FMO DATABASE

FMODB ID: 6NGMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-137218.582298
FMO2-HF: Nuclear repulsion	122949.982451
FMO2-HF: Total energy	-14268.599848
FMO2-MP2: Total energy	-14309.152597

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.
-67.773	-60.753	1.298	-3.144	-5.17	-0.019

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 : 1.010 / q_NPA : 0.989

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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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	C	65	SER	0	0.019	0.002	3.340	1.525	3.532	0.037	-0.703	-1.340	0.002
4	C	66	GLU	-1	-0.937	-0.956	2.687	-30.484	-29.235	0.211	-0.441	-1.020	-0.003
5	C	67	LEU	0	0.081	0.039	4.166	3.422	3.821	0.000	-0.087	-0.311	0.000
6	C	68	LEU	0	-0.027	-0.024	5.897	3.684	3.684	0.000	0.000	0.000	0.000
7	C	69	SER	0	-0.056	-0.048	6.809	3.164	3.164	0.000	0.000	0.000	0.000
8	C	70	LYS	1	1.006	1.007	7.905	24.538	24.538	0.000	0.000	0.000	0.000
9	C	71	ILE	0	0.011	0.008	9.431	1.741	1.741	0.000	0.000	0.000	0.000
10	C	72	ASN	0	-0.043	-0.034	11.957	2.247	2.247	0.000	0.000	0.000	0.000
11	C	73	ASP	-1	-0.914	-0.954	13.030	-17.830	-17.830	0.000	0.000	0.000	0.000
12	C	74	MET	0	-0.039	-0.003	13.102	1.061	1.061	0.000	0.000	0.000	0.000
13	C	75	PRO	0	-0.021	-0.003	16.426	0.418	0.418	0.000	0.000	0.000	0.000
14	C	76	ILE	0	-0.015	-0.008	16.325	0.518	0.518	0.000	0.000	0.000	0.000
15	C	77	THR	0	0.032	0.005	20.593	-0.205	-0.205	0.000	0.000	0.000	0.000
16	C	78	ASN	0	0.071	0.019	19.889	-0.846	-0.846	0.000	0.000	0.000	0.000
17	C	79	ASP	-1	-0.851	-0.953	19.225	-14.753	-14.753	0.000	0.000	0.000	0.000
18	C	80	GLN	0	0.067	0.042	18.474	-1.205	-1.205	0.000	0.000	0.000	0.000
19	C	81	LYS	1	0.917	0.992	15.370	14.931	14.931	0.000	0.000	0.000	0.000
20	C	82	LYS	1	0.810	0.908	14.476	13.686	13.686	0.000	0.000	0.000	0.000
21	C	83	LEU	0	-0.029	0.011	14.572	-1.020	-1.020	0.000	0.000	0.000	0.000
22	C	84	MET	0	0.068	0.033	12.214	-0.711	-0.711	0.000	0.000	0.000	0.000
23	C	85	SER	0	-0.020	-0.025	10.571	-2.677	-2.677	0.000	0.000	0.000	0.000
24	C	86	ASN	0	-0.028	-0.034	9.806	-3.039	-3.039	0.000	0.000	0.000	0.000
25	C	87	ASP	-1	-0.918	-0.964	10.134	-23.224	-23.224	0.000	0.000	0.000	0.000
26	C	88	VAL	0	-0.034	-0.010	5.427	-2.786	-2.786	0.000	0.000	0.000	0.000
27	C	89	LEU	0	-0.023	-0.028	5.213	-6.676	-6.676	0.000	0.000	0.000	0.000
28	C	90	LYS	1	0.958	0.994	6.269	21.988	21.988	0.000	0.000	0.000	0.000
29	C	91	PHE	0	0.041	0.023	4.886	0.479	0.479	0.000	0.000	0.000	0.000
30	C	92	ALA	0	-0.079	-0.044	2.360	-7.230	-6.144	0.988	-0.746	-1.328	-0.004
31	C	93	ALA	0	0.069	0.047	3.020	2.017	2.102	0.043	0.168	-0.295	-0.002
32	C	94	GLU	-1	-0.981	-0.994	6.677	-23.988	-23.988	0.000	0.000	0.000	0.000
33	C	95	ALA	0	-0.070	-0.044	4.272	2.930	3.007	-0.001	-0.006	-0.069	0.000
34	C	96	GLU	-1	-0.964	-0.971	3.199	-59.759	-57.642	0.020	-1.329	-0.807	-0.012
35	C	97	LYS	1	0.857	0.952	6.809	30.311	30.311	0.000	0.000	0.000	0.000

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