FMO DATABASE

FMODB ID: 3JLNL

Calculation Name: 4M78-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M78

Chain ID: D

ChEMBL ID:

UniProt ID: P38203

Base Structure: X-ray

Registration Date: 2023-09-23

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

Total energy (hartree)

FMO2-HF: Electronic energy	-456269.044562
FMO2-HF: Nuclear repulsion	427101.239914
FMO2-HF: Total energy	-29167.804648
FMO2-MP2: Total energy	-29252.874216

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:10:SER)

Summations of interaction energy for fragment #1(D:10:SER)

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.
-25.753	-18.804	8.669	-7.103	-8.516	0.006

Interaction energy analysis for fragmet #1(D:10:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.023

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	D	12	THR	0	-0.049	-0.020	2.094	-13.879	-10.189	4.381	-3.777	-4.294	0.032
4	D	13	THR	0	-0.019	-0.031	2.109	-5.821	-4.380	4.256	-2.401	-3.296	-0.021
5	D	14	GLU	-1	-0.901	-0.943	3.362	-6.523	-4.705	0.032	-0.925	-0.926	-0.005
6	D	15	PHE	0	-0.006	-0.004	5.677	0.829	0.829	0.000	0.000	0.000	0.000
7	D	16	LEU	0	-0.038	-0.034	6.976	0.172	0.172	0.000	0.000	0.000	0.000
8	D	17	SER	0	-0.036	-0.020	8.285	-0.039	-0.039	0.000	0.000	0.000	0.000
9	D	18	ASP	-1	-0.890	-0.930	9.866	-0.896	-0.896	0.000	0.000	0.000	0.000
10	D	19	ILE	0	-0.059	-0.038	11.837	0.181	0.181	0.000	0.000	0.000	0.000
11	D	20	ILE	0	-0.023	0.003	13.688	0.081	0.081	0.000	0.000	0.000	0.000
12	D	21	GLY	0	-0.026	-0.019	15.439	0.010	0.010	0.000	0.000	0.000	0.000
13	D	22	LYS	1	0.827	0.909	15.550	0.318	0.318	0.000	0.000	0.000	0.000
14	D	23	THR	0	-0.023	-0.016	19.487	-0.002	-0.002	0.000	0.000	0.000	0.000
15	D	24	VAL	0	-0.018	-0.013	16.856	0.006	0.006	0.000	0.000	0.000	0.000
16	D	25	ASN	0	-0.020	-0.007	19.501	0.007	0.007	0.000	0.000	0.000	0.000
17	D	26	VAL	0	0.033	0.012	17.688	0.016	0.016	0.000	0.000	0.000	0.000
18	D	27	LYS	1	0.807	0.907	19.596	-0.057	-0.057	0.000	0.000	0.000	0.000
19	D	28	LEU	0	0.036	0.014	19.978	0.007	0.007	0.000	0.000	0.000	0.000
20	D	29	ALA	0	-0.002	-0.014	21.415	0.009	0.009	0.000	0.000	0.000	0.000
21	D	30	SER	0	-0.033	-0.009	22.795	0.004	0.004	0.000	0.000	0.000	0.000
22	D	31	GLY	0	0.061	0.029	24.950	-0.002	-0.002	0.000	0.000	0.000	0.000
23	D	32	LEU	0	-0.040	-0.022	26.212	-0.001	-0.001	0.000	0.000	0.000	0.000
24	D	33	LEU	0	-0.023	-0.004	22.652	0.005	0.005	0.000	0.000	0.000	0.000
25	D	34	TYR	0	-0.019	-0.033	22.886	-0.004	-0.004	0.000	0.000	0.000	0.000
26	D	35	SER	0	0.019	-0.006	22.779	0.002	0.002	0.000	0.000	0.000	0.000
27	D	36	GLY	0	0.018	0.006	23.085	0.002	0.002	0.000	0.000	0.000	0.000
28	D	37	ARG	1	0.811	0.924	21.772	0.211	0.211	0.000	0.000	0.000	0.000
29	D	38	LEU	0	0.025	0.017	14.931	0.008	0.008	0.000	0.000	0.000	0.000
30	D	39	GLU	-1	-0.777	-0.853	18.549	-0.240	-0.240	0.000	0.000	0.000	0.000
31	D	40	SER	0	-0.036	-0.024	15.936	-0.031	-0.031	0.000	0.000	0.000	0.000
32	D	41	ILE	0	0.019	0.006	11.473	0.062	0.062	0.000	0.000	0.000	0.000
33	D	42	ASP	-1	-0.779	-0.866	11.488	-0.359	-0.359	0.000	0.000	0.000	0.000
34	D	43	GLY	0	0.037	0.006	8.461	0.008	0.008	0.000	0.000	0.000	0.000
35	D	44	PHE	0	-0.103	-0.043	9.294	0.094	0.094	0.000	0.000	0.000	0.000
36	D	45	MET	0	0.004	0.000	10.624	0.072	0.072	0.000	0.000	0.000	0.000
37	D	46	ASN	0	-0.051	-0.033	12.723	0.065	0.065	0.000	0.000	0.000	0.000
38	D	47	VAL	0	0.005	0.000	14.755	-0.048	-0.048	0.000	0.000	0.000	0.000
39	D	48	ALA	0	-0.002	0.010	17.113	0.026	0.026	0.000	0.000	0.000	0.000
40	D	49	LEU	0	-0.003	-0.001	19.260	-0.017	-0.017	0.000	0.000	0.000	0.000
41	D	50	SER	0	0.037	0.000	22.134	0.021	0.021	0.000	0.000	0.000	0.000
42	D	51	SER	0	-0.062	-0.051	25.228	0.009	0.009	0.000	0.000	0.000	0.000
43	D	52	ALA	0	0.014	0.023	25.130	0.008	0.008	0.000	0.000	0.000	0.000
44	D	53	THR	0	-0.011	-0.016	27.006	0.002	0.002	0.000	0.000	0.000	0.000
45	D	54	GLU	-1	-0.843	-0.910	27.319	-0.032	-0.032	0.000	0.000	0.000	0.000
46	D	55	HIS	0	0.028	0.005	28.496	-0.004	-0.004	0.000	0.000	0.000	0.000
47	D	56	TYR	0	0.015	-0.004	28.665	0.000	0.000	0.000	0.000	0.000	0.000
48	D	57	GLU	-1	-0.799	-0.853	26.313	0.043	0.043	0.000	0.000	0.000	0.000
49	D	58	SER	0	-0.027	-0.027	26.357	0.006	0.006	0.000	0.000	0.000	0.000
50	D	59	ASN	0	0.047	0.013	26.347	-0.010	-0.010	0.000	0.000	0.000	0.000
51	D	60	ASN	0	-0.018	-0.003	28.245	-0.007	-0.007	0.000	0.000	0.000	0.000
52	D	61	ASN	0	-0.041	-0.013	31.200	0.001	0.001	0.000	0.000	0.000	0.000
53	D	62	LYS	1	0.888	0.940	33.127	0.012	0.012	0.000	0.000	0.000	0.000
54	D	63	LEU	0	0.009	0.018	32.274	0.001	0.001	0.000	0.000	0.000	0.000
55	D	64	LEU	0	-0.040	-0.016	31.739	0.001	0.001	0.000	0.000	0.000	0.000
56	D	65	ASN	0	-0.034	-0.029	32.349	-0.004	-0.004	0.000	0.000	0.000	0.000
57	D	66	LYS	1	0.878	0.938	30.871	0.070	0.070	0.000	0.000	0.000	0.000
58	D	67	PHE	0	0.015	0.031	28.490	0.001	0.001	0.000	0.000	0.000	0.000
59	D	68	ASN	0	-0.022	-0.025	30.889	-0.004	-0.004	0.000	0.000	0.000	0.000
60	D	69	SER	0	-0.023	-0.021	29.991	0.000	0.000	0.000	0.000	0.000	0.000
61	D	70	ASP	-1	-0.883	-0.944	24.408	-0.137	-0.137	0.000	0.000	0.000	0.000
62	D	71	VAL	0	-0.040	-0.014	24.628	0.006	0.006	0.000	0.000	0.000	0.000
63	D	72	PHE	0	0.003	0.005	19.156	-0.007	-0.007	0.000	0.000	0.000	0.000
64	D	73	LEU	0	-0.005	-0.007	19.878	0.019	0.019	0.000	0.000	0.000	0.000
65	D	74	ARG	1	0.912	0.953	18.877	0.035	0.035	0.000	0.000	0.000	0.000
66	D	75	GLY	0	0.099	0.037	15.761	0.018	0.018	0.000	0.000	0.000	0.000
67	D	76	THR	0	-0.051	-0.047	16.622	0.022	0.022	0.000	0.000	0.000	0.000
68	D	77	GLN	0	-0.029	0.003	18.332	0.007	0.007	0.000	0.000	0.000	0.000
69	D	78	VAL	0	-0.011	0.007	15.321	0.007	0.007	0.000	0.000	0.000	0.000
70	D	79	MET	0	-0.041	-0.012	16.920	0.015	0.015	0.000	0.000	0.000	0.000
71	D	80	TYR	0	-0.007	-0.018	15.050	0.041	0.041	0.000	0.000	0.000	0.000
72	D	81	ILE	0	0.019	0.005	12.976	-0.038	-0.038	0.000	0.000	0.000	0.000
73	D	82	SER	0	-0.011	0.005	14.207	0.052	0.052	0.000	0.000	0.000	0.000
74	D	83	GLU	-1	-0.815	-0.894	15.855	-0.210	-0.210	0.000	0.000	0.000	0.000
75	D	84	GLN	0	-0.005	0.005	18.091	0.027	0.027	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:10:SER)