FMO DATABASE

FMODB ID: ZV4NN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-989424.68969
FMO2-HF: Nuclear repulsion	942717.440848
FMO2-HF: Total energy	-46707.248842
FMO2-MP2: Total energy	-46845.260038

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.
-4.826	-1.692	0.034	-1.232	-1.936	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 : 0.051 / q_NPA : 0.008

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	200	LYS	1	0.905	0.950	3.888	-3.125	-1.021	-0.009	-0.958	-1.137	0.001
4	A	201	GLN	0	-0.008	0.002	3.164	-1.277	-0.629	0.044	-0.164	-0.528	0.000
5	A	202	GLU	-1	-0.823	-0.934	4.197	-0.835	-0.453	-0.001	-0.110	-0.271	0.000
6	A	203	LEU	0	-0.024	0.005	6.201	0.093	0.093	0.000	0.000	0.000	0.000
7	A	204	ILE	0	0.013	0.004	8.155	-0.066	-0.066	0.000	0.000	0.000	0.000
8	A	205	SER	0	-0.039	-0.021	8.247	-0.043	-0.043	0.000	0.000	0.000	0.000
9	A	206	LYS	1	0.867	0.934	10.116	0.155	0.155	0.000	0.000	0.000	0.000
10	A	207	LEU	0	0.003	0.015	12.202	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	208	LYS	1	0.873	0.948	10.962	-0.130	-0.130	0.000	0.000	0.000	0.000
12	A	209	THR	0	-0.041	-0.045	13.905	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	210	GLY	0	0.069	0.043	15.880	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	211	LYS	1	0.958	0.957	17.768	-0.133	-0.133	0.000	0.000	0.000	0.000
15	A	212	THR	0	-0.045	-0.031	18.332	0.004	0.004	0.000	0.000	0.000	0.000
16	A	213	PHE	0	0.025	0.007	17.315	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	214	LEU	0	-0.004	0.011	21.942	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	215	ARG	1	0.857	0.939	20.322	-0.068	-0.068	0.000	0.000	0.000	0.000
19	A	216	ASN	0	-0.025	-0.005	23.480	0.007	0.007	0.000	0.000	0.000	0.000
20	A	217	GLN	0	-0.044	-0.012	26.459	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	218	GLU	-1	-0.811	-0.913	23.867	-0.021	-0.021	0.000	0.000	0.000	0.000
22	A	219	PRO	0	0.025	0.003	23.697	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	220	GLU	-1	-0.810	-0.917	23.859	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	221	LYS	1	0.908	0.978	20.206	0.036	0.036	0.000	0.000	0.000	0.000
25	A	222	ALA	0	-0.004	0.000	19.151	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	223	TYR	0	-0.032	-0.018	19.208	0.000	0.000	0.000	0.000	0.000	0.000
27	A	224	THR	0	-0.015	-0.021	16.738	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	225	GLU	-1	-0.772	-0.851	14.028	-0.121	-0.121	0.000	0.000	0.000	0.000
29	A	226	PHE	0	0.007	-0.007	14.436	0.007	0.007	0.000	0.000	0.000	0.000
30	A	227	LYS	1	0.918	0.973	16.136	0.049	0.049	0.000	0.000	0.000	0.000
31	A	228	ILE	0	0.031	0.022	10.357	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	229	ALA	0	-0.026	-0.017	11.597	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	230	LEU	0	0.009	-0.003	12.585	0.047	0.047	0.000	0.000	0.000	0.000
34	A	231	GLU	-1	-0.929	-0.949	11.653	-0.192	-0.192	0.000	0.000	0.000	0.000
35	A	232	LEU	0	-0.040	-0.034	6.578	-0.028	-0.028	0.000	0.000	0.000	0.000
36	A	233	ALA	0	0.000	-0.005	9.612	0.100	0.100	0.000	0.000	0.000	0.000
37	A	234	GLN	0	-0.021	-0.024	11.923	0.025	0.025	0.000	0.000	0.000	0.000
38	A	235	SER	0	-0.072	-0.034	9.428	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	236	LEU	0	-0.069	-0.029	5.608	0.051	0.051	0.000	0.000	0.000	0.000
40	A	237	LYS	1	0.927	0.969	9.770	-0.061	-0.061	0.000	0.000	0.000	0.000
41	A	238	ASP	-1	-0.785	-0.877	11.553	0.651	0.651	0.000	0.000	0.000	0.000
42	A	239	PRO	0	0.086	0.035	13.598	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	240	THR	0	0.024	-0.011	16.752	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	241	GLU	-1	-0.865	-0.933	11.819	0.476	0.476	0.000	0.000	0.000	0.000
45	A	242	GLU	-1	-0.820	-0.884	15.014	0.073	0.073	0.000	0.000	0.000	0.000
46	A	243	LYS	1	0.783	0.883	16.761	-0.202	-0.202	0.000	0.000	0.000	0.000
47	A	244	LYS	1	0.799	0.893	14.824	-0.404	-0.404	0.000	0.000	0.000	0.000
48	A	245	ALA	0	-0.003	0.001	15.237	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	246	ALA	0	-0.005	0.002	17.313	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	247	ARG	1	0.892	0.931	20.658	-0.153	-0.153	0.000	0.000	0.000	0.000
51	A	248	GLY	0	0.016	0.007	20.027	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	249	LEU	0	-0.038	-0.010	18.860	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	250	GLY	0	0.056	0.025	22.130	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	251	ALA	0	0.027	0.014	24.443	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	252	SER	0	-0.070	-0.063	22.596	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	253	LEU	0	-0.059	-0.023	25.065	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	254	GLN	0	0.056	0.027	27.547	0.001	0.001	0.000	0.000	0.000	0.000
58	A	255	ARG	1	0.820	0.909	27.289	-0.033	-0.033	0.000	0.000	0.000	0.000
59	A	256	GLN	0	-0.010	-0.001	24.948	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	257	GLY	0	0.061	0.043	30.375	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	258	LYS	1	0.804	0.913	27.122	0.016	0.016	0.000	0.000	0.000	0.000
62	A	259	TYR	0	0.007	-0.049	30.860	0.002	0.002	0.000	0.000	0.000	0.000
63	A	260	ARG	1	0.978	0.987	32.412	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	261	GLU	-1	-0.777	-0.883	26.104	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	262	ALA	0	-0.024	-0.016	27.633	0.004	0.004	0.000	0.000	0.000	0.000
66	A	263	ILE	0	0.045	0.022	28.105	0.007	0.007	0.000	0.000	0.000	0.000
67	A	264	GLN	0	-0.024	0.024	24.379	0.001	0.001	0.000	0.000	0.000	0.000
68	A	265	TYR	0	0.013	-0.016	21.627	0.003	0.003	0.000	0.000	0.000	0.000
69	A	266	HIS	0	0.049	0.012	24.545	0.016	0.016	0.000	0.000	0.000	0.000
70	A	267	SER	0	-0.007	-0.025	26.764	0.008	0.008	0.000	0.000	0.000	0.000
71	A	268	MET	0	-0.063	-0.023	20.495	0.000	0.000	0.000	0.000	0.000	0.000
72	A	269	VAL	0	0.016	0.019	22.685	0.011	0.011	0.000	0.000	0.000	0.000
73	A	270	LEU	0	-0.002	0.021	24.461	0.010	0.010	0.000	0.000	0.000	0.000
74	A	271	ALA	0	-0.018	-0.013	25.876	0.002	0.002	0.000	0.000	0.000	0.000
75	A	272	ILE	0	-0.036	-0.018	20.142	0.002	0.002	0.000	0.000	0.000	0.000
76	A	273	SER	0	-0.005	-0.024	23.493	0.012	0.012	0.000	0.000	0.000	0.000
77	A	274	LYS	1	0.872	0.945	25.381	-0.073	-0.073	0.000	0.000	0.000	0.000
78	A	275	ARG	1	0.712	0.851	19.457	-0.125	-0.125	0.000	0.000	0.000	0.000
79	A	276	GLU	-1	-0.784	-0.900	20.705	0.155	0.155	0.000	0.000	0.000	0.000
80	A	277	SER	0	-0.047	-0.007	23.892	0.003	0.003	0.000	0.000	0.000	0.000
81	A	278	GLU	-1	-0.725	-0.802	21.062	0.218	0.218	0.000	0.000	0.000	0.000
82	A	279	ASP	-1	-0.793	-0.894	24.792	0.128	0.128	0.000	0.000	0.000	0.000
83	A	280	SER	0	-0.042	-0.048	22.571	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	281	GLY	0	0.009	0.000	24.315	0.002	0.002	0.000	0.000	0.000	0.000
85	A	282	ILE	0	-0.021	-0.009	25.968	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	283	THR	0	-0.022	-0.021	28.777	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	284	GLU	-1	-0.832	-0.900	25.986	0.099	0.099	0.000	0.000	0.000	0.000
88	A	285	ALA	0	-0.017	-0.006	27.131	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	286	TYR	0	0.023	-0.010	29.050	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	287	GLY	0	0.075	0.036	32.674	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	288	ALA	0	0.003	0.006	29.773	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	289	ILE	0	-0.032	-0.018	29.912	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	290	ALA	0	0.023	0.017	33.071	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	291	ASP	-1	-0.878	-0.919	34.132	0.038	0.038	0.000	0.000	0.000	0.000
95	A	292	CYS	0	-0.103	-0.056	32.233	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	293	TYR	0	-0.014	-0.024	35.003	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	294	THR	0	-0.024	-0.022	38.018	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	295	GLU	-1	-0.868	-0.901	36.766	0.015	0.015	0.000	0.000	0.000	0.000
99	A	296	LEU	0	-0.129	-0.061	35.597	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	297	GLY	0	0.011	0.010	39.946	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	298	ASP	-1	-0.844	-0.897	40.430	0.018	0.018	0.000	0.000	0.000	0.000
102	A	299	LEU	0	0.083	0.027	41.988	0.003	0.003	0.000	0.000	0.000	0.000
103	A	300	GLU	-1	-0.903	-0.949	43.973	0.020	0.020	0.000	0.000	0.000	0.000
104	A	301	LYS	1	0.740	0.854	39.209	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	302	ALA	0	0.026	0.004	39.228	0.003	0.003	0.000	0.000	0.000	0.000
106	A	303	GLY	0	0.045	0.029	40.112	0.003	0.003	0.000	0.000	0.000	0.000
107	A	304	LYS	1	0.940	0.975	40.743	-0.026	-0.026	0.000	0.000	0.000	0.000
108	A	305	PHE	0	-0.028	-0.007	33.445	0.003	0.003	0.000	0.000	0.000	0.000
109	A	306	TYR	0	0.030	0.013	37.396	0.005	0.005	0.000	0.000	0.000	0.000
110	A	307	ASP	-1	-0.890	-0.948	39.440	0.039	0.039	0.000	0.000	0.000	0.000
111	A	308	THR	0	-0.084	-0.052	36.042	0.003	0.003	0.000	0.000	0.000	0.000
112	A	309	TYR	0	-0.051	-0.019	33.743	0.006	0.006	0.000	0.000	0.000	0.000
113	A	310	ILE	0	0.003	0.003	36.664	0.004	0.004	0.000	0.000	0.000	0.000
114	A	311	ALA	0	0.041	0.022	39.751	0.002	0.002	0.000	0.000	0.000	0.000
115	A	312	ARG	1	0.737	0.859	30.765	-0.098	-0.098	0.000	0.000	0.000	0.000
116	A	313	LEU	0	0.005	0.000	34.530	0.004	0.004	0.000	0.000	0.000	0.000
117	A	314	GLU	-1	-0.973	-0.979	37.329	0.050	0.050	0.000	0.000	0.000	0.000
118	A	315	THR	0	-0.101	-0.055	37.568	0.000	0.000	0.000	0.000	0.000	0.000
119	A	316	ASP	-1	-0.866	-0.914	33.236	0.098	0.098	0.000	0.000	0.000	0.000

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