FMO DATABASE

FMODB ID: 39N2L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1080065.290955
FMO2-HF: Nuclear repulsion	1030148.409354
FMO2-HF: Total energy	-49916.881601
FMO2-MP2: Total energy	-50064.592457

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.
-13.146	-8.601	13.396	-3.421	-14.521	-0.049

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 : -0.081 / q_NPA : -0.039

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	0.007	0.021	2.491	-8.066	-3.314	2.372	-2.292	-4.832	-0.021
4	A	1	MET	0	0.007	-0.007	4.990	0.839	0.924	-0.001	-0.006	-0.078	0.000
5	A	2	GLU	-1	-0.950	-0.982	6.894	-0.921	-0.921	0.000	0.000	0.000	0.000
6	A	3	ARG	1	0.975	0.985	5.694	-2.109	-2.109	0.000	0.000	0.000	0.000
7	A	4	PRO	0	-0.014	0.003	8.700	-0.190	-0.190	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.970	0.972	11.521	0.259	0.259	0.000	0.000	0.000	0.000
9	A	6	LEU	0	-0.012	0.003	14.742	0.036	0.036	0.000	0.000	0.000	0.000
10	A	7	GLY	0	0.024	0.019	14.198	0.035	0.035	0.000	0.000	0.000	0.000
11	A	8	LEU	0	0.001	0.004	14.941	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	9	ILE	0	-0.063	-0.036	16.129	0.075	0.075	0.000	0.000	0.000	0.000
13	A	10	VAL	0	0.018	0.012	14.969	-0.060	-0.060	0.000	0.000	0.000	0.000
14	A	11	ARG	1	0.927	0.966	17.956	-0.251	-0.251	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.770	-0.869	17.375	0.731	0.731	0.000	0.000	0.000	0.000
16	A	13	PRO	0	0.003	-0.018	19.255	-0.049	-0.049	0.000	0.000	0.000	0.000
17	A	14	TYR	0	0.048	0.003	16.930	0.061	0.061	0.000	0.000	0.000	0.000
18	A	15	ALA	0	-0.001	-0.001	14.550	0.029	0.029	0.000	0.000	0.000	0.000
19	A	16	SER	0	0.028	-0.006	12.945	0.164	0.164	0.000	0.000	0.000	0.000
20	A	17	LEU	0	-0.027	-0.001	12.600	0.138	0.138	0.000	0.000	0.000	0.000
21	A	18	ILE	0	-0.014	0.004	9.507	0.038	0.038	0.000	0.000	0.000	0.000
22	A	19	VAL	0	-0.044	-0.018	8.122	0.030	0.030	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.832	-0.896	7.762	2.301	2.301	0.000	0.000	0.000	0.000
24	A	21	GLY	0	-0.006	-0.006	7.846	0.008	0.008	0.000	0.000	0.000	0.000
25	A	22	ARG	1	0.913	0.956	8.500	-0.867	-0.867	0.000	0.000	0.000	0.000
26	A	23	LYS	1	0.768	0.895	11.510	-0.336	-0.336	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.067	0.032	9.536	0.035	0.035	0.000	0.000	0.000	0.000
28	A	25	TRP	0	0.017	0.021	11.687	-0.074	-0.074	0.000	0.000	0.000	0.000
29	A	26	GLU	-1	-0.812	-0.910	14.321	0.289	0.289	0.000	0.000	0.000	0.000
30	A	27	ILE	0	-0.006	0.005	15.982	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	28	ARG	1	0.808	0.906	18.193	-0.128	-0.128	0.000	0.000	0.000	0.000
32	A	29	ARG	1	0.922	0.950	21.709	-0.083	-0.083	0.000	0.000	0.000	0.000
33	A	30	ARG	1	0.932	0.969	23.470	0.013	0.013	0.000	0.000	0.000	0.000
34	A	31	LYS	1	0.958	1.003	21.474	0.099	0.099	0.000	0.000	0.000	0.000
35	A	32	THR	0	0.021	-0.008	17.628	0.007	0.007	0.000	0.000	0.000	0.000
36	A	33	ARG	1	0.843	0.889	19.516	0.132	0.132	0.000	0.000	0.000	0.000
37	A	34	HIS	0	-0.021	0.002	13.035	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	35	ARG	1	0.878	0.931	13.876	0.360	0.360	0.000	0.000	0.000	0.000
39	A	36	GLY	0	0.042	0.034	10.671	0.025	0.025	0.000	0.000	0.000	0.000
40	A	37	PRO	0	0.025	0.024	8.288	0.130	0.130	0.000	0.000	0.000	0.000
41	A	38	LEU	0	-0.049	-0.026	9.214	0.138	0.138	0.000	0.000	0.000	0.000
42	A	39	GLY	0	0.023	0.009	10.113	0.134	0.134	0.000	0.000	0.000	0.000
43	A	40	ILE	0	0.015	0.011	10.330	-0.155	-0.155	0.000	0.000	0.000	0.000
44	A	41	VAL	0	-0.042	-0.034	12.920	0.124	0.124	0.000	0.000	0.000	0.000
45	A	42	SER	0	0.036	0.016	16.415	-0.119	-0.119	0.000	0.000	0.000	0.000
46	A	43	GLY	0	0.007	-0.002	18.243	0.030	0.030	0.000	0.000	0.000	0.000
47	A	44	GLY	0	-0.108	-0.060	20.847	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	45	ARG	1	0.939	0.973	16.981	-0.600	-0.600	0.000	0.000	0.000	0.000
49	A	46	LEU	0	0.018	0.014	12.090	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	47	ILE	0	-0.002	-0.014	12.047	0.097	0.097	0.000	0.000	0.000	0.000
51	A	48	GLY	0	0.092	0.039	8.434	0.405	0.405	0.000	0.000	0.000	0.000
52	A	49	GLN	0	-0.014	0.029	5.782	0.050	0.050	0.000	0.000	0.000	0.000
53	A	50	ALA	0	0.052	0.024	5.532	0.384	0.384	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.819	-0.894	5.740	-2.325	-2.325	0.000	0.000	0.000	0.000
55	A	52	LEU	0	-0.065	-0.032	7.543	0.109	0.109	0.000	0.000	0.000	0.000
56	A	53	VAL	0	0.026	-0.001	9.291	0.003	0.003	0.000	0.000	0.000	0.000
57	A	54	GLY	0	-0.017	-0.011	12.108	0.020	0.020	0.000	0.000	0.000	0.000
58	A	55	VAL	0	-0.093	-0.043	15.413	0.038	0.038	0.000	0.000	0.000	0.000
59	A	56	GLU	-1	-0.882	-0.927	18.056	-0.247	-0.247	0.000	0.000	0.000	0.000
60	A	57	GLY	0	0.022	0.017	20.343	0.028	0.028	0.000	0.000	0.000	0.000
61	A	58	PRO	0	-0.109	-0.075	23.839	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	59	PHE	0	0.006	0.005	21.284	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	60	SER	0	0.032	0.018	26.532	0.013	0.013	0.000	0.000	0.000	0.000
64	A	61	VAL	0	0.018	-0.025	27.688	0.001	0.001	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.833	-0.931	27.821	0.019	0.019	0.000	0.000	0.000	0.000
66	A	63	GLU	-1	-0.865	-0.925	26.971	-0.050	-0.050	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.005	-0.009	21.801	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	65	LEU	0	-0.020	0.009	23.625	0.006	0.006	0.000	0.000	0.000	0.000
69	A	66	ALA	0	-0.027	0.001	25.400	0.007	0.007	0.000	0.000	0.000	0.000
70	A	67	HIS	0	-0.005	-0.015	20.004	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	68	GLN	0	0.019	0.009	20.145	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	69	GLU	-1	-0.846	-0.948	17.555	0.032	0.032	0.000	0.000	0.000	0.000
73	A	70	LYS	1	0.903	0.976	15.634	0.163	0.163	0.000	0.000	0.000	0.000
74	A	71	HIS	0	-0.027	-0.022	15.429	0.049	0.049	0.000	0.000	0.000	0.000
75	A	72	LEU	0	-0.029	-0.005	16.012	0.059	0.059	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.032	-0.015	19.566	0.030	0.030	0.000	0.000	0.000	0.000
77	A	74	GLU	-1	-0.869	-0.931	22.127	0.135	0.135	0.000	0.000	0.000	0.000
78	A	75	GLU	-1	-0.765	-0.867	25.753	0.056	0.056	0.000	0.000	0.000	0.000
79	A	76	ALA	0	-0.007	-0.004	28.304	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	77	PHE	0	-0.030	-0.034	25.368	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	78	LEU	0	0.030	0.020	23.353	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	79	ARG	1	0.835	0.906	27.083	-0.054	-0.054	0.000	0.000	0.000	0.000
83	A	80	ALA	0	-0.035	-0.007	30.574	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	81	TYR	0	-0.050	-0.027	23.948	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	82	ALA	0	0.041	-0.008	28.281	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	83	LYS	1	0.831	0.938	29.317	-0.082	-0.082	0.000	0.000	0.000	0.000
87	A	84	ASP	-1	-0.911	-0.947	32.916	0.014	0.014	0.000	0.000	0.000	0.000
88	A	85	GLU	-1	-0.957	-0.959	31.199	0.017	0.017	0.000	0.000	0.000	0.000
89	A	86	PRO	0	-0.031	-0.030	29.043	0.003	0.003	0.000	0.000	0.000	0.000
90	A	87	LEU	0	-0.055	-0.015	24.174	0.012	0.012	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.007	-0.007	21.539	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	89	ALA	0	0.036	0.017	17.943	0.032	0.032	0.000	0.000	0.000	0.000
93	A	90	TRP	0	-0.082	-0.048	14.893	-0.035	-0.035	0.000	0.000	0.000	0.000
94	A	91	VAL	0	0.042	0.008	12.004	0.060	0.060	0.000	0.000	0.000	0.000
95	A	92	LEU	0	-0.038	-0.037	8.828	-0.048	-0.048	0.000	0.000	0.000	0.000
96	A	93	GLU	-1	-0.881	-0.944	6.548	-1.422	-1.422	0.000	0.000	0.000	0.000
97	A	94	ASN	0	-0.030	-0.024	2.089	0.181	-1.231	4.288	-0.709	-2.167	0.001
98	A	95	ALA	0	-0.016	-0.007	2.349	-0.130	-2.188	2.590	1.350	-1.882	-0.026
99	A	96	PHE	0	0.010	0.005	2.977	-0.698	2.413	4.147	-1.727	-5.532	-0.003
100	A	97	ARG	1	0.804	0.881	5.086	-2.923	-2.856	0.000	-0.037	-0.030	0.000
101	A	98	TYR	0	-0.086	-0.069	6.199	0.449	0.449	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.886	-0.936	7.497	3.079	3.079	0.000	0.000	0.000	0.000
103	A	100	LYS	1	0.925	0.950	10.016	-1.513	-1.513	0.000	0.000	0.000	0.000
104	A	101	PRO	0	-0.003	0.014	12.387	0.055	0.055	0.000	0.000	0.000	0.000
105	A	102	LEU	0	0.040	0.021	11.482	-0.176	-0.176	0.000	0.000	0.000	0.000
106	A	103	HIS	0	-0.008	-0.008	15.378	-0.029	-0.029	0.000	0.000	0.000	0.000
107	A	104	VAL	0	0.034	0.025	17.464	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	105	PRO	0	0.020	0.024	19.832	-0.021	-0.021	0.000	0.000	0.000	0.000
109	A	106	ARG	1	0.989	0.982	23.352	-0.302	-0.302	0.000	0.000	0.000	0.000
110	A	107	ARG	1	0.956	1.001	25.879	-0.207	-0.207	0.000	0.000	0.000	0.000
111	A	108	PRO	0	0.027	-0.008	28.514	0.010	0.010	0.000	0.000	0.000	0.000
112	A	109	GLY	0	0.070	0.027	28.924	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	110	ARG	1	0.808	0.894	22.862	-0.309	-0.309	0.000	0.000	0.000	0.000
114	A	111	VAL	0	0.068	0.044	23.932	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	112	MET	0	-0.062	-0.030	22.265	0.031	0.031	0.000	0.000	0.000	0.000
116	A	113	PHE	0	0.030	0.013	21.887	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	114	VAL	0	0.004	0.001	23.741	0.008	0.008	0.000	0.000	0.000	0.000
118	A	115	ASP	-1	-0.775	-0.842	21.572	-0.094	-0.094	0.000	0.000	0.000	0.000
119	A	116	LEU	0	0.013	-0.010	23.586	0.003	0.003	0.000	0.000	0.000	0.000
120	A	117	SER	0	-0.022	-0.019	21.976	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	118	GLU	-1	-0.861	-0.935	23.541	-0.140	-0.140	0.000	0.000	0.000	0.000
122	A	119	VAL	0	-0.051	-0.003	26.266	0.008	0.008	0.000	0.000	0.000	0.000
123	A	120	ARG	1	0.915	0.958	29.571	0.067	0.067	0.000	0.000	0.000	0.000
124	A	121	TRP	0	0.050	0.035	28.337	0.013	0.013	0.000	0.000	0.000	0.000

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