FMO DATABASE

FMODB ID: 141KZ

Calculation Name: 3ZDM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZDM

Chain ID: A

ChEMBL ID:

UniProt ID: Q12285

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	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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-360210.827449
FMO2-HF: Nuclear repulsion	334018.312536
FMO2-HF: Total energy	-26192.514913
FMO2-MP2: Total energy	-26268.582994

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:SER)

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

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.
-33.963	-43.008	33.605	-14.012	-10.546	-0.121

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.098 / q_NPA : -0.089

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	SER	0	-0.022	-0.046	3.867	1.854	2.852	-0.006	-0.413	-0.579	0.002
4	A	5	LYS	1	0.854	0.890	6.556	0.209	0.209	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.753	-0.857	9.429	-0.065	-0.065	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.813	-0.870	6.951	-2.583	-2.583	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.022	-0.013	6.156	0.049	0.049	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.011	0.011	9.819	0.005	0.005	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.032	0.011	12.566	0.002	0.002	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.030	-0.024	8.338	0.008	0.008	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.031	-0.005	12.724	0.027	0.027	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.016	0.014	15.250	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	14	ASN	0	0.009	-0.002	15.406	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.063	-0.028	16.120	0.013	0.013	0.000	0.000	0.000	0.000
15	A	16	PHE	0	0.017	-0.018	17.915	0.014	0.014	0.000	0.000	0.000	0.000
16	A	17	SER	0	0.012	-0.023	20.442	0.009	0.009	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.043	-0.005	20.427	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.016	0.008	21.835	0.006	0.006	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.017	-0.003	24.557	0.007	0.007	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.883	-0.931	22.819	-0.191	-0.191	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.782	0.893	22.796	0.178	0.178	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.852	0.921	28.155	0.071	0.071	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.926	-0.955	24.402	-0.094	-0.094	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.060	-0.030	27.252	0.013	0.013	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.031	-0.025	30.034	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.832	-0.924	31.988	-0.046	-0.046	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.818	-0.885	32.959	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.010	0.015	30.573	0.005	0.005	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.007	-0.017	28.432	0.002	0.002	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.832	-0.914	28.509	-0.036	-0.036	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.106	-0.062	28.961	0.005	0.005	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.014	-0.013	23.241	0.009	0.009	0.000	0.000	0.000	0.000
33	A	34	ASN	0	-0.024	-0.005	24.710	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	35	VAL	0	0.049	0.028	25.948	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.007	0.004	22.891	0.005	0.005	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.034	-0.002	21.033	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.828	-0.879	21.818	-0.075	-0.075	0.000	0.000	0.000	0.000
38	A	39	CYS	0	-0.068	-0.040	23.548	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.043	-0.020	17.207	0.016	0.016	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.014	-0.036	18.781	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.921	-0.950	20.088	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.074	-0.036	19.584	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.095	-0.054	13.188	0.054	0.054	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.013	0.011	16.783	-0.047	-0.047	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.085	-0.046	14.778	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.863	-0.935	19.473	-0.119	-0.119	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.885	0.916	20.674	0.064	0.064	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.904	-0.964	20.910	-0.183	-0.183	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.043	-0.017	19.209	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.016	0.020	15.734	-0.081	-0.081	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.030	0.003	16.085	-0.075	-0.075	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.035	-0.011	17.635	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	54	ILE	0	-0.031	-0.023	12.098	-0.091	-0.091	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.008	0.005	11.324	-0.179	-0.179	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.033	0.020	13.301	-0.063	-0.063	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.877	0.950	11.887	0.847	0.847	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.002	-0.017	11.952	-0.141	-0.141	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.900	-0.942	9.279	-1.151	-1.151	0.000	0.000	0.000	0.000
59	A	60	PHE	0	0.062	0.043	6.650	-0.264	-0.264	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.850	0.919	7.216	0.261	0.261	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.000	0.004	9.080	-0.087	-0.087	0.000	0.000	0.000	0.000
62	A	63	GLN	0	-0.021	-0.014	2.338	2.922	4.428	1.493	-1.197	-1.801	-0.001
63	A	64	HIS	0	0.058	0.021	4.506	-2.112	-1.980	-0.001	-0.014	-0.117	0.000
64	A	65	LEU	0	-0.040	-0.018	5.567	0.517	0.517	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.008	-0.011	5.557	0.494	0.494	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.764	-0.853	1.671	-36.989	-48.777	32.120	-12.348	-7.983	-0.122
67	A	68	ILE	0	-0.057	-0.023	4.420	1.917	2.024	-0.001	-0.040	-0.066	0.000
68	A	69	LEU	0	-0.051	-0.024	7.867	0.538	0.538	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.124	-0.048	6.649	0.823	0.823	0.000	0.000	0.000	0.000

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