FMO DATABASE

FMODB ID: Z62NN

Calculation Name: 5LM7-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LM7

Chain ID: N

ChEMBL ID:

UniProt ID: P03045

Base Structure: X-ray

Registration Date: 2023-06-21

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-379617.274359
FMO2-HF: Nuclear repulsion	345628.73679
FMO2-HF: Total energy	-33988.537568
FMO2-MP2: Total energy	-34089.256957

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(N:-2:LEU)

Summations of interaction energy for fragment #1(N:-2:LEU)

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.
-3.146	-1.294	-0.013	-0.875	-0.963	0.001

Interaction energy analysis for fragmet #1(N:-2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.000

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	N	0	SER	0	0.009	0.005	3.802	-2.226	-0.374	-0.013	-0.875	-0.963	0.001
4	N	1	MET	0	0.086	0.036	5.645	-0.278	-0.278	0.000	0.000	0.000	0.000
5	N	2	ASP	-1	-0.873	-0.924	8.740	0.673	0.673	0.000	0.000	0.000	0.000
6	N	3	ALA	0	0.013	0.002	11.225	-0.128	-0.128	0.000	0.000	0.000	0.000
7	N	4	GLN	0	0.043	0.010	13.685	-0.076	-0.076	0.000	0.000	0.000	0.000
8	N	5	THR	0	0.016	-0.004	10.939	-0.066	-0.066	0.000	0.000	0.000	0.000
9	N	6	ARG	1	0.936	0.962	9.011	-0.141	-0.141	0.000	0.000	0.000	0.000
10	N	7	ARG	1	0.861	0.940	12.764	-0.107	-0.107	0.000	0.000	0.000	0.000
11	N	8	ARG	1	0.911	0.955	14.865	-0.224	-0.224	0.000	0.000	0.000	0.000
12	N	9	GLU	-1	-0.846	-0.930	9.929	-0.199	-0.199	0.000	0.000	0.000	0.000
13	N	10	ARG	1	0.946	0.981	14.206	0.072	0.072	0.000	0.000	0.000	0.000
14	N	11	ARG	1	0.887	0.943	16.792	-0.023	-0.023	0.000	0.000	0.000	0.000
15	N	12	ALA	0	0.029	0.016	17.358	0.015	0.015	0.000	0.000	0.000	0.000
16	N	13	GLU	-1	-0.854	-0.926	19.444	-0.052	-0.052	0.000	0.000	0.000	0.000
17	N	14	LYS	1	0.920	0.950	22.761	0.031	0.031	0.000	0.000	0.000	0.000
18	N	15	GLN	0	-0.004	0.003	19.173	0.014	0.014	0.000	0.000	0.000	0.000
19	N	16	ALA	0	-0.020	-0.020	22.986	0.006	0.006	0.000	0.000	0.000	0.000
20	N	17	GLN	0	-0.009	-0.005	24.579	0.000	0.000	0.000	0.000	0.000	0.000
21	N	18	TRP	0	-0.017	-0.004	26.657	0.003	0.003	0.000	0.000	0.000	0.000
22	N	19	LYS	1	0.919	0.975	20.977	0.036	0.036	0.000	0.000	0.000	0.000
23	N	20	ALA	0	0.001	0.014	26.969	0.002	0.002	0.000	0.000	0.000	0.000
24	N	21	ALA	0	0.016	0.006	30.534	0.003	0.003	0.000	0.000	0.000	0.000
25	N	22	ASN	0	-0.002	0.007	30.374	0.006	0.006	0.000	0.000	0.000	0.000
26	N	23	PRO	0	0.004	-0.008	29.815	0.001	0.001	0.000	0.000	0.000	0.000
27	N	24	LEU	0	0.004	0.006	24.587	0.006	0.006	0.000	0.000	0.000	0.000
28	N	25	LEU	0	-0.032	-0.018	21.338	0.009	0.009	0.000	0.000	0.000	0.000
29	N	26	VAL	0	0.007	0.009	25.339	-0.006	-0.006	0.000	0.000	0.000	0.000
30	N	27	GLY	0	0.015	-0.002	26.109	0.012	0.012	0.000	0.000	0.000	0.000
31	N	28	VAL	0	-0.006	0.006	27.205	-0.006	-0.006	0.000	0.000	0.000	0.000
32	N	29	SER	0	-0.015	-0.009	28.377	0.010	0.010	0.000	0.000	0.000	0.000
33	N	30	ALA	0	0.015	0.017	30.514	-0.008	-0.008	0.000	0.000	0.000	0.000
34	N	31	LYS	1	0.997	0.971	33.416	-0.108	-0.108	0.000	0.000	0.000	0.000
35	N	32	PRO	0	0.043	0.026	37.190	0.004	0.004	0.000	0.000	0.000	0.000
36	N	33	VAL	0	0.060	0.024	40.182	0.002	0.002	0.000	0.000	0.000	0.000
37	N	34	ASN	0	-0.070	-0.030	33.697	0.002	0.002	0.000	0.000	0.000	0.000
38	N	35	ARG	1	0.943	0.977	31.020	-0.130	-0.130	0.000	0.000	0.000	0.000
39	N	36	PRO	0	0.040	0.033	37.004	-0.001	-0.001	0.000	0.000	0.000	0.000
40	N	37	ILE	0	0.005	-0.009	35.181	0.002	0.002	0.000	0.000	0.000	0.000
41	N	38	LEU	0	0.018	0.012	38.775	0.001	0.001	0.000	0.000	0.000	0.000
42	N	39	SER	0	0.023	0.009	38.600	-0.003	-0.003	0.000	0.000	0.000	0.000
43	N	40	LEU	0	-0.004	0.009	40.770	0.000	0.000	0.000	0.000	0.000	0.000
44	N	41	ASN	0	0.064	0.020	43.728	0.000	0.000	0.000	0.000	0.000	0.000
45	N	42	ARG	1	0.878	0.917	41.609	-0.090	-0.090	0.000	0.000	0.000	0.000
46	N	43	LYS	1	1.006	1.018	45.166	-0.067	-0.067	0.000	0.000	0.000	0.000
47	N	44	PRO	0	-0.011	-0.001	46.323	-0.001	-0.001	0.000	0.000	0.000	0.000
48	N	45	LYS	1	0.838	0.933	47.962	-0.068	-0.068	0.000	0.000	0.000	0.000
49	N	46	SER	0	0.012	0.001	46.533	0.006	0.006	0.000	0.000	0.000	0.000
50	N	47	ARG	1	0.996	0.989	39.491	-0.097	-0.097	0.000	0.000	0.000	0.000
51	N	48	VAL	0	0.051	0.021	45.698	0.000	0.000	0.000	0.000	0.000	0.000
52	N	49	GLU	-1	-0.753	-0.861	48.954	0.059	0.059	0.000	0.000	0.000	0.000
53	N	50	SER	0	-0.068	-0.047	46.853	-0.001	-0.001	0.000	0.000	0.000	0.000
54	N	51	ALA	0	-0.019	-0.003	47.882	0.000	0.000	0.000	0.000	0.000	0.000
55	N	52	LEU	0	-0.019	-0.009	49.571	-0.001	-0.001	0.000	0.000	0.000	0.000
56	N	53	ASN	0	-0.067	-0.030	52.582	-0.003	-0.003	0.000	0.000	0.000	0.000
57	N	54	PRO	0	0.049	0.031	50.594	0.002	0.002	0.000	0.000	0.000	0.000
58	N	55	ILE	0	-0.037	-0.030	47.406	-0.002	-0.002	0.000	0.000	0.000	0.000
59	N	56	ASP	-1	-0.848	-0.917	51.499	0.057	0.057	0.000	0.000	0.000	0.000
60	N	57	LEU	0	-0.017	-0.024	52.708	0.000	0.000	0.000	0.000	0.000	0.000
61	N	58	THR	0	-0.028	0.000	56.450	-0.002	-0.002	0.000	0.000	0.000	0.000
62	N	59	VAL	0	0.054	0.007	59.002	-0.001	-0.001	0.000	0.000	0.000	0.000
63	N	60	LEU	0	-0.018	0.004	56.997	-0.002	-0.002	0.000	0.000	0.000	0.000
64	N	61	ALA	0	0.012	0.005	58.588	-0.001	-0.001	0.000	0.000	0.000	0.000
65	N	62	GLU	-1	-0.851	-0.900	60.582	0.040	0.040	0.000	0.000	0.000	0.000
66	N	63	TYR	0	0.014	0.006	64.020	-0.002	-0.002	0.000	0.000	0.000	0.000
67	N	64	HIS	0	-0.051	-0.035	61.987	0.000	0.000	0.000	0.000	0.000	0.000
68	N	65	LYS	1	0.996	0.997	64.168	-0.043	-0.043	0.000	0.000	0.000	0.000
69	N	66	GLN	0	-0.037	-0.049	65.813	-0.001	-0.001	0.000	0.000	0.000	0.000
70	N	67	ILE	0	-0.004	0.018	65.566	-0.002	-0.002	0.000	0.000	0.000	0.000
71	N	68	GLU	-1	-0.834	-0.908	65.034	0.039	0.039	0.000	0.000	0.000	0.000
72	N	69	SER	0	-0.092	-0.046	68.299	-0.002	-0.002	0.000	0.000	0.000	0.000
73	N	70	ASN	0	-0.003	-0.018	71.131	-0.002	-0.002	0.000	0.000	0.000	0.000
74	N	71	LEU	0	0.018	0.024	68.636	-0.001	-0.001	0.000	0.000	0.000	0.000
75	N	72	GLN	0	0.008	-0.018	70.729	-0.001	-0.001	0.000	0.000	0.000	0.000
76	N	73	ARG	1	0.828	0.913	73.401	-0.033	-0.033	0.000	0.000	0.000	0.000
77	N	74	ILE	0	-0.005	-0.004	74.975	-0.001	-0.001	0.000	0.000	0.000	0.000
78	N	75	GLU	-1	-0.891	-0.930	73.111	0.031	0.031	0.000	0.000	0.000	0.000
79	N	76	ARG	1	0.957	0.963	75.750	-0.030	-0.030	0.000	0.000	0.000	0.000
80	N	77	LYS	1	0.945	0.992	79.304	-0.027	-0.027	0.000	0.000	0.000	0.000
81	N	78	ASN	0	-0.023	-0.012	77.893	-0.001	-0.001	0.000	0.000	0.000	0.000
82	N	79	GLN	0	-0.011	0.005	79.878	0.000	0.000	0.000	0.000	0.000	0.000
83	N	80	ARG	1	0.870	0.929	81.627	-0.025	-0.025	0.000	0.000	0.000	0.000
84	N	81	THR	0	-0.009	-0.009	84.803	0.000	0.000	0.000	0.000	0.000	0.000
85	N	82	TRP	0	0.028	0.028	85.549	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(N:-2:LEU)