FMO DATABASE

FMODB ID: JK5L9

Calculation Name: 1NGK-A-Xray549

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | sulfate ion | cyanide ion

Ligand 3-letter code: HEM | SO4 | CYN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NGK

Chain ID: A

ChEMBL ID:

UniProt ID: P9WN23

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1142470.818581
FMO2-HF: Nuclear repulsion	1090511.050562
FMO2-HF: Total energy	-51959.76802
FMO2-MP2: Total energy	-52110.597378

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-343.11	-336.277	11.761	-9.089	-9.504	-0.096

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.720 / q_NPA : 1.847

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	5	PHE	0	0.066	0.035	3.209	-13.105	-11.067	0.050	-0.949	-1.139	-0.004
5	A	7	ASP	-1	-0.854	-0.933	2.169	-117.927	-115.661	4.726	-3.075	-3.917	-0.022
6	A	8	ALA	0	-0.117	-0.054	1.977	-38.813	-36.642	6.981	-5.010	-4.142	-0.069
7	A	9	VAL	0	0.059	0.053	3.603	7.034	7.339	0.005	-0.055	-0.255	-0.001
8	A	10	GLY	0	0.035	0.034	4.689	8.594	8.647	-0.001	0.000	-0.051	0.000
4	A	6	TYR	0	0.001	-0.017	5.864	-2.055	-2.055	0.000	0.000	0.000	0.000
9	A	11	GLY	0	-0.028	-0.012	6.217	5.567	5.567	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.022	0.001	7.578	4.439	4.439	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.964	0.985	10.565	44.356	44.356	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.004	-0.013	9.117	4.600	4.600	0.000	0.000	0.000	0.000
13	A	15	PHE	0	0.028	0.007	9.148	2.454	2.454	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.885	-0.955	13.433	-29.761	-29.761	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.028	0.013	14.903	2.123	2.123	0.000	0.000	0.000	0.000
16	A	18	ILE	0	-0.014	-0.010	13.622	1.713	1.713	0.000	0.000	0.000	0.000
17	A	19	VAL	0	0.008	-0.010	17.125	1.812	1.812	0.000	0.000	0.000	0.000
18	A	20	SER	0	0.054	0.024	19.281	1.771	1.771	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.853	0.922	18.125	31.655	31.655	0.000	0.000	0.000	0.000
20	A	22	PHE	0	-0.017	-0.013	21.360	0.815	0.815	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.065	0.017	23.044	1.133	1.133	0.000	0.000	0.000	0.000
22	A	24	ALA	0	-0.016	-0.003	24.979	1.007	1.007	0.000	0.000	0.000	0.000
23	A	25	GLN	0	-0.063	-0.032	25.464	0.932	0.932	0.000	0.000	0.000	0.000
24	A	26	VAL	0	-0.009	-0.012	26.672	0.823	0.823	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.027	-0.008	29.201	0.676	0.676	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.922	-0.957	31.276	-17.503	-17.503	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.784	-0.871	31.257	-18.681	-18.681	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.794	-0.872	33.233	-15.912	-15.912	0.000	0.000	0.000	0.000
29	A	31	VAL	0	-0.040	0.001	34.511	0.398	0.398	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.008	-0.011	28.801	0.040	0.040	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.897	0.941	32.893	16.544	16.544	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.762	0.861	34.720	16.200	16.200	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.057	-0.022	33.633	0.327	0.327	0.000	0.000	0.000	0.000
34	A	36	TYR	-1	-0.891	-0.967	27.238	-22.908	-22.908	0.000	0.000	0.000	0.000
35	A	37	PRO	0	-0.107	-0.079	32.674	0.471	0.471	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.937	-0.973	34.500	-16.085	-16.085	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.904	-0.922	35.964	-16.216	-16.216	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.935	-0.970	30.772	-20.452	-20.452	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.028	0.014	28.656	-0.402	-0.402	0.000	0.000	0.000	0.000
40	A	42	ALA	0	0.046	0.036	26.461	-1.000	-1.000	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.003	-0.013	25.436	-0.963	-0.963	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.085	-0.053	26.014	-0.569	-0.569	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.863	-0.944	21.784	-27.154	-27.154	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.965	-0.979	21.285	-27.140	-27.140	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.881	0.939	20.591	21.429	21.429	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.016	0.018	20.150	-1.269	-1.269	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.936	0.987	15.697	31.331	31.331	0.000	0.000	0.000	0.000
48	A	50	MET	0	-0.021	-0.013	16.516	-2.223	-2.223	0.000	0.000	0.000	0.000
49	A	51	PHE	0	-0.043	-0.024	16.593	-1.571	-1.571	0.000	0.000	0.000	0.000
50	A	52	LEU	0	0.020	0.013	15.084	-1.721	-1.721	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.828	-0.917	12.211	-45.785	-45.785	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.026	-0.009	11.583	-2.649	-2.649	0.000	0.000	0.000	0.000
53	A	55	TYR	0	-0.064	-0.024	12.215	-1.746	-1.746	0.000	0.000	0.000	0.000
54	A	56	TRP	0	0.008	0.011	9.254	-2.282	-2.282	0.000	0.000	0.000	0.000
55	A	57	GLY	0	-0.028	-0.028	7.693	-9.212	-9.212	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.018	0.016	7.755	-5.080	-5.080	0.000	0.000	0.000	0.000
57	A	59	PRO	0	-0.042	-0.025	9.830	2.578	2.578	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.959	0.976	12.475	41.429	41.429	0.000	0.000	0.000	0.000
59	A	61	THR	0	0.093	0.046	15.493	1.409	1.409	0.000	0.000	0.000	0.000
60	A	62	TYR	0	0.071	0.040	17.943	2.347	2.347	0.000	0.000	0.000	0.000
61	A	63	SER	0	-0.072	-0.045	18.421	1.477	1.477	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.943	-0.979	17.940	-31.364	-31.364	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.025	0.019	21.660	1.490	1.490	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.867	0.944	23.468	24.586	24.586	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.023	0.019	24.155	1.057	1.057	0.000	0.000	0.000	0.000
66	A	68	HIS	0	0.029	0.000	21.627	-1.408	-1.408	0.000	0.000	0.000	0.000
67	A	69	PRO	0	0.020	0.006	19.674	1.168	1.168	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.923	0.965	23.016	21.087	21.087	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.070	0.041	21.834	1.185	1.185	0.000	0.000	0.000	0.000
70	A	72	ARG	1	1.062	1.038	26.298	19.829	19.829	0.000	0.000	0.000	0.000
71	A	73	MET	0	-0.037	-0.027	29.343	0.670	0.670	0.000	0.000	0.000	0.000
72	A	74	ARG	1	0.835	0.916	26.989	22.725	22.725	0.000	0.000	0.000	0.000
73	A	75	HIS	0	0.065	0.024	25.574	-0.129	-0.129	0.000	0.000	0.000	0.000
74	A	76	ALA	0	-0.026	-0.012	30.969	0.459	0.459	0.000	0.000	0.000	0.000
75	A	77	PRO	0	-0.088	-0.032	33.516	0.497	0.497	0.000	0.000	0.000	0.000
76	A	78	PHE	0	0.017	0.023	32.062	0.329	0.329	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.882	0.944	35.259	15.295	15.295	0.000	0.000	0.000	0.000
78	A	80	ILE	0	0.050	0.023	30.139	-0.117	-0.117	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.017	-0.018	34.116	0.023	0.023	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.001	-0.027	33.686	-0.603	-0.603	0.000	0.000	0.000	0.000
81	A	83	ILE	0	0.017	0.018	33.560	-0.431	-0.431	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.767	-0.859	32.508	-18.035	-18.035	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.804	0.879	28.749	19.561	19.561	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.812	-0.883	28.953	-20.761	-20.761	0.000	0.000	0.000	0.000
85	A	87	ALA	0	-0.021	-0.003	29.815	-0.452	-0.452	0.000	0.000	0.000	0.000
86	A	88	TRP	0	0.017	0.015	21.756	-1.099	-1.099	0.000	0.000	0.000	0.000
87	A	89	LEU	0	0.028	0.007	23.675	-1.049	-1.049	0.000	0.000	0.000	0.000
88	A	90	ARG	1	0.856	0.927	24.882	19.385	19.385	0.000	0.000	0.000	0.000
89	A	91	CYS	0	-0.048	-0.008	25.788	-0.280	-0.280	0.000	0.000	0.000	0.000
90	A	92	MET	0	0.010	0.008	20.051	-1.379	-1.379	0.000	0.000	0.000	0.000
91	A	93	HIS	0	-0.048	-0.035	20.825	-1.832	-1.832	0.000	0.000	0.000	0.000
92	A	94	THR	0	-0.059	-0.036	21.607	-0.574	-0.574	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.002	0.014	20.032	-0.355	-0.355	0.000	0.000	0.000	0.000
94	A	96	VAL	0	0.007	0.012	15.798	-1.250	-1.250	0.000	0.000	0.000	0.000
95	A	97	ALA	0	-0.028	-0.013	17.338	-1.283	-1.283	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.079	-0.036	19.185	0.084	0.084	0.000	0.000	0.000	0.000
97	A	99	ILE	0	-0.030	-0.011	12.673	-0.394	-0.394	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.806	-0.877	13.107	-39.706	-39.706	0.000	0.000	0.000	0.000
99	A	101	SER	0	0.026	-0.022	13.354	-1.974	-1.974	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.971	-0.965	10.641	-47.936	-47.936	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.114	-0.065	8.892	-5.589	-5.589	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.050	-0.033	8.469	-6.015	-6.015	0.000	0.000	0.000	0.000
103	A	105	ASP	-1	-0.728	-0.820	8.983	-54.458	-54.458	0.000	0.000	0.000	0.000
104	A	106	ASP	-1	-0.861	-0.944	11.573	-34.681	-34.681	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.941	-0.973	11.753	-44.482	-44.482	0.000	0.000	0.000	0.000
106	A	108	HIS	1	0.815	0.874	7.105	65.679	65.679	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.799	0.895	11.427	38.626	38.626	0.000	0.000	0.000	0.000
108	A	110	ARG	1	0.873	0.951	14.523	32.832	32.832	0.000	0.000	0.000	0.000
109	A	111	GLU	-1	-0.861	-0.944	10.608	-53.607	-53.607	0.000	0.000	0.000	0.000
110	A	112	LEU	0	-0.030	-0.021	13.027	1.249	1.249	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.015	-0.011	14.875	1.748	1.748	0.000	0.000	0.000	0.000
112	A	114	ASP	-1	-0.818	-0.918	18.316	-29.892	-29.892	0.000	0.000	0.000	0.000
113	A	115	TYR	0	-0.043	-0.021	16.515	1.235	1.235	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.001	-0.014	17.279	1.372	1.372	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.874	-0.937	20.163	-23.254	-23.254	0.000	0.000	0.000	0.000
116	A	118	MET	0	-0.029	-0.013	20.000	1.038	1.038	0.000	0.000	0.000	0.000
117	A	119	ALA	0	-0.031	-0.009	20.960	1.130	1.130	0.000	0.000	0.000	0.000
118	A	120	ALA	0	0.027	0.013	23.030	1.045	1.045	0.000	0.000	0.000	0.000
119	A	121	HIS	0	-0.013	-0.015	25.699	1.693	1.693	0.000	0.000	0.000	0.000
120	A	122	SER	0	-0.091	-0.051	25.413	0.951	0.951	0.000	0.000	0.000	0.000
121	A	123	LEU	0	-0.083	-0.042	24.785	0.349	0.349	0.000	0.000	0.000	0.000
122	A	124	VAL	0	-0.020	0.011	28.773	0.530	0.530	0.000	0.000	0.000	0.000
123	A	125	ASN	0	-0.090	-0.051	32.042	0.415	0.415	0.000	0.000	0.000	0.000
124	A	126	SER	0	-0.049	-0.052	34.768	0.712	0.712	0.000	0.000	0.000	0.000
125	A	127	PRO	0	-0.050	-0.029	37.649	-0.247	-0.247	0.000	0.000	0.000	0.000
126	A	128	PHE	-1	-0.822	-0.866	39.743	-15.808	-15.808	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)