FMO DATABASE

FMODB ID: Z66YN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-784180.50138
FMO2-HF: Nuclear repulsion	741158.945104
FMO2-HF: Total energy	-43021.556276
FMO2-MP2: Total energy	-43147.132958

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.
-4.526	-0.27	-0.024	-2.153	-2.08	0.003

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 : 0.004 / 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

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	-0.017	-0.010	3.767	-2.331	1.352	-0.042	-2.047	-1.595	0.003
4	A	3	GLU	-1	-0.766	-0.853	3.404	1.904	2.477	0.018	-0.106	-0.485	0.000
5	A	4	ILE	0	0.005	0.006	5.951	-0.341	-0.341	0.000	0.000	0.000	0.000
6	A	5	MET	0	-0.035	-0.006	8.128	0.342	0.342	0.000	0.000	0.000	0.000
7	A	6	ILE	0	-0.007	-0.004	10.476	-0.160	-0.160	0.000	0.000	0.000	0.000
8	A	7	CYS	0	-0.029	-0.021	14.095	0.051	0.051	0.000	0.000	0.000	0.000
9	A	8	ALA	0	-0.017	0.000	16.730	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.048	0.017	19.708	0.009	0.009	0.000	0.000	0.000	0.000
11	A	10	GLY	0	0.001	-0.007	23.058	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	11	ASN	0	-0.034	-0.017	25.379	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.007	0.026	25.175	0.012	0.012	0.000	0.000	0.000	0.000
14	A	13	ALA	0	-0.008	-0.012	26.863	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	14	THR	0	-0.011	-0.017	27.216	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.021	0.001	28.101	0.008	0.008	0.000	0.000	0.000	0.000
17	A	16	PRO	0	-0.020	0.000	25.010	0.007	0.007	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.045	-0.014	25.477	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	18	PHE	0	0.011	0.003	23.654	0.028	0.028	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.907	0.947	23.403	-0.251	-0.251	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.808	-0.905	23.132	0.249	0.249	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.078	-0.036	19.132	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.048	0.017	21.576	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.007	-0.003	16.398	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	24	GLY	0	-0.004	0.002	17.606	0.040	0.040	0.000	0.000	0.000	0.000
26	A	25	PRO	0	0.027	0.025	19.950	0.005	0.005	0.000	0.000	0.000	0.000
27	A	26	SER	0	-0.029	-0.018	18.138	0.040	0.040	0.000	0.000	0.000	0.000
28	A	27	VAL	0	0.003	0.006	19.777	-0.037	-0.037	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.950	0.986	19.901	-0.204	-0.204	0.000	0.000	0.000	0.000
30	A	29	PHE	0	0.024	0.001	20.676	-0.030	-0.030	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.943	0.995	22.284	-0.157	-0.157	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.011	0.016	20.456	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.001	-0.005	23.888	0.003	0.003	0.000	0.000	0.000	0.000
34	A	33	VAL	0	0.024	0.005	22.021	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.014	0.004	25.462	0.001	0.001	0.000	0.000	0.000	0.000
36	A	35	ALA	0	-0.004	0.022	27.558	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.856	0.903	28.955	-0.097	-0.097	0.000	0.000	0.000	0.000
38	A	37	TYR	0	-0.011	-0.011	31.946	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	38	TRP	0	0.040	0.028	34.569	0.002	0.002	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.802	-0.917	37.654	0.034	0.034	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.808	0.873	39.408	-0.031	-0.031	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.816	-0.877	43.915	0.026	0.026	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.829	0.905	40.966	-0.042	-0.042	0.000	0.000	0.000	0.000
44	A	43	ASN	0	-0.056	-0.015	43.718	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	44	ALA	0	0.029	0.017	41.193	0.001	0.001	0.000	0.000	0.000	0.000
46	A	45	TRP	0	-0.012	0.001	33.454	0.000	0.000	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.016	-0.007	37.001	0.000	0.000	0.000	0.000	0.000	0.000
48	A	47	ASP	-1	-0.804	-0.889	33.736	0.086	0.086	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.000	-0.003	32.343	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	49	HIS	0	-0.020	-0.009	25.667	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.005	-0.020	27.844	0.000	0.000	0.000	0.000	0.000	0.000
52	A	51	ASN	0	-0.018	0.004	22.757	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	52	PHE	0	0.002	-0.020	24.238	0.003	0.003	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.018	0.006	18.250	0.007	0.007	0.000	0.000	0.000	0.000
55	A	54	THR	0	-0.033	-0.011	19.293	-0.038	-0.038	0.000	0.000	0.000	0.000
56	A	55	VAL	0	-0.029	-0.004	17.242	0.053	0.053	0.000	0.000	0.000	0.000
57	A	56	TRP	0	0.015	-0.006	15.420	-0.059	-0.059	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.039	0.016	15.584	0.066	0.066	0.000	0.000	0.000	0.000
59	A	58	ASN	0	0.022	-0.006	13.989	-0.075	-0.075	0.000	0.000	0.000	0.000
60	A	59	ARG	1	0.932	0.959	13.876	-0.513	-0.513	0.000	0.000	0.000	0.000
61	A	60	GLN	0	0.056	0.018	17.887	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	61	LEU	0	-0.004	0.008	15.697	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.005	-0.003	18.849	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	63	THR	0	0.029	0.015	20.513	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	64	ASN	0	0.020	0.013	22.197	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.000	-0.003	21.691	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	66	SER	0	-0.083	-0.046	23.680	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	67	GLY	0	0.015	0.013	26.094	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	68	SER	0	-0.069	-0.022	26.140	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	69	LEU	0	-0.015	0.002	22.855	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	70	ALA	0	0.024	0.004	27.536	0.001	0.001	0.000	0.000	0.000	0.000
72	A	71	VAL	0	-0.032	-0.027	29.884	0.004	0.004	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.011	0.004	30.634	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	73	ASP	-1	-0.782	-0.876	28.341	0.139	0.139	0.000	0.000	0.000	0.000
75	A	74	PRO	0	-0.041	-0.012	27.893	0.014	0.014	0.000	0.000	0.000	0.000
76	A	75	VAL	0	0.014	-0.001	23.035	0.003	0.003	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.007	-0.001	19.685	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	77	VAL	0	-0.003	-0.009	16.406	0.015	0.015	0.000	0.000	0.000	0.000
79	A	78	GLN	0	0.032	0.017	12.431	0.048	0.048	0.000	0.000	0.000	0.000
80	A	79	GLY	0	0.027	-0.002	11.184	0.026	0.026	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.952	0.989	5.356	-2.419	-2.419	0.000	0.000	0.000	0.000
82	A	81	LEU	0	-0.005	0.002	9.893	-0.117	-0.117	0.000	0.000	0.000	0.000
83	A	82	LYS	1	0.790	0.885	6.563	-1.424	-1.424	0.000	0.000	0.000	0.000
84	A	83	VAL	0	0.008	0.008	12.673	-0.051	-0.051	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.868	0.918	12.646	-0.524	-0.524	0.000	0.000	0.000	0.000
86	A	85	THR	0	0.010	0.003	17.563	-0.027	-0.027	0.000	0.000	0.000	0.000
87	A	86	ASP	-1	-0.816	-0.902	20.647	0.257	0.257	0.000	0.000	0.000	0.000
88	A	87	VAL	0	-0.011	-0.003	23.254	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.801	0.881	22.235	-0.194	-0.194	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.828	-0.904	29.032	0.102	0.102	0.000	0.000	0.000	0.000
91	A	90	GLY	0	0.008	0.009	31.934	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	91	GLN	0	0.036	0.036	30.253	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	92	SER	0	-0.013	0.001	25.529	0.014	0.014	0.000	0.000	0.000	0.000
94	A	93	ARG	1	0.809	0.873	25.521	-0.124	-0.124	0.000	0.000	0.000	0.000
95	A	94	THR	0	0.030	0.010	20.155	0.013	0.013	0.000	0.000	0.000	0.000
96	A	95	SER	0	-0.004	0.004	20.246	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	96	ALA	0	0.002	0.005	17.545	0.017	0.017	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.769	-0.862	15.260	0.383	0.383	0.000	0.000	0.000	0.000
99	A	98	ILE	0	-0.012	-0.015	13.791	0.039	0.039	0.000	0.000	0.000	0.000
100	A	99	ASP	-1	-0.894	-0.951	10.443	0.913	0.913	0.000	0.000	0.000	0.000
101	A	100	ALA	0	-0.045	-0.029	11.473	0.143	0.143	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.056	-0.040	9.281	0.082	0.082	0.000	0.000	0.000	0.000
103	A	102	ALA	0	-0.006	-0.001	12.505	-0.077	-0.077	0.000	0.000	0.000	0.000
104	A	103	ILE	0	-0.004	-0.017	15.909	0.019	0.019	0.000	0.000	0.000	0.000
105	A	104	GLY	0	0.002	0.015	19.276	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	105	HIS	0	0.010	0.006	22.606	0.001	0.001	0.000	0.000	0.000	0.000
107	A	106	ASP	-1	-0.851	-0.912	25.668	0.118	0.118	0.000	0.000	0.000	0.000
108	A	107	LEU	0	0.050	0.008	26.811	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	108	ALA	0	-0.057	-0.016	28.742	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.725	0.842	26.147	-0.139	-0.139	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.015	0.008	31.823	0.000	0.000	0.000	0.000	0.000	0.000
112	A	111	THR	0	-0.003	0.004	32.161	0.001	0.001	0.000	0.000	0.000	0.000
113	A	112	ALA	0	0.007	0.019	31.070	0.008	0.008	0.000	0.000	0.000	0.000

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