FMO DATABASE

FMODB ID: VR3V1

Calculation Name: 3RD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD4

Chain ID: A

ChEMBL ID:

UniProt ID: C0AZM8

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:

Apendix: None

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-499794.1985
FMO2-HF: Nuclear repulsion	468231.752173
FMO2-HF: Total energy	-31562.446326
FMO2-MP2: Total energy	-31653.945578

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-0.122	3.512	0.253	-1.716	-2.171	0.001

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.029

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	4	VAL	0	0.015	-0.003	3.530	-1.389	0.725	0.015	-1.188	-0.941	0.003
4	A	5	LYS	1	0.902	0.945	5.185	0.182	0.182	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.013	0.015	7.710	-0.017	-0.017	0.000	0.000	0.000	0.000
6	A	7	TYR	0	-0.023	-0.016	7.565	0.088	0.088	0.000	0.000	0.000	0.000
7	A	8	MET	0	0.031	0.025	13.580	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.040	-0.022	15.993	0.028	0.028	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.817	-0.900	18.736	-0.071	-0.071	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.034	-0.003	20.905	0.006	0.006	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.035	-0.017	22.341	0.008	0.008	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.817	-0.899	23.137	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.822	0.901	22.988	0.087	0.087	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.814	0.900	23.788	0.022	0.022	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.739	-0.839	23.797	-0.079	-0.079	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.045	-0.026	22.504	0.010	0.010	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.052	0.033	24.772	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.023	-0.008	23.868	0.007	0.007	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.040	-0.013	25.844	0.012	0.012	0.000	0.000	0.000	0.000
20	A	33	GLU	-1	-0.827	-0.901	29.511	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	34	ILE	0	-0.121	-0.068	25.241	0.000	0.000	0.000	0.000	0.000	0.000
22	A	35	THR	0	-0.010	-0.029	21.720	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	36	HIS	0	-0.070	-0.042	23.770	0.010	0.010	0.000	0.000	0.000	0.000
24	A	37	TYR	0	-0.046	-0.011	17.759	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	38	TYR	0	-0.015	-0.021	20.386	0.004	0.004	0.000	0.000	0.000	0.000
26	A	39	GLN	0	-0.023	-0.018	18.916	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	40	VAL	0	0.035	0.019	17.811	0.001	0.001	0.000	0.000	0.000	0.000
28	A	41	THR	0	-0.019	-0.004	18.511	0.006	0.006	0.000	0.000	0.000	0.000
29	A	42	PHE	0	0.035	0.017	15.904	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	43	ARG	1	0.842	0.890	17.278	0.022	0.022	0.000	0.000	0.000	0.000
31	A	44	LEU	0	-0.032	-0.027	14.342	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	45	THR	0	-0.045	-0.019	18.288	0.012	0.012	0.000	0.000	0.000	0.000
33	A	46	THR	0	-0.031	-0.036	18.179	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	47	ASP	-1	-0.896	-0.949	20.936	0.023	0.023	0.000	0.000	0.000	0.000
35	A	48	ASP	-1	-0.830	-0.873	16.003	0.035	0.035	0.000	0.000	0.000	0.000
36	A	49	ARG	1	0.902	0.920	18.161	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	50	LYS	1	0.852	0.926	13.141	-0.057	-0.057	0.000	0.000	0.000	0.000
38	A	51	ASP	-1	-0.748	-0.831	18.055	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	52	LEU	0	-0.020	-0.019	11.399	0.033	0.033	0.000	0.000	0.000	0.000
40	A	53	VAL	0	0.017	0.016	15.308	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.047	-0.027	11.902	0.014	0.014	0.000	0.000	0.000	0.000
42	A	55	ASN	0	0.018	0.005	14.856	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	56	ILE	0	-0.037	-0.016	14.426	-0.038	-0.038	0.000	0.000	0.000	0.000
44	A	57	ASP	-1	-0.824	-0.914	16.389	-0.246	-0.246	0.000	0.000	0.000	0.000
45	A	58	LYS	1	0.907	0.944	18.536	0.115	0.115	0.000	0.000	0.000	0.000
46	A	59	SER	0	-0.007	0.000	21.443	0.019	0.019	0.000	0.000	0.000	0.000
47	A	60	SER	0	0.012	0.004	17.535	0.018	0.018	0.000	0.000	0.000	0.000
48	A	61	TYR	0	-0.032	-0.044	20.486	0.012	0.012	0.000	0.000	0.000	0.000
49	A	62	GLN	0	-0.010	-0.011	22.178	0.015	0.015	0.000	0.000	0.000	0.000
50	A	63	ASN	0	-0.086	-0.035	23.083	0.011	0.011	0.000	0.000	0.000	0.000
51	A	64	ILE	0	-0.016	0.002	19.386	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	65	GLU	-1	-0.825	-0.932	23.799	-0.082	-0.082	0.000	0.000	0.000	0.000
53	A	66	PRO	0	0.017	-0.014	25.457	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	67	GLU	-1	-0.926	-0.948	26.374	-0.057	-0.057	0.000	0.000	0.000	0.000
55	A	68	MET	0	-0.024	0.037	24.240	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	69	LYS	1	0.846	0.889	22.573	0.082	0.082	0.000	0.000	0.000	0.000
57	A	70	GLY	0	0.036	0.031	20.814	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	71	ARG	1	0.749	0.846	16.204	0.267	0.267	0.000	0.000	0.000	0.000
59	A	72	LEU	0	0.006	0.017	12.425	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	73	PHE	0	0.026	-0.002	11.051	-0.034	-0.034	0.000	0.000	0.000	0.000
61	A	74	MET	0	-0.020	-0.002	7.800	0.080	0.080	0.000	0.000	0.000	0.000
62	A	75	GLN	0	0.012	0.004	2.748	0.711	1.588	0.164	-0.322	-0.719	-0.001
63	A	76	GLY	0	-0.016	-0.011	3.524	-0.082	0.490	0.061	-0.187	-0.445	-0.001
64	A	77	SER	0	-0.005	-0.006	3.859	-0.132	-0.061	0.013	-0.019	-0.066	0.000
65	A	78	ARG	1	0.905	0.963	6.061	1.368	1.368	0.000	0.000	0.000	0.000
66	A	79	PHE	0	0.092	0.038	7.872	-0.172	-0.172	0.000	0.000	0.000	0.000
67	A	80	VAL	0	-0.108	-0.054	8.097	-0.135	-0.135	0.000	0.000	0.000	0.000
68	A	81	GLN	0	0.093	0.043	11.094	0.041	0.041	0.000	0.000	0.000	0.000
69	A	82	PHE	0	-0.020	-0.020	14.317	0.000	0.000	0.000	0.000	0.000	0.000
70	A	83	GLU	-1	-0.870	-0.907	17.121	-0.346	-0.346	0.000	0.000	0.000	0.000
71	A	84	THR	0	0.016	0.005	19.673	0.015	0.015	0.000	0.000	0.000	0.000
72	A	85	ASP	-1	-0.840	-0.909	22.658	-0.200	-0.200	0.000	0.000	0.000	0.000
73	A	86	VAL	0	-0.033	-0.012	24.944	0.014	0.014	0.000	0.000	0.000	0.000
74	A	87	PRO	0	-0.015	-0.020	28.091	0.001	0.001	0.000	0.000	0.000	0.000
75	A	88	ILE	0	-0.034	-0.005	30.164	0.001	0.001	0.000	0.000	0.000	0.000
76	A	89	ASP	-1	-0.952	-0.967	31.999	-0.118	-0.118	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)