FMO DATABASE

FMODB ID: ZV9MN

Calculation Name: 1D9C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D9C

Chain ID: A

ChEMBL ID:

UniProt ID: P07353

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:

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-967304.215855
FMO2-HF: Nuclear repulsion	917810.432336
FMO2-HF: Total energy	-49493.783519
FMO2-MP2: Total energy	-49639.40157

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:1:GLN)

Summations of interaction energy for fragment #1(A:1: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.
-10.897	-8.376	4.58	-2.589	-4.51	0.012

Interaction energy analysis for fragmet #1(A:1:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.013

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	A	3	GLN	0	-0.052	-0.020	3.224	-3.881	-1.578	0.091	-0.875	-1.519	0.008
4	A	4	PHE	0	0.027	-0.013	2.359	-4.902	-4.912	4.489	-1.665	-2.813	0.004
5	A	5	PHE	0	0.035	0.032	4.098	-1.433	-1.205	0.000	-0.049	-0.178	0.000
6	A	6	ARG	1	0.916	0.946	5.797	-1.797	-1.797	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.770	-0.857	7.890	1.152	1.152	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.010	0.000	7.192	-0.188	-0.188	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.921	-0.960	9.899	-0.715	-0.715	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.057	-0.028	11.939	-0.049	-0.049	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.016	-0.016	12.388	-0.034	-0.034	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.907	0.948	12.534	0.579	0.579	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.916	-0.954	15.892	-0.030	-0.030	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.081	-0.075	17.811	0.000	0.000	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.036	-0.025	17.976	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.015	0.003	20.032	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.021	-0.011	17.369	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.026	-0.026	16.788	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.023	0.002	18.678	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.026	-0.021	22.476	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.969	-0.986	24.651	-0.161	-0.161	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.079	0.051	20.395	0.011	0.011	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.056	-0.024	23.135	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.887	0.948	24.190	0.179	0.179	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.054	0.029	27.699	0.014	0.014	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.021	0.011	26.845	0.009	0.009	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.036	-0.014	22.630	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.037	0.037	20.706	0.021	0.021	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.054	-0.010	18.051	0.003	0.003	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.022	-0.019	18.460	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.873	-0.941	19.723	-0.378	-0.378	0.000	0.000	0.000	0.000
32	A	32	ILE	0	0.009	0.013	22.523	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.018	-0.024	16.095	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.903	0.957	19.934	0.504	0.504	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.003	0.005	21.666	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.098	0.042	22.295	0.013	0.013	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.880	0.942	17.863	0.670	0.670	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.927	-0.983	20.457	-0.488	-0.488	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.902	-0.921	23.025	-0.215	-0.215	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.037	-0.026	23.708	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.825	-0.914	25.151	-0.159	-0.159	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.906	0.957	17.354	0.464	0.464	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.928	0.953	18.123	0.156	0.156	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.026	0.033	21.611	0.023	0.023	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.023	0.007	21.159	0.016	0.016	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.042	-0.037	16.469	0.036	0.036	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.042	0.027	18.986	0.029	0.029	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.028	0.007	21.125	0.032	0.032	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.021	0.008	17.032	0.009	0.009	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.010	-0.011	15.310	0.019	0.019	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.008	-0.011	17.692	0.044	0.044	0.000	0.000	0.000	0.000
52	A	52	PHE	0	-0.009	0.007	19.488	0.025	0.025	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.014	-0.003	15.896	0.013	0.013	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.025	-0.018	14.906	0.063	0.063	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.978	0.991	18.904	0.002	0.002	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.027	-0.002	18.778	0.010	0.010	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.032	-0.035	13.723	0.025	0.025	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.963	-0.983	19.167	0.261	0.261	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.033	-0.011	21.942	0.014	0.014	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.003	0.013	20.197	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.909	0.946	20.996	-0.217	-0.217	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.893	-0.947	22.072	0.269	0.269	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.028	0.048	21.458	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	64	GLN	0	0.068	0.012	20.795	0.013	0.013	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.036	-0.018	19.087	0.055	0.055	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.049	0.020	16.562	0.052	0.052	0.000	0.000	0.000	0.000
67	A	67	GLN	0	0.004	0.024	16.053	0.026	0.026	0.000	0.000	0.000	0.000
68	A	68	ARG	1	1.014	0.996	12.423	-1.125	-1.125	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.009	-0.023	11.536	0.127	0.127	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.032	0.009	11.421	0.051	0.051	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.898	-0.941	13.199	0.666	0.666	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.059	-0.038	7.186	0.114	0.114	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.009	0.007	8.240	0.048	0.048	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.943	0.972	9.654	-0.537	-0.537	0.000	0.000	0.000	0.000
75	A	75	GLN	0	0.020	0.021	9.584	-0.130	-0.130	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.797	-0.887	5.873	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.060	-0.026	8.366	-0.202	-0.202	0.000	0.000	0.000	0.000
78	A	78	PHE	0	-0.048	-0.014	11.347	-0.078	-0.078	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.012	-0.019	9.417	-0.152	-0.152	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.809	0.889	5.218	0.627	0.627	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.066	-0.026	11.399	-0.066	-0.066	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.033	-0.012	14.689	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	83	ASN	0	0.004	0.001	14.823	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.046	0.032	14.557	0.031	0.031	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.043	-0.016	15.182	0.026	0.026	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.002	-0.029	18.963	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.860	-0.915	20.247	0.154	0.154	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.985	0.989	20.061	-0.116	-0.116	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.056	-0.022	17.236	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.963	-0.973	20.353	0.184	0.184	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.853	-0.923	23.682	0.113	0.113	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.061	-0.036	19.405	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.926	0.938	19.475	-0.297	-0.297	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.974	0.998	23.400	-0.105	-0.105	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.004	-0.008	26.145	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.076	-0.040	21.722	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.008	-0.007	24.646	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.078	-0.009	27.937	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.001	0.023	31.338	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.038	-0.006	33.680	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.944	-0.950	36.135	0.030	0.030	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.805	-0.892	38.181	0.056	0.056	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.036	0.005	39.852	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	104	GLN	0	-0.026	-0.028	41.120	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.014	0.000	35.301	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.032	-0.038	39.128	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.920	0.963	40.830	-0.035	-0.035	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.925	0.971	38.618	-0.067	-0.067	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.066	0.035	37.805	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.020	-0.009	39.170	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.077	-0.044	42.446	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.983	-0.983	37.363	0.046	0.046	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.026	0.012	39.195	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	114	ILE	0	0.000	0.009	40.513	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.961	0.966	38.807	-0.040	-0.040	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.021	0.016	35.062	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	117	MET	0	0.017	-0.004	36.693	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.030	-0.015	38.880	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.996	-0.978	32.769	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.032	-0.013	32.989	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.092	-0.034	35.499	-0.009	-0.009	0.000	0.000	0.000	0.000

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