FMO DATABASE

FMODB ID: 1NMJZ

Calculation Name: 4M78-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M78

Chain ID: E

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	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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-499907.381627
FMO2-HF: Nuclear repulsion	468743.787362
FMO2-HF: Total energy	-31163.594265
FMO2-MP2: Total energy	-31255.12935

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(E:6:ILE)

Summations of interaction energy for fragment #1(E:6:ILE)

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.
-2.117	1.071	0.031	-1.086	-2.132	0

Interaction energy analysis for fragmet #1(E:6:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.022

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	E	8	PRO	0	0.023	0.000	3.754	-1.074	0.652	-0.022	-0.632	-1.071	0.002
4	E	9	LEU	0	0.057	0.017	5.539	0.304	0.304	0.000	0.000	0.000	0.000
5	E	10	GLU	-1	-0.870	-0.927	3.568	-0.726	0.161	0.017	-0.337	-0.567	-0.002
6	E	11	VAL	0	-0.054	-0.032	3.347	-0.231	0.344	0.036	-0.117	-0.494	0.000
7	E	12	ILE	0	-0.004	-0.011	5.802	0.333	0.333	0.000	0.000	0.000	0.000
8	E	13	ASP	-1	-0.887	-0.960	8.973	-0.211	-0.211	0.000	0.000	0.000	0.000
9	E	14	LYS	1	0.904	0.968	6.598	0.538	0.538	0.000	0.000	0.000	0.000
10	E	15	THR	0	-0.095	-0.052	9.437	0.108	0.108	0.000	0.000	0.000	0.000
11	E	16	ILE	0	0.030	0.029	11.491	0.059	0.059	0.000	0.000	0.000	0.000
12	E	17	ASN	0	-0.072	-0.038	14.493	0.027	0.027	0.000	0.000	0.000	0.000
13	E	18	GLN	0	-0.043	-0.014	11.876	0.002	0.002	0.000	0.000	0.000	0.000
14	E	19	LYS	1	0.910	0.969	16.261	0.199	0.199	0.000	0.000	0.000	0.000
15	E	20	VAL	0	0.011	0.006	13.511	-0.039	-0.039	0.000	0.000	0.000	0.000
16	E	21	LEU	0	0.010	0.017	15.454	0.035	0.035	0.000	0.000	0.000	0.000
17	E	22	ILE	0	-0.018	-0.005	15.538	-0.058	-0.058	0.000	0.000	0.000	0.000
18	E	23	VAL	0	0.032	0.015	17.123	0.041	0.041	0.000	0.000	0.000	0.000
19	E	24	LEU	0	0.028	0.007	18.281	-0.028	-0.028	0.000	0.000	0.000	0.000
20	E	25	GLN	0	0.006	-0.005	20.700	-0.005	-0.005	0.000	0.000	0.000	0.000
21	E	26	SER	0	-0.021	-0.005	22.088	0.014	0.014	0.000	0.000	0.000	0.000
22	E	27	ASN	0	-0.010	-0.010	23.748	-0.017	-0.017	0.000	0.000	0.000	0.000
23	E	28	ARG	1	0.924	0.982	24.544	0.177	0.177	0.000	0.000	0.000	0.000
24	E	29	GLU	-1	-0.872	-0.948	21.000	-0.272	-0.272	0.000	0.000	0.000	0.000
25	E	30	PHE	0	-0.018	-0.024	21.003	0.028	0.028	0.000	0.000	0.000	0.000
26	E	31	GLU	-1	-0.892	-0.930	19.628	-0.237	-0.237	0.000	0.000	0.000	0.000
27	E	32	GLY	0	0.046	0.019	19.648	0.026	0.026	0.000	0.000	0.000	0.000
28	E	33	THR	0	-0.038	-0.017	18.886	-0.027	-0.027	0.000	0.000	0.000	0.000
29	E	34	LEU	0	-0.027	0.012	13.510	0.021	0.021	0.000	0.000	0.000	0.000
30	E	35	VAL	0	0.013	0.000	17.511	0.017	0.017	0.000	0.000	0.000	0.000
31	E	36	GLY	0	-0.021	-0.019	17.168	0.022	0.022	0.000	0.000	0.000	0.000
32	E	37	PHE	0	-0.006	-0.007	11.231	-0.032	-0.032	0.000	0.000	0.000	0.000
33	E	38	ASP	-1	-0.796	-0.891	16.723	-0.242	-0.242	0.000	0.000	0.000	0.000
34	E	39	ASP	-1	-0.892	-0.955	15.246	-0.309	-0.309	0.000	0.000	0.000	0.000
35	E	40	PHE	0	-0.119	-0.060	15.804	-0.034	-0.034	0.000	0.000	0.000	0.000
36	E	41	VAL	0	-0.019	-0.005	13.355	-0.019	-0.019	0.000	0.000	0.000	0.000
37	E	42	ASN	0	0.005	0.010	16.319	0.002	0.002	0.000	0.000	0.000	0.000
38	E	43	VAL	0	0.013	0.015	16.286	-0.006	-0.006	0.000	0.000	0.000	0.000
39	E	44	ILE	0	-0.063	-0.025	18.935	0.037	0.037	0.000	0.000	0.000	0.000
40	E	45	LEU	0	0.027	0.010	18.666	-0.012	-0.012	0.000	0.000	0.000	0.000
41	E	46	GLU	-1	-0.967	-0.995	21.793	-0.125	-0.125	0.000	0.000	0.000	0.000
42	E	47	ASP	-1	-0.890	-0.952	23.737	-0.136	-0.136	0.000	0.000	0.000	0.000
43	E	48	ALA	0	-0.013	0.002	23.929	-0.005	-0.005	0.000	0.000	0.000	0.000
44	E	49	VAL	0	-0.008	-0.021	24.267	0.018	0.018	0.000	0.000	0.000	0.000
45	E	50	GLU	-1	-0.888	-0.952	24.724	-0.169	-0.169	0.000	0.000	0.000	0.000
46	E	51	TRP	0	0.010	-0.015	24.387	0.022	0.022	0.000	0.000	0.000	0.000
47	E	52	LEU	0	-0.015	-0.019	26.913	-0.009	-0.009	0.000	0.000	0.000	0.000
48	E	53	ILE	0	-0.019	-0.017	23.342	0.010	0.010	0.000	0.000	0.000	0.000
49	E	54	ASP	-1	-0.821	-0.923	26.942	-0.150	-0.150	0.000	0.000	0.000	0.000
50	E	55	PRO	0	-0.045	0.018	28.522	0.008	0.008	0.000	0.000	0.000	0.000
51	E	56	GLU	-1	-0.887	-0.953	31.404	-0.091	-0.091	0.000	0.000	0.000	0.000
52	E	57	ASP	-1	-0.919	-0.963	32.859	-0.093	-0.093	0.000	0.000	0.000	0.000
53	E	58	GLU	-1	-0.978	-0.979	29.948	-0.111	-0.111	0.000	0.000	0.000	0.000
54	E	59	SER	0	-0.087	-0.057	28.958	-0.008	-0.008	0.000	0.000	0.000	0.000
55	E	60	ARG	1	0.779	0.901	30.099	0.106	0.106	0.000	0.000	0.000	0.000
56	E	61	ASN	0	0.025	-0.011	26.127	-0.001	-0.001	0.000	0.000	0.000	0.000
57	E	62	GLU	-1	-0.913	-0.948	29.848	-0.110	-0.110	0.000	0.000	0.000	0.000
58	E	63	LYS	1	0.912	0.968	29.305	0.108	0.108	0.000	0.000	0.000	0.000
59	E	64	VAL	0	-0.009	0.014	30.127	0.009	0.009	0.000	0.000	0.000	0.000
60	E	65	MET	0	-0.032	-0.038	30.354	0.007	0.007	0.000	0.000	0.000	0.000
61	E	66	GLN	0	-0.030	-0.008	28.152	-0.014	-0.014	0.000	0.000	0.000	0.000
62	E	67	HIS	1	0.816	0.918	28.167	0.154	0.154	0.000	0.000	0.000	0.000
63	E	68	HIS	0	0.030	0.014	29.348	-0.005	-0.005	0.000	0.000	0.000	0.000
64	E	69	GLY	0	0.001	0.009	28.904	0.007	0.007	0.000	0.000	0.000	0.000
65	E	70	ARG	1	0.962	0.977	24.999	0.116	0.116	0.000	0.000	0.000	0.000
66	E	71	MET	0	-0.038	-0.007	23.710	0.016	0.016	0.000	0.000	0.000	0.000
67	E	72	LEU	0	0.003	0.000	23.193	-0.014	-0.014	0.000	0.000	0.000	0.000
68	E	73	LEU	0	-0.018	0.002	20.789	0.015	0.015	0.000	0.000	0.000	0.000
69	E	74	SER	0	-0.022	-0.027	21.668	-0.023	-0.023	0.000	0.000	0.000	0.000
70	E	75	GLY	0	0.130	0.039	19.376	-0.009	-0.009	0.000	0.000	0.000	0.000
71	E	76	ASN	0	-0.075	-0.037	19.428	-0.027	-0.027	0.000	0.000	0.000	0.000
72	E	77	ASN	0	-0.053	-0.013	21.713	0.007	0.007	0.000	0.000	0.000	0.000
73	E	78	ILE	0	-0.039	-0.007	15.737	0.001	0.001	0.000	0.000	0.000	0.000
74	E	79	ALA	0	-0.043	-0.006	16.672	-0.010	-0.010	0.000	0.000	0.000	0.000
75	E	80	ILE	0	-0.028	-0.023	12.507	-0.076	-0.076	0.000	0.000	0.000	0.000
76	E	81	LEU	0	0.004	0.005	11.185	0.052	0.052	0.000	0.000	0.000	0.000
77	E	82	VAL	0	0.012	-0.010	11.149	-0.099	-0.099	0.000	0.000	0.000	0.000
78	E	83	PRO	0	-0.026	-0.003	8.521	0.070	0.070	0.000	0.000	0.000	0.000
79	E	84	GLY	0	-0.017	-0.013	11.798	0.031	0.031	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:6:ILE)