FMO DATABASE

FMODB ID: K3MQ3

Calculation Name: 1O4W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O4W

Chain ID: A

ChEMBL ID:

UniProt ID: O29664

Base Structure: X-ray

Registration Date: 2023-06-19

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1063592.250613
FMO2-HF: Nuclear repulsion	1013765.091633
FMO2-HF: Total energy	-49827.15898
FMO2-MP2: Total energy	-49973.135494

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:10:LYS)

Summations of interaction energy for fragment #1(A:10:LYS)

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.
17.234	21.631	0.657	-1.96	-3.096	-0.004

Interaction energy analysis for fragmet #1(A:10:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.008 / q_NPA : 1.005

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	A	12	ARG	1	0.870	0.932	2.623	35.358	39.655	0.659	-1.950	-3.007	-0.004
4	A	13	CYS	0	-0.078	-0.019	4.729	-1.535	-1.435	-0.002	-0.010	-0.089	0.000
5	A	14	ALA	0	0.016	0.014	8.160	-0.904	-0.904	0.000	0.000	0.000	0.000
6	A	15	VAL	0	0.005	0.018	11.460	0.934	0.934	0.000	0.000	0.000	0.000
7	A	16	VAL	0	-0.030	-0.021	14.128	0.318	0.318	0.000	0.000	0.000	0.000
8	A	17	ASP	-1	-0.735	-0.842	17.426	-13.020	-13.020	0.000	0.000	0.000	0.000
9	A	18	THR	0	0.067	0.021	20.767	0.127	0.127	0.000	0.000	0.000	0.000
10	A	19	ASN	0	-0.040	-0.032	23.646	0.863	0.863	0.000	0.000	0.000	0.000
11	A	20	VAL	0	-0.033	-0.018	20.188	0.349	0.349	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.018	0.004	19.932	0.233	0.233	0.000	0.000	0.000	0.000
13	A	22	MET	0	-0.016	0.009	23.655	0.412	0.412	0.000	0.000	0.000	0.000
14	A	23	TYR	0	0.020	0.002	25.641	0.395	0.395	0.000	0.000	0.000	0.000
15	A	24	VAL	0	0.004	0.028	22.549	0.223	0.223	0.000	0.000	0.000	0.000
16	A	25	TYR	0	-0.015	-0.001	25.595	0.429	0.429	0.000	0.000	0.000	0.000
17	A	26	LEU	0	-0.045	-0.033	29.145	0.384	0.384	0.000	0.000	0.000	0.000
18	A	27	ASN	0	-0.036	-0.031	28.439	0.264	0.264	0.000	0.000	0.000	0.000
19	A	28	LYS	1	0.852	0.934	28.261	9.675	9.675	0.000	0.000	0.000	0.000
20	A	29	ALA	0	0.048	0.040	23.921	-0.073	-0.073	0.000	0.000	0.000	0.000
21	A	30	ASP	-1	-0.806	-0.913	20.659	-14.701	-14.701	0.000	0.000	0.000	0.000
22	A	31	VAL	0	0.009	-0.008	17.961	-0.542	-0.542	0.000	0.000	0.000	0.000
23	A	32	VAL	0	-0.018	-0.003	16.336	-1.054	-1.054	0.000	0.000	0.000	0.000
24	A	33	GLY	0	0.032	0.009	15.802	-1.125	-1.125	0.000	0.000	0.000	0.000
25	A	34	GLN	0	0.016	0.007	16.087	-0.964	-0.964	0.000	0.000	0.000	0.000
26	A	35	LEU	0	-0.047	-0.029	12.916	-0.991	-0.991	0.000	0.000	0.000	0.000
27	A	36	ARG	1	0.893	0.948	11.805	18.248	18.248	0.000	0.000	0.000	0.000
28	A	37	GLU	-1	-0.929	-0.953	11.628	-16.555	-16.555	0.000	0.000	0.000	0.000
29	A	38	PHE	0	-0.087	-0.042	11.546	-0.341	-0.341	0.000	0.000	0.000	0.000
30	A	39	GLY	0	0.010	0.014	7.743	-2.123	-2.123	0.000	0.000	0.000	0.000
31	A	40	PHE	0	-0.095	-0.049	7.293	-4.299	-4.299	0.000	0.000	0.000	0.000
32	A	41	SER	0	0.021	-0.001	7.261	2.048	2.048	0.000	0.000	0.000	0.000
33	A	42	ARG	1	0.829	0.883	6.669	34.972	34.972	0.000	0.000	0.000	0.000
34	A	43	PHE	0	-0.012	-0.005	10.423	-0.658	-0.658	0.000	0.000	0.000	0.000
35	A	44	LEU	0	0.007	0.009	10.855	0.389	0.389	0.000	0.000	0.000	0.000
36	A	45	ILE	0	-0.035	-0.018	14.424	0.545	0.545	0.000	0.000	0.000	0.000
37	A	46	THR	0	0.048	0.012	17.845	-0.195	-0.195	0.000	0.000	0.000	0.000
38	A	47	ALA	0	0.034	0.021	19.701	0.587	0.587	0.000	0.000	0.000	0.000
39	A	48	SER	0	-0.006	-0.023	22.786	0.500	0.500	0.000	0.000	0.000	0.000
40	A	49	VAL	0	0.011	0.000	22.058	0.522	0.522	0.000	0.000	0.000	0.000
41	A	50	LYS	1	0.905	0.949	22.598	12.916	12.916	0.000	0.000	0.000	0.000
42	A	51	ARG	1	0.865	0.920	24.530	11.456	11.456	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.777	-0.875	27.257	-9.897	-9.897	0.000	0.000	0.000	0.000
44	A	53	LEU	0	-0.020	-0.010	25.512	0.378	0.378	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.797	-0.876	27.693	-10.921	-10.921	0.000	0.000	0.000	0.000
46	A	55	LYS	1	0.804	0.872	30.496	10.336	10.336	0.000	0.000	0.000	0.000
47	A	56	LEU	0	0.000	0.014	29.977	0.344	0.344	0.000	0.000	0.000	0.000
48	A	57	GLU	-1	-0.742	-0.857	31.633	-8.691	-8.691	0.000	0.000	0.000	0.000
49	A	58	MET	0	-0.015	0.004	33.483	0.268	0.268	0.000	0.000	0.000	0.000
50	A	59	SER	0	-0.056	-0.030	35.958	0.282	0.282	0.000	0.000	0.000	0.000
51	A	60	LEU	0	-0.004	0.017	32.995	0.243	0.243	0.000	0.000	0.000	0.000
52	A	61	ARG	1	0.978	0.972	37.302	7.465	7.465	0.000	0.000	0.000	0.000
53	A	62	GLY	0	0.041	0.019	38.337	-0.137	-0.137	0.000	0.000	0.000	0.000
54	A	63	LYS	1	0.881	0.913	35.861	8.473	8.473	0.000	0.000	0.000	0.000
55	A	64	GLU	-1	-0.742	-0.858	33.848	-9.087	-9.087	0.000	0.000	0.000	0.000
56	A	65	LYS	1	0.789	0.915	33.398	8.232	8.232	0.000	0.000	0.000	0.000
57	A	66	VAL	0	-0.020	-0.006	33.287	-0.202	-0.202	0.000	0.000	0.000	0.000
58	A	67	ALA	0	0.005	0.003	30.186	-0.281	-0.281	0.000	0.000	0.000	0.000
59	A	68	ALA	0	0.037	0.014	29.123	-0.423	-0.423	0.000	0.000	0.000	0.000
60	A	69	ARG	1	0.825	0.878	29.113	8.659	8.659	0.000	0.000	0.000	0.000
61	A	70	PHE	0	-0.029	-0.011	25.459	-0.157	-0.157	0.000	0.000	0.000	0.000
62	A	71	ALA	0	0.026	0.007	25.063	-0.413	-0.413	0.000	0.000	0.000	0.000
63	A	72	LEU	0	-0.012	-0.022	24.515	-0.526	-0.526	0.000	0.000	0.000	0.000
64	A	73	LYS	1	0.955	0.990	25.460	10.914	10.914	0.000	0.000	0.000	0.000
65	A	74	LEU	0	-0.027	-0.015	21.517	-0.355	-0.355	0.000	0.000	0.000	0.000
66	A	75	LEU	0	-0.037	-0.024	20.107	-0.673	-0.673	0.000	0.000	0.000	0.000
67	A	76	GLU	-1	-0.892	-0.943	21.623	-12.016	-12.016	0.000	0.000	0.000	0.000
68	A	77	HIS	0	-0.119	-0.049	18.920	-0.698	-0.698	0.000	0.000	0.000	0.000
69	A	78	PHE	0	-0.035	-0.028	16.422	-1.167	-1.167	0.000	0.000	0.000	0.000
70	A	79	GLU	-1	-0.783	-0.859	11.691	-25.745	-25.745	0.000	0.000	0.000	0.000
71	A	80	VAL	0	-0.002	-0.010	15.911	-0.256	-0.256	0.000	0.000	0.000	0.000
72	A	81	VAL	0	-0.042	-0.015	14.151	-0.144	-0.144	0.000	0.000	0.000	0.000
73	A	82	GLU	-1	-0.843	-0.936	17.622	-13.222	-13.222	0.000	0.000	0.000	0.000
74	A	83	THR	0	-0.136	-0.083	17.772	-1.311	-1.311	0.000	0.000	0.000	0.000
75	A	84	GLU	-1	-0.907	-0.934	20.045	-12.994	-12.994	0.000	0.000	0.000	0.000
76	A	85	SER	0	-0.093	-0.058	20.645	0.607	0.607	0.000	0.000	0.000	0.000
77	A	86	GLU	-1	-0.824	-0.898	22.888	-11.796	-11.796	0.000	0.000	0.000	0.000
78	A	87	GLY	0	0.019	0.007	24.918	0.002	0.002	0.000	0.000	0.000	0.000
79	A	88	ASP	-1	-0.881	-0.935	22.913	-13.079	-13.079	0.000	0.000	0.000	0.000
80	A	89	PRO	0	-0.047	-0.036	21.324	-0.827	-0.827	0.000	0.000	0.000	0.000
81	A	90	SER	0	0.039	0.037	20.051	-0.962	-0.962	0.000	0.000	0.000	0.000
82	A	91	LEU	0	0.014	-0.005	17.553	-1.110	-1.110	0.000	0.000	0.000	0.000
83	A	92	ILE	0	-0.029	-0.022	15.933	-1.292	-1.292	0.000	0.000	0.000	0.000
84	A	93	GLU	-1	-0.719	-0.825	15.208	-17.926	-17.926	0.000	0.000	0.000	0.000
85	A	94	ALA	0	0.031	0.003	14.236	-1.406	-1.406	0.000	0.000	0.000	0.000
86	A	95	ALA	0	-0.037	-0.028	11.589	-2.056	-2.056	0.000	0.000	0.000	0.000
87	A	96	GLU	-1	-0.910	-0.967	10.418	-23.522	-23.522	0.000	0.000	0.000	0.000
88	A	97	LYS	1	0.810	0.904	9.970	16.110	16.110	0.000	0.000	0.000	0.000
89	A	98	TYR	0	0.000	-0.008	8.231	-0.629	-0.629	0.000	0.000	0.000	0.000
90	A	99	GLY	0	0.014	0.026	5.966	-5.463	-5.463	0.000	0.000	0.000	0.000
91	A	101	ILE	0	-0.024	0.000	8.477	0.991	0.991	0.000	0.000	0.000	0.000
92	A	102	LEU	0	0.003	0.004	10.997	0.673	0.673	0.000	0.000	0.000	0.000
93	A	103	ILE	0	-0.015	-0.005	13.918	0.822	0.822	0.000	0.000	0.000	0.000
94	A	104	THR	0	-0.012	-0.044	17.008	0.773	0.773	0.000	0.000	0.000	0.000
95	A	105	ASN	0	0.014	-0.015	20.547	-0.481	-0.481	0.000	0.000	0.000	0.000
96	A	106	ASP	-1	-0.709	-0.833	23.770	-11.432	-11.432	0.000	0.000	0.000	0.000
97	A	107	LYS	1	0.841	0.898	24.094	10.637	10.637	0.000	0.000	0.000	0.000
98	A	108	GLU	-1	-0.816	-0.880	25.299	-11.870	-11.870	0.000	0.000	0.000	0.000
99	A	109	LEU	0	0.001	0.013	20.391	-0.266	-0.266	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.940	0.978	20.180	13.270	13.270	0.000	0.000	0.000	0.000
101	A	111	ARG	1	0.835	0.904	20.272	11.404	11.404	0.000	0.000	0.000	0.000
102	A	112	LYS	1	0.891	0.940	21.258	12.048	12.048	0.000	0.000	0.000	0.000
103	A	113	ALA	0	0.072	0.044	16.378	-0.374	-0.374	0.000	0.000	0.000	0.000
104	A	114	LYS	1	0.983	0.989	16.461	13.671	13.671	0.000	0.000	0.000	0.000
105	A	115	GLN	0	-0.052	-0.023	17.820	-0.313	-0.313	0.000	0.000	0.000	0.000
106	A	116	ARG	1	0.881	0.932	15.349	16.582	16.582	0.000	0.000	0.000	0.000
107	A	117	GLY	0	-0.001	0.013	13.766	-1.122	-1.122	0.000	0.000	0.000	0.000
108	A	118	ILE	0	-0.029	0.006	11.752	-1.791	-1.791	0.000	0.000	0.000	0.000
109	A	119	PRO	0	-0.022	-0.006	9.498	1.785	1.785	0.000	0.000	0.000	0.000
110	A	120	VAL	0	-0.001	-0.013	12.780	0.170	0.170	0.000	0.000	0.000	0.000
111	A	121	GLY	0	0.018	0.005	15.846	0.084	0.084	0.000	0.000	0.000	0.000
112	A	122	TYR	0	-0.039	-0.032	17.064	0.708	0.708	0.000	0.000	0.000	0.000
113	A	123	LEU	0	0.036	0.035	20.539	-0.037	-0.037	0.000	0.000	0.000	0.000
114	A	124	LYS	1	0.910	0.941	22.959	12.689	12.689	0.000	0.000	0.000	0.000
115	A	125	GLU	-1	-0.821	-0.899	25.269	-9.798	-9.798	0.000	0.000	0.000	0.000
116	A	126	ASP	-1	-0.826	-0.900	28.030	-10.282	-10.282	0.000	0.000	0.000	0.000
117	A	127	LYS	1	0.831	0.899	29.747	9.313	9.313	0.000	0.000	0.000	0.000
118	A	128	ARG	1	0.876	0.934	27.575	10.473	10.473	0.000	0.000	0.000	0.000
119	A	129	VAL	0	0.003	0.001	34.278	0.075	0.075	0.000	0.000	0.000	0.000
120	A	130	PHE	0	-0.043	-0.019	36.308	-0.080	-0.080	0.000	0.000	0.000	0.000
121	A	131	VAL	0	0.010	0.001	39.102	0.110	0.110	0.000	0.000	0.000	0.000
122	A	132	GLU	-1	-0.827	-0.900	40.067	-7.608	-7.608	0.000	0.000	0.000	0.000
123	A	133	LEU	0	-0.051	-0.037	42.194	0.183	0.183	0.000	0.000	0.000	0.000
124	A	134	LEU	0	-0.083	-0.030	39.989	0.231	0.231	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:LYS)