FMO DATABASE

FMODB ID: VK521

Calculation Name: 4J8D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4J8D

Chain ID: A

ChEMBL ID:

UniProt ID: P50503

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1552210.956558
FMO2-HF: Nuclear repulsion	1487717.069178
FMO2-HF: Total energy	-64493.88738
FMO2-MP2: Total energy	-64680.881854

3D Structure Molmil

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:81:GLU)

Summations of interaction energy for fragment #1(A:81:GLU)

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.
-12.856	-9.1530000000001	0.05	-1.622	-2.13	0.005

Interaction energy analysis for fragmet #1(A:81:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.942 / q_NPA : -0.976

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	83	ASP	-1	-0.870	-0.931	3.663	49.102	51.662	0.013	-1.020	-1.552	0.001
4	A	84	ASN	0	-0.034	-0.021	5.400	-7.178	-7.178	0.000	0.000	0.000	0.000
5	A	85	GLU	-1	-0.903	-0.948	7.723	20.457	20.457	0.000	0.000	0.000	0.000
6	A	86	GLY	0	0.046	0.020	10.360	-0.739	-0.739	0.000	0.000	0.000	0.000
7	A	87	VAL	0	-0.106	-0.037	10.566	-1.144	-1.144	0.000	0.000	0.000	0.000
8	A	88	ILE	0	-0.036	-0.011	13.189	0.429	0.429	0.000	0.000	0.000	0.000
9	A	89	GLU	-1	-0.966	-0.979	15.749	16.211	16.211	0.000	0.000	0.000	0.000
10	A	90	ALA	0	-0.031	-0.019	17.888	-0.688	-0.688	0.000	0.000	0.000	0.000
11	A	91	ASP	-1	-0.788	-0.900	20.133	12.644	12.644	0.000	0.000	0.000	0.000
12	A	92	THR	0	-0.045	-0.026	23.838	0.070	0.070	0.000	0.000	0.000	0.000
13	A	93	ASP	-1	-0.913	-0.955	26.010	10.801	10.801	0.000	0.000	0.000	0.000
14	A	94	ALA	0	-0.034	-0.021	29.473	0.082	0.082	0.000	0.000	0.000	0.000
15	A	95	PRO	0	-0.049	-0.041	31.616	0.084	0.084	0.000	0.000	0.000	0.000
16	A	96	GLN	0	-0.035	-0.030	30.515	-0.108	-0.108	0.000	0.000	0.000	0.000
17	A	97	GLU	-1	-0.886	-0.950	34.500	7.769	7.769	0.000	0.000	0.000	0.000
18	A	98	MET	0	-0.034	-0.014	33.187	0.125	0.125	0.000	0.000	0.000	0.000
19	A	99	GLY	0	0.041	0.008	38.363	-0.149	-0.149	0.000	0.000	0.000	0.000
20	A	100	ASP	-1	-0.856	-0.910	41.765	7.116	7.116	0.000	0.000	0.000	0.000
21	A	101	GLU	-1	-0.925	-0.985	39.583	7.851	7.851	0.000	0.000	0.000	0.000
22	A	102	ASN	0	-0.062	-0.038	43.034	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	103	ALA	0	0.021	0.024	46.394	-0.167	-0.167	0.000	0.000	0.000	0.000
24	A	104	GLU	-1	-0.961	-0.985	48.785	5.857	5.857	0.000	0.000	0.000	0.000
25	A	105	ILE	0	-0.024	-0.016	46.529	0.051	0.051	0.000	0.000	0.000	0.000
26	A	106	THR	0	0.029	0.001	50.954	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	107	GLU	-1	-0.861	-0.936	52.949	5.722	5.722	0.000	0.000	0.000	0.000
28	A	108	ALA	0	0.043	0.021	53.953	0.071	0.071	0.000	0.000	0.000	0.000
29	A	109	MET	0	-0.017	0.025	50.402	0.124	0.124	0.000	0.000	0.000	0.000
30	A	110	MET	0	-0.024	-0.020	48.982	0.120	0.120	0.000	0.000	0.000	0.000
31	A	111	ASP	-1	-0.917	-0.953	49.532	6.089	6.089	0.000	0.000	0.000	0.000
32	A	112	GLU	-1	-0.993	-1.003	50.413	6.267	6.267	0.000	0.000	0.000	0.000
33	A	113	ALA	0	-0.013	-0.015	45.521	0.136	0.136	0.000	0.000	0.000	0.000
34	A	114	ASN	0	-0.066	-0.034	45.454	0.339	0.339	0.000	0.000	0.000	0.000
35	A	115	GLU	-1	-0.897	-0.953	46.488	6.413	6.413	0.000	0.000	0.000	0.000
36	A	116	LYS	1	0.891	0.959	44.419	-6.774	-6.774	0.000	0.000	0.000	0.000
37	A	117	LYS	1	0.943	0.975	41.222	-7.344	-7.344	0.000	0.000	0.000	0.000
38	A	118	GLY	0	-0.027	-0.016	42.127	0.186	0.186	0.000	0.000	0.000	0.000
39	A	119	ALA	0	0.077	0.039	43.615	0.093	0.093	0.000	0.000	0.000	0.000
40	A	120	ALA	0	-0.024	-0.017	39.297	0.104	0.104	0.000	0.000	0.000	0.000
41	A	121	ILE	0	-0.098	-0.058	38.778	0.328	0.328	0.000	0.000	0.000	0.000
42	A	122	ASP	-1	-0.857	-0.919	39.604	7.343	7.343	0.000	0.000	0.000	0.000
43	A	123	ALA	0	-0.019	-0.007	39.204	0.046	0.046	0.000	0.000	0.000	0.000
44	A	124	LEU	0	-0.078	-0.035	32.976	0.266	0.266	0.000	0.000	0.000	0.000
45	A	125	ASN	0	-0.097	-0.066	35.648	0.099	0.099	0.000	0.000	0.000	0.000
46	A	126	ASP	-1	-0.875	-0.923	37.260	7.818	7.818	0.000	0.000	0.000	0.000
47	A	127	GLY	0	-0.028	0.001	34.805	0.072	0.072	0.000	0.000	0.000	0.000
48	A	128	GLU	-1	-0.911	-0.959	34.577	8.342	8.342	0.000	0.000	0.000	0.000
49	A	129	LEU	0	-0.031	-0.040	30.221	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	130	GLN	0	0.002	-0.007	33.408	0.303	0.303	0.000	0.000	0.000	0.000
51	A	131	LYS	1	1.004	1.001	35.361	-7.460	-7.460	0.000	0.000	0.000	0.000
52	A	132	ALA	0	0.036	0.025	35.591	-0.172	-0.172	0.000	0.000	0.000	0.000
53	A	133	ILE	0	-0.015	-0.012	31.440	-0.080	-0.080	0.000	0.000	0.000	0.000
54	A	134	ASP	-1	-0.860	-0.893	36.049	8.217	8.217	0.000	0.000	0.000	0.000
55	A	135	LEU	0	-0.012	-0.003	39.371	-0.213	-0.213	0.000	0.000	0.000	0.000
56	A	136	PHE	0	-0.029	-0.025	35.479	-0.098	-0.098	0.000	0.000	0.000	0.000
57	A	137	THR	0	-0.032	-0.057	37.813	0.011	0.011	0.000	0.000	0.000	0.000
58	A	138	ASP	-1	-0.929	-0.963	39.729	7.224	7.224	0.000	0.000	0.000	0.000
59	A	139	ALA	0	-0.020	-0.003	41.992	-0.178	-0.178	0.000	0.000	0.000	0.000
60	A	140	ILE	0	-0.041	-0.030	37.227	-0.118	-0.118	0.000	0.000	0.000	0.000
61	A	141	LYS	1	0.924	0.965	41.693	-7.215	-7.215	0.000	0.000	0.000	0.000
62	A	142	LEU	0	-0.023	0.010	44.281	-0.136	-0.136	0.000	0.000	0.000	0.000
63	A	143	ASN	0	0.003	-0.013	44.258	-0.286	-0.286	0.000	0.000	0.000	0.000
64	A	144	PRO	0	0.044	0.035	42.100	0.205	0.205	0.000	0.000	0.000	0.000
65	A	145	ARG	1	0.840	0.923	41.420	-6.650	-6.650	0.000	0.000	0.000	0.000
66	A	146	LEU	0	0.018	0.012	41.701	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	147	ALA	0	0.077	0.031	36.965	0.147	0.147	0.000	0.000	0.000	0.000
68	A	148	ILE	0	-0.015	-0.022	36.581	0.272	0.272	0.000	0.000	0.000	0.000
69	A	149	LEU	0	-0.010	0.002	36.745	0.234	0.234	0.000	0.000	0.000	0.000
70	A	150	TYR	0	0.022	0.011	34.462	0.122	0.122	0.000	0.000	0.000	0.000
71	A	151	ALA	0	-0.031	-0.017	32.429	0.353	0.353	0.000	0.000	0.000	0.000
72	A	152	LYS	1	0.881	0.931	32.030	-8.036	-8.036	0.000	0.000	0.000	0.000
73	A	153	ARG	1	0.854	0.902	33.195	-8.884	-8.884	0.000	0.000	0.000	0.000
74	A	154	ALA	0	0.006	0.004	28.741	0.270	0.270	0.000	0.000	0.000	0.000
75	A	155	SER	0	-0.053	-0.017	28.256	0.423	0.423	0.000	0.000	0.000	0.000
76	A	156	VAL	0	-0.006	-0.007	28.638	0.378	0.378	0.000	0.000	0.000	0.000
77	A	157	PHE	0	0.037	0.003	27.818	0.320	0.320	0.000	0.000	0.000	0.000
78	A	158	VAL	0	-0.028	-0.009	22.843	0.448	0.448	0.000	0.000	0.000	0.000
79	A	159	LYS	1	0.929	0.970	24.008	-10.462	-10.462	0.000	0.000	0.000	0.000
80	A	160	LEU	0	-0.049	-0.015	25.589	0.244	0.244	0.000	0.000	0.000	0.000
81	A	161	GLN	0	-0.002	-0.006	19.997	0.288	0.288	0.000	0.000	0.000	0.000
82	A	162	LYS	1	0.966	0.999	23.229	-11.251	-11.251	0.000	0.000	0.000	0.000
83	A	163	PRO	0	0.021	0.009	20.032	-0.463	-0.463	0.000	0.000	0.000	0.000
84	A	164	ASN	0	-0.013	-0.014	22.355	0.045	0.045	0.000	0.000	0.000	0.000
85	A	165	ALA	0	0.016	0.012	24.736	-0.379	-0.379	0.000	0.000	0.000	0.000
86	A	166	ALA	0	0.023	0.022	25.282	-0.427	-0.427	0.000	0.000	0.000	0.000
87	A	167	ILE	0	-0.042	-0.041	22.010	-0.313	-0.313	0.000	0.000	0.000	0.000
88	A	168	ARG	1	0.939	0.985	26.590	-11.409	-11.409	0.000	0.000	0.000	0.000
89	A	169	ASP	-1	-0.746	-0.802	29.718	9.279	9.279	0.000	0.000	0.000	0.000
90	A	170	CYS	0	-0.076	-0.039	28.179	-0.167	-0.167	0.000	0.000	0.000	0.000
91	A	171	ASP	-1	-0.879	-0.955	27.896	11.096	11.096	0.000	0.000	0.000	0.000
92	A	172	ARG	1	0.931	0.982	30.568	-8.564	-8.564	0.000	0.000	0.000	0.000
93	A	173	ALA	0	-0.026	-0.021	32.983	-0.299	-0.299	0.000	0.000	0.000	0.000
94	A	174	ILE	0	-0.021	-0.019	29.079	-0.200	-0.200	0.000	0.000	0.000	0.000
95	A	175	GLU	-1	-0.974	-0.985	33.418	8.612	8.612	0.000	0.000	0.000	0.000
96	A	176	ILE	0	-0.090	-0.015	35.427	-0.279	-0.279	0.000	0.000	0.000	0.000
97	A	177	ASN	0	0.014	-0.002	36.899	-0.267	-0.267	0.000	0.000	0.000	0.000
98	A	178	PRO	0	-0.023	-0.010	33.654	0.269	0.269	0.000	0.000	0.000	0.000
99	A	179	ASP	-1	-0.845	-0.933	33.610	8.441	8.441	0.000	0.000	0.000	0.000
100	A	180	SER	0	-0.047	-0.008	35.185	0.071	0.071	0.000	0.000	0.000	0.000
101	A	181	ALA	0	0.106	0.036	31.368	0.250	0.250	0.000	0.000	0.000	0.000
102	A	182	GLN	0	-0.013	-0.015	30.224	0.541	0.541	0.000	0.000	0.000	0.000
103	A	183	PRO	0	0.015	0.001	29.503	0.433	0.433	0.000	0.000	0.000	0.000
104	A	184	TYR	0	-0.021	-0.012	26.716	0.468	0.468	0.000	0.000	0.000	0.000
105	A	185	LYS	1	0.809	0.889	25.428	-10.550	-10.550	0.000	0.000	0.000	0.000
106	A	186	TRP	0	0.015	-0.005	24.682	0.849	0.849	0.000	0.000	0.000	0.000
107	A	187	ARG	1	0.868	0.927	24.212	-11.247	-11.247	0.000	0.000	0.000	0.000
108	A	188	GLY	0	0.022	0.011	21.583	0.579	0.579	0.000	0.000	0.000	0.000
109	A	189	LYS	1	0.850	0.923	20.150	-12.769	-12.769	0.000	0.000	0.000	0.000
110	A	190	ALA	0	0.017	0.018	19.659	0.818	0.818	0.000	0.000	0.000	0.000
111	A	191	HIS	1	0.909	0.936	18.242	-14.527	-14.527	0.000	0.000	0.000	0.000
112	A	192	ARG	1	0.806	0.873	12.925	-20.718	-20.718	0.000	0.000	0.000	0.000
113	A	193	LEU	0	-0.025	-0.010	15.094	1.361	1.361	0.000	0.000	0.000	0.000
114	A	194	LEU	0	-0.002	0.004	15.621	0.860	0.860	0.000	0.000	0.000	0.000
115	A	195	GLY	0	0.036	0.032	12.484	0.975	0.975	0.000	0.000	0.000	0.000
116	A	196	HIS	0	-0.018	0.014	12.398	0.579	0.579	0.000	0.000	0.000	0.000
117	A	197	TRP	0	-0.018	-0.011	8.069	-2.768	-2.768	0.000	0.000	0.000	0.000
118	A	198	GLU	-1	-0.855	-0.964	13.185	17.711	17.711	0.000	0.000	0.000	0.000
119	A	199	GLU	-1	-0.959	-0.985	15.256	16.411	16.411	0.000	0.000	0.000	0.000
120	A	200	ALA	0	0.013	0.008	16.654	-0.908	-0.908	0.000	0.000	0.000	0.000
121	A	201	ALA	0	-0.013	-0.016	16.142	-0.672	-0.672	0.000	0.000	0.000	0.000
122	A	202	ARG	1	0.894	0.953	18.184	-14.342	-14.342	0.000	0.000	0.000	0.000
123	A	203	ASP	-1	-0.772	-0.875	21.208	12.589	12.589	0.000	0.000	0.000	0.000
124	A	204	LEU	0	0.043	0.027	19.425	-0.585	-0.585	0.000	0.000	0.000	0.000
125	A	205	ALA	0	0.030	0.013	21.972	-0.525	-0.525	0.000	0.000	0.000	0.000
126	A	206	LEU	0	-0.079	-0.025	23.797	-0.437	-0.437	0.000	0.000	0.000	0.000
127	A	207	ALA	0	0.049	0.010	26.317	-0.469	-0.469	0.000	0.000	0.000	0.000
128	A	208	CYS	0	-0.078	-0.037	25.064	-0.263	-0.263	0.000	0.000	0.000	0.000
129	A	209	LYS	1	0.924	0.953	27.835	-10.465	-10.465	0.000	0.000	0.000	0.000
130	A	210	LEU	0	-0.074	-0.021	30.242	-0.287	-0.287	0.000	0.000	0.000	0.000
131	A	211	ASP	-1	-0.954	-0.985	31.393	8.703	8.703	0.000	0.000	0.000	0.000
132	A	212	TYR	0	-0.079	-0.020	26.795	0.551	0.551	0.000	0.000	0.000	0.000
133	A	213	ASP	-1	-0.708	-0.820	28.106	10.138	10.138	0.000	0.000	0.000	0.000
134	A	214	GLU	-1	-0.873	-0.972	26.711	10.767	10.767	0.000	0.000	0.000	0.000
135	A	215	ASP	-1	-0.927	-0.952	24.658	11.992	11.992	0.000	0.000	0.000	0.000
136	A	216	ALA	0	-0.049	-0.037	23.204	0.653	0.653	0.000	0.000	0.000	0.000
137	A	217	SER	0	0.061	0.042	22.511	0.872	0.872	0.000	0.000	0.000	0.000
138	A	218	ALA	0	-0.023	-0.008	20.882	0.640	0.640	0.000	0.000	0.000	0.000
139	A	219	MET	0	0.030	0.026	17.354	0.367	0.367	0.000	0.000	0.000	0.000
140	A	220	LEU	0	0.020	0.023	17.514	1.072	1.072	0.000	0.000	0.000	0.000
141	A	221	ARG	1	0.886	0.922	17.477	-12.694	-12.694	0.000	0.000	0.000	0.000
142	A	222	GLU	-1	-0.822	-0.872	13.288	21.605	21.605	0.000	0.000	0.000	0.000
143	A	223	VAL	0	0.016	0.000	12.980	1.822	1.822	0.000	0.000	0.000	0.000
144	A	224	GLN	0	-0.002	-0.005	13.410	1.446	1.446	0.000	0.000	0.000	0.000
145	A	225	PRO	0	0.034	0.020	10.723	0.534	0.534	0.000	0.000	0.000	0.000
146	A	226	ARG	1	0.898	0.955	8.441	-25.449	-25.449	0.000	0.000	0.000	0.000
147	A	227	ALA	0	0.036	0.009	9.456	1.217	1.217	0.000	0.000	0.000	0.000
148	A	228	GLN	0	-0.025	-0.012	12.081	-0.481	-0.481	0.000	0.000	0.000	0.000
149	A	229	LYS	1	0.897	0.950	3.420	-55.510	-54.367	0.037	-0.602	-0.578	0.004
150	A	230	ILE	0	0.000	-0.005	7.608	0.823	0.823	0.000	0.000	0.000	0.000
151	A	231	ALA	0	0.089	0.060	8.550	-0.726	-0.726	0.000	0.000	0.000	0.000
152	A	232	GLU	-1	-1.005	-1.023	10.075	20.171	20.171	0.000	0.000	0.000	0.000
153	A	233	HIS	0	-0.059	-0.033	6.780	-0.119	-0.119	0.000	0.000	0.000	0.000
154	A	234	ARG	1	0.930	0.952	8.911	-20.960	-20.960	0.000	0.000	0.000	0.000
155	A	235	ARG	1	0.973	0.987	11.695	-18.453	-18.453	0.000	0.000	0.000	0.000
156	A	236	LYS	1	0.862	0.928	9.643	-24.646	-24.646	0.000	0.000	0.000	0.000
157	A	237	TYR	0	-0.010	0.016	11.160	-0.420	-0.420	0.000	0.000	0.000	0.000
158	A	238	GLU	-1	-0.763	-0.887	13.153	16.821	16.821	0.000	0.000	0.000	0.000
159	A	239	ARG	1	0.883	0.960	15.468	-16.518	-16.518	0.000	0.000	0.000	0.000
160	A	240	LYS	1	0.888	0.954	12.307	-19.785	-19.785	0.000	0.000	0.000	0.000
161	A	241	ARG	1	0.935	0.979	14.788	-17.685	-17.685	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:81:GLU)