FMO DATABASE

FMODB ID: 98YG2

Calculation Name: 3DML-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DML

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KM22

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-705665.201911
FMO2-HF: Nuclear repulsion	667365.788441
FMO2-HF: Total energy	-38299.41347
FMO2-MP2: Total energy	-38408.548823

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:GLU)

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

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.
94.862	99.559	3.798	-2.401	-6.091	0.038

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.919 / q_NPA : -0.988

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	A	4	ARG	1	0.805	0.885	3.817	-46.267	-44.799	-0.012	-0.617	-0.839	0.002
4	A	5	LEU	0	-0.005	0.007	6.446	-0.172	-0.172	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.004	0.009	10.209	-2.151	-2.151	0.000	0.000	0.000	0.000
6	A	7	MET	0	-0.028	0.006	12.404	-0.407	-0.407	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.002	-0.007	14.575	-0.780	-0.780	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.831	-0.955	18.681	13.917	13.917	0.000	0.000	0.000	0.000
9	A	10	GLN	0	0.014	0.000	21.925	-0.398	-0.398	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.025	0.002	25.386	-0.103	-0.103	0.000	0.000	0.000	0.000
11	A	12	GLY	0	0.002	0.005	28.461	-0.134	-0.134	0.000	0.000	0.000	0.000
12	A	13	CYS	0	-0.041	0.021	25.741	-0.196	-0.196	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.032	0.014	27.519	0.215	0.215	0.000	0.000	0.000	0.000
14	A	15	TYR	0	0.016	-0.007	25.937	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	16	CYS	0	0.004	-0.002	23.213	0.494	0.494	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.026	0.023	23.771	0.273	0.273	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.902	0.955	26.249	-10.649	-10.649	0.000	0.000	0.000	0.000
18	A	19	TRP	0	0.062	0.032	16.115	-0.065	-0.065	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.817	-0.908	21.167	14.738	14.738	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.046	-0.019	22.813	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.884	-0.913	24.858	11.698	11.698	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.005	0.025	18.544	0.122	0.122	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.037	-0.023	18.626	0.529	0.529	0.000	0.000	0.000	0.000
24	A	25	PRO	0	-0.035	-0.015	18.968	0.491	0.491	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.042	-0.041	20.467	0.254	0.254	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.017	-0.009	11.274	-0.161	-0.161	0.000	0.000	0.000	0.000
27	A	28	PRO	0	-0.017	0.004	14.036	1.132	1.132	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.042	-0.024	15.062	0.287	0.287	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.018	-0.001	15.753	-0.248	-0.248	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.838	-0.932	13.485	20.529	20.529	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.870	-0.947	11.642	22.821	22.821	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.017	-0.006	10.879	2.277	2.277	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.756	0.861	10.552	-20.096	-20.096	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.022	0.008	7.378	2.278	2.278	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.012	0.012	6.011	7.017	7.017	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.022	0.035	6.224	-4.435	-4.435	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.005	0.003	8.908	1.077	1.077	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.049	-0.026	9.516	0.375	0.375	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.826	0.904	12.628	-15.431	-15.431	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.008	-0.002	13.912	-0.067	-0.067	0.000	0.000	0.000	0.000
41	A	42	GLN	0	0.052	0.025	17.693	-0.793	-0.793	0.000	0.000	0.000	0.000
42	A	43	MET	0	-0.032	-0.018	20.817	0.215	0.215	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.812	0.889	22.003	-11.446	-11.446	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.893	-0.923	20.953	12.819	12.819	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.052	-0.035	20.793	0.357	0.357	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.030	0.015	15.126	0.176	0.176	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.006	-0.002	13.009	-0.536	-0.536	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.005	-0.022	14.132	0.566	0.566	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.011	-0.001	11.686	0.863	0.863	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.023	0.008	8.882	1.762	1.762	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.917	-0.955	10.524	18.789	18.789	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.027	-0.026	11.358	1.803	1.803	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.006	-0.002	13.770	-1.027	-1.027	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.802	0.865	15.196	-17.285	-17.285	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.037	0.026	17.721	0.681	0.681	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.046	0.029	17.698	0.074	0.074	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.008	-0.012	20.291	-0.420	-0.420	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.030	-0.008	22.595	-0.803	-0.803	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.017	0.056	22.249	0.491	0.491	0.000	0.000	0.000	0.000
60	A	61	PRO	0	0.028	-0.010	20.664	-0.759	-0.759	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.032	-0.037	16.984	-0.323	-0.323	0.000	0.000	0.000	0.000
62	A	63	PHE	0	-0.004	-0.016	15.037	0.044	0.044	0.000	0.000	0.000	0.000
63	A	64	VAL	0	0.003	-0.010	10.982	-0.274	-0.274	0.000	0.000	0.000	0.000
64	A	65	LEU	0	0.006	0.023	7.334	0.141	0.141	0.000	0.000	0.000	0.000
65	A	66	MET	0	-0.048	-0.008	6.727	-2.451	-2.451	0.000	0.000	0.000	0.000
66	A	67	ALA	0	0.067	0.032	2.631	-2.135	0.399	1.380	-1.754	-2.159	0.023
67	A	68	GLY	0	0.047	0.016	2.438	-10.488	-9.477	2.367	-0.684	-2.693	0.013
68	A	69	ASP	-1	-0.931	-0.949	3.077	29.127	28.655	0.064	0.655	-0.247	0.000
69	A	70	VAL	0	0.015	0.006	6.268	-5.566	-5.566	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.771	-0.855	6.850	26.366	26.366	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.038	-0.013	6.536	-2.291	-2.291	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.010	-0.021	8.617	-2.964	-2.964	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.721	0.813	11.727	-18.167	-18.167	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.026	0.003	14.397	-1.027	-1.027	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.825	-0.884	17.399	15.674	15.674	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.018	0.004	20.490	-0.596	-0.596	0.000	0.000	0.000	0.000
77	A	78	TYR	0	-0.072	-0.080	21.750	0.892	0.892	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.018	-0.016	23.921	-0.526	-0.526	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.040	0.029	25.149	-0.561	-0.561	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.833	-0.922	23.357	13.407	13.407	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.914	-0.957	22.639	12.814	12.814	0.000	0.000	0.000	0.000
82	A	83	PHE	0	-0.084	-0.047	23.392	0.106	0.106	0.000	0.000	0.000	0.000
83	A	84	PHE	0	0.003	-0.009	15.794	0.597	0.597	0.000	0.000	0.000	0.000
84	A	85	TRP	0	0.082	0.032	16.166	1.215	1.215	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.030	0.031	17.218	1.066	1.066	0.000	0.000	0.000	0.000
86	A	87	MET	0	-0.064	-0.039	17.665	0.386	0.386	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.016	0.017	11.862	0.986	0.986	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.054	0.030	12.944	2.100	2.100	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.853	0.928	13.192	-18.859	-18.859	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.058	-0.025	11.213	0.700	0.700	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.047	0.007	7.977	2.505	2.505	0.000	0.000	0.000	0.000
92	A	93	GLY	0	0.015	0.014	8.506	2.721	2.721	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.075	-0.032	10.703	-2.010	-2.010	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.039	-0.019	5.612	-0.267	-0.267	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-1.008	-0.979	5.061	48.266	48.422	-0.001	-0.001	-0.153	0.000

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