FMO DATABASE

FMODB ID: ZYM8N

Calculation Name: 2O8I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O8I

Chain ID: A

ChEMBL ID:

UniProt ID: A9CI02

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	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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1380535.299849
FMO2-HF: Nuclear repulsion	1322072.197749
FMO2-HF: Total energy	-58463.102101
FMO2-MP2: Total energy	-58635.892115

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:1:MET)

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

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.
0.634	2.526	-0.01	-0.7	-1.182	0.004

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.003

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

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	A	3	THR	0	0.049	0.040	3.881	0.227	1.746	-0.008	-0.663	-0.848	0.004
4	A	4	ARG	1	0.763	0.827	5.971	0.849	0.849	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.917	-0.954	9.080	-0.821	-0.821	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.793	-0.891	6.128	-2.434	-2.434	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.000	0.000	8.589	0.273	0.273	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.007	-0.010	10.322	0.199	0.199	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.017	-0.003	13.171	0.108	0.108	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.790	0.894	7.805	0.934	0.934	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.022	-0.017	10.054	0.106	0.106	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.033	-0.013	15.238	0.065	0.065	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.039	0.021	17.582	0.027	0.027	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.045	-0.013	17.216	0.027	0.027	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.009	-0.012	20.152	0.029	0.029	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.775	-0.868	22.759	-0.144	-0.144	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.011	0.005	24.176	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.027	-0.014	23.082	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.059	0.028	18.466	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.014	-0.005	17.896	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.017	-0.001	18.892	0.016	0.016	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.021	0.005	14.560	0.029	0.029	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.830	-0.910	13.909	-0.387	-0.387	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.879	0.921	14.151	0.083	0.083	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.008	0.001	14.366	0.047	0.047	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.053	-0.039	5.047	0.290	0.290	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.804	-0.872	10.596	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.084	-0.034	13.034	0.060	0.060	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.020	0.013	10.118	0.056	0.056	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.005	-0.007	9.267	0.264	0.264	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.027	-0.021	4.108	-0.137	-0.048	-0.001	-0.013	-0.075	0.000
32	A	32	GLY	0	-0.028	-0.008	5.028	1.119	1.403	-0.001	-0.024	-0.259	0.000
33	A	33	LEU	0	-0.077	-0.026	6.930	-0.275	-0.275	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.863	-0.940	8.370	0.830	0.830	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.024	0.001	6.782	-0.248	-0.248	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.005	-0.021	10.675	-0.106	-0.106	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.007	0.004	14.494	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.899	0.930	17.223	-0.205	-0.205	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.021	0.010	13.847	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.038	0.016	12.016	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.019	-0.019	14.678	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.017	0.016	18.452	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.002	0.006	14.840	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.008	0.000	15.397	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	45	CYS	0	-0.020	-0.024	18.187	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.035	-0.010	19.301	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.027	0.011	17.286	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.038	-0.021	20.889	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.785	0.852	23.831	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.022	0.008	22.321	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.026	0.001	24.175	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.000	-0.031	25.722	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.756	-0.890	29.387	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.018	-0.001	31.946	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.760	-0.838	25.465	-0.061	-0.061	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.804	0.888	27.525	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.001	0.000	29.231	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.007	0.005	30.032	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.012	-0.010	25.707	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.055	-0.032	28.447	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.861	0.912	31.757	0.048	0.048	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.001	0.021	28.305	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	HIS	0	0.008	0.014	27.969	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.032	0.034	28.940	0.005	0.005	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.770	-0.908	31.908	-0.051	-0.051	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.033	-0.014	34.356	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.009	0.008	36.396	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.032	0.009	34.469	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.811	0.890	30.245	0.054	0.054	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.037	-0.020	32.960	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.003	0.003	35.210	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.040	0.024	28.641	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.026	-0.015	31.350	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.011	0.009	32.648	0.003	0.003	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.960	-0.983	31.493	-0.106	-0.106	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.051	-0.017	27.386	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.113	-0.054	31.195	0.008	0.008	0.000	0.000	0.000	0.000
78	A	88	GLY	0	0.016	0.002	40.396	0.001	0.001	0.000	0.000	0.000	0.000
79	A	89	LEU	0	0.011	-0.018	36.836	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	90	ASP	-1	-0.824	-0.889	37.483	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	91	ARG	1	0.831	0.894	39.036	0.021	0.021	0.000	0.000	0.000	0.000
82	A	92	LEU	0	-0.020	0.016	40.326	0.002	0.002	0.000	0.000	0.000	0.000
83	A	93	SER	0	0.045	-0.004	43.855	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	94	PRO	0	0.025	0.008	45.874	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	95	GLN	0	0.045	0.008	47.016	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	96	GLU	-1	-0.812	-0.860	45.686	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	97	HIS	0	0.025	0.010	40.596	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	98	ALA	0	-0.001	0.017	43.848	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	99	ARG	1	0.985	0.989	46.420	0.018	0.018	0.000	0.000	0.000	0.000
90	A	100	PHE	0	0.033	-0.003	41.186	0.001	0.001	0.000	0.000	0.000	0.000
91	A	101	THR	0	0.017	0.003	42.236	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	102	GLN	0	-0.016	0.004	43.254	0.000	0.000	0.000	0.000	0.000	0.000
93	A	103	LEU	0	-0.034	-0.010	44.200	0.001	0.001	0.000	0.000	0.000	0.000
94	A	104	ASN	0	0.033	0.016	38.932	0.002	0.002	0.000	0.000	0.000	0.000
95	A	105	SER	0	-0.038	-0.026	41.820	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	106	ALA	0	0.015	0.004	44.116	0.000	0.000	0.000	0.000	0.000	0.000
97	A	107	TYR	0	-0.046	-0.049	38.232	0.001	0.001	0.000	0.000	0.000	0.000
98	A	108	THR	0	-0.027	-0.028	40.077	0.000	0.000	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.960	-0.956	41.659	-0.033	-0.033	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.781	0.902	45.188	0.016	0.016	0.000	0.000	0.000	0.000
101	A	111	PHE	0	-0.062	-0.038	40.526	0.003	0.003	0.000	0.000	0.000	0.000
102	A	112	GLY	0	0.019	0.025	40.450	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	113	PHE	0	-0.037	-0.029	35.604	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	114	PRO	0	0.073	0.034	34.822	0.004	0.004	0.000	0.000	0.000	0.000
105	A	115	PHE	0	0.017	0.002	36.407	0.003	0.003	0.000	0.000	0.000	0.000
106	A	116	ILE	0	-0.052	-0.002	31.238	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	117	ILE	0	0.026	0.002	33.769	0.007	0.007	0.000	0.000	0.000	0.000
108	A	118	ALA	0	-0.019	-0.001	30.242	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	119	VAL	0	0.033	0.004	31.795	0.006	0.006	0.000	0.000	0.000	0.000
110	A	120	LYS	1	0.954	0.982	27.153	0.021	0.021	0.000	0.000	0.000	0.000
111	A	121	GLY	0	0.015	0.001	32.063	0.006	0.006	0.000	0.000	0.000	0.000
112	A	122	LEU	0	-0.035	0.011	35.089	0.002	0.002	0.000	0.000	0.000	0.000
113	A	123	ASN	0	-0.017	-0.022	37.903	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	124	ARG	1	0.855	0.898	40.993	0.018	0.018	0.000	0.000	0.000	0.000
115	A	125	HIS	0	0.008	-0.003	42.985	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	126	ASP	-1	-0.777	-0.870	40.562	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	127	ILE	0	-0.006	-0.004	37.677	0.000	0.000	0.000	0.000	0.000	0.000
118	A	128	LEU	0	-0.032	-0.013	41.024	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	129	SER	0	0.059	0.036	44.449	0.001	0.001	0.000	0.000	0.000	0.000
120	A	130	ALA	0	-0.045	-0.010	40.062	0.001	0.001	0.000	0.000	0.000	0.000
121	A	131	PHE	0	-0.002	-0.017	42.198	0.000	0.000	0.000	0.000	0.000	0.000
122	A	132	ASP	-1	-0.909	-0.965	43.432	-0.012	-0.012	0.000	0.000	0.000	0.000
123	A	133	THR	0	-0.069	-0.038	43.934	0.002	0.002	0.000	0.000	0.000	0.000
124	A	134	ARG	1	0.745	0.851	36.576	0.017	0.017	0.000	0.000	0.000	0.000
125	A	135	ILE	0	-0.023	-0.002	43.472	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	136	ASP	-1	-0.824	-0.914	45.701	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	137	ASN	0	-0.109	-0.044	41.893	0.003	0.003	0.000	0.000	0.000	0.000
128	A	138	ASN	0	0.024	-0.008	43.846	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	139	ALA	0	0.069	0.011	41.815	0.000	0.000	0.000	0.000	0.000	0.000
130	A	140	ALA	0	0.013	0.015	39.679	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	141	GLN	0	0.030	0.019	38.958	0.000	0.000	0.000	0.000	0.000	0.000
132	A	142	GLU	-1	-0.682	-0.780	38.858	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	143	PHE	0	-0.018	0.011	32.630	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	144	ALA	0	0.009	0.016	34.484	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	145	THR	0	-0.025	-0.022	34.000	0.003	0.003	0.000	0.000	0.000	0.000
136	A	146	ALA	0	-0.006	-0.009	33.890	0.000	0.000	0.000	0.000	0.000	0.000
137	A	147	THR	0	-0.007	-0.023	30.173	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	148	GLY	0	0.062	0.036	29.251	0.000	0.000	0.000	0.000	0.000	0.000
139	A	149	GLN	0	-0.035	-0.025	29.653	0.000	0.000	0.000	0.000	0.000	0.000
140	A	150	VAL	0	0.002	0.009	25.931	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	151	GLU	-1	-0.772	-0.842	25.053	0.021	0.021	0.000	0.000	0.000	0.000
142	A	152	LYS	1	0.912	0.962	24.959	0.001	0.001	0.000	0.000	0.000	0.000
143	A	153	ILE	0	-0.025	-0.020	25.819	0.001	0.001	0.000	0.000	0.000	0.000
144	A	154	ALA	0	0.025	0.019	21.607	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	155	TRP	0	-0.034	-0.017	20.430	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	156	LEU	0	-0.031	-0.036	22.123	0.000	0.000	0.000	0.000	0.000	0.000
147	A	157	ARG	1	0.781	0.876	21.206	0.112	0.112	0.000	0.000	0.000	0.000
148	A	158	LEU	0	0.037	0.038	15.989	-0.011	-0.011	0.000	0.000	0.000	0.000
149	A	159	ALA	0	0.000	-0.008	18.417	0.004	0.004	0.000	0.000	0.000	0.000
150	A	160	SER	0	-0.124	-0.064	20.950	0.002	0.002	0.000	0.000	0.000	0.000
151	A	161	MET	0	-0.034	-0.020	16.312	-0.028	-0.028	0.000	0.000	0.000	0.000
152	A	162	LEU	0	-0.033	-0.003	12.517	-0.030	-0.030	0.000	0.000	0.000	0.000
153	A	163	PRO	0	0.033	0.021	14.669	0.000	0.000	0.000	0.000	0.000	0.000
154	A	164	GLU	-1	-0.853	-0.933	17.042	0.093	0.093	0.000	0.000	0.000	0.000
155	A	165	GLY	0	0.001	0.012	17.801	0.008	0.008	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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