FMO DATABASE

FMODB ID: 141MZ

Calculation Name: 3VH5-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VH5

Chain ID: D

ChEMBL ID:

UniProt ID: E1BSW7

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-424541.79066
FMO2-HF: Nuclear repulsion	395017.608958
FMO2-HF: Total energy	-29524.181702
FMO2-MP2: Total energy	-29612.041468

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(D:6:GLY)

Summations of interaction energy for fragment #1(D:6: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.
1.764	3.625	-0.026	-1.05	-0.784	0.003

Interaction energy analysis for fragmet #1(D:6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.005

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	D	8	PHE	0	0.015	0.022	3.792	0.255	2.017	-0.025	-1.027	-0.709	0.003
4	D	9	ARG	1	0.985	0.989	6.936	-0.871	-0.871	0.000	0.000	0.000	0.000
5	D	10	LYS	1	1.013	0.992	8.628	0.118	0.118	0.000	0.000	0.000	0.000
6	D	11	GLU	-1	-0.856	-0.917	12.070	0.157	0.157	0.000	0.000	0.000	0.000
7	D	12	THR	0	-0.027	-0.016	10.918	-0.012	-0.012	0.000	0.000	0.000	0.000
8	D	13	VAL	0	0.034	0.020	11.155	-0.001	-0.001	0.000	0.000	0.000	0.000
9	D	14	GLU	-1	-0.894	-0.957	13.819	0.036	0.036	0.000	0.000	0.000	0.000
10	D	15	ARG	1	0.904	0.944	16.559	-0.135	-0.135	0.000	0.000	0.000	0.000
11	D	16	LEU	0	0.008	0.013	14.452	-0.005	-0.005	0.000	0.000	0.000	0.000
12	D	17	LEU	0	-0.001	-0.008	17.217	-0.014	-0.014	0.000	0.000	0.000	0.000
13	D	18	ARG	1	0.871	0.925	19.683	-0.055	-0.055	0.000	0.000	0.000	0.000
14	D	19	LEU	0	-0.041	-0.003	20.546	-0.005	-0.005	0.000	0.000	0.000	0.000
15	D	20	HIS	0	-0.002	-0.006	20.271	0.001	0.001	0.000	0.000	0.000	0.000
16	D	21	PHE	0	-0.040	0.003	21.972	-0.009	-0.009	0.000	0.000	0.000	0.000
17	D	22	ARG	1	1.003	0.994	26.291	-0.015	-0.015	0.000	0.000	0.000	0.000
18	D	23	ASP	-1	-0.836	-0.921	29.231	0.010	0.010	0.000	0.000	0.000	0.000
19	D	24	GLY	0	0.055	0.034	29.151	0.000	0.000	0.000	0.000	0.000	0.000
20	D	25	ARG	1	0.896	0.942	29.231	0.000	0.000	0.000	0.000	0.000	0.000
21	D	26	THR	0	-0.026	0.004	25.442	-0.006	-0.006	0.000	0.000	0.000	0.000
22	D	27	ARG	1	0.843	0.908	24.268	-0.013	-0.013	0.000	0.000	0.000	0.000
23	D	28	VAL	0	0.039	0.025	18.846	-0.005	-0.005	0.000	0.000	0.000	0.000
24	D	29	ASN	0	0.023	0.026	20.809	-0.004	-0.004	0.000	0.000	0.000	0.000
25	D	30	GLY	0	0.055	-0.002	17.691	-0.003	-0.003	0.000	0.000	0.000	0.000
26	D	31	ASP	-1	-0.840	-0.919	16.405	-0.160	-0.160	0.000	0.000	0.000	0.000
27	D	32	ALA	0	0.014	0.003	16.705	-0.030	-0.030	0.000	0.000	0.000	0.000
28	D	33	LEU	0	-0.004	-0.003	14.756	-0.011	-0.011	0.000	0.000	0.000	0.000
29	D	34	LEU	0	-0.030	-0.017	11.370	-0.005	-0.005	0.000	0.000	0.000	0.000
30	D	35	LEU	0	0.024	0.016	12.186	-0.077	-0.077	0.000	0.000	0.000	0.000
31	D	36	MET	0	0.022	0.009	13.799	-0.035	-0.035	0.000	0.000	0.000	0.000
32	D	37	ALA	0	-0.029	-0.008	9.229	0.029	0.029	0.000	0.000	0.000	0.000
33	D	38	GLU	-1	-0.922	-0.968	8.685	-1.187	-1.187	0.000	0.000	0.000	0.000
34	D	39	LEU	0	0.001	0.010	10.704	-0.010	-0.010	0.000	0.000	0.000	0.000
35	D	40	LEU	0	0.019	-0.003	11.059	0.032	0.032	0.000	0.000	0.000	0.000
36	D	41	LYS	1	0.919	0.963	4.577	2.758	2.857	-0.001	-0.023	-0.075	0.000
37	D	42	VAL	0	-0.014	-0.008	8.533	0.028	0.028	0.000	0.000	0.000	0.000
38	D	43	PHE	0	0.018	0.022	11.084	0.053	0.053	0.000	0.000	0.000	0.000
39	D	44	VAL	0	0.014	-0.003	8.316	0.042	0.042	0.000	0.000	0.000	0.000
40	D	45	ARG	1	0.893	0.941	6.115	0.833	0.833	0.000	0.000	0.000	0.000
41	D	46	GLU	-1	-0.864	-0.921	9.766	-0.172	-0.172	0.000	0.000	0.000	0.000
42	D	47	ALA	0	0.026	0.004	13.357	0.020	0.020	0.000	0.000	0.000	0.000
43	D	48	ALA	0	-0.018	-0.006	10.873	0.012	0.012	0.000	0.000	0.000	0.000
44	D	49	ALA	0	-0.017	-0.007	12.877	-0.005	-0.005	0.000	0.000	0.000	0.000
45	D	50	ARG	1	0.793	0.892	14.220	0.091	0.091	0.000	0.000	0.000	0.000
46	D	51	ALA	0	0.049	0.031	16.412	0.004	0.004	0.000	0.000	0.000	0.000
47	D	52	ALA	0	0.018	0.005	15.140	0.003	0.003	0.000	0.000	0.000	0.000
48	D	53	ARG	1	0.962	0.974	16.569	0.124	0.124	0.000	0.000	0.000	0.000
49	D	54	GLN	0	-0.015	0.000	19.821	-0.004	-0.004	0.000	0.000	0.000	0.000
50	D	55	ALA	0	0.039	0.014	20.169	0.002	0.002	0.000	0.000	0.000	0.000
51	D	56	GLN	0	-0.028	-0.014	19.229	-0.013	-0.013	0.000	0.000	0.000	0.000
52	D	57	ALA	0	-0.064	-0.020	22.621	-0.001	-0.001	0.000	0.000	0.000	0.000
53	D	58	GLU	-1	-0.932	-0.977	25.194	0.015	0.015	0.000	0.000	0.000	0.000
54	D	59	ASP	-1	-0.979	-0.982	25.983	-0.008	-0.008	0.000	0.000	0.000	0.000
55	D	60	LEU	0	-0.043	-0.007	23.613	0.007	0.007	0.000	0.000	0.000	0.000
56	D	61	GLU	-1	-0.960	-0.990	20.574	0.000	0.000	0.000	0.000	0.000	0.000
57	D	62	LYS	1	0.823	0.918	19.155	-0.096	-0.096	0.000	0.000	0.000	0.000
58	D	63	VAL	0	-0.013	-0.007	16.344	-0.006	-0.006	0.000	0.000	0.000	0.000
59	D	64	ASP	-1	-0.862	-0.945	18.695	0.116	0.116	0.000	0.000	0.000	0.000
60	D	65	ILE	0	-0.053	-0.033	20.318	0.000	0.000	0.000	0.000	0.000	0.000
61	D	66	GLU	-1	-0.816	-0.916	21.313	0.066	0.066	0.000	0.000	0.000	0.000
62	D	67	HIS	0	0.038	0.036	20.351	-0.002	-0.002	0.000	0.000	0.000	0.000
63	D	68	VAL	0	-0.031	-0.022	17.181	-0.011	-0.011	0.000	0.000	0.000	0.000
64	D	69	GLU	-1	-0.925	-0.970	19.850	0.066	0.066	0.000	0.000	0.000	0.000
65	D	70	LYS	1	0.873	0.952	23.136	-0.005	-0.005	0.000	0.000	0.000	0.000
66	D	71	VAL	0	-0.073	-0.050	18.823	-0.010	-0.010	0.000	0.000	0.000	0.000
67	D	72	LEU	0	0.000	0.011	19.723	-0.011	-0.011	0.000	0.000	0.000	0.000
68	D	73	PRO	0	0.002	0.004	21.573	-0.008	-0.008	0.000	0.000	0.000	0.000
69	D	74	GLN	0	-0.022	-0.028	23.528	0.001	0.001	0.000	0.000	0.000	0.000
70	D	75	LEU	0	-0.020	0.000	16.411	-0.010	-0.010	0.000	0.000	0.000	0.000
71	D	76	LEU	0	-0.050	-0.049	19.971	-0.010	-0.010	0.000	0.000	0.000	0.000
72	D	77	LEU	0	-0.049	-0.013	21.963	-0.004	-0.004	0.000	0.000	0.000	0.000
73	D	78	ASP	-1	-0.817	-0.884	21.562	-0.065	-0.065	0.000	0.000	0.000	0.000
74	D	79	PHE	0	-0.088	-0.031	15.143	-0.016	-0.016	0.000	0.000	0.000	0.000
75	D	80	VAL	0	-0.003	-0.005	19.333	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:6:GLY)