FMO DATABASE

FMODB ID: R8438

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

Total energy (hartree)

FMO2-HF: Electronic energy	-967680.75746
FMO2-HF: Nuclear repulsion	918185.495345
FMO2-HF: Total energy	-49495.262114
FMO2-MP2: Total energy	-49640.85766

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.
-9.438	-7.664	5.89	-3.091	-4.573	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 : 0.033 / q_NPA : 0.009

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	-0.025	-0.008	3.431	-3.488	-0.824	0.046	-1.275	-1.435	0.007
4	A	4	PHE	0	0.040	-0.014	2.346	-4.068	-5.195	5.844	-1.763	-2.954	0.005
5	A	5	PHE	0	0.035	0.034	4.068	-1.360	-1.123	0.000	-0.053	-0.184	0.000
6	A	6	ARG	1	0.886	0.932	5.767	-1.321	-1.321	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.733	-0.833	7.824	0.830	0.830	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.001	0.007	6.922	-0.143	-0.143	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.809	-0.894	9.929	-0.865	-0.865	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.037	-0.005	11.892	-0.035	-0.035	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.024	-0.021	12.094	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.816	0.886	11.618	0.743	0.743	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.922	-0.953	15.855	-0.129	-0.129	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.061	-0.051	17.758	0.010	0.010	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.036	-0.023	17.414	0.011	0.011	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.031	-0.008	19.969	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.021	-0.013	17.383	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.035	-0.017	16.772	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.004	-0.013	18.664	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.025	-0.020	22.463	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.956	-0.967	24.645	-0.192	-0.192	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.062	0.043	20.369	0.016	0.016	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.039	-0.015	23.085	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.882	0.948	24.183	0.195	0.195	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.052	0.027	27.683	0.013	0.013	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.023	0.010	26.848	0.010	0.010	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.033	-0.020	22.544	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.029	0.037	20.474	0.021	0.021	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.050	-0.009	18.108	0.006	0.006	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.009	-0.003	18.387	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.788	-0.883	19.723	-0.389	-0.389	0.000	0.000	0.000	0.000
32	A	32	ILE	0	0.006	0.008	22.492	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.002	-0.015	16.141	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.803	0.899	20.022	0.398	0.398	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.027	-0.017	21.681	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.093	0.046	22.405	0.014	0.014	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.779	0.877	18.628	0.494	0.494	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.829	-0.905	20.476	-0.441	-0.441	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.861	-0.900	23.119	-0.182	-0.182	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.024	-0.019	23.717	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.861	-0.938	25.155	-0.126	-0.126	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.889	0.935	17.864	0.393	0.393	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.923	0.956	17.598	0.073	0.073	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.020	0.028	21.658	0.019	0.019	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.025	0.007	21.260	0.012	0.012	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.028	-0.028	16.170	0.030	0.030	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.055	0.032	19.086	0.026	0.026	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.014	-0.006	21.217	0.028	0.028	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.010	0.009	17.038	0.008	0.008	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.007	-0.011	15.344	0.016	0.016	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.033	-0.014	17.819	0.040	0.040	0.000	0.000	0.000	0.000
52	A	52	PHE	0	0.028	0.016	19.310	0.021	0.021	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.025	0.002	15.897	0.015	0.015	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.027	-0.019	14.797	0.050	0.050	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.922	0.958	19.061	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.004	0.016	18.619	0.010	0.010	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.036	-0.033	14.162	0.021	0.021	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.901	-0.941	19.350	0.227	0.227	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.054	-0.037	22.115	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.018	0.018	20.633	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.826	0.903	21.180	-0.182	-0.182	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.900	-0.942	22.253	0.205	0.205	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.054	0.013	21.644	-0.028	-0.028	0.000	0.000	0.000	0.000
64	A	64	GLN	0	0.015	-0.020	20.230	0.013	0.013	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.018	-0.008	19.118	0.046	0.046	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.049	0.021	16.560	0.033	0.033	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.017	0.008	16.168	0.024	0.024	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.962	0.964	12.090	-0.847	-0.847	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.001	-0.024	11.588	0.138	0.138	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.028	0.009	11.612	0.068	0.068	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.880	-0.923	13.372	0.566	0.566	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.060	-0.038	7.311	0.131	0.131	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.009	0.005	7.974	0.102	0.102	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.927	0.974	9.830	-0.436	-0.436	0.000	0.000	0.000	0.000
75	A	75	GLN	0	0.020	0.017	9.755	-0.108	-0.108	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.795	-0.885	6.060	0.051	0.051	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.040	-0.019	8.462	-0.190	-0.190	0.000	0.000	0.000	0.000
78	A	78	PHE	0	-0.036	-0.011	11.447	-0.082	-0.082	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.014	-0.014	9.425	-0.106	-0.106	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.797	0.879	5.078	0.522	0.522	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.057	-0.026	11.412	-0.062	-0.062	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.045	-0.022	14.729	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	83	ASN	0	0.001	0.002	14.797	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.044	0.032	14.576	0.032	0.032	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.052	-0.026	15.184	0.032	0.032	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.043	-0.002	18.971	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.760	-0.852	20.281	0.151	0.151	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.864	0.913	20.346	-0.149	-0.149	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.045	-0.015	17.262	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.967	-0.976	20.423	0.172	0.172	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.827	-0.914	23.759	0.086	0.086	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.015	-0.004	19.560	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.925	0.938	20.137	-0.240	-0.240	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.894	0.949	23.512	-0.109	-0.109	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.019	0.003	26.235	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.058	-0.025	21.809	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.010	-0.004	25.539	-0.022	-0.022	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.033	0.008	28.074	0.001	0.001	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.006	0.019	31.469	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.019	-0.012	33.751	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.923	-0.954	36.276	0.020	0.020	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.799	-0.891	38.281	0.045	0.045	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.026	0.007	39.995	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	GLN	0	-0.018	-0.013	41.265	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.021	-0.006	35.561	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.022	-0.017	39.244	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.916	0.959	40.952	-0.030	-0.030	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.928	0.963	38.997	-0.059	-0.059	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.048	0.027	37.872	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.011	-0.007	39.273	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.078	-0.040	42.546	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.883	-0.921	38.607	0.047	0.047	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.025	0.019	39.415	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	ILE	0	0.006	0.008	40.584	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.862	0.903	38.773	-0.043	-0.043	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.005	0.005	34.999	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	MET	0	0.021	-0.001	36.749	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.037	-0.022	38.928	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.980	-0.971	32.762	0.013	0.013	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.042	-0.016	32.925	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.088	-0.030	35.542	-0.007	-0.007	0.000	0.000	0.000	0.000

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