FMO DATABASE

FMODB ID: R5V48

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	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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1058891.50451
FMO2-HF: Nuclear repulsion	1009065.155433
FMO2-HF: Total energy	-49826.349077
FMO2-MP2: Total energy	-49972.226807

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.
20.02	24.604	0.874	-1.88	-3.58	0.001

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 : 1.005 / q_NPA : 1.003

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	0.921	0.974	2.306	40.217	44.654	0.876	-1.862	-3.452	0.001
4	A	13	CYS	0	-0.117	-0.044	4.539	-1.238	-1.091	-0.002	-0.018	-0.128	0.000
5	A	14	ALA	0	0.000	-0.006	7.341	-0.982	-0.982	0.000	0.000	0.000	0.000
6	A	15	VAL	0	0.023	0.027	10.498	0.989	0.989	0.000	0.000	0.000	0.000
7	A	16	VAL	0	-0.030	-0.024	13.430	0.248	0.248	0.000	0.000	0.000	0.000
8	A	17	ASP	-1	-0.775	-0.883	16.539	-13.510	-13.510	0.000	0.000	0.000	0.000
9	A	18	THR	0	0.073	0.020	19.891	0.093	0.093	0.000	0.000	0.000	0.000
10	A	19	ASN	0	-0.013	-0.009	22.769	0.775	0.775	0.000	0.000	0.000	0.000
11	A	20	VAL	0	-0.039	-0.013	19.502	0.354	0.354	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.019	0.004	19.206	0.288	0.288	0.000	0.000	0.000	0.000
13	A	22	MET	0	-0.013	0.019	22.896	0.468	0.468	0.000	0.000	0.000	0.000
14	A	23	TYR	0	0.025	-0.007	25.153	0.479	0.479	0.000	0.000	0.000	0.000
15	A	24	VAL	0	-0.019	0.018	22.445	0.189	0.189	0.000	0.000	0.000	0.000
16	A	25	TYR	0	-0.010	-0.006	25.431	0.459	0.459	0.000	0.000	0.000	0.000
17	A	26	LEU	0	-0.044	-0.029	28.895	0.424	0.424	0.000	0.000	0.000	0.000
18	A	27	ASN	0	-0.026	-0.018	28.105	0.244	0.244	0.000	0.000	0.000	0.000
19	A	28	LYS	1	0.857	0.939	28.022	9.927	9.927	0.000	0.000	0.000	0.000
20	A	29	ALA	0	0.044	0.037	23.745	-0.053	-0.053	0.000	0.000	0.000	0.000
21	A	30	ASP	-1	-0.833	-0.932	20.679	-14.822	-14.822	0.000	0.000	0.000	0.000
22	A	31	VAL	0	0.022	0.003	17.877	-0.620	-0.620	0.000	0.000	0.000	0.000
23	A	32	VAL	0	-0.013	-0.010	15.674	-0.940	-0.940	0.000	0.000	0.000	0.000
24	A	33	GLY	0	0.031	0.019	15.481	-1.258	-1.258	0.000	0.000	0.000	0.000
25	A	34	GLN	0	0.030	0.007	15.912	-0.857	-0.857	0.000	0.000	0.000	0.000
26	A	35	LEU	0	-0.038	-0.018	12.677	-1.073	-1.073	0.000	0.000	0.000	0.000
27	A	36	ARG	1	0.936	0.957	11.472	18.484	18.484	0.000	0.000	0.000	0.000
28	A	37	GLU	-1	-0.957	-0.955	10.996	-17.594	-17.594	0.000	0.000	0.000	0.000
29	A	38	PHE	0	-0.059	-0.024	10.917	-0.216	-0.216	0.000	0.000	0.000	0.000
30	A	39	GLY	0	-0.003	0.007	7.370	-2.213	-2.213	0.000	0.000	0.000	0.000
31	A	40	PHE	0	-0.094	-0.046	6.566	-5.595	-5.595	0.000	0.000	0.000	0.000
32	A	41	SER	0	-0.003	-0.017	7.388	2.137	2.137	0.000	0.000	0.000	0.000
33	A	42	ARG	1	0.841	0.925	7.042	34.627	34.627	0.000	0.000	0.000	0.000
34	A	43	PHE	0	0.006	-0.001	10.184	-1.351	-1.351	0.000	0.000	0.000	0.000
35	A	44	LEU	0	0.027	0.021	10.726	0.543	0.543	0.000	0.000	0.000	0.000
36	A	45	ILE	0	-0.033	-0.013	13.940	0.419	0.419	0.000	0.000	0.000	0.000
37	A	46	THR	0	0.058	0.017	17.337	-0.245	-0.245	0.000	0.000	0.000	0.000
38	A	47	ALA	0	0.036	0.016	19.205	0.574	0.574	0.000	0.000	0.000	0.000
39	A	48	SER	0	0.031	0.029	22.336	0.601	0.601	0.000	0.000	0.000	0.000
40	A	49	VAL	0	0.035	0.008	21.363	0.570	0.570	0.000	0.000	0.000	0.000
41	A	50	LYS	1	0.974	0.994	22.349	13.442	13.442	0.000	0.000	0.000	0.000
42	A	51	ARG	1	0.951	0.989	24.057	11.482	11.482	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.873	-0.948	26.731	-10.166	-10.166	0.000	0.000	0.000	0.000
44	A	53	LEU	0	-0.034	-0.006	25.038	0.391	0.391	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.915	-0.981	27.774	-11.007	-11.007	0.000	0.000	0.000	0.000
46	A	55	LYS	1	0.869	0.935	30.092	10.406	10.406	0.000	0.000	0.000	0.000
47	A	56	LEU	0	0.022	0.016	29.851	0.335	0.335	0.000	0.000	0.000	0.000
48	A	57	GLU	-1	-0.801	-0.902	31.245	-8.861	-8.861	0.000	0.000	0.000	0.000
49	A	58	MET	0	-0.047	-0.021	33.091	0.281	0.281	0.000	0.000	0.000	0.000
50	A	59	SER	0	-0.088	-0.037	35.664	0.291	0.291	0.000	0.000	0.000	0.000
51	A	60	LEU	0	-0.004	0.021	32.177	0.191	0.191	0.000	0.000	0.000	0.000
52	A	61	ARG	1	0.987	0.968	36.664	7.592	7.592	0.000	0.000	0.000	0.000
53	A	62	GLY	0	0.014	0.007	37.781	-0.136	-0.136	0.000	0.000	0.000	0.000
54	A	63	LYS	1	1.009	0.984	35.369	8.614	8.614	0.000	0.000	0.000	0.000
55	A	64	GLU	-1	-0.891	-0.942	33.356	-9.389	-9.389	0.000	0.000	0.000	0.000
56	A	65	LYS	1	0.876	0.960	32.744	8.364	8.364	0.000	0.000	0.000	0.000
57	A	66	VAL	0	-0.038	-0.017	32.931	-0.215	-0.215	0.000	0.000	0.000	0.000
58	A	67	ALA	0	-0.004	-0.008	29.667	-0.281	-0.281	0.000	0.000	0.000	0.000
59	A	68	ALA	0	0.072	0.030	28.543	-0.448	-0.448	0.000	0.000	0.000	0.000
60	A	69	ARG	1	0.892	0.938	28.475	8.729	8.729	0.000	0.000	0.000	0.000
61	A	70	PHE	0	-0.036	-0.016	25.112	-0.134	-0.134	0.000	0.000	0.000	0.000
62	A	71	ALA	0	0.030	0.005	24.562	-0.396	-0.396	0.000	0.000	0.000	0.000
63	A	72	LEU	0	0.011	-0.010	23.919	-0.569	-0.569	0.000	0.000	0.000	0.000
64	A	73	LYS	1	0.954	0.996	25.054	11.090	11.090	0.000	0.000	0.000	0.000
65	A	74	LEU	0	-0.039	-0.026	21.163	-0.365	-0.365	0.000	0.000	0.000	0.000
66	A	75	LEU	0	-0.023	-0.014	19.775	-0.718	-0.718	0.000	0.000	0.000	0.000
67	A	76	GLU	-1	-0.966	-0.968	20.757	-12.316	-12.316	0.000	0.000	0.000	0.000
68	A	77	HIS	0	-0.068	-0.028	18.372	-0.577	-0.577	0.000	0.000	0.000	0.000
69	A	78	PHE	0	-0.064	-0.036	16.118	-1.308	-1.308	0.000	0.000	0.000	0.000
70	A	79	GLU	-1	-0.828	-0.906	12.050	-25.038	-25.038	0.000	0.000	0.000	0.000
71	A	80	VAL	0	-0.017	-0.019	15.999	-0.077	-0.077	0.000	0.000	0.000	0.000
72	A	81	VAL	0	-0.049	-0.022	13.785	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	82	GLU	-1	-0.876	-0.965	17.199	-13.374	-13.374	0.000	0.000	0.000	0.000
74	A	83	THR	0	-0.153	-0.075	17.182	-1.239	-1.239	0.000	0.000	0.000	0.000
75	A	84	GLU	-1	-0.922	-0.959	19.559	-12.555	-12.555	0.000	0.000	0.000	0.000
76	A	85	SER	0	-0.099	-0.044	20.517	0.660	0.660	0.000	0.000	0.000	0.000
77	A	86	GLU	-1	-0.900	-0.960	22.655	-11.570	-11.570	0.000	0.000	0.000	0.000
78	A	87	GLY	0	0.017	-0.005	24.550	0.051	0.051	0.000	0.000	0.000	0.000
79	A	88	ASP	-1	-0.882	-0.933	22.486	-13.565	-13.565	0.000	0.000	0.000	0.000
80	A	89	PRO	0	-0.060	-0.044	20.828	-0.857	-0.857	0.000	0.000	0.000	0.000
81	A	90	SER	0	0.056	0.036	19.533	-0.941	-0.941	0.000	0.000	0.000	0.000
82	A	91	LEU	0	0.016	0.000	17.195	-1.219	-1.219	0.000	0.000	0.000	0.000
83	A	92	ILE	0	-0.034	-0.029	15.430	-1.387	-1.387	0.000	0.000	0.000	0.000
84	A	93	GLU	-1	-0.757	-0.852	14.633	-17.683	-17.683	0.000	0.000	0.000	0.000
85	A	94	ALA	0	0.022	0.005	13.815	-1.360	-1.360	0.000	0.000	0.000	0.000
86	A	95	ALA	0	-0.030	-0.025	11.165	-2.244	-2.244	0.000	0.000	0.000	0.000
87	A	96	GLU	-1	-0.902	-0.959	9.693	-24.666	-24.666	0.000	0.000	0.000	0.000
88	A	97	LYS	1	0.932	0.985	9.630	18.551	18.551	0.000	0.000	0.000	0.000
89	A	98	TYR	0	-0.039	-0.041	8.164	-1.146	-1.146	0.000	0.000	0.000	0.000
90	A	99	GLY	0	-0.001	0.019	5.369	-6.066	-6.066	0.000	0.000	0.000	0.000
91	A	101	ILE	0	-0.029	-0.009	8.054	1.315	1.315	0.000	0.000	0.000	0.000
92	A	102	LEU	0	0.022	0.015	10.153	0.746	0.746	0.000	0.000	0.000	0.000
93	A	103	ILE	0	-0.014	-0.009	13.358	0.751	0.751	0.000	0.000	0.000	0.000
94	A	104	THR	0	0.004	-0.022	16.160	0.908	0.908	0.000	0.000	0.000	0.000
95	A	105	ASN	0	0.009	-0.014	19.725	-0.604	-0.604	0.000	0.000	0.000	0.000
96	A	106	ASP	-1	-0.738	-0.850	22.617	-11.911	-11.911	0.000	0.000	0.000	0.000
97	A	107	LYS	1	0.870	0.923	23.047	10.981	10.981	0.000	0.000	0.000	0.000
98	A	108	GLU	-1	-0.784	-0.896	24.237	-12.402	-12.402	0.000	0.000	0.000	0.000
99	A	109	LEU	0	-0.002	0.000	19.872	-0.391	-0.391	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.941	0.977	19.244	13.456	13.456	0.000	0.000	0.000	0.000
101	A	111	ARG	1	0.815	0.916	19.354	11.989	11.989	0.000	0.000	0.000	0.000
102	A	112	LYS	1	0.887	0.943	20.498	12.546	12.546	0.000	0.000	0.000	0.000
103	A	113	ALA	0	0.068	0.033	15.526	-0.328	-0.328	0.000	0.000	0.000	0.000
104	A	114	LYS	1	0.946	0.977	15.679	13.686	13.686	0.000	0.000	0.000	0.000
105	A	115	GLN	0	-0.056	-0.040	17.158	-0.176	-0.176	0.000	0.000	0.000	0.000
106	A	116	ARG	1	0.932	0.975	15.468	16.695	16.695	0.000	0.000	0.000	0.000
107	A	117	GLY	0	0.010	0.023	13.176	-1.056	-1.056	0.000	0.000	0.000	0.000
108	A	118	ILE	0	-0.030	0.002	11.142	-2.180	-2.180	0.000	0.000	0.000	0.000
109	A	119	PRO	0	-0.022	-0.006	8.821	1.910	1.910	0.000	0.000	0.000	0.000
110	A	120	VAL	0	0.016	-0.006	12.092	0.115	0.115	0.000	0.000	0.000	0.000
111	A	121	GLY	0	0.003	0.000	14.888	-0.065	-0.065	0.000	0.000	0.000	0.000
112	A	122	TYR	0	-0.046	-0.021	16.144	0.737	0.737	0.000	0.000	0.000	0.000
113	A	123	LEU	0	0.027	0.015	19.596	-0.120	-0.120	0.000	0.000	0.000	0.000
114	A	124	LYS	1	0.930	0.949	22.316	13.020	13.020	0.000	0.000	0.000	0.000
115	A	125	GLU	-1	-0.941	-0.969	24.779	-10.261	-10.261	0.000	0.000	0.000	0.000
116	A	126	ASP	-1	-0.952	-0.966	27.044	-10.711	-10.711	0.000	0.000	0.000	0.000
117	A	127	LYS	1	0.950	0.971	28.949	9.470	9.470	0.000	0.000	0.000	0.000
118	A	128	ARG	1	0.995	0.999	29.502	10.157	10.157	0.000	0.000	0.000	0.000
119	A	129	VAL	0	0.001	-0.002	34.149	0.071	0.071	0.000	0.000	0.000	0.000
120	A	130	PHE	0	-0.045	-0.023	36.161	-0.081	-0.081	0.000	0.000	0.000	0.000
121	A	131	VAL	0	0.018	0.006	38.750	0.119	0.119	0.000	0.000	0.000	0.000
122	A	132	GLU	-1	-0.878	-0.940	40.019	-7.855	-7.855	0.000	0.000	0.000	0.000
123	A	133	LEU	0	-0.043	-0.027	42.112	0.182	0.182	0.000	0.000	0.000	0.000
124	A	134	LEU	0	-0.039	-0.002	39.797	0.187	0.187	0.000	0.000	0.000	0.000

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