FMO DATABASE

FMODB ID: 39Q2L

Calculation Name: 3WX6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WX6

Chain ID: B

ChEMBL ID:

UniProt ID: Q63K67

Base Structure: X-ray

Registration Date: 2023-06-21

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-856161.213849
FMO2-HF: Nuclear repulsion	811611.848052
FMO2-HF: Total energy	-44549.365797
FMO2-MP2: Total energy	-44677.615758

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(B:3:ALA)

Summations of interaction energy for fragment #1(B:3:ALA)

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.
-11.349	-7.525	7.302	-5.411	-5.715	-0.032

Interaction energy analysis for fragmet #1(B:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.004

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	B	5	ILE	0	-0.038	-0.030	3.784	-2.879	-0.323	-0.013	-1.507	-1.037	0.008
4	B	6	TYR	0	0.042	0.010	3.705	0.319	0.609	0.004	-0.044	-0.249	0.000
5	B	7	LEU	0	-0.024	-0.024	6.881	-0.155	-0.155	0.000	0.000	0.000	0.000
6	B	8	LYS	1	0.954	0.994	10.379	0.122	0.122	0.000	0.000	0.000	0.000
7	B	9	VAL	0	0.054	0.038	13.734	-0.054	-0.054	0.000	0.000	0.000	0.000
8	B	10	LYS	1	0.867	0.930	17.065	0.150	0.150	0.000	0.000	0.000	0.000
9	B	11	GLY	0	-0.124	-0.051	20.405	0.012	0.012	0.000	0.000	0.000	0.000
10	B	12	LYS	1	1.015	1.008	20.883	0.039	0.039	0.000	0.000	0.000	0.000
11	B	13	THR	0	-0.028	-0.023	18.769	-0.003	-0.003	0.000	0.000	0.000	0.000
12	B	14	GLN	0	0.061	0.001	12.873	-0.024	-0.024	0.000	0.000	0.000	0.000
13	B	15	GLY	0	0.008	0.031	13.259	0.010	0.010	0.000	0.000	0.000	0.000
14	B	16	GLU	-1	-0.796	-0.917	11.511	-0.158	-0.158	0.000	0.000	0.000	0.000
15	B	17	ILE	0	-0.048	-0.024	9.142	-0.025	-0.025	0.000	0.000	0.000	0.000
16	B	18	LYS	1	0.731	0.926	6.655	-0.033	-0.033	0.000	0.000	0.000	0.000
17	B	19	GLY	0	0.028	0.017	3.269	-0.183	0.038	0.022	-0.072	-0.171	0.000
18	B	20	SER	0	-0.016	-0.007	4.300	-0.208	-0.069	-0.001	-0.006	-0.132	0.000
19	B	35	PHE	0	0.022	-0.024	6.990	0.079	0.079	0.000	0.000	0.000	0.000
20	B	36	LYS	1	0.939	0.976	11.402	0.573	0.573	0.000	0.000	0.000	0.000
21	B	37	ASN	0	-0.012	-0.011	13.208	0.077	0.077	0.000	0.000	0.000	0.000
22	B	38	ASP	-1	-0.934	-0.954	15.112	-0.382	-0.382	0.000	0.000	0.000	0.000
23	B	39	TYR	0	-0.006	-0.017	18.881	0.001	0.001	0.000	0.000	0.000	0.000
24	B	40	ASP	-1	-0.915	-0.937	20.999	-0.247	-0.247	0.000	0.000	0.000	0.000
25	B	41	MET	0	-0.014	-0.012	24.788	0.008	0.008	0.000	0.000	0.000	0.000
26	B	42	PRO	0	0.025	0.028	27.565	0.007	0.007	0.000	0.000	0.000	0.000
27	B	43	ALA	0	0.019	-0.001	31.218	0.004	0.004	0.000	0.000	0.000	0.000
28	B	44	ARG	1	0.927	0.967	33.108	0.122	0.122	0.000	0.000	0.000	0.000
29	B	45	LEU	0	-0.002	0.008	32.475	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	46	GLN	0	-0.018	-0.015	35.244	0.004	0.004	0.000	0.000	0.000	0.000
31	B	47	GLU	-1	-0.923	-0.976	37.384	-0.093	-0.093	0.000	0.000	0.000	0.000
32	B	48	GLY	0	0.017	0.009	39.194	0.001	0.001	0.000	0.000	0.000	0.000
33	B	49	LEU	0	-0.049	-0.005	33.257	0.000	0.000	0.000	0.000	0.000	0.000
34	B	50	THR	0	0.026	0.002	31.270	-0.004	-0.004	0.000	0.000	0.000	0.000
35	B	51	PRO	0	0.074	0.009	28.584	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	52	ALA	0	-0.012	-0.006	26.339	-0.012	-0.012	0.000	0.000	0.000	0.000
37	B	53	ALA	0	-0.039	-0.009	27.129	-0.012	-0.012	0.000	0.000	0.000	0.000
38	B	54	ALA	0	-0.028	-0.011	29.747	0.001	0.001	0.000	0.000	0.000	0.000
39	B	55	ALA	0	-0.006	0.005	25.051	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	56	ARG	1	0.930	0.965	23.618	0.291	0.291	0.000	0.000	0.000	0.000
41	B	57	GLY	0	0.048	0.036	20.222	-0.013	-0.013	0.000	0.000	0.000	0.000
42	B	58	THR	0	-0.074	-0.052	18.784	0.030	0.030	0.000	0.000	0.000	0.000
43	B	59	ILE	0	0.044	0.032	10.903	-0.022	-0.022	0.000	0.000	0.000	0.000
44	B	60	THR	0	-0.059	-0.035	15.387	0.067	0.067	0.000	0.000	0.000	0.000
45	B	61	LEU	0	0.006	0.003	9.760	-0.108	-0.108	0.000	0.000	0.000	0.000
46	B	62	THR	0	0.035	0.022	12.219	0.169	0.169	0.000	0.000	0.000	0.000
47	B	63	LYS	1	0.839	0.929	10.847	0.264	0.264	0.000	0.000	0.000	0.000
48	B	64	GLU	-1	-0.813	-0.891	12.278	-0.363	-0.363	0.000	0.000	0.000	0.000
49	B	65	MET	0	-0.113	-0.072	14.403	-0.028	-0.028	0.000	0.000	0.000	0.000
50	B	66	ASP	-1	-0.820	-0.920	14.256	0.054	0.054	0.000	0.000	0.000	0.000
51	B	67	ARG	1	0.948	0.955	13.713	-0.136	-0.136	0.000	0.000	0.000	0.000
52	B	68	SER	0	0.093	0.049	11.964	-0.010	-0.010	0.000	0.000	0.000	0.000
53	B	69	SER	0	0.027	0.026	14.621	-0.048	-0.048	0.000	0.000	0.000	0.000
54	B	70	PRO	0	0.019	0.019	17.080	-0.012	-0.012	0.000	0.000	0.000	0.000
55	B	71	GLN	0	-0.002	0.001	15.595	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	72	PHE	0	0.012	0.002	11.436	-0.014	-0.014	0.000	0.000	0.000	0.000
57	B	73	LEU	0	-0.003	-0.014	17.556	-0.004	-0.004	0.000	0.000	0.000	0.000
58	B	74	GLN	0	-0.046	-0.024	21.032	0.015	0.015	0.000	0.000	0.000	0.000
59	B	75	ALA	0	0.059	0.026	19.101	0.006	0.006	0.000	0.000	0.000	0.000
60	B	76	LEU	0	-0.040	-0.025	20.953	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	77	GLY	0	-0.016	0.002	22.268	0.006	0.006	0.000	0.000	0.000	0.000
62	B	78	LYS	1	0.893	0.945	24.557	0.114	0.114	0.000	0.000	0.000	0.000
63	B	79	ARG	1	0.919	0.968	24.202	0.193	0.193	0.000	0.000	0.000	0.000
64	B	80	GLU	-1	-0.858	-0.923	19.784	-0.157	-0.157	0.000	0.000	0.000	0.000
65	B	81	MET	0	-0.046	-0.009	19.641	-0.025	-0.025	0.000	0.000	0.000	0.000
66	B	82	MET	0	-0.031	-0.017	14.701	0.017	0.017	0.000	0.000	0.000	0.000
67	B	83	GLU	-1	-0.899	-0.964	15.999	-0.087	-0.087	0.000	0.000	0.000	0.000
68	B	84	GLU	-1	-0.924	-0.962	9.501	-0.136	-0.136	0.000	0.000	0.000	0.000
69	B	85	PHE	0	0.009	-0.019	10.756	-0.019	-0.019	0.000	0.000	0.000	0.000
70	B	86	GLU	-1	-0.884	-0.940	6.151	-0.514	-0.514	0.000	0.000	0.000	0.000
71	B	87	ILE	0	-0.054	-0.018	5.344	0.047	0.047	0.000	0.000	0.000	0.000
72	B	88	THR	0	0.047	0.019	2.287	0.464	0.084	3.250	-1.030	-1.840	-0.005
73	B	89	ILE	0	0.030	0.019	2.118	-8.946	-7.948	4.040	-2.752	-2.286	-0.035
74	B	107	THR	0	-0.004	-0.008	6.612	-0.206	-0.206	0.000	0.000	0.000	0.000
75	B	108	TYR	0	-0.008	-0.004	7.751	0.433	0.433	0.000	0.000	0.000	0.000
76	B	109	LYS	1	0.946	0.979	9.141	0.324	0.324	0.000	0.000	0.000	0.000
77	B	110	PHE	0	-0.014	-0.009	11.203	0.055	0.055	0.000	0.000	0.000	0.000
78	B	111	GLU	-1	-0.820	-0.922	14.433	-0.223	-0.223	0.000	0.000	0.000	0.000
79	B	112	LYS	1	0.934	0.936	17.595	0.196	0.196	0.000	0.000	0.000	0.000
80	B	113	VAL	0	0.006	0.025	14.481	0.002	0.002	0.000	0.000	0.000	0.000
81	B	114	LEU	0	0.002	-0.007	17.690	0.039	0.039	0.000	0.000	0.000	0.000
82	B	115	ILE	0	0.001	0.010	17.243	-0.037	-0.037	0.000	0.000	0.000	0.000
83	B	116	THR	0	-0.050	-0.031	19.567	0.035	0.035	0.000	0.000	0.000	0.000
84	B	117	HIS	0	-0.020	-0.013	20.876	0.044	0.044	0.000	0.000	0.000	0.000
85	B	118	MET	0	-0.033	-0.008	18.686	-0.058	-0.058	0.000	0.000	0.000	0.000
86	B	119	ASP	-1	-0.876	-0.912	20.955	-0.250	-0.250	0.000	0.000	0.000	0.000
87	B	120	GLN	0	0.015	-0.006	19.839	-0.028	-0.028	0.000	0.000	0.000	0.000
88	B	144	ILE	0	-0.027	-0.029	14.423	0.031	0.031	0.000	0.000	0.000	0.000
89	B	145	LYS	1	0.944	0.994	15.744	0.276	0.276	0.000	0.000	0.000	0.000
90	B	146	PHE	0	0.016	-0.007	13.339	0.072	0.072	0.000	0.000	0.000	0.000
91	B	147	THR	0	-0.013	-0.016	17.353	-0.014	-0.014	0.000	0.000	0.000	0.000
92	B	148	TYR	0	-0.013	-0.001	16.365	0.027	0.027	0.000	0.000	0.000	0.000
93	B	149	SER	0	-0.045	-0.024	19.127	0.039	0.039	0.000	0.000	0.000	0.000
94	B	150	GLY	0	0.061	0.041	19.855	-0.005	-0.005	0.000	0.000	0.000	0.000
95	B	151	TYR	0	-0.044	-0.032	15.960	-0.049	-0.049	0.000	0.000	0.000	0.000
96	B	152	SER	0	-0.037	-0.019	14.442	0.075	0.075	0.000	0.000	0.000	0.000
97	B	153	LEU	0	0.002	0.008	10.520	-0.125	-0.125	0.000	0.000	0.000	0.000
98	B	154	GLU	-1	-0.935	-0.971	11.226	-0.121	-0.121	0.000	0.000	0.000	0.000
99	B	155	HIS	0	-0.014	-0.007	10.574	-0.165	-0.165	0.000	0.000	0.000	0.000
100	B	156	ALA	0	0.030	0.040	10.027	0.090	0.090	0.000	0.000	0.000	0.000
101	B	157	GLU	-1	-0.930	-0.977	11.962	0.138	0.138	0.000	0.000	0.000	0.000
102	B	158	SER	0	-0.095	-0.049	14.472	-0.084	-0.084	0.000	0.000	0.000	0.000
103	B	159	GLY	0	0.090	0.035	15.036	0.029	0.029	0.000	0.000	0.000	0.000
104	B	160	ILE	0	-0.062	-0.026	16.244	-0.007	-0.007	0.000	0.000	0.000	0.000
105	B	161	ALA	0	0.066	0.023	15.496	-0.058	-0.058	0.000	0.000	0.000	0.000
106	B	162	GLY	0	-0.039	0.005	16.452	0.046	0.046	0.000	0.000	0.000	0.000
107	B	163	ALA	0	-0.002	-0.031	17.084	-0.052	-0.052	0.000	0.000	0.000	0.000
108	B	164	ALA	0	-0.012	0.007	19.357	0.040	0.040	0.000	0.000	0.000	0.000
109	B	165	ASN	0	-0.014	-0.024	21.174	0.002	0.002	0.000	0.000	0.000	0.000
110	B	166	TRP	0	0.006	0.021	14.806	-0.027	-0.027	0.000	0.000	0.000	0.000
111	B	167	THR	0	-0.027	-0.017	20.917	0.032	0.032	0.000	0.000	0.000	0.000
112	B	168	ASN	0	-0.029	-0.002	21.536	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:ALA)