FMO DATABASE

FMODB ID: YZM12

Calculation Name: 4W6X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4W6X

Chain ID: B

ChEMBL ID:

UniProt ID: Q47212

Base Structure: X-ray

Registration Date: 2023-06-26

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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1018340.228951
FMO2-HF: Nuclear repulsion	969808.176356
FMO2-HF: Total energy	-48532.052594
FMO2-MP2: Total energy	-48669.730308

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:1:GLN)

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

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.
-19.124	-19.687	11.003	-5.787	-4.653	-0.05

Interaction energy analysis for fragmet #1(B:1:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.015

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

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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	3	GLN	0	0.022	0.014	1.811	-15.873	-17.141	10.987	-5.455	-4.264	-0.048
4	B	4	LEU	0	-0.001	0.012	4.553	1.813	1.948	-0.001	-0.034	-0.100	0.000
5	B	5	GLN	0	-0.023	-0.005	7.650	0.335	0.335	0.000	0.000	0.000	0.000
6	B	6	GLU	-1	-0.756	-0.881	10.425	-1.664	-1.664	0.000	0.000	0.000	0.000
7	B	7	SER	0	-0.011	-0.008	13.862	0.149	0.149	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.020	-0.003	17.591	-0.007	-0.007	0.000	0.000	0.000	0.000
9	B	9	GLY	0	0.015	0.020	20.077	0.057	0.057	0.000	0.000	0.000	0.000
10	B	10	GLY	0	-0.013	-0.013	21.607	0.018	0.018	0.000	0.000	0.000	0.000
11	B	11	SER	0	-0.037	-0.021	24.904	0.016	0.016	0.000	0.000	0.000	0.000
12	B	12	VAL	0	-0.026	-0.008	28.327	0.005	0.005	0.000	0.000	0.000	0.000
13	B	13	GLN	0	0.025	0.021	30.988	0.014	0.014	0.000	0.000	0.000	0.000
14	B	14	ALA	0	-0.001	-0.016	33.694	-0.017	-0.017	0.000	0.000	0.000	0.000
15	B	15	GLY	0	-0.018	-0.011	34.696	0.015	0.015	0.000	0.000	0.000	0.000
16	B	16	GLY	0	0.000	0.008	33.290	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	17	SER	0	-0.042	-0.029	30.188	0.003	0.003	0.000	0.000	0.000	0.000
18	B	18	LEU	0	0.015	0.006	25.165	0.004	0.004	0.000	0.000	0.000	0.000
19	B	19	ARG	1	0.880	0.939	21.640	0.824	0.824	0.000	0.000	0.000	0.000
20	B	20	LEU	0	0.021	0.041	18.841	-0.026	-0.026	0.000	0.000	0.000	0.000
21	B	21	SER	0	-0.029	-0.032	18.099	0.057	0.057	0.000	0.000	0.000	0.000
22	B	22	CYS	0	-0.066	-0.014	11.911	-0.089	-0.089	0.000	0.000	0.000	0.000
23	B	23	THR	0	0.000	0.021	11.346	0.275	0.275	0.000	0.000	0.000	0.000
24	B	24	ALA	0	0.026	0.001	8.837	-0.475	-0.475	0.000	0.000	0.000	0.000
25	B	25	SER	0	-0.004	-0.008	7.316	0.479	0.479	0.000	0.000	0.000	0.000
26	B	26	GLY	0	0.043	0.013	4.120	-1.356	-1.286	-0.001	-0.042	-0.027	0.000
27	B	27	TYR	0	-0.092	-0.042	3.404	-1.622	-1.171	0.019	-0.255	-0.215	-0.002
28	B	28	THR	0	0.042	0.007	5.481	0.582	0.582	0.000	0.000	0.000	0.000
29	B	29	TYR	0	-0.049	-0.033	7.808	0.847	0.847	0.000	0.000	0.000	0.000
30	B	30	ARG	1	0.901	0.933	10.761	0.986	0.986	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.892	0.941	14.126	0.566	0.566	0.000	0.000	0.000	0.000
32	B	32	TYR	0	-0.010	-0.011	13.280	0.000	0.000	0.000	0.000	0.000	0.000
33	B	33	CYS	0	-0.060	-0.007	15.201	0.140	0.140	0.000	0.000	0.000	0.000
34	B	34	MET	0	0.023	0.018	11.720	-0.163	-0.163	0.000	0.000	0.000	0.000
35	B	35	GLY	0	0.011	-0.012	14.776	0.220	0.220	0.000	0.000	0.000	0.000
36	B	36	TRP	0	-0.016	0.005	15.360	-0.193	-0.193	0.000	0.000	0.000	0.000
37	B	37	PHE	0	0.029	0.013	15.858	0.135	0.135	0.000	0.000	0.000	0.000
38	B	38	ARG	1	0.750	0.859	18.283	0.428	0.428	0.000	0.000	0.000	0.000
39	B	39	GLN	0	0.015	0.013	18.266	-0.043	-0.043	0.000	0.000	0.000	0.000
40	B	40	ALA	0	0.049	0.036	21.118	-0.009	-0.009	0.000	0.000	0.000	0.000
41	B	41	PRO	0	0.004	-0.010	24.020	0.006	0.006	0.000	0.000	0.000	0.000
42	B	42	GLY	0	0.006	0.004	24.404	0.024	0.024	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.866	0.926	24.453	0.288	0.288	0.000	0.000	0.000	0.000
44	B	44	GLU	-1	-0.801	-0.887	22.814	-0.283	-0.283	0.000	0.000	0.000	0.000
45	B	45	ARG	1	0.791	0.911	13.680	0.833	0.833	0.000	0.000	0.000	0.000
46	B	46	GLU	-1	-0.810	-0.885	20.368	-0.412	-0.412	0.000	0.000	0.000	0.000
47	B	47	GLY	0	0.048	0.015	20.034	-0.077	-0.077	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.031	-0.034	20.586	0.058	0.058	0.000	0.000	0.000	0.000
49	B	49	ALA	0	-0.007	-0.009	20.772	0.058	0.058	0.000	0.000	0.000	0.000
50	B	50	CYS	0	-0.051	0.022	19.060	-0.127	-0.127	0.000	0.000	0.000	0.000
51	B	51	ILE	0	0.011	0.004	18.756	0.095	0.095	0.000	0.000	0.000	0.000
52	B	52	ASN	0	0.088	0.038	18.834	-0.086	-0.086	0.000	0.000	0.000	0.000
53	B	53	SER	0	0.057	0.029	18.655	0.030	0.030	0.000	0.000	0.000	0.000
54	B	54	GLY	0	0.003	0.006	20.490	0.018	0.018	0.000	0.000	0.000	0.000
55	B	55	GLY	0	-0.023	-0.011	23.326	0.033	0.033	0.000	0.000	0.000	0.000
56	B	56	GLY	0	-0.016	0.005	24.678	0.022	0.022	0.000	0.000	0.000	0.000
57	B	57	THR	0	0.013	-0.006	23.681	-0.045	-0.045	0.000	0.000	0.000	0.000
58	B	58	SER	0	-0.031	-0.021	23.444	0.059	0.059	0.000	0.000	0.000	0.000
59	B	59	TYR	0	0.046	0.022	23.777	-0.067	-0.067	0.000	0.000	0.000	0.000
60	B	60	TYR	0	-0.033	-0.008	19.673	0.067	0.067	0.000	0.000	0.000	0.000
61	B	61	ALA	0	0.074	0.035	25.213	0.041	0.041	0.000	0.000	0.000	0.000
62	B	62	ASP	-1	-0.816	-0.919	27.122	-0.328	-0.328	0.000	0.000	0.000	0.000
63	B	63	SER	0	0.012	0.011	29.228	-0.006	-0.006	0.000	0.000	0.000	0.000
64	B	64	VAL	0	0.018	0.013	25.677	0.003	0.003	0.000	0.000	0.000	0.000
65	B	65	LYS	1	0.805	0.914	28.662	0.345	0.345	0.000	0.000	0.000	0.000
66	B	66	GLY	0	-0.004	0.007	30.585	0.023	0.023	0.000	0.000	0.000	0.000
67	B	67	ARG	1	0.746	0.842	29.895	0.378	0.378	0.000	0.000	0.000	0.000
68	B	68	PHE	0	0.004	-0.006	24.745	-0.018	-0.018	0.000	0.000	0.000	0.000
69	B	69	THR	0	-0.036	-0.023	26.217	0.028	0.028	0.000	0.000	0.000	0.000
70	B	70	ILE	0	-0.031	0.008	18.782	-0.032	-0.032	0.000	0.000	0.000	0.000
71	B	71	SER	0	-0.040	-0.028	21.572	0.058	0.058	0.000	0.000	0.000	0.000
72	B	72	GLN	0	0.016	0.000	19.106	-0.151	-0.151	0.000	0.000	0.000	0.000
73	B	73	ASP	-1	-0.814	-0.887	18.902	-1.020	-1.020	0.000	0.000	0.000	0.000
74	B	74	ASN	0	-0.051	-0.030	21.562	0.060	0.060	0.000	0.000	0.000	0.000
75	B	75	ALA	0	0.002	0.014	17.296	0.040	0.040	0.000	0.000	0.000	0.000
76	B	76	LYS	1	0.854	0.915	16.880	0.805	0.805	0.000	0.000	0.000	0.000
77	B	77	ASP	-1	-0.778	-0.848	12.536	-2.023	-2.023	0.000	0.000	0.000	0.000
78	B	78	THR	0	-0.015	-0.024	13.395	-0.294	-0.294	0.000	0.000	0.000	0.000
79	B	79	VAL	0	-0.032	-0.014	14.570	0.169	0.169	0.000	0.000	0.000	0.000
80	B	80	PHE	0	0.026	-0.020	17.067	-0.039	-0.039	0.000	0.000	0.000	0.000
81	B	81	LEU	0	-0.001	0.000	19.769	0.036	0.036	0.000	0.000	0.000	0.000
82	B	82	ARG	1	0.903	0.951	21.879	0.487	0.487	0.000	0.000	0.000	0.000
83	B	83	MET	0	-0.020	0.008	23.565	0.003	0.003	0.000	0.000	0.000	0.000
84	B	84	ASN	0	0.030	-0.002	27.276	0.012	0.012	0.000	0.000	0.000	0.000
85	B	85	SER	0	0.021	0.014	31.116	0.001	0.001	0.000	0.000	0.000	0.000
86	B	86	LEU	0	0.005	0.016	27.182	0.008	0.008	0.000	0.000	0.000	0.000
87	B	87	LYS	1	0.841	0.893	31.075	0.312	0.312	0.000	0.000	0.000	0.000
88	B	88	PRO	0	0.060	0.021	31.027	-0.019	-0.019	0.000	0.000	0.000	0.000
89	B	89	GLU	-1	-0.792	-0.874	30.701	-0.306	-0.306	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.782	-0.843	27.153	-0.429	-0.429	0.000	0.000	0.000	0.000
91	B	91	THR	0	-0.010	0.001	25.922	-0.050	-0.050	0.000	0.000	0.000	0.000
92	B	92	ALA	0	-0.015	-0.012	22.515	0.027	0.027	0.000	0.000	0.000	0.000
93	B	93	ILE	0	-0.013	0.011	17.314	-0.023	-0.023	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.013	-0.034	18.485	0.017	0.017	0.000	0.000	0.000	0.000
95	B	95	TYR	0	0.022	0.007	12.829	0.007	0.007	0.000	0.000	0.000	0.000
96	B	97	ALA	0	0.018	-0.001	10.980	-0.211	-0.211	0.000	0.000	0.000	0.000
97	B	98	LEU	0	-0.022	-0.009	8.061	0.159	0.159	0.000	0.000	0.000	0.000
98	B	99	SER	0	-0.012	-0.019	10.922	0.013	0.013	0.000	0.000	0.000	0.000
99	B	100	SER	0	0.016	0.009	12.121	-0.004	-0.004	0.000	0.000	0.000	0.000
100	B	101	ASN	0	-0.032	-0.016	13.923	0.202	0.202	0.000	0.000	0.000	0.000
101	B	102	SER	0	-0.009	-0.015	17.427	-0.083	-0.083	0.000	0.000	0.000	0.000
102	B	103	VAL	0	-0.009	-0.006	19.737	-0.004	-0.004	0.000	0.000	0.000	0.000
103	B	104	CYS	0	0.015	-0.018	20.255	-0.030	-0.030	0.000	0.000	0.000	0.000
104	B	105	PRO	0	0.011	0.025	17.477	0.065	0.065	0.000	0.000	0.000	0.000
105	B	106	PRO	0	0.027	0.003	20.798	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	107	GLY	0	0.025	0.017	20.480	-0.053	-0.053	0.000	0.000	0.000	0.000
107	B	108	HIS	0	-0.026	-0.023	19.503	-0.015	-0.015	0.000	0.000	0.000	0.000
108	B	109	VAL	0	0.040	0.003	15.162	-0.051	-0.051	0.000	0.000	0.000	0.000
109	B	110	ALA	0	0.008	-0.001	14.514	-0.090	-0.090	0.000	0.000	0.000	0.000
110	B	111	TRP	0	-0.022	0.001	15.398	0.049	0.049	0.000	0.000	0.000	0.000
111	B	112	TYR	0	0.008	0.000	12.240	0.011	0.011	0.000	0.000	0.000	0.000
112	B	113	ASN	0	0.026	0.020	8.624	0.145	0.145	0.000	0.000	0.000	0.000
113	B	114	ASP	-1	-0.785	-0.876	5.151	-5.002	-4.953	-0.001	-0.001	-0.047	0.000
114	B	115	TRP	0	-0.023	-0.035	6.809	0.737	0.737	0.000	0.000	0.000	0.000
115	B	116	GLY	0	0.012	0.020	7.256	-0.833	-0.833	0.000	0.000	0.000	0.000
116	B	117	GLN	0	-0.034	-0.034	8.949	0.372	0.372	0.000	0.000	0.000	0.000
117	B	118	GLY	0	-0.020	-0.019	10.948	0.304	0.304	0.000	0.000	0.000	0.000
118	B	119	THR	0	-0.050	-0.031	14.403	0.070	0.070	0.000	0.000	0.000	0.000
119	B	120	GLN	0	0.005	-0.001	17.491	0.061	0.061	0.000	0.000	0.000	0.000
120	B	121	VAL	0	0.020	0.013	21.078	-0.015	-0.015	0.000	0.000	0.000	0.000
121	B	122	THR	0	0.004	0.002	24.071	0.016	0.016	0.000	0.000	0.000	0.000
122	B	123	VAL	0	-0.006	0.006	27.533	0.000	0.000	0.000	0.000	0.000	0.000
123	B	124	SER	0	0.027	0.025	30.727	0.018	0.018	0.000	0.000	0.000	0.000
124	B	125	SER	0	0.018	0.003	34.002	0.001	0.001	0.000	0.000	0.000	0.000

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