FMO DATABASE

FMODB ID: MM71Z

Calculation Name: 2DGC-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DGC

Chain ID: A

ChEMBL ID:

UniProt ID: P03069

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	51
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-208237.303642
FMO2-HF: Nuclear repulsion	187664.943267
FMO2-HF: Total energy	-20572.360375
FMO2-MP2: Total energy	-20633.095017

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:228:ACE )

Summations of interaction energy for fragment #1(A:228:ACE )

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.
2.339	-1.421	7.887	-2.592	-1.533	0.01

Interaction energy analysis for fragmet #1(A:228:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.007

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	230	LEU	0	0.129	0.055	3.834	1.084	1.797	-0.005	-0.340	-0.367	0.001
4	A	231	LYS	1	1.012	1.007	7.061	1.089	1.089	0.000	0.000	0.000	0.000
5	A	232	ARG	1	0.933	0.987	1.978	-0.067	-4.540	7.892	-2.252	-1.166	0.009
6	A	233	ALA	0	0.061	0.047	5.952	0.236	0.236	0.000	0.000	0.000	0.000
7	A	234	ARG	1	1.004	0.995	7.261	0.217	0.217	0.000	0.000	0.000	0.000
8	A	235	ASN	0	0.015	0.008	10.196	0.035	0.035	0.000	0.000	0.000	0.000
9	A	236	THR	0	-0.018	-0.016	8.370	0.065	0.065	0.000	0.000	0.000	0.000
10	A	237	GLU	-1	-0.795	-0.877	10.867	0.203	0.203	0.000	0.000	0.000	0.000
11	A	238	ALA	0	-0.050	-0.021	13.454	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	239	ALA	0	0.009	0.003	14.244	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	240	ARG	1	0.863	0.907	12.380	-0.236	-0.236	0.000	0.000	0.000	0.000
14	A	241	ARG	1	0.999	0.991	15.888	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	242	SER	0	-0.007	-0.002	18.974	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	243	ARG	1	0.932	0.954	14.399	-0.161	-0.161	0.000	0.000	0.000	0.000
17	A	244	ALA	0	0.062	0.041	21.262	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	245	ARG	1	0.963	0.975	21.061	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	246	LYS	1	0.907	0.947	21.080	-0.043	-0.043	0.000	0.000	0.000	0.000
20	A	247	LEU	0	0.052	0.036	25.134	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	248	GLN	0	-0.019	-0.011	27.386	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	249	ARG	1	0.934	0.968	25.365	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	250	MET	0	0.000	0.022	30.367	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	251	LYS	1	1.015	1.007	29.766	-0.050	-0.050	0.000	0.000	0.000	0.000
25	A	252	GLN	0	0.003	0.015	33.561	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	253	LEU	0	-0.042	-0.029	34.989	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	254	GLU	-1	-0.908	-0.977	34.507	0.035	0.035	0.000	0.000	0.000	0.000
28	A	255	ASP	-1	-0.839	-0.908	37.945	0.027	0.027	0.000	0.000	0.000	0.000
29	A	256	LYS	1	0.879	0.942	39.633	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	257	VAL	0	-0.016	-0.005	40.714	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	258	GLU	-1	-0.913	-0.949	42.566	0.024	0.024	0.000	0.000	0.000	0.000
32	A	259	GLU	-1	-0.911	-0.966	44.019	0.011	0.011	0.000	0.000	0.000	0.000
33	A	260	LEU	0	-0.007	-0.018	44.516	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	261	LEU	0	0.011	0.012	45.964	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	262	SER	0	-0.048	-0.019	48.756	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	263	LYS	1	0.908	0.954	48.626	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	264	ASN	0	-0.015	-0.011	51.318	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	265	TYR	0	0.012	0.013	53.100	0.000	0.000	0.000	0.000	0.000	0.000
39	A	266	HIS	0	0.025	0.002	53.972	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	267	LEU	0	-0.002	0.001	54.733	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	268	GLU	-1	-0.917	-0.947	57.206	0.008	0.008	0.000	0.000	0.000	0.000
42	A	269	ASN	0	-0.041	-0.026	59.036	0.000	0.000	0.000	0.000	0.000	0.000
43	A	270	GLU	-1	-0.980	-0.992	60.522	0.007	0.007	0.000	0.000	0.000	0.000
44	A	271	VAL	0	0.008	0.002	61.305	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	272	ALA	0	0.009	0.010	63.464	0.000	0.000	0.000	0.000	0.000	0.000
46	A	273	ARG	1	0.912	0.958	65.246	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	274	LEU	0	-0.015	-0.028	64.670	0.000	0.000	0.000	0.000	0.000	0.000
48	A	275	LYS	1	0.913	0.965	65.947	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	276	LYS	1	0.920	0.975	69.217	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	277	LEU	0	-0.071	-0.035	70.978	0.000	0.000	0.000	0.000	0.000	0.000
51	A	278	NME	0	0.055	0.042	71.776	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:228:ACE )