FMO DATABASE

FMODB ID: 3Q53L

Calculation Name: 4NJC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NJC

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-346415.750334
FMO2-HF: Nuclear repulsion	320935.917431
FMO2-HF: Total energy	-25479.832903
FMO2-MP2: Total energy	-25554.030145

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:6:HIS)

Summations of interaction energy for fragment #1(A:6:HIS)

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.
-32.15	-28.103	8.693	-5.704	-7.036	-0.072

Interaction energy analysis for fragmet #1(A:6:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.097 / q_NPA : -0.057

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	8	MET	0	-0.021	0.000	3.580	0.941	2.563	-0.005	-0.585	-1.033	0.002
4	A	9	ILE	0	-0.014	-0.002	6.519	-0.225	-0.225	0.000	0.000	0.000	0.000
5	A	10	PHE	0	0.018	0.003	6.058	0.105	0.105	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.909	0.963	11.523	0.499	0.499	0.000	0.000	0.000	0.000
7	A	12	VAL	0	-0.015	-0.015	14.123	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	13	PHE	0	0.000	-0.014	16.502	0.107	0.107	0.000	0.000	0.000	0.000
9	A	14	TYR	0	-0.015	-0.008	19.891	-0.060	-0.060	0.000	0.000	0.000	0.000
10	A	15	GLN	0	0.021	0.004	21.677	0.060	0.060	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.857	-0.928	24.930	-0.462	-0.462	0.000	0.000	0.000	0.000
12	A	17	ASP	-1	-0.880	-0.924	26.327	-0.429	-0.429	0.000	0.000	0.000	0.000
13	A	18	ALA	0	-0.103	-0.039	27.717	0.026	0.026	0.000	0.000	0.000	0.000
14	A	19	ASP	-1	-0.886	-0.952	29.597	-0.308	-0.308	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.958	-0.978	31.206	-0.325	-0.325	0.000	0.000	0.000	0.000
16	A	21	ALA	0	-0.011	-0.019	34.160	0.017	0.017	0.000	0.000	0.000	0.000
17	A	22	PRO	0	-0.053	-0.022	35.418	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	23	VAL	0	0.012	0.019	34.254	0.021	0.021	0.000	0.000	0.000	0.000
19	A	24	ARG	1	0.891	0.945	34.009	0.172	0.172	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.774	-0.871	28.866	-0.298	-0.298	0.000	0.000	0.000	0.000
21	A	26	LYS	1	0.874	0.929	29.637	0.242	0.242	0.000	0.000	0.000	0.000
22	A	27	THR	0	0.000	-0.025	23.991	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	28	LYS	1	0.703	0.839	24.304	0.380	0.380	0.000	0.000	0.000	0.000
24	A	29	THR	0	-0.027	-0.018	20.279	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	30	MET	0	-0.025	-0.006	17.604	0.011	0.011	0.000	0.000	0.000	0.000
26	A	31	TYR	0	0.009	0.005	15.400	-0.055	-0.055	0.000	0.000	0.000	0.000
27	A	32	ILE	0	-0.003	0.004	11.918	0.087	0.087	0.000	0.000	0.000	0.000
28	A	33	GLU	-1	-0.798	-0.908	7.921	-2.109	-2.109	0.000	0.000	0.000	0.000
29	A	34	ALA	0	-0.023	-0.012	7.373	0.097	0.097	0.000	0.000	0.000	0.000
30	A	35	GLU	-1	-0.830	-0.917	1.915	-31.466	-30.574	7.920	-4.226	-4.587	-0.060
31	A	36	SER	0	-0.030	-0.023	2.580	-4.233	-2.744	0.779	-0.891	-1.376	-0.014
32	A	37	GLU	-1	-0.738	-0.867	5.292	-0.783	-0.739	-0.001	-0.002	-0.040	0.000
33	A	38	ARG	1	0.965	0.974	8.460	2.645	2.645	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.768	-0.875	6.740	-3.521	-3.521	0.000	0.000	0.000	0.000
35	A	40	VAL	0	0.030	0.021	8.814	0.499	0.499	0.000	0.000	0.000	0.000
36	A	41	ARG	1	0.840	0.897	11.063	1.517	1.517	0.000	0.000	0.000	0.000
37	A	42	ARG	1	0.869	0.933	9.703	2.727	2.727	0.000	0.000	0.000	0.000
38	A	43	LYS	1	0.750	0.876	8.793	2.757	2.757	0.000	0.000	0.000	0.000
39	A	44	LEU	0	-0.056	-0.032	14.198	0.214	0.214	0.000	0.000	0.000	0.000
40	A	45	GLU	-1	-0.913	-0.937	16.087	-1.213	-1.213	0.000	0.000	0.000	0.000
41	A	46	GLY	0	-0.011	-0.010	18.621	0.007	0.007	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.892	0.948	18.461	0.800	0.800	0.000	0.000	0.000	0.000
43	A	48	PRO	0	0.040	0.037	22.582	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	49	ILE	0	-0.024	-0.020	19.311	0.035	0.035	0.000	0.000	0.000	0.000
45	A	50	ASN	0	0.009	0.001	22.483	-0.072	-0.072	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.043	-0.032	15.875	0.016	0.016	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.833	-0.891	19.861	-0.412	-0.412	0.000	0.000	0.000	0.000
48	A	53	TYR	0	-0.035	-0.031	16.096	0.014	0.014	0.000	0.000	0.000	0.000
49	A	54	ILE	0	-0.025	-0.001	11.625	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	55	GLN	0	0.002	0.004	13.968	0.024	0.024	0.000	0.000	0.000	0.000
51	A	56	PRO	0	0.022	0.009	8.718	-0.085	-0.085	0.000	0.000	0.000	0.000
52	A	57	LEU	0	-0.040	-0.015	10.516	0.239	0.239	0.000	0.000	0.000	0.000
53	A	58	GLU	-1	-0.859	-0.938	9.099	-0.244	-0.244	0.000	0.000	0.000	0.000
54	A	59	GLY	0	-0.056	-0.026	9.767	0.034	0.034	0.000	0.000	0.000	0.000
55	A	60	ALA	0	-0.035	-0.003	10.919	0.021	0.021	0.000	0.000	0.000	0.000
56	A	61	HIS	1	0.830	0.868	9.358	-0.593	-0.593	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.043	-0.019	12.659	-0.107	-0.107	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.909	-0.941	14.870	0.094	0.094	0.000	0.000	0.000	0.000
59	A	64	TYR	0	-0.072	-0.049	16.722	0.081	0.081	0.000	0.000	0.000	0.000
60	A	65	GLU	-1	-0.808	-0.865	10.495	0.472	0.472	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:HIS)