FMO DATABASE

FMODB ID: 6Y1GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-985283.494572
FMO2-HF: Nuclear repulsion	938576.423915
FMO2-HF: Total energy	-46707.070657
FMO2-MP2: Total energy	-46845.077715

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.
-5.637	-2.1	0.026	-1.388	-2.176	0

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 : 0.043 / q_NPA : 0.005

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].
3	A	200	LYS	1	0.929	0.974	3.242	-2.393	0.016	-0.007	-1.070	-1.332
4	A	201	GLN	0	0.010	0.001	3.245	-1.747	-1.070	0.034	-0.165	-0.547
5	A	202	GLU	-1	-0.839	-0.929	4.191	-0.965	-0.514	-0.001	-0.153	-0.297
6	A	203	LEU	0	-0.016	0.009	6.061	0.079	0.079	0.000	0.000	0.000
7	A	204	ILE	0	-0.001	-0.005	8.190	-0.068	-0.068	0.000	0.000	0.000
8	A	205	SER	0	-0.021	-0.023	8.300	-0.089	-0.089	0.000	0.000	0.000
9	A	206	LYS	1	0.870	0.934	9.952	0.049	0.049	0.000	0.000	0.000
10	A	207	LEU	0	0.003	0.016	11.929	-0.028	-0.028	0.000	0.000	0.000
11	A	208	LYS	1	0.877	0.950	11.163	-0.392	-0.392	0.000	0.000	0.000
12	A	209	THR	0	-0.040	-0.059	13.630	-0.009	-0.009	0.000	0.000	0.000
13	A	210	GLY	0	0.072	0.042	15.694	-0.020	-0.020	0.000	0.000	0.000
14	A	211	LYS	1	0.941	0.956	17.729	-0.162	-0.162	0.000	0.000	0.000
15	A	212	THR	0	-0.033	-0.024	18.421	-0.003	-0.003	0.000	0.000	0.000
16	A	213	PHE	0	0.025	0.019	17.415	-0.007	-0.007	0.000	0.000	0.000
17	A	214	LEU	0	0.024	0.016	21.835	-0.005	-0.005	0.000	0.000	0.000
18	A	215	ARG	1	0.835	0.934	20.495	-0.123	-0.123	0.000	0.000	0.000
19	A	216	ASN	0	-0.010	0.008	23.668	0.004	0.004	0.000	0.000	0.000
20	A	217	GLN	0	-0.029	-0.008	26.364	-0.007	-0.007	0.000	0.000	0.000
21	A	218	GLU	-1	-0.851	-0.935	24.074	0.016	0.016	0.000	0.000	0.000
22	A	219	PRO	0	0.007	-0.001	23.765	0.001	0.001	0.000	0.000	0.000
23	A	220	GLU	-1	-0.822	-0.923	23.903	-0.006	-0.006	0.000	0.000	0.000
24	A	221	LYS	1	0.918	0.966	20.738	0.001	0.001	0.000	0.000	0.000
25	A	222	ALA	0	-0.005	-0.005	19.470	-0.003	-0.003	0.000	0.000	0.000
26	A	223	TYR	0	0.030	0.020	19.143	-0.004	-0.004	0.000	0.000	0.000
27	A	224	THR	0	-0.021	-0.013	16.449	-0.010	-0.010	0.000	0.000	0.000
28	A	225	GLU	-1	-0.775	-0.844	14.260	-0.051	-0.051	0.000	0.000	0.000
29	A	226	PHE	0	0.015	-0.004	14.504	0.003	0.003	0.000	0.000	0.000
30	A	227	LYS	1	0.926	0.973	16.128	0.065	0.065	0.000	0.000	0.000
31	A	228	ILE	0	0.030	0.020	10.609	-0.020	-0.020	0.000	0.000	0.000
32	A	229	ALA	0	-0.032	-0.015	11.520	-0.032	-0.032	0.000	0.000	0.000
33	A	230	LEU	0	0.011	-0.006	12.597	0.011	0.011	0.000	0.000	0.000
34	A	231	GLU	-1	-0.921	-0.946	12.106	-0.259	-0.259	0.000	0.000	0.000
35	A	232	LEU	0	-0.036	-0.031	6.580	-0.070	-0.070	0.000	0.000	0.000
36	A	233	ALA	0	-0.008	-0.010	9.722	0.005	0.005	0.000	0.000	0.000
37	A	234	GLN	0	-0.026	-0.020	11.728	-0.003	-0.003	0.000	0.000	0.000
38	A	235	SER	0	-0.079	-0.029	9.351	-0.068	-0.068	0.000	0.000	0.000
39	A	236	LEU	0	-0.080	-0.054	5.497	-0.026	-0.026	0.000	0.000	0.000
40	A	237	LYS	1	0.936	0.981	9.664	0.140	0.140	0.000	0.000	0.000
41	A	238	ASP	-1	-0.806	-0.891	11.307	0.425	0.425	0.000	0.000	0.000
42	A	239	PRO	0	0.100	0.039	13.347	-0.002	-0.002	0.000	0.000	0.000
43	A	240	THR	0	0.019	0.006	16.269	-0.003	-0.003	0.000	0.000	0.000
44	A	241	GLU	-1	-0.866	-0.938	11.651	0.397	0.397	0.000	0.000	0.000
45	A	242	GLU	-1	-0.854	-0.923	14.796	-0.012	-0.012	0.000	0.000	0.000
46	A	243	LYS	1	0.806	0.902	16.283	-0.124	-0.124	0.000	0.000	0.000
47	A	244	LYS	1	0.778	0.881	15.123	-0.331	-0.331	0.000	0.000	0.000
48	A	245	ALA	0	-0.006	0.004	15.390	-0.008	-0.008	0.000	0.000	0.000
49	A	246	ALA	0	0.007	0.010	17.472	-0.015	-0.015	0.000	0.000	0.000
50	A	247	ARG	1	0.886	0.923	20.794	-0.124	-0.124	0.000	0.000	0.000
51	A	248	GLY	0	0.007	0.005	20.245	-0.004	-0.004	0.000	0.000	0.000
52	A	249	LEU	0	-0.023	-0.007	18.912	-0.009	-0.009	0.000	0.000	0.000
53	A	250	GLY	0	0.050	0.026	22.173	-0.006	-0.006	0.000	0.000	0.000
54	A	251	ALA	0	0.012	0.005	24.536	-0.003	-0.003	0.000	0.000	0.000
55	A	252	SER	0	-0.076	-0.064	22.691	-0.002	-0.002	0.000	0.000	0.000
56	A	253	LEU	0	-0.031	-0.015	25.265	-0.005	-0.005	0.000	0.000	0.000
57	A	254	GLN	0	0.071	0.037	27.631	0.001	0.001	0.000	0.000	0.000
58	A	255	ARG	1	0.838	0.918	27.461	-0.045	-0.045	0.000	0.000	0.000
59	A	256	GLN	0	-0.005	0.008	25.463	-0.007	-0.007	0.000	0.000	0.000
60	A	257	GLY	0	0.042	0.039	30.833	-0.003	-0.003	0.000	0.000	0.000
61	A	258	LYS	1	0.850	0.932	28.066	0.017	0.017	0.000	0.000	0.000
62	A	259	TYR	0	0.025	-0.040	30.869	0.000	0.000	0.000	0.000	0.000
63	A	260	ARG	1	0.981	0.987	32.470	0.004	0.004	0.000	0.000	0.000
64	A	261	GLU	-1	-0.883	-0.947	27.551	-0.022	-0.022	0.000	0.000	0.000
65	A	262	ALA	0	-0.009	-0.007	27.722	0.001	0.001	0.000	0.000	0.000
66	A	263	ILE	0	0.024	0.013	28.109	0.004	0.004	0.000	0.000	0.000
67	A	264	GLN	0	-0.028	0.020	24.768	0.002	0.002	0.000	0.000	0.000
68	A	265	TYR	0	0.006	-0.017	21.473	-0.004	-0.004	0.000	0.000	0.000
69	A	266	HIS	0	0.042	0.004	24.750	0.009	0.009	0.000	0.000	0.000
70	A	267	SER	0	-0.027	-0.033	26.962	0.006	0.006	0.000	0.000	0.000
71	A	268	MET	0	-0.051	-0.018	20.232	-0.001	-0.001	0.000	0.000	0.000
72	A	269	VAL	0	0.024	0.026	22.878	0.005	0.005	0.000	0.000	0.000
73	A	270	LEU	0	-0.001	0.020	24.349	0.006	0.006	0.000	0.000	0.000
74	A	271	ALA	0	-0.027	-0.018	25.651	0.001	0.001	0.000	0.000	0.000
75	A	272	ILE	0	-0.039	-0.016	19.862	-0.001	-0.001	0.000	0.000	0.000
76	A	273	SER	0	0.004	-0.015	23.332	0.009	0.009	0.000	0.000	0.000
77	A	274	LYS	1	0.913	0.959	25.142	-0.033	-0.033	0.000	0.000	0.000
78	A	275	ARG	1	0.791	0.902	20.185	-0.022	-0.022	0.000	0.000	0.000
79	A	276	GLU	-1	-0.828	-0.919	20.398	0.046	0.046	0.000	0.000	0.000
80	A	277	SER	0	-0.049	-0.008	23.715	0.006	0.006	0.000	0.000	0.000
81	A	278	GLU	-1	-0.756	-0.834	20.887	0.145	0.145	0.000	0.000	0.000
82	A	279	ASP	-1	-0.809	-0.908	24.771	0.088	0.088	0.000	0.000	0.000
83	A	280	SER	0	-0.034	-0.041	22.167	-0.002	-0.002	0.000	0.000	0.000
84	A	281	GLY	0	-0.005	-0.009	24.330	-0.004	-0.004	0.000	0.000	0.000
85	A	282	ILE	0	-0.012	-0.003	25.692	-0.009	-0.009	0.000	0.000	0.000
86	A	283	THR	0	0.054	0.031	28.435	-0.005	-0.005	0.000	0.000	0.000
87	A	284	GLU	-1	-0.817	-0.893	26.337	0.087	0.087	0.000	0.000	0.000
88	A	285	ALA	0	0.000	0.003	27.292	-0.005	-0.005	0.000	0.000	0.000
89	A	286	TYR	0	-0.005	-0.011	29.222	-0.007	-0.007	0.000	0.000	0.000
90	A	287	GLY	0	0.080	0.042	32.808	-0.005	-0.005	0.000	0.000	0.000
91	A	288	ALA	0	0.011	0.015	29.985	-0.004	-0.004	0.000	0.000	0.000
92	A	289	ILE	0	-0.024	-0.016	29.976	-0.005	-0.005	0.000	0.000	0.000
93	A	290	ALA	0	0.002	0.004	33.199	-0.004	-0.004	0.000	0.000	0.000
94	A	291	ASP	-1	-0.867	-0.918	34.306	0.032	0.032	0.000	0.000	0.000
95	A	292	CYS	0	-0.119	-0.066	32.367	-0.004	-0.004	0.000	0.000	0.000
96	A	293	TYR	0	-0.021	-0.029	35.141	-0.005	-0.005	0.000	0.000	0.000
97	A	294	THR	0	-0.006	-0.011	38.130	-0.002	-0.002	0.000	0.000	0.000
98	A	295	GLU	-1	-0.877	-0.902	36.692	0.014	0.014	0.000	0.000	0.000
99	A	296	LEU	0	-0.138	-0.066	35.803	-0.003	-0.003	0.000	0.000	0.000
100	A	297	GLY	0	0.013	0.015	40.017	-0.002	-0.002	0.000	0.000	0.000
101	A	298	ASP	-1	-0.861	-0.909	40.700	0.005	0.005	0.000	0.000	0.000
102	A	299	LEU	0	0.086	0.021	42.139	0.002	0.002	0.000	0.000	0.000
103	A	300	GLU	-1	-0.894	-0.946	44.331	0.010	0.010	0.000	0.000	0.000
104	A	301	LYS	1	0.741	0.849	39.091	-0.004	-0.004	0.000	0.000	0.000
105	A	302	ALA	0	0.028	0.014	39.410	0.002	0.002	0.000	0.000	0.000
106	A	303	GLY	0	0.049	0.027	40.376	0.003	0.003	0.000	0.000	0.000
107	A	304	LYS	1	0.931	0.973	40.581	-0.012	-0.012	0.000	0.000	0.000
108	A	305	PHE	0	-0.029	-0.024	33.571	0.002	0.002	0.000	0.000	0.000
109	A	306	TYR	0	0.029	0.014	37.518	0.004	0.004	0.000	0.000	0.000
110	A	307	ASP	-1	-0.876	-0.935	39.513	0.028	0.028	0.000	0.000	0.000
111	A	308	THR	0	-0.088	-0.043	36.061	0.002	0.002	0.000	0.000	0.000
112	A	309	TYR	0	-0.045	-0.025	33.802	0.005	0.005	0.000	0.000	0.000
113	A	310	ILE	0	0.019	0.014	36.715	0.004	0.004	0.000	0.000	0.000
114	A	311	ALA	0	0.035	0.022	39.727	0.002	0.002	0.000	0.000	0.000
115	A	312	ARG	1	0.799	0.870	30.097	-0.070	-0.070	0.000	0.000	0.000
116	A	313	LEU	0	-0.003	0.006	34.686	0.003	0.003	0.000	0.000	0.000
117	A	314	GLU	-1	-0.963	-0.971	37.178	0.041	0.041	0.000	0.000	0.000
118	A	315	THR	0	-0.135	-0.073	36.918	-0.001	-0.001	0.000	0.000	0.000
119	A	316	ASP	-1	-1.014	-1.000	34.073	0.080	0.080	0.000	0.000	0.000

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