FMO DATABASE

FMODB ID: 94Y52

Calculation Name: 2DP9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DP9

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SM30

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1081436.032049
FMO2-HF: Nuclear repulsion	1031518.370939
FMO2-HF: Total energy	-49917.66111
FMO2-MP2: Total energy	-50065.316774

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:-2:MET)

Summations of interaction energy for fragment #1(A:-2: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.
-12.961	-4.782	6.849	-4.249	-10.779	-0.04

Interaction energy analysis for fragmet #1(A:-2:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.040

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

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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	0	TYR	0	-0.025	0.008	2.381	-5.961	-1.822	1.229	-1.922	-3.447	-0.012
4	A	1	MET	0	0.008	0.019	5.068	1.131	1.229	-0.001	-0.009	-0.087	0.000
5	A	2	GLU	-1	-0.909	-0.955	7.861	-1.466	-1.466	0.000	0.000	0.000	0.000
6	A	3	ARG	1	0.861	0.906	6.726	-0.667	-0.667	0.000	0.000	0.000	0.000
7	A	4	PRO	0	-0.016	0.009	8.937	-0.062	-0.062	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.955	0.967	11.805	0.542	0.542	0.000	0.000	0.000	0.000
9	A	6	LEU	0	-0.001	0.010	14.724	0.060	0.060	0.000	0.000	0.000	0.000
10	A	7	GLY	0	0.022	0.008	14.263	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	8	LEU	0	0.001	0.014	14.660	0.011	0.011	0.000	0.000	0.000	0.000
12	A	9	ILE	0	-0.039	-0.024	15.894	0.055	0.055	0.000	0.000	0.000	0.000
13	A	10	VAL	0	0.013	0.011	14.509	-0.036	-0.036	0.000	0.000	0.000	0.000
14	A	11	ARG	1	0.942	0.976	17.691	-0.147	-0.147	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.722	-0.798	16.850	0.489	0.489	0.000	0.000	0.000	0.000
16	A	13	PRO	0	0.014	-0.003	18.359	-0.037	-0.037	0.000	0.000	0.000	0.000
17	A	14	TYR	0	0.043	0.004	16.229	0.054	0.054	0.000	0.000	0.000	0.000
18	A	15	ALA	0	-0.001	-0.008	13.976	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	16	SER	0	-0.014	-0.038	12.285	0.086	0.086	0.000	0.000	0.000	0.000
20	A	17	LEU	0	-0.030	-0.007	11.718	0.117	0.117	0.000	0.000	0.000	0.000
21	A	18	ILE	0	-0.001	0.011	8.820	0.025	0.025	0.000	0.000	0.000	0.000
22	A	19	VAL	0	-0.025	-0.012	7.412	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.852	-0.912	7.323	1.751	1.751	0.000	0.000	0.000	0.000
24	A	21	GLY	0	0.027	0.009	7.042	0.135	0.135	0.000	0.000	0.000	0.000
25	A	22	ARG	1	0.866	0.940	7.697	-0.857	-0.857	0.000	0.000	0.000	0.000
26	A	23	LYS	1	0.772	0.890	10.514	-0.143	-0.143	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.047	0.026	9.383	-0.030	-0.030	0.000	0.000	0.000	0.000
28	A	25	TRP	0	0.011	0.016	11.570	-0.070	-0.070	0.000	0.000	0.000	0.000
29	A	26	GLU	-1	-0.783	-0.892	14.383	0.099	0.099	0.000	0.000	0.000	0.000
30	A	27	ILE	0	-0.020	0.018	16.124	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	28	ARG	1	0.768	0.861	17.867	0.026	0.026	0.000	0.000	0.000	0.000
32	A	29	ARG	1	0.834	0.898	22.044	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	30	ARG	1	0.905	0.966	23.762	0.104	0.104	0.000	0.000	0.000	0.000
34	A	31	LYS	1	0.958	1.002	21.571	0.158	0.158	0.000	0.000	0.000	0.000
35	A	32	THR	0	0.005	-0.021	17.794	0.002	0.002	0.000	0.000	0.000	0.000
36	A	33	ARG	1	0.807	0.875	19.987	0.205	0.205	0.000	0.000	0.000	0.000
37	A	34	HIS	0	0.003	0.014	13.424	0.024	0.024	0.000	0.000	0.000	0.000
38	A	35	ARG	1	0.837	0.911	14.300	0.469	0.469	0.000	0.000	0.000	0.000
39	A	36	GLY	0	0.044	0.039	10.896	0.028	0.028	0.000	0.000	0.000	0.000
40	A	37	PRO	0	0.024	0.021	7.991	0.125	0.125	0.000	0.000	0.000	0.000
41	A	38	LEU	0	-0.079	-0.037	9.397	0.251	0.251	0.000	0.000	0.000	0.000
42	A	39	GLY	0	0.034	0.011	9.838	0.001	0.001	0.000	0.000	0.000	0.000
43	A	40	ILE	0	-0.001	0.004	9.948	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	41	VAL	0	-0.034	-0.026	12.573	0.124	0.124	0.000	0.000	0.000	0.000
45	A	42	SER	0	0.003	-0.033	16.105	-0.070	-0.070	0.000	0.000	0.000	0.000
46	A	43	GLY	0	0.025	0.008	18.028	0.033	0.033	0.000	0.000	0.000	0.000
47	A	44	GLY	0	-0.078	-0.039	20.890	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	45	ARG	1	0.900	0.936	16.989	-0.425	-0.425	0.000	0.000	0.000	0.000
49	A	46	LEU	0	0.017	0.015	12.029	-0.044	-0.044	0.000	0.000	0.000	0.000
50	A	47	ILE	0	-0.017	-0.019	12.029	0.106	0.106	0.000	0.000	0.000	0.000
51	A	48	GLY	0	0.076	0.027	8.658	0.356	0.356	0.000	0.000	0.000	0.000
52	A	49	GLN	0	-0.015	0.027	5.551	0.349	0.349	0.000	0.000	0.000	0.000
53	A	50	ALA	0	0.048	0.021	5.473	0.114	0.114	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.778	-0.884	5.710	-2.932	-2.932	0.000	0.000	0.000	0.000
55	A	52	LEU	0	-0.052	-0.023	7.845	0.147	0.147	0.000	0.000	0.000	0.000
56	A	53	VAL	0	0.038	0.013	10.161	0.016	0.016	0.000	0.000	0.000	0.000
57	A	54	GLY	0	-0.008	-0.010	12.852	0.062	0.062	0.000	0.000	0.000	0.000
58	A	55	VAL	0	-0.098	-0.056	15.760	0.012	0.012	0.000	0.000	0.000	0.000
59	A	56	GLU	-1	-0.886	-0.925	18.412	-0.251	-0.251	0.000	0.000	0.000	0.000
60	A	57	GLY	0	0.037	0.032	20.604	0.019	0.019	0.000	0.000	0.000	0.000
61	A	58	PRO	0	-0.109	-0.077	24.163	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	59	PHE	0	-0.003	0.006	21.411	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	60	SER	0	0.011	-0.025	26.966	0.009	0.009	0.000	0.000	0.000	0.000
64	A	61	VAL	0	0.005	-0.019	27.473	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.769	-0.879	27.580	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	63	GLU	-1	-0.813	-0.874	26.538	-0.071	-0.071	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.023	-0.015	21.848	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	65	LEU	0	-0.001	0.010	23.385	0.007	0.007	0.000	0.000	0.000	0.000
69	A	66	ALA	0	-0.032	-0.004	25.268	0.010	0.010	0.000	0.000	0.000	0.000
70	A	67	HIS	0	-0.012	-0.010	20.150	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	68	GLN	0	0.035	0.009	19.843	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	69	GLU	-1	-0.818	-0.911	17.272	0.012	0.012	0.000	0.000	0.000	0.000
73	A	70	LYS	1	0.853	0.927	15.344	0.114	0.114	0.000	0.000	0.000	0.000
74	A	71	HIS	0	-0.018	-0.023	14.857	0.004	0.004	0.000	0.000	0.000	0.000
75	A	72	LEU	0	-0.003	0.002	15.616	0.033	0.033	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.019	-0.002	19.058	0.023	0.023	0.000	0.000	0.000	0.000
77	A	74	GLU	-1	-0.878	-0.935	21.760	0.106	0.106	0.000	0.000	0.000	0.000
78	A	75	GLU	-1	-0.766	-0.869	25.257	0.028	0.028	0.000	0.000	0.000	0.000
79	A	76	ALA	0	0.004	0.005	28.144	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	77	PHE	0	-0.018	-0.023	24.862	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	78	LEU	0	0.006	0.015	23.163	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	79	ARG	1	0.797	0.858	26.798	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	80	ALA	0	-0.030	-0.004	29.952	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	81	TYR	0	-0.019	-0.006	23.845	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	82	ALA	0	0.065	0.019	28.453	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	83	LYS	1	0.786	0.889	29.545	-0.036	-0.036	0.000	0.000	0.000	0.000
87	A	84	ASP	-1	-0.881	-0.934	32.873	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	85	GLU	-1	-0.899	-0.920	30.667	-0.035	-0.035	0.000	0.000	0.000	0.000
89	A	86	PRO	0	-0.022	-0.020	29.389	0.001	0.001	0.000	0.000	0.000	0.000
90	A	87	LEU	0	-0.061	-0.025	24.368	0.002	0.002	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.006	-0.009	21.788	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	89	ALA	0	0.035	0.016	18.198	0.022	0.022	0.000	0.000	0.000	0.000
93	A	90	TRP	0	-0.065	-0.051	15.218	-0.042	-0.042	0.000	0.000	0.000	0.000
94	A	91	VAL	0	0.023	0.011	12.634	0.038	0.038	0.000	0.000	0.000	0.000
95	A	92	LEU	0	-0.049	-0.033	8.972	-0.080	-0.080	0.000	0.000	0.000	0.000
96	A	93	GLU	-1	-0.822	-0.916	6.972	-1.490	-1.490	0.000	0.000	0.000	0.000
97	A	94	ASN	0	-0.065	-0.053	2.579	-0.445	0.079	0.823	-0.176	-1.171	0.000
98	A	95	ALA	0	-0.019	-0.009	2.438	-2.429	-2.341	2.143	-0.672	-1.559	-0.018
99	A	96	PHE	0	0.002	0.003	2.381	-1.557	1.723	2.656	-1.447	-4.489	-0.010
100	A	97	ARG	1	0.812	0.887	4.697	-2.008	-1.958	-0.001	-0.023	-0.026	0.000
101	A	98	TYR	0	-0.039	-0.044	6.269	0.767	0.767	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.861	-0.933	7.347	2.560	2.560	0.000	0.000	0.000	0.000
103	A	100	LYS	1	0.904	0.938	9.575	-1.490	-1.490	0.000	0.000	0.000	0.000
104	A	101	PRO	0	0.004	0.021	12.142	0.013	0.013	0.000	0.000	0.000	0.000
105	A	102	LEU	0	0.058	0.037	11.080	-0.128	-0.128	0.000	0.000	0.000	0.000
106	A	103	HIS	0	0.004	0.001	15.126	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	104	VAL	0	0.055	0.029	17.447	-0.022	-0.022	0.000	0.000	0.000	0.000
108	A	105	PRO	0	0.034	0.028	20.018	0.003	0.003	0.000	0.000	0.000	0.000
109	A	106	ARG	1	0.974	0.990	23.727	-0.182	-0.182	0.000	0.000	0.000	0.000
110	A	107	ARG	1	0.976	1.001	26.311	-0.075	-0.075	0.000	0.000	0.000	0.000
111	A	108	PRO	0	0.036	0.003	28.851	0.010	0.010	0.000	0.000	0.000	0.000
112	A	109	GLY	0	0.042	0.014	29.031	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	110	ARG	1	0.734	0.858	21.132	-0.156	-0.156	0.000	0.000	0.000	0.000
114	A	111	VAL	0	0.071	0.041	24.433	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	112	MET	0	-0.051	-0.025	21.367	0.017	0.017	0.000	0.000	0.000	0.000
116	A	113	PHE	0	0.024	0.007	21.742	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	114	VAL	0	0.009	0.008	23.818	0.001	0.001	0.000	0.000	0.000	0.000
118	A	115	ASP	-1	-0.752	-0.819	21.743	-0.223	-0.223	0.000	0.000	0.000	0.000
119	A	116	LEU	0	0.011	-0.002	23.989	0.010	0.010	0.000	0.000	0.000	0.000
120	A	117	SER	0	-0.031	-0.038	22.582	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	118	GLU	-1	-0.831	-0.916	24.385	-0.194	-0.194	0.000	0.000	0.000	0.000
122	A	119	VAL	0	-0.025	0.002	26.804	0.018	0.018	0.000	0.000	0.000	0.000
123	A	120	ARG	1	0.908	0.956	30.170	0.111	0.111	0.000	0.000	0.000	0.000
124	A	121	TRP	0	0.045	0.030	28.778	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:MET)