FMO DATABASE

FMODB ID: 3N2NL

Calculation Name: 3FMA-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FMA

Chain ID: A

ChEMBL ID:

UniProt ID: Q12186

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	83
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-563170.844589
FMO2-HF: Nuclear repulsion	530397.725843
FMO2-HF: Total energy	-32773.118747
FMO2-MP2: Total energy	-32868.460442

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:12:ACE )

Summations of interaction energy for fragment #1(A:12:ACE )

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.
0.401	1.118	-0.005	-0.309	-0.403	0

Interaction energy analysis for fragmet #1(A:12:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.011

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

Sort

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].
3	A	14	VAL	0	-0.014	0.010	3.849	1.046	1.763	-0.005	-0.309	-0.403
4	A	15	GLU	-1	-0.833	-0.907	6.758	-0.334	-0.334	0.000	0.000	0.000
5	A	16	SER	0	-0.051	-0.052	10.309	0.101	0.101	0.000	0.000	0.000
6	A	17	SER	0	-0.054	-0.026	13.213	0.044	0.044	0.000	0.000	0.000
7	A	18	TRP	0	-0.005	-0.024	16.027	0.021	0.021	0.000	0.000	0.000
8	A	19	ARG	1	0.955	0.977	19.576	0.072	0.072	0.000	0.000	0.000
9	A	20	TYR	0	0.006	-0.001	23.093	-0.005	-0.005	0.000	0.000	0.000
10	A	21	ILE	0	-0.014	0.012	26.488	0.007	0.007	0.000	0.000	0.000
11	A	22	ASP	-1	-0.779	-0.876	30.095	-0.046	-0.046	0.000	0.000	0.000
12	A	23	THR	0	0.039	-0.014	32.752	0.001	0.001	0.000	0.000	0.000
13	A	24	GLN	0	-0.083	-0.026	35.989	0.004	0.004	0.000	0.000	0.000
14	A	25	GLY	0	0.008	0.012	34.562	0.003	0.003	0.000	0.000	0.000
15	A	26	GLN	0	-0.046	-0.022	31.370	0.001	0.001	0.000	0.000	0.000
16	A	27	ILE	0	-0.007	0.000	26.509	-0.006	-0.006	0.000	0.000	0.000
17	A	28	HIS	1	0.823	0.903	27.020	0.054	0.054	0.000	0.000	0.000
18	A	29	GLY	0	0.048	0.033	22.961	-0.010	-0.010	0.000	0.000	0.000
19	A	30	PRO	0	-0.058	-0.050	18.401	0.011	0.011	0.000	0.000	0.000
20	A	31	PHE	0	0.008	-0.006	19.513	0.011	0.011	0.000	0.000	0.000
21	A	32	THR	0	0.059	0.032	14.587	0.000	0.000	0.000	0.000	0.000
22	A	33	THR	0	0.031	-0.001	14.171	0.049	0.049	0.000	0.000	0.000
23	A	34	GLN	0	0.021	0.033	15.215	0.025	0.025	0.000	0.000	0.000
24	A	35	MET	0	-0.033	-0.012	16.875	0.027	0.027	0.000	0.000	0.000
25	A	36	MET	0	-0.025	-0.004	19.557	0.023	0.023	0.000	0.000	0.000
26	A	37	SER	0	-0.040	-0.028	18.966	0.017	0.017	0.000	0.000	0.000
27	A	38	GLN	0	0.016	-0.003	20.906	0.013	0.013	0.000	0.000	0.000
28	A	39	TRP	0	-0.010	-0.002	22.971	0.010	0.010	0.000	0.000	0.000
29	A	40	TYR	0	0.023	-0.002	24.081	0.010	0.010	0.000	0.000	0.000
30	A	41	ILE	0	-0.022	-0.009	22.521	0.010	0.010	0.000	0.000	0.000
31	A	42	GLY	0	-0.050	-0.021	26.483	0.008	0.008	0.000	0.000	0.000
32	A	43	GLY	0	-0.021	-0.001	28.795	0.008	0.008	0.000	0.000	0.000
33	A	44	TYR	0	-0.070	-0.038	28.578	0.007	0.007	0.000	0.000	0.000
34	A	45	PHE	0	-0.047	-0.018	24.216	0.005	0.005	0.000	0.000	0.000
35	A	46	ALA	0	0.060	0.035	30.032	0.000	0.000	0.000	0.000	0.000
36	A	47	SER	0	0.057	0.006	30.916	-0.003	-0.003	0.000	0.000	0.000
37	A	48	THR	0	-0.008	-0.005	31.552	-0.004	-0.004	0.000	0.000	0.000
38	A	49	LEU	0	-0.028	0.002	27.781	0.003	0.003	0.000	0.000	0.000
39	A	50	GLN	0	0.017	0.013	29.224	-0.005	-0.005	0.000	0.000	0.000
40	A	51	ILE	0	0.002	-0.015	23.048	0.002	0.002	0.000	0.000	0.000
41	A	52	SER	0	0.002	-0.001	22.669	0.002	0.002	0.000	0.000	0.000
42	A	53	ARG	1	0.854	0.911	11.905	0.323	0.323	0.000	0.000	0.000
43	A	54	LEU	0	-0.031	-0.023	17.017	0.019	0.019	0.000	0.000	0.000
44	A	55	GLY	0	0.021	0.017	15.861	-0.035	-0.035	0.000	0.000	0.000
45	A	56	SER	0	-0.110	-0.062	12.242	0.003	0.003	0.000	0.000	0.000
46	A	57	THR	0	0.021	0.017	8.511	0.008	0.008	0.000	0.000	0.000
47	A	58	PRO	0	0.011	0.000	11.154	0.012	0.012	0.000	0.000	0.000
48	A	59	GLU	-1	-0.752	-0.872	12.687	-0.275	-0.275	0.000	0.000	0.000
49	A	60	THR	0	-0.022	-0.026	15.175	0.028	0.028	0.000	0.000	0.000
50	A	61	LEU	0	-0.052	-0.001	17.824	0.021	0.021	0.000	0.000	0.000
51	A	62	GLY	0	-0.047	-0.021	19.733	0.023	0.023	0.000	0.000	0.000
52	A	63	ILE	0	-0.076	-0.067	19.376	0.016	0.016	0.000	0.000	0.000
53	A	64	ASN	0	0.002	-0.002	15.789	-0.013	-0.013	0.000	0.000	0.000
54	A	65	ASP	-1	-0.865	-0.927	19.683	-0.079	-0.079	0.000	0.000	0.000
55	A	66	ILE	0	-0.030	0.014	21.869	0.015	0.015	0.000	0.000	0.000
56	A	67	PHE	0	-0.052	-0.038	24.462	-0.007	-0.007	0.000	0.000	0.000
57	A	68	ILE	0	0.022	0.026	24.314	0.005	0.005	0.000	0.000	0.000
58	A	69	THR	0	-0.010	-0.005	27.612	-0.003	-0.003	0.000	0.000	0.000
59	A	70	LEU	0	0.017	0.008	25.469	-0.008	-0.008	0.000	0.000	0.000
60	A	71	GLY	0	-0.002	-0.032	27.603	-0.008	-0.008	0.000	0.000	0.000
61	A	72	GLU	-1	-0.901	-0.950	28.902	-0.092	-0.092	0.000	0.000	0.000
62	A	73	LEU	0	0.014	0.022	21.472	-0.004	-0.004	0.000	0.000	0.000
63	A	74	MET	0	-0.040	-0.021	24.933	-0.012	-0.012	0.000	0.000	0.000
64	A	75	THR	0	-0.089	-0.051	26.739	-0.001	-0.001	0.000	0.000	0.000
65	A	76	LYS	1	0.941	0.976	24.734	0.116	0.116	0.000	0.000	0.000
66	A	77	LEU	0	-0.016	0.006	20.320	-0.008	-0.008	0.000	0.000	0.000
67	A	78	GLU	-1	-0.961	-0.958	24.008	-0.130	-0.130	0.000	0.000	0.000
68	A	79	LYS	1	0.902	0.932	24.402	0.147	0.147	0.000	0.000	0.000
69	A	80	TYR	0	-0.020	-0.015	22.834	-0.016	-0.016	0.000	0.000	0.000
70	A	81	ASP	-1	-0.950	-0.960	21.046	-0.206	-0.206	0.000	0.000	0.000
71	A	82	THR	0	0.005	0.003	21.468	0.012	0.012	0.000	0.000	0.000
72	A	83	ASP	-1	-0.757	-0.872	20.387	-0.216	-0.216	0.000	0.000	0.000
73	A	84	PRO	0	0.011	0.008	21.003	-0.025	-0.025	0.000	0.000	0.000
74	A	85	PHE	0	-0.004	0.004	18.538	-0.012	-0.012	0.000	0.000	0.000
75	A	86	THR	0	0.018	-0.013	15.536	-0.051	-0.051	0.000	0.000	0.000
76	A	87	THR	0	-0.052	-0.030	15.773	-0.053	-0.053	0.000	0.000	0.000
77	A	88	PHE	0	0.004	-0.003	15.336	-0.030	-0.030	0.000	0.000	0.000
78	A	89	ASP	-1	-0.678	-0.803	12.035	-0.499	-0.499	0.000	0.000	0.000
79	A	90	LYS	1	0.914	0.961	12.113	0.356	0.356	0.000	0.000	0.000
80	A	91	LEU	0	-0.068	-0.046	13.479	-0.032	-0.032	0.000	0.000	0.000
81	A	92	HIS	0	0.044	0.032	15.096	0.016	0.016	0.000	0.000	0.000
82	A	93	VAL	0	-0.040	0.001	9.265	0.054	0.054	0.000	0.000	0.000
83	A	94	NME	0	-0.019	0.006	8.916	-0.140	-0.140	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:ACE )