FMO DATABASE

FMODB ID: 3GQGL

Calculation Name: 6T6J-C-Xray547

Preferred Name:

Target Type:

Ligand Name: nickel (ii) ion

Ligand 3-letter code: NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6T6J

Chain ID: C

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-331986.820941
FMO2-HF: Nuclear repulsion	308525.852792
FMO2-HF: Total energy	-23460.968149
FMO2-MP2: Total energy	-23531.932298

3D Structure Molmil

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:213:GLY)

Summations of interaction energy for fragment #1(A:213: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.
64.209	65.068	-0.002	-0.368	-0.489	0

Interaction energy analysis for fragmet #1(A:213:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.885 / q_NPA : 0.931

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].
3	A	215	HIS	0	-0.014	-0.003	3.827	5.438	6.297	-0.002	-0.368	-0.489
4	A	216	HIS	0	-0.002	-0.011	6.360	2.693	2.693	0.000	0.000	0.000
5	A	217	HIS	0	-0.006	0.001	8.457	2.480	2.480	0.000	0.000	0.000
6	A	218	HIS	0	0.007	0.009	12.327	2.378	2.378	0.000	0.000	0.000
7	A	219	HIS	0	0.015	0.011	15.159	-0.334	-0.334	0.000	0.000	0.000
8	A	220	ILE	0	-0.040	-0.026	18.329	0.537	0.537	0.000	0.000	0.000
9	A	221	GLN	0	0.021	0.003	21.341	-0.139	-0.139	0.000	0.000	0.000
10	A	222	ASN	0	-0.019	-0.007	23.622	0.010	0.010	0.000	0.000	0.000
11	A	223	PHE	0	0.006	0.008	25.168	0.572	0.572	0.000	0.000	0.000
12	A	224	ARG	1	0.929	0.982	24.605	12.348	12.348	0.000	0.000	0.000
13	A	225	VAL	0	-0.022	-0.022	24.369	0.442	0.442	0.000	0.000	0.000
14	A	226	TYR	0	0.051	0.043	26.097	-0.276	-0.276	0.000	0.000	0.000
15	A	227	TYR	0	-0.071	-0.090	23.346	0.127	0.127	0.000	0.000	0.000
16	A	228	ARG	1	0.893	0.939	27.479	10.030	10.030	0.000	0.000	0.000
17	A	229	ASP	-1	-0.769	-0.874	24.086	-13.547	-13.547	0.000	0.000	0.000
18	A	230	SER	0	-0.019	-0.022	26.644	0.560	0.560	0.000	0.000	0.000
19	A	231	ARG	1	0.961	0.952	28.284	9.480	9.480	0.000	0.000	0.000
20	A	232	ASP	-1	-0.794	-0.867	30.114	-9.931	-9.931	0.000	0.000	0.000
21	A	233	PRO	0	-0.015	-0.007	32.010	-0.122	-0.122	0.000	0.000	0.000
22	A	234	ILE	0	-0.002	0.005	31.484	0.146	0.146	0.000	0.000	0.000
23	A	235	TRP	0	-0.073	-0.039	30.436	-0.426	-0.426	0.000	0.000	0.000
24	A	236	LYS	1	0.884	0.942	24.450	12.849	12.849	0.000	0.000	0.000
25	A	237	GLY	0	0.037	0.026	25.561	-0.019	-0.019	0.000	0.000	0.000
26	A	238	PRO	0	-0.034	-0.017	26.538	0.377	0.377	0.000	0.000	0.000
27	A	239	ALA	0	-0.002	-0.002	21.906	-0.335	-0.335	0.000	0.000	0.000
28	A	240	GLN	0	-0.018	-0.015	17.504	0.778	0.778	0.000	0.000	0.000
29	A	241	LEU	0	0.007	-0.004	20.771	-0.045	-0.045	0.000	0.000	0.000
30	A	242	LEU	0	-0.003	0.006	14.576	-0.208	-0.208	0.000	0.000	0.000
31	A	243	TRP	0	0.039	0.012	18.329	-0.232	-0.232	0.000	0.000	0.000
32	A	244	LYS	1	0.908	0.950	20.230	12.922	12.922	0.000	0.000	0.000
33	A	245	GLY	0	0.031	0.024	23.752	0.037	0.037	0.000	0.000	0.000
34	A	246	GLU	-1	-0.858	-0.918	24.410	-12.130	-12.130	0.000	0.000	0.000
35	A	247	GLY	0	-0.029	-0.002	26.697	0.132	0.132	0.000	0.000	0.000
36	A	248	ALA	0	-0.062	-0.036	24.157	0.281	0.281	0.000	0.000	0.000
37	A	249	VAL	0	-0.013	-0.017	22.866	0.147	0.147	0.000	0.000	0.000
38	A	250	VAL	0	-0.003	0.012	16.498	-0.019	-0.019	0.000	0.000	0.000
39	A	251	ILE	0	-0.001	-0.003	19.678	0.218	0.218	0.000	0.000	0.000
40	A	252	GLN	0	0.038	-0.002	13.877	-1.387	-1.387	0.000	0.000	0.000
41	A	253	ASP	-1	-0.833	-0.879	18.072	-13.375	-13.375	0.000	0.000	0.000
42	A	254	LYS	1	0.993	0.984	18.616	14.397	14.397	0.000	0.000	0.000
43	A	255	SER	0	0.027	0.015	14.375	-0.529	-0.529	0.000	0.000	0.000
44	A	256	ASP	-1	-0.870	-0.910	14.257	-18.508	-18.508	0.000	0.000	0.000
45	A	257	ILE	0	-0.001	0.002	11.677	1.012	1.012	0.000	0.000	0.000
46	A	258	LYS	1	0.831	0.917	15.664	15.761	15.761	0.000	0.000	0.000
47	A	259	VAL	0	0.020	0.013	18.374	0.035	0.035	0.000	0.000	0.000
48	A	260	VAL	0	-0.002	-0.001	20.692	0.513	0.513	0.000	0.000	0.000
49	A	261	PRO	0	0.031	0.005	24.404	0.112	0.112	0.000	0.000	0.000
50	A	262	ARG	1	0.950	0.970	27.456	10.823	10.823	0.000	0.000	0.000
51	A	263	ARG	1	0.945	0.966	29.113	9.426	9.426	0.000	0.000	0.000
52	A	264	LYS	1	0.869	0.950	28.822	10.823	10.823	0.000	0.000	0.000
53	A	265	ALA	0	0.053	0.029	26.976	-0.267	-0.267	0.000	0.000	0.000
54	A	266	LYS	1	0.944	0.973	28.888	9.501	9.501	0.000	0.000	0.000
55	A	267	ILE	0	-0.041	-0.020	26.830	-0.200	-0.200	0.000	0.000	0.000
56	A	268	ILE	0	-0.022	-0.017	29.157	0.494	0.494	0.000	0.000	0.000
57	A	269	ARG	1	0.920	0.965	29.300	9.913	9.913	0.000	0.000	0.000
58	A	270	ASP	-2	-1.774	-1.885	28.049	-21.554	-21.554	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:213:GLY)