FMO DATABASE

FMODB ID: LZV29

Calculation Name: 1CDC-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CDC

Chain ID: B

ChEMBL ID:

UniProt ID: P08921

Base Structure: X-ray

Registration Date: 2023-06-26

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-568088.982323
FMO2-HF: Nuclear repulsion	530573.165501
FMO2-HF: Total energy	-37515.816822
FMO2-MP2: Total energy	-37625.887049

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(B:4:GLY)

Summations of interaction energy for fragment #1(B:4:GLY)

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.
1.984	2.89	-0.01	-0.348	-0.548	0.001

Interaction energy analysis for fragmet #1(B:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.002

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	B	6	VAL	0	-0.017	0.004	3.833	2.189	2.983	-0.010	-0.324	-0.461	0.001
4	B	7	TRP	0	0.013	0.002	6.136	-0.357	-0.357	0.000	0.000	0.000	0.000
5	B	8	GLY	0	0.028	0.012	9.803	0.053	0.053	0.000	0.000	0.000	0.000
6	B	9	ALA	0	-0.019	0.009	12.805	0.000	0.000	0.000	0.000	0.000	0.000
7	B	10	LEU	0	0.016	-0.025	16.523	-0.019	-0.019	0.000	0.000	0.000	0.000
8	B	11	GLY	0	0.017	0.016	18.976	0.021	0.021	0.000	0.000	0.000	0.000
9	B	12	HIS	0	-0.031	-0.009	17.756	0.021	0.021	0.000	0.000	0.000	0.000
10	B	13	GLY	0	-0.016	0.006	17.323	-0.025	-0.025	0.000	0.000	0.000	0.000
11	B	14	ILE	0	-0.008	-0.013	10.339	0.028	0.028	0.000	0.000	0.000	0.000
12	B	15	ASN	0	0.011	0.010	11.831	-0.044	-0.044	0.000	0.000	0.000	0.000
13	B	16	LEU	0	-0.006	-0.009	7.636	0.015	0.015	0.000	0.000	0.000	0.000
14	B	17	ASN	0	0.003	0.001	7.446	0.029	0.029	0.000	0.000	0.000	0.000
15	B	18	ILE	0	0.009	0.004	6.202	-0.282	-0.282	0.000	0.000	0.000	0.000
16	B	19	PRO	0	0.000	0.003	3.947	0.127	0.239	0.000	-0.024	-0.087	0.000
17	B	20	ASN	0	-0.043	-0.027	6.589	0.042	0.042	0.000	0.000	0.000	0.000
18	B	21	PHE	0	0.037	0.014	9.577	-0.038	-0.038	0.000	0.000	0.000	0.000
19	B	22	GLN	0	0.017	0.009	11.972	0.032	0.032	0.000	0.000	0.000	0.000
20	B	23	MET	0	-0.019	0.005	15.312	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	24	THR	0	0.000	-0.018	17.433	0.017	0.017	0.000	0.000	0.000	0.000
22	B	25	ASP	-1	-0.878	-0.963	20.491	-0.052	-0.052	0.000	0.000	0.000	0.000
23	B	26	ASP	-1	-0.966	-0.963	20.497	-0.067	-0.067	0.000	0.000	0.000	0.000
24	B	27	ILE	0	0.005	0.025	17.331	-0.014	-0.014	0.000	0.000	0.000	0.000
25	B	28	ASP	-1	-0.836	-0.935	20.375	-0.089	-0.089	0.000	0.000	0.000	0.000
26	B	29	GLU	-1	-0.932	-0.978	19.447	-0.164	-0.164	0.000	0.000	0.000	0.000
27	B	30	VAL	0	0.007	0.017	13.627	-0.010	-0.010	0.000	0.000	0.000	0.000
28	B	31	ARG	1	0.908	0.968	15.204	0.242	0.242	0.000	0.000	0.000	0.000
29	B	32	TRP	0	0.032	0.028	8.188	-0.081	-0.081	0.000	0.000	0.000	0.000
30	B	33	GLU	-1	-0.844	-0.921	12.751	-0.273	-0.273	0.000	0.000	0.000	0.000
31	B	34	ARG	1	0.948	0.973	12.180	0.273	0.273	0.000	0.000	0.000	0.000
32	B	35	GLY	0	0.015	0.011	13.158	0.057	0.057	0.000	0.000	0.000	0.000
33	B	36	SER	0	0.006	-0.002	15.014	0.007	0.007	0.000	0.000	0.000	0.000
34	B	37	THR	0	-0.051	-0.019	17.455	0.043	0.043	0.000	0.000	0.000	0.000
35	B	38	LEU	0	0.032	0.019	17.065	-0.045	-0.045	0.000	0.000	0.000	0.000
36	B	39	VAL	0	-0.085	-0.042	15.341	0.015	0.015	0.000	0.000	0.000	0.000
37	B	40	ALA	0	0.015	0.002	16.583	0.028	0.028	0.000	0.000	0.000	0.000
38	B	41	GLU	-1	-0.895	-0.967	17.434	-0.207	-0.207	0.000	0.000	0.000	0.000
39	B	42	PHE	0	-0.028	0.006	18.134	0.018	0.018	0.000	0.000	0.000	0.000
40	B	43	LYS	1	0.885	0.931	19.808	0.149	0.149	0.000	0.000	0.000	0.000
41	B	44	ARG	1	0.855	0.937	21.318	0.089	0.089	0.000	0.000	0.000	0.000
42	B	45	LYS	1	0.872	0.943	24.723	0.082	0.082	0.000	0.000	0.000	0.000
43	B	46	MET	0	0.055	0.021	27.428	-0.006	-0.006	0.000	0.000	0.000	0.000
44	B	47	LYS	1	0.845	0.931	29.907	0.067	0.067	0.000	0.000	0.000	0.000
45	B	48	PRO	0	0.076	0.038	28.829	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	49	PHE	0	0.042	0.016	26.302	0.008	0.008	0.000	0.000	0.000	0.000
47	B	50	LEU	0	0.004	-0.012	28.346	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	51	LYS	1	0.935	0.996	26.344	0.077	0.077	0.000	0.000	0.000	0.000
49	B	52	SER	0	0.054	0.011	29.944	0.004	0.004	0.000	0.000	0.000	0.000
50	B	53	GLY	0	0.057	0.033	33.676	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	54	ALA	0	0.036	0.027	35.211	0.002	0.002	0.000	0.000	0.000	0.000
52	B	55	PHE	0	0.018	0.016	31.930	0.000	0.000	0.000	0.000	0.000	0.000
53	B	56	GLU	-1	-0.963	-0.996	35.390	-0.050	-0.050	0.000	0.000	0.000	0.000
54	B	57	ILE	0	-0.001	0.015	30.713	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	58	LEU	0	0.003	-0.001	34.382	0.004	0.004	0.000	0.000	0.000	0.000
56	B	59	ALA	0	0.011	-0.001	35.648	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	60	ASN	0	-0.054	-0.030	36.809	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	61	GLY	0	-0.018	-0.011	32.850	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	62	ASP	-1	-0.891	-0.925	32.142	-0.078	-0.078	0.000	0.000	0.000	0.000
60	B	63	LEU	0	-0.015	-0.011	30.456	0.001	0.001	0.000	0.000	0.000	0.000
61	B	64	LYS	1	0.929	0.971	33.887	0.054	0.054	0.000	0.000	0.000	0.000
62	B	65	ILE	0	0.043	0.010	33.504	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	66	LYS	1	0.791	0.873	36.974	0.050	0.050	0.000	0.000	0.000	0.000
64	B	67	ASN	0	-0.015	-0.011	39.667	0.003	0.003	0.000	0.000	0.000	0.000
65	B	68	LEU	0	0.004	0.008	37.079	0.000	0.000	0.000	0.000	0.000	0.000
66	B	69	THR	0	-0.038	-0.009	36.910	0.004	0.004	0.000	0.000	0.000	0.000
67	B	70	ARG	1	0.873	0.905	37.537	0.026	0.026	0.000	0.000	0.000	0.000
68	B	71	ASP	-1	-0.963	-0.983	32.066	-0.047	-0.047	0.000	0.000	0.000	0.000
69	B	72	ASP	-1	-0.843	-0.895	32.558	-0.054	-0.054	0.000	0.000	0.000	0.000
70	B	73	SER	0	-0.051	-0.022	32.997	-0.004	-0.004	0.000	0.000	0.000	0.000
71	B	74	GLY	0	0.059	0.030	29.907	0.000	0.000	0.000	0.000	0.000	0.000
72	B	75	THR	0	-0.065	-0.043	26.064	0.000	0.000	0.000	0.000	0.000	0.000
73	B	76	TYR	0	-0.041	-0.014	26.854	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	77	ASN	0	-0.005	-0.017	22.864	0.008	0.008	0.000	0.000	0.000	0.000
75	B	78	VAL	0	0.018	0.018	24.903	0.000	0.000	0.000	0.000	0.000	0.000
76	B	79	THR	0	-0.011	-0.019	20.612	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	80	VAL	0	0.011	0.014	24.039	0.006	0.006	0.000	0.000	0.000	0.000
78	B	81	TYR	0	-0.057	-0.062	18.686	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	82	SER	0	-0.002	-0.002	25.209	0.010	0.010	0.000	0.000	0.000	0.000
80	B	83	THR	0	0.057	0.009	26.480	-0.008	-0.008	0.000	0.000	0.000	0.000
81	B	84	ASN	0	-0.034	-0.003	26.286	-0.006	-0.006	0.000	0.000	0.000	0.000
82	B	85	GLY	0	0.070	0.048	22.473	-0.011	-0.011	0.000	0.000	0.000	0.000
83	B	86	THR	0	-0.035	-0.020	21.717	-0.024	-0.024	0.000	0.000	0.000	0.000
84	B	87	ARG	1	0.941	0.978	17.142	0.270	0.270	0.000	0.000	0.000	0.000
85	B	88	ILE	0	-0.041	-0.026	22.846	0.001	0.001	0.000	0.000	0.000	0.000
86	B	89	LEU	0	-0.036	-0.019	25.381	0.006	0.006	0.000	0.000	0.000	0.000
87	B	90	ASP	-1	-0.861	-0.951	20.400	-0.204	-0.204	0.000	0.000	0.000	0.000
88	B	91	LYS	1	0.867	0.944	23.792	0.133	0.133	0.000	0.000	0.000	0.000
89	B	92	ALA	0	0.045	0.026	25.001	-0.004	-0.004	0.000	0.000	0.000	0.000
90	B	93	LEU	0	-0.027	-0.015	26.816	0.005	0.005	0.000	0.000	0.000	0.000
91	B	94	ASP	-1	-0.861	-0.932	29.653	-0.066	-0.066	0.000	0.000	0.000	0.000
92	B	95	LEU	0	-0.027	0.001	31.653	0.003	0.003	0.000	0.000	0.000	0.000
93	B	96	ARG	1	0.922	0.955	34.202	0.054	0.054	0.000	0.000	0.000	0.000
94	B	97	ILE	0	0.011	0.007	36.438	0.000	0.000	0.000	0.000	0.000	0.000
95	B	98	LEU	0	-0.020	-0.007	39.806	0.002	0.002	0.000	0.000	0.000	0.000
96	B	99	GLU	-1	-0.855	-0.911	42.669	-0.029	-0.029	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:GLY)