FMO DATABASE

FMODB ID: 6Y8QZ

Calculation Name: 4C92-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C92

Chain ID: B

ChEMBL ID:

UniProt ID: P47017

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	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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-794136.619716
FMO2-HF: Nuclear repulsion	751461.985543
FMO2-HF: Total energy	-42674.634173
FMO2-MP2: Total energy	-42799.422784

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:-9:SER)

Summations of interaction energy for fragment #1(B:-9: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.
-7.125	-4.197	2.621	-2.529	-3.019	0.016

Interaction energy analysis for fragmet #1(B:-9: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 : 0.004

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	B	-7	ASN	0	-0.043	-0.055	3.853	-0.084	1.812	-0.022	-0.943	-0.931	0.003
4	B	-6	LEU	0	0.026	0.021	6.823	-0.094	-0.094	0.000	0.000	0.000	0.000
5	B	-5	TYR	0	0.016	-0.005	10.154	0.038	0.038	0.000	0.000	0.000	0.000
6	B	-4	PHE	0	-0.014	-0.031	8.499	0.192	0.192	0.000	0.000	0.000	0.000
7	B	-3	GLN	0	0.047	0.037	9.405	-0.193	-0.193	0.000	0.000	0.000	0.000
8	B	-2	GLY	0	0.011	0.007	11.645	-0.108	-0.108	0.000	0.000	0.000	0.000
9	B	-1	SER	0	-0.045	-0.018	12.670	0.061	0.061	0.000	0.000	0.000	0.000
10	B	0	GLY	0	0.114	0.075	14.346	0.066	0.066	0.000	0.000	0.000	0.000
11	B	1	SER	0	-0.069	-0.057	15.513	-0.028	-0.028	0.000	0.000	0.000	0.000
12	B	2	LEU	0	0.004	0.051	13.199	-0.029	-0.029	0.000	0.000	0.000	0.000
13	B	3	PHE	0	0.044	0.003	14.977	-0.022	-0.022	0.000	0.000	0.000	0.000
14	B	4	PHE	0	0.076	0.036	18.223	-0.013	-0.013	0.000	0.000	0.000	0.000
15	B	5	SER	0	-0.051	-0.030	13.844	-0.027	-0.027	0.000	0.000	0.000	0.000
16	B	6	PHE	0	-0.022	-0.009	15.892	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	7	PHE	0	0.035	-0.001	16.698	-0.004	-0.004	0.000	0.000	0.000	0.000
18	B	8	LYS	1	0.802	0.900	17.048	0.372	0.372	0.000	0.000	0.000	0.000
19	B	9	THR	0	-0.036	-0.016	15.189	-0.029	-0.029	0.000	0.000	0.000	0.000
20	B	10	LEU	0	-0.053	-0.015	17.906	0.015	0.015	0.000	0.000	0.000	0.000
21	B	11	VAL	0	-0.006	0.003	21.038	0.019	0.019	0.000	0.000	0.000	0.000
22	B	12	ASP	-1	-0.906	-0.960	23.181	-0.160	-0.160	0.000	0.000	0.000	0.000
23	B	13	GLN	0	-0.074	-0.026	22.510	0.027	0.027	0.000	0.000	0.000	0.000
24	B	14	GLU	-1	-0.849	-0.902	25.714	-0.040	-0.040	0.000	0.000	0.000	0.000
25	B	15	VAL	0	-0.010	-0.010	25.576	0.005	0.005	0.000	0.000	0.000	0.000
26	B	16	VAL	0	0.007	0.000	28.592	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	17	VAL	0	-0.025	-0.005	29.237	0.003	0.003	0.000	0.000	0.000	0.000
28	B	18	GLU	-1	-0.744	-0.839	31.511	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	19	LEU	0	0.015	0.005	33.069	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	20	LYS	1	0.792	0.856	32.294	0.029	0.029	0.000	0.000	0.000	0.000
31	B	21	ASN	0	-0.057	-0.022	36.956	0.001	0.001	0.000	0.000	0.000	0.000
32	B	22	ASP	-1	-0.810	-0.882	38.453	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	23	ILE	0	-0.036	0.009	38.470	0.000	0.000	0.000	0.000	0.000	0.000
34	B	24	GLU	-1	-0.893	-0.951	35.163	-0.014	-0.014	0.000	0.000	0.000	0.000
35	B	25	ILE	0	-0.033	-0.035	34.854	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	26	LYS	1	0.841	0.914	33.187	0.032	0.032	0.000	0.000	0.000	0.000
37	B	27	GLY	0	0.021	-0.004	32.193	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	28	THR	0	-0.003	0.014	28.933	0.001	0.001	0.000	0.000	0.000	0.000
39	B	29	LEU	0	-0.011	-0.007	23.828	0.000	0.000	0.000	0.000	0.000	0.000
40	B	30	GLN	0	-0.016	-0.012	26.553	-0.022	-0.022	0.000	0.000	0.000	0.000
41	B	31	SER	0	-0.047	-0.033	25.624	-0.013	-0.013	0.000	0.000	0.000	0.000
42	B	32	VAL	0	0.023	0.012	22.249	0.016	0.016	0.000	0.000	0.000	0.000
43	B	33	ASP	-1	-0.778	-0.874	24.376	-0.159	-0.159	0.000	0.000	0.000	0.000
44	B	34	GLN	0	0.013	-0.002	22.486	-0.010	-0.010	0.000	0.000	0.000	0.000
45	B	35	PHE	0	-0.078	-0.039	23.495	0.008	0.008	0.000	0.000	0.000	0.000
46	B	36	LEU	0	-0.020	-0.008	21.558	0.018	0.018	0.000	0.000	0.000	0.000
47	B	37	ASN	0	-0.079	-0.052	25.573	0.027	0.027	0.000	0.000	0.000	0.000
48	B	38	LEU	0	0.014	0.012	25.585	-0.014	-0.014	0.000	0.000	0.000	0.000
49	B	39	LYS	1	0.875	0.933	28.812	0.141	0.141	0.000	0.000	0.000	0.000
50	B	40	LEU	0	0.026	0.023	29.697	-0.006	-0.006	0.000	0.000	0.000	0.000
51	B	41	ASP	-1	-0.769	-0.890	32.037	-0.101	-0.101	0.000	0.000	0.000	0.000
52	B	42	ASN	0	-0.062	-0.045	33.826	0.006	0.006	0.000	0.000	0.000	0.000
53	B	43	ILE	0	-0.008	0.001	34.891	0.003	0.003	0.000	0.000	0.000	0.000
54	B	44	SER	0	-0.036	-0.016	36.903	0.004	0.004	0.000	0.000	0.000	0.000
55	B	45	CYS	0	-0.019	-0.010	37.733	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	46	THR	0	0.017	0.016	39.527	0.002	0.002	0.000	0.000	0.000	0.000
57	B	47	ASP	-1	-0.867	-0.932	41.788	-0.027	-0.027	0.000	0.000	0.000	0.000
58	B	48	GLU	-1	-0.858	-0.952	44.311	-0.018	-0.018	0.000	0.000	0.000	0.000
59	B	49	LYS	1	0.924	0.943	46.765	0.010	0.010	0.000	0.000	0.000	0.000
60	B	50	LYS	1	0.881	0.964	46.176	0.024	0.024	0.000	0.000	0.000	0.000
61	B	51	TYR	0	-0.013	-0.006	44.127	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	52	PRO	0	0.014	0.024	48.426	0.001	0.001	0.000	0.000	0.000	0.000
63	B	53	HIS	0	0.108	0.041	44.604	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	54	LEU	0	-0.012	0.006	45.111	0.000	0.000	0.000	0.000	0.000	0.000
65	B	55	GLY	0	0.026	0.011	45.448	-0.003	-0.003	0.000	0.000	0.000	0.000
66	B	56	SER	0	-0.030	-0.010	46.069	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	57	VAL	0	-0.001	0.003	40.528	-0.004	-0.004	0.000	0.000	0.000	0.000
68	B	58	ARG	1	0.856	0.924	38.992	0.054	0.054	0.000	0.000	0.000	0.000
69	B	59	ASN	0	0.032	0.017	35.247	0.004	0.004	0.000	0.000	0.000	0.000
70	B	60	ILE	0	-0.021	0.000	35.225	0.003	0.003	0.000	0.000	0.000	0.000
71	B	61	PHE	0	-0.009	-0.006	31.596	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	62	ILE	0	0.027	0.017	32.003	0.007	0.007	0.000	0.000	0.000	0.000
73	B	63	ARG	1	0.950	0.978	31.727	0.068	0.068	0.000	0.000	0.000	0.000
74	B	64	GLY	0	0.143	0.075	29.416	0.008	0.008	0.000	0.000	0.000	0.000
75	B	65	SER	0	-0.009	-0.008	30.267	0.006	0.006	0.000	0.000	0.000	0.000
76	B	66	THR	0	-0.087	-0.056	32.320	0.008	0.008	0.000	0.000	0.000	0.000
77	B	67	VAL	0	0.052	0.041	29.161	0.004	0.004	0.000	0.000	0.000	0.000
78	B	68	ARG	1	0.682	0.817	31.992	0.007	0.007	0.000	0.000	0.000	0.000
79	B	69	TYR	0	-0.005	-0.006	28.876	0.007	0.007	0.000	0.000	0.000	0.000
80	B	70	VAL	0	0.015	-0.005	25.917	-0.009	-0.009	0.000	0.000	0.000	0.000
81	B	71	TYR	0	-0.069	-0.033	26.447	0.011	0.011	0.000	0.000	0.000	0.000
82	B	72	LEU	0	0.017	-0.003	21.807	-0.011	-0.011	0.000	0.000	0.000	0.000
83	B	73	ASN	0	0.013	-0.005	24.545	0.018	0.018	0.000	0.000	0.000	0.000
84	B	74	LYS	1	0.909	0.939	17.432	-0.081	-0.081	0.000	0.000	0.000	0.000
85	B	75	ASN	0	-0.032	-0.035	19.861	0.013	0.013	0.000	0.000	0.000	0.000
86	B	76	MET	0	0.006	0.037	19.757	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	77	VAL	0	0.033	0.024	16.014	-0.017	-0.017	0.000	0.000	0.000	0.000
88	B	78	ASP	-1	-0.749	-0.848	10.858	0.213	0.213	0.000	0.000	0.000	0.000
89	B	79	THR	0	0.023	-0.008	13.034	0.021	0.021	0.000	0.000	0.000	0.000
90	B	80	ASN	0	-0.109	-0.055	10.220	0.095	0.095	0.000	0.000	0.000	0.000
91	B	81	LEU	0	0.062	0.017	6.697	0.208	0.208	0.000	0.000	0.000	0.000
92	B	82	LEU	0	0.034	0.031	9.245	0.073	0.073	0.000	0.000	0.000	0.000
93	B	83	GLN	0	0.014	0.022	11.893	0.072	0.072	0.000	0.000	0.000	0.000
94	B	84	ASP	-1	-0.871	-0.909	5.474	3.704	3.702	-0.001	-0.001	0.004	0.000
95	B	85	ALA	0	0.038	0.017	8.535	0.066	0.066	0.000	0.000	0.000	0.000
96	B	86	THR	0	-0.009	-0.021	9.865	-0.133	-0.133	0.000	0.000	0.000	0.000
97	B	87	ARG	1	0.866	0.928	9.553	-0.885	-0.885	0.000	0.000	0.000	0.000
98	B	88	ARG	1	0.820	0.906	2.218	-9.964	-8.930	2.644	-1.585	-2.092	0.013
99	B	89	GLU	-1	-0.816	-0.923	9.751	-0.188	-0.188	0.000	0.000	0.000	0.000
100	B	90	VAL	0	-0.036	-0.014	13.359	-0.047	-0.047	0.000	0.000	0.000	0.000
101	B	91	MET	0	-0.047	-0.029	10.282	-0.070	-0.070	0.000	0.000	0.000	0.000
102	B	92	THR	0	-0.070	-0.057	11.824	-0.068	-0.068	0.000	0.000	0.000	0.000
103	B	93	GLU	-1	-0.831	-0.912	14.407	-0.149	-0.149	0.000	0.000	0.000	0.000
104	B	94	ARG	1	0.887	0.973	15.483	-0.129	-0.129	0.000	0.000	0.000	0.000
105	B	95	DLY	1	0.910	0.959	17.571	0.097	0.097	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:-9:SER)