FMO DATABASE

FMODB ID: R9YZ8

Calculation Name: 4N9G-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N9G

Chain ID: C

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptAll
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	35
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-137192.549487
FMO2-HF: Nuclear repulsion	122923.544407
FMO2-HF: Total energy	-14269.005079
FMO2-MP2: Total energy	-14309.550909

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(C:63:ARG)

Summations of interaction energy for fragment #1(C:63:ARG)

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.
-139.844	-142.054	30.895	-15.284	-13.4	-0.169

Interaction energy analysis for fragmet #1(C:63:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.890

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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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	C	65	SER	0	0.058	0.017	3.422	2.821	4.304	0.027	-0.477	-1.032	0.002
4	C	66	GLU	-1	-0.839	-0.895	1.884	-25.906	-25.677	2.874	-1.292	-1.811	-0.007
5	C	67	LEU	0	0.051	0.031	3.870	3.312	3.838	0.002	-0.172	-0.356	0.000
6	C	68	LEU	0	-0.004	-0.006	5.967	3.354	3.354	0.000	0.000	0.000	0.000
7	C	69	SER	0	-0.048	-0.032	6.841	2.943	2.943	0.000	0.000	0.000	0.000
8	C	70	LYS	1	0.896	0.934	7.153	26.027	26.027	0.000	0.000	0.000	0.000
9	C	71	ILE	0	-0.027	-0.005	9.224	1.573	1.573	0.000	0.000	0.000	0.000
10	C	72	ASN	0	-0.018	-0.020	11.960	1.755	1.755	0.000	0.000	0.000	0.000
11	C	73	ASP	-1	-0.898	-0.942	12.589	-16.990	-16.990	0.000	0.000	0.000	0.000
12	C	74	MET	0	0.013	0.016	13.513	1.244	1.244	0.000	0.000	0.000	0.000
13	C	75	PRO	0	-0.014	0.010	16.406	0.302	0.302	0.000	0.000	0.000	0.000
14	C	76	ILE	0	-0.023	-0.014	16.169	0.455	0.455	0.000	0.000	0.000	0.000
15	C	77	THR	0	0.054	0.012	20.421	-0.237	-0.237	0.000	0.000	0.000	0.000
16	C	78	ASN	0	0.053	0.008	20.122	-0.628	-0.628	0.000	0.000	0.000	0.000
17	C	79	ASP	-1	-0.843	-0.901	19.722	-14.284	-14.284	0.000	0.000	0.000	0.000
18	C	80	GLN	0	0.046	0.012	18.702	-0.929	-0.929	0.000	0.000	0.000	0.000
19	C	81	LYS	1	0.809	0.920	15.758	14.776	14.776	0.000	0.000	0.000	0.000
20	C	82	LYS	1	0.857	0.917	14.795	13.511	13.511	0.000	0.000	0.000	0.000
21	C	83	LEU	0	-0.027	0.006	15.139	-1.066	-1.066	0.000	0.000	0.000	0.000
22	C	84	MET	0	0.044	0.004	12.485	-0.807	-0.807	0.000	0.000	0.000	0.000
23	C	85	SER	0	-0.010	-0.019	10.611	-2.381	-2.381	0.000	0.000	0.000	0.000
24	C	86	ASN	0	0.003	-0.013	10.323	-3.099	-3.099	0.000	0.000	0.000	0.000
25	C	87	ASP	-1	-0.812	-0.895	11.056	-23.545	-23.545	0.000	0.000	0.000	0.000
26	C	88	VAL	0	-0.005	0.001	5.372	-2.532	-2.532	0.000	0.000	0.000	0.000
27	C	89	LEU	0	-0.022	-0.013	6.292	-5.950	-5.950	0.000	0.000	0.000	0.000
28	C	90	LYS	1	0.823	0.912	6.777	20.224	20.224	0.000	0.000	0.000	0.000
29	C	91	PHE	0	0.009	0.000	5.662	-0.080	-0.080	0.000	0.000	0.000	0.000
30	C	92	ALA	0	-0.040	-0.009	2.456	-4.953	-3.993	0.687	-0.537	-1.110	0.000
31	C	93	ALA	0	0.030	0.010	3.278	-0.583	-0.490	0.007	0.159	-0.259	-0.001
32	C	94	GLU	-1	-0.863	-0.921	6.319	-23.734	-23.734	0.000	0.000	0.000	0.000
33	C	95	ALA	0	-0.033	-0.009	3.515	3.718	3.886	0.002	-0.034	-0.136	0.000
34	C	96	GLU	-1	-0.842	-0.897	1.734	-140.778	-146.447	27.296	-12.931	-8.696	-0.163
35	C	97	LYS	1	0.745	0.869	5.872	32.623	32.623	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:63:ARG)