FMO DATABASE

FMODB ID: JQNM9

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	OptHSide
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	-456762.38679
FMO2-HF: Nuclear repulsion	427594.984522
FMO2-HF: Total energy	-29167.402268
FMO2-MP2: Total energy	-29252.495666

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.
-14.022	-9.266	7.826	-5.774	-6.807	-0.02

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 : 0.017 / q_NPA : 0.005

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	D	12	THR	0	-0.027	-0.015	2.974	-6.442	-2.061	0.165	-2.200	-2.346	0.010
4	D	13	THR	0	-0.027	-0.036	1.987	-4.360	-4.763	7.654	-3.374	-3.877	-0.030
5	D	14	GLU	-1	-0.889	-0.936	3.463	-3.583	-2.805	0.007	-0.200	-0.584	0.000
6	D	15	PHE	0	0.028	0.005	5.775	0.956	0.956	0.000	0.000	0.000	0.000
7	D	16	LEU	0	-0.067	-0.036	7.253	0.390	0.390	0.000	0.000	0.000	0.000
8	D	17	SER	0	-0.040	-0.013	8.597	-0.021	-0.021	0.000	0.000	0.000	0.000
9	D	18	ASP	-1	-0.922	-0.946	10.269	-0.983	-0.983	0.000	0.000	0.000	0.000
10	D	19	ILE	0	-0.052	-0.041	12.070	0.200	0.200	0.000	0.000	0.000	0.000
11	D	20	ILE	0	-0.015	0.015	13.618	0.095	0.095	0.000	0.000	0.000	0.000
12	D	21	GLY	0	-0.020	-0.006	15.310	0.027	0.027	0.000	0.000	0.000	0.000
13	D	22	LYS	1	0.809	0.894	16.031	0.490	0.490	0.000	0.000	0.000	0.000
14	D	23	THR	0	-0.030	-0.022	19.179	-0.008	-0.008	0.000	0.000	0.000	0.000
15	D	24	VAL	0	-0.006	-0.011	16.740	0.003	0.003	0.000	0.000	0.000	0.000
16	D	25	ASN	0	-0.026	-0.018	19.610	0.032	0.032	0.000	0.000	0.000	0.000
17	D	26	VAL	0	0.031	0.011	17.733	-0.008	-0.008	0.000	0.000	0.000	0.000
18	D	27	LYS	1	0.826	0.915	19.456	0.122	0.122	0.000	0.000	0.000	0.000
19	D	28	LEU	0	0.005	0.006	19.897	-0.020	-0.020	0.000	0.000	0.000	0.000
20	D	29	ALA	0	0.009	-0.003	21.752	0.018	0.018	0.000	0.000	0.000	0.000
21	D	30	SER	0	-0.034	-0.017	22.814	0.011	0.011	0.000	0.000	0.000	0.000
22	D	31	GLY	0	0.085	0.045	24.856	0.011	0.011	0.000	0.000	0.000	0.000
23	D	32	LEU	0	-0.054	-0.031	25.966	0.004	0.004	0.000	0.000	0.000	0.000
24	D	33	LEU	0	-0.041	-0.020	22.761	-0.013	-0.013	0.000	0.000	0.000	0.000
25	D	34	TYR	0	-0.017	-0.042	22.710	0.006	0.006	0.000	0.000	0.000	0.000
26	D	35	SER	0	0.008	0.001	22.649	-0.014	-0.014	0.000	0.000	0.000	0.000
27	D	36	GLY	0	0.039	0.013	22.749	0.015	0.015	0.000	0.000	0.000	0.000
28	D	37	ARG	1	0.824	0.942	21.719	0.305	0.305	0.000	0.000	0.000	0.000
29	D	38	LEU	0	0.022	0.011	15.007	0.013	0.013	0.000	0.000	0.000	0.000
30	D	39	GLU	-1	-0.762	-0.858	18.483	-0.353	-0.353	0.000	0.000	0.000	0.000
31	D	40	SER	0	-0.019	-0.019	15.788	-0.030	-0.030	0.000	0.000	0.000	0.000
32	D	41	ILE	0	0.008	0.002	11.436	0.063	0.063	0.000	0.000	0.000	0.000
33	D	42	ASP	-1	-0.801	-0.883	11.430	-0.683	-0.683	0.000	0.000	0.000	0.000
34	D	43	GLY	0	0.042	0.015	8.835	-0.120	-0.120	0.000	0.000	0.000	0.000
35	D	44	PHE	0	-0.109	-0.052	9.705	0.016	0.016	0.000	0.000	0.000	0.000
36	D	45	MET	0	0.021	0.005	10.588	0.046	0.046	0.000	0.000	0.000	0.000
37	D	46	ASN	0	-0.034	-0.026	12.846	0.117	0.117	0.000	0.000	0.000	0.000
38	D	47	VAL	0	0.008	0.003	14.994	-0.071	-0.071	0.000	0.000	0.000	0.000
39	D	48	ALA	0	-0.003	0.022	17.334	0.057	0.057	0.000	0.000	0.000	0.000
40	D	49	LEU	0	-0.023	-0.007	19.431	-0.028	-0.028	0.000	0.000	0.000	0.000
41	D	50	SER	0	0.039	0.008	22.111	0.030	0.030	0.000	0.000	0.000	0.000
42	D	51	SER	0	-0.057	-0.043	25.230	0.008	0.008	0.000	0.000	0.000	0.000
43	D	52	ALA	0	0.015	0.024	25.459	-0.001	-0.001	0.000	0.000	0.000	0.000
44	D	53	THR	0	-0.018	-0.017	27.009	0.012	0.012	0.000	0.000	0.000	0.000
45	D	54	GLU	-1	-0.860	-0.912	27.534	-0.136	-0.136	0.000	0.000	0.000	0.000
46	D	55	HIS	0	0.014	-0.003	28.478	0.005	0.005	0.000	0.000	0.000	0.000
47	D	56	TYR	0	0.000	-0.001	28.691	-0.005	-0.005	0.000	0.000	0.000	0.000
48	D	57	GLU	-1	-0.814	-0.867	26.328	-0.071	-0.071	0.000	0.000	0.000	0.000
49	D	58	SER	0	-0.029	-0.032	26.657	-0.002	-0.002	0.000	0.000	0.000	0.000
50	D	59	ASN	0	0.041	0.014	26.860	-0.011	-0.011	0.000	0.000	0.000	0.000
51	D	60	ASN	0	-0.017	-0.011	28.725	-0.007	-0.007	0.000	0.000	0.000	0.000
52	D	61	ASN	0	-0.023	0.001	31.765	0.010	0.010	0.000	0.000	0.000	0.000
53	D	62	LYS	1	0.927	0.959	33.725	0.069	0.069	0.000	0.000	0.000	0.000
54	D	63	LEU	0	0.001	0.014	32.178	-0.002	-0.002	0.000	0.000	0.000	0.000
55	D	64	LEU	0	-0.057	-0.032	31.819	0.007	0.007	0.000	0.000	0.000	0.000
56	D	65	ASN	0	-0.025	-0.023	32.085	0.000	0.000	0.000	0.000	0.000	0.000
57	D	66	LYS	1	0.980	0.991	31.435	0.142	0.142	0.000	0.000	0.000	0.000
58	D	67	PHE	0	0.016	0.022	28.718	0.005	0.005	0.000	0.000	0.000	0.000
59	D	68	ASN	0	-0.064	-0.045	30.530	-0.009	-0.009	0.000	0.000	0.000	0.000
60	D	69	SER	0	-0.028	-0.012	29.910	0.003	0.003	0.000	0.000	0.000	0.000
61	D	70	ASP	-1	-0.862	-0.948	24.373	-0.240	-0.240	0.000	0.000	0.000	0.000
62	D	71	VAL	0	-0.065	-0.027	24.579	0.015	0.015	0.000	0.000	0.000	0.000
63	D	72	PHE	0	-0.005	-0.001	19.550	-0.023	-0.023	0.000	0.000	0.000	0.000
64	D	73	LEU	0	0.002	-0.017	19.753	0.026	0.026	0.000	0.000	0.000	0.000
65	D	74	ARG	1	0.895	0.948	19.123	0.163	0.163	0.000	0.000	0.000	0.000
66	D	75	GLY	0	0.119	0.053	16.064	0.011	0.011	0.000	0.000	0.000	0.000
67	D	76	THR	0	-0.037	-0.029	16.698	0.009	0.009	0.000	0.000	0.000	0.000
68	D	77	GLN	0	-0.056	-0.022	18.201	0.028	0.028	0.000	0.000	0.000	0.000
69	D	78	VAL	0	-0.015	-0.005	15.145	0.026	0.026	0.000	0.000	0.000	0.000
70	D	79	MET	0	-0.023	0.003	16.548	-0.006	-0.006	0.000	0.000	0.000	0.000
71	D	80	TYR	0	-0.021	-0.021	15.093	0.025	0.025	0.000	0.000	0.000	0.000
72	D	81	ILE	0	0.013	0.001	12.942	0.001	0.001	0.000	0.000	0.000	0.000
73	D	82	SER	0	0.008	0.014	14.702	-0.003	-0.003	0.000	0.000	0.000	0.000
74	D	83	GLU	-1	-0.814	-0.884	16.212	-0.393	-0.393	0.000	0.000	0.000	0.000
75	D	84	GLN	0	-0.023	-0.001	18.459	0.032	0.032	0.000	0.000	0.000	0.000

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