FMO DATABASE

FMODB ID: GY6Q1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1557050.584343
FMO2-HF: Nuclear repulsion	1492554.494676
FMO2-HF: Total energy	-64496.089667
FMO2-MP2: Total energy	-64682.941233

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.
-33.907	-30.074	2.647	-2.796	-3.684	0.018

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 : -0.893 / q_NPA : -0.949

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	-0.770	-0.865	3.726	42.174	44.869	0.038	-1.111	-1.622	0.002
4	A	84	ASN	0	-0.036	-0.018	4.632	-10.555	-10.402	-0.001	-0.009	-0.143	0.000
5	A	85	GLU	-1	-0.857	-0.939	7.556	20.646	20.646	0.000	0.000	0.000	0.000
6	A	86	GLY	0	0.029	0.016	9.968	-0.464	-0.464	0.000	0.000	0.000	0.000
7	A	87	VAL	0	-0.099	-0.034	10.304	-1.057	-1.057	0.000	0.000	0.000	0.000
8	A	88	ILE	0	-0.034	-0.015	12.989	0.119	0.119	0.000	0.000	0.000	0.000
9	A	89	GLU	-1	-0.959	-0.978	15.759	16.281	16.281	0.000	0.000	0.000	0.000
10	A	90	ALA	0	-0.007	0.000	17.730	-0.573	-0.573	0.000	0.000	0.000	0.000
11	A	91	ASP	-1	-0.789	-0.892	19.873	12.313	12.313	0.000	0.000	0.000	0.000
12	A	92	THR	0	-0.004	-0.011	23.074	0.053	0.053	0.000	0.000	0.000	0.000
13	A	93	ASP	-1	-0.807	-0.885	25.543	11.048	11.048	0.000	0.000	0.000	0.000
14	A	94	ALA	0	-0.015	-0.007	29.066	0.094	0.094	0.000	0.000	0.000	0.000
15	A	95	PRO	0	-0.047	-0.035	31.152	0.106	0.106	0.000	0.000	0.000	0.000
16	A	96	GLN	0	-0.005	0.001	30.088	-0.095	-0.095	0.000	0.000	0.000	0.000
17	A	97	GLU	-1	-0.786	-0.878	33.943	7.892	7.892	0.000	0.000	0.000	0.000
18	A	98	MET	0	-0.052	-0.021	32.803	0.176	0.176	0.000	0.000	0.000	0.000
19	A	99	GLY	0	0.071	0.023	38.116	-0.206	-0.206	0.000	0.000	0.000	0.000
20	A	100	ASP	-1	-0.856	-0.912	41.112	7.248	7.248	0.000	0.000	0.000	0.000
21	A	101	GLU	-1	-0.774	-0.894	38.907	8.034	8.034	0.000	0.000	0.000	0.000
22	A	102	ASN	0	-0.056	-0.023	42.885	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	103	ALA	0	-0.005	0.013	46.252	-0.165	-0.165	0.000	0.000	0.000	0.000
24	A	104	GLU	-1	-0.932	-0.970	48.716	5.892	5.892	0.000	0.000	0.000	0.000
25	A	105	ILE	0	-0.027	-0.015	46.317	0.093	0.093	0.000	0.000	0.000	0.000
26	A	106	THR	0	0.004	-0.005	50.808	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	107	GLU	-1	-0.867	-0.948	52.562	5.775	5.775	0.000	0.000	0.000	0.000
28	A	108	ALA	0	0.027	0.018	53.323	0.080	0.080	0.000	0.000	0.000	0.000
29	A	109	MET	0	0.013	0.035	49.967	0.091	0.091	0.000	0.000	0.000	0.000
30	A	110	MET	0	-0.004	-0.001	47.929	0.135	0.135	0.000	0.000	0.000	0.000
31	A	111	ASP	-1	-0.928	-0.966	48.941	6.159	6.159	0.000	0.000	0.000	0.000
32	A	112	GLU	-1	-0.965	-0.989	49.716	6.415	6.415	0.000	0.000	0.000	0.000
33	A	113	ALA	0	0.009	-0.006	45.299	0.137	0.137	0.000	0.000	0.000	0.000
34	A	114	ASN	0	-0.062	-0.027	45.307	0.346	0.346	0.000	0.000	0.000	0.000
35	A	115	GLU	-1	-0.849	-0.922	45.989	6.605	6.605	0.000	0.000	0.000	0.000
36	A	116	LYS	1	0.784	0.888	44.457	-6.959	-6.959	0.000	0.000	0.000	0.000
37	A	117	LYS	1	0.891	0.929	41.693	-7.060	-7.060	0.000	0.000	0.000	0.000
38	A	118	GLY	0	-0.027	-0.007	41.789	0.178	0.178	0.000	0.000	0.000	0.000
39	A	119	ALA	0	0.068	0.034	42.936	0.137	0.137	0.000	0.000	0.000	0.000
40	A	120	ALA	0	-0.020	-0.010	39.101	0.118	0.118	0.000	0.000	0.000	0.000
41	A	121	ILE	0	-0.066	-0.045	38.487	0.324	0.324	0.000	0.000	0.000	0.000
42	A	122	ASP	-1	-0.878	-0.936	39.087	7.417	7.417	0.000	0.000	0.000	0.000
43	A	123	ALA	0	0.005	0.003	39.298	0.095	0.095	0.000	0.000	0.000	0.000
44	A	124	LEU	0	-0.076	-0.039	32.494	0.283	0.283	0.000	0.000	0.000	0.000
45	A	125	ASN	0	-0.098	-0.055	35.306	0.210	0.210	0.000	0.000	0.000	0.000
46	A	126	ASP	-1	-0.886	-0.934	37.141	7.821	7.821	0.000	0.000	0.000	0.000
47	A	127	GLY	0	-0.041	-0.013	34.431	0.071	0.071	0.000	0.000	0.000	0.000
48	A	128	GLU	-1	-0.802	-0.882	34.508	8.036	8.036	0.000	0.000	0.000	0.000
49	A	129	LEU	0	-0.024	-0.036	29.860	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	130	GLN	0	-0.046	-0.034	33.477	0.312	0.312	0.000	0.000	0.000	0.000
51	A	131	LYS	1	0.870	0.923	35.040	-7.708	-7.708	0.000	0.000	0.000	0.000
52	A	132	ALA	0	0.022	0.015	35.438	-0.164	-0.164	0.000	0.000	0.000	0.000
53	A	133	ILE	0	-0.025	-0.014	31.093	-0.056	-0.056	0.000	0.000	0.000	0.000
54	A	134	ASP	-1	-0.841	-0.894	35.588	8.425	8.425	0.000	0.000	0.000	0.000
55	A	135	LEU	0	-0.009	-0.003	38.821	-0.184	-0.184	0.000	0.000	0.000	0.000
56	A	136	PHE	0	0.013	-0.015	35.845	-0.128	-0.128	0.000	0.000	0.000	0.000
57	A	137	THR	0	-0.023	-0.018	37.291	0.059	0.059	0.000	0.000	0.000	0.000
58	A	138	ASP	-1	-0.815	-0.882	39.267	7.248	7.248	0.000	0.000	0.000	0.000
59	A	139	ALA	0	0.001	-0.004	41.514	-0.147	-0.147	0.000	0.000	0.000	0.000
60	A	140	ILE	0	-0.059	-0.029	36.818	-0.091	-0.091	0.000	0.000	0.000	0.000
61	A	141	LYS	1	0.777	0.871	41.254	-7.556	-7.556	0.000	0.000	0.000	0.000
62	A	142	LEU	0	-0.036	0.014	43.809	-0.142	-0.142	0.000	0.000	0.000	0.000
63	A	143	ASN	0	-0.001	-0.022	43.989	-0.279	-0.279	0.000	0.000	0.000	0.000
64	A	144	PRO	0	0.016	0.033	41.843	0.182	0.182	0.000	0.000	0.000	0.000
65	A	145	ARG	1	0.793	0.875	41.466	-6.783	-6.783	0.000	0.000	0.000	0.000
66	A	146	LEU	0	0.028	0.013	41.206	-0.090	-0.090	0.000	0.000	0.000	0.000
67	A	147	ALA	0	0.066	0.039	36.525	0.143	0.143	0.000	0.000	0.000	0.000
68	A	148	ILE	0	-0.018	-0.027	36.183	0.273	0.273	0.000	0.000	0.000	0.000
69	A	149	LEU	0	-0.001	0.016	36.633	0.162	0.162	0.000	0.000	0.000	0.000
70	A	150	TYR	0	0.029	0.007	34.078	0.154	0.154	0.000	0.000	0.000	0.000
71	A	151	ALA	0	-0.017	-0.010	32.044	0.343	0.343	0.000	0.000	0.000	0.000
72	A	152	LYS	1	0.892	0.955	31.691	-8.175	-8.175	0.000	0.000	0.000	0.000
73	A	153	ARG	1	0.812	0.860	32.649	-8.927	-8.927	0.000	0.000	0.000	0.000
74	A	154	ALA	0	0.021	0.013	28.512	0.300	0.300	0.000	0.000	0.000	0.000
75	A	155	SER	0	-0.021	-0.015	28.073	0.432	0.432	0.000	0.000	0.000	0.000
76	A	156	VAL	0	-0.036	-0.006	28.479	0.307	0.307	0.000	0.000	0.000	0.000
77	A	157	PHE	0	0.034	0.008	27.307	0.243	0.243	0.000	0.000	0.000	0.000
78	A	158	VAL	0	-0.039	-0.019	22.757	0.453	0.453	0.000	0.000	0.000	0.000
79	A	159	LYS	1	0.846	0.925	23.973	-10.371	-10.371	0.000	0.000	0.000	0.000
80	A	160	LEU	0	-0.014	-0.012	25.924	0.159	0.159	0.000	0.000	0.000	0.000
81	A	161	GLN	0	-0.023	-0.002	20.372	0.361	0.361	0.000	0.000	0.000	0.000
82	A	162	LYS	1	0.815	0.906	22.880	-11.308	-11.308	0.000	0.000	0.000	0.000
83	A	163	PRO	0	0.042	0.013	19.512	-0.480	-0.480	0.000	0.000	0.000	0.000
84	A	164	ASN	0	-0.021	-0.025	21.750	0.143	0.143	0.000	0.000	0.000	0.000
85	A	165	ALA	0	-0.011	-0.003	24.108	-0.429	-0.429	0.000	0.000	0.000	0.000
86	A	166	ALA	0	0.033	0.008	24.909	-0.415	-0.415	0.000	0.000	0.000	0.000
87	A	167	ILE	0	-0.020	-0.007	21.379	-0.292	-0.292	0.000	0.000	0.000	0.000
88	A	168	ARG	1	0.849	0.930	26.031	-11.834	-11.834	0.000	0.000	0.000	0.000
89	A	169	ASP	-1	-0.726	-0.825	29.209	9.337	9.337	0.000	0.000	0.000	0.000
90	A	170	CYS	0	-0.084	-0.043	27.649	-0.222	-0.222	0.000	0.000	0.000	0.000
91	A	171	ASP	-1	-0.850	-0.923	27.521	11.523	11.523	0.000	0.000	0.000	0.000
92	A	172	ARG	1	0.821	0.894	30.322	-8.696	-8.696	0.000	0.000	0.000	0.000
93	A	173	ALA	0	-0.008	-0.014	32.654	-0.293	-0.293	0.000	0.000	0.000	0.000
94	A	174	ILE	0	-0.038	-0.023	28.942	-0.203	-0.203	0.000	0.000	0.000	0.000
95	A	175	GLU	-1	-0.932	-0.944	33.216	8.732	8.732	0.000	0.000	0.000	0.000
96	A	176	ILE	0	-0.080	-0.019	35.518	-0.296	-0.296	0.000	0.000	0.000	0.000
97	A	177	ASN	0	-0.053	-0.053	36.621	-0.278	-0.278	0.000	0.000	0.000	0.000
98	A	178	PRO	0	0.013	0.012	33.565	0.253	0.253	0.000	0.000	0.000	0.000
99	A	179	ASP	-1	-0.849	-0.900	33.286	8.610	8.610	0.000	0.000	0.000	0.000
100	A	180	SER	0	-0.007	0.002	34.615	0.094	0.094	0.000	0.000	0.000	0.000
101	A	181	ALA	0	0.065	0.024	30.867	0.285	0.285	0.000	0.000	0.000	0.000
102	A	182	GLN	0	0.006	-0.006	29.583	0.615	0.615	0.000	0.000	0.000	0.000
103	A	183	PRO	0	0.026	0.007	28.955	0.410	0.410	0.000	0.000	0.000	0.000
104	A	184	TYR	0	-0.034	-0.027	26.377	0.586	0.586	0.000	0.000	0.000	0.000
105	A	185	LYS	1	0.780	0.875	24.938	-10.522	-10.522	0.000	0.000	0.000	0.000
106	A	186	TRP	0	-0.008	-0.015	24.121	0.782	0.782	0.000	0.000	0.000	0.000
107	A	187	ARG	1	0.855	0.891	23.837	-11.567	-11.567	0.000	0.000	0.000	0.000
108	A	188	GLY	0	0.000	-0.005	21.234	0.679	0.679	0.000	0.000	0.000	0.000
109	A	189	LYS	1	0.820	0.902	19.663	-12.432	-12.432	0.000	0.000	0.000	0.000
110	A	190	ALA	0	0.019	0.022	19.520	0.728	0.728	0.000	0.000	0.000	0.000
111	A	191	HIS	1	0.906	0.923	18.165	-14.889	-14.889	0.000	0.000	0.000	0.000
112	A	192	ARG	1	0.755	0.833	12.095	-21.590	-21.590	0.000	0.000	0.000	0.000
113	A	193	LEU	0	-0.011	0.004	14.698	1.430	1.430	0.000	0.000	0.000	0.000
114	A	194	LEU	0	0.003	0.013	15.551	0.579	0.579	0.000	0.000	0.000	0.000
115	A	195	GLY	0	0.026	0.020	11.711	0.945	0.945	0.000	0.000	0.000	0.000
116	A	196	HIS	0	-0.026	0.021	12.145	0.465	0.465	0.000	0.000	0.000	0.000
117	A	197	TRP	0	0.043	0.001	8.749	-2.382	-2.382	0.000	0.000	0.000	0.000
118	A	198	GLU	-1	-0.895	-0.962	12.805	19.154	19.154	0.000	0.000	0.000	0.000
119	A	199	GLU	-1	-0.932	-0.979	15.180	16.759	16.759	0.000	0.000	0.000	0.000
120	A	200	ALA	0	0.030	0.014	16.459	-0.970	-0.970	0.000	0.000	0.000	0.000
121	A	201	ALA	0	-0.010	-0.006	16.065	-0.711	-0.711	0.000	0.000	0.000	0.000
122	A	202	ARG	1	0.821	0.897	18.117	-14.770	-14.770	0.000	0.000	0.000	0.000
123	A	203	ASP	-1	-0.750	-0.831	21.040	12.579	12.579	0.000	0.000	0.000	0.000
124	A	204	LEU	0	0.040	0.018	18.897	-0.606	-0.606	0.000	0.000	0.000	0.000
125	A	205	ALA	0	0.004	0.004	21.895	-0.506	-0.506	0.000	0.000	0.000	0.000
126	A	206	LEU	0	-0.047	-0.017	23.689	-0.487	-0.487	0.000	0.000	0.000	0.000
127	A	207	ALA	0	0.036	0.013	25.971	-0.475	-0.475	0.000	0.000	0.000	0.000
128	A	208	CYS	0	-0.065	-0.034	24.728	-0.361	-0.361	0.000	0.000	0.000	0.000
129	A	209	LYS	1	0.889	0.943	27.396	-10.563	-10.563	0.000	0.000	0.000	0.000
130	A	210	LEU	0	-0.055	-0.009	29.756	-0.307	-0.307	0.000	0.000	0.000	0.000
131	A	211	ASP	-1	-0.916	-0.966	31.194	8.889	8.889	0.000	0.000	0.000	0.000
132	A	212	TYR	0	-0.105	-0.044	26.837	0.536	0.536	0.000	0.000	0.000	0.000
133	A	213	ASP	-1	-0.749	-0.864	28.027	10.545	10.545	0.000	0.000	0.000	0.000
134	A	214	GLU	-1	-0.772	-0.857	25.921	12.064	12.064	0.000	0.000	0.000	0.000
135	A	215	ASP	-1	-0.770	-0.876	24.007	12.429	12.429	0.000	0.000	0.000	0.000
136	A	216	ALA	0	0.015	0.001	22.911	0.627	0.627	0.000	0.000	0.000	0.000
137	A	217	SER	0	0.055	0.012	22.002	0.925	0.925	0.000	0.000	0.000	0.000
138	A	218	ALA	0	-0.049	-0.016	20.933	0.568	0.568	0.000	0.000	0.000	0.000
139	A	219	MET	0	0.017	0.007	17.342	0.413	0.413	0.000	0.000	0.000	0.000
140	A	220	LEU	0	0.003	0.018	17.237	1.031	1.031	0.000	0.000	0.000	0.000
141	A	221	ARG	1	0.798	0.859	17.239	-12.483	-12.483	0.000	0.000	0.000	0.000
142	A	222	GLU	-1	-0.789	-0.840	12.857	22.478	22.478	0.000	0.000	0.000	0.000
143	A	223	VAL	0	0.024	0.022	12.708	1.974	1.974	0.000	0.000	0.000	0.000
144	A	224	GLN	0	-0.027	-0.017	12.928	1.192	1.192	0.000	0.000	0.000	0.000
145	A	225	PRO	0	0.022	0.008	10.377	0.619	0.619	0.000	0.000	0.000	0.000
146	A	226	ARG	1	0.786	0.871	7.673	-27.118	-27.118	0.000	0.000	0.000	0.000
147	A	227	ALA	0	0.026	0.014	9.111	1.036	1.036	0.000	0.000	0.000	0.000
148	A	228	GLN	0	-0.009	-0.007	11.502	-0.552	-0.552	0.000	0.000	0.000	0.000
149	A	229	LYS	1	0.872	0.924	2.450	-68.124	-67.139	2.610	-1.676	-1.919	0.016
150	A	230	ILE	0	0.019	0.014	7.069	1.585	1.585	0.000	0.000	0.000	0.000
151	A	231	ALA	0	0.084	0.047	8.208	-1.115	-1.115	0.000	0.000	0.000	0.000
152	A	232	GLU	-1	-0.872	-0.926	9.005	19.145	19.145	0.000	0.000	0.000	0.000
153	A	233	HIS	0	-0.018	-0.001	6.327	-0.011	-0.011	0.000	0.000	0.000	0.000
154	A	234	ARG	1	0.948	0.965	8.401	-21.997	-21.997	0.000	0.000	0.000	0.000
155	A	235	ARG	1	0.878	0.923	11.665	-19.016	-19.016	0.000	0.000	0.000	0.000
156	A	236	LYS	1	0.798	0.887	9.679	-24.048	-24.048	0.000	0.000	0.000	0.000
157	A	237	TYR	0	-0.020	0.008	10.670	-0.460	-0.460	0.000	0.000	0.000	0.000
158	A	238	GLU	-1	-0.768	-0.900	12.640	17.327	17.327	0.000	0.000	0.000	0.000
159	A	239	ARG	1	0.879	0.955	15.149	-16.566	-16.566	0.000	0.000	0.000	0.000
160	A	240	LYS	1	0.894	0.957	12.523	-19.437	-19.437	0.000	0.000	0.000	0.000
161	A	241	ARG	1	0.920	0.971	15.096	-17.301	-17.301	0.000	0.000	0.000	0.000

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