FMO DATABASE

FMODB ID: NNK3Q

Calculation Name: 4M78-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4M78

Chain ID: D

ChEMBL ID:

UniProt ID: P38203

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-456980.173909
FMO2-HF: Nuclear repulsion	427813.511236
FMO2-HF: Total energy	-29166.662673
FMO2-MP2: Total energy	-29251.82468

3D Structure Molmil

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(D:10:SER)

Summations of interaction energy for fragment #1(D:10: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.
-14.503	-8.031	6.244	-5.351	-7.365	-0.001

Interaction energy analysis for fragmet #1(D:10:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	D	12	THR	0	-0.030	-0.017	2.727	-7.607	-2.978	0.367	-2.317	-2.679	0.016
4	D	13	THR	0	-0.025	-0.024	1.990	-3.158	-2.335	5.876	-2.744	-3.955	-0.016
5	D	14	GLU	-1	-0.910	-0.946	3.765	-4.007	-2.987	0.001	-0.290	-0.731	-0.001
6	D	15	PHE	0	0.036	0.014	5.707	0.799	0.799	0.000	0.000	0.000	0.000
7	D	16	LEU	0	-0.075	-0.049	7.211	0.292	0.292	0.000	0.000	0.000	0.000
8	D	17	SER	0	-0.031	-0.008	8.648	-0.043	-0.043	0.000	0.000	0.000	0.000
9	D	18	ASP	-1	-0.910	-0.936	10.124	-0.940	-0.940	0.000	0.000	0.000	0.000
10	D	19	ILE	0	-0.043	-0.037	12.005	0.172	0.172	0.000	0.000	0.000	0.000
11	D	20	ILE	0	0.002	0.028	13.128	0.077	0.077	0.000	0.000	0.000	0.000
12	D	21	GLY	0	-0.010	0.001	15.266	0.016	0.016	0.000	0.000	0.000	0.000
13	D	22	LYS	1	0.870	0.926	16.081	0.411	0.411	0.000	0.000	0.000	0.000
14	D	23	THR	0	-0.023	-0.013	19.129	0.002	0.002	0.000	0.000	0.000	0.000
15	D	24	VAL	0	-0.008	-0.016	16.762	0.007	0.007	0.000	0.000	0.000	0.000
16	D	25	ASN	0	0.020	0.045	19.686	0.006	0.006	0.000	0.000	0.000	0.000
17	D	26	VAL	0	0.023	0.003	17.853	0.003	0.003	0.000	0.000	0.000	0.000
18	D	27	LYS	1	0.852	0.961	19.363	0.052	0.052	0.000	0.000	0.000	0.000
19	D	28	LEU	0	-0.006	0.005	19.751	-0.010	-0.010	0.000	0.000	0.000	0.000
20	D	29	ALA	0	0.018	-0.001	21.539	0.013	0.013	0.000	0.000	0.000	0.000
21	D	30	SER	0	-0.032	-0.016	22.522	0.008	0.008	0.000	0.000	0.000	0.000
22	D	31	GLY	0	0.076	0.035	24.549	0.007	0.007	0.000	0.000	0.000	0.000
23	D	32	LEU	0	-0.060	-0.028	25.678	0.003	0.003	0.000	0.000	0.000	0.000
24	D	33	LEU	0	-0.058	-0.028	22.501	-0.006	-0.006	0.000	0.000	0.000	0.000
25	D	34	TYR	0	-0.016	-0.020	22.995	0.001	0.001	0.000	0.000	0.000	0.000
26	D	35	SER	0	0.000	-0.035	22.956	-0.006	-0.006	0.000	0.000	0.000	0.000
27	D	36	GLY	0	0.033	0.008	22.951	0.008	0.008	0.000	0.000	0.000	0.000
28	D	37	ARG	1	0.897	0.984	21.361	0.228	0.228	0.000	0.000	0.000	0.000
29	D	38	LEU	0	0.011	0.004	14.982	0.010	0.010	0.000	0.000	0.000	0.000
30	D	39	GLU	-1	-0.862	-0.934	18.448	-0.290	-0.290	0.000	0.000	0.000	0.000
31	D	40	SER	0	-0.021	-0.028	15.776	-0.024	-0.024	0.000	0.000	0.000	0.000
32	D	41	ILE	0	-0.004	-0.005	11.179	0.052	0.052	0.000	0.000	0.000	0.000
33	D	42	ASP	-1	-0.807	-0.889	11.431	-0.519	-0.519	0.000	0.000	0.000	0.000
34	D	43	GLY	0	0.045	0.013	8.893	-0.077	-0.077	0.000	0.000	0.000	0.000
35	D	44	PHE	0	-0.108	-0.057	9.737	0.032	0.032	0.000	0.000	0.000	0.000
36	D	45	MET	0	0.018	0.004	10.936	0.050	0.050	0.000	0.000	0.000	0.000
37	D	46	ASN	0	-0.018	-0.002	13.006	0.088	0.088	0.000	0.000	0.000	0.000
38	D	47	VAL	0	0.003	0.000	15.147	-0.053	-0.053	0.000	0.000	0.000	0.000
39	D	48	ALA	0	0.007	0.027	17.513	0.042	0.042	0.000	0.000	0.000	0.000
40	D	49	LEU	0	-0.025	-0.006	19.505	-0.022	-0.022	0.000	0.000	0.000	0.000
41	D	50	SER	0	0.078	0.055	22.094	0.020	0.020	0.000	0.000	0.000	0.000
42	D	51	SER	0	-0.082	-0.051	25.206	0.007	0.007	0.000	0.000	0.000	0.000
43	D	52	ALA	0	0.025	0.025	25.609	0.000	0.000	0.000	0.000	0.000	0.000
44	D	53	THR	0	-0.038	-0.030	27.143	0.007	0.007	0.000	0.000	0.000	0.000
45	D	54	GLU	-1	-0.859	-0.922	27.830	-0.084	-0.084	0.000	0.000	0.000	0.000
46	D	55	HIS	0	0.026	0.006	28.597	0.002	0.002	0.000	0.000	0.000	0.000
47	D	56	TYR	0	0.042	0.028	28.647	-0.003	-0.003	0.000	0.000	0.000	0.000
48	D	57	GLU	-1	-0.874	-0.946	26.320	-0.022	-0.022	0.000	0.000	0.000	0.000
49	D	58	SER	0	-0.054	-0.055	26.396	0.001	0.001	0.000	0.000	0.000	0.000
50	D	59	ASN	0	0.081	0.031	26.937	-0.005	-0.005	0.000	0.000	0.000	0.000
51	D	60	ASN	0	-0.022	-0.006	28.624	-0.007	-0.007	0.000	0.000	0.000	0.000
52	D	61	ASN	0	-0.007	0.015	31.616	0.005	0.005	0.000	0.000	0.000	0.000
53	D	62	LYS	1	0.918	0.955	33.556	0.041	0.041	0.000	0.000	0.000	0.000
54	D	63	LEU	0	0.009	0.010	32.347	-0.001	-0.001	0.000	0.000	0.000	0.000
55	D	64	LEU	0	-0.049	-0.026	31.888	0.004	0.004	0.000	0.000	0.000	0.000
56	D	65	ASN	0	-0.026	-0.023	32.301	-0.001	-0.001	0.000	0.000	0.000	0.000
57	D	66	LYS	1	0.966	0.989	31.282	0.101	0.101	0.000	0.000	0.000	0.000
58	D	67	PHE	0	0.018	0.020	29.269	0.003	0.003	0.000	0.000	0.000	0.000
59	D	68	ASN	0	-0.059	-0.043	30.512	-0.006	-0.006	0.000	0.000	0.000	0.000
60	D	69	SER	0	-0.038	-0.017	29.865	0.001	0.001	0.000	0.000	0.000	0.000
61	D	70	ASP	-1	-0.841	-0.937	24.389	-0.185	-0.185	0.000	0.000	0.000	0.000
62	D	71	VAL	0	-0.069	-0.022	23.968	0.012	0.012	0.000	0.000	0.000	0.000
63	D	72	PHE	0	-0.003	-0.004	20.096	-0.017	-0.017	0.000	0.000	0.000	0.000
64	D	73	LEU	0	0.012	-0.014	19.939	0.020	0.020	0.000	0.000	0.000	0.000
65	D	74	ARG	1	0.936	0.962	19.282	0.107	0.107	0.000	0.000	0.000	0.000
66	D	75	GLY	0	0.107	0.043	16.211	0.011	0.011	0.000	0.000	0.000	0.000
67	D	76	THR	0	-0.043	-0.027	16.822	0.013	0.013	0.000	0.000	0.000	0.000
68	D	77	GLN	0	-0.088	-0.043	18.215	0.022	0.022	0.000	0.000	0.000	0.000
69	D	78	VAL	0	-0.021	0.003	15.292	0.021	0.021	0.000	0.000	0.000	0.000
70	D	79	MET	0	-0.017	0.001	16.278	0.001	0.001	0.000	0.000	0.000	0.000
71	D	80	TYR	0	-0.023	-0.022	14.800	0.028	0.028	0.000	0.000	0.000	0.000
72	D	81	ILE	0	0.009	-0.002	13.207	-0.014	-0.014	0.000	0.000	0.000	0.000
73	D	82	SER	0	0.008	0.010	14.651	0.012	0.012	0.000	0.000	0.000	0.000
74	D	83	GLU	-1	-0.915	-0.940	16.330	-0.241	-0.241	0.000	0.000	0.000	0.000
75	D	84	GLN	0	-0.046	-0.017	18.388	0.027	0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:10:SER)