FMO DATABASE

FMODB ID: 2NLRR

Calculation Name: 2IC9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IC9

Chain ID: A

ChEMBL ID:

UniProt ID: Q89462

Base Structure: X-ray

Registration Date: 2023-09-22

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-411519.559431
FMO2-HF: Nuclear repulsion	382528.626534
FMO2-HF: Total energy	-28990.932896
FMO2-MP2: Total energy	-29076.546878

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-10.214	-8.731	16.111	-6.922	-10.674	-0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : 0.020

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	3	THR	0	-0.041	-0.027	2.511	-6.457	-2.602	2.715	-2.700	-3.870	-0.022
4	A	4	LEU	0	0.022	-0.001	2.408	-1.404	-0.451	3.138	-1.003	-3.089	0.000
5	A	5	LYS	1	0.855	0.928	2.994	2.814	3.510	0.031	-0.188	-0.539	0.000
6	A	6	GLU	-1	-0.778	-0.904	4.748	-3.910	-3.872	-0.001	-0.015	-0.022	0.000
7	A	7	VAL	0	0.023	0.024	7.145	0.383	0.383	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.048	0.027	7.711	0.328	0.328	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.828	-0.894	9.001	-1.735	-1.735	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.018	-0.003	11.045	0.226	0.226	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.007	0.016	11.271	0.122	0.122	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.012	-0.024	12.544	0.094	0.094	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.006	-0.002	14.884	0.079	0.079	0.000	0.000	0.000	0.000
14	A	14	HIS	0	-0.045	-0.030	16.540	0.105	0.105	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.814	-0.896	16.802	-0.169	-0.169	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.003	0.002	17.940	0.030	0.030	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.903	0.951	20.126	0.422	0.422	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.003	0.028	22.419	0.026	0.026	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.005	0.006	23.308	0.025	0.025	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.007	0.001	25.556	0.021	0.021	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.049	-0.042	26.386	0.019	0.019	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.889	0.916	26.175	0.118	0.118	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.059	-0.021	29.890	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.977	0.977	28.708	0.210	0.210	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.027	-0.002	32.408	0.004	0.004	0.000	0.000	0.000	0.000
26	A	26	LYS	1	1.000	1.003	31.408	0.108	0.108	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.871	-0.925	35.504	-0.113	-0.113	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.010	0.007	37.418	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.842	-0.916	36.928	-0.070	-0.070	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.838	0.900	37.654	0.097	0.097	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.004	0.012	41.894	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.006	-0.013	42.926	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.967	-0.978	44.446	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.083	-0.038	46.271	0.003	0.003	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.870	-0.933	47.708	-0.057	-0.057	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.003	0.001	47.801	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.741	-0.866	47.663	-0.068	-0.068	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.862	-0.917	47.179	-0.058	-0.058	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.002	0.018	44.222	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.006	0.001	43.378	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.790	0.877	42.404	0.052	0.052	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.028	-0.026	41.824	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.028	-0.016	38.584	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.008	-0.011	37.654	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	45	GLN	0	0.005	0.002	37.175	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.029	-0.027	35.678	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.864	0.945	33.272	0.122	0.122	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.909	0.936	32.282	0.061	0.061	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.018	0.033	32.148	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.015	-0.010	29.492	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.001	-0.008	27.758	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.014	-0.006	27.041	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.004	0.017	26.728	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.022	-0.013	22.603	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.805	-0.898	22.212	-0.101	-0.101	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.030	-0.018	22.752	0.018	0.018	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.862	0.940	16.897	0.213	0.213	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.019	-0.022	17.318	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.001	0.005	17.992	0.021	0.021	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.894	-0.945	18.389	-0.093	-0.093	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.025	-0.011	13.797	0.036	0.036	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.845	0.904	13.463	0.172	0.172	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.916	0.975	14.444	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.846	-0.931	12.420	-0.170	-0.170	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.006	0.000	7.204	0.116	0.116	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.005	-0.001	9.641	0.348	0.348	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.874	-0.944	11.665	0.521	0.521	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.012	-0.006	6.575	0.098	0.098	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.011	-0.008	7.311	0.511	0.511	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.038	-0.021	8.432	0.104	0.104	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.024	0.006	8.916	0.029	0.029	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.037	-0.042	2.313	-1.510	-5.569	10.228	-3.016	-3.154	0.016
73	A	73	LYS	1	0.844	0.943	7.175	-1.588	-1.588	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.056	-0.013	10.228	-0.246	-0.246	0.000	0.000	0.000	0.000

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