FMO DATABASE

FMODB ID: 7JR4K

Calculation Name: 1O4W-A-Xray310

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	126
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1064198.562419
FMO2-HF: Nuclear repulsion	1014201.34799
FMO2-HF: Total energy	-49997.214429
FMO2-MP2: Total energy	-50143.616056

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:9:ACE )

Summations of interaction energy for fragment #1(A:9:ACE )

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.
1.403	2.2	-0.005	-0.383	-0.409	0

Interaction energy analysis for fragmet #1(A:9:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.012

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].
3	A	11	VAL	0	0.050	0.025	3.853	0.920	1.717	-0.005	-0.383	-0.409
4	A	12	ARG	1	0.923	0.976	6.326	0.385	0.385	0.000	0.000	0.000
5	A	100	CYS	0	-0.123	-0.046	8.831	0.033	0.033	0.000	0.000	0.000
6	A	14	ALA	0	-0.001	-0.007	12.640	0.024	0.024	0.000	0.000	0.000
7	A	15	VAL	0	0.027	0.029	15.675	-0.002	-0.002	0.000	0.000	0.000
8	A	16	VAL	0	-0.032	-0.025	19.245	0.016	0.016	0.000	0.000	0.000
9	A	17	ASP	-1	-0.771	-0.882	21.639	-0.044	-0.044	0.000	0.000	0.000
10	A	18	THR	0	0.069	0.020	25.258	0.006	0.006	0.000	0.000	0.000
11	A	19	ASN	0	-0.009	-0.007	27.821	0.007	0.007	0.000	0.000	0.000
12	A	20	VAL	0	-0.047	-0.017	23.430	0.006	0.006	0.000	0.000	0.000
13	A	21	LEU	0	0.022	0.006	23.145	0.006	0.006	0.000	0.000	0.000
14	A	22	MET	0	-0.013	0.020	26.799	0.005	0.005	0.000	0.000	0.000
15	A	23	TYR	0	0.023	-0.008	28.514	0.003	0.003	0.000	0.000	0.000
16	A	24	VAL	0	-0.020	0.018	25.300	0.004	0.004	0.000	0.000	0.000
17	A	25	TYR	0	-0.009	-0.005	28.088	0.005	0.005	0.000	0.000	0.000
18	A	26	LEU	0	-0.044	-0.028	31.469	0.003	0.003	0.000	0.000	0.000
19	A	27	ASN	0	-0.026	-0.019	30.567	-0.001	-0.001	0.000	0.000	0.000
20	A	28	LYS	1	0.856	0.938	29.905	-0.001	-0.001	0.000	0.000	0.000
21	A	29	ALA	0	0.044	0.037	25.878	0.005	0.005	0.000	0.000	0.000
22	A	30	ASP	-1	-0.829	-0.931	21.931	0.015	0.015	0.000	0.000	0.000
23	A	31	VAL	0	0.018	0.001	20.910	0.006	0.006	0.000	0.000	0.000
24	A	32	VAL	0	-0.013	-0.009	17.980	0.001	0.001	0.000	0.000	0.000
25	A	33	GLY	0	0.031	0.019	17.366	0.000	0.000	0.000	0.000	0.000
26	A	34	GLN	0	0.029	0.006	17.071	0.013	0.013	0.000	0.000	0.000
27	A	35	LEU	0	-0.038	-0.018	15.369	0.013	0.013	0.000	0.000	0.000
28	A	36	ARG	1	0.939	0.959	12.926	0.050	0.050	0.000	0.000	0.000
29	A	37	GLU	-1	-0.958	-0.955	12.036	0.166	0.166	0.000	0.000	0.000
30	A	38	PHE	0	-0.061	-0.025	12.144	0.055	0.055	0.000	0.000	0.000
31	A	39	GLY	0	-0.004	0.006	8.447	0.037	0.037	0.000	0.000	0.000
32	A	40	PHE	0	-0.094	-0.046	8.479	-0.141	-0.141	0.000	0.000	0.000
33	A	41	SER	0	-0.003	-0.017	9.073	0.022	0.022	0.000	0.000	0.000
34	A	42	ARG	1	0.840	0.924	11.605	0.394	0.394	0.000	0.000	0.000
35	A	43	PHE	0	0.007	0.000	13.750	0.005	0.005	0.000	0.000	0.000
36	A	44	LEU	0	0.028	0.021	16.367	-0.005	-0.005	0.000	0.000	0.000
37	A	45	ILE	0	-0.032	-0.013	19.516	0.016	0.016	0.000	0.000	0.000
38	A	46	THR	0	0.055	0.015	23.190	-0.008	-0.008	0.000	0.000	0.000
39	A	47	ALA	0	0.039	0.017	25.665	0.008	0.008	0.000	0.000	0.000
40	A	48	SER	0	0.030	0.028	28.716	0.008	0.008	0.000	0.000	0.000
41	A	49	VAL	0	0.033	0.007	27.634	0.006	0.006	0.000	0.000	0.000
42	A	50	LYS	1	0.975	0.994	27.538	0.076	0.076	0.000	0.000	0.000
43	A	51	ARG	1	0.953	0.990	29.759	0.061	0.061	0.000	0.000	0.000
44	A	52	GLU	-1	-0.873	-0.947	32.822	-0.039	-0.039	0.000	0.000	0.000
45	A	53	LEU	0	-0.033	-0.006	29.983	0.005	0.005	0.000	0.000	0.000
46	A	54	GLU	-1	-0.917	-0.981	32.690	-0.049	-0.049	0.000	0.000	0.000
47	A	55	LYS	1	0.871	0.936	35.318	0.044	0.044	0.000	0.000	0.000
48	A	56	LEU	0	0.024	0.017	35.011	0.003	0.003	0.000	0.000	0.000
49	A	57	GLU	-1	-0.803	-0.902	35.970	-0.022	-0.022	0.000	0.000	0.000
50	A	58	MET	0	-0.046	-0.020	37.954	0.002	0.002	0.000	0.000	0.000
51	A	59	SER	0	-0.089	-0.037	40.928	0.002	0.002	0.000	0.000	0.000
52	A	60	LEU	0	-0.003	0.021	36.986	0.002	0.002	0.000	0.000	0.000
53	A	61	ARG	1	0.988	0.967	41.370	0.013	0.013	0.000	0.000	0.000
54	A	62	GLY	0	0.013	0.007	41.826	0.000	0.000	0.000	0.000	0.000
55	A	63	LYS	1	1.007	0.983	38.538	0.004	0.004	0.000	0.000	0.000
56	A	64	GLU	-1	-0.891	-0.942	37.241	-0.013	-0.013	0.000	0.000	0.000
57	A	65	LYS	1	0.878	0.961	36.818	0.018	0.018	0.000	0.000	0.000
58	A	66	VAL	0	-0.035	-0.016	35.674	-0.002	-0.002	0.000	0.000	0.000
59	A	67	ALA	0	-0.009	-0.010	33.278	-0.001	-0.001	0.000	0.000	0.000
60	A	68	ALA	0	0.077	0.030	32.231	-0.002	-0.002	0.000	0.000	0.000
61	A	69	ARG	1	0.885	0.937	32.525	0.018	0.018	0.000	0.000	0.000
62	A	70	PHE	0	-0.030	-0.014	27.318	-0.002	-0.002	0.000	0.000	0.000
63	A	71	ALA	0	0.025	0.004	28.167	-0.002	-0.002	0.000	0.000	0.000
64	A	72	LEU	0	0.013	-0.010	27.740	-0.006	-0.006	0.000	0.000	0.000
65	A	73	LYS	1	0.957	0.997	28.105	0.015	0.015	0.000	0.000	0.000
66	A	74	LEU	0	-0.042	-0.027	23.907	-0.003	-0.003	0.000	0.000	0.000
67	A	75	LEU	0	-0.023	-0.014	23.684	-0.008	-0.008	0.000	0.000	0.000
68	A	76	GLU	-1	-0.966	-0.967	24.580	-0.055	-0.055	0.000	0.000	0.000
69	A	77	HIS	0	-0.067	-0.028	20.429	-0.010	-0.010	0.000	0.000	0.000
70	A	78	PHE	0	-0.065	-0.037	19.710	-0.010	-0.010	0.000	0.000	0.000
71	A	79	GLU	-1	-0.830	-0.907	16.109	-0.274	-0.274	0.000	0.000	0.000
72	A	80	VAL	0	-0.016	-0.018	20.640	0.006	0.006	0.000	0.000	0.000
73	A	81	VAL	0	-0.048	-0.022	20.401	-0.006	-0.006	0.000	0.000	0.000
74	A	82	GLU	-1	-0.877	-0.965	23.784	-0.080	-0.080	0.000	0.000	0.000
75	A	83	THR	0	-0.148	-0.073	25.113	-0.013	-0.013	0.000	0.000	0.000
76	A	84	GLU	-1	-0.927	-0.961	27.554	-0.077	-0.077	0.000	0.000	0.000
77	A	85	SER	0	-0.100	-0.044	28.673	0.008	0.008	0.000	0.000	0.000
78	A	86	GLU	-1	-0.899	-0.960	30.475	-0.059	-0.059	0.000	0.000	0.000
79	A	87	GLY	0	0.018	-0.005	31.752	0.003	0.003	0.000	0.000	0.000
80	A	88	ASP	-1	-0.878	-0.930	28.979	-0.052	-0.052	0.000	0.000	0.000
81	A	89	PRO	0	-0.061	-0.044	27.737	-0.005	-0.005	0.000	0.000	0.000
82	A	90	SER	0	0.054	0.035	27.229	-0.009	-0.009	0.000	0.000	0.000
83	A	91	LEU	0	0.010	-0.003	23.968	-0.013	-0.013	0.000	0.000	0.000
84	A	92	ILE	0	-0.026	-0.025	22.496	-0.010	-0.010	0.000	0.000	0.000
85	A	93	GLU	-1	-0.755	-0.851	22.497	-0.116	-0.116	0.000	0.000	0.000
86	A	94	ALA	0	0.019	0.002	21.222	-0.017	-0.017	0.000	0.000	0.000
87	A	95	ALA	0	-0.033	-0.026	18.359	-0.026	-0.026	0.000	0.000	0.000
88	A	96	GLU	-1	-0.902	-0.958	17.552	-0.150	-0.150	0.000	0.000	0.000
89	A	97	LYS	1	0.937	0.986	18.360	0.152	0.152	0.000	0.000	0.000
90	A	98	TYR	0	-0.040	-0.042	15.937	-0.022	-0.022	0.000	0.000	0.000
91	A	99	GLY	0	0.000	0.020	13.814	-0.066	-0.066	0.000	0.000	0.000
92	A	101	ILE	0	-0.031	-0.010	14.254	0.025	0.025	0.000	0.000	0.000
93	A	102	LEU	0	0.023	0.017	15.789	-0.005	-0.005	0.000	0.000	0.000
94	A	103	ILE	0	-0.015	-0.008	17.287	0.019	0.019	0.000	0.000	0.000
95	A	104	THR	0	0.021	-0.012	20.975	-0.001	-0.001	0.000	0.000	0.000
96	A	105	ASN	0	0.008	-0.012	24.722	0.004	0.004	0.000	0.000	0.000
97	A	106	ASP	-1	-0.819	-0.885	27.615	-0.028	-0.028	0.000	0.000	0.000
98	A	107	LYS	1	0.913	0.927	28.469	0.013	0.013	0.000	0.000	0.000
99	A	108	GLU	-1	-0.734	-0.842	29.862	-0.036	-0.036	0.000	0.000	0.000
100	A	109	LEU	0	0.001	-0.004	26.149	-0.003	-0.003	0.000	0.000	0.000
101	A	110	LYS	1	0.922	0.967	24.852	0.007	0.007	0.000	0.000	0.000
102	A	111	ARG	1	0.815	0.908	25.295	0.032	0.032	0.000	0.000	0.000
103	A	112	LYS	1	0.877	0.930	27.052	0.043	0.043	0.000	0.000	0.000
104	A	113	ALA	0	0.064	0.030	21.895	-0.005	-0.005	0.000	0.000	0.000
105	A	114	LYS	1	0.944	0.976	22.542	0.013	0.013	0.000	0.000	0.000
106	A	115	GLN	0	-0.058	-0.040	23.791	0.001	0.001	0.000	0.000	0.000
107	A	116	ARG	1	0.934	0.977	23.289	0.074	0.074	0.000	0.000	0.000
108	A	117	GLY	0	0.008	0.022	20.394	-0.011	-0.011	0.000	0.000	0.000
109	A	118	ILE	0	-0.032	0.000	18.136	-0.012	-0.012	0.000	0.000	0.000
110	A	119	PRO	0	-0.019	-0.005	14.380	0.021	0.021	0.000	0.000	0.000
111	A	120	VAL	0	0.021	-0.004	17.527	-0.009	-0.009	0.000	0.000	0.000
112	A	121	GLY	0	0.002	0.000	19.196	0.016	0.016	0.000	0.000	0.000
113	A	122	TYR	0	-0.050	-0.022	19.983	-0.008	-0.008	0.000	0.000	0.000
114	A	123	LEU	0	0.028	0.015	23.060	0.009	0.009	0.000	0.000	0.000
115	A	124	LYS	1	0.931	0.950	25.355	-0.029	-0.029	0.000	0.000	0.000
116	A	125	GLU	-1	-0.941	-0.969	27.147	0.017	0.017	0.000	0.000	0.000
117	A	126	ASP	-1	-0.951	-0.966	28.296	0.047	0.047	0.000	0.000	0.000
118	A	127	LYS	1	0.949	0.971	30.331	-0.019	-0.019	0.000	0.000	0.000
119	A	128	ARG	1	0.996	0.999	29.828	-0.053	-0.053	0.000	0.000	0.000
120	A	129	VAL	0	0.000	-0.002	34.927	-0.002	-0.002	0.000	0.000	0.000
121	A	130	PHE	0	-0.044	-0.022	36.717	0.002	0.002	0.000	0.000	0.000
122	A	131	VAL	0	0.020	0.007	39.044	-0.002	-0.002	0.000	0.000	0.000
123	A	132	GLU	-1	-0.902	-0.939	40.559	0.033	0.033	0.000	0.000	0.000
124	A	133	LEU	0	-0.040	-0.031	42.470	-0.002	-0.002	0.000	0.000	0.000
125	A	134	LEU	0	-0.011	-0.002	40.121	-0.001	-0.001	0.000	0.000	0.000
126	A	135	NME	0	-0.014	0.000	44.151	-0.001	-0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ACE )