FMO DATABASE

FMODB ID: 3M34L

Calculation Name: 1HLM-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | cyanide ion | acetyl group

Ligand 3-letter code: HEM | CYN | ACE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HLM

Chain ID: A

ChEMBL ID:

UniProt ID: P80017

Base Structure: X-ray

Registration Date: 2025-10-05

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1495368.788187
FMO2-HF: Nuclear repulsion	1433237.598422
FMO2-HF: Total energy	-62131.189765
FMO2-MP2: Total energy	-62311.543739

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-17.879	-16.578	-0.018	-0.53	-0.753	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.915

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	A	3	THR	0	0.043	0.012	3.827	2.131	3.293	-0.017	-0.522	-0.623	-0.002
157	A	157	ALA	0	-0.031	0.000	4.663	-7.328	-7.189	-0.001	-0.008	-0.130	0.000
4	A	4	GLN	0	0.014	0.022	6.825	-0.938	-0.938	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.017	0.007	9.540	1.341	1.341	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.029	-0.018	11.232	-0.951	-0.951	0.000	0.000	0.000	0.000
7	A	7	GLN	0	0.056	0.028	12.771	0.751	0.751	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.058	0.021	14.297	-1.782	-1.782	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.064	-0.032	13.146	0.991	0.991	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.002	0.013	16.004	-0.238	-0.238	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.891	-0.955	19.293	-15.158	-15.158	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.054	-0.030	20.840	0.800	0.800	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.036	0.009	22.697	0.071	0.071	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.008	-0.005	25.721	0.124	0.124	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.021	0.013	29.177	0.210	0.210	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.925	-0.975	24.322	-12.698	-12.698	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.851	0.903	25.298	12.244	12.244	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.883	-0.945	27.912	-9.330	-9.330	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.007	0.002	30.584	0.227	0.227	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.006	0.002	25.065	0.228	0.228	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.903	0.962	29.336	9.140	9.140	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.023	0.000	31.491	0.230	0.230	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.038	-0.018	31.370	0.270	0.270	0.000	0.000	0.000	0.000
24	A	24	TRP	0	-0.013	-0.021	28.610	-0.085	-0.085	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.881	-0.940	32.452	-8.703	-8.703	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.047	-0.020	35.980	0.291	0.291	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.014	0.011	31.023	0.102	0.102	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.113	-0.025	33.050	0.001	0.001	0.000	0.000	0.000	0.000
29	A	29	THR	0	0.047	0.020	35.094	0.203	0.203	0.000	0.000	0.000	0.000
30	A	30	HIS	0	-0.067	-0.025	37.602	0.259	0.259	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.957	0.973	34.930	8.496	8.496	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.001	-0.024	34.841	-0.225	-0.225	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.026	-0.008	36.958	0.025	0.025	0.000	0.000	0.000	0.000
34	A	34	PHE	0	0.088	0.032	29.200	-0.114	-0.114	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.026	0.014	29.369	-0.252	-0.252	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.012	-0.010	31.143	-0.257	-0.257	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.843	-0.917	33.419	-9.036	-9.036	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.026	0.013	27.424	-0.112	-0.112	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.014	-0.019	25.754	-0.356	-0.356	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.013	-0.015	29.995	-0.121	-0.121	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.821	0.898	31.000	9.651	9.651	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.009	0.004	25.145	-0.238	-0.238	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.049	-0.043	28.161	-0.191	-0.191	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.015	0.002	30.418	0.464	0.464	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.053	-0.010	26.585	-0.279	-0.279	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.760	-0.879	24.515	-13.218	-13.218	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.003	-0.001	26.649	0.295	0.295	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.098	-0.068	22.875	0.194	0.194	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.001	-0.005	25.360	0.068	0.068	0.000	0.000	0.000	0.000
50	A	50	GLN	0	0.037	0.023	26.281	0.063	0.063	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.941	0.977	27.648	11.408	11.408	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.790	0.885	20.536	14.404	14.404	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.018	0.025	25.521	-0.346	-0.346	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.011	-0.016	27.500	0.378	0.378	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.018	0.003	29.811	0.095	0.095	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.007	0.002	30.803	0.311	0.311	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.032	-0.016	32.490	0.196	0.196	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.016	0.012	33.065	0.131	0.131	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.036	-0.009	34.166	0.200	0.200	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.013	-0.007	37.250	-0.067	-0.067	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.026	-0.026	33.882	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.026	0.007	35.553	-0.114	-0.114	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.961	-0.972	37.787	-7.646	-7.646	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.017	0.008	35.074	0.136	0.136	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.933	0.951	36.969	8.338	8.338	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.046	-0.028	38.253	-0.127	-0.127	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.076	0.046	39.933	0.221	0.221	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.950	0.961	40.142	6.716	6.716	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.013	-0.002	36.547	-0.202	-0.202	0.000	0.000	0.000	0.000
70	A	70	MET	0	0.044	0.041	31.995	-0.276	-0.276	0.000	0.000	0.000	0.000
71	A	71	HIS	0	0.028	0.012	35.187	-0.338	-0.338	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.005	0.003	36.149	-0.088	-0.088	0.000	0.000	0.000	0.000
73	A	73	HIS	0	-0.010	-0.009	27.466	0.030	0.030	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.042	0.025	31.683	-0.234	-0.234	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.008	-0.004	32.918	-0.123	-0.123	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.934	0.974	29.939	9.777	9.777	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.001	-0.004	26.371	-0.189	-0.189	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.025	0.014	28.657	-0.193	-0.193	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.014	-0.015	31.023	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.011	0.010	25.385	-0.045	-0.045	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.035	-0.022	25.328	-0.494	-0.494	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.027	0.003	27.285	-0.063	-0.063	0.000	0.000	0.000	0.000
83	A	83	THR	0	0.037	0.023	27.472	0.046	0.046	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.017	-0.016	21.919	-0.315	-0.315	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.043	-0.006	25.283	-0.292	-0.292	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.894	-0.944	27.808	-9.749	-9.749	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.955	-1.008	24.662	-11.076	-11.076	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.060	-0.002	24.289	-0.511	-0.511	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.881	-0.934	23.370	-12.300	-12.300	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.009	0.010	24.804	0.069	0.069	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.936	-0.981	23.548	-12.422	-12.422	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.014	0.013	22.542	-0.606	-0.606	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.013	0.015	19.644	-0.427	-0.427	0.000	0.000	0.000	0.000
94	A	94	PRO	0	-0.019	-0.022	17.192	-0.472	-0.472	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.862	-0.928	18.174	-15.476	-15.476	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.033	-0.007	20.440	0.061	0.061	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.006	0.010	16.918	0.012	0.012	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.037	0.035	16.452	-0.646	-0.646	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.037	-0.021	17.415	-0.070	-0.070	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.007	0.002	19.708	0.326	0.326	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.010	-0.017	13.451	-0.289	-0.289	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.986	0.985	16.797	14.320	14.320	0.000	0.000	0.000	0.000
103	A	103	THR	0	-0.102	-0.032	18.267	0.820	0.820	0.000	0.000	0.000	0.000
104	A	104	HIS	0	-0.065	-0.050	17.461	0.548	0.548	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.904	-0.958	13.359	-21.057	-21.057	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.857	0.932	16.012	13.906	13.906	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.025	0.004	18.835	0.184	0.184	0.000	0.000	0.000	0.000
108	A	108	HIS	0	0.092	0.029	16.994	0.476	0.476	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.014	0.007	16.376	0.813	0.813	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.072	0.032	13.539	-1.185	-1.185	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.929	0.965	10.889	27.166	27.166	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.956	0.988	13.740	17.645	17.645	0.000	0.000	0.000	0.000
113	A	113	ASN	0	0.025	0.002	16.950	0.215	0.215	0.000	0.000	0.000	0.000
114	A	114	TYR	0	0.040	0.028	13.483	0.555	0.555	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.931	-0.976	17.544	-15.826	-15.826	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.015	0.014	19.352	0.595	0.595	0.000	0.000	0.000	0.000
117	A	117	PHE	0	0.014	-0.002	21.549	0.473	0.473	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.028	0.008	20.907	0.469	0.469	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.926	0.966	21.295	14.546	14.546	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.038	0.018	24.197	0.471	0.471	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.003	0.008	24.359	0.493	0.493	0.000	0.000	0.000	0.000
122	A	122	MET	0	0.012	0.001	22.983	0.378	0.378	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.861	-0.906	27.585	-9.928	-9.928	0.000	0.000	0.000	0.000
124	A	124	ALA	0	0.004	0.001	30.183	0.427	0.427	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.010	0.003	28.221	0.343	0.343	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.752	0.880	30.597	10.307	10.307	0.000	0.000	0.000	0.000
127	A	127	ALA	0	0.012	0.013	34.093	0.254	0.254	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.874	-0.920	36.056	-8.388	-8.388	0.000	0.000	0.000	0.000
129	A	129	LEU	0	-0.010	0.000	37.548	-0.085	-0.085	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.007	0.008	38.872	0.266	0.266	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.036	-0.029	40.523	0.004	0.004	0.000	0.000	0.000	0.000
132	A	132	GLY	0	-0.019	-0.015	36.970	-0.199	-0.199	0.000	0.000	0.000	0.000
133	A	133	PHE	0	0.047	0.025	30.159	-0.014	-0.014	0.000	0.000	0.000	0.000
134	A	134	THR	0	0.027	0.010	32.185	-0.203	-0.203	0.000	0.000	0.000	0.000
135	A	135	LYS	1	0.987	0.970	29.876	9.429	9.429	0.000	0.000	0.000	0.000
136	A	136	GLN	0	0.017	0.019	28.404	-0.347	-0.347	0.000	0.000	0.000	0.000
137	A	137	VAL	0	0.062	0.028	27.467	-0.419	-0.419	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.069	-0.042	25.936	-0.184	-0.184	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.907	-0.926	22.197	-14.497	-14.497	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.084	0.042	23.026	-0.564	-0.564	0.000	0.000	0.000	0.000
141	A	141	TRP	0	0.058	0.032	23.191	-0.686	-0.686	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.023	-0.008	20.849	-0.511	-0.511	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.923	0.961	17.450	15.764	15.764	0.000	0.000	0.000	0.000
144	A	144	THR	0	0.042	-0.006	18.451	-0.747	-0.747	0.000	0.000	0.000	0.000
145	A	145	PHE	0	-0.021	-0.007	18.413	-0.836	-0.836	0.000	0.000	0.000	0.000
146	A	146	ALA	0	-0.046	-0.022	14.993	-0.952	-0.952	0.000	0.000	0.000	0.000
147	A	147	ILE	0	-0.039	-0.007	13.998	-1.840	-1.840	0.000	0.000	0.000	0.000
148	A	148	VAL	0	0.061	0.023	14.956	-0.702	-0.702	0.000	0.000	0.000	0.000
149	A	149	GLN	0	-0.050	-0.025	13.688	-1.092	-1.092	0.000	0.000	0.000	0.000
150	A	150	GLY	0	0.012	0.004	13.930	-1.332	-1.332	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.018	0.008	12.251	-1.204	-1.204	0.000	0.000	0.000	0.000
152	A	152	LEU	0	-0.020	-0.006	7.496	-2.668	-2.668	0.000	0.000	0.000	0.000
153	A	153	ILE	0	0.000	0.002	7.782	-1.546	-1.546	0.000	0.000	0.000	0.000
154	A	154	THR	0	0.016	-0.002	9.261	-0.687	-0.687	0.000	0.000	0.000	0.000
155	A	155	LYS	1	1.005	1.010	7.987	31.848	31.848	0.000	0.000	0.000	0.000
156	A	156	HIS	0	-0.170	-0.100	5.037	-3.582	-3.582	0.000	0.000	0.000	0.000
158	A	158	SER	-1	-0.947	-0.962	5.351	-34.207	-34.207	0.000	0.000	0.000	0.000

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