FMO DATABASE

FMODB ID: QY2RY

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	OptHSide
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	-404660.256741
FMO2-HF: Nuclear repulsion	377762.623321
FMO2-HF: Total energy	-26897.63342
FMO2-MP2: Total energy	-26977.822238

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.
-3.678	-0.3	0.045	-1.351	-2.071	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 : 0.010 / q_NPA : -0.008

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	0.005	-0.002	2.958	-1.773	0.931	0.029	-1.184	-1.549	0.002
4	D	81	LEU	0	0.004	0.010	4.521	-0.320	-0.061	-0.001	-0.044	-0.214	0.000
5	D	82	ALA	0	0.047	0.009	6.407	0.147	0.147	0.000	0.000	0.000	0.000
6	D	83	LEU	0	-0.092	-0.034	8.118	0.017	0.017	0.000	0.000	0.000	0.000
7	D	84	PHE	0	0.000	-0.024	8.006	-0.007	-0.007	0.000	0.000	0.000	0.000
8	D	85	GLU	-1	-0.830	-0.895	10.263	-0.273	-0.273	0.000	0.000	0.000	0.000
9	D	86	GLU	-1	-0.859	-0.924	12.910	0.298	0.298	0.000	0.000	0.000	0.000
10	D	87	LEU	0	-0.028	-0.024	13.808	-0.015	-0.015	0.000	0.000	0.000	0.000
11	D	88	VAL	0	-0.036	-0.010	15.266	-0.025	-0.025	0.000	0.000	0.000	0.000
12	D	89	GLU	-1	-0.976	-0.979	16.990	0.104	0.104	0.000	0.000	0.000	0.000
13	D	90	THR	0	-0.099	-0.049	18.393	-0.015	-0.015	0.000	0.000	0.000	0.000
14	D	91	ASP	-1	-0.982	-0.989	19.548	0.171	0.171	0.000	0.000	0.000	0.000
15	D	92	PRO	0	0.024	0.028	20.184	-0.006	-0.006	0.000	0.000	0.000	0.000
16	D	93	ASP	-1	-0.969	-0.978	21.235	0.053	0.053	0.000	0.000	0.000	0.000
17	D	94	TYR	0	0.000	0.002	19.672	0.002	0.002	0.000	0.000	0.000	0.000
18	D	95	VAL	0	0.036	0.006	19.854	-0.003	-0.003	0.000	0.000	0.000	0.000
19	D	96	GLY	0	-0.014	-0.010	19.114	-0.013	-0.013	0.000	0.000	0.000	0.000
20	D	97	THR	0	0.009	-0.012	14.343	-0.006	-0.006	0.000	0.000	0.000	0.000
21	D	98	TYR	0	-0.048	-0.021	14.570	-0.032	-0.032	0.000	0.000	0.000	0.000
22	D	99	TYR	0	-0.007	0.019	15.243	-0.045	-0.045	0.000	0.000	0.000	0.000
23	D	100	HIS	0	0.011	-0.024	11.864	-0.066	-0.066	0.000	0.000	0.000	0.000
24	D	101	LEU	0	0.044	0.027	8.362	-0.068	-0.068	0.000	0.000	0.000	0.000
25	D	102	GLY	0	0.076	-0.020	9.935	-0.163	-0.163	0.000	0.000	0.000	0.000
26	D	103	LYS	1	0.781	0.885	12.023	0.226	0.226	0.000	0.000	0.000	0.000
27	D	104	LEU	0	-0.073	-0.028	4.597	-0.077	-0.007	-0.001	-0.005	-0.064	0.000
28	D	105	TYR	0	-0.016	-0.034	7.539	-0.357	-0.357	0.000	0.000	0.000	0.000
29	D	106	GLU	-1	-0.715	-0.805	9.128	-0.383	-0.383	0.000	0.000	0.000	0.000
30	D	107	ARG	1	0.875	0.944	7.919	0.533	0.533	0.000	0.000	0.000	0.000
31	D	108	LEU	0	-0.106	-0.053	3.216	-0.870	-0.525	0.018	-0.118	-0.244	-0.001
32	D	109	ASP	-1	-0.924	-0.954	7.488	-0.924	-0.924	0.000	0.000	0.000	0.000
33	D	110	ARG	1	0.798	0.901	8.992	0.721	0.721	0.000	0.000	0.000	0.000
34	D	111	THR	0	0.042	-0.011	11.535	-0.025	-0.025	0.000	0.000	0.000	0.000
35	D	112	ASP	-1	-0.921	-0.953	14.431	-0.244	-0.244	0.000	0.000	0.000	0.000
36	D	113	ASP	-1	-0.805	-0.900	13.204	-0.307	-0.307	0.000	0.000	0.000	0.000
37	D	114	ALA	0	-0.033	-0.027	12.591	0.017	0.017	0.000	0.000	0.000	0.000
38	D	115	ILE	0	-0.024	-0.006	14.099	0.040	0.040	0.000	0.000	0.000	0.000
39	D	116	ASP	-1	-0.869	-0.936	17.845	-0.121	-0.121	0.000	0.000	0.000	0.000
40	D	117	THR	0	-0.039	-0.011	13.509	0.024	0.024	0.000	0.000	0.000	0.000
41	D	118	TYR	0	-0.074	-0.020	14.708	0.031	0.031	0.000	0.000	0.000	0.000
42	D	119	ALA	0	0.011	0.021	16.350	0.012	0.012	0.000	0.000	0.000	0.000
43	D	120	GLN	0	-0.043	-0.018	19.537	0.011	0.011	0.000	0.000	0.000	0.000
44	D	121	GLY	0	0.067	0.022	20.545	0.016	0.016	0.000	0.000	0.000	0.000
45	D	122	ILE	0	-0.019	-0.017	21.370	0.011	0.011	0.000	0.000	0.000	0.000
46	D	123	GLU	-1	-0.861	-0.942	24.433	-0.040	-0.040	0.000	0.000	0.000	0.000
47	D	124	VAL	0	0.043	0.038	22.314	0.006	0.006	0.000	0.000	0.000	0.000
48	D	125	ALA	0	-0.054	-0.022	23.976	0.008	0.008	0.000	0.000	0.000	0.000
49	D	126	ARG	1	0.734	0.877	25.799	0.029	0.029	0.000	0.000	0.000	0.000
50	D	127	GLU	-1	-0.950	-0.978	28.424	0.000	0.000	0.000	0.000	0.000	0.000
51	D	128	GLU	-1	-0.927	-0.955	26.600	0.034	0.034	0.000	0.000	0.000	0.000
52	D	129	GLY	0	-0.040	-0.015	26.558	0.004	0.004	0.000	0.000	0.000	0.000
53	D	130	THR	0	-0.053	-0.057	27.029	-0.002	-0.002	0.000	0.000	0.000	0.000
54	D	131	GLN	0	0.087	0.017	27.812	-0.007	-0.007	0.000	0.000	0.000	0.000
55	D	132	LYS	1	0.731	0.856	23.216	0.007	0.007	0.000	0.000	0.000	0.000
56	D	133	ASP	-1	-0.795	-0.858	23.674	-0.002	-0.002	0.000	0.000	0.000	0.000
57	D	134	LEU	0	0.020	0.020	23.840	-0.008	-0.008	0.000	0.000	0.000	0.000
58	D	135	SER	0	-0.055	-0.037	25.439	-0.009	-0.009	0.000	0.000	0.000	0.000
59	D	136	GLU	-1	-0.852	-0.931	20.456	-0.040	-0.040	0.000	0.000	0.000	0.000
60	D	137	LEU	0	0.054	0.023	19.315	-0.018	-0.018	0.000	0.000	0.000	0.000
61	D	138	GLN	0	-0.050	-0.015	21.713	-0.011	-0.011	0.000	0.000	0.000	0.000
62	D	139	ASP	-1	-0.932	-0.970	22.934	-0.089	-0.089	0.000	0.000	0.000	0.000
63	D	140	ALA	0	-0.081	-0.038	18.032	-0.015	-0.015	0.000	0.000	0.000	0.000
64	D	141	LYS	1	0.897	0.922	19.836	0.101	0.101	0.000	0.000	0.000	0.000
65	D	142	LEU	0	0.000	0.012	20.852	-0.007	-0.007	0.000	0.000	0.000	0.000
66	D	143	LYS	1	0.789	0.879	17.151	0.257	0.257	0.000	0.000	0.000	0.000
67	D	144	ALA	0	-0.075	-0.020	17.781	-0.023	-0.023	0.000	0.000	0.000	0.000
68	D	145	GLU	-1	-0.861	-0.899	19.189	-0.149	-0.149	0.000	0.000	0.000	0.000

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