FMO DATABASE

FMODB ID: R9LZ8

Calculation Name: 5X2D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X2D

Chain ID: A

ChEMBL ID:

UniProt ID: Q2PMV7

Base Structure: X-ray

Registration Date: 2023-06-22

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-695102.333415
FMO2-HF: Nuclear repulsion	657022.577772
FMO2-HF: Total energy	-38079.755642
FMO2-MP2: Total energy	-38189.998988

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:83:PRO)

Summations of interaction energy for fragment #1(A:83:PRO)

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.
-3.434	0.62	0.248	-2.089	-2.212	-0.002

Interaction energy analysis for fragmet #1(A:83:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.030

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	85	LEU	0	-0.007	0.005	3.502	-2.602	0.742	-0.008	-1.852	-1.484	0.000
4	A	86	PRO	0	-0.037	-0.011	6.180	-0.030	-0.030	0.000	0.000	0.000	0.000
5	A	87	PRO	0	0.009	0.000	8.295	-0.009	-0.009	0.000	0.000	0.000	0.000
6	A	88	GLU	-1	-0.898	-0.955	11.400	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	89	ILE	0	-0.054	-0.019	10.416	0.010	0.010	0.000	0.000	0.000	0.000
8	A	90	ILE	0	0.030	0.030	12.343	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	91	VAL	0	-0.040	-0.029	11.687	0.011	0.011	0.000	0.000	0.000	0.000
10	A	92	ILE	0	0.003	-0.002	14.716	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	93	SER	0	-0.035	-0.027	17.389	0.001	0.001	0.000	0.000	0.000	0.000
12	A	94	ALA	0	0.013	-0.007	14.107	0.005	0.005	0.000	0.000	0.000	0.000
13	A	95	ASN	0	-0.058	-0.001	16.099	0.006	0.006	0.000	0.000	0.000	0.000
14	A	96	MET	0	0.021	0.000	12.032	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	97	SER	0	0.025	0.032	9.747	0.034	0.034	0.000	0.000	0.000	0.000
16	A	98	LEU	0	0.083	0.010	5.659	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	99	GLU	-1	-0.949	-0.964	5.560	0.224	0.224	0.000	0.000	0.000	0.000
18	A	100	ASP	-1	-0.839	-0.952	6.586	0.057	0.057	0.000	0.000	0.000	0.000
19	A	101	GLN	0	-0.003	0.002	8.792	-0.074	-0.074	0.000	0.000	0.000	0.000
20	A	102	ILE	0	0.011	-0.002	2.643	-0.819	-0.109	0.256	-0.237	-0.728	-0.002
21	A	103	LYS	1	0.854	0.936	6.937	-0.196	-0.196	0.000	0.000	0.000	0.000
22	A	104	ILE	0	0.051	0.039	9.406	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	105	ALA	0	0.002	0.019	8.365	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	106	ARG	1	0.905	0.930	8.551	-0.054	-0.054	0.000	0.000	0.000	0.000
25	A	107	GLU	-1	-0.929	-0.949	10.566	0.029	0.029	0.000	0.000	0.000	0.000
26	A	108	THR	0	-0.012	-0.022	13.648	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	109	ILE	0	-0.025	-0.027	10.891	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	110	PRO	0	-0.066	-0.023	13.926	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	111	ILE	0	0.017	0.002	16.863	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	112	ALA	0	-0.006	0.006	18.391	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	113	PRO	0	-0.041	-0.030	18.459	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	114	GLY	0	-0.024	0.000	21.400	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	115	ALA	0	-0.015	0.001	23.830	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	116	GLN	0	0.066	0.029	25.864	0.001	0.001	0.000	0.000	0.000	0.000
35	A	117	THR	0	-0.026	-0.015	28.680	0.000	0.000	0.000	0.000	0.000	0.000
36	A	118	SER	0	0.031	-0.005	30.001	0.001	0.001	0.000	0.000	0.000	0.000
37	A	119	GLU	-1	-0.971	-0.977	31.337	0.009	0.009	0.000	0.000	0.000	0.000
38	A	120	GLU	-1	-0.829	-0.902	27.931	0.008	0.008	0.000	0.000	0.000	0.000
39	A	121	LEU	0	-0.002	-0.006	25.293	0.001	0.001	0.000	0.000	0.000	0.000
40	A	122	GLY	0	0.004	0.008	26.776	0.001	0.001	0.000	0.000	0.000	0.000
41	A	123	ARG	1	0.979	0.964	27.643	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	124	LEU	0	-0.003	0.024	21.054	0.001	0.001	0.000	0.000	0.000	0.000
43	A	125	THR	0	0.009	0.003	23.024	0.002	0.002	0.000	0.000	0.000	0.000
44	A	126	GLU	-1	-0.914	-0.945	23.407	0.022	0.022	0.000	0.000	0.000	0.000
45	A	127	ASN	0	-0.090	-0.048	22.367	0.002	0.002	0.000	0.000	0.000	0.000
46	A	128	LEU	0	0.051	0.029	17.823	0.002	0.002	0.000	0.000	0.000	0.000
47	A	129	LYS	1	0.826	0.912	19.897	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	130	SER	0	-0.036	-0.025	21.731	0.002	0.002	0.000	0.000	0.000	0.000
49	A	131	PHE	0	-0.002	0.012	13.186	0.001	0.001	0.000	0.000	0.000	0.000
50	A	132	ALA	0	0.010	0.025	17.249	0.004	0.004	0.000	0.000	0.000	0.000
51	A	133	ASP	-1	-0.751	-0.891	18.321	0.037	0.037	0.000	0.000	0.000	0.000
52	A	134	LYS	1	0.873	0.947	18.879	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	135	THR	0	-0.101	-0.071	14.574	0.002	0.002	0.000	0.000	0.000	0.000
54	A	136	PHE	0	-0.020	-0.022	12.023	0.005	0.005	0.000	0.000	0.000	0.000
55	A	137	GLY	0	0.020	0.040	16.977	0.000	0.000	0.000	0.000	0.000	0.000
56	A	138	GLY	0	0.014	-0.001	20.720	0.002	0.002	0.000	0.000	0.000	0.000
57	A	139	CYS	0	-0.057	-0.023	23.517	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	140	TRP	0	0.048	0.039	16.964	0.001	0.001	0.000	0.000	0.000	0.000
59	A	141	GLN	0	-0.055	-0.027	23.311	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	142	VAL	0	0.012	0.006	20.770	0.002	0.002	0.000	0.000	0.000	0.000
61	A	143	MET	0	-0.032	-0.006	22.946	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	144	VAL	0	0.003	-0.001	22.158	0.001	0.001	0.000	0.000	0.000	0.000
63	A	145	VAL	0	-0.045	-0.021	23.890	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	146	ASP	-1	-0.910	-0.953	24.810	0.003	0.003	0.000	0.000	0.000	0.000
65	A	147	GLY	0	0.007	-0.003	26.695	0.000	0.000	0.000	0.000	0.000	0.000
66	A	148	SER	0	-0.021	-0.005	26.631	0.000	0.000	0.000	0.000	0.000	0.000
67	A	149	TYR	0	-0.032	-0.023	22.579	0.000	0.000	0.000	0.000	0.000	0.000
68	A	150	TRP	0	0.026	0.002	28.141	0.000	0.000	0.000	0.000	0.000	0.000
69	A	151	ILE	0	0.003	0.008	26.048	0.000	0.000	0.000	0.000	0.000	0.000
70	A	152	THR	0	-0.043	-0.009	29.352	0.000	0.000	0.000	0.000	0.000	0.000
71	A	153	GLN	0	0.031	0.016	28.425	0.002	0.002	0.000	0.000	0.000	0.000
72	A	154	THR	0	0.003	-0.015	28.502	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	155	PHE	0	-0.007	-0.003	26.173	0.001	0.001	0.000	0.000	0.000	0.000
74	A	156	VAL	0	0.013	-0.007	23.971	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	157	PRO	0	-0.060	-0.007	24.354	0.004	0.004	0.000	0.000	0.000	0.000
76	A	158	ASN	0	0.002	0.007	22.059	0.004	0.004	0.000	0.000	0.000	0.000
77	A	159	MET	0	0.007	0.003	16.309	0.005	0.005	0.000	0.000	0.000	0.000
78	A	160	SER	0	-0.022	-0.010	18.267	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	161	PHE	0	0.003	-0.004	11.460	0.012	0.012	0.000	0.000	0.000	0.000
80	A	162	GLN	0	-0.004	0.008	16.510	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	163	PHE	0	0.029	0.024	14.428	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	164	GLU	-1	-0.895	-0.945	16.415	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	165	LEU	0	-0.008	-0.001	14.123	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	166	TYR	0	-0.030	-0.035	16.577	0.001	0.001	0.000	0.000	0.000	0.000
85	A	167	ASN	0	0.000	-0.001	19.940	0.001	0.001	0.000	0.000	0.000	0.000
86	A	168	ARG	1	0.905	0.956	20.921	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	169	ALA	0	-0.006	0.013	20.210	0.000	0.000	0.000	0.000	0.000	0.000
88	A	170	TYR	0	0.018	0.004	17.741	0.002	0.002	0.000	0.000	0.000	0.000
89	A	171	LEU	0	-0.024	-0.013	18.845	0.002	0.002	0.000	0.000	0.000	0.000
90	A	172	PHE	0	-0.002	-0.010	17.146	0.000	0.000	0.000	0.000	0.000	0.000
91	A	173	TRP	0	0.038	0.010	19.811	0.002	0.002	0.000	0.000	0.000	0.000
92	A	174	GLN	0	0.073	0.045	20.236	0.000	0.000	0.000	0.000	0.000	0.000
93	A	175	THR	0	-0.069	-0.070	22.183	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	176	SER	0	-0.049	-0.040	24.974	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	177	GLU	-1	-0.944	-0.956	22.753	0.049	0.049	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:83:PRO)