FMO DATABASE

FMODB ID: 3JNZL

Calculation Name: 3M20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M20

Chain ID: A

ChEMBL ID:

UniProt ID: O29588

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	59
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-269594.764657
FMO2-HF: Nuclear repulsion	247514.639025
FMO2-HF: Total energy	-22080.125632
FMO2-MP2: Total energy	-22145.47928

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:1:PRO)

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

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.
-14.913	-9.37	13.038	-6.277	-12.303	-0.047

Interaction energy analysis for fragmet #1(A:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.004

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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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	3	LEU	0	0.017	0.015	3.638	-0.860	1.018	-0.002	-0.858	-1.018	0.002
4	A	4	ILE	0	-0.019	-0.016	6.387	-0.073	-0.073	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.006	0.004	10.154	0.028	0.028	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.033	0.006	12.987	0.011	0.011	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.001	0.005	16.743	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.000	-0.002	19.463	0.006	0.006	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.872	0.930	21.243	0.006	0.006	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.006	0.010	18.471	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.798	-0.886	22.222	-0.124	-0.124	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.029	-0.009	20.315	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.001	0.014	19.779	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.954	0.944	19.631	0.090	0.090	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.813	0.899	16.691	0.089	0.089	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.948	0.979	15.207	0.190	0.190	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.856	-0.911	14.989	-0.256	-0.256	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.008	-0.009	13.439	-0.032	-0.032	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.046	0.017	10.143	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.818	-0.850	10.181	-0.704	-0.704	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.860	0.914	11.239	0.175	0.175	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.007	0.000	8.369	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.020	-0.027	6.360	-0.097	-0.097	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.002	-0.011	6.918	-0.214	-0.214	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.014	-0.002	8.905	-0.029	-0.029	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.004	-0.005	3.709	-0.145	0.048	0.006	-0.049	-0.150	0.000
27	A	27	ALA	0	-0.006	-0.004	4.731	-0.408	-0.228	-0.001	-0.009	-0.169	0.000
28	A	28	GLU	-1	-0.943	-0.963	5.769	-0.440	-0.440	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.061	-0.027	6.385	0.064	0.064	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.043	-0.031	2.665	-1.736	0.040	1.658	-0.867	-2.566	-0.010
31	A	31	GLY	0	-0.005	0.022	5.250	-0.031	0.005	-0.001	-0.002	-0.033	0.000
32	A	32	MET	0	-0.079	-0.044	2.567	-1.767	-1.868	3.363	-0.765	-2.498	-0.004
33	A	33	ASP	-1	-0.845	-0.917	5.606	-1.062	-1.062	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.838	0.861	5.845	0.190	0.190	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.071	-0.044	7.301	0.187	0.187	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.009	0.011	3.309	0.031	0.520	0.015	-0.161	-0.343	0.000
37	A	37	ILE	0	-0.014	-0.006	2.039	-9.863	-8.989	7.976	-3.856	-4.994	-0.034
38	A	38	THR	0	-0.028	0.002	3.223	1.822	2.040	0.024	0.290	-0.532	-0.001
39	A	39	ILE	0	0.001	-0.001	5.701	0.098	0.098	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.022	-0.007	8.113	0.091	0.091	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.003	-0.015	11.223	0.027	0.027	0.000	0.000	0.000	0.000
42	A	42	HIS	0	0.006	0.019	14.029	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.754	-0.876	17.391	-0.093	-0.093	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.014	0.022	20.154	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.020	-0.014	23.084	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.040	0.018	26.187	0.005	0.005	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.867	-0.956	27.684	0.012	0.012	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.035	-0.016	25.498	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.000	0.001	22.989	0.009	0.009	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.030	0.026	25.467	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.038	-0.028	24.849	0.005	0.005	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.007	0.003	27.382	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.024	-0.008	29.611	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.825	0.909	31.068	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.063	0.037	29.735	0.002	0.002	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.049	-0.033	24.574	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.006	0.004	28.965	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.839	-0.898	31.718	0.014	0.014	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.925	0.960	32.012	0.001	0.001	0.000	0.000	0.000	0.000

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