FMO DATABASE

FMODB ID: R9Q18

Calculation Name: 4XVV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XVV

Chain ID: A

ChEMBL ID:

UniProt ID: A6TE95

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	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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-490832.386137
FMO2-HF: Nuclear repulsion	459042.798527
FMO2-HF: Total energy	-31789.58761
FMO2-MP2: Total energy	-31877.462798

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-13.914	-9.76	4.611	-4.389	-4.377	-0.03

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / 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	27	GLU	-1	-0.878	-0.925	3.320	-2.538	-0.080	0.013	-1.286	-1.185	0.006
4	A	28	GLU	-1	-0.897	-0.943	2.154	-14.159	-12.585	4.599	-3.093	-3.081	-0.036
5	A	29	THR	0	-0.107	-0.049	5.183	1.330	1.452	-0.001	-0.010	-0.111	0.000
6	A	30	THR	0	-0.086	-0.046	7.882	0.873	0.873	0.000	0.000	0.000	0.000
7	A	31	PRO	0	0.050	-0.002	9.491	-0.140	-0.140	0.000	0.000	0.000	0.000
8	A	32	GLN	0	0.013	0.028	9.333	0.266	0.266	0.000	0.000	0.000	0.000
9	A	33	ASN	0	-0.034	-0.056	7.839	0.469	0.469	0.000	0.000	0.000	0.000
10	A	34	MET	0	0.011	0.044	11.324	0.056	0.056	0.000	0.000	0.000	0.000
11	A	35	THR	0	-0.025	-0.047	13.642	0.114	0.114	0.000	0.000	0.000	0.000
12	A	36	CYS	0	-0.047	-0.034	17.029	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	37	GLN	0	-0.055	-0.041	20.387	0.029	0.029	0.000	0.000	0.000	0.000
14	A	38	GLU	-1	-0.794	-0.870	14.980	-0.777	-0.777	0.000	0.000	0.000	0.000
15	A	39	PHE	0	-0.014	-0.025	18.835	0.000	0.000	0.000	0.000	0.000	0.000
16	A	40	MET	0	-0.090	-0.043	19.929	0.029	0.029	0.000	0.000	0.000	0.000
17	A	41	ASP	-1	-0.849	-0.894	21.486	-0.337	-0.337	0.000	0.000	0.000	0.000
18	A	42	MET	0	-0.081	-0.010	18.442	-0.042	-0.042	0.000	0.000	0.000	0.000
19	A	43	ASN	0	-0.005	-0.015	21.181	0.070	0.070	0.000	0.000	0.000	0.000
20	A	44	PRO	0	0.095	0.013	22.606	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	45	LYS	1	0.915	0.959	23.970	0.298	0.298	0.000	0.000	0.000	0.000
22	A	46	SER	0	0.014	0.013	18.844	0.016	0.016	0.000	0.000	0.000	0.000
23	A	47	MET	0	-0.032	0.005	20.140	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	48	THR	0	0.027	-0.021	21.852	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	49	PRO	0	-0.011	-0.006	18.952	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	50	VAL	0	0.006	0.010	16.105	-0.031	-0.031	0.000	0.000	0.000	0.000
27	A	51	ALA	0	0.044	0.004	18.208	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	52	PHE	0	0.017	0.007	19.360	0.018	0.018	0.000	0.000	0.000	0.000
29	A	53	TRP	0	0.010	0.010	11.272	0.026	0.026	0.000	0.000	0.000	0.000
30	A	54	VAL	0	0.000	-0.001	17.076	0.021	0.021	0.000	0.000	0.000	0.000
31	A	55	VAL	0	-0.029	-0.009	18.353	0.038	0.038	0.000	0.000	0.000	0.000
32	A	56	ASN	0	-0.019	-0.022	19.704	0.063	0.063	0.000	0.000	0.000	0.000
33	A	57	ARG	1	0.834	0.934	12.213	0.539	0.539	0.000	0.000	0.000	0.000
34	A	58	ASN	0	-0.069	-0.039	15.447	0.014	0.014	0.000	0.000	0.000	0.000
35	A	59	THR	0	-0.023	-0.006	17.424	0.036	0.036	0.000	0.000	0.000	0.000
36	A	60	ASP	-1	-0.808	-0.892	20.923	-0.086	-0.086	0.000	0.000	0.000	0.000
37	A	61	PHE	0	-0.015	-0.028	18.594	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	62	SER	0	-0.073	-0.042	23.889	0.002	0.002	0.000	0.000	0.000	0.000
39	A	63	GLY	0	-0.022	-0.005	26.494	0.007	0.007	0.000	0.000	0.000	0.000
40	A	64	GLY	0	-0.037	-0.015	28.004	0.003	0.003	0.000	0.000	0.000	0.000
41	A	65	ASP	-1	-0.958	-0.956	26.471	-0.132	-0.132	0.000	0.000	0.000	0.000
42	A	66	TYR	0	-0.095	-0.062	23.812	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	67	VAL	0	-0.025	0.007	24.716	0.010	0.010	0.000	0.000	0.000	0.000
44	A	68	ASP	-1	-0.784	-0.899	25.229	-0.215	-0.215	0.000	0.000	0.000	0.000
45	A	69	TRP	0	0.045	0.001	20.534	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	70	HIS	0	0.026	0.023	26.954	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	71	GLU	-1	-0.892	-0.938	29.038	-0.171	-0.171	0.000	0.000	0.000	0.000
48	A	72	VAL	0	-0.029	-0.018	23.369	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	73	GLU	-1	-0.871	-0.925	26.686	-0.273	-0.273	0.000	0.000	0.000	0.000
50	A	74	THR	0	-0.068	-0.056	28.201	0.006	0.006	0.000	0.000	0.000	0.000
51	A	75	VAL	0	-0.023	0.001	30.095	0.010	0.010	0.000	0.000	0.000	0.000
52	A	76	SER	0	-0.010	-0.012	25.090	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	77	VAL	0	0.014	0.016	24.374	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	78	PRO	0	0.008	0.001	26.396	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	79	LYS	1	0.829	0.931	27.820	0.195	0.195	0.000	0.000	0.000	0.000
56	A	80	MET	0	0.016	0.006	19.787	0.003	0.003	0.000	0.000	0.000	0.000
57	A	81	LEU	0	0.012	0.012	25.078	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	82	GLN	0	-0.005	0.014	26.760	0.013	0.013	0.000	0.000	0.000	0.000
59	A	83	GLU	-1	-0.855	-0.930	25.392	-0.182	-0.182	0.000	0.000	0.000	0.000
60	A	85	HIS	0	-0.002	-0.023	24.771	0.008	0.008	0.000	0.000	0.000	0.000
61	A	86	LYS	1	0.734	0.872	28.027	0.190	0.190	0.000	0.000	0.000	0.000
62	A	87	ASN	0	-0.024	-0.021	23.922	0.005	0.005	0.000	0.000	0.000	0.000
63	A	88	PRO	0	0.077	0.035	23.245	-0.023	-0.023	0.000	0.000	0.000	0.000
64	A	89	ALA	0	-0.003	0.002	20.598	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	90	ALA	0	-0.044	-0.003	19.341	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	91	LYS	1	0.904	0.940	13.573	0.388	0.388	0.000	0.000	0.000	0.000
67	A	92	LEU	0	0.046	0.000	15.549	0.061	0.061	0.000	0.000	0.000	0.000
68	A	93	GLY	0	-0.034	-0.003	14.067	0.035	0.035	0.000	0.000	0.000	0.000
69	A	94	ASP	-1	-0.882	-0.922	14.953	-0.283	-0.283	0.000	0.000	0.000	0.000
70	A	95	LEU	0	-0.028	-0.019	18.240	0.053	0.053	0.000	0.000	0.000	0.000
71	A	96	SER	0	0.002	-0.021	18.551	0.016	0.016	0.000	0.000	0.000	0.000
72	A	97	ALA	0	0.004	-0.001	20.787	0.019	0.019	0.000	0.000	0.000	0.000
73	A	98	VAL	0	-0.002	0.000	23.751	0.016	0.016	0.000	0.000	0.000	0.000
74	A	99	ILE	0	0.016	0.004	22.942	0.015	0.015	0.000	0.000	0.000	0.000
75	A	100	LYS	1	0.988	1.018	22.751	0.209	0.209	0.000	0.000	0.000	0.000
76	A	101	LYS	1	0.923	0.981	26.216	0.131	0.131	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:0:GLY)