FMO DATABASE

FMODB ID: YVQ32

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

Total energy (hartree)

FMO2-HF: Electronic energy	-327996.27752
FMO2-HF: Nuclear repulsion	303963.03421
FMO2-HF: Total energy	-24033.24331
FMO2-MP2: Total energy	-24102.677898

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.
-46.077	-41.666	37.804	-18.445	-23.772	0.045

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 : -0.019 / q_NPA : 0.015

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	D	13	PHE	0	0.073	0.054	3.793	-2.622	-0.056	-0.029	-0.901	-1.637	0.006
4	D	14	PHE	0	0.000	-0.009	2.602	-3.647	-0.487	1.336	-1.378	-3.119	-0.012
5	D	15	GLU	-1	-0.925	-0.963	3.529	-7.067	-6.184	0.009	-0.246	-0.645	0.000
6	D	16	SER	0	0.030	0.008	5.297	1.232	1.295	-0.002	-0.005	-0.056	0.000
7	D	17	HIS	0	-0.023	-0.008	8.870	-0.049	-0.049	0.000	0.000	0.000	0.000
8	D	18	VAL	0	0.023	0.022	5.732	-0.100	-0.100	0.000	0.000	0.000	0.000
9	D	19	ALA	0	0.019	0.009	9.135	0.480	0.480	0.000	0.000	0.000	0.000
10	D	20	ARG	1	1.029	1.007	10.234	-1.234	-1.234	0.000	0.000	0.000	0.000
11	D	21	ALA	0	-0.002	-0.003	11.607	0.265	0.265	0.000	0.000	0.000	0.000
12	D	22	ASN	0	-0.007	-0.017	8.930	0.140	0.140	0.000	0.000	0.000	0.000
13	D	23	VAL	0	0.012	0.014	7.042	0.057	0.057	0.000	0.000	0.000	0.000
14	D	24	LYS	1	0.894	0.945	8.900	-1.638	-1.638	0.000	0.000	0.000	0.000
15	D	25	HIS	0	0.004	-0.003	8.675	0.127	0.127	0.000	0.000	0.000	0.000
16	D	26	LEU	0	0.018	0.010	5.989	1.416	1.416	0.000	0.000	0.000	0.000
17	D	27	LYS	1	0.927	0.961	6.230	-6.253	-6.253	0.000	0.000	0.000	0.000
18	D	28	ILE	0	0.026	0.015	6.561	2.282	2.282	0.000	0.000	0.000	0.000
19	D	29	LEU	0	-0.051	-0.023	3.775	-1.109	-0.867	0.000	-0.034	-0.209	0.000
20	D	30	ASN	0	0.004	-0.008	7.335	-0.314	-0.314	0.000	0.000	0.000	0.000
21	D	31	THR	0	0.003	0.002	6.103	0.081	0.081	0.000	0.000	0.000	0.000
22	D	32	PRO	0	0.055	0.056	3.908	-0.861	-0.611	0.002	-0.078	-0.174	0.000
23	D	33	ASN	0	-0.017	-0.024	3.684	-1.660	-1.321	0.002	-0.106	-0.235	-0.001
24	D	34	CYS	0	-0.012	0.008	2.476	0.013	1.309	0.917	-0.716	-1.497	-0.001
25	D	35	ALA	0	0.052	0.001	4.529	0.710	0.810	-0.002	-0.011	-0.087	0.000
26	D	36	LEU	0	-0.018	0.004	6.463	0.709	0.709	0.000	0.000	0.000	0.000
27	D	37	GLN	0	0.037	0.011	1.907	-5.015	-6.017	8.094	-2.836	-4.256	-0.005
28	D	38	ILE	0	0.011	0.011	3.543	0.255	0.540	0.000	0.012	-0.297	0.000
29	D	39	VAL	0	0.009	-0.004	2.376	-4.147	0.186	5.366	-4.330	-5.369	0.010
30	D	40	ALA	0	0.006	0.005	1.634	-12.123	-25.388	22.108	-5.767	-3.075	0.047
31	D	41	ARG	1	0.853	0.935	3.499	-5.884	-5.409	0.063	0.069	-0.607	0.001
32	D	42	LEU	0	0.000	-0.002	4.419	-0.254	-0.133	-0.002	-0.016	-0.103	0.000
33	D	43	LYS	1	0.880	0.941	7.284	-1.220	-1.220	0.000	0.000	0.000	0.000
34	D	44	ASN	0	0.055	0.036	10.076	-0.132	-0.132	0.000	0.000	0.000	0.000
35	D	45	ASN	0	0.056	0.017	8.024	-0.090	-0.090	0.000	0.000	0.000	0.000
36	D	46	ASN	0	0.032	0.025	9.301	0.125	0.125	0.000	0.000	0.000	0.000
37	D	47	ARG	1	0.985	1.006	5.115	3.039	3.072	-0.002	-0.001	-0.031	0.000
38	D	48	GLN	0	-0.006	-0.012	3.803	0.179	2.391	-0.032	-1.022	-1.158	-0.005
41	D	52	ASP	-1	-0.800	-0.921	3.806	-2.415	-0.095	-0.024	-1.079	-1.217	0.005
42	D	53	PRO	0	-0.009	-0.019	5.664	0.601	0.601	0.000	0.000	0.000	0.000
43	D	54	LYS	1	0.942	0.984	8.428	0.315	0.315	0.000	0.000	0.000	0.000
44	D	55	LEU	0	-0.001	0.018	8.818	-0.149	-0.149	0.000	0.000	0.000	0.000
45	D	56	LYS	1	1.012	0.995	11.912	-0.244	-0.244	0.000	0.000	0.000	0.000
46	D	57	TRP	0	0.026	-0.009	8.143	0.149	0.149	0.000	0.000	0.000	0.000
47	D	58	ILE	0	-0.003	0.005	8.200	0.267	0.267	0.000	0.000	0.000	0.000
48	D	59	GLN	0	0.000	-0.013	11.485	0.083	0.083	0.000	0.000	0.000	0.000
49	D	60	GLU	-1	-0.854	-0.912	14.394	0.922	0.922	0.000	0.000	0.000	0.000
50	D	61	TYR	0	-0.135	-0.073	11.711	0.079	0.079	0.000	0.000	0.000	0.000
51	D	62	LEU	0	0.002	-0.023	10.964	0.053	0.053	0.000	0.000	0.000	0.000
52	D	63	GLU	-1	-0.888	-0.933	14.590	0.884	0.884	0.000	0.000	0.000	0.000
53	D	64	LYS	1	0.919	0.958	17.227	-1.173	-1.173	0.000	0.000	0.000	0.000
54	D	65	ALA	0	-0.022	0.003	15.558	-0.064	-0.064	0.000	0.000	0.000	0.000
55	D	66	LEU	0	-0.059	-0.023	16.366	-0.074	-0.074	0.000	0.000	0.000	0.000
56	D	67	ASN	0	-0.017	-0.012	19.819	-0.102	-0.102	0.000	0.000	0.000	0.000
57	D	68	LYS	1	0.977	1.012	21.531	-0.900	-0.900	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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