FMO DATABASE

FMODB ID: 6YNYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1006369.395179
FMO2-HF: Nuclear repulsion	958361.706519
FMO2-HF: Total energy	-48007.688659
FMO2-MP2: Total energy	-48146.608268

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.
-224.4	-224.997	33.244	-16.542	-16.103	0.174

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 : -0.774 / q_NPA : -0.894

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	-0.719	-0.850	2.199	41.924	45.400	1.213	-1.917	-2.771	0.008
4	B	30	LYS	1	0.891	0.924	1.791	-163.831	-168.957	31.989	-14.173	-12.690	0.163
5	B	31	GLY	0	0.035	0.023	4.113	-11.749	-11.345	0.010	-0.190	-0.223	0.001
6	B	32	TYR	0	-0.013	-0.017	6.323	-6.512	-6.512	0.000	0.000	0.000	0.000
7	B	33	GLN	0	0.073	0.035	6.817	-6.272	-6.272	0.000	0.000	0.000	0.000
8	B	34	SER	0	0.029	0.010	8.416	-3.928	-3.928	0.000	0.000	0.000	0.000
9	B	35	GLN	0	-0.033	0.001	9.372	-4.861	-4.861	0.000	0.000	0.000	0.000
10	B	36	LEU	0	0.021	0.014	11.529	-2.133	-2.133	0.000	0.000	0.000	0.000
11	B	37	TYR	0	0.056	0.015	12.516	-1.462	-1.462	0.000	0.000	0.000	0.000
12	B	38	THR	0	-0.023	-0.017	14.256	-1.737	-1.737	0.000	0.000	0.000	0.000
13	B	39	GLU	-1	-0.806	-0.894	16.237	15.510	15.510	0.000	0.000	0.000	0.000
14	B	40	MET	0	-0.044	-0.006	16.536	-0.688	-0.688	0.000	0.000	0.000	0.000
15	B	41	VAL	0	0.052	0.023	18.432	-1.004	-1.004	0.000	0.000	0.000	0.000
16	B	42	GLY	0	-0.004	0.013	20.599	-0.883	-0.883	0.000	0.000	0.000	0.000
17	B	43	ILE	0	0.008	-0.003	20.415	-0.783	-0.783	0.000	0.000	0.000	0.000
18	B	44	ASN	0	0.026	0.015	22.464	-1.318	-1.318	0.000	0.000	0.000	0.000
19	B	45	ASN	0	0.004	-0.001	24.412	-0.773	-0.773	0.000	0.000	0.000	0.000
20	B	46	ILE	0	-0.022	-0.007	25.975	-0.603	-0.603	0.000	0.000	0.000	0.000
21	B	47	SER	0	-0.022	-0.019	26.641	-0.551	-0.551	0.000	0.000	0.000	0.000
22	B	48	LYS	1	0.873	0.926	26.092	-12.511	-12.511	0.000	0.000	0.000	0.000
23	B	49	GLN	0	0.000	-0.008	30.497	-0.724	-0.724	0.000	0.000	0.000	0.000
24	B	50	PHE	0	-0.022	0.000	32.027	-0.366	-0.366	0.000	0.000	0.000	0.000
25	B	51	ILE	0	0.030	0.019	31.866	-0.382	-0.382	0.000	0.000	0.000	0.000
26	B	52	LEU	0	-0.024	-0.024	33.777	-0.296	-0.296	0.000	0.000	0.000	0.000
27	B	53	LYS	1	0.866	0.949	35.239	-9.320	-9.320	0.000	0.000	0.000	0.000
28	B	54	ASN	0	-0.003	0.005	37.256	-0.326	-0.326	0.000	0.000	0.000	0.000
29	B	55	PRO	0	0.035	0.010	39.531	0.098	0.098	0.000	0.000	0.000	0.000
30	B	56	LEU	0	0.005	-0.003	41.121	-0.048	-0.048	0.000	0.000	0.000	0.000
31	B	57	ASP	-1	-0.799	-0.871	38.599	8.155	8.155	0.000	0.000	0.000	0.000
32	B	58	ASP	-1	-0.744	-0.857	40.851	7.948	7.948	0.000	0.000	0.000	0.000
33	B	59	ASN	0	0.014	-0.003	38.133	0.299	0.299	0.000	0.000	0.000	0.000
34	B	60	GLN	0	0.001	-0.001	37.021	0.351	0.351	0.000	0.000	0.000	0.000
35	B	61	THR	0	-0.028	-0.025	37.319	0.205	0.205	0.000	0.000	0.000	0.000
36	B	62	ILE	0	-0.043	-0.021	34.024	0.233	0.233	0.000	0.000	0.000	0.000
37	B	63	LYS	1	0.819	0.894	32.433	-9.466	-9.466	0.000	0.000	0.000	0.000
38	B	64	SER	0	-0.001	-0.015	32.356	0.293	0.293	0.000	0.000	0.000	0.000
39	B	65	LYS	1	0.813	0.894	33.269	-8.124	-8.124	0.000	0.000	0.000	0.000
40	B	66	LEU	0	0.007	0.009	29.059	0.254	0.254	0.000	0.000	0.000	0.000
41	B	67	GLU	-1	-0.762	-0.870	28.523	10.622	10.622	0.000	0.000	0.000	0.000
42	B	68	ARG	1	0.858	0.963	28.675	-10.067	-10.067	0.000	0.000	0.000	0.000
43	B	69	PHE	0	0.015	-0.003	28.548	0.138	0.138	0.000	0.000	0.000	0.000
44	B	70	VAL	0	0.007	0.003	23.283	0.367	0.367	0.000	0.000	0.000	0.000
45	B	71	SER	0	-0.044	-0.033	24.210	0.396	0.396	0.000	0.000	0.000	0.000
46	B	72	GLY	0	-0.008	-0.010	26.288	-0.253	-0.253	0.000	0.000	0.000	0.000
47	B	73	TYR	0	-0.035	-0.034	20.686	-0.553	-0.553	0.000	0.000	0.000	0.000
48	B	74	LYS	1	0.829	0.914	23.553	-11.356	-11.356	0.000	0.000	0.000	0.000
49	B	75	MET	0	0.038	0.031	18.104	0.355	0.355	0.000	0.000	0.000	0.000
50	B	76	ASN	0	0.034	0.017	15.787	0.335	0.335	0.000	0.000	0.000	0.000
51	B	77	PRO	0	0.050	0.013	16.993	0.860	0.860	0.000	0.000	0.000	0.000
52	B	78	LYS	1	0.877	0.931	11.988	-21.143	-21.143	0.000	0.000	0.000	0.000
53	B	79	ILE	0	0.007	0.009	11.725	1.328	1.328	0.000	0.000	0.000	0.000
54	B	80	ALA	0	0.026	0.012	14.255	0.151	0.151	0.000	0.000	0.000	0.000
55	B	81	GLU	-1	-0.873	-0.922	14.698	18.495	18.495	0.000	0.000	0.000	0.000
56	B	82	LYS	1	0.814	0.891	11.272	-21.705	-21.705	0.000	0.000	0.000	0.000
57	B	83	TYR	0	0.016	0.009	7.890	0.573	0.573	0.000	0.000	0.000	0.000
58	B	84	ASN	0	-0.031	-0.003	14.686	-1.422	-1.422	0.000	0.000	0.000	0.000
59	B	85	VAL	0	0.033	0.007	17.139	0.849	0.849	0.000	0.000	0.000	0.000
60	B	86	SER	0	-0.038	-0.007	19.258	-0.858	-0.858	0.000	0.000	0.000	0.000
61	B	87	VAL	0	0.007	0.000	22.025	0.408	0.408	0.000	0.000	0.000	0.000
62	B	88	HIS	0	-0.027	-0.006	22.064	-0.706	-0.706	0.000	0.000	0.000	0.000
63	B	89	PHE	0	0.018	0.000	26.394	-0.156	-0.156	0.000	0.000	0.000	0.000
64	B	90	VAL	0	0.060	0.038	27.708	-0.259	-0.259	0.000	0.000	0.000	0.000
65	B	91	ASN	0	0.015	-0.015	30.101	-0.320	-0.320	0.000	0.000	0.000	0.000
66	B	92	LYS	1	0.903	0.936	30.777	-10.189	-10.189	0.000	0.000	0.000	0.000
67	B	93	GLU	-1	-0.778	-0.852	35.318	8.077	8.077	0.000	0.000	0.000	0.000
68	B	94	LYS	1	0.837	0.904	36.014	-8.379	-8.379	0.000	0.000	0.000	0.000
69	B	95	PRO	0	0.010	0.015	32.958	0.265	0.265	0.000	0.000	0.000	0.000
70	B	96	ARG	1	0.879	0.919	31.965	-8.231	-8.231	0.000	0.000	0.000	0.000
71	B	97	ALA	0	-0.021	0.011	30.883	0.219	0.219	0.000	0.000	0.000	0.000
72	B	98	TYR	0	-0.052	-0.028	25.513	-0.116	-0.116	0.000	0.000	0.000	0.000
73	B	99	SER	0	0.008	-0.017	23.239	-0.094	-0.094	0.000	0.000	0.000	0.000
74	B	100	LEU	0	-0.040	-0.029	20.920	-0.333	-0.333	0.000	0.000	0.000	0.000
75	B	101	VAL	0	0.035	0.014	17.571	0.575	0.575	0.000	0.000	0.000	0.000
76	B	102	GLY	0	-0.007	-0.009	15.638	-0.789	-0.789	0.000	0.000	0.000	0.000
77	B	103	VAL	0	-0.007	-0.007	13.551	1.383	1.383	0.000	0.000	0.000	0.000
78	B	104	PRO	0	0.020	0.017	10.241	-1.428	-1.428	0.000	0.000	0.000	0.000
79	B	105	LYS	1	0.798	0.916	12.961	-18.793	-18.793	0.000	0.000	0.000	0.000
80	B	106	THR	0	-0.008	-0.018	14.915	0.939	0.939	0.000	0.000	0.000	0.000
81	B	107	GLY	0	0.046	0.021	15.569	-1.082	-1.082	0.000	0.000	0.000	0.000
82	B	108	THR	0	-0.047	-0.025	11.239	-0.219	-0.219	0.000	0.000	0.000	0.000
83	B	109	GLY	0	-0.003	0.007	10.967	1.548	1.548	0.000	0.000	0.000	0.000
84	B	110	TYR	0	-0.054	-0.024	6.772	0.814	0.814	0.000	0.000	0.000	0.000
85	B	111	THR	0	-0.046	-0.034	7.224	-3.383	-3.383	0.000	0.000	0.000	0.000
86	B	112	LEU	0	-0.017	0.004	3.427	-3.565	-2.916	0.032	-0.262	-0.419	0.002
87	B	113	SER	0	-0.034	-0.040	7.865	-3.271	-3.271	0.000	0.000	0.000	0.000
88	B	114	VAL	0	-0.041	-0.023	11.282	1.147	1.147	0.000	0.000	0.000	0.000
89	B	115	TRP	0	-0.014	-0.008	13.860	-1.255	-1.255	0.000	0.000	0.000	0.000
90	B	116	MET	0	0.000	0.019	17.565	0.096	0.096	0.000	0.000	0.000	0.000
91	B	117	ASN	0	0.021	0.002	20.459	-0.457	-0.457	0.000	0.000	0.000	0.000
92	B	118	SER	0	-0.048	-0.025	24.324	0.213	0.213	0.000	0.000	0.000	0.000
93	B	119	VAL	0	0.018	0.014	26.994	-0.270	-0.270	0.000	0.000	0.000	0.000
94	B	120	GLY	0	-0.032	-0.023	24.309	-0.273	-0.273	0.000	0.000	0.000	0.000
95	B	121	ASP	-1	-0.816	-0.883	22.332	13.513	13.513	0.000	0.000	0.000	0.000
96	B	122	GLY	0	0.021	0.000	18.825	-0.187	-0.187	0.000	0.000	0.000	0.000
97	B	123	TYR	0	-0.072	-0.055	15.920	0.372	0.372	0.000	0.000	0.000	0.000
98	B	124	LYS	1	0.884	0.948	9.902	-28.303	-28.303	0.000	0.000	0.000	0.000
99	B	125	CYS	0	-0.138	-0.054	10.968	0.457	0.457	0.000	0.000	0.000	0.000
100	B	126	ARG	1	0.834	0.884	7.768	-31.208	-31.208	0.000	0.000	0.000	0.000
101	B	127	ASP	-1	-0.716	-0.818	9.232	24.410	24.410	0.000	0.000	0.000	0.000
102	B	128	ALA	0	0.046	0.007	11.646	-1.308	-1.308	0.000	0.000	0.000	0.000
103	B	129	ALA	0	-0.069	-0.023	14.095	-1.684	-1.684	0.000	0.000	0.000	0.000
104	B	130	SER	0	0.007	-0.040	14.899	-1.739	-1.739	0.000	0.000	0.000	0.000
105	B	131	ALA	0	0.019	-0.003	14.340	-0.719	-0.719	0.000	0.000	0.000	0.000
106	B	132	ARG	1	0.864	0.925	16.393	-18.615	-18.615	0.000	0.000	0.000	0.000
107	B	133	ALA	0	-0.029	-0.007	19.524	-0.877	-0.877	0.000	0.000	0.000	0.000
108	B	134	HIS	0	-0.030	0.004	20.025	-0.803	-0.803	0.000	0.000	0.000	0.000
109	B	135	LEU	0	0.012	0.026	17.715	-0.483	-0.483	0.000	0.000	0.000	0.000
110	B	136	GLU	-1	-0.846	-0.898	18.498	14.868	14.868	0.000	0.000	0.000	0.000
111	B	137	THR	0	-0.008	-0.001	18.897	-0.263	-0.263	0.000	0.000	0.000	0.000
112	B	138	LEU	0	-0.021	-0.003	12.247	0.641	0.641	0.000	0.000	0.000	0.000
113	B	139	SER	0	-0.018	-0.012	16.056	-1.179	-1.179	0.000	0.000	0.000	0.000
114	B	140	SER	0	-0.009	-0.018	15.152	0.186	0.186	0.000	0.000	0.000	0.000
115	B	141	ASP	-1	-0.873	-0.929	9.624	33.060	33.060	0.000	0.000	0.000	0.000
116	B	142	VAL	0	0.011	0.025	11.445	1.964	1.964	0.000	0.000	0.000	0.000
117	B	143	GLY	0	0.041	0.007	13.851	-1.239	-1.239	0.000	0.000	0.000	0.000
118	B	145	GLU	-1	-0.813	-0.887	10.721	29.325	29.325	0.000	0.000	0.000	0.000
119	B	146	ALA	0	0.030	0.014	14.688	0.635	0.635	0.000	0.000	0.000	0.000
120	B	147	PHE	0	-0.066	-0.032	14.082	0.929	0.929	0.000	0.000	0.000	0.000

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