FMO DATABASE

FMODB ID: M3KJZ

Calculation Name: 2DX5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DX5

Chain ID: A

ChEMBL ID:

UniProt ID: P0CH28

Base Structure: X-ray

Registration Date: 2023-06-21

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-835553.823434
FMO2-HF: Nuclear repulsion	793173.320307
FMO2-HF: Total energy	-42380.503127
FMO2-MP2: Total energy	-42503.743181

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:10:LEU)

Summations of interaction energy for fragment #1(A:10: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.
-7.585	-4.278	1.364	-1.398	-3.273	0.004

Interaction energy analysis for fragmet #1(A:10:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / 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

Sort

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	12	GLU	-1	-0.807	-0.892	3.879	-2.918	-1.540	-0.015	-0.591	-0.772	0.001
4	A	13	ILE	0	0.013	-0.008	6.606	0.231	0.231	0.000	0.000	0.000	0.000
5	A	14	ASN	0	-0.059	-0.035	9.653	0.102	0.102	0.000	0.000	0.000	0.000
6	A	15	GLU	-1	-0.754	-0.801	6.690	-0.940	-0.940	0.000	0.000	0.000	0.000
7	A	16	THR	0	-0.006	-0.011	8.502	-0.072	-0.072	0.000	0.000	0.000	0.000
8	A	17	LEU	0	-0.031	-0.019	7.242	0.083	0.083	0.000	0.000	0.000	0.000
9	A	18	VAL	0	0.000	0.014	8.975	-0.096	-0.096	0.000	0.000	0.000	0.000
10	A	19	ILE	0	-0.015	-0.017	11.952	-0.036	-0.036	0.000	0.000	0.000	0.000
11	A	20	GLN	0	0.026	0.019	7.851	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	21	GLN	0	-0.031	-0.025	11.703	-0.099	-0.099	0.000	0.000	0.000	0.000
13	A	22	ARG	1	0.918	0.953	14.142	-0.439	-0.439	0.000	0.000	0.000	0.000
14	A	23	GLY	0	0.024	0.009	15.913	-0.060	-0.060	0.000	0.000	0.000	0.000
15	A	24	VAL	0	-0.018	0.001	15.181	-0.059	-0.059	0.000	0.000	0.000	0.000
16	A	25	ARG	1	0.923	0.962	16.509	-0.197	-0.197	0.000	0.000	0.000	0.000
17	A	26	VAL	0	0.037	0.016	13.983	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	27	TYR	0	-0.063	-0.032	17.449	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	28	ASP	-1	-0.806	-0.891	20.269	0.110	0.110	0.000	0.000	0.000	0.000
20	A	29	GLY	0	0.043	0.015	21.790	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	30	GLU	-1	-0.824	-0.900	25.149	0.111	0.111	0.000	0.000	0.000	0.000
22	A	31	GLU	-1	-0.841	-0.910	22.532	0.093	0.093	0.000	0.000	0.000	0.000
23	A	32	LYS	1	0.979	0.977	25.872	-0.070	-0.070	0.000	0.000	0.000	0.000
24	A	33	ILE	0	-0.033	-0.023	24.589	0.010	0.010	0.000	0.000	0.000	0.000
25	A	34	LYS	1	0.809	0.876	21.183	-0.121	-0.121	0.000	0.000	0.000	0.000
26	A	35	PHE	0	-0.023	0.011	19.662	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	36	ASP	-1	-0.808	-0.879	14.788	0.226	0.226	0.000	0.000	0.000	0.000
28	A	37	ALA	0	-0.034	-0.040	15.978	0.006	0.006	0.000	0.000	0.000	0.000
29	A	38	GLY	0	0.030	0.009	12.624	0.011	0.011	0.000	0.000	0.000	0.000
30	A	39	THR	0	-0.099	-0.057	10.248	-0.121	-0.121	0.000	0.000	0.000	0.000
31	A	40	LEU	0	-0.004	0.011	10.360	0.161	0.161	0.000	0.000	0.000	0.000
32	A	41	LEU	0	-0.048	-0.026	5.267	0.139	0.139	0.000	0.000	0.000	0.000
33	A	42	LEU	0	0.002	0.019	8.804	-0.047	-0.047	0.000	0.000	0.000	0.000
34	A	43	SER	0	0.001	-0.050	8.091	0.120	0.120	0.000	0.000	0.000	0.000
35	A	44	THR	0	0.064	0.007	10.201	-0.030	-0.030	0.000	0.000	0.000	0.000
36	A	45	HIS	0	-0.016	0.005	9.859	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	46	ARG	1	0.718	0.833	3.005	1.770	2.455	0.022	-0.264	-0.444	0.001
38	A	47	LEU	0	-0.030	-0.020	9.362	0.147	0.147	0.000	0.000	0.000	0.000
39	A	48	ILE	0	0.009	0.011	3.863	-0.210	0.048	0.001	-0.044	-0.214	0.000
40	A	49	TRP	0	-0.034	-0.011	7.146	0.189	0.189	0.000	0.000	0.000	0.000
41	A	50	ARG	1	0.909	0.938	3.844	-5.510	-5.048	0.004	-0.129	-0.337	0.001
42	A	51	ASP	-1	-0.754	-0.871	7.581	0.324	0.324	0.000	0.000	0.000	0.000
43	A	52	GLN	0	0.017	0.003	10.446	0.061	0.061	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.742	0.869	12.816	-0.308	-0.308	0.000	0.000	0.000	0.000
45	A	54	ASN	0	0.015	-0.015	9.583	0.012	0.012	0.000	0.000	0.000	0.000
46	A	55	ASN	0	-0.026	-0.011	8.795	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	56	GLU	-1	-0.825	-0.916	8.955	0.179	0.179	0.000	0.000	0.000	0.000
48	A	57	CYS	0	-0.095	-0.027	7.041	0.206	0.206	0.000	0.000	0.000	0.000
49	A	58	CYS	0	-0.075	-0.035	2.324	0.070	0.439	1.353	-0.355	-1.367	0.001
50	A	59	MET	0	0.038	0.027	4.348	-0.536	-0.381	-0.001	-0.015	-0.139	0.000
51	A	60	ALA	0	-0.010	0.000	7.059	-0.137	-0.137	0.000	0.000	0.000	0.000
52	A	61	ILE	0	0.109	0.031	5.982	0.180	0.180	0.000	0.000	0.000	0.000
53	A	62	PRO	0	0.043	0.020	9.073	-0.058	-0.058	0.000	0.000	0.000	0.000
54	A	63	LEU	0	-0.024	0.005	11.802	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	64	SER	0	0.001	-0.012	13.658	-0.070	-0.070	0.000	0.000	0.000	0.000
56	A	65	GLN	0	-0.010	0.010	15.180	0.014	0.014	0.000	0.000	0.000	0.000
57	A	66	ILE	0	-0.035	0.006	16.155	0.010	0.010	0.000	0.000	0.000	0.000
58	A	67	VAL	0	0.049	0.031	18.981	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	68	PHE	0	-0.003	-0.011	22.530	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	69	ILE	0	-0.024	-0.023	19.177	0.010	0.010	0.000	0.000	0.000	0.000
61	A	70	GLU	-1	-0.831	-0.889	22.564	0.068	0.068	0.000	0.000	0.000	0.000
62	A	71	GLU	-1	-0.839	-0.926	24.082	0.158	0.158	0.000	0.000	0.000	0.000
63	A	72	GLN	0	-0.023	0.000	26.359	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	73	ALA	0	-0.010	0.002	27.744	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	81	LYS	1	0.896	0.945	22.974	-0.153	-0.153	0.000	0.000	0.000	0.000
66	A	82	ILE	0	-0.034	-0.015	19.492	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	83	VAL	0	-0.010	-0.009	21.076	0.018	0.018	0.000	0.000	0.000	0.000
68	A	84	VAL	0	0.020	-0.006	16.902	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	85	HIS	0	0.009	-0.009	20.283	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	86	LEU	0	-0.033	-0.036	16.625	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	87	HIS	0	-0.026	-0.005	18.563	-0.027	-0.027	0.000	0.000	0.000	0.000
72	A	101	SER	0	-0.008	-0.017	30.181	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.946	0.969	24.853	0.007	0.007	0.000	0.000	0.000	0.000
74	A	103	ASN	0	-0.010	0.002	21.573	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	104	SER	0	0.008	-0.001	24.010	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	105	TYR	0	-0.040	-0.011	21.799	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	106	ILE	0	0.034	0.041	15.868	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	107	ARG	1	0.778	0.859	20.324	-0.117	-0.117	0.000	0.000	0.000	0.000
79	A	108	LEU	0	0.022	0.021	15.531	0.018	0.018	0.000	0.000	0.000	0.000
80	A	109	SER	0	-0.010	-0.019	19.090	-0.032	-0.032	0.000	0.000	0.000	0.000
81	A	110	PHE	0	0.040	0.024	17.281	0.012	0.012	0.000	0.000	0.000	0.000
82	A	111	LYS	1	0.901	0.964	21.126	-0.260	-0.260	0.000	0.000	0.000	0.000
83	A	112	GLU	-1	-0.885	-0.938	19.595	0.363	0.363	0.000	0.000	0.000	0.000
84	A	113	HIS	0	0.047	0.019	21.332	0.006	0.006	0.000	0.000	0.000	0.000
85	A	114	GLY	0	0.085	0.032	20.118	0.031	0.031	0.000	0.000	0.000	0.000
86	A	115	GLN	0	0.018	0.003	20.601	0.029	0.029	0.000	0.000	0.000	0.000
87	A	116	ILE	0	-0.025	-0.013	22.403	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	117	GLU	-1	-0.952	-0.969	20.392	0.228	0.228	0.000	0.000	0.000	0.000
89	A	118	PHE	0	0.002	-0.012	12.926	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	119	TYR	0	0.002	0.001	18.658	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	120	ARG	1	0.839	0.917	20.996	-0.139	-0.139	0.000	0.000	0.000	0.000
92	A	121	ARG	1	0.917	0.951	16.851	-0.193	-0.193	0.000	0.000	0.000	0.000
93	A	122	LEU	0	-0.007	-0.011	15.729	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	123	SER	0	0.005	-0.010	17.698	-0.030	-0.030	0.000	0.000	0.000	0.000
95	A	124	GLU	-1	-0.814	-0.884	20.321	0.106	0.106	0.000	0.000	0.000	0.000
96	A	125	GLU	-1	-0.870	-0.924	14.744	0.036	0.036	0.000	0.000	0.000	0.000
97	A	126	MET	0	-0.056	-0.007	17.898	-0.038	-0.038	0.000	0.000	0.000	0.000
98	A	127	THR	0	0.022	-0.012	18.751	-0.019	-0.019	0.000	0.000	0.000	0.000
99	A	128	GLN	0	0.011	0.016	20.784	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	129	ARG	1	0.879	0.972	14.067	0.149	0.149	0.000	0.000	0.000	0.000
101	A	130	ARG	1	0.779	0.888	18.326	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:10:LEU)