FMO DATABASE

FMODB ID: YV4Q2

Calculation Name: 4M78-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M78

Chain ID: G

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-445388.21386
FMO2-HF: Nuclear repulsion	416852.001274
FMO2-HF: Total energy	-28536.212586
FMO2-MP2: Total energy	-28618.967468

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(G:1:MET)

Summations of interaction energy for fragment #1(G:1:MET)

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.
-6.489	-2.08	1.489	-1.498	-4.399	0.003

Interaction energy analysis for fragmet #1(G:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.046

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	G	3	PRO	0	0.040	0.018	3.740	-3.064	-1.358	-0.013	-0.352	-1.341	0.010
4	G	4	LEU	0	0.023	0.022	6.030	0.099	0.099	0.000	0.000	0.000	0.000
5	G	5	TYR	0	-0.022	-0.017	2.271	-1.591	0.015	1.099	-0.726	-1.979	-0.004
6	G	6	LEU	0	0.005	-0.008	2.413	-1.654	-0.641	0.404	-0.413	-1.004	-0.003
7	G	7	LEU	0	0.031	0.021	4.768	-0.002	0.082	-0.001	-0.007	-0.075	0.000
8	G	8	THR	0	-0.025	-0.018	7.891	-0.007	-0.007	0.000	0.000	0.000	0.000
9	G	9	ASN	0	-0.062	-0.026	6.482	-0.162	-0.162	0.000	0.000	0.000	0.000
10	G	10	ALA	0	0.051	0.023	8.622	-0.069	-0.069	0.000	0.000	0.000	0.000
11	G	11	LYS	1	0.855	0.931	10.802	-0.161	-0.161	0.000	0.000	0.000	0.000
12	G	12	GLY	0	-0.023	-0.007	13.975	-0.003	-0.003	0.000	0.000	0.000	0.000
13	G	13	GLN	0	-0.009	0.009	10.347	-0.015	-0.015	0.000	0.000	0.000	0.000
14	G	14	GLN	0	0.010	0.005	15.434	0.004	0.004	0.000	0.000	0.000	0.000
15	G	15	MET	0	-0.025	-0.007	12.016	-0.019	-0.019	0.000	0.000	0.000	0.000
16	G	16	GLN	0	0.003	-0.008	15.961	0.017	0.017	0.000	0.000	0.000	0.000
17	G	17	ILE	0	0.009	0.014	15.853	-0.028	-0.028	0.000	0.000	0.000	0.000
18	G	18	GLU	-1	-0.807	-0.877	18.011	-0.043	-0.043	0.000	0.000	0.000	0.000
19	G	19	LEU	0	0.036	0.018	19.503	-0.004	-0.004	0.000	0.000	0.000	0.000
20	G	20	LYS	1	0.872	0.931	19.210	0.016	0.016	0.000	0.000	0.000	0.000
21	G	21	ASN	0	-0.038	-0.029	23.773	-0.003	-0.003	0.000	0.000	0.000	0.000
22	G	22	GLY	0	-0.036	-0.019	24.746	0.001	0.001	0.000	0.000	0.000	0.000
23	G	23	GLU	-1	-0.887	-0.917	25.465	-0.011	-0.011	0.000	0.000	0.000	0.000
24	G	24	ILE	0	-0.038	-0.017	21.653	-0.007	-0.007	0.000	0.000	0.000	0.000
25	G	25	ILE	0	0.017	0.016	20.631	0.006	0.006	0.000	0.000	0.000	0.000
26	G	26	GLN	0	-0.016	-0.017	20.391	-0.011	-0.011	0.000	0.000	0.000	0.000
27	G	27	GLY	0	0.055	0.029	19.889	0.009	0.009	0.000	0.000	0.000	0.000
28	G	28	ILE	0	-0.031	-0.011	18.328	-0.012	-0.012	0.000	0.000	0.000	0.000
29	G	29	LEU	0	0.008	0.011	12.714	0.011	0.011	0.000	0.000	0.000	0.000
30	G	30	THR	0	0.000	-0.006	16.945	0.008	0.008	0.000	0.000	0.000	0.000
31	G	31	ASN	0	0.015	-0.005	16.058	0.034	0.034	0.000	0.000	0.000	0.000
32	G	32	VAL	0	0.001	0.003	11.642	-0.017	-0.017	0.000	0.000	0.000	0.000
33	G	33	ASP	-1	-0.761	-0.854	14.633	0.173	0.173	0.000	0.000	0.000	0.000
34	G	34	ASN	0	0.021	-0.021	13.180	0.074	0.074	0.000	0.000	0.000	0.000
35	G	35	TRP	0	-0.090	-0.035	14.268	0.025	0.025	0.000	0.000	0.000	0.000
36	G	36	MET	0	-0.024	-0.018	9.906	-0.061	-0.061	0.000	0.000	0.000	0.000
37	G	37	ASN	0	-0.054	-0.032	14.683	-0.054	-0.054	0.000	0.000	0.000	0.000
38	G	38	LEU	0	-0.013	-0.002	14.461	0.017	0.017	0.000	0.000	0.000	0.000
39	G	39	THR	0	-0.023	-0.014	17.925	0.000	0.000	0.000	0.000	0.000	0.000
40	G	40	LEU	0	-0.005	0.013	17.410	-0.003	-0.003	0.000	0.000	0.000	0.000
41	G	41	SER	0	0.091	0.037	20.851	0.003	0.003	0.000	0.000	0.000	0.000
42	G	42	ASN	0	-0.074	-0.047	22.671	-0.006	-0.006	0.000	0.000	0.000	0.000
43	G	43	VAL	0	0.006	0.019	23.420	-0.004	-0.004	0.000	0.000	0.000	0.000
44	G	44	THR	0	-0.003	0.001	24.718	0.004	0.004	0.000	0.000	0.000	0.000
45	G	45	GLU	-1	-0.933	-0.968	25.094	-0.009	-0.009	0.000	0.000	0.000	0.000
46	G	46	TYR	0	-0.032	-0.017	25.138	0.004	0.004	0.000	0.000	0.000	0.000
47	G	47	SER	0	0.042	0.020	27.796	0.000	0.000	0.000	0.000	0.000	0.000
48	G	64	VAL	0	0.003	-0.001	30.761	0.000	0.000	0.000	0.000	0.000	0.000
49	G	65	LYS	1	0.890	0.946	28.867	0.010	0.010	0.000	0.000	0.000	0.000
50	G	66	LEU	0	0.032	0.004	28.010	0.002	0.002	0.000	0.000	0.000	0.000
51	G	67	ASN	0	-0.007	-0.005	27.939	-0.003	-0.003	0.000	0.000	0.000	0.000
52	G	68	GLU	-1	-0.857	-0.946	23.102	0.023	0.023	0.000	0.000	0.000	0.000
53	G	69	ILE	0	-0.029	0.012	23.006	0.001	0.001	0.000	0.000	0.000	0.000
54	G	70	TYR	0	0.036	0.012	21.280	0.001	0.001	0.000	0.000	0.000	0.000
55	G	71	ILE	0	0.014	0.007	19.434	-0.003	-0.003	0.000	0.000	0.000	0.000
56	G	72	ARG	1	0.925	0.963	20.292	-0.043	-0.043	0.000	0.000	0.000	0.000
57	G	73	GLY	0	0.127	0.052	17.725	-0.013	-0.013	0.000	0.000	0.000	0.000
58	G	74	THR	0	-0.045	-0.031	18.261	-0.014	-0.014	0.000	0.000	0.000	0.000
59	G	75	PHE	0	-0.003	-0.013	20.574	-0.008	-0.008	0.000	0.000	0.000	0.000
60	G	76	ILE	0	0.030	0.021	15.754	-0.010	-0.010	0.000	0.000	0.000	0.000
61	G	77	LYS	1	0.697	0.842	18.367	0.049	0.049	0.000	0.000	0.000	0.000
62	G	78	PHE	0	-0.015	-0.013	14.412	-0.019	-0.019	0.000	0.000	0.000	0.000
63	G	79	ILE	0	0.038	0.018	12.115	0.033	0.033	0.000	0.000	0.000	0.000
64	G	80	LYS	1	0.877	0.935	12.405	0.017	0.017	0.000	0.000	0.000	0.000
65	G	81	LEU	0	0.022	0.003	7.821	0.016	0.016	0.000	0.000	0.000	0.000
66	G	82	GLN	0	0.042	0.020	11.972	0.039	0.039	0.000	0.000	0.000	0.000
67	G	83	ASP	-1	-0.871	-0.933	11.512	-0.076	-0.076	0.000	0.000	0.000	0.000
68	G	84	ASN	0	-0.089	-0.041	12.201	0.032	0.032	0.000	0.000	0.000	0.000
69	G	85	ILE	0	-0.017	0.000	7.494	-0.007	-0.007	0.000	0.000	0.000	0.000
70	G	86	ILE	0	-0.020	-0.002	6.345	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:1:MET)