FMO DATABASE

FMODB ID: MV9RZ

Calculation Name: 3PZ8-A-Xray372

Preferred Name: Segment polarity protein dishevelled homolog DVL-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3PZ8

Chain ID: A

ChEMBL ID: CHEMBL3813590

UniProt ID: P51141

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-561900.312371
FMO2-HF: Nuclear repulsion	528685.1022
FMO2-HF: Total energy	-33215.210171
FMO2-MP2: Total energy	-33312.089644

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:3:ASP)

Summations of interaction energy for fragment #1(A:3:ASP)

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.
-5.42	-0.56999999999998	8.003	-5.417	-7.438	-0.03

Interaction energy analysis for fragmet #1(A:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.947 / q_NPA : -0.971

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	A	5	LYS	1	0.915	0.938	3.876	-37.504	-35.470	-0.018	-1.131	-0.885	0.005
4	A	6	ILE	0	-0.003	0.016	6.902	-1.574	-1.574	0.000	0.000	0.000	0.000
5	A	7	ILE	0	-0.029	-0.017	10.075	-0.111	-0.111	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.057	-0.084	13.098	0.094	0.094	0.000	0.000	0.000	0.000
7	A	9	HIS	0	-0.031	-0.019	16.327	-0.347	-0.347	0.000	0.000	0.000	0.000
8	A	10	MET	0	0.020	0.017	18.561	0.425	0.425	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.857	-0.948	22.609	11.150	11.150	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.981	-0.983	25.899	9.469	9.469	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.807	-0.876	21.897	13.144	13.144	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.942	-0.962	24.855	10.377	10.377	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.056	-0.033	21.188	-0.039	-0.039	0.000	0.000	0.000	0.000
14	A	16	PRO	0	-0.061	-0.020	17.507	0.048	0.048	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.722	-0.804	15.152	16.179	16.179	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.040	-0.042	10.834	0.820	0.820	0.000	0.000	0.000	0.000
17	A	19	VAL	0	0.002	0.018	9.075	0.774	0.774	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.858	0.904	5.050	-25.541	-25.522	-0.001	-0.006	-0.012	0.000
19	A	21	LEU	0	0.029	0.020	4.069	-3.565	-3.196	-0.001	-0.107	-0.261	0.000
20	A	22	PRO	0	0.031	0.001	2.153	3.673	3.600	4.539	-2.106	-2.361	-0.023
21	A	23	VAL	0	-0.014	0.018	3.141	3.881	5.587	0.223	-0.524	-1.405	-0.006
22	A	24	ALA	0	0.049	0.020	2.292	3.279	4.316	3.015	-2.238	-1.814	-0.007
23	A	25	PRO	0	-0.029	-0.026	2.594	-6.222	-6.464	0.246	0.695	-0.700	0.001
24	A	26	GLU	-1	-0.879	-0.936	5.575	31.031	31.031	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.874	0.918	7.066	-25.269	-25.269	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.008	0.026	6.738	-1.232	-1.232	0.000	0.000	0.000	0.000
27	A	29	THR	0	-0.050	-0.050	8.546	-2.281	-2.281	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.023	0.013	11.642	0.860	0.860	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.026	0.020	13.991	-0.164	-0.164	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.839	-0.900	8.500	25.600	25.600	0.000	0.000	0.000	0.000
31	A	33	PHE	0	-0.005	-0.001	10.502	0.578	0.578	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.894	0.928	11.515	-14.889	-14.889	0.000	0.000	0.000	0.000
33	A	35	ASN	0	-0.061	-0.042	10.260	-1.264	-1.264	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.065	-0.024	9.618	-0.183	-0.183	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.032	-0.001	12.392	-0.479	-0.479	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.015	0.008	15.835	-1.096	-1.096	0.000	0.000	0.000	0.000
37	A	39	ASN	0	-0.020	-0.006	17.973	-0.217	-0.217	0.000	0.000	0.000	0.000
38	A	40	ARG	1	0.760	0.836	18.035	-14.906	-14.906	0.000	0.000	0.000	0.000
39	A	41	PRO	0	0.026	0.021	21.170	0.195	0.195	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.012	-0.006	18.125	-0.342	-0.342	0.000	0.000	0.000	0.000
41	A	43	HIS	0	-0.011	-0.017	21.122	0.264	0.264	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.025	0.000	24.018	-0.358	-0.358	0.000	0.000	0.000	0.000
43	A	45	TYR	0	-0.032	-0.014	21.711	-0.207	-0.207	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.808	0.874	23.075	-10.646	-10.646	0.000	0.000	0.000	0.000
45	A	47	PHE	0	-0.030	-0.006	17.398	0.310	0.310	0.000	0.000	0.000	0.000
46	A	48	PHE	0	0.049	0.038	20.103	0.017	0.017	0.000	0.000	0.000	0.000
47	A	49	PHE	0	0.011	-0.003	14.125	0.882	0.882	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.820	0.937	17.479	-15.578	-15.578	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.026	-0.048	17.231	0.841	0.841	0.000	0.000	0.000	0.000
50	A	52	MET	0	-0.042	-0.032	19.178	-0.514	-0.514	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.769	-0.881	21.183	11.627	11.627	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.130	-0.077	23.826	0.193	0.193	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.876	-0.916	25.568	9.896	9.896	0.000	0.000	0.000	0.000
54	A	56	PHE	0	-0.083	-0.046	27.869	-0.420	-0.420	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.003	0.011	25.350	-0.083	-0.083	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.060	-0.049	22.105	0.456	0.456	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.000	0.013	22.816	-0.523	-0.523	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.877	0.936	22.178	-11.238	-11.238	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.815	-0.881	20.066	14.022	14.022	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.804	-0.888	20.716	11.691	11.691	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.049	-0.021	17.349	0.039	0.039	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.043	0.016	19.994	0.279	0.279	0.000	0.000	0.000	0.000
63	A	65	ASP	-1	-0.890	-0.945	20.574	12.669	12.669	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.834	-0.917	17.665	15.319	15.319	0.000	0.000	0.000	0.000
65	A	67	ASN	0	-0.035	-0.019	15.974	0.596	0.596	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.001	0.008	16.169	0.420	0.420	0.000	0.000	0.000	0.000
67	A	69	LYS	1	0.941	0.951	12.807	-18.693	-18.693	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.007	0.015	10.506	-0.958	-0.958	0.000	0.000	0.000	0.000
69	A	71	PRO	0	0.002	0.018	12.452	1.170	1.170	0.000	0.000	0.000	0.000
70	A	72	CYS	0	-0.001	-0.005	9.159	0.783	0.783	0.000	0.000	0.000	0.000
71	A	73	PHE	0	0.053	0.023	12.738	-0.770	-0.770	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.030	-0.028	14.291	0.454	0.454	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.048	0.023	10.091	0.292	0.292	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.901	0.947	9.331	-19.660	-19.660	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.073	0.053	9.473	-1.618	-1.618	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.055	-0.033	11.925	0.230	0.230	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.006	-0.008	15.029	-0.465	-0.465	0.000	0.000	0.000	0.000
78	A	80	TRP	0	-0.003	-0.012	17.042	-0.048	-0.048	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.004	0.012	17.377	-0.051	-0.051	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.016	0.008	21.096	-0.277	-0.277	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.015	0.017	24.852	0.181	0.181	0.000	0.000	0.000	0.000
82	A	84	ALA	0	-0.049	-0.019	27.102	-0.296	-0.296	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASP)