FMO DATABASE

FMODB ID: 2NQRR

Calculation Name: 3M9Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M9Q

Chain ID: A

ChEMBL ID:

UniProt ID: P50536

Base Structure: X-ray

Registration Date: 2023-09-23

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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-650401.273753
FMO2-HF: Nuclear repulsion	613634.966762
FMO2-HF: Total energy	-36766.306991
FMO2-MP2: Total energy	-36875.917331

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:4:LEU)

Summations of interaction energy for fragment #1(A:4:LEU)

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.
-10.194	-2.634	1.193	-1.252	-7.501	-0.052

Interaction energy analysis for fragmet #1(A:4:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.014

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	6	ASP	-1	-0.829	-0.906	3.166	-3.578	0.132	0.069	-1.917	-1.862	-0.008
4	A	7	GLU	-1	-0.823	-0.910	5.671	-0.292	-0.292	0.000	0.000	0.000	0.000
5	A	8	THR	0	-0.005	-0.008	7.053	0.026	0.026	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.020	0.005	10.730	-0.008	-0.008	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.021	-0.004	11.518	0.024	0.024	0.000	0.000	0.000	0.000
8	A	11	PHE	0	-0.024	-0.012	14.633	0.017	0.017	0.000	0.000	0.000	0.000
9	A	12	HIS	0	0.019	0.013	17.925	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.955	0.961	20.682	0.088	0.088	0.000	0.000	0.000	0.000
11	A	14	GLY	0	-0.053	-0.034	23.001	0.006	0.006	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.784	-0.871	20.929	-0.072	-0.072	0.000	0.000	0.000	0.000
13	A	16	ILE	0	-0.005	-0.010	23.965	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	17	VAL	0	0.004	0.005	19.851	0.001	0.001	0.000	0.000	0.000	0.000
15	A	18	LEU	0	0.013	0.009	21.552	0.001	0.001	0.000	0.000	0.000	0.000
16	A	19	CYS	0	-0.027	-0.020	19.283	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	20	TYR	0	-0.001	-0.004	17.435	0.007	0.007	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.798	-0.863	19.601	-0.090	-0.090	0.000	0.000	0.000	0.000
19	A	22	PRO	0	-0.093	-0.042	18.564	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.792	-0.870	19.377	-0.084	-0.084	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.949	0.955	15.145	0.150	0.150	0.000	0.000	0.000	0.000
22	A	25	SER	0	-0.071	-0.042	21.334	0.007	0.007	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.844	0.926	24.341	0.069	0.069	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.057	0.034	24.585	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.912	0.955	17.613	0.075	0.075	0.000	0.000	0.000	0.000
26	A	29	VAL	0	0.097	0.052	23.726	0.005	0.005	0.000	0.000	0.000	0.000
27	A	30	LEU	0	0.005	0.001	20.881	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	31	TYR	0	-0.044	-0.058	23.289	0.007	0.007	0.000	0.000	0.000	0.000
29	A	32	THR	0	0.077	0.044	24.020	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.047	-0.029	22.639	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.961	0.994	24.749	0.066	0.066	0.000	0.000	0.000	0.000
32	A	35	VAL	0	0.014	0.018	19.782	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.060	-0.039	22.120	0.007	0.007	0.000	0.000	0.000	0.000
34	A	37	ASN	0	-0.076	-0.062	20.043	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.023	0.020	15.626	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	39	PHE	0	-0.016	0.009	15.689	0.003	0.003	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.835	-0.887	12.045	-0.265	-0.265	0.000	0.000	0.000	0.000
38	A	41	ARG	1	0.844	0.920	10.485	0.325	0.325	0.000	0.000	0.000	0.000
39	A	42	ARG	1	0.966	0.974	8.470	0.377	0.377	0.000	0.000	0.000	0.000
40	A	43	ASN	0	0.009	0.010	2.795	-0.710	-0.085	0.144	-0.207	-0.562	-0.001
41	A	44	GLU	-1	-0.857	-0.941	6.178	-0.888	-0.888	0.000	0.000	0.000	0.000
42	A	45	HIS	0	-0.037	-0.013	3.468	-1.109	-0.147	0.048	-0.253	-0.757	-0.001
43	A	46	GLY	0	-0.027	-0.003	5.683	-0.039	-0.039	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.081	0.058	2.174	-5.369	-3.106	0.932	1.125	-4.320	-0.042
45	A	48	ARG	1	0.924	0.956	5.816	0.458	0.458	0.000	0.000	0.000	0.000
46	A	49	PHE	0	-0.047	-0.020	6.156	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	50	TYR	0	-0.054	-0.060	8.123	0.035	0.035	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.889	-0.933	11.156	-0.261	-0.261	0.000	0.000	0.000	0.000
49	A	52	TYR	0	0.040	0.015	12.051	0.029	0.029	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.971	0.994	16.308	0.113	0.113	0.000	0.000	0.000	0.000
51	A	54	ILE	0	-0.004	-0.009	18.969	0.008	0.008	0.000	0.000	0.000	0.000
52	A	55	HIS	1	0.815	0.903	21.617	0.071	0.071	0.000	0.000	0.000	0.000
53	A	56	PHE	0	0.045	0.022	21.444	0.001	0.001	0.000	0.000	0.000	0.000
54	A	57	GLN	0	0.029	-0.002	26.529	0.001	0.001	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.004	0.006	29.496	0.001	0.001	0.000	0.000	0.000	0.000
56	A	59	TRP	0	0.005	0.023	29.317	0.002	0.002	0.000	0.000	0.000	0.000
57	A	60	ARG	1	0.948	0.962	31.301	0.057	0.057	0.000	0.000	0.000	0.000
58	A	61	PRO	0	0.079	0.005	29.146	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	62	SER	0	-0.012	0.013	28.053	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	63	TYR	0	-0.026	-0.013	26.958	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.819	-0.897	24.241	-0.088	-0.088	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.935	0.970	17.869	0.121	0.121	0.000	0.000	0.000	0.000
63	A	66	ALA	0	-0.001	0.011	16.398	0.004	0.004	0.000	0.000	0.000	0.000
64	A	67	VAL	0	-0.021	-0.007	14.681	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.936	0.952	5.057	0.472	0.472	0.000	0.000	0.000	0.000
66	A	69	ALA	0	0.078	0.023	10.478	0.024	0.024	0.000	0.000	0.000	0.000
67	A	70	THR	0	0.010	0.006	8.613	0.016	0.016	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.053	-0.020	11.606	0.022	0.022	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.039	-0.007	14.783	0.016	0.016	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.012	0.015	16.356	0.000	0.000	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.842	0.901	18.375	0.071	0.071	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.822	-0.892	21.159	-0.042	-0.042	0.000	0.000	0.000	0.000
73	A	76	THR	0	0.005	0.000	23.423	0.001	0.001	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.807	-0.904	25.995	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.882	-0.951	25.448	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	79	ASN	0	-0.029	-0.028	21.026	0.001	0.001	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.842	0.912	24.912	0.033	0.033	0.000	0.000	0.000	0.000
78	A	81	GLN	0	-0.044	-0.026	28.157	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.039	0.035	22.401	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	83	GLN	0	-0.087	-0.060	26.281	0.000	0.000	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.906	0.944	27.361	0.025	0.025	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.893	-0.928	28.540	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.024	-0.028	23.869	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	87	ALA	0	-0.057	-0.026	28.443	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.965	-0.981	30.712	-0.020	-0.020	0.000	0.000	0.000	0.000
86	A	89	ALA	0	0.036	0.018	30.041	0.001	0.001	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.081	-0.043	29.508	0.000	0.000	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.856	0.931	31.295	0.032	0.032	0.000	0.000	0.000	0.000
89	A	92	LEU	0	-0.004	0.020	34.503	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LEU)