FMO DATABASE

FMODB ID: YY582

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

Total energy (hartree)

FMO2-HF: Electronic energy	-357813.95226
FMO2-HF: Nuclear repulsion	331621.931168
FMO2-HF: Total energy	-26192.021092
FMO2-MP2: Total energy	-26268.045616

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.
-39.715	-47.047	31.531	-14.281	-9.918	-0.127

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 : -0.101 / q_NPA : -0.090

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	0.019	0.025	3.815	1.824	3.061	-0.013	-0.559	-0.665	0.002
4	A	5	LYS	1	0.913	0.937	6.492	-0.113	-0.113	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.805	-0.910	9.531	-0.046	-0.046	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.867	-0.942	5.891	-3.019	-3.019	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.019	-0.012	6.235	-0.019	-0.019	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.012	0.011	9.691	-0.018	-0.018	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.038	0.016	12.284	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.021	-0.020	8.226	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.040	-0.010	12.610	0.032	0.032	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.023	0.011	15.019	0.002	0.002	0.000	0.000	0.000	0.000
13	A	14	ASN	0	0.004	-0.005	15.202	0.011	0.011	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.056	-0.019	16.139	0.013	0.013	0.000	0.000	0.000	0.000
15	A	16	PHE	0	0.013	-0.013	17.846	0.019	0.019	0.000	0.000	0.000	0.000
16	A	17	SER	0	0.022	-0.009	20.272	0.018	0.018	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.019	0.011	20.269	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.007	0.008	21.833	0.010	0.010	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.003	0.004	24.383	0.009	0.009	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.940	-0.956	23.600	-0.233	-0.233	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.819	0.904	22.691	0.244	0.244	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.896	0.953	27.967	0.107	0.107	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.938	-0.968	25.043	-0.143	-0.143	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.034	-0.016	26.851	0.011	0.011	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.009	-0.003	29.949	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.883	-0.955	31.993	-0.052	-0.052	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.854	-0.916	33.199	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.055	-0.036	30.394	0.005	0.005	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.007	-0.013	28.423	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.884	-0.932	28.767	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.075	-0.042	28.518	0.007	0.007	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.011	-0.011	23.281	0.007	0.007	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.036	0.030	24.673	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	35	VAL	0	0.027	0.024	26.196	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.019	-0.003	22.857	0.006	0.006	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.036	-0.027	20.995	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.818	-0.893	21.855	-0.082	-0.082	0.000	0.000	0.000	0.000
38	A	39	CYS	0	-0.072	-0.042	23.488	0.007	0.007	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.044	-0.014	17.195	0.018	0.018	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.009	-0.017	18.712	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.929	-0.960	20.003	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.089	-0.037	19.224	0.010	0.010	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.100	-0.070	13.522	0.056	0.056	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.000	0.023	16.483	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.084	-0.037	14.613	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.863	-0.935	18.953	-0.101	-0.101	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.939	0.949	20.168	0.077	0.077	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.932	-0.975	20.842	-0.196	-0.196	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.056	-0.027	18.796	-0.029	-0.029	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.021	0.014	15.532	-0.080	-0.080	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.024	0.000	15.590	-0.097	-0.097	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.019	-0.005	16.506	-0.063	-0.063	0.000	0.000	0.000	0.000
53	A	54	ILE	0	-0.023	-0.017	11.797	-0.087	-0.087	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.008	0.004	10.900	-0.184	-0.184	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.002	0.002	12.484	-0.105	-0.105	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.913	0.956	11.696	0.718	0.718	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.011	-0.016	11.657	-0.159	-0.159	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.944	-0.956	8.552	-1.219	-1.219	0.000	0.000	0.000	0.000
59	A	60	PHE	0	0.060	0.039	6.337	-0.280	-0.280	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.894	0.946	6.973	0.314	0.314	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.001	-0.001	8.680	-0.192	-0.192	0.000	0.000	0.000	0.000
62	A	63	GLN	0	0.029	0.015	2.590	1.651	2.996	0.370	-0.635	-1.080	0.003
63	A	64	HIS	0	0.035	0.026	4.359	-2.967	-2.807	-0.001	-0.031	-0.128	0.000
64	A	65	LEU	0	-0.040	-0.021	5.432	0.439	0.439	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.022	-0.020	5.351	0.487	0.487	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.788	-0.870	1.626	-38.887	-49.154	31.176	-12.950	-7.959	-0.132
67	A	68	ILE	0	-0.065	-0.025	4.301	1.834	2.027	-0.001	-0.106	-0.086	0.000
68	A	69	LEU	0	-0.107	-0.054	7.953	0.575	0.575	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.047	-0.008	6.930	0.348	0.348	0.000	0.000	0.000	0.000

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