FMO DATABASE

FMODB ID: LNYL9

Calculation Name: 4M78-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M78

Chain ID: A

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-381803.757042
FMO2-HF: Nuclear repulsion	356265.358645
FMO2-HF: Total energy	-25538.398397
FMO2-MP2: Total energy	-25614.307872

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:MET)

Summations of interaction energy for fragment #1(A: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.
-0.468	1.854	0.07	-0.929	-1.463	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / 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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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	A	3	ALA	0	0.063	0.036	3.321	-1.463	0.788	0.071	-0.923	-1.399	-0.001
4	A	4	THR	0	-0.010	-0.005	4.961	0.507	0.578	-0.001	-0.006	-0.064	0.000
5	A	5	LEU	0	0.062	0.033	8.245	0.060	0.060	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.985	0.976	10.700	0.259	0.259	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.885	-0.937	10.009	-0.340	-0.340	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.002	-0.014	11.245	0.042	0.042	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.058	-0.028	15.436	0.032	0.032	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.057	-0.045	17.434	0.022	0.022	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.908	0.977	16.823	0.163	0.163	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.859	0.952	21.095	0.088	0.088	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.005	-0.014	17.826	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.029	-0.020	19.657	0.019	0.019	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.002	0.004	19.124	-0.028	-0.028	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.035	-0.017	19.578	0.023	0.023	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.034	0.010	20.194	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.001	-0.010	20.665	0.003	0.003	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.854	-0.922	22.964	-0.121	-0.121	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.033	-0.017	24.596	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.905	-0.939	25.582	-0.094	-0.094	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.107	-0.069	24.686	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.010	0.008	24.140	0.010	0.010	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.046	-0.029	24.010	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.014	0.015	23.613	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.045	-0.020	22.889	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.058	0.052	16.025	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.018	-0.002	20.337	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.041	0.018	19.265	0.016	0.016	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.022	-0.003	12.332	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.771	-0.857	16.405	-0.255	-0.255	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.963	0.965	10.822	0.518	0.518	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.065	-0.034	13.270	-0.095	-0.095	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.025	-0.004	12.741	0.008	0.008	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.024	0.003	15.827	0.032	0.032	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.020	-0.019	16.435	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.019	-0.007	20.208	0.023	0.023	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.007	0.001	20.944	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.020	-0.018	24.214	0.014	0.014	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.080	-0.047	26.858	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.031	0.008	26.494	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.009	0.004	28.154	0.009	0.009	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.138	0.072	28.466	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.915	0.957	24.447	0.116	0.116	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.016	0.007	30.090	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.060	0.022	32.467	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.839	0.919	31.870	0.071	0.071	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.861	-0.911	33.898	-0.060	-0.060	0.000	0.000	0.000	0.000
49	A	49	PHE	0	-0.081	-0.066	32.560	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.022	0.022	29.733	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.008	-0.015	30.760	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.929	0.988	30.972	0.055	0.055	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.025	-0.002	29.032	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.024	0.023	26.649	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.003	0.003	23.913	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.019	0.018	22.081	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.986	0.976	21.910	0.155	0.155	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.098	0.039	18.669	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.060	-0.025	18.961	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.933	-0.955	21.003	-0.148	-0.148	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.069	-0.031	16.798	0.012	0.012	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.002	0.021	17.602	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.041	-0.031	15.262	-0.047	-0.047	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.031	0.014	14.462	0.030	0.030	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.014	0.003	14.535	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.003	-0.005	14.999	0.013	0.013	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.016	-0.004	17.554	0.018	0.018	0.000	0.000	0.000	0.000

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