FMO DATABASE

FMODB ID: 7626K

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	OptH
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	-1002448.617828
FMO2-HF: Nuclear repulsion	954442.333087
FMO2-HF: Total energy	-48006.28474
FMO2-MP2: Total energy	-48145.155941

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.
-125.754	-118.533	1.4	-3.22	-5.401	0.019

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 : -0.901 / q_NPA : -0.978

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	-0.721	-0.855	2.832	45.925	49.973	0.154	-1.720	-2.483	0.005
4	B	30	LYS	1	1.000	0.994	2.255	-78.210	-75.247	1.248	-1.466	-2.744	0.014
5	B	31	GLY	0	0.037	0.026	4.494	-6.186	-6.058	-0.001	-0.031	-0.096	0.000
6	B	32	TYR	0	0.025	-0.002	6.586	-4.627	-4.627	0.000	0.000	0.000	0.000
7	B	33	GLN	0	0.074	0.046	7.353	-3.899	-3.899	0.000	0.000	0.000	0.000
8	B	34	SER	0	-0.046	-0.037	8.391	-3.184	-3.184	0.000	0.000	0.000	0.000
9	B	35	GLN	0	-0.059	-0.034	9.645	-3.500	-3.500	0.000	0.000	0.000	0.000
10	B	36	LEU	0	0.008	0.008	11.754	-1.725	-1.725	0.000	0.000	0.000	0.000
11	B	37	TYR	0	0.053	0.022	13.002	-1.216	-1.216	0.000	0.000	0.000	0.000
12	B	38	THR	0	0.007	0.000	14.719	-1.565	-1.565	0.000	0.000	0.000	0.000
13	B	39	GLU	-1	-0.828	-0.924	16.346	14.970	14.970	0.000	0.000	0.000	0.000
14	B	40	MET	0	-0.054	-0.010	17.353	-0.554	-0.554	0.000	0.000	0.000	0.000
15	B	41	VAL	0	0.037	0.009	18.673	-0.901	-0.901	0.000	0.000	0.000	0.000
16	B	42	GLY	0	-0.020	0.007	20.920	-0.787	-0.787	0.000	0.000	0.000	0.000
17	B	43	ILE	0	0.022	0.007	21.476	-0.686	-0.686	0.000	0.000	0.000	0.000
18	B	44	ASN	0	0.036	0.016	23.322	-1.033	-1.033	0.000	0.000	0.000	0.000
19	B	45	ASN	0	-0.052	-0.023	24.611	-0.570	-0.570	0.000	0.000	0.000	0.000
20	B	46	ILE	0	0.007	0.007	26.732	-0.520	-0.520	0.000	0.000	0.000	0.000
21	B	47	SER	0	-0.026	-0.014	27.425	-0.454	-0.454	0.000	0.000	0.000	0.000
22	B	48	LYS	1	0.972	0.987	26.353	-11.847	-11.847	0.000	0.000	0.000	0.000
23	B	49	GLN	0	-0.025	-0.012	31.072	-0.632	-0.632	0.000	0.000	0.000	0.000
24	B	50	PHE	0	-0.001	0.005	32.786	-0.349	-0.349	0.000	0.000	0.000	0.000
25	B	51	ILE	0	0.008	0.001	32.483	-0.315	-0.315	0.000	0.000	0.000	0.000
26	B	52	LEU	0	-0.012	-0.022	34.361	-0.247	-0.247	0.000	0.000	0.000	0.000
27	B	53	LYS	1	0.898	0.959	35.823	-8.802	-8.802	0.000	0.000	0.000	0.000
28	B	54	ASN	0	-0.060	-0.013	37.772	-0.369	-0.369	0.000	0.000	0.000	0.000
29	B	55	PRO	0	0.015	0.005	40.320	0.086	0.086	0.000	0.000	0.000	0.000
30	B	56	LEU	0	-0.013	-0.014	41.704	-0.031	-0.031	0.000	0.000	0.000	0.000
31	B	57	ASP	-1	-0.812	-0.879	40.239	7.759	7.759	0.000	0.000	0.000	0.000
32	B	58	ASP	-1	-0.820	-0.891	42.009	7.556	7.556	0.000	0.000	0.000	0.000
33	B	59	ASN	0	0.030	-0.022	39.582	0.243	0.243	0.000	0.000	0.000	0.000
34	B	60	GLN	0	-0.013	-0.003	38.360	0.320	0.320	0.000	0.000	0.000	0.000
35	B	61	THR	0	-0.011	-0.031	38.310	0.241	0.241	0.000	0.000	0.000	0.000
36	B	62	ILE	0	-0.014	-0.001	34.784	0.221	0.221	0.000	0.000	0.000	0.000
37	B	63	LYS	1	0.868	0.920	33.166	-9.417	-9.417	0.000	0.000	0.000	0.000
38	B	64	SER	0	0.011	0.004	33.361	0.326	0.326	0.000	0.000	0.000	0.000
39	B	65	LYS	1	0.872	0.924	34.073	-7.876	-7.876	0.000	0.000	0.000	0.000
40	B	66	LEU	0	-0.010	-0.003	30.181	0.242	0.242	0.000	0.000	0.000	0.000
41	B	67	GLU	-1	-0.834	-0.893	29.466	10.409	10.409	0.000	0.000	0.000	0.000
42	B	68	ARG	1	0.948	1.006	29.507	-9.602	-9.602	0.000	0.000	0.000	0.000
43	B	69	PHE	0	-0.040	-0.037	29.155	0.202	0.202	0.000	0.000	0.000	0.000
44	B	70	VAL	0	0.011	0.013	24.143	0.331	0.331	0.000	0.000	0.000	0.000
45	B	71	SER	0	-0.031	-0.032	24.826	0.365	0.365	0.000	0.000	0.000	0.000
46	B	72	GLY	0	-0.059	-0.020	26.350	0.108	0.108	0.000	0.000	0.000	0.000
47	B	73	TYR	0	0.014	0.013	21.768	-0.408	-0.408	0.000	0.000	0.000	0.000
48	B	74	LYS	1	0.840	0.915	24.038	-10.921	-10.921	0.000	0.000	0.000	0.000
49	B	75	MET	0	0.013	0.020	18.512	0.292	0.292	0.000	0.000	0.000	0.000
50	B	76	ASN	0	0.041	0.005	15.892	-0.449	-0.449	0.000	0.000	0.000	0.000
51	B	77	PRO	0	0.037	0.016	17.915	0.683	0.683	0.000	0.000	0.000	0.000
52	B	78	LYS	1	0.957	0.991	12.411	-19.823	-19.823	0.000	0.000	0.000	0.000
53	B	79	ILE	0	-0.023	-0.009	12.504	1.232	1.232	0.000	0.000	0.000	0.000
54	B	80	ALA	0	0.007	-0.007	14.984	0.272	0.272	0.000	0.000	0.000	0.000
55	B	81	GLU	-1	-0.970	-0.979	15.643	17.505	17.505	0.000	0.000	0.000	0.000
56	B	82	LYS	1	0.915	0.963	10.846	-24.775	-24.775	0.000	0.000	0.000	0.000
57	B	83	TYR	0	0.003	0.007	9.132	0.750	0.750	0.000	0.000	0.000	0.000
58	B	84	ASN	0	-0.013	0.003	15.560	-1.576	-1.576	0.000	0.000	0.000	0.000
59	B	85	VAL	0	0.041	0.006	18.334	0.601	0.601	0.000	0.000	0.000	0.000
60	B	86	SER	0	-0.032	-0.005	20.433	-0.777	-0.777	0.000	0.000	0.000	0.000
61	B	87	VAL	0	0.007	0.006	23.345	0.338	0.338	0.000	0.000	0.000	0.000
62	B	88	HIS	0	-0.036	-0.016	23.505	-0.726	-0.726	0.000	0.000	0.000	0.000
63	B	89	PHE	0	0.004	-0.019	27.835	-0.166	-0.166	0.000	0.000	0.000	0.000
64	B	90	VAL	0	0.051	0.035	29.238	-0.128	-0.128	0.000	0.000	0.000	0.000
65	B	91	ASN	0	0.047	0.019	31.655	-0.266	-0.266	0.000	0.000	0.000	0.000
66	B	92	LYS	1	0.932	0.955	32.357	-9.839	-9.839	0.000	0.000	0.000	0.000
67	B	93	GLU	-1	-0.911	-0.939	36.498	7.671	7.671	0.000	0.000	0.000	0.000
68	B	94	LYS	1	0.918	0.947	36.895	-8.337	-8.337	0.000	0.000	0.000	0.000
69	B	95	PRO	0	0.031	0.020	34.269	0.270	0.270	0.000	0.000	0.000	0.000
70	B	96	ARG	1	0.937	0.958	33.248	-7.980	-7.980	0.000	0.000	0.000	0.000
71	B	97	ALA	0	-0.034	0.012	31.600	0.178	0.178	0.000	0.000	0.000	0.000
72	B	98	TYR	0	-0.059	-0.048	26.471	-0.212	-0.212	0.000	0.000	0.000	0.000
73	B	99	SER	0	-0.027	-0.096	24.264	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	100	LEU	0	-0.018	-0.019	21.571	-0.237	-0.237	0.000	0.000	0.000	0.000
75	B	101	VAL	0	0.044	0.020	18.940	0.534	0.534	0.000	0.000	0.000	0.000
76	B	102	GLY	0	0.020	-0.001	16.494	-0.500	-0.500	0.000	0.000	0.000	0.000
77	B	103	VAL	0	-0.056	-0.023	14.765	1.165	1.165	0.000	0.000	0.000	0.000
78	B	104	PRO	0	0.049	0.024	11.077	-1.254	-1.254	0.000	0.000	0.000	0.000
79	B	105	LYS	1	0.854	0.933	13.426	-17.984	-17.984	0.000	0.000	0.000	0.000
80	B	106	THR	0	-0.003	-0.017	14.260	1.083	1.083	0.000	0.000	0.000	0.000
81	B	107	GLY	0	0.011	0.000	14.835	-0.719	-0.719	0.000	0.000	0.000	0.000
82	B	108	THR	0	-0.021	-0.014	10.157	-0.279	-0.279	0.000	0.000	0.000	0.000
83	B	109	GLY	0	-0.012	0.010	9.437	1.862	1.862	0.000	0.000	0.000	0.000
84	B	110	TYR	0	-0.025	0.005	5.581	1.047	1.047	0.000	0.000	0.000	0.000
85	B	111	THR	0	-0.051	-0.039	7.155	-3.832	-3.832	0.000	0.000	0.000	0.000
86	B	112	LEU	0	-0.027	0.001	4.683	-4.030	-3.948	-0.001	-0.003	-0.078	0.000
87	B	113	SER	0	-0.021	-0.029	9.270	-2.259	-2.259	0.000	0.000	0.000	0.000
88	B	114	VAL	0	-0.034	-0.018	12.372	0.678	0.678	0.000	0.000	0.000	0.000
89	B	115	TRP	0	-0.028	0.005	14.902	-0.761	-0.761	0.000	0.000	0.000	0.000
90	B	116	MET	0	-0.009	-0.001	18.134	0.001	0.001	0.000	0.000	0.000	0.000
91	B	117	ASN	0	0.024	0.025	21.153	-0.339	-0.339	0.000	0.000	0.000	0.000
92	B	118	SER	0	-0.048	-0.021	24.942	0.143	0.143	0.000	0.000	0.000	0.000
93	B	119	VAL	0	0.014	0.001	27.782	-0.235	-0.235	0.000	0.000	0.000	0.000
94	B	120	GLY	0	-0.078	-0.054	24.928	-0.259	-0.259	0.000	0.000	0.000	0.000
95	B	121	ASP	-1	-0.842	-0.894	22.975	12.778	12.778	0.000	0.000	0.000	0.000
96	B	122	GLY	0	0.029	0.005	19.181	-0.048	-0.048	0.000	0.000	0.000	0.000
97	B	123	TYR	0	-0.020	0.012	16.791	0.186	0.186	0.000	0.000	0.000	0.000
98	B	124	LYS	1	0.936	0.969	10.330	-24.083	-24.083	0.000	0.000	0.000	0.000
99	B	125	CYS	0	-0.160	-0.061	12.319	0.950	0.950	0.000	0.000	0.000	0.000
100	B	126	ARG	1	0.965	0.974	8.745	-28.156	-28.156	0.000	0.000	0.000	0.000
101	B	127	ASP	-1	-0.762	-0.872	10.173	24.247	24.247	0.000	0.000	0.000	0.000
102	B	128	ALA	0	0.019	-0.011	12.722	-1.554	-1.554	0.000	0.000	0.000	0.000
103	B	129	ALA	0	-0.045	-0.024	15.517	-1.308	-1.308	0.000	0.000	0.000	0.000
104	B	130	SER	0	0.024	0.009	15.885	-1.455	-1.455	0.000	0.000	0.000	0.000
105	B	131	ALA	0	0.029	-0.001	15.995	-0.864	-0.864	0.000	0.000	0.000	0.000
106	B	132	ARG	1	0.855	0.928	18.052	-17.857	-17.857	0.000	0.000	0.000	0.000
107	B	133	ALA	0	0.000	0.005	20.765	-0.821	-0.821	0.000	0.000	0.000	0.000
108	B	134	HIS	0	0.012	0.083	21.064	-0.566	-0.566	0.000	0.000	0.000	0.000
109	B	135	LEU	0	0.007	0.003	18.976	-0.515	-0.515	0.000	0.000	0.000	0.000
110	B	136	GLU	-1	-0.895	-0.953	19.802	13.629	13.629	0.000	0.000	0.000	0.000
111	B	137	THR	0	-0.023	-0.011	20.057	0.100	0.100	0.000	0.000	0.000	0.000
112	B	138	LEU	0	0.001	0.009	12.901	1.042	1.042	0.000	0.000	0.000	0.000
113	B	139	SER	0	-0.038	-0.015	16.593	-0.924	-0.924	0.000	0.000	0.000	0.000
114	B	140	SER	0	0.021	-0.004	15.408	0.336	0.336	0.000	0.000	0.000	0.000
115	B	141	ASP	-1	-0.933	-0.953	10.611	28.593	28.593	0.000	0.000	0.000	0.000
116	B	142	VAL	0	-0.008	-0.002	11.692	1.767	1.767	0.000	0.000	0.000	0.000
117	B	143	GLY	0	0.030	0.011	14.407	-1.150	-1.150	0.000	0.000	0.000	0.000
118	B	145	GLU	-1	-0.884	-0.952	13.683	21.314	21.314	0.000	0.000	0.000	0.000
119	B	146	ALA	0	0.012	0.008	15.722	0.493	0.493	0.000	0.000	0.000	0.000
120	B	147	PHE	0	-0.069	-0.039	14.942	0.682	0.682	0.000	0.000	0.000	0.000

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