FMO DATABASE

FMODB ID: LJ9R9

Calculation Name: 1PDN-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PDN

Chain ID: C

ChEMBL ID:

UniProt ID: P06601

Base Structure: X-ray

Registration Date: 2023-06-19

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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-818504.51948
FMO2-HF: Nuclear repulsion	770441.714045
FMO2-HF: Total energy	-48062.805435
FMO2-MP2: Total energy	-48201.82637

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(C:2:GLN)

Summations of interaction energy for fragment #1(C:2:GLN)

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.
-10.578	-6.201	0.757	-2.112	-3.022	-0.003

Interaction energy analysis for fragmet #1(C:2:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.011

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	C	4	ARG	1	0.909	0.951	2.801	-3.720	-0.642	0.352	-1.545	-1.885	-0.008
4	C	5	VAL	0	0.052	0.021	5.261	0.694	0.763	-0.001	-0.003	-0.064	0.000
5	C	6	ASN	0	-0.034	-0.021	8.997	-0.370	-0.370	0.000	0.000	0.000	0.000
6	C	7	GLN	0	0.056	0.005	12.080	0.055	0.055	0.000	0.000	0.000	0.000
7	C	8	LEU	0	-0.021	0.014	15.499	-0.017	-0.017	0.000	0.000	0.000	0.000
8	C	9	GLY	0	0.023	0.020	13.984	0.023	0.023	0.000	0.000	0.000	0.000
9	C	10	GLY	0	0.015	0.013	13.461	0.098	0.098	0.000	0.000	0.000	0.000
10	C	11	VAL	0	-0.011	-0.010	7.952	-0.122	-0.122	0.000	0.000	0.000	0.000
11	C	12	PHE	0	-0.062	-0.033	8.032	-0.070	-0.070	0.000	0.000	0.000	0.000
12	C	13	ILE	0	0.080	0.033	2.812	-1.345	-0.320	0.407	-0.547	-0.886	0.005
13	C	14	ASN	0	0.002	-0.002	4.026	-0.510	-0.305	-0.001	-0.017	-0.187	0.000
14	C	15	GLY	0	0.071	0.041	5.574	-0.406	-0.406	0.000	0.000	0.000	0.000
15	C	16	ARG	1	0.862	0.933	5.751	-2.064	-2.064	0.000	0.000	0.000	0.000
16	C	17	PRO	0	-0.007	-0.006	8.407	-0.202	-0.202	0.000	0.000	0.000	0.000
17	C	18	LEU	0	0.034	0.021	10.580	0.320	0.320	0.000	0.000	0.000	0.000
18	C	19	PRO	0	0.051	0.018	10.850	-0.114	-0.114	0.000	0.000	0.000	0.000
19	C	20	ASN	0	0.044	0.008	13.587	-0.194	-0.194	0.000	0.000	0.000	0.000
20	C	21	ASN	0	0.075	0.038	16.165	-0.011	-0.011	0.000	0.000	0.000	0.000
21	C	22	ILE	0	0.019	0.016	13.891	-0.092	-0.092	0.000	0.000	0.000	0.000
22	C	23	ARG	1	0.815	0.898	15.618	-0.908	-0.908	0.000	0.000	0.000	0.000
23	C	24	LEU	0	0.027	0.020	18.862	-0.070	-0.070	0.000	0.000	0.000	0.000
24	C	25	LYS	1	0.906	0.939	21.109	-0.583	-0.583	0.000	0.000	0.000	0.000
25	C	26	ILE	0	-0.040	-0.028	18.386	-0.057	-0.057	0.000	0.000	0.000	0.000
26	C	27	VAL	0	0.002	-0.001	22.564	-0.048	-0.048	0.000	0.000	0.000	0.000
27	C	28	GLU	-1	-0.828	-0.903	25.059	0.501	0.501	0.000	0.000	0.000	0.000
28	C	29	MET	0	0.020	0.009	25.261	-0.018	-0.018	0.000	0.000	0.000	0.000
29	C	30	ALA	0	-0.024	-0.019	27.043	-0.030	-0.030	0.000	0.000	0.000	0.000
30	C	31	ALA	0	-0.033	-0.006	28.748	-0.025	-0.025	0.000	0.000	0.000	0.000
31	C	32	ASP	-1	-0.921	-0.952	30.303	0.316	0.316	0.000	0.000	0.000	0.000
32	C	33	GLY	0	-0.004	0.008	32.048	-0.018	-0.018	0.000	0.000	0.000	0.000
33	C	34	ILE	0	-0.056	-0.023	28.594	-0.019	-0.019	0.000	0.000	0.000	0.000
34	C	35	ARG	1	1.023	1.000	29.530	-0.138	-0.138	0.000	0.000	0.000	0.000
35	C	36	PRO	0	0.100	0.031	25.715	0.008	0.008	0.000	0.000	0.000	0.000
36	C	37	CYS	0	-0.026	-0.012	25.032	0.022	0.022	0.000	0.000	0.000	0.000
37	C	38	VAL	0	-0.012	0.001	25.763	-0.011	-0.011	0.000	0.000	0.000	0.000
38	C	39	ILE	0	0.029	0.029	22.631	0.019	0.019	0.000	0.000	0.000	0.000
39	C	40	SER	0	-0.088	-0.055	20.666	0.024	0.024	0.000	0.000	0.000	0.000
40	C	41	ARG	1	0.936	0.941	20.363	-0.162	-0.162	0.000	0.000	0.000	0.000
41	C	42	GLN	0	0.003	0.012	21.440	-0.005	-0.005	0.000	0.000	0.000	0.000
42	C	43	LEU	0	-0.007	-0.012	19.268	0.039	0.039	0.000	0.000	0.000	0.000
43	C	44	ARG	1	0.893	0.961	16.466	-0.289	-0.289	0.000	0.000	0.000	0.000
44	C	45	VAL	0	0.022	0.026	15.510	0.057	0.057	0.000	0.000	0.000	0.000
45	C	46	SER	0	0.059	0.035	15.984	-0.041	-0.041	0.000	0.000	0.000	0.000
46	C	47	HIS	0	0.109	0.036	18.158	0.065	0.065	0.000	0.000	0.000	0.000
47	C	48	GLY	0	0.026	0.022	20.169	0.009	0.009	0.000	0.000	0.000	0.000
48	C	49	CYS	0	-0.055	-0.024	14.762	0.030	0.030	0.000	0.000	0.000	0.000
49	C	50	VAL	0	0.047	0.016	18.060	0.032	0.032	0.000	0.000	0.000	0.000
50	C	51	SER	0	-0.003	0.007	20.828	0.007	0.007	0.000	0.000	0.000	0.000
51	C	52	LYS	1	0.978	0.990	16.522	-0.361	-0.361	0.000	0.000	0.000	0.000
52	C	53	ILE	0	-0.060	-0.028	16.922	0.021	0.021	0.000	0.000	0.000	0.000
53	C	54	LEU	0	0.043	0.015	21.155	-0.004	-0.004	0.000	0.000	0.000	0.000
54	C	55	ASN	0	-0.010	-0.011	24.679	-0.018	-0.018	0.000	0.000	0.000	0.000
55	C	56	ARG	1	0.801	0.890	21.037	-0.360	-0.360	0.000	0.000	0.000	0.000
56	C	57	TYR	0	0.017	0.019	24.235	-0.007	-0.007	0.000	0.000	0.000	0.000
57	C	58	GLN	0	-0.028	-0.017	26.127	-0.027	-0.027	0.000	0.000	0.000	0.000
58	C	59	GLU	-1	-0.804	-0.875	26.214	0.252	0.252	0.000	0.000	0.000	0.000
59	C	60	THR	0	-0.085	-0.065	25.180	0.008	0.008	0.000	0.000	0.000	0.000
60	C	61	GLY	0	0.055	0.046	27.939	0.006	0.006	0.000	0.000	0.000	0.000
61	C	62	SER	0	-0.021	-0.012	24.384	0.036	0.036	0.000	0.000	0.000	0.000
62	C	63	ILE	0	0.061	0.030	20.407	0.006	0.006	0.000	0.000	0.000	0.000
63	C	64	ARG	1	0.905	0.958	17.600	-0.643	-0.643	0.000	0.000	0.000	0.000
64	C	65	PRO	0	-0.040	-0.009	15.337	-0.047	-0.047	0.000	0.000	0.000	0.000
65	C	66	GLY	0	0.062	0.016	17.797	-0.039	-0.039	0.000	0.000	0.000	0.000
66	C	67	VAL	0	0.024	0.018	17.875	0.095	0.095	0.000	0.000	0.000	0.000
67	C	68	ILE	0	-0.039	-0.031	12.845	-0.004	-0.004	0.000	0.000	0.000	0.000
68	C	69	GLY	0	0.026	0.022	16.195	0.065	0.065	0.000	0.000	0.000	0.000
69	C	70	GLY	0	0.014	0.010	16.934	-0.008	-0.008	0.000	0.000	0.000	0.000
70	C	71	SER	0	-0.005	-0.012	20.381	-0.029	-0.029	0.000	0.000	0.000	0.000
71	C	72	LYS	1	0.884	0.934	23.358	-0.082	-0.082	0.000	0.000	0.000	0.000
72	C	73	PRO	0	0.028	-0.006	26.586	-0.013	-0.013	0.000	0.000	0.000	0.000
73	C	74	ARG	1	0.815	0.905	28.884	-0.084	-0.084	0.000	0.000	0.000	0.000
74	C	75	ILE	0	-0.001	-0.004	31.609	-0.004	-0.004	0.000	0.000	0.000	0.000
75	C	76	ALA	0	0.021	0.023	34.756	-0.007	-0.007	0.000	0.000	0.000	0.000
76	C	77	THR	0	-0.015	-0.043	32.955	0.003	0.003	0.000	0.000	0.000	0.000
77	C	78	PRO	0	0.018	0.004	33.452	-0.004	-0.004	0.000	0.000	0.000	0.000
78	C	79	GLU	-1	-0.896	-0.934	35.068	0.004	0.004	0.000	0.000	0.000	0.000
79	C	80	ILE	0	0.069	0.046	36.483	-0.002	-0.002	0.000	0.000	0.000	0.000
80	C	81	GLU	-1	-0.804	-0.872	32.266	0.069	0.069	0.000	0.000	0.000	0.000
81	C	82	ASN	0	-0.069	-0.031	33.429	-0.007	-0.007	0.000	0.000	0.000	0.000
82	C	83	ARG	0	0.002	-0.004	37.124	0.000	0.000	0.000	0.000	0.000	0.000
83	C	84	ILE	0	-0.014	-0.018	39.890	0.001	0.001	0.000	0.000	0.000	0.000
84	C	85	GLU	-1	-0.875	-0.913	36.486	0.004	0.004	0.000	0.000	0.000	0.000
85	C	86	GLU	-1	-0.836	-0.911	39.633	-0.013	-0.013	0.000	0.000	0.000	0.000
86	C	87	TYR	0	-0.070	-0.070	41.766	0.000	0.000	0.000	0.000	0.000	0.000
87	C	88	LYS	1	0.784	0.875	38.676	0.004	0.004	0.000	0.000	0.000	0.000
88	C	89	ARG	0	-0.004	0.018	44.331	0.003	0.003	0.000	0.000	0.000	0.000
89	C	90	SER	0	-0.011	-0.035	47.577	-0.002	-0.002	0.000	0.000	0.000	0.000
90	C	91	SER	0	-0.065	-0.017	45.185	0.004	0.004	0.000	0.000	0.000	0.000
91	C	92	PRO	0	-0.021	-0.006	47.490	0.004	0.004	0.000	0.000	0.000	0.000
92	C	93	GLY	0	0.007	-0.014	50.258	-0.002	-0.002	0.000	0.000	0.000	0.000
93	C	94	MET	0	-0.025	0.014	48.305	0.001	0.001	0.000	0.000	0.000	0.000
94	C	95	PHE	0	0.011	0.004	49.144	0.005	0.005	0.000	0.000	0.000	0.000
95	C	96	SER	0	-0.013	-0.026	46.329	-0.002	-0.002	0.000	0.000	0.000	0.000
96	C	97	TRP	0	-0.003	-0.024	48.122	0.001	0.001	0.000	0.000	0.000	0.000
97	C	98	GLU	-1	-0.843	-0.908	50.819	0.023	0.023	0.000	0.000	0.000	0.000
98	C	99	ILE	0	0.008	0.006	44.596	-0.002	-0.002	0.000	0.000	0.000	0.000
99	C	100	ARG	1	0.839	0.903	46.949	-0.050	-0.050	0.000	0.000	0.000	0.000
100	C	101	GLU	-1	-0.802	-0.882	47.996	0.026	0.026	0.000	0.000	0.000	0.000
101	C	102	LYN	0	-0.057	-0.013	47.805	-0.002	-0.002	0.000	0.000	0.000	0.000
102	C	103	LEU	0	0.028	0.019	42.550	-0.002	-0.002	0.000	0.000	0.000	0.000
103	C	104	ILE	0	-0.058	-0.023	46.708	-0.002	-0.002	0.000	0.000	0.000	0.000
104	C	105	ARG	1	0.802	0.885	48.990	-0.019	-0.019	0.000	0.000	0.000	0.000
105	C	106	GLU	-1	-0.765	-0.860	46.287	0.003	0.003	0.000	0.000	0.000	0.000
106	C	107	GLY	0	-0.040	-0.008	47.945	-0.004	-0.004	0.000	0.000	0.000	0.000
107	C	108	VAL	0	-0.030	-0.005	41.615	0.000	0.000	0.000	0.000	0.000	0.000
108	C	109	CYM	-1	-0.774	-0.795	42.808	0.043	0.043	0.000	0.000	0.000	0.000
109	C	110	ASP	-1	-0.799	-0.923	44.956	0.027	0.027	0.000	0.000	0.000	0.000
110	C	111	ARG	1	0.781	0.849	47.608	-0.025	-0.025	0.000	0.000	0.000	0.000
111	C	112	SER	0	-0.078	-0.037	47.192	0.004	0.004	0.000	0.000	0.000	0.000
112	C	113	THR	0	-0.114	-0.115	42.851	0.004	0.004	0.000	0.000	0.000	0.000
113	C	114	ALA	0	0.057	0.029	43.369	0.005	0.005	0.000	0.000	0.000	0.000
114	C	115	PRO	0	0.018	0.015	40.926	0.005	0.005	0.000	0.000	0.000	0.000
115	C	116	SER	0	0.017	0.007	43.296	-0.004	-0.004	0.000	0.000	0.000	0.000
116	C	117	VAL	0	0.113	0.051	44.469	0.002	0.002	0.000	0.000	0.000	0.000
117	C	118	SER	0	-0.017	0.019	44.151	0.002	0.002	0.000	0.000	0.000	0.000
118	C	119	ALA	0	-0.036	-0.031	40.261	0.003	0.003	0.000	0.000	0.000	0.000
119	C	120	ILE	0	0.068	0.036	40.492	0.003	0.003	0.000	0.000	0.000	0.000
120	C	121	SER	0	0.007	-0.014	42.007	-0.003	-0.003	0.000	0.000	0.000	0.000
121	C	122	ARG	1	0.855	0.943	37.746	-0.101	-0.101	0.000	0.000	0.000	0.000
122	C	123	LEU	0	-0.050	-0.017	35.165	0.007	0.007	0.000	0.000	0.000	0.000
123	C	124	VAL	0	-0.034	-0.008	38.380	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:GLN)