FMO DATABASE

FMODB ID: J3Z69

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

Total energy (hartree)

FMO2-HF: Electronic energy	-345533.96376
FMO2-HF: Nuclear repulsion	320054.54023
FMO2-HF: Total energy	-25479.423529
FMO2-MP2: Total energy	-25553.568355

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.
-5.868	-1.851	0.32	-1.457	-2.883	-0.003

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 : 0.000 / q_NPA : -0.017

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	-0.018	-0.005	3.432	0.838	2.735	-0.001	-0.741	-1.156	0.002
4	A	9	ILE	0	-0.001	0.007	6.482	-0.073	-0.073	0.000	0.000	0.000	0.000
5	A	10	PHE	0	0.013	-0.001	5.802	-0.061	-0.061	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.912	0.963	11.498	0.762	0.762	0.000	0.000	0.000	0.000
7	A	12	VAL	0	-0.009	-0.012	14.195	-0.084	-0.084	0.000	0.000	0.000	0.000
8	A	13	PHE	0	0.003	-0.013	16.413	0.150	0.150	0.000	0.000	0.000	0.000
9	A	14	TYR	0	0.006	-0.004	19.690	-0.061	-0.061	0.000	0.000	0.000	0.000
10	A	15	GLN	0	0.022	0.012	21.597	0.057	0.057	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.936	-0.975	24.982	-0.466	-0.466	0.000	0.000	0.000	0.000
12	A	17	ASP	-1	-0.856	-0.932	26.706	-0.459	-0.459	0.000	0.000	0.000	0.000
13	A	18	ALA	0	-0.105	-0.039	28.003	0.028	0.028	0.000	0.000	0.000	0.000
14	A	19	ASP	-1	-0.887	-0.943	29.933	-0.315	-0.315	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.962	-0.987	31.488	-0.363	-0.363	0.000	0.000	0.000	0.000
16	A	21	ALA	0	-0.012	-0.024	34.331	0.022	0.022	0.000	0.000	0.000	0.000
17	A	22	PRO	0	-0.053	-0.010	35.377	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	23	VAL	0	-0.015	0.005	34.271	0.025	0.025	0.000	0.000	0.000	0.000
19	A	24	ARG	1	0.904	0.960	33.822	0.221	0.221	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.812	-0.916	29.291	-0.337	-0.337	0.000	0.000	0.000	0.000
21	A	26	LYS	1	0.835	0.914	29.660	0.295	0.295	0.000	0.000	0.000	0.000
22	A	27	THR	0	0.034	0.017	23.897	0.002	0.002	0.000	0.000	0.000	0.000
23	A	28	LYS	1	0.819	0.922	24.251	0.415	0.415	0.000	0.000	0.000	0.000
24	A	29	THR	0	-0.031	-0.018	20.316	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	30	MET	0	-0.010	0.001	17.790	0.037	0.037	0.000	0.000	0.000	0.000
26	A	31	TYR	0	0.009	0.008	15.647	-0.087	-0.087	0.000	0.000	0.000	0.000
27	A	32	ILE	0	-0.013	-0.002	12.366	0.124	0.124	0.000	0.000	0.000	0.000
28	A	33	GLU	-1	-0.885	-0.946	7.308	-1.477	-1.477	0.000	0.000	0.000	0.000
29	A	34	ALA	0	-0.013	-0.017	8.212	0.128	0.128	0.000	0.000	0.000	0.000
30	A	35	GLU	-1	-0.881	-0.946	3.576	-5.732	-4.777	0.007	-0.175	-0.787	0.000
31	A	36	SER	0	-0.054	-0.034	2.891	-4.332	-3.235	0.315	-0.538	-0.875	-0.005
32	A	37	GLU	-1	-0.837	-0.922	5.185	-1.082	-1.014	-0.001	-0.003	-0.065	0.000
33	A	38	ARG	1	0.956	0.968	7.805	3.102	3.102	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.787	-0.896	6.883	-2.541	-2.541	0.000	0.000	0.000	0.000
35	A	40	VAL	0	0.023	0.017	8.931	0.573	0.573	0.000	0.000	0.000	0.000
36	A	41	ARG	1	0.942	0.959	11.425	1.793	1.793	0.000	0.000	0.000	0.000
37	A	42	ARG	1	0.908	0.968	10.525	2.087	2.087	0.000	0.000	0.000	0.000
38	A	43	LYS	1	0.826	0.915	10.154	2.120	2.120	0.000	0.000	0.000	0.000
39	A	44	LEU	0	-0.050	-0.031	14.709	0.196	0.196	0.000	0.000	0.000	0.000
40	A	45	GLU	-1	-0.929	-0.940	16.942	-1.065	-1.065	0.000	0.000	0.000	0.000
41	A	46	GLY	0	-0.009	-0.008	18.776	0.031	0.031	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.894	0.947	19.253	0.753	0.753	0.000	0.000	0.000	0.000
43	A	48	PRO	0	0.046	0.045	23.030	-0.040	-0.040	0.000	0.000	0.000	0.000
44	A	49	ILE	0	-0.027	-0.026	19.718	0.028	0.028	0.000	0.000	0.000	0.000
45	A	50	ASN	0	0.049	0.028	22.436	-0.076	-0.076	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.059	-0.039	15.870	0.006	0.006	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.902	-0.959	19.709	-0.563	-0.563	0.000	0.000	0.000	0.000
48	A	53	TYR	0	-0.039	-0.034	15.865	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	54	ILE	0	-0.015	0.003	11.278	0.032	0.032	0.000	0.000	0.000	0.000
50	A	55	GLN	0	0.009	0.007	13.239	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	56	PRO	0	0.030	0.013	8.339	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	57	LEU	0	-0.048	-0.018	10.341	0.316	0.316	0.000	0.000	0.000	0.000
53	A	58	GLU	-1	-0.850	-0.934	8.878	-0.910	-0.910	0.000	0.000	0.000	0.000
54	A	59	GLY	0	-0.055	-0.025	9.754	0.104	0.104	0.000	0.000	0.000	0.000
55	A	60	ALA	0	-0.033	-0.002	10.910	0.080	0.080	0.000	0.000	0.000	0.000
56	A	61	HIS	1	0.809	0.863	9.884	-0.550	-0.550	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.040	-0.013	12.627	-0.107	-0.107	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.950	-0.975	14.834	0.147	0.147	0.000	0.000	0.000	0.000
59	A	64	TYR	0	-0.035	-0.017	16.507	0.095	0.095	0.000	0.000	0.000	0.000
60	A	65	GLU	-1	-0.796	-0.869	11.033	0.414	0.414	0.000	0.000	0.000	0.000

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