FMO DATABASE

FMODB ID: R5688

Calculation Name: 2YV4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YV4

Chain ID: A

ChEMBL ID:

UniProt ID: O73972

Base Structure: X-ray

Registration Date: 2023-06-19

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-795951.800693
FMO2-HF: Nuclear repulsion	756268.558734
FMO2-HF: Total energy	-39683.241959
FMO2-MP2: Total energy	-39800.642508

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:236:ALA)

Summations of interaction energy for fragment #1(A:236:ALA)

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.
-7.554	-5.408	0.011	-1.081	-1.076	0.003

Interaction energy analysis for fragmet #1(A:236:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.016

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	238	ASN	0	-0.105	-0.069	3.663	-1.020	0.691	0.004	-0.960	-0.755	0.003
4	A	239	ALA	0	0.043	0.041	6.452	0.545	0.545	0.000	0.000	0.000	0.000
5	A	240	GLU	-1	-0.831	-0.897	7.332	-0.557	-0.557	0.000	0.000	0.000	0.000
6	A	241	VAL	0	-0.007	-0.003	6.726	0.084	0.084	0.000	0.000	0.000	0.000
7	A	242	ILE	0	-0.009	-0.012	9.700	0.160	0.160	0.000	0.000	0.000	0.000
8	A	243	VAL	0	0.006	0.008	12.096	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	244	VAL	0	0.000	0.000	14.432	0.008	0.008	0.000	0.000	0.000	0.000
10	A	245	GLU	-1	-0.921	-0.960	18.193	0.111	0.111	0.000	0.000	0.000	0.000
11	A	246	GLY	0	0.034	0.012	20.164	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	247	PRO	0	0.013	0.015	23.780	0.000	0.000	0.000	0.000	0.000	0.000
13	A	248	ARG	1	0.916	0.923	24.182	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	249	GLU	-1	-0.851	-0.900	25.912	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	250	LYS	1	0.871	0.920	27.198	0.004	0.004	0.000	0.000	0.000	0.000
16	A	251	VAL	0	-0.019	-0.001	21.109	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	252	LYS	1	0.804	0.875	23.379	0.074	0.074	0.000	0.000	0.000	0.000
18	A	253	GLY	0	0.012	0.023	25.227	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	254	LYS	1	0.856	0.904	21.921	0.070	0.070	0.000	0.000	0.000	0.000
20	A	255	ILE	0	0.010	0.003	19.258	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	256	THR	0	-0.015	-0.022	21.835	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	257	GLU	-1	-0.883	-0.915	24.969	-0.104	-0.104	0.000	0.000	0.000	0.000
23	A	258	LEU	0	0.028	0.002	19.025	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	259	VAL	0	-0.001	0.005	20.144	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	260	LYS	1	0.929	0.969	21.861	0.124	0.124	0.000	0.000	0.000	0.000
26	A	261	GLU	-1	-0.869	-0.920	22.215	-0.192	-0.192	0.000	0.000	0.000	0.000
27	A	262	LEU	0	-0.026	-0.028	17.156	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	263	LYS	1	0.826	0.916	20.865	0.277	0.277	0.000	0.000	0.000	0.000
29	A	264	GLU	-1	-0.936	-0.952	22.959	-0.183	-0.183	0.000	0.000	0.000	0.000
30	A	265	ARG	1	0.787	0.883	18.710	0.253	0.253	0.000	0.000	0.000	0.000
31	A	266	GLY	0	0.003	0.010	22.031	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	267	LYS	1	0.775	0.877	15.262	0.525	0.525	0.000	0.000	0.000	0.000
33	A	268	LYS	1	0.830	0.909	17.189	0.617	0.617	0.000	0.000	0.000	0.000
34	A	269	VAL	0	0.005	-0.002	16.311	-0.082	-0.082	0.000	0.000	0.000	0.000
35	A	270	GLY	0	0.024	-0.001	15.305	0.022	0.022	0.000	0.000	0.000	0.000
36	A	271	VAL	0	-0.035	-0.015	15.564	0.009	0.009	0.000	0.000	0.000	0.000
37	A	272	ILE	0	-0.009	-0.005	10.762	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	273	GLY	0	0.040	-0.008	15.065	0.052	0.052	0.000	0.000	0.000	0.000
39	A	274	SER	0	-0.081	-0.080	18.387	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	275	GLU	-1	-0.849	-0.908	21.741	-0.115	-0.115	0.000	0.000	0.000	0.000
41	A	276	SER	0	0.033	0.007	20.952	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	277	TYR	0	0.036	-0.008	20.771	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	278	ASN	0	-0.047	-0.020	24.073	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	279	ALA	0	0.039	0.017	19.248	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	280	ASP	-1	-0.832	-0.910	19.465	-0.344	-0.344	0.000	0.000	0.000	0.000
46	A	281	GLU	-1	-0.770	-0.856	16.423	-0.534	-0.534	0.000	0.000	0.000	0.000
47	A	282	PHE	0	-0.039	-0.033	17.921	0.018	0.018	0.000	0.000	0.000	0.000
48	A	283	PHE	0	-0.010	-0.004	14.947	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	284	PHE	0	0.016	0.019	17.032	0.021	0.021	0.000	0.000	0.000	0.000
50	A	285	LEU	0	-0.002	0.001	14.466	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	286	GLY	0	0.000	-0.006	16.776	0.035	0.035	0.000	0.000	0.000	0.000
52	A	287	SER	0	-0.077	-0.055	19.591	0.000	0.000	0.000	0.000	0.000	0.000
53	A	288	SER	0	-0.009	-0.037	21.173	0.018	0.018	0.000	0.000	0.000	0.000
54	A	289	VAL	0	0.079	0.023	18.450	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	290	GLU	-1	-0.805	-0.872	17.755	0.149	0.149	0.000	0.000	0.000	0.000
56	A	291	GLU	-1	-0.741	-0.818	17.694	0.022	0.022	0.000	0.000	0.000	0.000
57	A	292	VAL	0	0.028	0.023	14.217	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	293	ALA	0	-0.012	-0.004	13.523	0.014	0.014	0.000	0.000	0.000	0.000
59	A	294	LYS	1	0.806	0.891	12.866	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	295	ASN	0	-0.010	-0.020	13.154	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	296	LEU	0	0.031	0.031	8.983	-0.114	-0.114	0.000	0.000	0.000	0.000
62	A	297	PHE	0	0.035	-0.005	6.220	-0.142	-0.142	0.000	0.000	0.000	0.000
63	A	298	LYS	1	0.899	0.967	7.898	-0.025	-0.025	0.000	0.000	0.000	0.000
64	A	299	ALA	0	0.016	0.007	10.690	-0.145	-0.145	0.000	0.000	0.000	0.000
65	A	300	LEU	0	0.035	0.010	5.384	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	301	ARG	1	0.946	0.966	6.397	0.528	0.528	0.000	0.000	0.000	0.000
67	A	302	TYR	0	-0.103	-0.063	8.344	0.028	0.028	0.000	0.000	0.000	0.000
68	A	303	MET	0	0.007	0.016	10.429	0.055	0.055	0.000	0.000	0.000	0.000
69	A	304	ASP	-1	-0.770	-0.883	6.542	-3.498	-3.498	0.000	0.000	0.000	0.000
70	A	305	LYS	1	0.904	0.955	9.999	0.853	0.853	0.000	0.000	0.000	0.000
71	A	306	ALA	0	-0.037	-0.007	12.430	0.136	0.136	0.000	0.000	0.000	0.000
72	A	307	GLY	0	0.007	0.013	13.451	0.118	0.118	0.000	0.000	0.000	0.000
73	A	308	VAL	0	-0.062	-0.032	12.677	0.108	0.108	0.000	0.000	0.000	0.000
74	A	309	ASP	-1	-0.776	-0.859	12.173	-0.804	-0.804	0.000	0.000	0.000	0.000
75	A	310	VAL	0	-0.037	-0.024	11.956	-0.085	-0.085	0.000	0.000	0.000	0.000
76	A	311	VAL	0	0.007	-0.002	10.214	0.050	0.050	0.000	0.000	0.000	0.000
77	A	312	ILE	0	0.019	0.016	12.113	0.051	0.051	0.000	0.000	0.000	0.000
78	A	313	ALA	0	-0.009	-0.013	12.081	-0.018	-0.018	0.000	0.000	0.000	0.000
79	A	314	GLU	-1	-0.762	-0.820	14.233	-0.053	-0.053	0.000	0.000	0.000	0.000
80	A	315	GLY	0	-0.004	-0.002	17.319	0.029	0.029	0.000	0.000	0.000	0.000
81	A	316	VAL	0	-0.018	-0.017	17.887	0.017	0.017	0.000	0.000	0.000	0.000
82	A	317	GLU	-1	-0.855	-0.935	21.406	0.073	0.073	0.000	0.000	0.000	0.000
83	A	318	GLU	-1	-0.827	-0.910	23.750	0.027	0.027	0.000	0.000	0.000	0.000
84	A	319	ARG	1	0.885	0.923	23.836	-0.043	-0.043	0.000	0.000	0.000	0.000
85	A	320	GLY	0	0.024	0.013	22.036	0.014	0.014	0.000	0.000	0.000	0.000
86	A	321	LEU	0	-0.036	-0.009	18.783	0.031	0.031	0.000	0.000	0.000	0.000
87	A	322	GLY	0	0.076	0.045	17.016	0.013	0.013	0.000	0.000	0.000	0.000
88	A	323	LEU	0	0.015	0.016	16.060	0.032	0.032	0.000	0.000	0.000	0.000
89	A	324	ALA	0	-0.034	-0.014	15.924	0.067	0.067	0.000	0.000	0.000	0.000
90	A	325	VAL	0	0.010	-0.002	11.820	0.079	0.079	0.000	0.000	0.000	0.000
91	A	326	MET	0	0.014	0.009	11.439	0.094	0.094	0.000	0.000	0.000	0.000
92	A	327	ASN	0	-0.003	-0.007	11.517	0.173	0.173	0.000	0.000	0.000	0.000
93	A	328	ARG	1	0.783	0.902	9.333	-0.581	-0.581	0.000	0.000	0.000	0.000
94	A	329	LEU	0	0.004	0.000	5.953	0.329	0.329	0.000	0.000	0.000	0.000
95	A	330	ARG	1	0.867	0.946	5.040	-3.864	-3.864	0.000	0.000	0.000	0.000
96	A	331	LYS	1	1.032	1.014	9.381	-1.107	-1.107	0.000	0.000	0.000	0.000
97	A	332	ALA	0	-0.023	-0.023	7.187	0.350	0.350	0.000	0.000	0.000	0.000
98	A	333	SER	0	-0.013	-0.017	3.558	0.852	1.170	0.008	-0.093	-0.233	0.000
99	A	334	GLY	0	0.029	0.026	4.231	-0.857	-0.740	-0.001	-0.028	-0.088	0.000
100	A	335	TYR	0	-0.052	-0.026	6.418	-0.349	-0.349	0.000	0.000	0.000	0.000
101	A	336	LYS	1	0.820	0.907	9.228	0.358	0.358	0.000	0.000	0.000	0.000
102	A	337	ILE	0	0.022	0.008	12.927	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	338	VAL	0	-0.011	-0.007	15.968	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	339	LYS	1	0.989	1.001	19.225	-0.038	-0.038	0.000	0.000	0.000	0.000
105	A	340	ALA	0	-0.031	-0.018	22.269	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:236:ALA)