FMO DATABASE

FMODB ID: 2NM4R

Calculation Name: 2OGK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OGK

Chain ID: A

ChEMBL ID:

UniProt ID: O27966

Base Structure: X-ray

Registration Date: 2023-09-23

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1219785.780223
FMO2-HF: Nuclear repulsion	1166971.441445
FMO2-HF: Total energy	-52814.338778
FMO2-MP2: Total energy	-52971.048529

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:4:GLY)

Summations of interaction energy for fragment #1(A:4:GLY)

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.
-11.734	-7.087	8.204	-6.572	-6.28	-0.04

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.009

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	6	ILE	0	0.043	0.029	3.866	-0.150	1.756	-0.013	-1.075	-0.818	0.003
4	A	7	GLU	-1	-0.931	-0.958	7.087	-0.366	-0.366	0.000	0.000	0.000	0.000
5	A	8	TRP	0	0.043	-0.003	9.383	0.085	0.085	0.000	0.000	0.000	0.000
6	A	9	VAL	0	-0.016	-0.005	11.872	-0.071	-0.071	0.000	0.000	0.000	0.000
7	A	10	ARG	1	0.808	0.877	14.333	0.342	0.342	0.000	0.000	0.000	0.000
8	A	11	VAL	0	0.013	0.005	17.585	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	12	SER	0	-0.029	-0.008	20.495	0.024	0.024	0.000	0.000	0.000	0.000
10	A	13	ALA	0	0.051	0.022	23.607	0.000	0.000	0.000	0.000	0.000	0.000
11	A	14	VAL	0	0.004	0.003	26.981	0.005	0.005	0.000	0.000	0.000	0.000
12	A	15	VAL	0	0.019	0.034	30.348	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	16	HIS	1	0.840	0.889	32.805	0.099	0.099	0.000	0.000	0.000	0.000
14	A	17	SER	0	0.014	-0.008	36.710	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	18	THR	0	-0.048	-0.016	40.146	0.001	0.001	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.771	-0.854	34.245	-0.109	-0.109	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.822	-0.910	38.141	-0.107	-0.107	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.826	0.874	33.911	0.104	0.104	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.789	-0.883	33.804	-0.135	-0.135	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.858	0.943	34.224	0.098	0.098	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.005	-0.005	29.928	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	25	GLY	0	0.006	-0.004	29.860	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.848	-0.909	29.592	-0.157	-0.157	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.011	0.010	29.729	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	28	ILE	0	-0.038	-0.015	24.404	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	29	SER	0	-0.028	-0.037	25.237	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	30	THR	0	-0.067	-0.028	26.346	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	31	LEU	0	-0.032	-0.013	21.291	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.009	-0.009	19.773	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	33	PRO	0	0.004	0.022	21.056	0.022	0.022	0.000	0.000	0.000	0.000
31	A	34	PHE	0	-0.086	-0.073	18.568	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.895	-0.940	24.481	-0.235	-0.235	0.000	0.000	0.000	0.000
33	A	36	PHE	0	-0.040	-0.026	23.262	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	37	GLU	-1	-0.921	-0.953	24.584	-0.191	-0.191	0.000	0.000	0.000	0.000
35	A	38	ILE	0	-0.005	-0.015	25.151	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.000	0.019	26.654	0.016	0.016	0.000	0.000	0.000	0.000
37	A	40	VAL	0	0.027	-0.005	28.423	0.000	0.000	0.000	0.000	0.000	0.000
38	A	41	SER	0	-0.010	-0.012	28.708	0.016	0.016	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.810	0.871	31.635	0.105	0.105	0.000	0.000	0.000	0.000
40	A	51	MET	0	0.010	0.008	33.067	0.002	0.002	0.000	0.000	0.000	0.000
41	A	52	GLU	-1	-0.844	-0.896	33.709	-0.099	-0.099	0.000	0.000	0.000	0.000
42	A	53	TYR	0	-0.015	-0.003	28.247	0.001	0.001	0.000	0.000	0.000	0.000
43	A	54	LEU	0	-0.018	0.003	28.396	0.002	0.002	0.000	0.000	0.000	0.000
44	A	55	GLU	-1	-0.895	-0.927	24.128	-0.166	-0.166	0.000	0.000	0.000	0.000
45	A	56	VAL	0	0.026	0.024	21.084	0.003	0.003	0.000	0.000	0.000	0.000
46	A	57	GLU	-1	-0.843	-0.902	17.338	-0.358	-0.358	0.000	0.000	0.000	0.000
47	A	58	LEU	0	0.011	0.015	15.805	0.002	0.002	0.000	0.000	0.000	0.000
48	A	59	THR	0	0.048	0.009	14.387	-0.082	-0.082	0.000	0.000	0.000	0.000
49	A	60	LYS	1	0.842	0.908	14.031	0.412	0.412	0.000	0.000	0.000	0.000
50	A	61	SER	0	0.036	0.007	11.431	0.036	0.036	0.000	0.000	0.000	0.000
51	A	62	SER	0	-0.013	-0.005	12.838	-0.096	-0.096	0.000	0.000	0.000	0.000
52	A	63	GLU	-1	-0.738	-0.852	15.616	-0.563	-0.563	0.000	0.000	0.000	0.000
53	A	64	ILE	0	-0.010	0.015	10.521	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	65	LYS	1	0.881	0.946	8.840	1.946	1.946	0.000	0.000	0.000	0.000
55	A	66	LYS	1	0.880	0.937	12.862	0.508	0.508	0.000	0.000	0.000	0.000
56	A	67	PHE	0	0.037	0.018	15.077	0.035	0.035	0.000	0.000	0.000	0.000
57	A	68	TRP	0	0.015	-0.016	11.519	-0.036	-0.036	0.000	0.000	0.000	0.000
58	A	69	LYS	1	0.846	0.903	14.216	0.613	0.613	0.000	0.000	0.000	0.000
59	A	70	ASN	0	-0.021	-0.026	15.707	0.080	0.080	0.000	0.000	0.000	0.000
60	A	71	LEU	0	0.022	0.016	15.715	0.053	0.053	0.000	0.000	0.000	0.000
61	A	72	LEU	0	0.004	0.000	13.546	0.056	0.056	0.000	0.000	0.000	0.000
62	A	73	GLU	-1	-0.880	-0.915	17.997	-0.427	-0.427	0.000	0.000	0.000	0.000
63	A	74	LEU	0	-0.030	-0.013	20.812	0.040	0.040	0.000	0.000	0.000	0.000
64	A	75	LEU	0	-0.015	0.008	18.558	0.029	0.029	0.000	0.000	0.000	0.000
65	A	76	GLY	0	0.041	0.030	22.008	0.035	0.035	0.000	0.000	0.000	0.000
66	A	77	GLU	-1	-0.868	-0.951	21.523	-0.208	-0.208	0.000	0.000	0.000	0.000
67	A	78	GLN	0	-0.052	-0.021	22.378	0.024	0.024	0.000	0.000	0.000	0.000
68	A	79	ALA	0	0.008	-0.002	17.369	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	80	GLU	-1	-0.860	-0.943	17.647	-0.254	-0.254	0.000	0.000	0.000	0.000
70	A	81	GLU	-1	-0.862	-0.900	19.768	-0.115	-0.115	0.000	0.000	0.000	0.000
71	A	82	ILE	0	-0.022	-0.016	14.635	0.021	0.021	0.000	0.000	0.000	0.000
72	A	83	LEU	0	0.014	0.005	13.585	0.039	0.039	0.000	0.000	0.000	0.000
73	A	84	SER	0	-0.087	-0.052	16.153	0.060	0.060	0.000	0.000	0.000	0.000
74	A	85	THR	0	-0.028	0.000	17.726	0.022	0.022	0.000	0.000	0.000	0.000
75	A	86	LEU	0	-0.007	-0.004	11.539	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	87	GLU	-1	-0.889	-0.934	14.003	0.289	0.289	0.000	0.000	0.000	0.000
77	A	88	ASP	-1	-0.894	-0.943	15.843	0.037	0.037	0.000	0.000	0.000	0.000
78	A	89	ARG	1	0.749	0.854	15.609	0.144	0.144	0.000	0.000	0.000	0.000
79	A	90	ILE	0	0.002	0.011	9.904	-0.064	-0.064	0.000	0.000	0.000	0.000
80	A	91	ASP	-1	-0.735	-0.828	13.677	0.040	0.040	0.000	0.000	0.000	0.000
81	A	92	GLU	-1	-0.882	-0.941	13.596	0.225	0.225	0.000	0.000	0.000	0.000
82	A	93	GLN	0	-0.115	-0.070	13.796	0.025	0.025	0.000	0.000	0.000	0.000
83	A	94	ASN	0	-0.017	-0.013	8.551	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	95	VAL	0	-0.025	-0.017	9.580	-0.168	-0.168	0.000	0.000	0.000	0.000
85	A	96	LEU	0	0.019	0.020	10.834	0.077	0.077	0.000	0.000	0.000	0.000
86	A	97	HIS	0	-0.043	-0.032	12.592	-0.086	-0.086	0.000	0.000	0.000	0.000
87	A	98	ILE	0	0.021	-0.002	14.693	0.019	0.019	0.000	0.000	0.000	0.000
88	A	99	ARG	1	0.851	0.916	18.334	0.111	0.111	0.000	0.000	0.000	0.000
89	A	100	ILE	0	0.064	0.031	20.943	0.006	0.006	0.000	0.000	0.000	0.000
90	A	101	ASP	-1	-0.835	-0.914	23.762	-0.120	-0.120	0.000	0.000	0.000	0.000
91	A	102	LYS	1	0.771	0.854	27.572	0.117	0.117	0.000	0.000	0.000	0.000
92	A	103	GLN	0	0.007	0.005	29.248	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	104	LYS	1	0.813	0.893	28.894	0.147	0.147	0.000	0.000	0.000	0.000
94	A	105	ALA	0	0.034	0.027	27.094	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	106	TYR	0	-0.099	-0.061	29.008	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	107	LEU	0	-0.060	-0.022	32.245	0.003	0.003	0.000	0.000	0.000	0.000
97	A	108	GLY	0	0.008	0.012	30.325	0.003	0.003	0.000	0.000	0.000	0.000
98	A	109	GLU	-1	-0.915	-0.974	28.649	-0.169	-0.169	0.000	0.000	0.000	0.000
99	A	110	VAL	0	-0.008	-0.008	22.187	0.001	0.001	0.000	0.000	0.000	0.000
100	A	111	SER	0	0.015	0.015	25.184	0.007	0.007	0.000	0.000	0.000	0.000
101	A	112	LEU	0	-0.001	0.011	20.348	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	113	THR	0	0.021	0.006	24.263	0.024	0.024	0.000	0.000	0.000	0.000
103	A	114	SER	0	0.007	-0.002	24.968	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	115	GLY	0	0.011	0.030	27.208	0.013	0.013	0.000	0.000	0.000	0.000
105	A	116	GLY	0	-0.015	-0.024	28.019	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	117	ASP	-1	-0.852	-0.920	29.442	-0.107	-0.107	0.000	0.000	0.000	0.000
107	A	118	PRO	0	-0.031	-0.005	24.560	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	119	ILE	0	0.032	0.021	23.001	0.004	0.004	0.000	0.000	0.000	0.000
109	A	120	ALA	0	-0.040	-0.023	21.378	-0.014	-0.014	0.000	0.000	0.000	0.000
110	A	121	VAL	0	0.039	0.024	16.264	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	122	LYS	1	0.856	0.920	15.448	0.233	0.233	0.000	0.000	0.000	0.000
112	A	123	LEU	0	0.010	0.008	10.388	-0.069	-0.069	0.000	0.000	0.000	0.000
113	A	124	ARG	1	0.855	0.957	9.122	0.183	0.183	0.000	0.000	0.000	0.000
114	A	125	LEU	0	0.019	0.013	5.706	-0.437	-0.437	0.000	0.000	0.000	0.000
115	A	126	VAL	0	-0.028	-0.018	4.050	0.496	0.610	0.000	-0.047	-0.066	0.000
116	A	127	THR	0	0.028	0.005	2.305	-1.229	-1.180	5.589	-3.570	-2.069	-0.020
117	A	128	TYR	0	0.009	0.017	2.708	-2.652	-2.322	1.453	-0.469	-1.314	-0.005
118	A	129	PRO	0	0.041	0.002	5.455	-0.060	-0.060	0.000	0.000	0.000	0.000
119	A	130	SER	0	0.022	0.031	6.955	0.631	0.631	0.000	0.000	0.000	0.000
120	A	131	LYS	1	0.813	0.884	7.866	-1.334	-1.334	0.000	0.000	0.000	0.000
121	A	132	ARG	1	0.869	0.886	9.031	-0.054	-0.054	0.000	0.000	0.000	0.000
122	A	133	GLU	-1	-0.765	-0.860	10.282	0.859	0.859	0.000	0.000	0.000	0.000
123	A	134	LYS	1	0.937	0.961	6.098	-3.816	-3.816	0.000	0.000	0.000	0.000
124	A	135	VAL	0	-0.051	-0.014	5.789	0.098	0.098	0.000	0.000	0.000	0.000
125	A	136	ILE	0	0.023	0.007	6.850	-0.454	-0.454	0.000	0.000	0.000	0.000
126	A	137	GLU	-1	-0.977	-0.986	7.700	1.041	1.041	0.000	0.000	0.000	0.000
127	A	138	PHE	0	-0.005	-0.011	2.953	-3.644	-1.470	1.176	-1.400	-1.951	-0.018
128	A	139	ALA	0	0.010	-0.002	5.647	-0.652	-0.652	0.000	0.000	0.000	0.000
129	A	140	ARG	1	0.962	0.982	8.218	-0.206	-0.206	0.000	0.000	0.000	0.000
130	A	141	GLU	-1	-0.898	-0.946	4.548	-1.986	-1.912	-0.001	-0.011	-0.062	0.000
131	A	142	LEU	0	-0.060	-0.024	5.815	-0.147	-0.147	0.000	0.000	0.000	0.000
132	A	143	CYS	0	-0.054	-0.012	9.062	0.078	0.078	0.000	0.000	0.000	0.000
133	A	144	THR	0	-0.022	0.004	11.655	0.150	0.150	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)