FMO DATABASE

FMODB ID: J3VK9

Calculation Name: 3G8L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G8L

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JIP9

Base Structure: X-ray

Registration Date: 2023-03-14

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	OptH
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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1632406.765113
FMO2-HF: Nuclear repulsion	1566253.511922
FMO2-HF: Total energy	-66153.25319
FMO2-MP2: Total energy	-66341.809047

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:109:PRO)

Summations of interaction energy for fragment #1(A:109: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.
27.552	6.727	28.628	0.278	-8.081	-0.052

Interaction energy analysis for fragmet #1(A:109:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.190 / q_NPA : -0.007

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	111	ASN	0	-0.054	-0.039	3.458	-0.757	0.722	0.004	-0.577	-0.906	0.004
4	A	112	ASP	-1	-0.706	-0.725	2.197	26.966	4.538	28.625	0.859	-7.056	-0.056
5	A	113	LEU	0	-0.039	0.002	5.348	-0.714	-0.590	-0.001	-0.004	-0.119	0.000
6	A	114	LEU	0	0.002	-0.007	7.117	0.063	0.063	0.000	0.000	0.000	0.000
7	A	115	GLU	-1	-0.921	-0.960	6.984	2.105	2.105	0.000	0.000	0.000	0.000
8	A	116	SER	0	-0.043	-0.026	8.880	-0.083	-0.083	0.000	0.000	0.000	0.000
9	A	117	LEU	0	0.007	-0.023	9.450	-0.083	-0.083	0.000	0.000	0.000	0.000
10	A	118	HIS	0	-0.032	-0.012	12.377	0.019	0.019	0.000	0.000	0.000	0.000
11	A	119	LYS	1	0.971	0.984	14.042	-0.412	-0.412	0.000	0.000	0.000	0.000
12	A	120	GLU	-1	-0.914	-0.948	14.159	0.203	0.203	0.000	0.000	0.000	0.000
13	A	121	GLN	0	0.010	0.026	16.708	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	122	ASN	0	-0.053	-0.038	18.586	0.008	0.008	0.000	0.000	0.000	0.000
15	A	123	ARG	1	0.891	0.958	16.345	-0.269	-0.269	0.000	0.000	0.000	0.000
16	A	124	TRP	0	0.084	0.030	16.081	-0.036	-0.036	0.000	0.000	0.000	0.000
17	A	125	TYR	0	-0.041	0.016	22.413	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	126	SER	0	-0.060	-0.030	24.688	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	127	GLU	-1	-0.914	-0.957	23.006	0.105	0.105	0.000	0.000	0.000	0.000
20	A	128	THR	0	-0.030	-0.054	25.709	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	129	LYS	1	0.846	0.933	28.164	-0.041	-0.041	0.000	0.000	0.000	0.000
22	A	130	THR	0	-0.039	-0.026	30.188	0.003	0.003	0.000	0.000	0.000	0.000
23	A	131	PHE	0	-0.009	0.033	33.603	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	132	SER	0	-0.057	-0.048	36.829	0.001	0.001	0.000	0.000	0.000	0.000
25	A	133	ASP	-1	-0.789	-0.901	38.690	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	134	SER	0	-0.028	0.007	39.458	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	135	SER	0	0.042	0.026	41.264	0.000	0.000	0.000	0.000	0.000	0.000
28	A	136	GLN	0	-0.077	-0.076	43.056	0.000	0.000	0.000	0.000	0.000	0.000
29	A	137	HIS	0	-0.048	-0.021	43.343	0.000	0.000	0.000	0.000	0.000	0.000
30	A	138	THR	0	0.096	0.014	45.521	0.002	0.002	0.000	0.000	0.000	0.000
31	A	139	GLY	0	-0.006	0.038	45.129	0.000	0.000	0.000	0.000	0.000	0.000
32	A	140	ARG	1	0.790	0.896	40.941	0.011	0.011	0.000	0.000	0.000	0.000
33	A	141	GLY	0	0.040	0.019	41.257	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	142	PHE	0	-0.113	-0.063	34.620	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	143	GLU	-1	-0.756	-0.890	32.793	0.024	0.024	0.000	0.000	0.000	0.000
36	A	144	LYS	1	0.851	0.905	31.364	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	145	TYR	0	-0.001	-0.015	22.508	0.004	0.004	0.000	0.000	0.000	0.000
38	A	146	TRP	0	0.006	0.012	25.012	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	147	PHE	0	0.040	0.021	19.305	0.009	0.009	0.000	0.000	0.000	0.000
40	A	148	CYS	0	-0.067	-0.016	21.372	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	149	TYR	0	0.064	0.008	12.246	0.016	0.016	0.000	0.000	0.000	0.000
42	A	150	GLY	0	-0.010	0.013	17.990	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	151	ILE	0	0.058	0.032	18.614	0.019	0.019	0.000	0.000	0.000	0.000
44	A	152	LYS	1	0.773	0.877	21.441	0.162	0.162	0.000	0.000	0.000	0.000
45	A	154	TYR	0	-0.047	-0.025	20.423	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	155	TYR	0	0.049	0.022	25.196	0.011	0.011	0.000	0.000	0.000	0.000
47	A	156	PHE	0	0.032	0.000	23.048	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	157	VAL	0	-0.004	0.003	28.942	0.010	0.010	0.000	0.000	0.000	0.000
49	A	158	MET	0	-0.017	-0.026	29.429	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	159	ASP	-1	-0.888	-0.889	32.742	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	160	ARG	1	0.952	0.961	34.211	0.010	0.010	0.000	0.000	0.000	0.000
52	A	161	LYS	1	0.976	1.029	35.900	0.029	0.029	0.000	0.000	0.000	0.000
53	A	162	THR	0	0.039	0.025	36.762	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	163	TRP	0	0.027	0.037	33.694	0.003	0.003	0.000	0.000	0.000	0.000
55	A	164	SER	0	0.041	-0.030	37.174	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	165	GLY	0	0.021	-0.007	39.661	0.001	0.001	0.000	0.000	0.000	0.000
57	A	166	CYS	0	-0.021	0.000	31.036	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	167	LYS	1	0.921	0.984	36.101	0.057	0.057	0.000	0.000	0.000	0.000
59	A	168	GLN	0	0.073	0.005	37.084	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	169	THR	0	0.029	0.012	35.773	0.003	0.003	0.000	0.000	0.000	0.000
61	A	170	CYS	0	-0.080	0.010	28.710	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	171	GLN	0	0.001	-0.004	35.462	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	172	ILE	0	0.021	0.011	38.224	0.001	0.001	0.000	0.000	0.000	0.000
64	A	173	SER	0	-0.045	-0.017	35.369	0.004	0.004	0.000	0.000	0.000	0.000
65	A	174	SER	0	-0.056	-0.017	36.031	0.000	0.000	0.000	0.000	0.000	0.000
66	A	175	LEU	0	-0.061	-0.028	31.019	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	176	SER	0	-0.029	-0.031	32.346	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	177	LEU	0	0.032	0.008	30.813	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	178	LEU	0	-0.046	-0.035	23.656	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	179	LYS	1	0.902	0.955	26.968	0.092	0.092	0.000	0.000	0.000	0.000
71	A	180	ILE	0	-0.005	-0.017	21.956	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	181	ASP	-1	-0.773	-0.898	22.463	-0.152	-0.152	0.000	0.000	0.000	0.000
73	A	182	ASN	0	-0.046	0.017	18.727	-0.020	-0.020	0.000	0.000	0.000	0.000
74	A	183	GLU	-1	-0.851	-0.960	16.590	-0.424	-0.424	0.000	0.000	0.000	0.000
75	A	184	ASP	-1	-0.860	-0.907	14.595	-0.488	-0.488	0.000	0.000	0.000	0.000
76	A	185	GLU	-1	-0.763	-0.883	15.735	-0.176	-0.176	0.000	0.000	0.000	0.000
77	A	186	LEU	0	-0.064	-0.020	17.993	0.006	0.006	0.000	0.000	0.000	0.000
78	A	187	LYS	1	0.926	0.935	13.669	0.449	0.449	0.000	0.000	0.000	0.000
79	A	188	PHE	0	0.013	0.010	9.581	0.005	0.005	0.000	0.000	0.000	0.000
80	A	189	LEU	0	-0.002	-0.008	14.887	0.037	0.037	0.000	0.000	0.000	0.000
81	A	190	LYS	1	0.904	0.971	17.186	0.297	0.297	0.000	0.000	0.000	0.000
82	A	191	LEU	0	0.006	-0.021	12.431	0.034	0.034	0.000	0.000	0.000	0.000
83	A	192	LEU	0	0.013	0.024	14.441	0.046	0.046	0.000	0.000	0.000	0.000
84	A	193	VAL	0	-0.021	0.011	16.790	0.031	0.031	0.000	0.000	0.000	0.000
85	A	194	PRO	0	0.034	0.005	20.199	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	195	SER	0	-0.021	-0.007	22.220	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	196	ASP	-1	-0.869	-0.929	23.485	-0.031	-0.031	0.000	0.000	0.000	0.000
88	A	197	SER	0	-0.074	-0.028	26.359	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	198	TYR	0	0.019	-0.021	24.278	0.011	0.011	0.000	0.000	0.000	0.000
90	A	199	TRP	0	0.003	0.024	28.844	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	200	ILE	0	0.002	-0.005	26.454	0.000	0.000	0.000	0.000	0.000	0.000
92	A	201	GLY	0	-0.007	-0.013	29.958	0.004	0.004	0.000	0.000	0.000	0.000
93	A	202	LEU	0	-0.018	0.012	29.702	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	203	SER	0	0.015	-0.032	32.000	0.002	0.002	0.000	0.000	0.000	0.000
95	A	204	TYR	0	0.031	0.038	35.523	0.000	0.000	0.000	0.000	0.000	0.000
96	A	205	ASP	-1	-0.788	-0.879	38.670	-0.051	-0.051	0.000	0.000	0.000	0.000
97	A	206	ASN	0	-0.035	-0.041	41.710	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	207	LYS	1	0.908	0.959	44.764	0.063	0.063	0.000	0.000	0.000	0.000
99	A	208	LYS	1	0.860	0.908	40.701	0.062	0.062	0.000	0.000	0.000	0.000
100	A	209	LYS	1	0.961	0.995	42.149	0.060	0.060	0.000	0.000	0.000	0.000
101	A	210	ASP	-1	-0.823	-0.926	36.879	-0.101	-0.101	0.000	0.000	0.000	0.000
102	A	211	TRP	0	-0.063	0.003	33.911	0.004	0.004	0.000	0.000	0.000	0.000
103	A	212	ALA	0	0.006	0.015	34.768	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	213	TRP	0	0.040	0.021	26.939	0.002	0.002	0.000	0.000	0.000	0.000
105	A	214	ILE	0	-0.047	-0.059	32.920	0.003	0.003	0.000	0.000	0.000	0.000
106	A	215	ASN	0	-0.071	-0.036	34.586	0.006	0.006	0.000	0.000	0.000	0.000
107	A	216	ASN	0	0.057	0.055	35.893	0.001	0.001	0.000	0.000	0.000	0.000
108	A	217	GLY	0	-0.040	-0.007	32.792	0.001	0.001	0.000	0.000	0.000	0.000
109	A	218	PRO	0	-0.022	-0.022	30.128	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	219	SER	0	0.002	0.011	25.618	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	220	LYS	1	0.931	0.956	22.804	0.211	0.211	0.000	0.000	0.000	0.000
112	A	221	LEU	0	-0.019	-0.019	22.027	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	222	ALA	0	0.018	0.032	23.904	0.012	0.012	0.000	0.000	0.000	0.000
114	A	223	LEU	0	0.013	0.020	25.307	0.016	0.016	0.000	0.000	0.000	0.000
115	A	224	ASN	0	0.020	-0.008	27.154	0.003	0.003	0.000	0.000	0.000	0.000
116	A	225	THR	0	0.055	0.014	30.021	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	226	MET	0	0.021	0.027	33.158	0.001	0.001	0.000	0.000	0.000	0.000
118	A	227	LYS	1	0.889	0.954	25.473	0.174	0.174	0.000	0.000	0.000	0.000
119	A	228	TYR	0	-0.054	-0.048	27.684	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	229	ASN	0	-0.032	-0.006	34.070	0.004	0.004	0.000	0.000	0.000	0.000
121	A	230	ILE	0	0.105	0.030	37.437	0.001	0.001	0.000	0.000	0.000	0.000
122	A	231	ARG	1	0.819	0.925	39.296	0.067	0.067	0.000	0.000	0.000	0.000
123	A	232	ASP	-1	-0.893	-0.920	36.556	-0.074	-0.074	0.000	0.000	0.000	0.000
124	A	233	GLY	0	0.046	-0.008	37.315	0.002	0.002	0.000	0.000	0.000	0.000
125	A	234	GLY	0	-0.010	0.004	38.096	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	235	CYS	0	-0.147	-0.063	35.150	0.001	0.001	0.000	0.000	0.000	0.000
127	A	236	MET	0	0.009	-0.003	28.395	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	237	LEU	0	0.023	0.042	29.110	0.003	0.003	0.000	0.000	0.000	0.000
129	A	238	LEU	0	-0.043	-0.047	22.618	-0.014	-0.014	0.000	0.000	0.000	0.000
130	A	239	SER	0	0.036	0.034	24.266	0.009	0.009	0.000	0.000	0.000	0.000
131	A	240	LYS	1	0.837	0.922	17.393	0.114	0.114	0.000	0.000	0.000	0.000
132	A	241	THR	0	-0.042	-0.013	19.327	-0.033	-0.033	0.000	0.000	0.000	0.000
133	A	242	ARG	1	0.871	0.920	21.286	0.108	0.108	0.000	0.000	0.000	0.000
134	A	243	LEU	0	0.001	0.005	22.944	0.011	0.011	0.000	0.000	0.000	0.000
135	A	244	ASP	-1	-0.897	-0.960	25.882	-0.115	-0.115	0.000	0.000	0.000	0.000
136	A	245	ASN	0	-0.010	-0.006	29.435	0.006	0.006	0.000	0.000	0.000	0.000
137	A	246	ASP	-1	-0.653	-0.838	33.073	-0.058	-0.058	0.000	0.000	0.000	0.000
138	A	247	ASN	0	0.025	0.054	35.731	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	249	ASP	-1	-0.970	-1.047	38.945	-0.039	-0.039	0.000	0.000	0.000	0.000
140	A	250	LYS	1	0.987	1.037	36.234	0.048	0.048	0.000	0.000	0.000	0.000
141	A	251	SER	0	-0.070	-0.101	37.408	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	252	PHE	0	-0.026	-0.018	31.993	0.002	0.002	0.000	0.000	0.000	0.000
143	A	253	ILE	0	0.073	0.055	28.586	0.000	0.000	0.000	0.000	0.000	0.000
144	A	255	ILE	0	-0.029	0.000	24.716	0.004	0.004	0.000	0.000	0.000	0.000
145	A	257	GLY	0	0.087	0.013	27.141	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	258	LYS	1	0.951	0.984	27.176	0.052	0.052	0.000	0.000	0.000	0.000
147	A	259	ARG	1	0.928	0.959	26.286	0.104	0.104	0.000	0.000	0.000	0.000
148	A	260	LEU	0	-0.015	-0.018	24.139	0.008	0.008	0.000	0.000	0.000	0.000
149	A	261	ASP	-1	-0.916	-0.979	27.539	-0.064	-0.064	0.000	0.000	0.000	0.000
150	A	262	LYS	1	0.913	0.987	29.376	0.048	0.048	0.000	0.000	0.000	0.000
151	A	263	PHE	0	-0.025	0.019	23.568	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	264	PRO	0	0.030	-0.012	26.240	0.003	0.003	0.000	0.000	0.000	0.000
153	A	265	HIS	0	0.029	0.020	28.971	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:109:PRO)