FMO DATABASE

FMODB ID: MN4GZ

Calculation Name: 1R7J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R7J

Chain ID: A

ChEMBL ID:

UniProt ID: Q5W1E8

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	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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-624261.861215
FMO2-HF: Nuclear repulsion	586523.332845
FMO2-HF: Total energy	-37738.528369
FMO2-MP2: Total energy	-37844.651408

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
53.471	57.417	0.848	-2.206	-2.587	-0.013

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.995 / q_NPA : 0.998

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	5	SER	0	0.004	-0.033	2.604	-14.237	-10.449	0.850	-2.201	-2.437	-0.013
4	A	6	LYS	1	0.934	0.939	5.124	29.600	29.668	-0.001	-0.002	-0.065	0.000
5	A	7	LEU	0	0.050	0.031	7.205	2.488	2.488	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.746	-0.839	6.391	-35.331	-35.331	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.065	-0.021	4.783	1.453	1.543	-0.001	-0.003	-0.085	0.000
8	A	10	ILE	0	0.004	-0.011	8.597	2.267	2.267	0.000	0.000	0.000	0.000
9	A	11	GLN	0	0.009	-0.001	11.772	0.590	0.590	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.007	-0.001	10.575	1.343	1.343	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.028	-0.018	12.107	1.244	1.244	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.010	0.006	14.821	1.192	1.192	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.733	-0.850	14.990	-15.133	-15.133	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.041	-0.010	16.173	0.879	0.879	0.000	0.000	0.000	0.000
15	A	17	CYS	0	-0.076	-0.046	17.993	0.820	0.820	0.000	0.000	0.000	0.000
16	A	18	LYS	1	0.836	0.909	20.470	13.230	13.230	0.000	0.000	0.000	0.000
17	A	19	SER	0	0.018	0.010	22.483	0.414	0.414	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.017	0.035	23.678	0.371	0.371	0.000	0.000	0.000	0.000
19	A	21	SER	0	0.001	-0.012	19.242	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	22	PRO	0	0.026	0.039	20.997	-0.149	-0.149	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.906	0.943	16.801	16.303	16.303	0.000	0.000	0.000	0.000
22	A	24	THR	0	0.013	0.005	16.937	-1.032	-1.032	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.957	0.976	16.232	12.728	12.728	0.000	0.000	0.000	0.000
24	A	26	ILE	0	0.009	0.017	14.374	-0.826	-0.826	0.000	0.000	0.000	0.000
25	A	27	MET	0	-0.042	-0.008	12.733	-1.242	-1.242	0.000	0.000	0.000	0.000
26	A	28	TYR	0	0.016	0.001	11.286	-1.647	-1.647	0.000	0.000	0.000	0.000
27	A	29	GLY	0	0.044	0.035	10.424	-1.121	-1.121	0.000	0.000	0.000	0.000
28	A	30	ALA	0	-0.017	-0.027	9.513	-1.316	-1.316	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.050	-0.024	5.939	-1.821	-1.821	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.019	0.005	6.588	-4.370	-4.370	0.000	0.000	0.000	0.000
31	A	33	SER	0	0.097	0.043	8.944	2.372	2.372	0.000	0.000	0.000	0.000
32	A	34	TYR	0	0.136	0.050	11.240	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	35	ALA	0	0.019	0.009	13.700	0.698	0.698	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.013	-0.005	6.890	0.682	0.682	0.000	0.000	0.000	0.000
35	A	37	THR	0	0.041	-0.010	11.451	-0.145	-0.145	0.000	0.000	0.000	0.000
36	A	38	GLY	0	-0.019	-0.002	13.118	0.868	0.868	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.959	0.980	11.200	24.852	24.852	0.000	0.000	0.000	0.000
38	A	40	TYR	0	0.019	0.004	7.214	0.817	0.817	0.000	0.000	0.000	0.000
39	A	41	ILE	0	0.020	0.013	13.598	0.613	0.613	0.000	0.000	0.000	0.000
40	A	42	LYS	1	0.883	0.917	17.001	14.945	14.945	0.000	0.000	0.000	0.000
41	A	43	MET	0	0.000	0.009	12.528	-0.243	-0.243	0.000	0.000	0.000	0.000
42	A	44	LEU	0	0.011	-0.005	14.784	0.429	0.429	0.000	0.000	0.000	0.000
43	A	45	MET	0	-0.028	-0.005	18.230	0.621	0.621	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.823	-0.885	20.717	-13.877	-13.877	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.026	-0.005	17.863	0.358	0.358	0.000	0.000	0.000	0.000
46	A	48	GLU	-1	-0.846	-0.898	21.910	-11.295	-11.295	0.000	0.000	0.000	0.000
47	A	49	ILE	0	-0.024	0.021	18.464	0.203	0.203	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.022	-0.023	18.345	0.025	0.025	0.000	0.000	0.000	0.000
49	A	51	ARG	1	0.830	0.893	22.160	11.185	11.185	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.015	-0.021	24.385	-0.780	-0.780	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.772	-0.860	26.230	-9.877	-9.877	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.049	0.019	29.002	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.919	0.953	26.397	10.153	10.153	0.000	0.000	0.000	0.000
54	A	56	GLN	0	-0.026	0.002	24.686	-0.816	-0.816	0.000	0.000	0.000	0.000
55	A	57	TYR	0	-0.037	-0.034	21.176	-0.038	-0.038	0.000	0.000	0.000	0.000
56	A	58	MET	0	0.009	-0.007	23.140	0.021	0.021	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.023	0.027	20.078	-0.320	-0.320	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.024	-0.025	23.667	0.583	0.583	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.860	0.916	25.352	10.615	10.615	0.000	0.000	0.000	0.000
60	A	62	LYS	1	0.937	0.945	23.830	12.439	12.439	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.035	0.005	21.559	-0.535	-0.535	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.898	-0.932	21.285	-11.940	-11.940	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.884	-0.944	22.976	-11.489	-11.489	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.022	0.015	17.381	-0.371	-0.371	0.000	0.000	0.000	0.000
65	A	67	LEU	0	-0.038	-0.016	17.480	-0.804	-0.804	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.787	-0.879	19.209	-13.620	-13.620	0.000	0.000	0.000	0.000
67	A	69	ASP	-1	-0.855	-0.928	20.690	-13.400	-13.400	0.000	0.000	0.000	0.000
68	A	70	ILE	0	-0.070	-0.035	14.213	-0.637	-0.637	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.752	0.828	16.821	13.685	13.685	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.937	0.971	18.212	12.390	12.390	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.003	-0.008	13.521	-0.036	-0.036	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.008	-0.006	13.043	-1.272	-1.272	0.000	0.000	0.000	0.000
73	A	75	GLU	-1	-0.764	-0.837	15.882	-13.272	-13.272	0.000	0.000	0.000	0.000
74	A	76	MET	0	-0.029	-0.020	18.859	0.522	0.522	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.890	0.955	11.338	21.312	21.312	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.874	0.918	16.568	13.462	13.462	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.015	-0.023	17.553	0.390	0.390	0.000	0.000	0.000	0.000
78	A	80	MET	0	-0.019	-0.001	19.312	0.336	0.336	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.885	-0.951	15.246	-16.855	-16.855	0.000	0.000	0.000	0.000
80	A	82	GLN	0	-0.020	-0.009	18.660	0.150	0.150	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.038	-0.018	21.168	0.548	0.548	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.916	0.963	19.561	14.383	14.383	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.800	-0.896	19.541	-12.975	-12.975	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.926	0.976	22.356	10.090	10.090	0.000	0.000	0.000	0.000
85	A	87	ILE	0	-0.023	-0.011	25.368	0.412	0.412	0.000	0.000	0.000	0.000
86	A	88	ASN	0	0.011	-0.015	21.117	0.520	0.520	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.050	-0.017	25.320	0.375	0.375	0.000	0.000	0.000	0.000
88	A	90	VAL	0	-0.055	-0.027	27.415	0.295	0.295	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.025	-0.007	27.674	0.261	0.261	0.000	0.000	0.000	0.000
90	A	92	SER	0	-0.098	-0.048	26.545	-0.128	-0.128	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)