FMO DATABASE

FMODB ID: K3L53

Calculation Name: 1NVP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NVP

Chain ID: B

ChEMBL ID:

UniProt ID: P52657

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	43
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-200977.515935
FMO2-HF: Nuclear repulsion	182972.375331
FMO2-HF: Total energy	-18005.140603
FMO2-MP2: Total energy	-18057.063084

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(B:9:THR)

Summations of interaction energy for fragment #1(B:9:THR)

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.
-8.076	-3.798	0.986	-1.982	-3.282	0.005

Interaction energy analysis for fragmet #1(B:9:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.019

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	B	11	PRO	0	0.035	0.015	3.234	-2.044	0.834	0.197	-1.359	-1.716	0.004
4	B	12	LYS	1	0.959	0.977	2.441	-6.217	-5.053	0.790	-0.587	-1.368	0.001
5	B	13	LEU	0	0.042	0.041	4.463	-0.102	0.134	-0.001	-0.036	-0.198	0.000
6	B	14	TYR	0	0.031	0.005	6.036	0.315	0.315	0.000	0.000	0.000	0.000
7	B	15	ARG	1	0.877	0.931	8.016	-0.533	-0.533	0.000	0.000	0.000	0.000
8	B	16	SER	0	0.005	-0.002	8.227	0.012	0.012	0.000	0.000	0.000	0.000
9	B	17	VAL	0	0.013	0.007	9.788	0.011	0.011	0.000	0.000	0.000	0.000
10	B	18	ILE	0	-0.031	-0.012	11.943	0.063	0.063	0.000	0.000	0.000	0.000
11	B	19	GLU	-1	-0.864	-0.935	12.925	0.260	0.260	0.000	0.000	0.000	0.000
12	B	20	ASP	-1	-0.911	-0.948	12.916	-0.122	-0.122	0.000	0.000	0.000	0.000
13	B	21	VAL	0	-0.009	-0.005	15.821	0.005	0.005	0.000	0.000	0.000	0.000
14	B	22	ILE	0	-0.021	-0.022	17.745	0.018	0.018	0.000	0.000	0.000	0.000
15	B	23	ASN	0	-0.049	-0.046	17.529	0.017	0.017	0.000	0.000	0.000	0.000
16	B	24	ASP	-1	-0.903	-0.948	19.100	-0.083	-0.083	0.000	0.000	0.000	0.000
17	B	25	VAL	0	-0.079	-0.031	21.603	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	26	ARG	1	0.827	0.903	21.947	-0.063	-0.063	0.000	0.000	0.000	0.000
19	B	27	ASP	-1	-0.866	-0.945	25.774	0.009	0.009	0.000	0.000	0.000	0.000
20	B	28	ILE	0	-0.001	0.013	25.718	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	29	PHE	0	0.000	-0.010	25.733	0.002	0.002	0.000	0.000	0.000	0.000
22	B	30	LEU	0	-0.038	-0.018	29.630	0.004	0.004	0.000	0.000	0.000	0.000
23	B	31	ASP	-1	-0.960	-0.973	31.753	-0.013	-0.013	0.000	0.000	0.000	0.000
24	B	32	ASP	-1	-0.990	-0.989	31.911	-0.034	-0.034	0.000	0.000	0.000	0.000
25	B	33	GLY	0	-0.091	-0.035	34.368	0.001	0.001	0.000	0.000	0.000	0.000
26	B	34	VAL	0	-0.093	-0.050	30.509	0.004	0.004	0.000	0.000	0.000	0.000
27	B	35	ASP	-1	-0.854	-0.928	31.822	0.049	0.049	0.000	0.000	0.000	0.000
28	B	36	GLU	-1	-0.777	-0.885	25.984	0.067	0.067	0.000	0.000	0.000	0.000
29	B	37	GLN	0	-0.057	-0.046	27.327	0.004	0.004	0.000	0.000	0.000	0.000
30	B	38	VAL	0	0.021	0.011	27.406	0.005	0.005	0.000	0.000	0.000	0.000
31	B	39	LEU	0	-0.006	0.027	23.012	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	40	MET	0	-0.002	-0.013	21.217	0.002	0.002	0.000	0.000	0.000	0.000
33	B	41	GLU	-1	-0.930	-0.948	22.887	0.055	0.055	0.000	0.000	0.000	0.000
34	B	42	LEU	0	0.004	0.010	21.561	0.003	0.003	0.000	0.000	0.000	0.000
35	B	43	LYS	1	0.843	0.905	15.362	-0.236	-0.236	0.000	0.000	0.000	0.000
36	B	44	THR	0	-0.009	-0.012	18.561	0.028	0.028	0.000	0.000	0.000	0.000
37	B	45	LEU	0	-0.050	-0.025	20.019	0.013	0.013	0.000	0.000	0.000	0.000
38	B	46	TRP	0	-0.027	-0.016	15.749	0.009	0.009	0.000	0.000	0.000	0.000
39	B	47	GLU	-1	-0.794	-0.887	13.939	0.317	0.317	0.000	0.000	0.000	0.000
40	B	48	ASN	0	-0.057	-0.046	15.694	0.068	0.068	0.000	0.000	0.000	0.000
41	B	49	LYS	1	0.923	0.977	18.083	0.015	0.015	0.000	0.000	0.000	0.000
42	B	50	LEU	0	-0.061	-0.006	11.801	-0.018	-0.018	0.000	0.000	0.000	0.000
43	B	51	MET	0	-0.105	-0.044	13.674	0.043	0.043	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:THR)