.000	18.441	0.480	0.480	0.000	0.000	0.000	0.000
82	A	318	ALA	0	0.011	-0.007	20.207	0.583	0.583	0.000	0.000	0.000	0.000
83	A	319	LEU	0	0.007	0.004	23.115	0.493	0.493	0.000	0.000	0.000	0.000
84	A	320	HIS	0	-0.005	-0.007	21.810	0.027	0.027	0.000	0.000	0.000	0.000
85	A	321	CYS	0	-0.085	-0.035	23.292	0.363	0.363	0.000	0.000	0.000	0.000
86	A	322	LEU	0	-0.059	-0.041	25.999	0.429	0.429	0.000	0.000	0.000	0.000
87	A	323	ASP	-1	-0.889	-0.943	27.796	-9.457	-9.457	0.000	0.000	0.000	0.000
88	A	324	GLU	-1	-0.844	-0.912	25.981	-11.434	-11.434	0.000	0.000	0.000	0.000
89	A	325	GLU	-1	-0.832	-0.911	27.135	-10.238	-10.238	0.000	0.000	0.000	0.000
90	A	326	ALA	0	0.006	0.005	28.860	-0.168	-0.168	0.000	0.000	0.000	0.000
91	A	327	SER	0	-0.099	-0.044	23.148	-0.518	-0.518	0.000	0.000	0.000	0.000
92	A	328	ASN	0	-0.028	-0.041	24.110	-0.966	-0.966	0.000	0.000	0.000	0.000
93	A	329	ALA	0	0.015	0.012	25.360	-0.228	-0.228	0.000	0.000	0.000	0.000
94	A	330	LEU	0	-0.016	-0.007	23.193	-0.118	-0.118	0.000	0.000	0.000	0.000
95	A	331	ARG	1	0.731	0.829	19.401	13.819	13.819	0.000	0.000	0.000	0.000
96	A	332	ARG	1	0.913	0.938	22.305	10.765	10.765	0.000	0.000	0.000	0.000
97	A	333	ALA	0	0.048	0.037	24.787	-0.072	-0.072	0.000	0.000	0.000	0.000
98	A	334	PHE	0	-0.039	-0.043	20.424	-0.097	-0.097	0.000	0.000	0.000	0.000
99	A	335	LYS	1	0.793	0.882	20.655	12.907	12.907	0.000	0.000	0.000	0.000
100	A	336	GLU	-1	-0.950	-0.959	21.645	-10.896	-10.896	0.000	0.000	0.000	0.000
101	A	337	ARG	1	0.813	0.891	23.710	12.661	12.661	0.000	0.000	0.000	0.000
102	A	338	GLY	0	-0.002	0.013	20.535	-0.098	-0.098	0.000	0.000	0.000	0.000
103	A	339	GLU	-1	-0.841	-0.894	19.350	-15.077	-15.077	0.000	0.000	0.000	0.000
104	A	340	ASN	0	-0.002	-0.001	13.796	-1.453	-1.453	0.000	0.000	0.000	0.000
105	A	341	VAL	0	0.031	-0.004	12.021	0.626	0.626	0.000	0.000	0.000	0.000
106	A	342	GLY	0	-0.013	0.000	13.615	0.563	0.563	0.000	0.000	0.000	0.000
107	A	343	SER	0	0.001	-0.009	14.645	0.465	0.465	0.000	0.000	0.000	0.000
108	A	344	TRP	0	0.071	0.028	15.934	0.202	0.202	0.000	0.000	0.000	0.000
109	A	345	ARG	1	0.861	0.919	14.580	19.232	19.232	0.000	0.000	0.000	0.000
110	A	346	GLN	0	-0.034	-0.012	17.865	1.062	1.062	0.000	0.000	0.000	0.000
111	A	347	ALA	0	0.029	0.019	20.286	0.679	0.679	0.000	0.000	0.000	0.000
112	A	348	CYS	0	0.010	0.027	20.677	0.493	0.493	0.000	0.000	0.000	0.000
113	A	349	TYR	0	-0.054	-0.030	19.844	0.173	0.173	0.000	0.000	0.000	0.000
114	A	350	LYS	1	1.015	1.015	24.645	10.358	10.358	0.000	0.000	0.000	0.000
115	A	351	PRO	0	0.044	0.022	26.249	0.403	0.403	0.000	0.000	0.000	0.000
116	A	352	LEU	0	0.009	0.007	23.813	0.279	0.279	0.000	0.000	0.000	0.000
117	A	353	VAL	0	0.008	-0.006	28.111	0.269	0.269	0.000	0.000	0.000	0.000
118	A	354	ASN	0	-0.002	-0.001	30.418	0.312	0.312	0.000	0.000	0.000	0.000
119	A	355	ILE	0	0.001	0.001	29.522	0.332	0.332	0.000	0.000	0.000	0.000
120	A	356	ALA	0	0.021	0.012	31.400	0.239	0.239	0.000	0.000	0.000	0.000
121	A	357	CYS	0	-0.050	-0.008	33.352	0.314	0.314	0.000	0.000	0.000	0.000
122	A	358	ARG	1	0.921	0.962	33.992	9.118	9.118	0.000	0.000	0.000	0.000
123	A	359	HIS	0	-0.042	-0.027	35.078	0.256	0.256	0.000	0.000	0.000	0.000
124	A	360	GLY	0	0.047	0.028	37.672	-0.029	-0.029	0.000	0.000	0.000	0.000
125	A	361	TRP	0	-0.013	-0.025	34.190	-0.101	-0.101	0.000	0.000	0.000	0.000
126	A	362	ASP	-1	-0.827	-0.896	34.642	-9.157	-9.157	0.000	0.000	0.000	0.000
127	A	363	ILE	0	0.012	-0.014	28.058	-0.145	-0.145	0.000	0.000	0.000	0.000
128	A	364	ASP	-1	-0.808	-0.872	29.916	-10.634	-10.634	0.000	0.000	0.000	0.000
129	A	365	ALA	0	0.008	0.017	31.216	-0.134	-0.134	0.000	0.000	0.000	0.000
130	A	366	VAL	0	-0.004	0.001	29.775	-0.016	-0.016	0.000	0.000	0.000	0.000
131	A	367	PHE	0	-0.005	-0.031	23.417	-0.297	-0.297	0.000	0.000	0.000	0.000
132	A	368	ASN	0	-0.080	-0.073	28.912	-0.216	-0.216	0.000	0.000	0.000	0.000
133	A	369	ALA	0	0.039	0.046	31.237	0.115	0.115	0.000	0.000	0.000	0.000
134	A	370	HIS	0	0.032	0.023	27.648	0.044	0.044	0.000	0.000	0.000	0.000
135	A	371	PRO	0	0.052	0.014	29.193	-0.319	-0.319	0.000	0.000	0.000	0.000
136	A	372	ARG	1	0.831	0.908	24.269	11.205	11.205	0.000	0.000	0.000	0.000
137	A	373	LEU	0	0.015	0.015	23.562	-0.523	-0.523	0.000	0.000	0.000	0.000
138	A	374	SER	0	0.032	0.036	25.402	-0.304	-0.304	0.000	0.000	0.000	0.000
139	A	375	ILE	0	-0.030	-0.002	22.174	-0.008	-0.008	0.000	0.000	0.000	0.000
140	A	376	TRP	0	-0.059	-0.037	17.076	-1.081	-1.081	0.000	0.000	0.000	0.000
141	A	377	TYR	0	-0.016	-0.020	21.904	0.201	0.201	0.000	0.000	0.000	0.000
142	A	378	VAL	0	0.049	0.037	22.622	-0.532	-0.532	0.000	0.000	0.000	0.000
143	A	379	PRO	0	-0.040	-0.006	20.254	-0.127	-0.127	0.000	0.000	0.000	0.000
144	A	380	THR	0	0.036	0.000	22.184	0.405	0.405	0.000	0.000	0.000	0.000
145	A	381	LYS	1	0.984	1.005	21.850	13.441	13.441	0.000	0.000	0.000	0.000
146	A	382	LEU	0	0.048	0.022	23.630	0.315	0.315	0.000	0.000	0.000	0.000
147	A	383	ARG	1	0.869	0.896	25.326	11.257	11.257	0.000	0.000	0.000	0.000
148	A	384	GLN	0	-0.013	-0.020	25.332	0.089	0.089	0.000	0.000	0.000	0.000
149	A	385	LEU	0	-0.005	0.000	25.084	0.270	0.270	0.000	0.000	0.000	0.000
150	A	386	CYS	0	0.009	0.010	28.908	0.315	0.315	0.000	0.000	0.000	0.000
151	A	387	HIS	0	-0.015	0.008	31.388	0.364	0.364	0.000	0.000	0.000	0.000
152	A	388	LEU	0	-0.023	-0.023	29.724	0.214	0.214	0.000	0.000	0.000	0.000
153	A	389	GLU	-1	-0.866	-0.922	32.809	-9.140	-9.140	0.000	0.000	0.000	0.000
154	A	390	ARG	1	0.964	0.988	34.695	8.858	8.858	0.000	0.000	0.000	0.000
155	A	391	ASN	0	-0.035	-0.027	36.445	0.393	0.393	0.000	0.000	0.000	0.000
156	A	392	ASN	0	-0.010	-0.014	35.161	0.332	0.332	0.000	0.000	0.000	0.000
157	A	393	ALA	0	-0.034	-0.011	38.837	0.199	0.199	0.000	0.000	0.000	0.000
158	A	394	VAL	0	-0.035	-0.024	40.634	0.184	0.184	0.000	0.000	0.000	0.000
159	A	395	ALA	0	-0.023	-0.007	41.947	0.182	0.182	0.000	0.000	0.000	0.000
160	A	396	ALA	0	0.003	0.002	42.259	0.166	0.166	0.000	0.000	0.000	0.000
161	A	397	ALA	0	-0.063	-0.026	44.064	0.157	0.157	0.000	0.000	0.000	0.000
162	A	398	ALA	0	-0.045	-0.001	45.821	0.252	0.252	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:237:ARG)