FMO DATABASE

FMODB ID: 2NJNR

Calculation Name: 2OPD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OPD

Chain ID: B

ChEMBL ID:

UniProt ID: A0A0U1

Base Structure: X-ray

Registration Date: 2023-09-21

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	OptHSide
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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1004749.961767
FMO2-HF: Nuclear repulsion	956742.648797
FMO2-HF: Total energy	-48007.312971
FMO2-MP2: Total energy	-48146.210123

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(B:27:GLU)

Summations of interaction energy for fragment #1(B:27:GLU)

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.
-181.099	-181.379	22.529	-10.791	-11.458	0.104

Interaction energy analysis for fragmet #1(B:27:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.842 / q_NPA : -0.931

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	B	29	GLU	-1	-0.728	-0.853	1.943	40.942	43.841	1.832	-1.908	-2.823	0.006
4	B	30	LYS	1	0.944	0.956	1.718	-134.752	-138.268	20.699	-8.821	-8.362	0.098
5	B	31	GLY	0	0.052	0.033	4.411	-7.488	-7.328	-0.001	-0.031	-0.128	0.000
6	B	32	TYR	0	0.013	0.001	6.516	-4.939	-4.939	0.000	0.000	0.000	0.000
7	B	33	GLN	0	0.064	0.044	7.470	-4.269	-4.269	0.000	0.000	0.000	0.000
8	B	34	SER	0	-0.007	-0.023	8.315	-3.290	-3.290	0.000	0.000	0.000	0.000
9	B	35	GLN	0	-0.026	-0.014	9.925	-3.970	-3.970	0.000	0.000	0.000	0.000
10	B	36	LEU	0	-0.001	0.006	11.822	-1.859	-1.859	0.000	0.000	0.000	0.000
11	B	37	TYR	0	0.064	0.022	12.971	-1.303	-1.303	0.000	0.000	0.000	0.000
12	B	38	THR	0	-0.006	-0.006	14.390	-1.575	-1.575	0.000	0.000	0.000	0.000
13	B	39	GLU	-1	-0.817	-0.918	16.350	15.121	15.121	0.000	0.000	0.000	0.000
14	B	40	MET	0	-0.046	-0.012	17.362	-0.586	-0.586	0.000	0.000	0.000	0.000
15	B	41	VAL	0	0.037	0.009	18.555	-0.923	-0.923	0.000	0.000	0.000	0.000
16	B	42	GLY	0	-0.020	0.007	20.828	-0.818	-0.818	0.000	0.000	0.000	0.000
17	B	43	ILE	0	0.013	0.001	21.220	-0.705	-0.705	0.000	0.000	0.000	0.000
18	B	44	ASN	0	0.023	0.010	23.132	-1.168	-1.168	0.000	0.000	0.000	0.000
19	B	45	ASN	0	-0.035	-0.015	24.277	-0.666	-0.666	0.000	0.000	0.000	0.000
20	B	46	ILE	0	0.001	0.004	26.816	-0.534	-0.534	0.000	0.000	0.000	0.000
21	B	47	SER	0	-0.026	-0.016	27.402	-0.474	-0.474	0.000	0.000	0.000	0.000
22	B	48	LYS	1	0.927	0.961	26.490	-12.034	-12.034	0.000	0.000	0.000	0.000
23	B	49	GLN	0	0.000	-0.004	30.982	-0.659	-0.659	0.000	0.000	0.000	0.000
24	B	50	PHE	0	-0.017	0.003	32.748	-0.349	-0.349	0.000	0.000	0.000	0.000
25	B	51	ILE	0	0.018	0.007	32.526	-0.331	-0.331	0.000	0.000	0.000	0.000
26	B	52	LEU	0	-0.022	-0.029	34.514	-0.265	-0.265	0.000	0.000	0.000	0.000
27	B	53	LYS	1	0.880	0.956	35.559	-9.002	-9.002	0.000	0.000	0.000	0.000
28	B	54	ASN	0	-0.040	-0.009	37.877	-0.340	-0.340	0.000	0.000	0.000	0.000
29	B	55	PRO	0	0.035	0.006	40.306	0.085	0.085	0.000	0.000	0.000	0.000
30	B	56	LEU	0	-0.001	-0.004	41.654	-0.025	-0.025	0.000	0.000	0.000	0.000
31	B	57	ASP	-1	-0.807	-0.874	39.719	7.920	7.920	0.000	0.000	0.000	0.000
32	B	58	ASP	-1	-0.784	-0.895	42.030	7.700	7.700	0.000	0.000	0.000	0.000
33	B	59	ASN	0	0.004	-0.019	39.631	0.254	0.254	0.000	0.000	0.000	0.000
34	B	60	GLN	0	-0.020	-0.005	38.424	0.322	0.322	0.000	0.000	0.000	0.000
35	B	61	THR	0	-0.026	-0.035	38.238	0.230	0.230	0.000	0.000	0.000	0.000
36	B	62	ILE	0	-0.018	-0.002	34.978	0.212	0.212	0.000	0.000	0.000	0.000
37	B	63	LYS	1	0.836	0.912	33.111	-9.344	-9.344	0.000	0.000	0.000	0.000
38	B	64	SER	0	0.012	0.006	33.271	0.321	0.321	0.000	0.000	0.000	0.000
39	B	65	LYS	1	0.834	0.899	33.876	-7.928	-7.928	0.000	0.000	0.000	0.000
40	B	66	LEU	0	0.009	0.005	30.047	0.242	0.242	0.000	0.000	0.000	0.000
41	B	67	GLU	-1	-0.784	-0.879	29.278	10.465	10.465	0.000	0.000	0.000	0.000
42	B	68	ARG	1	0.917	0.991	29.222	-9.704	-9.704	0.000	0.000	0.000	0.000
43	B	69	PHE	0	-0.013	-0.026	29.107	0.202	0.202	0.000	0.000	0.000	0.000
44	B	70	VAL	0	0.009	0.011	24.015	0.331	0.331	0.000	0.000	0.000	0.000
45	B	71	SER	0	-0.039	-0.027	24.567	0.364	0.364	0.000	0.000	0.000	0.000
46	B	72	GLY	0	-0.052	-0.026	25.857	0.088	0.088	0.000	0.000	0.000	0.000
47	B	73	TYR	0	0.006	0.013	21.318	-0.419	-0.419	0.000	0.000	0.000	0.000
48	B	74	LYS	1	0.849	0.923	23.617	-10.898	-10.898	0.000	0.000	0.000	0.000
49	B	75	MET	0	0.017	0.024	18.210	0.305	0.305	0.000	0.000	0.000	0.000
50	B	76	ASN	0	0.053	0.020	15.974	0.228	0.228	0.000	0.000	0.000	0.000
51	B	77	PRO	0	0.037	0.010	17.362	0.655	0.655	0.000	0.000	0.000	0.000
52	B	78	LYS	1	0.880	0.941	12.223	-19.978	-19.978	0.000	0.000	0.000	0.000
53	B	79	ILE	0	-0.011	-0.005	12.008	1.028	1.028	0.000	0.000	0.000	0.000
54	B	80	ALA	0	0.016	0.002	14.365	0.227	0.227	0.000	0.000	0.000	0.000
55	B	81	GLU	-1	-0.875	-0.932	14.843	17.887	17.887	0.000	0.000	0.000	0.000
56	B	82	LYS	1	0.842	0.913	11.069	-21.597	-21.597	0.000	0.000	0.000	0.000
57	B	83	TYR	0	0.010	0.009	8.530	0.506	0.506	0.000	0.000	0.000	0.000
58	B	84	ASN	0	-0.022	0.001	15.105	-1.217	-1.217	0.000	0.000	0.000	0.000
59	B	85	VAL	0	0.036	0.006	18.072	0.640	0.640	0.000	0.000	0.000	0.000
60	B	86	SER	0	-0.026	-0.001	20.145	-0.779	-0.779	0.000	0.000	0.000	0.000
61	B	87	VAL	0	-0.001	-0.003	23.315	0.380	0.380	0.000	0.000	0.000	0.000
62	B	88	HIS	0	-0.039	-0.010	23.351	-0.720	-0.720	0.000	0.000	0.000	0.000
63	B	89	PHE	0	0.017	-0.007	27.590	-0.139	-0.139	0.000	0.000	0.000	0.000
64	B	90	VAL	0	0.057	0.032	28.846	-0.156	-0.156	0.000	0.000	0.000	0.000
65	B	91	ASN	0	0.024	-0.012	31.112	-0.275	-0.275	0.000	0.000	0.000	0.000
66	B	92	LYS	1	0.914	0.957	31.626	-10.067	-10.067	0.000	0.000	0.000	0.000
67	B	93	GLU	-1	-0.818	-0.868	36.168	7.891	7.891	0.000	0.000	0.000	0.000
68	B	94	LYS	1	0.842	0.896	36.656	-8.324	-8.324	0.000	0.000	0.000	0.000
69	B	95	PRO	0	0.024	0.018	34.175	0.275	0.275	0.000	0.000	0.000	0.000
70	B	96	ARG	1	0.914	0.955	33.257	-8.084	-8.084	0.000	0.000	0.000	0.000
71	B	97	ALA	0	-0.024	0.016	31.515	0.199	0.199	0.000	0.000	0.000	0.000
72	B	98	TYR	0	-0.055	-0.041	26.329	-0.222	-0.222	0.000	0.000	0.000	0.000
73	B	99	SER	0	0.017	-0.019	23.955	-0.088	-0.088	0.000	0.000	0.000	0.000
74	B	100	LEU	0	-0.042	-0.030	21.749	-0.267	-0.267	0.000	0.000	0.000	0.000
75	B	101	VAL	0	0.039	0.020	18.571	0.596	0.596	0.000	0.000	0.000	0.000
76	B	102	GLY	0	0.020	0.000	16.472	-0.580	-0.580	0.000	0.000	0.000	0.000
77	B	103	VAL	0	-0.040	-0.023	14.562	1.321	1.321	0.000	0.000	0.000	0.000
78	B	104	PRO	0	0.031	0.020	10.948	-1.372	-1.372	0.000	0.000	0.000	0.000
79	B	105	LYS	1	0.804	0.918	13.494	-18.115	-18.115	0.000	0.000	0.000	0.000
80	B	106	THR	0	-0.002	-0.018	14.840	1.015	1.015	0.000	0.000	0.000	0.000
81	B	107	GLY	0	0.010	-0.002	15.517	-0.717	-0.717	0.000	0.000	0.000	0.000
82	B	108	THR	0	-0.020	-0.007	10.902	-0.432	-0.432	0.000	0.000	0.000	0.000
83	B	109	GLY	0	-0.014	0.004	10.126	1.462	1.462	0.000	0.000	0.000	0.000
84	B	110	TYR	0	-0.046	-0.004	6.619	2.105	2.105	0.000	0.000	0.000	0.000
85	B	111	THR	0	-0.046	-0.040	7.272	-3.283	-3.283	0.000	0.000	0.000	0.000
86	B	112	LEU	0	-0.008	0.009	4.265	-3.647	-3.470	-0.001	-0.031	-0.145	0.000
87	B	113	SER	0	-0.030	-0.043	8.561	-2.884	-2.884	0.000	0.000	0.000	0.000
88	B	114	VAL	0	-0.035	-0.019	12.115	0.963	0.963	0.000	0.000	0.000	0.000
89	B	115	TRP	0	-0.026	0.007	14.805	-1.027	-1.027	0.000	0.000	0.000	0.000
90	B	116	MET	0	-0.014	0.000	18.268	-0.013	-0.013	0.000	0.000	0.000	0.000
91	B	117	ASN	0	0.009	-0.020	21.056	-0.414	-0.414	0.000	0.000	0.000	0.000
92	B	118	SER	0	-0.047	-0.015	24.825	0.129	0.129	0.000	0.000	0.000	0.000
93	B	119	VAL	0	0.044	0.016	27.503	-0.277	-0.277	0.000	0.000	0.000	0.000
94	B	120	GLY	0	-0.074	-0.046	24.723	-0.289	-0.289	0.000	0.000	0.000	0.000
95	B	121	ASP	-1	-0.825	-0.870	22.741	13.053	13.053	0.000	0.000	0.000	0.000
96	B	122	GLY	0	0.037	0.014	18.965	-0.087	-0.087	0.000	0.000	0.000	0.000
97	B	123	TYR	0	-0.063	-0.045	16.535	0.259	0.259	0.000	0.000	0.000	0.000
98	B	124	LYS	1	0.910	0.964	10.239	-25.771	-25.771	0.000	0.000	0.000	0.000
99	B	125	CYS	0	-0.150	-0.055	11.847	0.962	0.962	0.000	0.000	0.000	0.000
100	B	126	ARG	1	0.856	0.909	8.073	-29.893	-29.893	0.000	0.000	0.000	0.000
101	B	127	ASP	-1	-0.760	-0.855	9.580	24.381	24.381	0.000	0.000	0.000	0.000
102	B	128	ALA	0	0.025	-0.008	12.143	-1.538	-1.538	0.000	0.000	0.000	0.000
103	B	129	ALA	0	-0.053	-0.023	15.009	-1.391	-1.391	0.000	0.000	0.000	0.000
104	B	130	SER	0	0.009	-0.016	15.134	-1.638	-1.638	0.000	0.000	0.000	0.000
105	B	131	ALA	0	0.033	0.000	15.235	-0.894	-0.894	0.000	0.000	0.000	0.000
106	B	132	ARG	1	0.876	0.937	17.231	-18.010	-18.010	0.000	0.000	0.000	0.000
107	B	133	ALA	0	-0.001	0.005	20.028	-0.888	-0.888	0.000	0.000	0.000	0.000
108	B	134	HIS	0	-0.031	0.013	20.178	-0.769	-0.769	0.000	0.000	0.000	0.000
109	B	135	LEU	0	-0.012	0.004	17.923	-0.517	-0.517	0.000	0.000	0.000	0.000
110	B	136	GLU	-1	-0.838	-0.899	18.952	14.253	14.253	0.000	0.000	0.000	0.000
111	B	137	THR	0	-0.004	-0.001	19.154	-0.247	-0.247	0.000	0.000	0.000	0.000
112	B	138	LEU	0	-0.024	-0.001	12.120	0.852	0.852	0.000	0.000	0.000	0.000
113	B	139	SER	0	-0.012	-0.003	15.974	-1.021	-1.021	0.000	0.000	0.000	0.000
114	B	140	SER	0	-0.008	-0.021	15.109	0.304	0.304	0.000	0.000	0.000	0.000
115	B	141	ASP	-1	-0.858	-0.913	9.669	32.328	32.328	0.000	0.000	0.000	0.000
116	B	142	VAL	0	-0.023	-0.007	11.239	1.841	1.841	0.000	0.000	0.000	0.000
117	B	143	GLY	0	0.044	0.013	13.891	-1.195	-1.195	0.000	0.000	0.000	0.000
118	B	145	GLU	-1	-0.824	-0.917	11.396	26.149	26.149	0.000	0.000	0.000	0.000
119	B	146	ALA	0	0.024	0.011	15.406	0.554	0.554	0.000	0.000	0.000	0.000
120	B	147	PHE	0	-0.064	-0.036	14.448	0.793	0.793	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:27:GLU)