FMO DATABASE

FMODB ID: R97Z8

Calculation Name: 3MA5-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MA5

Chain ID: D

ChEMBL ID:

UniProt ID: Q2S6C5

Base Structure: X-ray

Registration Date: 2023-09-20

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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-405257.898657
FMO2-HF: Nuclear repulsion	378361.323486
FMO2-HF: Total energy	-26896.575171
FMO2-MP2: Total energy	-26976.838491

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(D:78:SER)

Summations of interaction energy for fragment #1(D:78: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.
-4.126	-0.498	0.075	-1.483	-2.221	0.001

Interaction energy analysis for fragmet #1(D:78:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.003

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	D	80	ALA	0	0.001	-0.003	2.867	-2.254	0.686	0.054	-1.315	-1.679	0.002
4	D	81	LEU	0	0.014	0.012	4.428	-0.347	-0.078	-0.001	-0.045	-0.224	0.000
5	D	82	ALA	0	0.037	0.009	6.323	0.154	0.154	0.000	0.000	0.000	0.000
6	D	83	LEU	0	-0.094	-0.030	8.005	-0.001	-0.001	0.000	0.000	0.000	0.000
7	D	84	PHE	0	0.004	-0.043	8.388	-0.015	-0.015	0.000	0.000	0.000	0.000
8	D	85	GLU	-1	-0.864	-0.928	10.164	-0.187	-0.187	0.000	0.000	0.000	0.000
9	D	86	GLU	-1	-0.872	-0.940	12.828	0.302	0.302	0.000	0.000	0.000	0.000
10	D	87	LEU	0	-0.063	-0.026	13.184	-0.015	-0.015	0.000	0.000	0.000	0.000
11	D	88	VAL	0	-0.007	0.003	15.095	-0.026	-0.026	0.000	0.000	0.000	0.000
12	D	89	GLU	-1	-0.960	-0.971	16.641	0.109	0.109	0.000	0.000	0.000	0.000
13	D	90	THR	0	-0.113	-0.052	17.974	-0.016	-0.016	0.000	0.000	0.000	0.000
14	D	91	ASP	-1	-0.967	-0.992	18.971	0.178	0.178	0.000	0.000	0.000	0.000
15	D	92	PRO	0	0.022	0.034	20.098	-0.006	-0.006	0.000	0.000	0.000	0.000
16	D	93	ASP	-1	-0.966	-0.966	21.147	0.054	0.054	0.000	0.000	0.000	0.000
17	D	94	TYR	0	0.006	0.004	19.724	0.001	0.001	0.000	0.000	0.000	0.000
18	D	95	VAL	0	0.027	-0.003	19.764	-0.003	-0.003	0.000	0.000	0.000	0.000
19	D	96	GLY	0	-0.012	-0.008	19.028	-0.012	-0.012	0.000	0.000	0.000	0.000
20	D	97	THR	0	0.006	-0.006	14.078	-0.004	-0.004	0.000	0.000	0.000	0.000
21	D	98	TYR	0	-0.053	-0.031	14.489	-0.033	-0.033	0.000	0.000	0.000	0.000
22	D	99	TYR	0	0.015	0.031	15.167	-0.046	-0.046	0.000	0.000	0.000	0.000
23	D	100	HIS	0	0.004	-0.030	11.791	-0.067	-0.067	0.000	0.000	0.000	0.000
24	D	101	LEU	0	0.047	0.025	8.044	-0.084	-0.084	0.000	0.000	0.000	0.000
25	D	102	GLY	0	0.094	-0.024	9.889	-0.166	-0.166	0.000	0.000	0.000	0.000
26	D	103	LYS	1	0.834	0.922	11.993	0.199	0.199	0.000	0.000	0.000	0.000
27	D	104	LEU	0	-0.086	-0.026	4.463	-0.101	-0.024	-0.001	-0.007	-0.069	0.000
28	D	105	TYR	0	-0.030	0.010	7.537	-0.309	-0.309	0.000	0.000	0.000	0.000
29	D	106	GLU	-1	-0.784	-0.872	9.126	-0.387	-0.387	0.000	0.000	0.000	0.000
30	D	107	ARG	1	0.878	0.944	7.273	0.493	0.493	0.000	0.000	0.000	0.000
31	D	108	LEU	0	-0.131	-0.064	3.121	-0.841	-0.499	0.023	-0.116	-0.249	-0.001
32	D	109	ASP	-1	-0.909	-0.948	7.536	-0.887	-0.887	0.000	0.000	0.000	0.000
33	D	110	ARG	1	0.882	0.955	9.779	0.637	0.637	0.000	0.000	0.000	0.000
34	D	111	THR	0	0.060	-0.008	11.568	-0.020	-0.020	0.000	0.000	0.000	0.000
35	D	112	ASP	-1	-0.934	-0.951	14.450	-0.221	-0.221	0.000	0.000	0.000	0.000
36	D	113	ASP	-1	-0.894	-0.959	13.587	-0.236	-0.236	0.000	0.000	0.000	0.000
37	D	114	ALA	0	-0.038	-0.042	12.802	0.011	0.011	0.000	0.000	0.000	0.000
38	D	115	ILE	0	-0.006	-0.006	14.081	0.037	0.037	0.000	0.000	0.000	0.000
39	D	116	ASP	-1	-0.892	-0.951	17.826	-0.124	-0.124	0.000	0.000	0.000	0.000
40	D	117	THR	0	0.009	0.004	13.388	0.033	0.033	0.000	0.000	0.000	0.000
41	D	118	TYR	0	-0.111	-0.016	14.562	0.030	0.030	0.000	0.000	0.000	0.000
42	D	119	ALA	0	0.003	0.013	16.301	0.012	0.012	0.000	0.000	0.000	0.000
43	D	120	GLN	0	0.049	0.017	19.627	0.011	0.011	0.000	0.000	0.000	0.000
44	D	121	GLY	0	-0.024	-0.029	20.492	0.016	0.016	0.000	0.000	0.000	0.000
45	D	122	ILE	0	-0.039	-0.023	21.302	0.012	0.012	0.000	0.000	0.000	0.000
46	D	123	GLU	-1	-0.936	-0.981	23.633	-0.045	-0.045	0.000	0.000	0.000	0.000
47	D	124	VAL	0	0.068	0.054	22.111	0.006	0.006	0.000	0.000	0.000	0.000
48	D	125	ALA	0	-0.059	-0.029	23.830	0.008	0.008	0.000	0.000	0.000	0.000
49	D	126	ARG	1	0.855	0.942	25.723	0.024	0.024	0.000	0.000	0.000	0.000
50	D	127	GLU	-1	-0.968	-0.983	28.328	0.005	0.005	0.000	0.000	0.000	0.000
51	D	128	GLU	-1	-0.938	-0.959	26.543	0.038	0.038	0.000	0.000	0.000	0.000
52	D	129	GLY	0	-0.039	-0.009	26.479	0.004	0.004	0.000	0.000	0.000	0.000
53	D	130	THR	0	-0.026	-0.018	26.951	-0.002	-0.002	0.000	0.000	0.000	0.000
54	D	131	GLN	0	0.112	0.032	27.741	-0.006	-0.006	0.000	0.000	0.000	0.000
55	D	132	LYS	1	0.773	0.891	24.359	-0.009	-0.009	0.000	0.000	0.000	0.000
56	D	133	ASP	-1	-0.819	-0.913	23.696	0.004	0.004	0.000	0.000	0.000	0.000
57	D	134	LEU	0	0.000	0.008	23.776	-0.007	-0.007	0.000	0.000	0.000	0.000
58	D	135	SER	0	-0.059	-0.038	25.385	-0.009	-0.009	0.000	0.000	0.000	0.000
59	D	136	GLU	-1	-0.886	-0.948	20.350	-0.040	-0.040	0.000	0.000	0.000	0.000
60	D	137	LEU	0	0.060	0.029	19.016	-0.018	-0.018	0.000	0.000	0.000	0.000
61	D	138	GLN	0	-0.066	-0.021	21.673	-0.009	-0.009	0.000	0.000	0.000	0.000
62	D	139	ASP	-1	-0.946	-0.971	23.025	-0.083	-0.083	0.000	0.000	0.000	0.000
63	D	140	ALA	0	-0.087	-0.046	18.112	-0.014	-0.014	0.000	0.000	0.000	0.000
64	D	141	LYS	1	0.958	0.955	19.819	0.091	0.091	0.000	0.000	0.000	0.000
65	D	142	LEU	0	-0.030	-0.005	20.827	-0.005	-0.005	0.000	0.000	0.000	0.000
66	D	143	LYS	1	0.851	0.934	17.706	0.217	0.217	0.000	0.000	0.000	0.000
67	D	144	ALA	0	-0.039	-0.011	17.912	-0.019	-0.019	0.000	0.000	0.000	0.000
68	D	145	GLU	-1	-0.923	-0.931	19.189	-0.138	-0.138	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:78:SER)