FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 64L7Z

Calculation Name: 1GV3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: manganese (ii) ion

Ligand 3-letter code: MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1GV3

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Z0M1

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 213
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2659126.086958
FMO2-HF: Nuclear repulsion 2574371.542319
FMO2-HF: Total energy -84754.544639
FMO2-MP2: Total energy -85004.946217


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:25:SER)


Summations of interaction energy for fragment #1(A:25:SER)
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.
-157.168-151.96527.311-16.424-16.088-0.17
Interaction energy analysis for fragmet #1(A:25:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.736 / q_NPA : 0.854
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   
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].
3A27GLY00.0600.0333.8518.47310.714-0.022-1.200-1.019-0.003
4A28PHE00.0060.0103.9627.6737.908-0.001-0.070-0.1650.000
5A29ILE00.0540.0292.357-18.405-15.8171.731-2.040-2.279-0.025
6A30ASP-1-0.867-0.9241.696-67.532-70.92512.146-5.488-3.264-0.056
7A31ARG10.8940.9633.26235.36536.2050.079-0.215-0.705-0.001
8A32GLN00.006-0.0121.978-40.979-40.40410.877-5.286-6.166-0.057
9A33LEU0-0.015-0.0033.3658.7058.4130.0390.316-0.0620.000
64A88SER0-0.020-0.0324.7581.2911.309-0.001-0.003-0.0130.000
66A90GLU-1-0.740-0.8662.385-70.855-68.5212.464-2.433-2.365-0.028
70A94ARG10.9240.9704.20845.81045.867-0.001-0.005-0.0500.000
10A34GLY00.0130.0015.8991.7701.7700.0000.0000.0000.000
11A35THR0-0.014-0.0378.7561.8191.8190.0000.0000.0000.000
12A36ASN0-0.0150.02711.9742.2162.2160.0000.0000.0000.000
13A37PRO00.0130.00814.8010.4100.4100.0000.0000.0000.000
14A38ALA00.0270.00012.515-1.527-1.5270.0000.0000.0000.000
15A39GLU-1-0.936-0.96012.647-18.660-18.6600.0000.0000.0000.000
16A40LEU0-0.020-0.01513.110-1.315-1.3150.0000.0000.0000.000
17A41PRO0-0.0030.00511.2590.4810.4810.0000.0000.0000.000
18A42PRO00.0230.00813.7520.9710.9710.0000.0000.0000.000
19A43LEU0-0.0100.01715.328-1.055-1.0550.0000.0000.0000.000
20A44PRO0-0.044-0.02714.3230.5400.5400.0000.0000.0000.000
21A45TYR0-0.001-0.01916.8180.6840.6840.0000.0000.0000.000
22A46GLY00.0310.02120.815-0.038-0.0380.0000.0000.0000.000
23A47TYR0-0.047-0.06422.908-0.163-0.1630.0000.0000.0000.000
24A48ASP-1-0.870-0.94124.664-10.937-10.9370.0000.0000.0000.000
25A49ALA0-0.014-0.00423.6500.2110.2110.0000.0000.0000.000
26A50LEU00.015-0.00720.387-0.144-0.1440.0000.0000.0000.000
27A51GLU-1-0.750-0.87224.968-10.154-10.1540.0000.0000.0000.000
28A52LYS10.8010.93125.71312.16612.1660.0000.0000.0000.000
29A53ALA0-0.052-0.02425.3230.0750.0750.0000.0000.0000.000
30A54ILE00.0000.00122.3100.1510.1510.0000.0000.0000.000
31A55ASP-1-0.765-0.85026.539-10.727-10.7270.0000.0000.0000.000
32A56ALA00.0690.02027.157-0.435-0.4350.0000.0000.0000.000
33A57GLU-1-0.904-0.95227.382-10.238-10.2380.0000.0000.0000.000
34A58THR0-0.043-0.04524.951-0.231-0.2310.0000.0000.0000.000
35A59MET0-0.0070.01320.141-0.625-0.6250.0000.0000.0000.000
36A60LYS10.8680.93722.9289.8689.8680.0000.0000.0000.000
37A61LEU0-0.016-0.00524.292-0.359-0.3590.0000.0000.0000.000
38A62HIS0-0.038-0.02220.0080.0010.0010.0000.0000.0000.000
39A63HIS10.8870.91416.85415.45215.4520.0000.0000.0000.000
40A64ASP-1-0.816-0.88320.256-13.697-13.6970.0000.0000.0000.000
41A65LYS10.8540.93222.76711.70411.7040.0000.0000.0000.000
42A66HIS00.0180.00721.231-0.441-0.4410.0000.0000.0000.000
43A67HIS0-0.0010.00913.1350.6680.6680.0000.0000.0000.000
44A68ALA00.0400.01617.602-0.628-0.6280.0000.0000.0000.000
45A69ALA0-0.024-0.00419.807-0.045-0.0450.0000.0000.0000.000
46A70TYR0-0.0190.00116.425-0.003-0.0030.0000.0000.0000.000
47A71VAL00.0510.02214.284-0.357-0.3570.0000.0000.0000.000
48A72ASN0-0.016-0.01216.523-0.242-0.2420.0000.0000.0000.000
49A73ASN0-0.065-0.03419.6080.7000.7000.0000.0000.0000.000
50A74LEU00.0090.01112.3960.2350.2350.0000.0000.0000.000
51A75ASN00.015-0.00216.736-0.278-0.2780.0000.0000.0000.000
52A76ASN0-0.035-0.02818.2600.4810.4810.0000.0000.0000.000
53A77ALA0-0.025-0.00518.5640.6110.6110.0000.0000.0000.000
54A78LEU00.0400.00613.8620.3750.3750.0000.0000.0000.000
55A79LYS10.9400.97918.41913.73113.7310.0000.0000.0000.000
56A80LYS10.8910.95521.55712.88312.8830.0000.0000.0000.000
57A81HIS10.7790.87119.81314.23014.2300.0000.0000.0000.000
58A82PRO00.0650.03818.843-0.939-0.9390.0000.0000.0000.000
59A83GLU-1-0.818-0.91018.242-15.242-15.2420.0000.0000.0000.000
60A84LEU0-0.009-0.00814.926-0.961-0.9610.0000.0000.0000.000
61A85GLN0-0.0280.00013.513-1.133-1.1330.0000.0000.0000.000
62A86ASN0-0.048-0.00913.434-0.818-0.8180.0000.0000.0000.000
63A87SER0-0.040-0.02710.123-1.694-1.6940.0000.0000.0000.000
65A89VAL00.0430.0117.3221.6351.6350.0000.0000.0000.000
67A91ALA0-0.034-0.0105.9901.7151.7150.0000.0000.0000.000
68A92LEU00.0130.0018.2892.8682.8680.0000.0000.0000.000
69A93LEU0-0.040-0.0269.4282.2512.2510.0000.0000.0000.000
71A95ASP-1-0.811-0.90910.353-17.664-17.6640.0000.0000.0000.000
72A96LEU00.0130.00313.5410.9520.9520.0000.0000.0000.000
73A97ASN0-0.046-0.01915.9851.3551.3550.0000.0000.0000.000
74A98SER0-0.051-0.01715.2330.6900.6900.0000.0000.0000.000
75A99VAL0-0.0170.00215.0260.4520.4520.0000.0000.0000.000
76A100PRO00.0180.01217.8920.6780.6780.0000.0000.0000.000
77A101GLU-1-0.854-0.94321.472-12.179-12.1790.0000.0000.0000.000
78A102ASP-1-0.879-0.91923.799-12.913-12.9130.0000.0000.0000.000
79A103ILE0-0.064-0.03318.7140.0940.0940.0000.0000.0000.000
80A104ARG10.8700.96019.02513.77613.7760.0000.0000.0000.000
81A105THR00.0330.00218.614-0.932-0.9320.0000.0000.0000.000
82A106THR0-0.019-0.00319.743-0.252-0.2520.0000.0000.0000.000
83A107VAL00.0530.02114.203-0.481-0.4810.0000.0000.0000.000
84A108ARG10.8600.90314.84114.79414.7940.0000.0000.0000.000
85A109ASN0-0.007-0.01015.331-1.170-1.1700.0000.0000.0000.000
86A110ASN0-0.050-0.03916.5830.2310.2310.0000.0000.0000.000
87A111GLY00.0520.03112.527-0.467-0.4670.0000.0000.0000.000
88A112GLY00.0550.02811.553-1.930-1.9300.0000.0000.0000.000
89A113GLY0-0.007-0.00413.021-0.524-0.5240.0000.0000.0000.000
90A114HIS00.0350.02611.1790.4550.4550.0000.0000.0000.000
91A115LEU00.0190.0206.467-0.890-0.8900.0000.0000.0000.000
92A116ASN00.014-0.0039.938-2.666-2.6660.0000.0000.0000.000
93A117HIS00.000-0.01912.6191.1281.1280.0000.0000.0000.000
94A118THR0-0.039-0.0278.3440.6420.6420.0000.0000.0000.000
95A119ILE0-0.0140.0128.319-0.405-0.4050.0000.0000.0000.000
96A120PHE0-0.004-0.01010.3980.8580.8580.0000.0000.0000.000
97A121TRP0-0.020-0.02913.6661.1231.1230.0000.0000.0000.000
98A122GLN0-0.037-0.0257.6330.0240.0240.0000.0000.0000.000
99A123ILE0-0.0270.00211.9190.7700.7700.0000.0000.0000.000
100A124MET0-0.0200.02114.3671.4531.4530.0000.0000.0000.000
101A125SER0-0.004-0.01517.246-0.393-0.3930.0000.0000.0000.000
102A126PRO00.0410.02519.8170.3800.3800.0000.0000.0000.000
103A127ASP-1-0.953-0.97822.432-12.133-12.1330.0000.0000.0000.000
104A128GLY0-0.044-0.01321.524-0.083-0.0830.0000.0000.0000.000
105A129GLY0-0.021-0.00822.1580.6850.6850.0000.0000.0000.000
106A130GLY0-0.008-0.00824.024-0.082-0.0820.0000.0000.0000.000
107A131GLN0-0.053-0.02924.958-0.313-0.3130.0000.0000.0000.000
108A132PRO00.0020.01021.222-0.136-0.1360.0000.0000.0000.000
109A133THR00.0140.00520.6890.2880.2880.0000.0000.0000.000
110A134GLY00.0200.01119.216-0.657-0.6570.0000.0000.0000.000
111A135ASP-1-0.842-0.92216.409-16.583-16.5830.0000.0000.0000.000
112A136ILE0-0.015-0.01116.3660.4830.4830.0000.0000.0000.000
113A137ALA00.001-0.00118.3090.4870.4870.0000.0000.0000.000
114A138GLN0-0.040-0.01221.5970.8840.8840.0000.0000.0000.000
115A139GLU-1-0.769-0.86716.890-18.244-18.2440.0000.0000.0000.000
116A140ILE0-0.010-0.00219.9370.2670.2670.0000.0000.0000.000
117A141ASN0-0.004-0.01422.5000.3880.3880.0000.0000.0000.000
118A142GLN0-0.052-0.02723.2510.0550.0550.0000.0000.0000.000
119A143THR0-0.048-0.01421.5530.1070.1070.0000.0000.0000.000
120A144PHE0-0.022-0.02321.1610.1910.1910.0000.0000.0000.000
121A145GLY0-0.0030.01826.5880.4470.4470.0000.0000.0000.000
122A146SER0-0.036-0.02528.4720.2720.2720.0000.0000.0000.000
123A147PHE00.0600.02423.503-0.328-0.3280.0000.0000.0000.000
124A148GLU-1-0.858-0.94726.735-10.877-10.8770.0000.0000.0000.000
125A149GLU-1-0.855-0.90029.552-10.127-10.1270.0000.0000.0000.000
126A150PHE00.0490.01620.180-0.151-0.1510.0000.0000.0000.000
127A151LYS10.9130.97325.47510.95610.9560.0000.0000.0000.000
128A152LYS10.8260.90926.5419.8169.8160.0000.0000.0000.000
129A153GLN00.012-0.00226.092-0.373-0.3730.0000.0000.0000.000
130A154PHE0-0.0010.00318.866-0.188-0.1880.0000.0000.0000.000
131A155ASN00.018-0.00424.287-0.500-0.5000.0000.0000.0000.000
132A156GLN0-0.0110.00626.993-0.047-0.0470.0000.0000.0000.000
133A157ALA00.0300.02023.5170.1100.1100.0000.0000.0000.000
134A158GLY00.005-0.01524.753-0.291-0.2910.0000.0000.0000.000
135A159GLY0-0.054-0.02725.5070.1580.1580.0000.0000.0000.000
136A160ASP-1-0.879-0.95027.880-10.559-10.5590.0000.0000.0000.000
137A161ARG10.8260.92522.55313.57113.5710.0000.0000.0000.000
138A162PHE00.0090.00326.2770.0350.0350.0000.0000.0000.000
139A163GLY0-0.0070.00427.516-0.251-0.2510.0000.0000.0000.000
140A164SER00.0230.00423.685-0.008-0.0080.0000.0000.0000.000
141A165GLY00.004-0.00520.959-0.003-0.0030.0000.0000.0000.000
142A166TRP0-0.026-0.01216.319-0.183-0.1830.0000.0000.0000.000
143A167VAL0-0.0030.01719.3210.2270.2270.0000.0000.0000.000
144A168TRP0-0.031-0.03712.742-1.534-1.5340.0000.0000.0000.000
145A169LEU0-0.0070.00916.2781.1321.1320.0000.0000.0000.000
146A170VAL0-0.024-0.03213.142-1.795-1.7950.0000.0000.0000.000
147A171ARG10.8360.92011.42123.79523.7950.0000.0000.0000.000
148A172ASN00.007-0.01512.371-1.942-1.9420.0000.0000.0000.000
149A173PRO00.029-0.01013.809-0.326-0.3260.0000.0000.0000.000
150A174GLN0-0.061-0.01614.8150.5640.5640.0000.0000.0000.000
151A175GLY00.0150.01214.8170.6240.6240.0000.0000.0000.000
152A176GLN0-0.0020.00815.891-0.060-0.0600.0000.0000.0000.000
153A177LEU00.0180.02115.836-1.104-1.1040.0000.0000.0000.000
154A178GLN00.0170.00817.3900.6970.6970.0000.0000.0000.000
155A179VAL00.0120.00817.900-0.924-0.9240.0000.0000.0000.000
156A180VAL00.0010.00516.5860.5890.5890.0000.0000.0000.000
157A181SER00.0490.02019.512-0.224-0.2240.0000.0000.0000.000
158A182THR0-0.0040.00815.9380.5280.5280.0000.0000.0000.000
159A183PRO00.0180.01119.3140.4340.4340.0000.0000.0000.000
160A184ASN00.003-0.02419.814-0.484-0.4840.0000.0000.0000.000
161A185GLN00.0370.03716.299-1.021-1.0210.0000.0000.0000.000
162A186ASP-1-0.745-0.82115.304-18.086-18.0860.0000.0000.0000.000
163A187ASN00.015-0.00610.125-1.573-1.5730.0000.0000.0000.000
164A188PRO00.0680.02711.805-0.232-0.2320.0000.0000.0000.000
165A189ILE0-0.0270.0046.505-0.783-0.7830.0000.0000.0000.000
166A190MET0-0.085-0.0259.5500.0280.0280.0000.0000.0000.000
167A191GLU-1-0.978-0.97412.592-17.413-17.4130.0000.0000.0000.000
168A192GLY0-0.036-0.02410.5120.6170.6170.0000.0000.0000.000
169A193SER00.0030.00610.598-0.519-0.5190.0000.0000.0000.000
170A194TYR00.0190.0075.170-1.396-1.3960.0000.0000.0000.000
171A195PRO0-0.021-0.0198.0902.6412.6410.0000.0000.0000.000
172A196ILE0-0.0020.0179.822-2.573-2.5730.0000.0000.0000.000
173A197MET0-0.004-0.00211.543-0.634-0.6340.0000.0000.0000.000
174A198GLY00.0450.00514.0190.2770.2770.0000.0000.0000.000
175A199ASN0-0.0050.00716.306-0.025-0.0250.0000.0000.0000.000
176A200ASP-1-0.778-0.88319.118-15.137-15.1370.0000.0000.0000.000
177A201VAL00.001-0.01020.3720.6500.6500.0000.0000.0000.000
178A202TRP0-0.054-0.04520.5091.0291.0290.0000.0000.0000.000
179A203GLU-1-0.886-0.94324.475-10.272-10.2720.0000.0000.0000.000
180A204HIS10.8200.91520.99014.16914.1690.0000.0000.0000.000
181A205ALA0-0.0170.00322.797-0.041-0.0410.0000.0000.0000.000
182A206TYR00.0280.02924.546-0.039-0.0390.0000.0000.0000.000
183A207TYR00.0090.00327.9310.4890.4890.0000.0000.0000.000
184A208LEU0-0.014-0.01230.1520.4010.4010.0000.0000.0000.000
185A209ARG10.8290.92429.82210.53810.5380.0000.0000.0000.000
186A210TYR0-0.028-0.04028.6760.3120.3120.0000.0000.0000.000
187A211GLN0-0.0230.01732.9200.3310.3310.0000.0000.0000.000
188A212ASN00.0590.00932.574-0.257-0.2570.0000.0000.0000.000
189A213ARG10.7870.88433.6898.7828.7820.0000.0000.0000.000
190A214ARG10.8490.89927.03911.67311.6730.0000.0000.0000.000
191A215PRO00.022-0.00229.177-0.323-0.3230.0000.0000.0000.000
192A216GLU-1-0.824-0.89030.609-9.121-9.1210.0000.0000.0000.000
193A217TYR0-0.018-0.01121.9970.0180.0180.0000.0000.0000.000
194A218LEU0-0.055-0.02124.454-0.355-0.3550.0000.0000.0000.000
195A219ASN0-0.032-0.02126.120-0.411-0.4110.0000.0000.0000.000
196A220ASN00.007-0.01328.2170.0350.0350.0000.0000.0000.000
197A221TRP00.007-0.00417.8650.0350.0350.0000.0000.0000.000
198A222TRP00.006-0.02621.334-0.503-0.5030.0000.0000.0000.000
199A223ASN0-0.036-0.00924.574-0.010-0.0100.0000.0000.0000.000
200A224VAL00.005-0.00221.5970.2330.2330.0000.0000.0000.000
201A225VAL00.0080.02818.553-0.716-0.7160.0000.0000.0000.000
202A226ASN00.018-0.00215.3411.0861.0860.0000.0000.0000.000
203A227TRP00.0460.00216.168-1.675-1.6750.0000.0000.0000.000
204A228SER0-0.0040.00516.620-0.376-0.3760.0000.0000.0000.000
205A229GLU-1-0.888-0.9299.504-28.192-28.1920.0000.0000.0000.000
206A230ILE00.015-0.00811.761-1.832-1.8320.0000.0000.0000.000
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208A232ARG10.9250.9619.39421.25121.2510.0000.0000.0000.000
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