FMO DATABASE

FMODB ID: VQ2M1

Calculation Name: 4LMQ-D-Xray372

Preferred Name: Stromal cell-derived factor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4LMQ

Chain ID: D

ChEMBL ID: CHEMBL3286074

UniProt ID: P48061

Base Structure: X-ray

Registration Date: 2023-09-20

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-328085.39945
FMO2-HF: Nuclear repulsion	304051.723126
FMO2-HF: Total energy	-24033.676324
FMO2-MP2: Total energy	-24103.081748

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(D:11:CYS)

Summations of interaction energy for fragment #1(D:11:CYS)

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.
-49.473	-45.189	37.551	-17.048	-24.784	0.039

Interaction energy analysis for fragmet #1(D:11:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : 0.035

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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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	D	13	PHE	0	0.064	0.046	3.793	-1.819	-0.017	0.024	0.009	-1.834	0.009
4	D	14	PHE	0	0.004	-0.020	2.507	-5.560	-1.909	2.549	-1.837	-4.362	-0.016
5	D	15	GLU	-1	-0.834	-0.903	3.499	-10.068	-9.038	0.010	-0.310	-0.731	0.000
6	D	16	SER	0	0.024	0.002	5.388	1.351	1.400	-0.002	-0.005	-0.042	0.000
7	D	17	HIS	0	-0.033	-0.012	9.042	-0.101	-0.101	0.000	0.000	0.000	0.000
8	D	18	VAL	0	0.017	0.022	5.758	-0.106	-0.106	0.000	0.000	0.000	0.000
9	D	19	ALA	0	0.024	0.009	9.135	0.510	0.510	0.000	0.000	0.000	0.000
10	D	20	ARG	1	1.007	0.999	10.234	-1.243	-1.243	0.000	0.000	0.000	0.000
11	D	21	ALA	0	0.016	0.009	11.607	0.247	0.247	0.000	0.000	0.000	0.000
12	D	22	ASN	0	-0.002	-0.016	8.779	0.163	0.163	0.000	0.000	0.000	0.000
13	D	23	VAL	0	0.010	0.010	6.709	0.007	0.007	0.000	0.000	0.000	0.000
14	D	24	LYS	1	0.894	0.953	8.897	-1.350	-1.350	0.000	0.000	0.000	0.000
15	D	25	HIS	0	0.005	-0.006	8.686	0.166	0.166	0.000	0.000	0.000	0.000
16	D	26	LEU	0	0.017	0.013	6.018	1.376	1.376	0.000	0.000	0.000	0.000
17	D	27	LYS	1	0.918	0.950	6.233	-5.966	-5.966	0.000	0.000	0.000	0.000
18	D	28	ILE	0	0.023	0.015	6.557	2.065	2.065	0.000	0.000	0.000	0.000
19	D	29	LEU	0	-0.045	-0.017	3.634	-1.179	-0.832	0.005	-0.064	-0.288	0.000
20	D	30	ASN	0	0.004	-0.007	6.918	-0.075	-0.075	0.000	0.000	0.000	0.000
21	D	31	THR	0	-0.001	-0.004	6.076	0.067	0.067	0.000	0.000	0.000	0.000
22	D	32	PRO	0	0.038	0.047	3.897	-0.733	-0.513	0.001	-0.059	-0.161	0.000
23	D	33	ASN	0	-0.002	-0.013	3.746	-1.615	-1.307	0.001	-0.110	-0.200	-0.001
24	D	34	CYS	0	-0.021	-0.018	2.643	-1.669	-0.553	1.690	-0.966	-1.841	-0.003
25	D	35	ALA	0	0.028	0.016	4.366	0.058	0.158	-0.002	-0.024	-0.074	0.000
26	D	36	LEU	0	-0.008	0.005	6.478	0.563	0.563	0.000	0.000	0.000	0.000
27	D	37	GLN	0	0.075	0.024	2.228	-2.393	-2.872	5.071	-1.568	-3.024	-0.008
28	D	38	ILE	0	0.002	0.002	3.738	-0.662	-0.316	0.002	0.005	-0.352	0.000
29	D	39	VAL	0	0.004	-0.007	2.361	-3.982	-0.183	6.022	-4.246	-5.574	0.009
30	D	40	ALA	0	0.015	0.009	1.633	-12.281	-25.495	22.176	-5.809	-3.153	0.047
31	D	41	ARG	1	0.850	0.939	3.499	-5.645	-5.191	0.063	0.070	-0.586	0.001
32	D	42	LEU	0	0.007	0.001	4.508	-0.162	-0.046	-0.002	-0.013	-0.101	0.000
33	D	43	LYS	1	0.864	0.929	7.284	-1.075	-1.075	0.000	0.000	0.000	0.000
34	D	44	ASN	0	0.036	0.028	9.982	-0.201	-0.201	0.000	0.000	0.000	0.000
35	D	45	ASN	0	0.057	0.020	7.802	-0.163	-0.163	0.000	0.000	0.000	0.000
36	D	46	ASN	0	0.028	0.022	9.284	0.129	0.129	0.000	0.000	0.000	0.000
37	D	47	ARG	1	0.992	1.006	5.210	3.196	3.228	-0.002	-0.001	-0.029	0.000
38	D	48	GLN	0	0.003	-0.001	3.803	0.737	2.958	-0.032	-1.021	-1.168	-0.005
41	D	52	ASP	-1	-0.783	-0.889	3.806	-2.041	0.345	-0.023	-1.099	-1.264	0.006
42	D	53	PRO	0	0.004	-0.014	5.683	0.449	0.449	0.000	0.000	0.000	0.000
43	D	54	LYS	1	0.890	0.943	8.519	-0.081	-0.081	0.000	0.000	0.000	0.000
44	D	55	LEU	0	-0.005	0.018	8.616	-0.224	-0.224	0.000	0.000	0.000	0.000
45	D	56	LYS	1	1.029	1.000	11.867	-0.301	-0.301	0.000	0.000	0.000	0.000
46	D	57	TRP	0	0.023	-0.008	8.210	0.196	0.196	0.000	0.000	0.000	0.000
47	D	58	ILE	0	0.015	0.004	8.175	0.209	0.209	0.000	0.000	0.000	0.000
48	D	59	GLN	0	0.019	-0.001	11.485	0.089	0.089	0.000	0.000	0.000	0.000
49	D	60	GLU	-1	-0.810	-0.883	14.380	0.877	0.877	0.000	0.000	0.000	0.000
50	D	61	TYR	0	-0.081	-0.058	11.671	0.101	0.101	0.000	0.000	0.000	0.000
51	D	62	LEU	0	0.006	-0.014	10.738	0.032	0.032	0.000	0.000	0.000	0.000
52	D	63	GLU	-1	-0.893	-0.940	14.590	0.880	0.880	0.000	0.000	0.000	0.000
53	D	64	LYS	1	0.834	0.910	17.361	-1.061	-1.061	0.000	0.000	0.000	0.000
54	D	65	ALA	0	-0.022	0.005	15.521	-0.066	-0.066	0.000	0.000	0.000	0.000
55	D	66	LEU	0	-0.054	-0.024	16.429	-0.073	-0.073	0.000	0.000	0.000	0.000
56	D	67	ASN	0	-0.031	-0.018	19.819	-0.117	-0.117	0.000	0.000	0.000	0.000
57	D	68	LYS	1	0.970	1.013	21.504	-0.929	-0.929	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:11:CYS)