FMO DATABASE

FMODB ID: 2NVLR

Calculation Name: 4YVO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YVO

Chain ID: A

ChEMBL ID:

UniProt ID: Q940U6

Base Structure: X-ray

Registration Date: 2023-09-23

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-983895.897646
FMO2-HF: Nuclear repulsion	937189.286648
FMO2-HF: Total energy	-46706.610998
FMO2-MP2: Total energy	-46844.555616

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:198:PRO)

Summations of interaction energy for fragment #1(A:198:PRO)

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.
-3.217	0.781	0.047	-1.663	-2.382	0.001

Interaction energy analysis for fragmet #1(A:198:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.021

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

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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	200	LYS	1	0.940	0.983	2.970	-1.871	1.005	0.014	-1.367	-1.522	0.001
4	A	201	GLN	0	0.019	0.003	3.281	-0.579	0.078	0.034	-0.144	-0.548	0.000
5	A	202	GLU	-1	-0.846	-0.925	4.212	-0.627	-0.162	-0.001	-0.152	-0.312	0.000
6	A	203	LEU	0	0.002	0.011	6.077	0.241	0.241	0.000	0.000	0.000	0.000
7	A	204	ILE	0	-0.015	-0.010	7.881	0.100	0.100	0.000	0.000	0.000	0.000
8	A	205	SER	0	-0.055	-0.031	8.550	0.044	0.044	0.000	0.000	0.000	0.000
9	A	206	LYS	1	0.917	0.965	9.872	0.196	0.196	0.000	0.000	0.000	0.000
10	A	207	LEU	0	0.007	0.017	11.946	0.027	0.027	0.000	0.000	0.000	0.000
11	A	208	LYS	1	0.914	0.968	12.321	-0.171	-0.171	0.000	0.000	0.000	0.000
12	A	209	THR	0	-0.053	-0.087	13.626	0.007	0.007	0.000	0.000	0.000	0.000
13	A	210	GLY	0	0.083	0.047	15.710	0.002	0.002	0.000	0.000	0.000	0.000
14	A	211	LYS	1	0.932	0.952	17.746	0.002	0.002	0.000	0.000	0.000	0.000
15	A	212	THR	0	-0.036	-0.018	18.493	0.009	0.009	0.000	0.000	0.000	0.000
16	A	213	PHE	0	0.030	0.020	17.618	0.002	0.002	0.000	0.000	0.000	0.000
17	A	214	LEU	0	0.011	0.010	21.852	0.001	0.001	0.000	0.000	0.000	0.000
18	A	215	ARG	1	0.844	0.932	20.696	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	216	ASN	0	0.007	0.017	23.552	0.004	0.004	0.000	0.000	0.000	0.000
20	A	217	GLN	0	-0.030	-0.007	26.379	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	218	GLU	-1	-0.891	-0.945	24.236	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	219	PRO	0	0.007	-0.004	23.764	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	220	GLU	-1	-0.843	-0.930	23.901	-0.043	-0.043	0.000	0.000	0.000	0.000
24	A	221	LYS	1	0.946	0.968	20.777	0.024	0.024	0.000	0.000	0.000	0.000
25	A	222	ALA	0	0.014	0.005	19.475	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	223	TYR	0	0.036	0.025	19.145	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	224	THR	0	-0.024	-0.011	16.526	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	225	GLU	-1	-0.832	-0.873	14.382	-0.124	-0.124	0.000	0.000	0.000	0.000
29	A	226	PHE	0	0.009	-0.004	14.504	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	227	LYS	1	0.921	0.968	15.985	0.109	0.109	0.000	0.000	0.000	0.000
31	A	228	ILE	0	0.031	0.020	10.375	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	229	ALA	0	-0.031	-0.016	11.463	-0.059	-0.059	0.000	0.000	0.000	0.000
33	A	230	LEU	0	0.005	-0.008	12.416	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	231	GLU	-1	-0.923	-0.944	11.685	-0.289	-0.289	0.000	0.000	0.000	0.000
35	A	232	LEU	0	-0.043	-0.035	6.417	-0.065	-0.065	0.000	0.000	0.000	0.000
36	A	233	ALA	0	-0.012	-0.009	9.528	-0.042	-0.042	0.000	0.000	0.000	0.000
37	A	234	GLN	0	-0.012	-0.004	11.728	0.004	0.004	0.000	0.000	0.000	0.000
38	A	235	SER	0	-0.089	-0.040	9.106	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	236	LEU	0	-0.084	-0.058	5.726	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	237	LYS	1	0.939	0.984	9.857	0.218	0.218	0.000	0.000	0.000	0.000
41	A	238	ASP	-1	-0.798	-0.896	11.152	-0.082	-0.082	0.000	0.000	0.000	0.000
42	A	239	PRO	0	0.110	0.047	13.226	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	240	THR	0	0.030	0.019	15.653	0.014	0.014	0.000	0.000	0.000	0.000
44	A	241	GLU	-1	-0.882	-0.952	11.376	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	242	GLU	-1	-0.865	-0.936	14.463	-0.144	-0.144	0.000	0.000	0.000	0.000
46	A	243	LYS	1	0.792	0.899	16.135	0.044	0.044	0.000	0.000	0.000	0.000
47	A	244	LYS	1	0.786	0.890	15.150	0.012	0.012	0.000	0.000	0.000	0.000
48	A	245	ALA	0	-0.001	0.003	15.370	0.009	0.009	0.000	0.000	0.000	0.000
49	A	246	ALA	0	0.010	0.011	17.453	0.006	0.006	0.000	0.000	0.000	0.000
50	A	247	ARG	1	0.950	0.980	20.298	0.027	0.027	0.000	0.000	0.000	0.000
51	A	248	GLY	0	-0.012	-0.005	20.244	0.007	0.007	0.000	0.000	0.000	0.000
52	A	249	LEU	0	-0.021	-0.010	18.555	0.005	0.005	0.000	0.000	0.000	0.000
53	A	250	GLY	0	0.058	0.028	22.165	0.004	0.004	0.000	0.000	0.000	0.000
54	A	251	ALA	0	0.009	0.001	24.577	0.005	0.005	0.000	0.000	0.000	0.000
55	A	252	SER	0	-0.063	-0.052	22.657	0.005	0.005	0.000	0.000	0.000	0.000
56	A	253	LEU	0	-0.026	-0.015	25.113	0.002	0.002	0.000	0.000	0.000	0.000
57	A	254	GLN	0	0.064	0.034	27.566	0.001	0.001	0.000	0.000	0.000	0.000
58	A	255	ARG	1	0.839	0.919	27.366	0.017	0.017	0.000	0.000	0.000	0.000
59	A	256	GLN	0	0.001	0.006	25.596	0.001	0.001	0.000	0.000	0.000	0.000
60	A	257	GLY	0	0.044	0.038	30.829	0.000	0.000	0.000	0.000	0.000	0.000
61	A	258	LYS	1	0.863	0.938	28.385	0.050	0.050	0.000	0.000	0.000	0.000
62	A	259	TYR	0	0.106	0.030	30.630	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	260	ARG	1	0.987	0.989	32.241	0.032	0.032	0.000	0.000	0.000	0.000
64	A	261	GLU	-1	-0.904	-0.952	27.385	-0.062	-0.062	0.000	0.000	0.000	0.000
65	A	262	ALA	0	-0.010	-0.007	27.541	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	263	ILE	0	0.024	0.012	27.950	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	264	GLN	0	-0.014	0.020	24.678	0.003	0.003	0.000	0.000	0.000	0.000
68	A	265	TYR	0	-0.002	-0.020	21.020	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	266	HIS	0	0.034	0.002	24.644	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	267	SER	0	-0.028	-0.029	26.803	0.003	0.003	0.000	0.000	0.000	0.000
71	A	268	MET	0	-0.053	-0.016	19.937	0.000	0.000	0.000	0.000	0.000	0.000
72	A	269	VAL	0	0.021	0.027	22.612	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	270	LEU	0	0.003	0.015	24.169	0.002	0.002	0.000	0.000	0.000	0.000
74	A	271	ALA	0	-0.034	-0.025	25.667	0.002	0.002	0.000	0.000	0.000	0.000
75	A	272	ILE	0	-0.031	-0.020	19.672	0.001	0.001	0.000	0.000	0.000	0.000
76	A	273	SER	0	0.009	-0.003	23.253	0.003	0.003	0.000	0.000	0.000	0.000
77	A	274	LYS	1	0.919	0.964	24.951	0.036	0.036	0.000	0.000	0.000	0.000
78	A	275	ARG	1	0.903	0.954	21.743	0.084	0.084	0.000	0.000	0.000	0.000
79	A	276	GLU	-1	-0.916	-0.968	20.470	-0.074	-0.074	0.000	0.000	0.000	0.000
80	A	277	SER	0	-0.069	-0.013	23.590	0.006	0.006	0.000	0.000	0.000	0.000
81	A	278	GLU	-1	-0.762	-0.864	21.357	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	279	ASP	-1	-0.909	-0.960	24.478	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	280	SER	0	-0.017	-0.024	21.674	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	281	GLY	0	-0.036	-0.022	23.960	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	282	ILE	0	-0.016	-0.011	25.282	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	283	THR	0	0.052	0.027	28.099	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	284	GLU	-1	-0.854	-0.933	26.333	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	285	ALA	0	-0.011	-0.005	27.030	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	286	TYR	0	-0.012	-0.012	28.922	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	287	GLY	0	0.077	0.042	32.458	0.000	0.000	0.000	0.000	0.000	0.000
91	A	288	ALA	0	0.016	0.016	29.846	0.000	0.000	0.000	0.000	0.000	0.000
92	A	289	ILE	0	-0.039	-0.025	29.889	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	290	ALA	0	-0.001	0.001	33.058	0.000	0.000	0.000	0.000	0.000	0.000
94	A	291	ASP	-1	-0.862	-0.923	34.317	-0.014	-0.014	0.000	0.000	0.000	0.000
95	A	292	CYS	0	-0.112	-0.058	32.346	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	293	TYR	0	-0.026	-0.030	35.141	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	294	THR	0	0.009	0.005	38.064	0.001	0.001	0.000	0.000	0.000	0.000
98	A	295	GLU	-1	-0.946	-0.967	36.725	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	296	LEU	0	-0.158	-0.074	35.602	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	297	GLY	0	0.013	0.014	39.840	0.000	0.000	0.000	0.000	0.000	0.000
101	A	298	ASP	-1	-0.917	-0.959	40.537	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	299	LEU	0	0.075	0.011	42.047	0.000	0.000	0.000	0.000	0.000	0.000
103	A	300	GLU	-1	-0.886	-0.934	44.168	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	301	LYS	1	0.796	0.898	38.639	0.027	0.027	0.000	0.000	0.000	0.000
105	A	302	ALA	0	0.029	0.014	39.243	0.000	0.000	0.000	0.000	0.000	0.000
106	A	303	GLY	0	0.052	0.029	40.134	0.001	0.001	0.000	0.000	0.000	0.000
107	A	304	LYS	1	0.943	0.976	40.367	0.021	0.021	0.000	0.000	0.000	0.000
108	A	305	PHE	0	-0.046	-0.034	33.440	0.000	0.000	0.000	0.000	0.000	0.000
109	A	306	TYR	0	0.037	0.016	37.228	0.001	0.001	0.000	0.000	0.000	0.000
110	A	307	ASP	-1	-0.866	-0.928	39.206	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	308	THR	0	-0.084	-0.042	35.764	0.001	0.001	0.000	0.000	0.000	0.000
112	A	309	TYR	0	-0.059	-0.031	33.289	0.001	0.001	0.000	0.000	0.000	0.000
113	A	310	ILE	0	0.026	0.017	36.349	0.002	0.002	0.000	0.000	0.000	0.000
114	A	311	ALA	0	0.034	0.023	39.312	0.001	0.001	0.000	0.000	0.000	0.000
115	A	312	ARG	1	0.882	0.933	29.902	0.010	0.010	0.000	0.000	0.000	0.000
116	A	313	LEU	0	0.002	0.009	34.120	0.002	0.002	0.000	0.000	0.000	0.000
117	A	314	GLU	-1	-0.963	-0.973	36.691	0.000	0.000	0.000	0.000	0.000	0.000
118	A	315	THR	0	-0.158	-0.081	36.381	0.001	0.001	0.000	0.000	0.000	0.000
119	A	316	ASP	-1	-0.997	-0.993	33.584	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:198:PRO)