FMO DATABASE

FMODB ID: Q12KY

Calculation Name: 3R84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R84

Chain ID: A

ChEMBL ID:

UniProt ID: Q99278

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptHSide
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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-494991.026784
FMO2-HF: Nuclear repulsion	461884.105975
FMO2-HF: Total energy	-33106.920809
FMO2-MP2: Total energy	-33204.082458

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:GLY)

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

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.
-0.907	2.631	5.161	-4.166	-4.533	-0.012

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.082 / q_NPA : 0.038

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	ILE	0	0.060	0.017	3.566	-0.976	0.852	0.003	-0.973	-0.858	0.005
4	A	7	GLN	0	0.050	0.025	1.957	-2.249	-1.533	5.145	-2.803	-3.058	-0.015
5	A	8	GLU	-1	-0.815	-0.886	3.507	-5.092	-4.169	0.014	-0.386	-0.551	-0.002
6	A	9	ARG	1	0.816	0.892	5.818	2.990	2.990	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.026	0.007	7.293	0.415	0.415	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.864	0.916	4.486	3.730	3.801	-0.001	-0.004	-0.066	0.000
9	A	12	SER	0	-0.049	-0.032	9.301	0.327	0.327	0.000	0.000	0.000	0.000
10	A	13	LEU	0	-0.005	-0.013	11.518	0.202	0.202	0.000	0.000	0.000	0.000
11	A	14	ASN	0	-0.021	-0.018	11.542	0.032	0.032	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.837	-0.898	13.406	-0.535	-0.535	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.001	-0.011	15.240	0.101	0.101	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.859	-0.926	16.062	-0.426	-0.426	0.000	0.000	0.000	0.000
15	A	18	THR	0	-0.003	0.006	17.237	0.072	0.072	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.049	-0.035	17.833	0.088	0.088	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.023	0.009	21.171	0.041	0.041	0.000	0.000	0.000	0.000
18	A	21	CYS	0	-0.026	-0.011	22.082	0.038	0.038	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.054	-0.037	23.378	0.028	0.028	0.000	0.000	0.000	0.000
20	A	23	MET	0	-0.022	0.001	25.809	0.013	0.013	0.000	0.000	0.000	0.000
21	A	24	LEU	0	0.020	0.014	26.759	0.019	0.019	0.000	0.000	0.000	0.000
22	A	25	GLN	0	0.042	0.017	28.003	0.022	0.022	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.797	-0.857	29.520	-0.169	-0.169	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.026	0.020	31.946	0.012	0.012	0.000	0.000	0.000	0.000
25	A	28	SER	0	-0.005	0.008	33.011	0.013	0.013	0.000	0.000	0.000	0.000
26	A	29	GLN	0	-0.043	-0.032	32.101	0.015	0.015	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.004	0.006	35.921	0.008	0.008	0.000	0.000	0.000	0.000
28	A	31	THR	0	-0.025	-0.020	37.675	0.008	0.008	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.007	-0.012	39.308	0.006	0.006	0.000	0.000	0.000	0.000
30	A	33	ILE	0	0.000	-0.012	38.752	0.005	0.005	0.000	0.000	0.000	0.000
31	A	34	PHE	0	-0.002	0.009	42.166	0.006	0.006	0.000	0.000	0.000	0.000
32	A	35	GLY	0	0.005	0.001	44.161	0.004	0.004	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.810	-0.870	44.877	-0.065	-0.065	0.000	0.000	0.000	0.000
34	A	37	LEU	0	-0.008	0.002	44.599	0.004	0.004	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.877	0.951	48.138	0.074	0.074	0.000	0.000	0.000	0.000
36	A	39	ARG	1	0.831	0.888	48.785	0.067	0.067	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.013	0.014	51.577	0.003	0.003	0.000	0.000	0.000	0.000
38	A	41	ASN	0	-0.053	-0.017	47.326	0.002	0.002	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.756	-0.886	48.241	-0.079	-0.079	0.000	0.000	0.000	0.000
40	A	43	SER	0	-0.065	-0.043	47.570	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.011	-0.008	42.978	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.857	0.931	42.976	0.075	0.075	0.000	0.000	0.000	0.000
43	A	46	PRO	0	0.060	0.018	42.369	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.036	0.013	38.984	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	48	PHE	0	-0.031	-0.007	38.337	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.880	-0.951	38.889	-0.105	-0.105	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.027	-0.020	33.873	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	51	HIS	1	0.844	0.897	33.266	0.132	0.132	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.022	0.019	33.983	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.832	0.919	32.936	0.158	0.158	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.012	0.013	29.360	0.000	0.000	0.000	0.000	0.000	0.000
52	A	55	PHE	0	-0.028	-0.007	29.693	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	56	TYR	0	-0.033	-0.024	29.917	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.803	-0.908	28.507	-0.203	-0.203	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.827	0.890	25.040	0.217	0.217	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.028	0.026	25.223	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.882	-0.901	26.257	-0.274	-0.274	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.899	0.957	18.116	0.487	0.487	0.000	0.000	0.000	0.000
59	A	62	SER	0	0.008	-0.018	21.094	-0.037	-0.037	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.042	-0.038	21.235	-0.037	-0.037	0.000	0.000	0.000	0.000
61	A	64	THR	0	0.006	0.004	21.796	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.068	-0.052	14.819	0.051	0.051	0.000	0.000	0.000	0.000
63	A	66	LEU	0	0.026	0.002	17.850	-0.069	-0.069	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.891	0.949	19.322	0.377	0.377	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.874	0.928	13.679	0.942	0.942	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.763	-0.842	12.886	-1.262	-1.262	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.023	0.014	15.672	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	71	GLN	0	-0.005	0.008	18.235	0.035	0.035	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.031	-0.019	11.932	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.035	-0.008	13.480	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.899	-0.951	15.285	-0.287	-0.287	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.892	-0.932	15.397	-0.526	-0.526	0.000	0.000	0.000	0.000
73	A	76	ASN	0	-0.072	-0.057	11.156	-0.042	-0.042	0.000	0.000	0.000	0.000
74	A	77	VAL	0	0.049	0.036	14.058	0.029	0.029	0.000	0.000	0.000	0.000
75	A	78	GLY	0	-0.027	-0.009	16.444	0.020	0.020	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.042	-0.017	12.981	0.014	0.014	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.848	0.913	7.648	0.798	0.798	0.000	0.000	0.000	0.000
78	A	81	LEU	0	-0.034	-0.004	10.908	0.018	0.018	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.009	0.007	13.546	0.039	0.039	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.036	0.013	16.693	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	84	ILE	0	-0.016	0.007	19.913	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:4:GLY)