FMO DATABASE

FMODB ID: Z6GYN

Calculation Name: 4JVU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JVU

Chain ID: A

ChEMBL ID:

UniProt ID: P01872

Base Structure: X-ray

Registration Date: 2023-06-26

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-839590.370059
FMO2-HF: Nuclear repulsion	795732.836148
FMO2-HF: Total energy	-43857.53391
FMO2-MP2: Total energy	-43985.020847

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:224:GLY)

Summations of interaction energy for fragment #1(A:224:GLY)

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.
0.705	2.212	-0.009	-0.772	-0.726	0.003

Interaction energy analysis for fragmet #1(A:224:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.020

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	226	PRO	0	-0.014	0.007	3.868	0.489	1.996	-0.009	-0.772	-0.726	0.003
4	A	227	ALA	0	0.005	-0.005	6.484	0.212	0.212	0.000	0.000	0.000	0.000
5	A	228	VAL	0	0.003	-0.008	9.455	0.000	0.000	0.000	0.000	0.000	0.000
6	A	229	ALA	0	-0.007	0.000	12.539	0.080	0.080	0.000	0.000	0.000	0.000
7	A	230	GLU	-1	-0.765	-0.852	13.511	-0.295	-0.295	0.000	0.000	0.000	0.000
8	A	231	MET	0	-0.070	-0.028	16.515	0.000	0.000	0.000	0.000	0.000	0.000
9	A	232	ASN	0	0.071	0.024	18.930	0.013	0.013	0.000	0.000	0.000	0.000
10	A	233	PRO	0	-0.042	0.000	20.487	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	234	ASN	0	0.001	0.013	22.535	0.002	0.002	0.000	0.000	0.000	0.000
12	A	235	VAL	0	0.002	-0.015	25.165	0.009	0.009	0.000	0.000	0.000	0.000
13	A	236	ASN	0	-0.031	-0.015	27.481	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	237	VAL	0	0.012	-0.012	29.969	0.008	0.008	0.000	0.000	0.000	0.000
15	A	238	PHE	0	-0.031	-0.001	30.912	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	239	VAL	0	0.020	-0.001	35.298	0.006	0.006	0.000	0.000	0.000	0.000
17	A	240	PRO	0	-0.006	0.018	38.405	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	241	PRO	0	0.026	0.013	41.325	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	242	ARG	1	0.951	0.959	44.457	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	243	ASP	-1	-0.884	-0.941	47.553	0.017	0.017	0.000	0.000	0.000	0.000
21	A	244	GLY	0	0.001	0.015	44.100	0.001	0.001	0.000	0.000	0.000	0.000
22	A	245	PHE	0	-0.019	-0.008	42.830	0.004	0.004	0.000	0.000	0.000	0.000
23	A	246	SER	0	-0.059	-0.023	43.721	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	247	GLY	0	0.048	0.017	45.888	0.003	0.003	0.000	0.000	0.000	0.000
25	A	248	PRO	0	0.024	-0.005	47.152	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	249	ALA	0	0.009	0.022	48.593	0.001	0.001	0.000	0.000	0.000	0.000
27	A	250	PRO	0	-0.027	-0.010	46.889	0.001	0.001	0.000	0.000	0.000	0.000
28	A	251	ARG	1	0.852	0.890	46.646	-0.028	-0.028	0.000	0.000	0.000	0.000
29	A	252	LYS	1	0.935	0.961	41.299	-0.060	-0.060	0.000	0.000	0.000	0.000
30	A	253	SER	0	0.015	-0.005	40.841	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	254	LYS	1	0.945	0.966	34.407	-0.059	-0.059	0.000	0.000	0.000	0.000
32	A	255	LEU	0	0.000	0.031	34.536	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	256	ILE	0	-0.001	-0.003	30.475	0.007	0.007	0.000	0.000	0.000	0.000
34	A	257	CYS	0	-0.056	-0.002	28.114	0.000	0.000	0.000	0.000	0.000	0.000
35	A	258	GLU	-1	-0.833	-0.901	26.259	0.014	0.014	0.000	0.000	0.000	0.000
36	A	259	ALA	0	0.017	0.014	22.549	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	260	THR	0	-0.011	-0.024	22.621	0.002	0.002	0.000	0.000	0.000	0.000
38	A	261	ASN	0	0.004	-0.009	21.820	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	262	PHE	0	0.028	0.040	16.536	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	263	THR	0	-0.014	-0.039	14.157	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	264	PRO	0	0.047	0.025	10.470	0.007	0.007	0.000	0.000	0.000	0.000
42	A	265	LYS	1	0.883	0.959	11.302	-0.099	-0.099	0.000	0.000	0.000	0.000
43	A	266	PRO	0	-0.028	-0.019	10.257	0.028	0.028	0.000	0.000	0.000	0.000
44	A	267	ILE	0	-0.009	0.006	13.212	-0.052	-0.052	0.000	0.000	0.000	0.000
45	A	268	THR	0	0.008	0.015	17.011	0.049	0.049	0.000	0.000	0.000	0.000
46	A	269	VAL	0	0.021	0.005	19.862	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	270	SER	0	-0.041	-0.021	23.418	0.020	0.020	0.000	0.000	0.000	0.000
48	A	271	TRP	0	0.029	0.012	26.699	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	272	LEU	0	-0.015	-0.008	30.447	0.006	0.006	0.000	0.000	0.000	0.000
50	A	273	LYS	1	0.839	0.902	33.430	-0.056	-0.056	0.000	0.000	0.000	0.000
51	A	274	ASP	-1	-0.803	-0.899	37.177	0.045	0.045	0.000	0.000	0.000	0.000
52	A	275	GLY	0	-0.018	-0.011	36.017	0.000	0.000	0.000	0.000	0.000	0.000
53	A	276	LYS	1	0.855	0.926	35.991	-0.049	-0.049	0.000	0.000	0.000	0.000
54	A	277	LEU	0	0.035	0.013	28.967	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	278	VAL	0	-0.033	-0.013	32.115	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	279	GLU	-1	-0.900	-0.955	30.599	0.126	0.126	0.000	0.000	0.000	0.000
57	A	280	SER	0	-0.034	-0.014	31.101	0.007	0.007	0.000	0.000	0.000	0.000
58	A	281	GLY	0	0.041	0.013	32.725	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	282	PHE	0	-0.019	-0.003	26.201	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	283	THR	0	-0.029	-0.011	26.858	0.011	0.011	0.000	0.000	0.000	0.000
61	A	284	THR	0	-0.031	-0.024	22.300	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	285	ASP	-1	-0.877	-0.926	23.330	0.122	0.122	0.000	0.000	0.000	0.000
63	A	286	PRO	0	-0.011	-0.023	18.526	0.008	0.008	0.000	0.000	0.000	0.000
64	A	287	VAL	0	-0.002	0.008	16.045	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	288	THR	0	0.009	0.004	16.704	0.020	0.020	0.000	0.000	0.000	0.000
66	A	289	ILE	0	-0.013	-0.007	14.130	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	290	GLU	-1	-0.766	-0.845	17.870	-0.066	-0.066	0.000	0.000	0.000	0.000
68	A	291	ASN	0	-0.046	-0.058	19.060	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	292	LYS	1	0.880	0.924	21.626	0.168	0.168	0.000	0.000	0.000	0.000
70	A	293	GLY	0	0.025	0.027	22.917	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	294	SER	0	0.021	0.016	22.243	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	295	THR	0	-0.048	-0.028	19.219	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	296	PRO	0	0.016	0.027	16.874	-0.053	-0.053	0.000	0.000	0.000	0.000
74	A	297	GLN	0	0.037	0.009	14.014	0.046	0.046	0.000	0.000	0.000	0.000
75	A	298	THR	0	-0.015	-0.013	15.379	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	299	TYR	0	-0.054	-0.045	11.997	0.035	0.035	0.000	0.000	0.000	0.000
77	A	300	LYS	1	0.854	0.920	17.973	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	301	VAL	0	-0.039	-0.019	19.880	0.021	0.021	0.000	0.000	0.000	0.000
79	A	302	ILE	0	0.034	0.030	21.768	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	303	SER	0	0.042	0.019	24.787	0.020	0.020	0.000	0.000	0.000	0.000
81	A	304	THR	0	0.026	0.012	27.086	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	305	LEU	0	0.003	0.011	30.616	0.010	0.010	0.000	0.000	0.000	0.000
83	A	306	THR	0	-0.050	-0.034	33.098	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	307	ILE	0	-0.027	-0.007	36.483	0.002	0.002	0.000	0.000	0.000	0.000
85	A	308	SER	0	-0.009	-0.026	39.355	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	309	GLU	-1	-0.753	-0.857	43.032	0.029	0.029	0.000	0.000	0.000	0.000
87	A	310	ILE	0	0.014	0.005	45.863	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	311	ASP	-1	-0.806	-0.867	42.586	0.048	0.048	0.000	0.000	0.000	0.000
89	A	312	TRP	0	0.022	0.008	39.568	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	313	LEU	0	0.011	0.014	44.304	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	314	ASN	0	-0.099	-0.048	47.117	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	315	LEU	0	-0.030	-0.020	45.780	0.000	0.000	0.000	0.000	0.000	0.000
93	A	316	ASN	0	-0.004	0.024	41.720	0.003	0.003	0.000	0.000	0.000	0.000
94	A	317	VAL	0	0.001	0.000	38.222	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	318	TYR	0	0.020	0.005	35.745	0.006	0.006	0.000	0.000	0.000	0.000
96	A	319	THR	0	-0.030	-0.036	31.287	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	321	ARG	1	0.857	0.891	24.874	-0.088	-0.088	0.000	0.000	0.000	0.000
98	A	322	VAL	0	0.026	0.005	22.133	0.012	0.012	0.000	0.000	0.000	0.000
99	A	323	ASP	-1	-0.798	-0.853	20.997	0.071	0.071	0.000	0.000	0.000	0.000
100	A	324	HIS	0	-0.010	-0.024	15.587	0.030	0.030	0.000	0.000	0.000	0.000
101	A	325	ARG	1	0.835	0.867	12.531	0.149	0.149	0.000	0.000	0.000	0.000
102	A	326	GLY	0	-0.004	0.013	16.560	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	327	LEU	0	-0.039	-0.001	19.541	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	328	THR	0	-0.008	-0.031	22.156	0.010	0.010	0.000	0.000	0.000	0.000
105	A	329	PHE	0	-0.025	-0.012	21.772	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	330	LEU	0	0.005	-0.004	26.588	0.013	0.013	0.000	0.000	0.000	0.000
107	A	331	LYS	1	0.903	0.957	29.724	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	332	ASN	0	0.037	0.032	32.129	0.011	0.011	0.000	0.000	0.000	0.000
109	A	333	VAL	0	-0.030	-0.021	35.466	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	334	SER	0	0.041	0.008	37.994	0.004	0.004	0.000	0.000	0.000	0.000
111	A	335	SER	0	-0.006	-0.016	41.496	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	336	THR	0	-0.017	0.003	44.679	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	337	CYS	0	-0.001	0.010	45.490	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:224:GLY)