FMO DATABASE

FMODB ID: MV6GZ

Calculation Name: 4XD9-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XD9

Chain ID: B

ChEMBL ID:

UniProt ID: C8VMF9

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptAll
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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-467741.445444
FMO2-HF: Nuclear repulsion	435180.678035
FMO2-HF: Total energy	-32560.767409
FMO2-MP2: Total energy	-32657.349027

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(B:17:GLU)

Summations of interaction energy for fragment #1(B:17: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.
-14.458	-10.688	-0.027	-2.042	-1.701	0.002

Interaction energy analysis for fragmet #1(B:17:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.943 / q_NPA : -0.975

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	B	19	LEU	0	0.004	0.000	3.705	-10.556	-6.908	-0.026	-2.039	-1.584	0.002
4	B	20	PRO	0	-0.014	0.011	5.028	3.546	3.668	-0.001	-0.003	-0.117	0.000
5	B	21	ILE	0	0.057	0.027	6.307	-2.400	-2.400	0.000	0.000	0.000	0.000
6	B	22	THR	0	-0.010	0.006	8.551	-1.489	-1.489	0.000	0.000	0.000	0.000
7	B	23	VAL	0	-0.018	-0.013	10.850	0.047	0.047	0.000	0.000	0.000	0.000
8	B	24	SER	0	-0.032	-0.015	14.402	0.093	0.093	0.000	0.000	0.000	0.000
9	B	25	LYS	1	0.814	0.906	16.481	-13.577	-13.577	0.000	0.000	0.000	0.000
10	B	26	PRO	0	0.003	-0.004	20.211	0.058	0.058	0.000	0.000	0.000	0.000
11	B	27	THR	0	-0.002	0.012	23.413	-0.369	-0.369	0.000	0.000	0.000	0.000
12	B	28	PRO	0	-0.014	0.003	21.523	0.406	0.406	0.000	0.000	0.000	0.000
13	B	29	TYR	0	0.001	-0.043	18.889	-0.159	-0.159	0.000	0.000	0.000	0.000
14	B	30	THR	0	-0.025	-0.002	22.366	-0.084	-0.084	0.000	0.000	0.000	0.000
15	B	31	PHE	0	0.025	-0.016	19.182	0.180	0.180	0.000	0.000	0.000	0.000
16	B	32	ASP	-1	-0.703	-0.790	24.981	9.077	9.077	0.000	0.000	0.000	0.000
17	B	33	LEU	0	0.023	0.007	21.785	-0.105	-0.105	0.000	0.000	0.000	0.000
18	B	34	GLY	0	0.043	0.038	25.457	0.063	0.063	0.000	0.000	0.000	0.000
19	B	35	HIS	0	-0.100	-0.066	28.703	-0.388	-0.388	0.000	0.000	0.000	0.000
20	B	36	LEU	0	-0.051	-0.026	23.660	0.078	0.078	0.000	0.000	0.000	0.000
21	B	37	LEU	0	0.006	0.018	24.787	0.251	0.251	0.000	0.000	0.000	0.000
22	B	38	ALA	0	0.012	-0.018	22.103	0.257	0.257	0.000	0.000	0.000	0.000
23	B	39	ASN	0	-0.036	-0.012	24.061	-0.410	-0.410	0.000	0.000	0.000	0.000
24	B	40	ASP	-1	-0.722	-0.839	22.127	12.832	12.832	0.000	0.000	0.000	0.000
25	B	41	PRO	0	-0.025	-0.010	24.391	-0.299	-0.299	0.000	0.000	0.000	0.000
26	B	42	ASN	0	-0.043	-0.027	22.983	-0.347	-0.347	0.000	0.000	0.000	0.000
27	B	43	PRO	0	0.025	0.003	26.439	-0.151	-0.151	0.000	0.000	0.000	0.000
28	B	44	LEU	0	-0.014	-0.002	26.685	0.350	0.350	0.000	0.000	0.000	0.000
29	B	45	GLU	-1	-0.920	-0.954	25.036	10.162	10.162	0.000	0.000	0.000	0.000
30	B	46	LEU	0	-0.041	-0.033	26.778	0.151	0.151	0.000	0.000	0.000	0.000
31	B	47	PRO	0	0.032	0.025	26.105	-0.383	-0.383	0.000	0.000	0.000	0.000
32	B	48	LYS	1	0.955	0.959	29.435	-8.056	-8.056	0.000	0.000	0.000	0.000
33	B	49	SER	0	-0.052	-0.049	28.397	-0.274	-0.274	0.000	0.000	0.000	0.000
34	B	50	GLU	-1	-0.861	-0.887	25.722	11.095	11.095	0.000	0.000	0.000	0.000
35	B	51	PRO	0	-0.016	-0.015	27.333	-0.268	-0.268	0.000	0.000	0.000	0.000
36	B	52	LEU	0	0.065	0.034	28.019	0.335	0.335	0.000	0.000	0.000	0.000
37	B	53	ASN	0	0.016	-0.010	28.140	0.149	0.149	0.000	0.000	0.000	0.000
38	B	54	ALA	0	-0.005	0.004	24.268	0.334	0.334	0.000	0.000	0.000	0.000
39	B	55	SER	0	0.051	0.033	23.422	0.582	0.582	0.000	0.000	0.000	0.000
40	B	56	LEU	0	0.005	0.005	24.119	0.307	0.307	0.000	0.000	0.000	0.000
41	B	57	LYS	1	0.955	0.979	20.255	-12.624	-12.624	0.000	0.000	0.000	0.000
42	B	58	ALA	0	-0.007	0.000	19.495	0.557	0.557	0.000	0.000	0.000	0.000
43	B	59	THR	0	0.024	0.008	19.379	0.544	0.544	0.000	0.000	0.000	0.000
44	B	60	ALA	0	-0.003	-0.006	20.945	0.225	0.225	0.000	0.000	0.000	0.000
45	B	61	ARG	1	0.811	0.902	12.084	-18.169	-18.169	0.000	0.000	0.000	0.000
46	B	62	ASP	-1	-0.763	-0.873	16.188	16.499	16.499	0.000	0.000	0.000	0.000
47	B	63	GLY	0	0.028	0.023	17.305	0.281	0.281	0.000	0.000	0.000	0.000
48	B	64	VAL	0	0.001	-0.009	17.342	-0.011	-0.011	0.000	0.000	0.000	0.000
49	B	65	GLN	0	-0.036	-0.006	10.820	0.728	0.728	0.000	0.000	0.000	0.000
50	B	66	SER	0	-0.014	-0.019	14.788	0.587	0.587	0.000	0.000	0.000	0.000
51	B	67	LEU	0	-0.004	-0.003	16.631	0.039	0.039	0.000	0.000	0.000	0.000
52	B	68	LEU	0	-0.004	0.004	13.815	-0.170	-0.170	0.000	0.000	0.000	0.000
53	B	69	ASN	0	0.003	-0.007	11.589	0.534	0.534	0.000	0.000	0.000	0.000
54	B	70	GLN	0	0.015	0.030	14.286	0.517	0.517	0.000	0.000	0.000	0.000
55	B	71	LEU	0	-0.020	-0.010	17.678	-0.355	-0.355	0.000	0.000	0.000	0.000
56	B	72	LEU	0	-0.013	-0.018	13.391	-0.279	-0.279	0.000	0.000	0.000	0.000
57	B	73	THR	0	-0.058	-0.030	14.374	0.581	0.581	0.000	0.000	0.000	0.000
58	B	74	THR	0	-0.085	-0.063	16.256	-0.514	-0.514	0.000	0.000	0.000	0.000
59	B	75	CYS	0	-0.024	0.016	20.089	-0.762	-0.762	0.000	0.000	0.000	0.000
60	B	76	PRO	0	-0.002	0.000	20.932	0.427	0.427	0.000	0.000	0.000	0.000
61	B	77	ILE	0	0.023	0.027	17.327	-0.391	-0.391	0.000	0.000	0.000	0.000
62	B	78	THR	0	0.002	0.012	21.897	-0.199	-0.199	0.000	0.000	0.000	0.000
63	B	79	SER	0	-0.012	-0.014	22.566	0.229	0.229	0.000	0.000	0.000	0.000
64	B	80	SER	0	-0.026	-0.012	24.648	-0.348	-0.348	0.000	0.000	0.000	0.000
65	B	81	GLN	0	0.012	0.003	27.817	0.163	0.163	0.000	0.000	0.000	0.000
66	B	82	GLN	0	0.000	-0.009	30.500	0.085	0.085	0.000	0.000	0.000	0.000
67	B	83	GLY	0	0.020	0.024	26.624	-0.027	-0.027	0.000	0.000	0.000	0.000
68	B	84	VAL	0	-0.022	-0.015	20.217	0.000	0.000	0.000	0.000	0.000	0.000
69	B	85	LEU	0	-0.018	-0.010	23.611	-0.042	-0.042	0.000	0.000	0.000	0.000
70	B	86	LEU	0	0.016	0.011	19.242	0.204	0.204	0.000	0.000	0.000	0.000
71	B	87	THR	0	-0.033	-0.032	23.304	-0.555	-0.555	0.000	0.000	0.000	0.000
72	B	88	LEU	0	0.000	-0.005	24.195	0.212	0.212	0.000	0.000	0.000	0.000
73	B	89	PRO	0	-0.005	0.006	25.360	-0.308	-0.308	0.000	0.000	0.000	0.000
74	B	90	ALA	0	0.009	-0.009	28.412	-0.094	-0.094	0.000	0.000	0.000	0.000
75	B	91	PRO	0	-0.043	-0.021	31.105	0.129	0.129	0.000	0.000	0.000	0.000
76	B	92	SER	0	-0.050	-0.037	30.363	-0.199	-0.199	0.000	0.000	0.000	0.000
77	B	93	THR	0	-0.052	-0.053	31.553	-0.180	-0.180	0.000	0.000	0.000	0.000
78	B	94	ILE	0	-0.016	-0.011	34.067	-0.118	-0.118	0.000	0.000	0.000	0.000
79	B	95	LEU	0	0.014	0.010	35.649	-0.044	-0.044	0.000	0.000	0.000	0.000
80	B	96	PRO	0	-0.019	-0.001	39.609	-0.112	-0.112	0.000	0.000	0.000	0.000
81	B	97	ARG	1	0.876	0.917	42.925	-6.372	-6.372	0.000	0.000	0.000	0.000
82	B	98	HIS	0	0.061	0.032	44.867	-0.127	-0.127	0.000	0.000	0.000	0.000
83	B	99	LYS	1	0.918	0.956	46.786	-6.116	-6.116	0.000	0.000	0.000	0.000
84	B	100	PRO	0	0.084	0.044	48.668	0.130	0.130	0.000	0.000	0.000	0.000
85	B	101	LEU	0	0.009	0.009	46.828	0.072	0.072	0.000	0.000	0.000	0.000
86	B	102	PRO	0	0.000	-0.007	49.317	-0.097	-0.097	0.000	0.000	0.000	0.000
87	B	103	THR	0	0.007	0.009	52.467	0.007	0.007	0.000	0.000	0.000	0.000
88	B	104	PRO	0	0.008	0.020	53.998	-0.033	-0.033	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:17:GLU)