FMO DATABASE

FMODB ID: QYK8Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-492935.75475
FMO2-HF: Nuclear repulsion	461146.092259
FMO2-HF: Total energy	-31789.662491
FMO2-MP2: Total energy	-31877.561156

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.
-16.59	-15.953	11.233	-6.719	-5.15	-0.06

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 : 0.044 / q_NPA : 0.016

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	-0.871	-0.914	3.658	-2.441	-0.264	0.000	-1.111	-1.065	0.004
4	A	28	GLU	-1	-0.863	-0.919	1.827	-17.185	-18.863	11.234	-5.595	-3.961	-0.064
5	A	29	THR	0	-0.114	-0.060	5.226	1.427	1.565	-0.001	-0.013	-0.124	0.000
6	A	30	THR	0	-0.057	-0.040	7.738	0.878	0.878	0.000	0.000	0.000	0.000
7	A	31	PRO	0	0.030	-0.004	9.528	-0.110	-0.110	0.000	0.000	0.000	0.000
8	A	32	GLN	0	-0.006	0.007	8.639	0.274	0.274	0.000	0.000	0.000	0.000
9	A	33	ASN	0	-0.030	-0.057	7.698	0.487	0.487	0.000	0.000	0.000	0.000
10	A	34	MET	0	0.014	0.045	11.131	0.076	0.076	0.000	0.000	0.000	0.000
11	A	35	THR	0	-0.022	-0.048	13.419	0.113	0.113	0.000	0.000	0.000	0.000
12	A	36	CYS	0	-0.040	-0.029	16.831	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	37	GLN	0	-0.049	-0.035	20.089	0.036	0.036	0.000	0.000	0.000	0.000
14	A	38	GLU	-1	-0.787	-0.862	14.786	-0.801	-0.801	0.000	0.000	0.000	0.000
15	A	39	PHE	0	-0.023	-0.030	18.761	0.001	0.001	0.000	0.000	0.000	0.000
16	A	40	MET	0	-0.075	-0.034	19.858	0.034	0.034	0.000	0.000	0.000	0.000
17	A	41	ASP	-1	-0.858	-0.906	21.241	-0.348	-0.348	0.000	0.000	0.000	0.000
18	A	42	MET	0	-0.079	-0.013	18.475	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	43	ASN	0	0.002	-0.016	21.076	0.066	0.066	0.000	0.000	0.000	0.000
20	A	44	PRO	0	0.073	0.008	22.578	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	45	LYS	1	0.920	0.968	24.017	0.284	0.284	0.000	0.000	0.000	0.000
22	A	46	SER	0	0.023	0.011	18.847	0.016	0.016	0.000	0.000	0.000	0.000
23	A	47	MET	0	-0.040	0.005	20.032	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	48	THR	0	0.039	-0.025	21.506	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	49	PRO	0	-0.017	-0.012	18.792	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	50	VAL	0	0.006	0.009	15.919	-0.035	-0.035	0.000	0.000	0.000	0.000
27	A	51	ALA	0	0.040	0.004	17.789	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	52	PHE	0	0.020	0.008	19.398	0.012	0.012	0.000	0.000	0.000	0.000
29	A	53	TRP	0	0.018	0.010	11.102	0.022	0.022	0.000	0.000	0.000	0.000
30	A	54	VAL	0	-0.002	-0.003	16.794	0.021	0.021	0.000	0.000	0.000	0.000
31	A	55	VAL	0	-0.027	-0.007	17.994	0.032	0.032	0.000	0.000	0.000	0.000
32	A	56	ASN	0	0.003	-0.011	19.750	0.055	0.055	0.000	0.000	0.000	0.000
33	A	57	ARG	1	0.781	0.892	12.415	0.633	0.633	0.000	0.000	0.000	0.000
34	A	58	ASN	0	-0.058	-0.032	15.520	0.016	0.016	0.000	0.000	0.000	0.000
35	A	59	THR	0	-0.018	-0.006	17.877	0.025	0.025	0.000	0.000	0.000	0.000
36	A	60	ASP	-1	-0.812	-0.883	21.520	-0.104	-0.104	0.000	0.000	0.000	0.000
37	A	61	PHE	0	-0.015	-0.027	19.161	0.004	0.004	0.000	0.000	0.000	0.000
38	A	62	SER	0	-0.085	-0.052	24.549	0.006	0.006	0.000	0.000	0.000	0.000
39	A	63	GLY	0	-0.021	-0.009	26.753	0.009	0.009	0.000	0.000	0.000	0.000
40	A	64	GLY	0	-0.019	-0.004	27.888	0.004	0.004	0.000	0.000	0.000	0.000
41	A	65	ASP	-1	-0.872	-0.929	25.901	-0.170	-0.170	0.000	0.000	0.000	0.000
42	A	66	TYR	0	-0.092	-0.050	23.881	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	67	VAL	0	0.008	0.020	24.948	0.012	0.012	0.000	0.000	0.000	0.000
44	A	68	ASP	-1	-0.765	-0.879	25.411	-0.219	-0.219	0.000	0.000	0.000	0.000
45	A	69	TRP	0	0.024	-0.003	20.465	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	70	HIS	0	0.031	0.027	26.823	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	71	GLU	-1	-0.889	-0.934	29.221	-0.178	-0.178	0.000	0.000	0.000	0.000
48	A	72	VAL	0	-0.034	-0.027	23.299	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	73	GLU	-1	-0.864	-0.901	26.468	-0.273	-0.273	0.000	0.000	0.000	0.000
50	A	74	THR	0	-0.061	-0.060	28.025	0.006	0.006	0.000	0.000	0.000	0.000
51	A	75	VAL	0	-0.028	-0.002	29.757	0.011	0.011	0.000	0.000	0.000	0.000
52	A	76	SER	0	-0.016	-0.011	24.923	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	77	VAL	0	0.010	0.017	23.893	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	78	PRO	0	0.005	0.000	25.910	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	79	LYS	1	0.817	0.920	27.326	0.212	0.212	0.000	0.000	0.000	0.000
56	A	80	MET	0	0.007	0.006	19.476	0.004	0.004	0.000	0.000	0.000	0.000
57	A	81	LEU	0	0.025	0.014	24.662	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	82	GLN	0	-0.002	0.018	26.427	0.014	0.014	0.000	0.000	0.000	0.000
59	A	83	GLU	-1	-0.854	-0.926	24.724	-0.201	-0.201	0.000	0.000	0.000	0.000
60	A	85	HIS	0	0.004	-0.016	24.572	0.011	0.011	0.000	0.000	0.000	0.000
61	A	86	LYS	1	0.729	0.860	27.805	0.206	0.206	0.000	0.000	0.000	0.000
62	A	87	ASN	0	-0.020	-0.024	23.214	0.006	0.006	0.000	0.000	0.000	0.000
63	A	88	PRO	0	0.057	0.031	23.036	-0.026	-0.026	0.000	0.000	0.000	0.000
64	A	89	ALA	0	-0.001	0.001	20.315	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	90	ALA	0	-0.036	0.001	19.212	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	91	LYS	1	0.903	0.950	12.926	0.546	0.546	0.000	0.000	0.000	0.000
67	A	92	LEU	0	0.029	-0.003	15.218	0.060	0.060	0.000	0.000	0.000	0.000
68	A	93	GLY	0	-0.023	0.006	13.269	0.034	0.034	0.000	0.000	0.000	0.000
69	A	94	ASP	-1	-0.889	-0.929	14.163	-0.395	-0.395	0.000	0.000	0.000	0.000
70	A	95	LEU	0	-0.024	-0.015	17.400	0.062	0.062	0.000	0.000	0.000	0.000
71	A	96	SER	0	0.008	-0.013	18.118	0.021	0.021	0.000	0.000	0.000	0.000
72	A	97	ALA	0	0.000	0.005	20.305	0.026	0.026	0.000	0.000	0.000	0.000
73	A	98	VAL	0	-0.007	-0.001	23.126	0.022	0.022	0.000	0.000	0.000	0.000
74	A	99	ILE	0	0.002	-0.008	22.397	0.019	0.019	0.000	0.000	0.000	0.000
75	A	100	LYS	1	0.908	0.966	23.212	0.216	0.216	0.000	0.000	0.000	0.000
76	A	101	LYS	1	0.911	0.978	25.842	0.158	0.158	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)