FMO DATABASE

FMODB ID: 6NN6Z

Calculation Name: 4DAM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DAM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KYI9

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:

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-783656.692865
FMO2-HF: Nuclear repulsion	740635.522564
FMO2-HF: Total energy	-43021.170301
FMO2-MP2: Total energy	-43146.771779

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:0:SER)

Summations of interaction energy for fragment #1(A:0: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.
-6.144	-1.148	0.485	-2.639	-2.842	0.002

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / 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	A	2	ASN	0	0.002	-0.002	3.767	-3.321	0.484	-0.043	-2.093	-1.669	0.003
4	A	3	GLU	-1	-0.841	-0.891	2.314	-5.192	-4.068	0.530	-0.541	-1.113	-0.001
5	A	4	ILE	0	0.009	0.006	5.343	0.246	0.242	-0.001	-0.001	0.006	0.000
6	A	5	MET	0	-0.042	-0.001	7.298	-0.197	-0.197	0.000	0.000	0.000	0.000
7	A	6	ILE	0	-0.005	-0.006	9.547	0.054	0.054	0.000	0.000	0.000	0.000
8	A	7	CYS	0	-0.017	-0.017	13.130	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	8	ALA	0	-0.026	-0.003	15.888	0.010	0.010	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.043	0.014	18.752	0.002	0.002	0.000	0.000	0.000	0.000
11	A	10	GLY	0	-0.012	-0.011	22.166	0.002	0.002	0.000	0.000	0.000	0.000
12	A	11	ASN	0	-0.020	-0.002	24.401	0.001	0.001	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.013	0.026	24.202	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.002	-0.007	25.792	0.007	0.007	0.000	0.000	0.000	0.000
15	A	14	THR	0	-0.020	-0.021	26.122	0.001	0.001	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.021	0.000	27.087	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	16	PRO	0	-0.023	-0.002	24.174	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.034	-0.008	24.548	0.008	0.008	0.000	0.000	0.000	0.000
19	A	18	PHE	0	0.019	0.006	23.261	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.904	0.942	23.088	0.036	0.036	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.809	-0.908	22.950	0.004	0.004	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.084	-0.034	19.314	0.001	0.001	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.054	0.017	21.811	0.006	0.006	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.022	-0.010	16.652	0.031	0.031	0.000	0.000	0.000	0.000
25	A	24	GLY	0	-0.023	-0.012	17.692	0.010	0.010	0.000	0.000	0.000	0.000
26	A	25	PRO	0	0.030	0.025	19.905	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	26	SER	0	-0.038	-0.010	18.636	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	27	VAL	0	0.024	0.006	19.047	0.010	0.010	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.943	0.980	19.022	0.054	0.054	0.000	0.000	0.000	0.000
30	A	29	PHE	0	0.019	-0.001	20.093	0.015	0.015	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.960	1.001	21.194	0.076	0.076	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.012	0.016	19.476	0.007	0.007	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.003	-0.002	22.782	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	33	VAL	0	0.016	-0.002	20.932	0.003	0.003	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.004	-0.002	24.371	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	35	ALA	0	-0.020	-0.005	26.517	0.001	0.001	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.949	0.973	27.917	0.070	0.070	0.000	0.000	0.000	0.000
38	A	37	TYR	0	-0.006	-0.008	31.000	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	38	TRP	0	0.037	0.022	33.618	0.001	0.001	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.818	-0.916	36.758	-0.040	-0.040	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.813	0.870	38.397	0.043	0.043	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.817	-0.875	43.011	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.842	0.907	40.166	0.042	0.042	0.000	0.000	0.000	0.000
44	A	43	ASN	0	-0.032	0.002	42.872	0.000	0.000	0.000	0.000	0.000	0.000
45	A	44	ALA	0	0.015	0.009	40.275	0.001	0.001	0.000	0.000	0.000	0.000
46	A	45	TRP	0	-0.020	-0.003	32.953	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.002	-0.003	36.025	0.002	0.002	0.000	0.000	0.000	0.000
48	A	47	ASP	-1	-0.906	-0.952	32.896	-0.058	-0.058	0.000	0.000	0.000	0.000
49	A	48	GLY	0	-0.032	-0.023	31.253	0.002	0.002	0.000	0.000	0.000	0.000
50	A	49	HIS	0	-0.012	0.000	25.115	0.007	0.007	0.000	0.000	0.000	0.000
51	A	50	THR	0	0.025	0.018	26.744	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	51	ASN	0	-0.006	0.007	21.452	0.004	0.004	0.000	0.000	0.000	0.000
53	A	52	PHE	0	-0.018	-0.026	23.228	0.003	0.003	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.006	0.001	17.235	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	54	THR	0	-0.043	-0.009	18.758	0.026	0.026	0.000	0.000	0.000	0.000
56	A	55	VAL	0	-0.010	0.003	16.234	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	56	TRP	0	0.031	0.012	14.458	0.053	0.053	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.045	0.016	14.677	-0.037	-0.037	0.000	0.000	0.000	0.000
59	A	58	ASN	0	0.012	-0.008	13.437	0.048	0.048	0.000	0.000	0.000	0.000
60	A	59	ARG	1	0.965	0.984	13.781	-0.103	-0.103	0.000	0.000	0.000	0.000
61	A	60	GLN	0	0.043	0.010	17.717	0.000	0.000	0.000	0.000	0.000	0.000
62	A	61	LEU	0	-0.002	0.011	15.096	0.000	0.000	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.007	-0.004	18.362	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	63	THR	0	0.014	0.013	19.950	0.004	0.004	0.000	0.000	0.000	0.000
65	A	64	ASN	0	0.029	0.012	21.946	0.005	0.005	0.000	0.000	0.000	0.000
66	A	65	ALA	0	-0.003	-0.003	21.049	0.000	0.000	0.000	0.000	0.000	0.000
67	A	66	SER	0	-0.087	-0.052	23.061	0.001	0.001	0.000	0.000	0.000	0.000
68	A	67	GLY	0	0.019	0.015	25.442	0.002	0.002	0.000	0.000	0.000	0.000
69	A	68	SER	0	-0.055	-0.011	25.530	0.001	0.001	0.000	0.000	0.000	0.000
70	A	69	LEU	0	-0.024	0.001	22.091	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	70	ALA	0	0.028	0.012	26.772	0.002	0.002	0.000	0.000	0.000	0.000
72	A	71	VAL	0	-0.027	-0.024	28.989	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.002	0.001	29.643	0.004	0.004	0.000	0.000	0.000	0.000
74	A	73	ASP	-1	-0.771	-0.884	27.523	-0.048	-0.048	0.000	0.000	0.000	0.000
75	A	74	PRO	0	-0.061	-0.029	26.996	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	75	VAL	0	0.018	0.008	22.124	0.001	0.001	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.008	-0.001	18.972	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	77	VAL	0	-0.005	-0.010	15.456	0.001	0.001	0.000	0.000	0.000	0.000
79	A	78	GLN	0	0.039	0.022	12.091	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	79	GLY	0	0.028	-0.006	10.357	0.006	0.006	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.951	0.984	4.358	1.353	1.424	-0.001	-0.004	-0.066	0.000
82	A	81	LEU	0	0.004	0.010	8.748	0.069	0.069	0.000	0.000	0.000	0.000
83	A	82	LYS	1	0.841	0.907	6.349	1.103	1.103	0.000	0.000	0.000	0.000
84	A	83	VAL	0	0.017	0.018	12.211	0.051	0.051	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.897	0.951	12.226	0.272	0.272	0.000	0.000	0.000	0.000
86	A	85	THR	0	0.035	0.011	17.527	0.011	0.011	0.000	0.000	0.000	0.000
87	A	86	ASP	-1	-0.851	-0.926	20.799	-0.120	-0.120	0.000	0.000	0.000	0.000
88	A	87	VAL	0	-0.006	-0.010	23.323	0.002	0.002	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.813	0.893	21.824	0.105	0.105	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.831	-0.905	28.954	-0.050	-0.050	0.000	0.000	0.000	0.000
91	A	90	GLY	0	0.010	0.009	31.971	0.002	0.002	0.000	0.000	0.000	0.000
92	A	91	GLN	0	0.038	0.039	29.946	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	92	SER	0	-0.034	-0.010	25.742	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	93	ARG	1	0.843	0.890	25.586	0.062	0.062	0.000	0.000	0.000	0.000
95	A	94	THR	0	0.020	0.019	20.033	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	95	SER	0	0.000	-0.003	19.487	0.013	0.013	0.000	0.000	0.000	0.000
97	A	96	ALA	0	-0.011	0.001	16.963	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.815	-0.911	14.434	-0.186	-0.186	0.000	0.000	0.000	0.000
99	A	98	ILE	0	-0.025	-0.025	12.667	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	99	ASP	-1	-0.901	-0.948	9.612	-0.458	-0.458	0.000	0.000	0.000	0.000
101	A	100	ALA	0	-0.049	-0.033	10.514	-0.085	-0.085	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.063	-0.041	8.784	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	102	ALA	0	0.000	0.000	11.947	0.054	0.054	0.000	0.000	0.000	0.000
104	A	103	ILE	0	-0.002	-0.016	15.399	-0.021	-0.021	0.000	0.000	0.000	0.000
105	A	104	GLY	0	-0.007	0.009	18.642	0.013	0.013	0.000	0.000	0.000	0.000
106	A	105	HIS	0	0.005	-0.003	22.037	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	106	ASP	-1	-0.854	-0.935	25.050	-0.064	-0.064	0.000	0.000	0.000	0.000
108	A	107	LEU	0	0.041	0.007	26.161	0.003	0.003	0.000	0.000	0.000	0.000
109	A	108	ALA	0	-0.056	-0.013	28.123	0.003	0.003	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.735	0.859	25.412	0.071	0.071	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.022	0.014	31.181	0.001	0.001	0.000	0.000	0.000	0.000
112	A	111	THR	0	0.012	0.009	31.576	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	112	ALA	0	-0.004	0.016	30.629	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)