FMO DATABASE

FMODB ID: 167JZ

Calculation Name: 4J8D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1552586.070651
FMO2-HF: Nuclear repulsion	1488090.852568
FMO2-HF: Total energy	-64495.218083
FMO2-MP2: Total energy	-64682.151706

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: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.
-17.267	-13.158	0.12	-1.801	-2.428	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 : -0.930 / q_NPA : -0.977

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	-0.803	-0.891	3.469	46.456	49.186	0.069	-1.092	-1.708	0.001
4	A	84	ASN	0	-0.047	-0.024	5.161	-9.456	-9.352	-0.001	-0.002	-0.101	0.000
5	A	85	GLU	-1	-0.880	-0.946	7.551	20.766	20.766	0.000	0.000	0.000	0.000
6	A	86	GLY	0	0.065	0.035	10.265	-0.618	-0.618	0.000	0.000	0.000	0.000
7	A	87	VAL	0	-0.117	-0.043	10.414	-1.136	-1.136	0.000	0.000	0.000	0.000
8	A	88	ILE	0	-0.021	-0.007	13.002	0.384	0.384	0.000	0.000	0.000	0.000
9	A	89	GLU	-1	-0.967	-0.980	15.531	16.627	16.627	0.000	0.000	0.000	0.000
10	A	90	ALA	0	-0.031	-0.017	17.679	-0.728	-0.728	0.000	0.000	0.000	0.000
11	A	91	ASP	-1	-0.796	-0.901	19.896	12.618	12.618	0.000	0.000	0.000	0.000
12	A	92	THR	0	-0.013	-0.012	23.452	0.032	0.032	0.000	0.000	0.000	0.000
13	A	93	ASP	-1	-0.814	-0.897	25.772	11.002	11.002	0.000	0.000	0.000	0.000
14	A	94	ALA	0	-0.021	-0.015	29.237	0.089	0.089	0.000	0.000	0.000	0.000
15	A	95	PRO	0	-0.044	-0.033	31.782	0.092	0.092	0.000	0.000	0.000	0.000
16	A	96	GLN	0	-0.012	-0.006	30.557	-0.087	-0.087	0.000	0.000	0.000	0.000
17	A	97	GLU	-1	-0.830	-0.899	34.256	7.784	7.784	0.000	0.000	0.000	0.000
18	A	98	MET	0	-0.016	0.005	32.953	0.085	0.085	0.000	0.000	0.000	0.000
19	A	99	GLY	0	0.057	0.017	38.109	-0.163	-0.163	0.000	0.000	0.000	0.000
20	A	100	ASP	-1	-0.903	-0.935	41.510	7.155	7.155	0.000	0.000	0.000	0.000
21	A	101	GLU	-1	-0.808	-0.919	39.453	7.966	7.966	0.000	0.000	0.000	0.000
22	A	102	ASN	0	-0.076	-0.033	42.947	-0.061	-0.061	0.000	0.000	0.000	0.000
23	A	103	ALA	0	0.027	0.029	46.308	-0.166	-0.166	0.000	0.000	0.000	0.000
24	A	104	GLU	-1	-0.941	-0.970	48.699	5.892	5.892	0.000	0.000	0.000	0.000
25	A	105	ILE	0	-0.029	-0.014	46.258	0.045	0.045	0.000	0.000	0.000	0.000
26	A	106	THR	0	0.013	-0.012	50.707	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	107	GLU	-1	-0.866	-0.941	52.713	5.738	5.738	0.000	0.000	0.000	0.000
28	A	108	ALA	0	0.036	0.020	53.727	0.073	0.073	0.000	0.000	0.000	0.000
29	A	109	MET	0	0.009	0.036	50.152	0.110	0.110	0.000	0.000	0.000	0.000
30	A	110	MET	0	-0.029	-0.016	48.382	0.122	0.122	0.000	0.000	0.000	0.000
31	A	111	ASP	-1	-0.921	-0.960	49.313	6.114	6.114	0.000	0.000	0.000	0.000
32	A	112	GLU	-1	-0.988	-1.001	50.078	6.349	6.349	0.000	0.000	0.000	0.000
33	A	113	ALA	0	-0.001	-0.004	45.362	0.135	0.135	0.000	0.000	0.000	0.000
34	A	114	ASN	0	-0.054	-0.026	45.242	0.367	0.367	0.000	0.000	0.000	0.000
35	A	115	GLU	-1	-0.863	-0.937	46.290	6.539	6.539	0.000	0.000	0.000	0.000
36	A	116	LYS	1	0.813	0.911	44.226	-6.890	-6.890	0.000	0.000	0.000	0.000
37	A	117	LYS	1	0.904	0.942	41.693	-7.065	-7.065	0.000	0.000	0.000	0.000
38	A	118	GLY	0	-0.037	-0.017	41.939	0.188	0.188	0.000	0.000	0.000	0.000
39	A	119	ALA	0	0.078	0.041	43.442	0.098	0.098	0.000	0.000	0.000	0.000
40	A	120	ALA	0	-0.025	-0.013	39.102	0.110	0.110	0.000	0.000	0.000	0.000
41	A	121	ILE	0	-0.095	-0.061	38.602	0.337	0.337	0.000	0.000	0.000	0.000
42	A	122	ASP	-1	-0.866	-0.926	39.448	7.381	7.381	0.000	0.000	0.000	0.000
43	A	123	ALA	0	-0.014	-0.002	39.042	0.053	0.053	0.000	0.000	0.000	0.000
44	A	124	LEU	0	-0.078	-0.039	32.745	0.271	0.271	0.000	0.000	0.000	0.000
45	A	125	ASN	0	-0.097	-0.059	35.508	0.149	0.149	0.000	0.000	0.000	0.000
46	A	126	ASP	-1	-0.868	-0.927	37.243	7.860	7.860	0.000	0.000	0.000	0.000
47	A	127	GLY	0	-0.040	-0.005	34.674	0.060	0.060	0.000	0.000	0.000	0.000
48	A	128	GLU	-1	-0.829	-0.902	34.441	8.083	8.083	0.000	0.000	0.000	0.000
49	A	129	LEU	0	-0.002	-0.025	30.026	-0.065	-0.065	0.000	0.000	0.000	0.000
50	A	130	GLN	0	-0.017	-0.025	33.475	0.319	0.319	0.000	0.000	0.000	0.000
51	A	131	LYS	1	0.856	0.922	35.183	-7.714	-7.714	0.000	0.000	0.000	0.000
52	A	132	ALA	0	0.036	0.021	35.454	-0.162	-0.162	0.000	0.000	0.000	0.000
53	A	133	ILE	0	-0.023	-0.012	31.281	-0.075	-0.075	0.000	0.000	0.000	0.000
54	A	134	ASP	-1	-0.850	-0.899	35.847	8.335	8.335	0.000	0.000	0.000	0.000
55	A	135	LEU	0	0.004	0.005	39.166	-0.201	-0.201	0.000	0.000	0.000	0.000
56	A	136	PHE	0	-0.019	-0.025	35.686	-0.102	-0.102	0.000	0.000	0.000	0.000
57	A	137	THR	0	-0.004	-0.018	37.453	0.004	0.004	0.000	0.000	0.000	0.000
58	A	138	ASP	-1	-0.844	-0.904	39.504	7.173	7.173	0.000	0.000	0.000	0.000
59	A	139	ALA	0	-0.011	0.001	41.762	-0.179	-0.179	0.000	0.000	0.000	0.000
60	A	140	ILE	0	-0.045	-0.028	36.989	-0.123	-0.123	0.000	0.000	0.000	0.000
61	A	141	LYS	1	0.857	0.912	41.457	-7.366	-7.366	0.000	0.000	0.000	0.000
62	A	142	LEU	0	-0.034	0.006	44.039	-0.137	-0.137	0.000	0.000	0.000	0.000
63	A	143	ASN	0	-0.006	-0.025	44.067	-0.257	-0.257	0.000	0.000	0.000	0.000
64	A	144	PRO	0	0.034	0.040	41.821	0.189	0.189	0.000	0.000	0.000	0.000
65	A	145	ARG	1	0.820	0.888	41.250	-6.728	-6.728	0.000	0.000	0.000	0.000
66	A	146	LEU	0	0.013	0.012	41.361	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	147	ALA	0	0.079	0.035	36.919	0.156	0.156	0.000	0.000	0.000	0.000
68	A	148	ILE	0	-0.005	-0.018	36.353	0.289	0.289	0.000	0.000	0.000	0.000
69	A	149	LEU	0	-0.009	0.004	36.530	0.238	0.238	0.000	0.000	0.000	0.000
70	A	150	TYR	0	0.025	0.017	34.200	0.150	0.150	0.000	0.000	0.000	0.000
71	A	151	ALA	0	-0.036	-0.020	32.205	0.367	0.367	0.000	0.000	0.000	0.000
72	A	152	LYS	1	0.906	0.945	31.820	-8.127	-8.127	0.000	0.000	0.000	0.000
73	A	153	ARG	1	0.815	0.869	32.996	-8.883	-8.883	0.000	0.000	0.000	0.000
74	A	154	ALA	0	0.016	0.013	28.555	0.279	0.279	0.000	0.000	0.000	0.000
75	A	155	SER	0	-0.026	-0.005	28.047	0.467	0.467	0.000	0.000	0.000	0.000
76	A	156	VAL	0	-0.035	-0.022	28.452	0.416	0.416	0.000	0.000	0.000	0.000
77	A	157	PHE	0	0.047	0.011	27.598	0.313	0.313	0.000	0.000	0.000	0.000
78	A	158	VAL	0	-0.026	-0.008	22.755	0.440	0.440	0.000	0.000	0.000	0.000
79	A	159	LYS	1	0.884	0.947	23.826	-10.384	-10.384	0.000	0.000	0.000	0.000
80	A	160	LEU	0	-0.039	-0.012	25.431	0.235	0.235	0.000	0.000	0.000	0.000
81	A	161	GLN	0	-0.012	-0.012	19.930	0.265	0.265	0.000	0.000	0.000	0.000
82	A	162	LYS	1	0.845	0.925	23.029	-11.340	-11.340	0.000	0.000	0.000	0.000
83	A	163	PRO	0	0.019	0.007	19.762	-0.471	-0.471	0.000	0.000	0.000	0.000
84	A	164	ASN	0	-0.025	-0.018	21.925	0.011	0.011	0.000	0.000	0.000	0.000
85	A	165	ALA	0	0.022	0.020	24.481	-0.388	-0.388	0.000	0.000	0.000	0.000
86	A	166	ALA	0	0.031	0.018	25.075	-0.425	-0.425	0.000	0.000	0.000	0.000
87	A	167	ILE	0	-0.024	-0.025	21.695	-0.323	-0.323	0.000	0.000	0.000	0.000
88	A	168	ARG	1	0.882	0.951	26.336	-11.599	-11.599	0.000	0.000	0.000	0.000
89	A	169	ASP	-1	-0.724	-0.817	29.458	9.254	9.254	0.000	0.000	0.000	0.000
90	A	170	CYS	0	-0.091	-0.049	28.038	-0.163	-0.163	0.000	0.000	0.000	0.000
91	A	171	ASP	-1	-0.862	-0.933	27.659	11.280	11.280	0.000	0.000	0.000	0.000
92	A	172	ARG	1	0.824	0.893	30.470	-8.620	-8.620	0.000	0.000	0.000	0.000
93	A	173	ALA	0	-0.020	-0.017	32.881	-0.299	-0.299	0.000	0.000	0.000	0.000
94	A	174	ILE	0	-0.025	-0.019	28.829	-0.211	-0.211	0.000	0.000	0.000	0.000
95	A	175	GLU	-1	-0.925	-0.943	33.305	8.643	8.643	0.000	0.000	0.000	0.000
96	A	176	ILE	0	-0.080	-0.009	35.321	-0.283	-0.283	0.000	0.000	0.000	0.000
97	A	177	ASN	0	-0.042	-0.042	36.804	-0.275	-0.275	0.000	0.000	0.000	0.000
98	A	178	PRO	0	-0.008	-0.005	33.366	0.248	0.248	0.000	0.000	0.000	0.000
99	A	179	ASP	-1	-0.851	-0.911	33.481	8.467	8.467	0.000	0.000	0.000	0.000
100	A	180	SER	0	-0.013	0.008	35.008	0.079	0.079	0.000	0.000	0.000	0.000
101	A	181	ALA	0	0.102	0.035	31.413	0.257	0.257	0.000	0.000	0.000	0.000
102	A	182	GLN	0	0.011	-0.006	30.095	0.605	0.605	0.000	0.000	0.000	0.000
103	A	183	PRO	0	0.018	0.008	29.380	0.440	0.440	0.000	0.000	0.000	0.000
104	A	184	TYR	0	-0.050	-0.035	26.598	0.506	0.506	0.000	0.000	0.000	0.000
105	A	185	LYS	1	0.752	0.866	25.303	-10.327	-10.327	0.000	0.000	0.000	0.000
106	A	186	TRP	0	0.013	-0.012	24.635	0.832	0.832	0.000	0.000	0.000	0.000
107	A	187	ARG	1	0.858	0.901	23.957	-11.358	-11.358	0.000	0.000	0.000	0.000
108	A	188	GLY	0	0.018	0.006	21.465	0.595	0.595	0.000	0.000	0.000	0.000
109	A	189	LYS	1	0.884	0.943	19.936	-12.678	-12.678	0.000	0.000	0.000	0.000
110	A	190	ALA	0	0.014	0.017	19.447	0.841	0.841	0.000	0.000	0.000	0.000
111	A	191	HIS	1	0.897	0.925	18.182	-14.719	-14.719	0.000	0.000	0.000	0.000
112	A	192	ARG	1	0.786	0.868	12.625	-21.451	-21.451	0.000	0.000	0.000	0.000
113	A	193	LEU	0	-0.041	-0.020	14.883	1.331	1.331	0.000	0.000	0.000	0.000
114	A	194	LEU	0	0.001	0.003	15.402	0.856	0.856	0.000	0.000	0.000	0.000
115	A	195	GLY	0	0.034	0.030	12.229	1.007	1.007	0.000	0.000	0.000	0.000
116	A	196	HIS	0	-0.009	0.023	12.309	0.710	0.710	0.000	0.000	0.000	0.000
117	A	197	TRP	0	0.025	-0.004	8.354	-2.731	-2.731	0.000	0.000	0.000	0.000
118	A	198	GLU	-1	-0.871	-0.963	12.930	18.223	18.223	0.000	0.000	0.000	0.000
119	A	199	GLU	-1	-0.944	-0.977	15.130	16.819	16.819	0.000	0.000	0.000	0.000
120	A	200	ALA	0	0.015	-0.001	16.513	-1.028	-1.028	0.000	0.000	0.000	0.000
121	A	201	ALA	0	-0.010	-0.014	15.985	-0.699	-0.699	0.000	0.000	0.000	0.000
122	A	202	ARG	1	0.820	0.909	18.045	-14.559	-14.559	0.000	0.000	0.000	0.000
123	A	203	ASP	-1	-0.748	-0.848	21.072	12.584	12.584	0.000	0.000	0.000	0.000
124	A	204	LEU	0	0.051	0.036	19.433	-0.582	-0.582	0.000	0.000	0.000	0.000
125	A	205	ALA	0	0.043	0.019	21.806	-0.556	-0.556	0.000	0.000	0.000	0.000
126	A	206	LEU	0	-0.071	-0.024	23.653	-0.457	-0.457	0.000	0.000	0.000	0.000
127	A	207	ALA	0	0.052	0.014	26.174	-0.485	-0.485	0.000	0.000	0.000	0.000
128	A	208	CYS	0	-0.085	-0.046	25.160	-0.264	-0.264	0.000	0.000	0.000	0.000
129	A	209	LYS	1	0.905	0.946	27.795	-10.575	-10.575	0.000	0.000	0.000	0.000
130	A	210	LEU	0	-0.063	-0.015	30.096	-0.292	-0.292	0.000	0.000	0.000	0.000
131	A	211	ASP	-1	-0.950	-0.984	31.349	8.754	8.754	0.000	0.000	0.000	0.000
132	A	212	TYR	0	-0.087	-0.044	26.959	0.472	0.472	0.000	0.000	0.000	0.000
133	A	213	ASP	-1	-0.732	-0.846	28.198	10.180	10.180	0.000	0.000	0.000	0.000
134	A	214	GLU	-1	-0.847	-0.925	26.537	11.329	11.329	0.000	0.000	0.000	0.000
135	A	215	ASP	-1	-0.832	-0.908	24.759	11.832	11.832	0.000	0.000	0.000	0.000
136	A	216	ALA	0	-0.035	-0.030	23.255	0.688	0.688	0.000	0.000	0.000	0.000
137	A	217	SER	0	0.035	0.029	22.570	0.889	0.889	0.000	0.000	0.000	0.000
138	A	218	ALA	0	-0.024	-0.007	20.963	0.649	0.649	0.000	0.000	0.000	0.000
139	A	219	MET	0	0.015	0.010	17.667	0.380	0.380	0.000	0.000	0.000	0.000
140	A	220	LEU	0	0.021	0.029	17.571	1.087	1.087	0.000	0.000	0.000	0.000
141	A	221	ARG	1	0.872	0.912	17.549	-12.573	-12.573	0.000	0.000	0.000	0.000
142	A	222	GLU	-1	-0.784	-0.835	13.076	22.482	22.482	0.000	0.000	0.000	0.000
143	A	223	VAL	0	0.016	0.011	13.051	1.903	1.903	0.000	0.000	0.000	0.000
144	A	224	GLN	0	-0.014	-0.007	13.361	1.292	1.292	0.000	0.000	0.000	0.000
145	A	225	PRO	0	0.041	0.020	10.966	0.530	0.530	0.000	0.000	0.000	0.000
146	A	226	ARG	1	0.811	0.883	7.933	-27.223	-27.223	0.000	0.000	0.000	0.000
147	A	227	ALA	0	0.032	0.010	9.310	1.182	1.182	0.000	0.000	0.000	0.000
148	A	228	GLN	0	-0.035	-0.019	11.990	-0.533	-0.533	0.000	0.000	0.000	0.000
149	A	229	LYS	1	0.888	0.937	3.596	-56.105	-54.830	0.052	-0.707	-0.619	0.004
150	A	230	ILE	0	0.000	0.001	7.511	0.725	0.725	0.000	0.000	0.000	0.000
151	A	231	ALA	0	0.102	0.064	8.426	-0.771	-0.771	0.000	0.000	0.000	0.000
152	A	232	GLU	-1	-0.953	-0.992	10.085	19.852	19.852	0.000	0.000	0.000	0.000
153	A	233	HIS	0	-0.060	-0.027	6.674	0.052	0.052	0.000	0.000	0.000	0.000
154	A	234	ARG	1	0.922	0.949	8.836	-21.178	-21.178	0.000	0.000	0.000	0.000
155	A	235	ARG	1	0.970	0.988	11.627	-18.579	-18.579	0.000	0.000	0.000	0.000
156	A	236	LYS	1	0.818	0.895	9.904	-23.798	-23.798	0.000	0.000	0.000	0.000
157	A	237	TYR	0	0.001	0.020	11.136	-0.534	-0.534	0.000	0.000	0.000	0.000
158	A	238	GLU	-1	-0.771	-0.892	13.138	16.974	16.974	0.000	0.000	0.000	0.000
159	A	239	ARG	1	0.885	0.957	15.763	-16.224	-16.224	0.000	0.000	0.000	0.000
160	A	240	LYS	1	0.886	0.953	12.443	-19.592	-19.592	0.000	0.000	0.000	0.000
161	A	241	ARG	1	0.941	0.984	14.869	-17.681	-17.681	0.000	0.000	0.000	0.000

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