FMO DATABASE

FMODB ID: LJ2M9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-346744.686166
FMO2-HF: Nuclear repulsion	321264.662566
FMO2-HF: Total energy	-25480.0236
FMO2-MP2: Total energy	-25554.242866

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.
-32.547	-32.505	14.2	-6.868	-7.374	-0.077

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 : -0.085 / q_NPA : -0.063

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	-0.025	0.000	3.616	0.935	2.338	0.010	-0.508	-0.904	0.002
4	A	9	ILE	0	-0.006	0.006	6.317	-0.213	-0.213	0.000	0.000	0.000	0.000
5	A	10	PHE	0	0.009	-0.005	6.269	0.104	0.104	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.899	0.961	11.533	0.490	0.490	0.000	0.000	0.000	0.000
7	A	12	VAL	0	-0.011	-0.011	14.206	-0.080	-0.080	0.000	0.000	0.000	0.000
8	A	13	PHE	0	0.006	-0.009	16.655	0.098	0.098	0.000	0.000	0.000	0.000
9	A	14	TYR	0	-0.073	-0.049	19.998	-0.065	-0.065	0.000	0.000	0.000	0.000
10	A	15	GLN	0	0.035	0.024	22.043	0.056	0.056	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.804	-0.906	24.866	-0.460	-0.460	0.000	0.000	0.000	0.000
12	A	17	ASP	-1	-0.909	-0.934	26.232	-0.435	-0.435	0.000	0.000	0.000	0.000
13	A	18	ALA	0	-0.075	-0.047	28.017	0.026	0.026	0.000	0.000	0.000	0.000
14	A	19	ASP	-1	-0.885	-0.928	29.905	-0.298	-0.298	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.969	-0.981	31.587	-0.314	-0.314	0.000	0.000	0.000	0.000
16	A	21	ALA	0	-0.014	-0.013	34.581	0.022	0.022	0.000	0.000	0.000	0.000
17	A	22	PRO	0	-0.027	-0.018	35.390	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	23	VAL	0	0.007	0.013	34.042	0.021	0.021	0.000	0.000	0.000	0.000
19	A	24	ARG	1	0.895	0.945	34.155	0.167	0.167	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.787	-0.870	28.890	-0.289	-0.289	0.000	0.000	0.000	0.000
21	A	26	LYS	1	0.876	0.930	29.480	0.245	0.245	0.000	0.000	0.000	0.000
22	A	27	THR	0	-0.007	-0.008	24.360	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	28	LYS	1	0.702	0.841	24.305	0.379	0.379	0.000	0.000	0.000	0.000
24	A	29	THR	0	-0.049	-0.038	20.315	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	30	MET	0	-0.005	0.023	17.450	0.021	0.021	0.000	0.000	0.000	0.000
26	A	31	TYR	0	0.019	-0.006	15.493	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	32	ILE	0	-0.011	0.000	11.561	0.078	0.078	0.000	0.000	0.000	0.000
28	A	33	GLU	-1	-0.784	-0.890	7.632	-2.305	-2.305	0.000	0.000	0.000	0.000
29	A	34	ALA	0	-0.019	-0.009	6.984	0.053	0.053	0.000	0.000	0.000	0.000
30	A	35	GLU	-1	-0.830	-0.898	1.763	-34.294	-36.997	13.962	-5.742	-5.518	-0.070
31	A	36	SER	0	-0.009	-0.017	2.895	-1.249	0.093	0.228	-0.618	-0.952	-0.009
32	A	37	GLU	-1	-0.747	-0.863	5.610	-0.862	-0.862	0.000	0.000	0.000	0.000
33	A	38	ARG	1	0.965	0.980	8.454	2.570	2.570	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.749	-0.866	6.612	-3.695	-3.695	0.000	0.000	0.000	0.000
35	A	40	VAL	0	0.024	0.015	8.637	0.492	0.492	0.000	0.000	0.000	0.000
36	A	41	ARG	1	0.839	0.893	10.859	1.438	1.438	0.000	0.000	0.000	0.000
37	A	42	ARG	1	0.873	0.939	9.469	2.731	2.731	0.000	0.000	0.000	0.000
38	A	43	LYS	1	0.700	0.841	8.235	2.866	2.866	0.000	0.000	0.000	0.000
39	A	44	LEU	0	-0.071	-0.045	13.814	0.228	0.228	0.000	0.000	0.000	0.000
40	A	45	GLU	-1	-0.893	-0.937	15.425	-1.251	-1.251	0.000	0.000	0.000	0.000
41	A	46	GLY	0	-0.027	-0.011	18.414	0.012	0.012	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.895	0.945	18.541	0.778	0.778	0.000	0.000	0.000	0.000
43	A	48	PRO	0	0.038	0.030	22.513	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	49	ILE	0	-0.034	-0.032	19.299	0.037	0.037	0.000	0.000	0.000	0.000
45	A	50	ASN	0	0.002	-0.004	22.481	-0.075	-0.075	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.032	-0.030	16.076	0.017	0.017	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.809	-0.888	19.984	-0.422	-0.422	0.000	0.000	0.000	0.000
48	A	53	TYR	0	-0.044	-0.033	16.133	0.018	0.018	0.000	0.000	0.000	0.000
49	A	54	ILE	0	-0.024	-0.011	11.810	-0.032	-0.032	0.000	0.000	0.000	0.000
50	A	55	GLN	0	-0.006	0.005	14.240	0.032	0.032	0.000	0.000	0.000	0.000
51	A	56	PRO	0	0.040	0.016	9.135	-0.081	-0.081	0.000	0.000	0.000	0.000
52	A	57	LEU	0	-0.038	-0.018	10.573	0.212	0.212	0.000	0.000	0.000	0.000
53	A	58	GLU	-1	-0.862	-0.936	9.469	-0.267	-0.267	0.000	0.000	0.000	0.000
54	A	59	GLY	0	-0.039	-0.013	9.581	0.060	0.060	0.000	0.000	0.000	0.000
55	A	60	ALA	0	-0.051	-0.020	11.268	0.067	0.067	0.000	0.000	0.000	0.000
56	A	61	HIS	1	0.830	0.873	8.969	-0.706	-0.706	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.032	-0.014	12.658	-0.121	-0.121	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.908	-0.929	14.995	0.110	0.110	0.000	0.000	0.000	0.000
59	A	64	TYR	0	-0.069	-0.058	16.480	0.070	0.070	0.000	0.000	0.000	0.000
60	A	65	GLU	-1	-0.803	-0.871	10.001	0.601	0.601	0.000	0.000	0.000	0.000

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