FMO DATABASE

FMODB ID: 1N9VZ

Calculation Name: 3C4S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C4S

Chain ID: A

ChEMBL ID:

UniProt ID: P74795

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	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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-307162.397412
FMO2-HF: Nuclear repulsion	284773.136072
FMO2-HF: Total energy	-22389.26134
FMO2-MP2: Total energy	-22455.501761

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:1:MET)

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

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.
-1.641	0.953	0.589	-0.911	-2.271	0.001

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.005

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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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	3	PHE	0	-0.016	-0.007	3.799	-0.959	0.750	-0.007	-0.614	-1.088	0.002
4	A	4	PRO	0	0.000	-0.018	6.018	0.272	0.272	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.021	0.012	9.807	-0.043	-0.043	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.039	-0.004	6.235	0.099	0.099	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.032	0.014	8.281	0.161	0.161	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.039	-0.023	6.190	-0.098	-0.098	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.831	0.906	7.990	0.244	0.244	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.020	-0.001	9.249	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.005	-0.016	9.122	0.020	0.020	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.013	-0.014	12.075	0.017	0.017	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.010	-0.014	15.113	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.898	-0.936	18.224	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	ASH	0	-0.125	-0.087	16.105	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.006	-0.015	19.160	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.004	-0.014	17.190	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.031	0.040	15.062	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.905	0.934	13.951	0.054	0.054	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.020	0.017	14.963	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.849	-0.936	12.088	-0.162	-0.162	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.012	0.003	12.207	0.029	0.029	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.003	0.010	11.702	-0.058	-0.058	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.019	-0.002	7.703	0.078	0.078	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.015	-0.019	11.084	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.933	0.959	11.406	0.221	0.221	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.008	0.002	5.971	0.055	0.055	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.006	-0.005	9.249	-0.053	-0.053	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.902	-0.944	10.954	-0.076	-0.076	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.004	0.004	8.651	0.037	0.037	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.902	0.946	9.695	0.148	0.148	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.047	0.019	8.522	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.043	0.001	10.610	0.038	0.038	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.004	-0.012	11.331	-0.063	-0.063	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.023	0.013	13.988	0.031	0.031	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.053	-0.028	14.158	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.839	-0.938	18.099	-0.133	-0.133	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.050	-0.027	20.635	0.003	0.003	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.028	0.022	23.414	0.006	0.006	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.018	-0.017	26.174	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	TRP	0	-0.058	-0.016	20.917	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.857	-0.925	22.045	-0.115	-0.115	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.920	0.950	21.017	0.091	0.091	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.017	0.011	17.062	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.042	-0.025	17.219	0.017	0.017	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.034	-0.011	14.198	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.015	0.012	12.485	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.975	0.979	12.071	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.052	0.007	5.212	-0.073	-0.073	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.015	-0.001	7.958	0.006	0.006	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.844	-0.882	9.526	-0.057	-0.057	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.032	-0.015	7.854	-0.062	-0.062	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.843	-0.893	4.605	-0.339	-0.230	-0.001	-0.008	-0.100	0.000
54	A	54	ALA	0	-0.008	-0.013	2.497	-0.621	0.014	0.598	-0.284	-0.948	-0.001
55	A	55	VAL	0	-0.019	-0.004	4.147	0.064	0.205	-0.001	-0.005	-0.135	0.000
56	A	56	LYS	1	0.924	0.953	7.220	-0.202	-0.202	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.054	0.039	10.023	0.002	0.002	0.000	0.000	0.000	0.000

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