FMO DATABASE

FMODB ID: 2N35R

Calculation Name: 2IVY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IVY

Chain ID: A

ChEMBL ID:

UniProt ID: Q97YC2

Base Structure: X-ray

Registration Date: 2023-09-23

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-627270.169002
FMO2-HF: Nuclear repulsion	591286.2866
FMO2-HF: Total energy	-35983.882403
FMO2-MP2: Total energy	-36090.231064

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:ALA)

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

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.
-10.008	-5.57	2.05	-2.51	-3.976	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.010

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	LEU	0	0.071	0.049	3.715	-1.605	0.824	-0.014	-1.251	-1.163	0.006
4	A	5	TYR	0	-0.021	-0.021	4.894	0.609	0.609	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.008	0.012	8.482	0.055	0.055	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.009	-0.019	10.496	0.078	0.078	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.035	0.027	13.958	0.014	0.014	0.000	0.000	0.000	0.000
8	A	9	TYR	0	0.009	-0.007	17.738	0.024	0.024	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.822	-0.873	20.368	-0.138	-0.138	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.008	-0.006	21.360	0.013	0.013	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.061	0.036	25.603	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.819	-0.893	28.667	-0.040	-0.040	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.744	-0.879	27.885	-0.081	-0.081	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.051	-0.021	27.675	0.000	0.000	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.018	-0.019	25.219	0.003	0.003	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.815	0.885	23.551	0.098	0.098	0.000	0.000	0.000	0.000
17	A	18	ASN	0	-0.009	-0.008	22.684	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.943	0.987	22.730	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	20	VAL	0	0.017	0.012	17.972	0.008	0.008	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.007	0.002	18.128	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.889	-0.945	18.391	-0.034	-0.034	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.067	-0.021	14.271	0.015	0.015	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.032	0.004	13.093	0.021	0.021	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.984	0.992	13.588	0.084	0.084	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.814	0.904	15.057	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.806	0.898	10.790	-0.173	-0.173	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.009	-0.003	10.323	0.034	0.034	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.068	-0.009	8.183	-0.089	-0.089	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.866	-0.924	11.137	-0.572	-0.572	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.797	0.889	13.474	0.183	0.183	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.003	-0.018	15.307	0.007	0.007	0.000	0.000	0.000	0.000
32	A	33	GLN	0	0.030	0.020	18.072	0.024	0.024	0.000	0.000	0.000	0.000
33	A	34	TYR	0	0.027	0.019	20.375	0.003	0.003	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.011	-0.006	20.681	0.015	0.015	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.009	0.006	16.185	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.008	-0.008	13.111	0.035	0.035	0.000	0.000	0.000	0.000
37	A	38	MET	0	0.001	0.012	10.923	0.026	0.026	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.078	0.031	7.918	0.181	0.181	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.846	-0.910	2.471	-4.365	-4.117	0.676	-0.329	-0.595	-0.001
40	A	41	LEU	0	-0.061	-0.027	3.022	0.669	1.428	0.150	-0.252	-0.657	-0.002
41	A	42	ASN	0	0.057	0.022	2.560	-1.794	-0.736	1.203	-0.775	-1.486	-0.003
42	A	43	SER	0	0.082	0.030	3.595	-1.326	-1.382	0.035	0.097	-0.075	0.000
43	A	44	SER	0	-0.009	-0.002	6.993	-0.374	-0.374	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.916	0.941	5.069	-0.551	-0.551	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.042	0.036	6.681	-0.217	-0.217	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.904	0.937	8.201	-1.007	-1.007	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.855	-0.902	10.887	0.201	0.201	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.035	0.008	9.663	-0.072	-0.072	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.857	-0.917	12.158	0.026	0.026	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.000	-0.007	14.069	-0.025	-0.025	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.012	0.005	15.657	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.014	-0.016	14.496	-0.022	-0.022	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.865	0.917	17.312	-0.039	-0.039	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.023	-0.005	20.022	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.087	-0.039	19.418	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.029	0.015	22.284	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	58	ASN	0	-0.074	-0.012	24.100	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.886	0.927	26.087	0.026	0.026	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.948	0.981	29.278	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.822	0.912	31.326	0.060	0.060	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.072	-0.053	32.622	0.005	0.005	0.000	0.000	0.000	0.000
62	A	63	GLN	0	-0.047	-0.038	35.291	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.849	-0.910	35.199	-0.046	-0.046	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.845	-0.911	34.878	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.881	-0.933	30.667	-0.049	-0.049	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.816	0.860	27.908	0.110	0.110	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.037	0.007	21.569	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	69	PHE	0	-0.007	0.006	21.283	0.007	0.007	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.016	-0.004	16.409	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.012	0.011	16.705	0.021	0.021	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.006	-0.010	10.767	-0.037	-0.037	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.004	-0.006	12.573	0.057	0.057	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.006	0.012	8.560	-0.111	-0.111	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.022	-0.012	9.439	0.236	0.236	0.000	0.000	0.000	0.000
75	A	76	THR	0	0.007	-0.015	9.046	-0.419	-0.419	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.823	-0.928	9.589	-1.010	-1.010	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.048	-0.011	11.419	0.195	0.195	0.000	0.000	0.000	0.000
78	A	79	GLN	0	0.098	0.061	13.368	-0.046	-0.046	0.000	0.000	0.000	0.000
79	A	80	PHE	0	0.020	0.010	13.240	0.121	0.121	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.818	0.891	12.975	1.018	1.018	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.883	-0.935	17.413	-0.526	-0.526	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.843	0.940	17.485	0.609	0.609	0.000	0.000	0.000	0.000
83	A	84	ILE	0	0.031	0.010	20.298	0.027	0.027	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.045	-0.025	21.837	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.011	0.005	24.448	0.015	0.015	0.000	0.000	0.000	0.000
86	A	87	GLY	0	0.024	0.010	27.643	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.024	-0.013	29.716	0.006	0.006	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.001	0.012	33.056	0.000	0.000	0.000	0.000	0.000	0.000

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