FMO DATABASE

FMODB ID: 2NL5R

Calculation Name: 4GHJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GHJ

Chain ID: A

ChEMBL ID:

UniProt ID: A0A3Q0

Base Structure: X-ray

Registration Date: 2023-09-22

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-418060.8834
FMO2-HF: Nuclear repulsion	390106.924243
FMO2-HF: Total energy	-27953.959157
FMO2-MP2: Total energy	-28035.812599

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-108.01	-114.894	36.218	-15.205	-14.129	-0.161

Interaction energy analysis for fragmet #1(A:2:LYS)

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 : 0.905

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	4	VAL	0	-0.005	0.001	2.462	-0.204	2.027	2.787	-1.710	-3.308	0.002
4	A	5	THR	0	0.039	0.019	4.114	1.264	1.315	0.000	-0.008	-0.043	0.000
5	A	6	ALA	0	0.064	0.016	6.846	-3.752	-3.752	0.000	0.000	0.000	0.000
6	A	7	ALA	0	0.011	0.009	8.368	-1.291	-1.291	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.040	0.021	7.058	0.161	0.161	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.004	0.003	2.099	-8.253	-9.228	4.462	-1.035	-2.452	-0.011
9	A	10	ALA	0	0.033	0.008	4.985	-2.127	-2.072	-0.001	0.000	-0.053	0.000
10	A	11	GLU	-1	-0.918	-0.966	7.975	-23.554	-23.554	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.752	-0.839	1.713	-148.302	-157.470	28.899	-11.976	-7.755	-0.149
12	A	13	ILE	0	-0.039	-0.026	4.931	1.425	1.425	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.051	0.033	7.388	3.660	3.660	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.871	-0.939	8.944	-23.983	-23.983	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.839	0.908	2.497	65.077	65.999	0.071	-0.476	-0.518	-0.003
16	A	17	LEU	0	0.008	0.011	9.063	2.400	2.400	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.808	0.896	12.231	24.812	24.812	0.000	0.000	0.000	0.000
18	A	19	GLN	0	-0.017	-0.015	11.966	1.171	1.171	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.010	-0.002	12.792	1.301	1.301	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.798	0.867	14.494	17.617	17.617	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.020	-0.016	16.335	0.989	0.989	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.040	-0.014	15.804	0.757	0.757	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.843	0.909	16.519	17.038	17.038	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.898	-0.934	21.421	-12.221	-12.221	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.022	0.012	21.942	0.191	0.191	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.028	-0.059	22.005	-0.800	-0.800	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.037	-0.053	18.558	0.690	0.690	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.035	-0.026	22.344	-0.170	-0.170	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.721	-0.808	25.511	-11.644	-11.644	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.031	0.020	19.752	0.019	0.019	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.056	-0.031	23.227	-0.104	-0.104	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.962	-0.974	24.670	-10.036	-10.036	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.002	0.000	25.270	0.216	0.216	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.017	-0.010	22.958	0.049	0.049	0.000	0.000	0.000	0.000
35	A	36	GLY	0	-0.006	0.022	25.068	0.057	0.057	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.078	-0.042	22.066	0.017	0.017	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.044	0.015	26.408	0.164	0.164	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.973	0.960	23.235	12.301	12.301	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.851	0.919	21.621	13.638	13.638	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.041	0.016	20.617	-0.524	-0.524	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.089	0.054	18.876	-0.988	-0.988	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.062	-0.017	17.998	-0.977	-0.977	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.007	-0.004	17.807	-0.489	-0.489	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.069	0.044	15.113	-1.276	-1.276	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.766	-0.845	13.424	-19.860	-19.860	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.900	0.948	13.028	17.819	17.819	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.062	0.041	11.154	-0.487	-0.487	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.759	0.885	11.927	22.390	22.390	0.000	0.000	0.000	0.000
49	A	50	VAL	0	0.002	-0.010	13.939	1.266	1.266	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.034	-0.016	15.487	-0.781	-0.781	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.044	0.012	13.880	-0.193	-0.193	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.775	-0.876	16.524	-15.025	-15.025	0.000	0.000	0.000	0.000
53	A	54	ILE	0	0.004	-0.001	19.360	0.127	0.127	0.000	0.000	0.000	0.000
54	A	55	MET	0	-0.020	-0.011	11.492	0.199	0.199	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.017	0.007	16.391	-0.248	-0.248	0.000	0.000	0.000	0.000
56	A	57	ALA	0	0.036	0.019	17.872	0.298	0.298	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.028	-0.024	17.315	0.330	0.330	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.030	-0.019	13.339	-0.155	-0.155	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.005	-0.006	17.594	0.282	0.282	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.014	-0.001	21.185	0.451	0.451	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.070	-0.031	16.527	0.163	0.163	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.907	-0.934	20.119	-13.904	-13.904	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.044	-0.019	13.657	-0.637	-0.637	0.000	0.000	0.000	0.000
64	A	65	THR	0	0.048	0.010	16.148	-1.127	-1.127	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.880	-0.921	18.076	-14.325	-14.325	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.035	-0.037	12.861	0.892	0.892	0.000	0.000	0.000	0.000
67	A	68	ILE	0	-0.059	-0.037	13.899	-1.250	-1.250	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.866	-0.919	16.112	-15.027	-15.027	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.058	-0.036	15.190	0.372	0.372	0.000	0.000	0.000	0.000
70	A	71	PHE	0	-0.066	-0.033	9.646	-1.817	-1.817	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.060	-0.031	12.468	0.907	0.907	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.059	0.065	15.110	0.963	0.963	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.901	0.934	18.189	16.048	16.048	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)