FMO DATABASE

FMODB ID: R8NK8

Calculation Name: 2I4R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I4R

Chain ID: A

ChEMBL ID:

UniProt ID: O29102

Base Structure: X-ray

Registration Date: 2023-09-20

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-510083.316577
FMO2-HF: Nuclear repulsion	479071.929477
FMO2-HF: Total energy	-31011.3871
FMO2-MP2: Total energy	-31101.434347

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:SER)

Summations of interaction energy for fragment #1(A:-2:SER)

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.
-22.979	-18.488	9.432	-6.49	-7.433	-0.046

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.027

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	MET	0	-0.042	-0.011	2.205	2.121	5.824	0.923	-2.101	-2.525	0.009
4	A	4	LEU	0	-0.007	-0.008	4.251	-0.576	-0.535	-0.001	-0.022	-0.018	0.000
5	A	5	ALA	0	0.053	0.033	8.037	0.306	0.306	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.035	-0.026	9.570	0.076	0.076	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.011	0.003	13.424	0.036	0.036	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.022	-0.036	16.152	0.019	0.019	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.784	-0.880	19.708	-0.230	-0.230	0.000	0.000	0.000	0.000
10	A	10	PRO	0	0.060	0.031	21.451	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.932	-0.958	22.440	-0.105	-0.105	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.056	-0.029	17.907	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.015	-0.030	17.162	0.011	0.011	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.016	0.009	18.350	0.026	0.026	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.002	0.001	20.505	0.035	0.035	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.017	-0.016	15.197	0.016	0.016	0.000	0.000	0.000	0.000
17	A	17	MET	0	0.010	0.016	15.976	0.060	0.060	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.064	-0.027	17.256	0.064	0.064	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.069	-0.024	17.117	0.032	0.032	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.019	-0.006	15.568	0.044	0.044	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.048	-0.017	10.799	0.100	0.100	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.049	0.003	10.747	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.857	-0.880	6.711	-1.438	-1.438	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.010	-0.010	10.092	-0.170	-0.170	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.006	0.012	10.385	-0.045	-0.045	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.895	-0.965	15.446	-0.148	-0.148	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.078	-0.025	19.002	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.071	-0.054	21.059	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.034	-0.030	24.784	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.816	-0.919	24.716	-0.300	-0.300	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.891	-0.950	24.614	-0.277	-0.277	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.801	-0.870	21.761	-0.291	-0.291	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.025	-0.017	20.346	-0.053	-0.053	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.021	-0.013	19.689	-0.064	-0.064	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.878	0.925	18.046	0.412	0.412	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.004	0.005	16.200	-0.066	-0.066	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.006	-0.010	14.740	-0.123	-0.123	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.837	-0.910	15.052	-0.682	-0.682	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.845	-0.902	13.775	-0.727	-0.727	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.069	-0.026	9.547	-0.128	-0.128	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.003	-0.003	10.100	-0.374	-0.374	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.734	0.843	12.104	0.679	0.679	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.650	0.772	5.231	2.671	2.671	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.904	-0.952	6.099	-2.385	-2.385	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.821	-0.878	2.133	-7.562	-6.337	2.895	-2.029	-2.091	-0.003
46	A	46	VAL	0	0.001	0.009	1.950	-12.488	-13.043	5.616	-2.328	-2.733	-0.052
47	A	47	GLY	0	0.054	0.030	4.796	0.282	0.359	-0.001	-0.010	-0.066	0.000
48	A	48	VAL	0	-0.089	-0.041	6.881	0.959	0.959	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.041	0.029	8.885	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.036	-0.008	11.507	0.140	0.140	0.000	0.000	0.000	0.000
51	A	51	MET	0	0.013	0.015	14.735	0.015	0.015	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.866	0.957	17.732	0.311	0.311	0.000	0.000	0.000	0.000
53	A	53	GLN	0	0.008	-0.015	21.559	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.858	-0.937	23.232	-0.286	-0.286	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.054	0.021	20.220	0.033	0.033	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.044	0.029	20.416	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.800	0.895	23.444	0.282	0.282	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.839	0.910	24.501	0.303	0.303	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.019	0.034	20.080	0.008	0.008	0.000	0.000	0.000	0.000
60	A	60	PRO	0	0.037	0.010	23.480	0.027	0.027	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.043	-0.033	24.791	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.017	0.009	23.588	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.116	0.064	18.317	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.830	0.901	20.574	0.340	0.340	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.732	0.819	22.730	0.462	0.462	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.882	-0.916	17.599	-0.790	-0.790	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.011	0.009	16.327	-0.079	-0.079	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.885	-0.894	18.100	-0.513	-0.513	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.887	-0.963	16.899	-0.766	-0.766	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.771	0.878	15.595	0.771	0.771	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.012	0.009	11.860	-0.057	-0.057	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.821	-0.900	6.792	-3.612	-3.612	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.009	0.016	8.376	0.089	0.089	0.000	0.000	0.000	0.000
74	A	74	THR	0	0.009	-0.002	9.954	0.536	0.536	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.003	-0.015	12.265	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.028	-0.017	14.480	0.112	0.112	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.016	-0.007	16.747	0.023	0.023	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.021	0.009	19.163	0.045	0.045	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.005	0.008	21.767	0.016	0.016	0.000	0.000	0.000	0.000

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