FMO DATABASE

FMODB ID: 767GK

Calculation Name: 3F8X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F8X

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D504

Base Structure: X-ray

Registration Date: 2023-09-23

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1115614.033407
FMO2-HF: Nuclear repulsion	1065116.306053
FMO2-HF: Total energy	-50497.727354
FMO2-MP2: Total energy	-50645.469768

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:16:SER)

Summations of interaction energy for fragment #1(A:16:SER)

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.
-24.918	-21.424	4.544	-3.19	-4.85	0.02

Interaction energy analysis for fragmet #1(A:16:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / 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	18	ASN	0	0.025	0.030	3.719	-0.488	0.776	-0.008	-0.540	-0.717	0.001
4	A	19	ALA	0	0.078	0.021	6.218	-0.457	-0.457	0.000	0.000	0.000	0.000
5	A	20	ALA	0	0.019	0.017	8.569	-0.088	-0.088	0.000	0.000	0.000	0.000
6	A	21	VAL	0	0.037	0.019	7.430	-0.056	-0.056	0.000	0.000	0.000	0.000
7	A	22	GLN	0	-0.071	-0.032	5.341	0.101	0.101	0.000	0.000	0.000	0.000
8	A	23	SER	0	-0.020	-0.016	8.531	0.197	0.197	0.000	0.000	0.000	0.000
9	A	24	GLY	0	0.041	0.031	11.935	0.103	0.103	0.000	0.000	0.000	0.000
10	A	25	LEU	0	-0.037	-0.018	8.883	0.076	0.076	0.000	0.000	0.000	0.000
11	A	26	GLN	0	-0.044	-0.026	12.006	0.155	0.155	0.000	0.000	0.000	0.000
12	A	27	GLU	-1	-0.793	-0.888	14.169	-0.310	-0.310	0.000	0.000	0.000	0.000
13	A	28	TRP	0	0.006	-0.009	14.726	0.057	0.057	0.000	0.000	0.000	0.000
14	A	29	HIS	0	-0.022	-0.024	12.892	0.130	0.130	0.000	0.000	0.000	0.000
15	A	30	ARG	1	0.672	0.829	17.145	0.376	0.376	0.000	0.000	0.000	0.000
16	A	31	ILE	0	-0.002	0.004	19.883	0.039	0.039	0.000	0.000	0.000	0.000
17	A	32	ILE	0	-0.039	-0.008	19.277	0.039	0.039	0.000	0.000	0.000	0.000
18	A	33	ALA	0	-0.068	-0.036	21.157	0.033	0.033	0.000	0.000	0.000	0.000
19	A	34	GLU	-1	-0.917	-0.962	22.874	-0.238	-0.238	0.000	0.000	0.000	0.000
20	A	35	ALA	0	-0.039	-0.005	24.837	0.025	0.025	0.000	0.000	0.000	0.000
21	A	36	ASP	-1	-0.823	-0.900	24.622	-0.234	-0.234	0.000	0.000	0.000	0.000
22	A	37	TRP	0	0.045	-0.004	23.056	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.899	-0.955	26.449	-0.222	-0.222	0.000	0.000	0.000	0.000
24	A	39	ARG	1	0.909	0.955	23.556	0.229	0.229	0.000	0.000	0.000	0.000
25	A	40	LEU	0	0.004	0.013	20.301	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	41	PRO	0	0.048	0.001	22.026	-0.025	-0.025	0.000	0.000	0.000	0.000
27	A	42	ASP	-1	-0.898	-0.928	22.569	-0.235	-0.235	0.000	0.000	0.000	0.000
28	A	43	LEU	0	-0.063	-0.016	15.615	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	44	LEU	0	-0.012	0.005	17.993	-0.060	-0.060	0.000	0.000	0.000	0.000
30	A	45	ALA	0	0.003	0.000	18.466	0.044	0.044	0.000	0.000	0.000	0.000
31	A	46	GLU	-1	-0.977	-1.016	20.394	-0.201	-0.201	0.000	0.000	0.000	0.000
32	A	47	ASP	-1	-0.970	-0.988	21.019	-0.271	-0.271	0.000	0.000	0.000	0.000
33	A	48	VAL	0	-0.027	0.010	19.142	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	49	VAL	0	0.035	0.023	19.823	0.042	0.042	0.000	0.000	0.000	0.000
35	A	50	PHE	0	-0.003	-0.017	20.176	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	51	SER	0	0.006	0.007	21.277	0.048	0.048	0.000	0.000	0.000	0.000
37	A	52	ASN	0	0.042	0.030	22.421	-0.030	-0.030	0.000	0.000	0.000	0.000
38	A	53	PRO	0	0.032	-0.007	24.462	0.008	0.008	0.000	0.000	0.000	0.000
39	A	54	SER	0	-0.070	-0.025	26.185	0.017	0.017	0.000	0.000	0.000	0.000
40	A	55	THR	0	-0.036	-0.025	28.845	0.022	0.022	0.000	0.000	0.000	0.000
41	A	56	PHE	0	-0.034	-0.004	25.626	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	57	ASP	-1	-0.915	-0.960	26.546	-0.217	-0.217	0.000	0.000	0.000	0.000
43	A	58	PRO	0	-0.041	-0.016	23.577	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	59	TYR	0	-0.038	-0.019	25.559	0.029	0.029	0.000	0.000	0.000	0.000
45	A	60	HIS	0	0.017	-0.002	24.201	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	61	GLY	0	0.020	0.024	24.653	0.024	0.024	0.000	0.000	0.000	0.000
47	A	62	LYS	1	0.886	0.925	23.437	0.254	0.254	0.000	0.000	0.000	0.000
48	A	63	GLY	0	-0.008	0.005	25.976	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	64	PRO	0	0.027	0.001	27.901	0.001	0.001	0.000	0.000	0.000	0.000
50	A	65	LEU	0	0.032	0.031	21.169	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	66	MET	0	-0.012	-0.011	25.778	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	67	VAL	0	-0.030	0.004	27.635	0.010	0.010	0.000	0.000	0.000	0.000
53	A	68	ILE	0	-0.026	-0.023	27.336	0.002	0.002	0.000	0.000	0.000	0.000
54	A	69	LEU	0	-0.001	0.007	21.609	0.001	0.001	0.000	0.000	0.000	0.000
55	A	70	PRO	0	0.059	0.026	26.091	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	71	ALA	0	0.012	0.022	28.192	0.010	0.010	0.000	0.000	0.000	0.000
57	A	72	VAL	0	-0.011	0.010	26.188	0.010	0.010	0.000	0.000	0.000	0.000
58	A	73	PHE	0	0.028	-0.009	21.376	0.007	0.007	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.098	-0.049	27.525	0.014	0.014	0.000	0.000	0.000	0.000
60	A	75	VAL	0	-0.042	-0.033	30.775	0.016	0.016	0.000	0.000	0.000	0.000
61	A	76	LEU	0	-0.055	-0.011	25.480	0.004	0.004	0.000	0.000	0.000	0.000
62	A	77	GLU	-1	-0.855	-0.919	29.346	-0.192	-0.192	0.000	0.000	0.000	0.000
63	A	78	ASN	0	-0.100	-0.080	28.331	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	79	PHE	0	0.030	0.025	20.141	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	80	GLN	0	-0.025	-0.013	22.167	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	81	TYR	0	0.010	-0.013	16.668	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	82	ALA	0	-0.042	-0.024	17.740	0.041	0.041	0.000	0.000	0.000	0.000
68	A	83	ARG	1	0.757	0.865	14.920	0.446	0.446	0.000	0.000	0.000	0.000
69	A	84	HIS	0	0.008	0.005	10.152	-0.165	-0.165	0.000	0.000	0.000	0.000
70	A	85	PHE	0	-0.038	-0.012	8.813	0.021	0.021	0.000	0.000	0.000	0.000
71	A	86	SER	0	-0.006	-0.005	4.288	-0.661	-0.535	-0.001	-0.025	-0.100	0.000
72	A	87	SER	0	0.042	0.029	4.605	-0.038	0.081	-0.001	-0.016	-0.102	0.000
73	A	88	LYS	1	0.795	0.873	2.311	-19.825	-17.728	4.547	-2.767	-3.878	0.019
74	A	89	SER	0	-0.002	-0.026	3.298	0.046	-0.066	0.007	0.158	-0.053	0.000
75	A	90	GLY	0	0.098	0.064	6.369	0.457	0.457	0.000	0.000	0.000	0.000
76	A	91	TYR	0	-0.048	-0.031	5.741	-1.236	-1.236	0.000	0.000	0.000	0.000
77	A	92	VAL	0	0.011	0.014	8.965	0.294	0.294	0.000	0.000	0.000	0.000
78	A	93	LEU	0	-0.009	-0.006	11.256	-0.101	-0.101	0.000	0.000	0.000	0.000
79	A	94	GLU	-1	-0.760	-0.871	14.037	-0.442	-0.442	0.000	0.000	0.000	0.000
80	A	95	PHE	0	0.006	0.014	17.098	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	96	ASN	0	-0.044	-0.031	20.164	0.029	0.029	0.000	0.000	0.000	0.000
82	A	97	ALA	0	0.039	0.017	23.764	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	98	ASN	0	-0.020	-0.007	26.741	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	99	MET	0	0.051	0.038	30.405	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	100	GLY	0	0.018	0.008	33.139	0.009	0.009	0.000	0.000	0.000	0.000
86	A	101	ASP	-1	-0.977	-0.980	34.952	-0.165	-0.165	0.000	0.000	0.000	0.000
87	A	102	GLH	0	-0.077	-0.046	34.101	0.002	0.002	0.000	0.000	0.000	0.000
88	A	103	LEU	0	-0.030	-0.026	29.945	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	104	LEU	0	-0.022	-0.010	25.587	0.004	0.004	0.000	0.000	0.000	0.000
90	A	105	THR	0	-0.011	-0.004	22.858	0.005	0.005	0.000	0.000	0.000	0.000
91	A	106	GLY	0	0.026	0.003	21.778	0.028	0.028	0.000	0.000	0.000	0.000
92	A	107	VAL	0	-0.061	-0.024	16.510	-0.038	-0.038	0.000	0.000	0.000	0.000
93	A	108	ASP	-1	-0.752	-0.867	16.147	-0.545	-0.545	0.000	0.000	0.000	0.000
94	A	109	LEU	0	-0.053	-0.027	13.150	-0.119	-0.119	0.000	0.000	0.000	0.000
95	A	110	ILE	0	0.012	-0.006	12.110	0.109	0.109	0.000	0.000	0.000	0.000
96	A	111	GLU	-1	-0.853	-0.909	9.982	-1.729	-1.729	0.000	0.000	0.000	0.000
97	A	112	PHE	0	0.006	-0.008	9.959	0.141	0.141	0.000	0.000	0.000	0.000
98	A	113	ASN	0	0.057	0.033	10.956	-0.048	-0.048	0.000	0.000	0.000	0.000
99	A	114	ASP	-1	-0.900	-0.971	10.713	-0.252	-0.252	0.000	0.000	0.000	0.000
100	A	115	ALA	0	-0.094	-0.044	12.495	0.044	0.044	0.000	0.000	0.000	0.000
101	A	116	GLY	0	-0.023	-0.013	12.380	0.013	0.013	0.000	0.000	0.000	0.000
102	A	117	LYS	1	0.814	0.903	13.409	0.372	0.372	0.000	0.000	0.000	0.000
103	A	118	ILE	0	0.007	0.008	14.675	-0.055	-0.055	0.000	0.000	0.000	0.000
104	A	119	THR	0	-0.021	-0.047	14.719	0.071	0.071	0.000	0.000	0.000	0.000
105	A	120	ASP	-1	-0.856	-0.895	15.174	-0.514	-0.514	0.000	0.000	0.000	0.000
106	A	121	LEU	0	0.002	0.005	15.703	-0.097	-0.097	0.000	0.000	0.000	0.000
107	A	122	VAL	0	-0.013	-0.009	17.292	0.078	0.078	0.000	0.000	0.000	0.000
108	A	123	VAL	0	0.023	0.021	18.311	-0.050	-0.050	0.000	0.000	0.000	0.000
109	A	124	MET	0	-0.049	-0.024	20.800	0.037	0.037	0.000	0.000	0.000	0.000
110	A	125	MET	0	0.019	0.008	22.087	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.857	0.961	24.330	0.334	0.334	0.000	0.000	0.000	0.000
112	A	127	PRO	0	0.068	0.007	27.086	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	128	ALA	0	0.087	0.014	29.863	0.001	0.001	0.000	0.000	0.000	0.000
114	A	129	SER	0	-0.005	-0.005	31.003	0.000	0.000	0.000	0.000	0.000	0.000
115	A	130	VAL	0	0.055	0.042	31.080	0.007	0.007	0.000	0.000	0.000	0.000
116	A	131	VAL	0	0.023	0.016	28.032	0.000	0.000	0.000	0.000	0.000	0.000
117	A	132	ILE	0	-0.040	-0.019	30.923	0.003	0.003	0.000	0.000	0.000	0.000
118	A	133	ASP	-1	-0.829	-0.898	34.244	-0.170	-0.170	0.000	0.000	0.000	0.000
119	A	134	LEU	0	0.002	-0.011	28.559	0.005	0.005	0.000	0.000	0.000	0.000
120	A	135	SER	0	0.010	-0.005	31.754	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	136	VAL	0	-0.047	-0.010	33.345	0.008	0.008	0.000	0.000	0.000	0.000
122	A	137	GLU	-1	-0.880	-0.934	35.153	-0.155	-0.155	0.000	0.000	0.000	0.000
123	A	138	VAL	0	0.019	0.000	30.780	0.004	0.004	0.000	0.000	0.000	0.000
124	A	139	GLY	0	0.024	0.013	33.931	0.003	0.003	0.000	0.000	0.000	0.000
125	A	140	LYS	1	0.903	0.952	36.353	0.150	0.150	0.000	0.000	0.000	0.000
126	A	141	ARG	1	0.855	0.922	34.439	0.193	0.193	0.000	0.000	0.000	0.000
127	A	142	ILE	0	0.023	0.030	32.037	0.003	0.003	0.000	0.000	0.000	0.000
128	A	143	ALA	0	-0.041	-0.018	36.101	0.006	0.006	0.000	0.000	0.000	0.000
129	A	144	ALA	0	-0.057	-0.031	39.722	0.006	0.006	0.000	0.000	0.000	0.000
130	A	145	ALA	0	-0.024	-0.001	36.763	0.005	0.005	0.000	0.000	0.000	0.000
131	A	146	GLN	0	-0.096	-0.044	35.967	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:SER)