FMO DATABASE

FMODB ID: YVYZ2

Calculation Name: 5MR1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MR1

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WWN9

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	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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-810844.708613
FMO2-HF: Nuclear repulsion	769524.750555
FMO2-HF: Total energy	-41319.958058
FMO2-MP2: Total energy	-41440.725506

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:42:ALA)

Summations of interaction energy for fragment #1(A:42:ALA)

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.
-25.103	-21.31	10.881	-6.774	-7.898	0.02

Interaction energy analysis for fragmet #1(A:42:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.013

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	44	CYS	0	-0.028	-0.010	2.963	-0.338	1.336	0.029	-0.778	-0.925	0.001
4	A	45	GLN	0	0.019	0.010	3.141	-1.884	-0.310	0.153	-0.708	-1.019	-0.006
5	A	46	GLY	0	0.037	0.018	4.847	0.156	0.149	-0.001	-0.004	0.013	0.000
6	A	47	TRP	0	-0.002	0.005	8.567	0.059	0.059	0.000	0.000	0.000	0.000
7	A	48	LEU	0	0.000	0.010	10.749	0.031	0.031	0.000	0.000	0.000	0.000
8	A	49	TYR	0	-0.089	-0.083	13.535	0.039	0.039	0.000	0.000	0.000	0.000
9	A	50	LYS	1	0.981	0.996	15.950	0.142	0.142	0.000	0.000	0.000	0.000
10	A	51	LYS	1	0.814	0.928	17.820	0.119	0.119	0.000	0.000	0.000	0.000
11	A	52	LYS	1	0.972	0.971	21.212	0.119	0.119	0.000	0.000	0.000	0.000
12	A	53	GLU	-1	-0.787	-0.881	23.099	-0.047	-0.047	0.000	0.000	0.000	0.000
13	A	54	LYS	1	0.997	0.994	24.563	0.041	0.041	0.000	0.000	0.000	0.000
14	A	55	GLY	0	-0.032	-0.002	26.543	0.002	0.002	0.000	0.000	0.000	0.000
15	A	56	SER	0	0.062	0.028	27.680	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	57	PHE	0	0.065	0.025	25.474	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	58	LEU	0	0.043	0.023	28.087	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	59	SER	0	-0.037	-0.006	27.897	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	60	ASN	0	0.064	0.010	25.932	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	61	LYS	1	0.929	0.966	25.247	0.095	0.095	0.000	0.000	0.000	0.000
21	A	62	TRP	0	-0.023	-0.025	19.488	0.007	0.007	0.000	0.000	0.000	0.000
22	A	63	LYS	1	0.882	0.965	17.449	0.201	0.201	0.000	0.000	0.000	0.000
23	A	64	LYS	1	0.865	0.928	15.552	0.340	0.340	0.000	0.000	0.000	0.000
24	A	65	PHE	0	0.003	-0.005	12.836	0.034	0.034	0.000	0.000	0.000	0.000
25	A	66	TRP	0	0.054	0.044	6.573	0.040	0.040	0.000	0.000	0.000	0.000
26	A	67	VAL	0	-0.015	-0.020	7.931	0.087	0.087	0.000	0.000	0.000	0.000
27	A	68	ILE	0	0.055	0.018	2.401	-0.594	-0.553	1.278	-0.392	-0.927	-0.001
28	A	69	LEU	0	-0.014	0.003	3.763	0.379	0.558	0.000	-0.041	-0.138	0.000
29	A	70	LYS	1	0.862	0.918	2.015	-24.049	-23.792	9.413	-4.815	-4.854	0.026
30	A	71	GLY	0	0.016	0.015	3.776	-0.297	-0.222	0.009	-0.036	-0.048	0.000
31	A	72	SER	0	0.013	0.011	6.834	-0.331	-0.331	0.000	0.000	0.000	0.000
32	A	73	SER	0	0.007	0.006	7.900	-0.175	-0.175	0.000	0.000	0.000	0.000
33	A	74	LEU	0	-0.017	-0.005	7.196	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	75	TYR	0	0.046	0.021	6.839	0.025	0.025	0.000	0.000	0.000	0.000
35	A	76	TRP	0	-0.019	-0.003	8.583	-0.169	-0.169	0.000	0.000	0.000	0.000
36	A	77	TYR	0	0.063	0.032	7.414	0.057	0.057	0.000	0.000	0.000	0.000
37	A	78	SER	0	-0.011	-0.036	12.107	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	79	ASN	0	-0.035	-0.025	13.589	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	80	GLN	0	0.009	-0.016	10.232	0.072	0.072	0.000	0.000	0.000	0.000
40	A	81	MET	0	0.008	0.017	10.784	-0.045	-0.045	0.000	0.000	0.000	0.000
41	A	82	ALA	0	-0.058	-0.005	12.930	0.050	0.050	0.000	0.000	0.000	0.000
42	A	83	GLU	-1	-0.748	-0.861	11.586	-0.078	-0.078	0.000	0.000	0.000	0.000
43	A	84	LYS	1	0.804	0.889	12.140	0.045	0.045	0.000	0.000	0.000	0.000
44	A	85	ALA	0	-0.026	-0.015	10.845	-0.040	-0.040	0.000	0.000	0.000	0.000
45	A	86	ASP	-1	-0.825	-0.913	12.784	-0.163	-0.163	0.000	0.000	0.000	0.000
46	A	87	GLY	0	-0.040	-0.032	14.058	0.026	0.026	0.000	0.000	0.000	0.000
47	A	88	PHE	0	-0.021	-0.014	11.858	-0.037	-0.037	0.000	0.000	0.000	0.000
48	A	89	VAL	0	-0.033	-0.003	12.437	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	90	ASN	0	-0.016	-0.017	12.119	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	91	LEU	0	0.025	-0.003	10.187	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	92	PRO	0	0.005	0.009	13.703	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	93	ASP	-1	-0.841	-0.893	16.373	0.121	0.121	0.000	0.000	0.000	0.000
53	A	94	PHE	0	-0.063	-0.032	16.463	-0.030	-0.030	0.000	0.000	0.000	0.000
54	A	95	THR	0	-0.014	0.008	18.587	0.004	0.004	0.000	0.000	0.000	0.000
55	A	96	VAL	0	0.005	-0.022	15.238	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	97	GLU	-1	-0.809	-0.872	18.243	-0.058	-0.058	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.882	0.928	20.117	0.143	0.143	0.000	0.000	0.000	0.000
58	A	99	ALA	0	0.030	0.010	21.507	0.014	0.014	0.000	0.000	0.000	0.000
59	A	100	SER	0	-0.045	-0.045	23.313	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	101	GLU	-1	-0.773	-0.879	25.690	-0.097	-0.097	0.000	0.000	0.000	0.000
61	A	102	CYS	0	-0.121	-0.044	24.147	0.002	0.002	0.000	0.000	0.000	0.000
62	A	103	LYS	1	0.992	1.002	26.202	0.102	0.102	0.000	0.000	0.000	0.000
63	A	104	LYS	1	0.830	0.941	20.534	0.227	0.227	0.000	0.000	0.000	0.000
64	A	105	LYS	1	0.947	0.960	23.227	0.204	0.204	0.000	0.000	0.000	0.000
65	A	106	HIS	0	0.038	0.020	19.104	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	107	ALA	0	0.032	0.018	18.562	-0.030	-0.030	0.000	0.000	0.000	0.000
67	A	108	PHE	0	0.041	0.018	12.979	0.012	0.012	0.000	0.000	0.000	0.000
68	A	109	LYS	1	0.855	0.915	18.564	0.056	0.056	0.000	0.000	0.000	0.000
69	A	110	ILE	0	0.024	0.009	13.874	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	111	SER	0	-0.042	-0.038	18.005	0.004	0.004	0.000	0.000	0.000	0.000
71	A	112	HIS	0	0.127	0.062	19.878	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	113	PRO	0	0.013	0.010	22.022	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	114	GLN	0	-0.019	-0.008	24.252	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	115	ILE	0	-0.025	0.008	19.030	0.002	0.002	0.000	0.000	0.000	0.000
75	A	116	LYS	1	0.842	0.900	20.423	0.020	0.020	0.000	0.000	0.000	0.000
76	A	117	THR	0	0.020	0.031	21.107	0.003	0.003	0.000	0.000	0.000	0.000
77	A	118	PHE	0	-0.057	-0.028	17.169	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	119	TYR	0	-0.009	-0.013	18.948	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	120	PHE	0	0.016	-0.001	13.738	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	121	ALA	0	-0.007	-0.003	16.442	0.023	0.023	0.000	0.000	0.000	0.000
81	A	122	ALA	0	0.038	0.032	14.677	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	123	GLU	-1	-0.794	-0.872	16.034	-0.276	-0.276	0.000	0.000	0.000	0.000
83	A	124	ASN	0	-0.050	-0.034	16.671	0.033	0.033	0.000	0.000	0.000	0.000
84	A	125	VAL	0	0.021	0.001	17.663	-0.023	-0.023	0.000	0.000	0.000	0.000
85	A	126	GLN	0	0.077	0.038	17.021	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	127	GLU	-1	-0.831	-0.912	12.852	-0.575	-0.575	0.000	0.000	0.000	0.000
87	A	128	MET	0	-0.062	-0.025	13.095	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	129	ASN	0	0.014	-0.007	14.739	0.011	0.011	0.000	0.000	0.000	0.000
89	A	130	VAL	0	0.013	0.021	9.584	0.020	0.020	0.000	0.000	0.000	0.000
90	A	131	TRP	0	0.023	0.002	6.360	-0.048	-0.048	0.000	0.000	0.000	0.000
91	A	132	LEU	0	-0.005	-0.007	11.388	0.056	0.056	0.000	0.000	0.000	0.000
92	A	133	ASN	0	-0.043	-0.010	12.756	0.025	0.025	0.000	0.000	0.000	0.000
93	A	134	LYS	1	0.918	0.942	6.939	1.156	1.156	0.000	0.000	0.000	0.000
94	A	135	LEU	0	-0.003	-0.015	10.144	0.112	0.112	0.000	0.000	0.000	0.000
95	A	136	GLY	0	0.008	0.009	11.892	0.078	0.078	0.000	0.000	0.000	0.000
96	A	137	SER	0	-0.016	-0.010	11.655	0.051	0.051	0.000	0.000	0.000	0.000
97	A	138	ALA	0	-0.036	-0.011	9.599	0.078	0.078	0.000	0.000	0.000	0.000
98	A	139	VAL	0	-0.029	-0.001	11.455	0.065	0.065	0.000	0.000	0.000	0.000
99	A	140	ILE	0	-0.006	0.005	14.899	0.007	0.007	0.000	0.000	0.000	0.000
100	A	141	HIS	1	0.804	0.870	15.171	-0.136	-0.136	0.000	0.000	0.000	0.000
101	A	142	GLN	0	0.047	0.038	17.399	-0.054	-0.054	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:42:ALA)